%0 Journal Article %J J Clin Microbiol %D 2024 %T Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. %A Bogaerts, Bert %E Van den Bossche, An %E Verhaegen, Bavo %E Laurence Delbrassinne %E Wesley Mattheus %E Nouws, Stéphanie %E Godfroid, Maxime %E Hoffman, Stefan %E Nancy Roosens %E De Keersmaecker, Sigrid C J %E Vanneste, Kevin %K Illumina %K nanopore sequencing %K outbreak %K public health %K whole-genome sequencing. %X

Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing and by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.

%B J Clin Microbiol %8 2024 Mar 05 %G eng %R 10.1128/jcm.01576-23 %0 Journal Article %J J Clin Microbiol %D 2024 %T Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. %A Bogaerts, Bert %E Van den Bossche, An %E Verhaegen, Bavo %E Laurence Delbrassinne %E Wesley Mattheus %E Nouws, Stéphanie %E Godfroid, Maxime %E Hoffman, Stefan %E Nancy Roosens %E De Keersmaecker, Sigrid C J %E Vanneste, Kevin %K Illumina %K nanopore sequencing %K outbreak %K public health %K whole-genome sequencing. %X

Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing and by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.

%B J Clin Microbiol %8 2024 Mar 05 %G eng %R 10.1128/jcm.01576-23 %0 Journal Article %J J Clin Microbiol %D 2024 %T Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. %A Bogaerts, Bert %E Van den Bossche, An %E Verhaegen, Bavo %E Laurence Delbrassinne %E Wesley Mattheus %E Nouws, Stéphanie %E Godfroid, Maxime %E Hoffman, Stefan %E Nancy Roosens %E De Keersmaecker, Sigrid C J %E Vanneste, Kevin %K Illumina %K nanopore sequencing %K outbreak %K public health %K whole-genome sequencing. %X

Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing and by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.

%B J Clin Microbiol %8 2024 Mar 05 %G eng %R 10.1128/jcm.01576-23 %0 Journal Article %J J Clin Microbiol %D 2024 %T Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. %A Bert Bogaerts %A An Van den Bossche %A Bavo Verhaegen %A Laurence Delbrassinne %A Wesley Mattheus %A Stéphanie Nouws %A Maxime Godfroid %A Stefan Hoffman %A Nancy Roosens %A Sigrid C.J. De Keersmaecker %A Kevin Vanneste %X

Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing and by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.

%B J Clin Microbiol %8 2024 Mar 05 %G eng %R 10.1128/jcm.01576-23 %0 Generic %D 2023 %T BSFM 2023 - L. monocytogenes in Plant-Based Foods : insights from of a recent foodborne outbreak linked to vegan alternative to cheese %A Laurence Delbrassinne %A An Van den Bossche %A Marie Polet %A Wesley Mattheus %A Anneline Christiaens %A Bavo Verhaegen %A Koenraad Van Hoorde %K foodborne outbreak %K foodborne outbreak investigation %K Listeria monocytogenes %X

Introduction

Listeriosis outbreaks have been associated with a wide range of animal-derived foods, including unpasteurized milk, dairy products, raw or undercooked meat and raw or smoked fish products.

A survey conducted by Smartproteinproject (funded by the EU Horizon 2020) on European consumer attitudes towards plant-based foods has indicated an increasing consumption of plant-based food products in Europe over the years. In Belgium, there was an 8 % increase in sales volume between 2019-2020, with plant-based plain milk (primarily made from soy, almond and oat) showing the highest sales volume. Recently, a foodborne outbreak caused by L. monocytogenes was traced back to the consumption of almond-milk & cashew alternative to cheese. This report presents the first occurrence of such a matrix in listeriosis outbreaks in Belgium.

Materials and Methods

Food samples were collected by the Belgian Federal Agency for the Safety of the Food Chain (FASFC) and analysed at the National Reference Laboratory (NRL) for Foodborne outbreaks following ISO 11290 – 1 and – 2. A human strain was collected at the NRC Listeria. All isolated strains underwent serotyping for further characterisation at the NRC Listeria, and Whole Genome Sequencing (WGS) was performed for clustering analysis.

Discussion

Due to the growing demand for novel and alternative food products among the population, concerns are raised about the potential risks associated with plant-based food production. For example, challenge tests performed on bovine milk and plant-based milk demonstrated similar growth of L. monocytogenes. The outbreak described here provides strong evidence of the contamination of plant-based alternative to cheese with L. monocytogenes: the strain isolated from the affected individual (case) matched the strain found in the consumed vegan cheese-like product, indicating it as the source of contamination. A third isolate was obtained by analysing a different product of vegan alternative to cheese from the same brand, suggesting a potential contamination in the processing environment. The company has voluntarily implemented withdrawal and recall measures on all its cheese-like vegetable specialties (RASFF 2023.0500). Additional cases were also reported in Germany, France and The Netherlands (EpiPulse 2022-FWD-00102).

In conclusion, this report underscores the occurrence of L. monocytogenes in plant-based foods. It emphasizes the need for further investigation into the prevalence of this pathogen in plant-based foods and its survival throughout the plant-based food supply chain.  

%B BSFM %I Belgian Society for Food Microbiology (BSFM) %C Brussels, Belgium %8 10/2023 %G eng %0 Report %D 2023 %T Epidemiologische surveillance van invasieve meningokokkeninfecties, Neisseria Meningitidis - 2022 %A Stéphanie Jacquinet %A Wesley Mattheus %X %I Sciensano %C Brussels, Belgium %P 16 %8 13/09/2023 %G eng %0 Journal Article %J Pathogens %D 2023 %T Genital Infection Caused by Salmonella enterica Serovar Hvittingfoss: A Case Report %A Emilie De Hert %A Sarah Baïli %A Marleen Vanden Driessche %A Hilde Jansens %A Sarah Vandamme %A Yves Jacquemyn %A Alexandra Vodolazkaia %A Marina Mukovnikova %A Wesley Mattheus %A Veerle Matheeussen %B Pathogens %V 12 %8 Jan-11-2023 %G eng %N 11 %R 10.3390/pathogens12111316 %0 Journal Article %J Nat Commun %D 2023 %T A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa. %A Sandra Van Puyvelde %A Tessa de Block %A Sushmita Sridhar %A Matt Bawn %A Robert A Kingsley %A Brecht Ingelbeen %A Mathew A Beale %A Barbé, Barbara %A Jeon, Hyon Jin %A Lisette Mbuyi-Kalonji %A Phoba, Marie-France %A Falay, Dadi %A Martiny, Delphine %A Vandenberg, Olivier %A Affolabi, Dissou %A Jean Pierre Rutanga %A Pieter-Jan Ceyssens %A Wesley Mattheus %A Wim L Cuypers %A Marianne A B van der Sande %A Park Se Eun %A Simon Kariuki %A Kephas Otieno %A John P A Lusingu %A Joyce R Mbwana %A Samuel Adjei %A Anima Sarfo %A Seth O Agyei %A Kwaku P Asante %A Walter Otieno %A Lucas Otieno %A Marc C Tahita %A Lompo, Palpouguini %A Irving F Hoffman %A Mvalo, Tisungane %A Msefula, Chisomo %A Hassan-Hanga, Fatimah %A Stephen Obaro %A Mackenzie, Grant %A Stijn Deborggraeve %A Nicholas Feasey %A Florian Marks %A Calman A MacLennan %A Nicholas R Thomson %A Jacobs, Jan %A Gordon Dougan %A Samuel Kariuki %A Lunguya, Octavie %K Africa South of the Sahara %K Drug Resistance, Microbial %K Genomics %K Humans %K Salmonella Infections %K Salmonella typhimurium %X

Invasive non-typhoidal Salmonella (iNTS) disease manifesting as bloodstream infection with high mortality is responsible for a huge public health burden in sub-Saharan Africa. Salmonella enterica serovar Typhimurium (S. Typhimurium) is the main cause of iNTS disease in Africa. By analysing whole genome sequence data from 1303 S. Typhimurium isolates originating from 19 African countries and isolated between 1979 and 2017, here we show a thorough scaled appraisal of the population structure of iNTS disease caused by S. Typhimurium across many of Africa's most impacted countries. At least six invasive S. Typhimurium clades have already emerged, with ST313 lineage 2 or ST313-L2 driving the current pandemic. ST313-L2 likely emerged in the Democratic Republic of Congo around 1980 and further spread in the mid 1990s. We observed plasmid-borne as well as chromosomally encoded fluoroquinolone resistance underlying emergences of extensive-drug and pan-drug resistance. Our work provides an overview of the evolution of invasive S. Typhimurium disease, and can be exploited to target control measures.

%B Nat Commun %V 14 %8 2023 Oct 23 %G eng %N 1 %R 10.1038/s41467-023-41152-6 %0 Journal Article %J Nature Communications %D 2023 %T A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan AfricaAbstract %A Sandra Van Puyvelde %A Tessa de Block %A Sushmita Sridhar %A Matt Bawn %A Robert A. Kingsley %A Brecht Ingelbeen %A Mathew A. Beale %A Barbé, Barbara %A Jeon, Hyon Jin %A Lisette Mbuyi-Kalonji %A Phoba, Marie-France %A Falay, Dadi %A Martiny, Delphine %A Vandenberg, Olivier %A Affolabi, Dissou %A Jean Pierre Rutanga %A Pieter-Jan Ceyssens %A Wesley Mattheus %A Wim L. Cuypers %A Marianne A. B. van der Sande %A Park Se Eun %A Simon Kariuki %A Kephas Otieno %A John P.A. Lusingu %A Joyce R. Mbwana %A Samuel Adjei %A Anima Sarfo %A Seth O. Agyei %A Kwaku P. Asante %A Walter Otieno %A Lucas Otieno %A Marc C. Tahita %A Lompo, Palpouguini %A Irving F. Hoffman %A Mvalo, Tisungane %A Msefula, Chisomo %A Hassan-Hanga, Fatimah %A Stephen Obaro %A Mackenzie, Grant %A Stijn Deborggraeve %A Nicholas Feasey %A Florian Marks %A Calman A. MacLennan %A Nicholas R. Thomson %A Jacobs, Jan %A Gordon Dougan %A Samuel Kariuki %A Lunguya, Octavie %B Nature Communications %V 14 %8 Jan-12-2023 %G eng %N 1 %R 10.1038/s41467-023-41152-6 %0 Journal Article %J BMC Infect Dis %D 2023 %T Salmonella Durban meningitis: case report and genomics study. %A Christelle Nanga Diasi %A Pieter-Jan Ceyssens %A Alexandra Vodolazkaia %A Marina Mukovnikova %A Sarah Dorval %A Olivia Bauraind %A Wesley Mattheus %K Genomics %K Humans %K Infant %K Male %K Meningitis, Bacterial %K Salmonella %K Salmonella Infections %K South Africa %X

BACKGROUND: Bacterial meningitis caused by non-typhoid Salmonella can be a fatal condition which is more common in low and middle-income countries.

CASE PRESENTATION: We report the case of a Salmonella meningitis in a Belgian six-month old male infant. The first clinical examination was reassuring, but after a few hours, his general state deteriorated. A blood test and a lumbar puncture were therefore performed. The cerebrospinal fluid analysis was compatible with a bacterial meningitis which was later identified by the NRC (National Reference Center) as Salmonella enterica serovar Durban.

CONCLUSIONS: In this paper, we present the clinical presentation, genomic typing, and probable sources of infection for an unusually rare serovar of Salmonella. Through an extended genomic analysis, we established its relationship to historical cases with links to Guinea.

%B BMC Infect Dis %V 23 %8 2023 May 20 %G eng %N 1 %R 10.1186/s12879-023-08308-7 %0 Report %D 2023 %T Surveillance épidémiologique des infections invasives à méningocoques, Neisseria Meningitidis - 2022 %A Stéphanie Jacquinet %A Wesley Mattheus %X %I Sciensano %C Ixelles, Belgium %P 16 %8 13/09/2023 %G eng %0 Journal Article %J Zoonoses Public Health %D 2022 %T Assessing evidence of a potential Salmonella transmission across the poultry food chain. %A Mickael Cargnel %A Maria‐Eleni Filippitzi %A Dieter Van Cauteren %A Wesley Mattheus %A N Botteldoorn %A Cambier,L. %A Sarah Welby %X

Enhanced Salmonella surveillance programmes in poultry were implemented in all European Member States, with minimum prevalence targets for a list of targeted serotypes to safeguard food and public health. Based on the Belgian Salmonella surveillance programme and focusing on poultry, the overarching aim of this study was to highlight possible Salmonella transmissions across the food chain (FC). For this purpose, firstly, the prevalence patterns of Salmonella (targeted and the most prevalent non-targeted) serotypes along the FC were described over time. Secondly, the effectiveness of the control measures against vertical transmission (breeders to 1-day-old broiler and layer chicks) was indirectly assessed by looking into the odds of targeted serotypes detection. Thirdly, it was appraised if Salmonella prevalence can significantly increase during broilers and layers production. In addition, it was tested if being tested negative at the end of production in broilers when tested positive at the entrance is serotype dependent (targeted vs. non-targeted serotypes). Results showed that, firstly, the prevalence patterns of the listed serotypes were inconstant over time and across the FC. Secondly, the odds of Salmonella targeted serotype detection in 1-day-old broiler and in 1-day-old layer flocks were lower than in breeder flocks while, thirdly, infection during broiler and layer production can lead to significant increase in positivity in subsequent samples. Finally, being infected by a targeted or by non-targeted serotype at the entrance of the flock poorly reflects the Salmonella status at the end of production. Note that this study did not make a distinction between the different sources of contamination and the effects of sampling methods and isolation methods should be subject to further investigation.

%B Zoonoses Public Health %8 2022 Sep 08 %G eng %R 10.1111/zph.12998 %0 Generic %D 2022 %T BSFM 2022 - International outbreak of Salmonella Typhimurium linked to a chocolate factory in 2022: Belgian findings %A Laurence Delbrassinne %E Dieter Van Cauteren %E Bavo Verhaegen %E Valeska Laisnez %E Wesley Mattheus %Y Vera Cantaert %Y Géraldine de Muylder %Y Tiffany Dierinck %Y Naïma Hammami %Y Veronica Jaramillo %Y Inne Nauwelaers %Y Koenraad Van Hoorde %K foodborne outbreak %K foodborne outbreak investigation %K Salmonella %X

Introduction

A multi-country outbreak caused by monophasic Salmonella Typhimurium is presented. A link with chocolate products from a Belgian factory was established by epidemiological, microbiological and traceback investigations. Whole genome sequencing (WGS) analysis of human and food isolates revealed the presence of two clusters:  HC5_296366 (cluster 1) and HC5_298160 (cluster 2).  The investigation of the outbreak as well as  measures taken are presented.

Materials and Methods

Probable and confirmed cases were identified using ECDC case definitions. Raw materials and finished food products collected at the factory were analysed for Salmonella spp. using ISO 6579-1:2017 and real-time PCR. WGS analysis of selected food and human isolates was performed.

Results & Discussion

In Belgium 64 confirmed and 2 probable cases were identified (89% children aged 1-9 years old, 43% hospitalizations), with illness onset from mid-January until April and a peak in cases mid-February 2022. WGS data revealed two distinct clusters at 62 allelic differences from each other. Seven of 229 food products tested positive for Salmonella Typhimurium. WGS analysis of the food isolates indicated matches with both clusters. Moreover, in December 2021, Salmonella isolates matching with the later identified clusters had also been found in samples during an own-check in the factory. Eleven types of products were recalled worldwide and food safety authorities shut down the factory 8 April 2022. A strong collaboration and information sharing between different stakeholders resulted in comprehensive measures to stop the spread of this international outbreak.

References

Joint ECDC-EFSA Rapid Outbreak Assessment  https://www.ecdc.europa.eu/sites/default/files/documents/1st-update-ROA_monophasic-S-Typhimurium-ST34_2022-00014_UK-amended-8-June.pdf

RASFF 2022.1799 ; RASFF 2022.2201; RASFF 2022.2452

%B BSFM %I Sciensano %C Brussels, Belgium %P 1 %8 2022/10 %G eng %0 Journal Article %J Euro Surveill %D 2022 %T Changing epidemiology of Enteritidis human infections in the Netherlands and Belgium, 2006 to 2019: a registry-based population study. %A Linda Chanamé Pinedo %A Franz, Eelco %A Maaike van den Beld %A Nina Van Goethem %A Wesley Mattheus %A Kees Veldman %A Thijs Bosch %A Lapo Mughini-Gras %A Roan Pijnacker %K Animals %K Belgium %K Disease Outbreaks %K Humans %K Netherlands %K REGISTRIES %K Salmonella enteritidis %K Salmonella Infections %K Travel %K Travel-Related Illness %X

BackgroundSalmonellosis remains the second most common zoonosis in the European Union despite a long-term decreasing trend. However, this trend has been reported to have stagnated in recent years, particularly for serotype Enteritidis (SE).AimTo describe temporal changes in the incidence of SE human infections, and in its associated factors between 2006 and 2019. In addition, we aim to determine which factors influenced the stagnated trend seen in recent years.MethodsData on culture-confirmed SE human infections from national surveillance registries in the Netherlands and Belgium between 2006 and 2019 were analysed using multivariable negative-binomial regression models with restricted cubic splines.ResultsSE incidence was significantly higher in summer and autumn than winter, in persons aged 0-4 years and 5-14 years than in persons ≥ 60 years, and increased with increasing proportions of travel-related and resistant SE infections. SE incidence decreased significantly in both countries until 2015, followed by an increasing trend, which was particularly pronounced in the Netherlands. Potential SE outbreaks in both countries and invasive infections in the Netherlands also increased after 2015.ConclusionThe increase in potential outbreaks and invasive infections since 2015 may partially explain the observed reversal of the decreasing trend. While these results provide insights into the possible causes of this trend reversal, attention should also be given to factors known to influence SE epidemiology at primary (animal) production and pathogen genomic levels.

%B Euro Surveill %V 27 %8 2022 09 %G eng %N 38 %R 10.2807/1560-7917.ES.2022.27.38.2101174 %0 Journal Article %J Clin Microbiol Infect %D 2022 %T Epidemiological cut-off value and antibiotic susceptibility test methods for azithromycin in a collection of multi-country invasive non-typhoidal Salmonella. %A Bieke Tack %A Phoba, Marie-France %A Thong, Phe %A Lompo, Palpouguini %A Charlien Hupko %A Stefanie Desmet %A Martiny, Delphine %A Wesley Mattheus %A Maria Pardos de la Gandara %A Lisette Mbuyi-Kalonji %A Kuijpers, Laura %A Benoit Prevost %A Barbé, Barbara %A Vandenberg, Olivier %A Lunguya, Octavie %A Joaquim Ruiz %A Jacobs, Jan %A Liselotte Hardy %X

OBJECTIVE: Azithromycin is an alternative to treat invasive non-typhoidal Salmonella (iNTS) infections. We determined its epidemiological cut-off (ECOFF) and compared azithromycin susceptibility testing methods for iNTS.

METHODS: We used EUCAST ECOFFinder to determine the minimum inhibitory concentrations (MIC; obtained by broth microdilution) ECOFF and corresponding disk zone diameters of 515 iNTS from blood cultures in Democratic Republic of Congo, Burkina Faso, Rwanda, and Cambodia. Transferable resistance mechanisms were determined by polymerase chain reaction. We compared azithromycin susceptibility testing by semi-automated broth microdilution (customized Sensititre panel; reference), agar dilution, gradient tests (bioMérieux, Liofilchem, HiMedia; read at 80% (MIC80%) and 100% inhibition (MIC100%)), and disk diffusion (Rosco, Oxoid, BD, Liofilchem) for 161 wild- and 198 non-wild-type iNTS.

RESULTS: Azithromycin MIC ECOFF was 16 mg/L corresponding to a 12 mm zone diameter; mphA was detected in 192/197 non-wild- and 0/47 wild-type iNTS. Categorical agreement was excellent (≥98%) for all methods. Essential agreement was very good for agar dilution (>90%) but moderate for gradient tests (MIC80%: 52% to 71% and MIC100%: 72% to 91%). Repeatability was good for all methods/brands. Interreader agreement was high for broth microdilution and agar dilution (all ≤1 twofold dilution difference) and disk diffusion (>96% ≤3 mm difference) but lower for gradient tests (MIC80% & MIC100%: 83% to 94% ≤1 twofold dilution difference).

DISCUSSION: Azithromycin ECOFF of iNTS was 16 mg/L, i.e. equal to Salmonella Typhi. Disk diffusion is an accurate, precise, and user-friendly alternative for agar dilution and broth microdilution. Reading gradient tests at 100% instead of 80% inhibition improved accuracy and precision.

%B Clin Microbiol Infect %8 2022 Jun 20 %G eng %R 10.1016/j.cmi.2022.06.009 %0 Report %D 2022 %T Epidemiologische surveillance van invasieve meningokokkeninfecties - 2021 %A Stéphanie Jacquinet %A Wesley Mattheus %X %P 13 %8 1/08/2022 %G eng %0 Generic %D 2022 %T ESCAIDE 2022 Oral presentation: International outbreak of Salmonella Typhimurium linked to a chocolate factory in 2022: Belgian findings %A Valeska Laisnez %A Vera Cantaert %A Laurence Delbrassinne %A Géraldine de Muylder %A Tiffany Dierinck %A Hammami, Naïma %A Veronica Jaramillo %A Wesley Mattheus %A Inne Nauwelaers %A Bavo Verhaegen %A Dieter Van Cauteren %X

Background

Mid-February 2022, the United Kingdom reported via EpiPulse a cluster of monophasic Salmonella Typhimurium infections. Epidemiological and traceback investigations revealed a multi-country outbreak linked to chocolate products from a Belgian factory of an international brand. Microbiological investigations indicated two clusters:  HC5_296366 (cluster 1) and HC5_298160 (cluster 2).  We assessed the extent of the outbreak in Belgium and took measures to limit further spread.

Methods

Probable and confirmed cases were identified using ECDC case definitions. Case-interviews focused on exposure to chocolate products of the concerned brand. Raw materials and finished food products collected at the factory were analysed for Salmonella spp. using real-time PCR. Whole genome sequence (WGS) analysis of isolates of probable cases and positive food samples is still ongoing.

Results

We identified 62 probable cases (39 cluster 1, 23 cluster 2), with illness onset from mid-January until April and a peak in cases mid-February 2022. Of these 62 cases, 54 were aged 1-9 years old. Among the 44 interviewed cases, 19 have been hospitalized and 41 reported consumption of products of the factory among whom 35 reported consumption of Kinder Surprise. Seven of 229 food products tested positive for Salmonella; WGS analysis indicated matches with both clusters. In December 2021, Salmonella was found in samples during a self-check in the factory, these isolates matched with the later identified clusters. Eleven types of products were recalled worldwide and food safety authorities shut down the factory 8 April 2022.

Conclusions

Epidemiological and microbiological investigations confirmed the link between Salmonella cases and products from a Belgian chocolate factory. A strong collaboration and information sharing between different stakeholders resulted in comprehensive measures to stop the spread of this international outbreak.

%B ESCAIDE %8 2022-11-25 %G eng %0 Journal Article %J Euro Surveill %D 2022 %T Investigation of an international outbreak of multidrug-resistant monophasic Typhimurium associated with chocolate products, EU/EEA and United Kingdom, February to April 2022. %A Lesley Larkin %A Maria Pardos de la Gandara %A Ann Hoban %A Caisey Pulford %A Nathalie Jourdan-Da Silva %A Henriette de Valk %A Lynda Browning %A Gerhard Falkenhorst %A Sandra Simon %A Raskit Lachmann %A Dryselius, Rikard %A Nadja Karamehmedovic %A Stefan Börjesson %A Dieter Van Cauteren %A Valeska Laisnez %A Wesley Mattheus %A Roan Pijnacker %A Maaike van den Beld %A Mossong, Joel %A Ragimbeau, Catherine %A Vergison, Anne %A Lin Thorstensen Brandal %A Heidi Lange %A Patricia Garvey %A Charlotte Salgaard Nielsen %A Silvia Herrera León %A Carmen Varela %A Marie Chattaway %A Weill, François-Xavier %A Derek Brown %A Paul McKeown %K Child %K Child, Preschool %K chocolate %K Disease Outbreaks %K Humans %K Salmonella typhimurium %K United Kingdom %X

An extensive multi-country outbreak of multidrug-resistant monophasic Typhimurium infection in 10 countries with 150 reported cases, predominantly affecting young children, has been linked to chocolate products produced by a large multinational company. Extensive withdrawals and recalls of multiple product lines have been undertaken. With Easter approaching, widespread product distribution and the vulnerability of the affected population, early and effective real-time sharing of microbiological and epidemiological information has been of critical importance in effectively managing this serious food-borne incident.

%B Euro Surveill %V 27 %8 2022 04 %G eng %N 15 %R 10.2807/1560-7917.ES.2022.27.15.2200314 %0 Generic %D 2022 %T The key role of WGS-based surveillance of Listeria monocytogenes in both human and food isolates in outbreak investigations %A An Van den Bossche %A Sigrid C.J. De Keersmaecker %A Wesley Mattheus %A Nancy Roosens %A Bert Bogaerts %A Kevin Vanneste %A Koenraad Van Hoorde %A Bavo Verhaegen %K cgMLST %K Listeria monocytogenes %K NGS %K outbreak %B 26th Conference on Food Microbiology %I BSFM %C Brussels, Belgium %8 13-14/10/2022 %G eng %N BSFM %0 Journal Article %J Acta Clin Belg %D 2022 %T Meningococcal pericarditis caused by the MenW:cc11 strain in an older adult. %A Gaëlle Moerman %A D Verleyen %A Ph Rogiers %A J Hoste %A Wesley Mattheus %A K Floré %X

INTRODUCTION: Invasive meningococcal disease (IMD) caused by is a disease with a high mortality and morbidity rate. Serogroup W meningococci (MenW) used to be associated with sporadic disease worldwide. In recent years, a surge in MenW incidence is being observed.

REPORT: An older adult presenting with acute onset shortness of breath, chest pain and fever, was diagnosed with pericarditis with meningococcemia due to MenW:ST11 strain. MenW infections are reported to have a higher case fatality rate and atypical clinical presentations: MenW has been identified in patients presenting with pneumonia, gastro-intestinal symptoms, arthritis, and pericarditis.

DISCUSSION: In Belgium, the National Reference Laboratory is also noticing an increase in serogroup Wmeningococcal disease. Recent epidemiological data for Belgium is reported in the article. MenW infections are reported to have a higher case fatality rate and atypical clinical presentations: MenW has been identified in patients presenting with pneumonia, gastro-intestinal symptoms, arthritis, and pericarditis.

CONCLUSION: When factors for poor prognosis are present in patients with pericarditi clinicians should be vigilant and search for the underlying aetiology .

%B Acta Clin Belg %8 2022 Jul 29 %G eng %R 10.1080/17843286.2022.2107315 %0 Journal Article %J Eurosurveillance %D 2022 %T Outbreak of invasive meningococcal disease caused by a meningococcus serogroup B in a nursery school, Wallonia, Belgium, 2018 %A Stéphanie Jacquinet %A Wesley Mattheus %A Sophie Quoilin %A Chloé Wyndham-Thomas %A Charlotte Martin %A Dimitri Van der Linden %A André Mulder %A Julie Frère %A Schirvel, Carole %B Eurosurveillance %V 27 %8 Mar-03-2022 %G eng %N 9 %R 10.2807/1560-7917.ES.2022.27.9.2100224 %0 Generic %D 2022 %T Shotgun metagenomics as a ONE Health tool for better protecting human health %A Mathieu Gand %A Florence E Buytaers %A Bram Bloemen %A Assia Saltykova %A Sarah Denayer %A Bavo Verhaegen %A Wesley Mattheus %A Denis Piérard %A Bert Bogaerts %A Kathleen Marchal %A The FARMED consortium %A Nancy Roosens %A Kevin Vanneste %A Sigrid C.J. De Keersmaecker %X

Introduction: Open approaches to identify all biological material in a sample without a priori knowing what to look for, could transform the way specific key public health questions can be addressed, in a ONE Health context. Metagenomics is defined as the study of all genetic material within a sample, using sequencing technologies. Shotgun metagenomics is capable of detecting a wide range of microorganisms in a sample, as well as their composing genes such as virulence or antimicrobial resistance (AMR) genes, without prior knowledge, nor the need to isolate. Such approaches could offer efficient and fast solutions to limitations faced by conventional methods in e.g. the field of pathogen detection/characterization along the food chain, starting from the food production environment (including detection of AMR genes) until foodborne outbreak investigation and clinical/veterinary diagnostics. This could also allow a better understanding of infectious diseases and accurate risk (safety) assessment in food safety issues. However, before it can be used in these settings, this approach should be appropriately developed and validated from sampling and DNA extraction to sequencing and data analysis.

Methodology: Third generation sequencing technologies have had a breakthrough with the launch of nanopore sequencing, which through the production of long sequencing reads, portability and real-time data generation, represents a disruptive innovation for microbiology. Compared to short read sequencing (Illumina), this technology allows to unambiguously detect and scaffold microbial genes to their host chromosomes, even for complex metagenomics samples, allowing taxonomic classification up to an unprecedented sensitivity, including the identification of linked specific genes, such as AMR or virulence genes. We are developing and optimizing the protocols (from DNA extraction to data analysis) for sensitive metagenomics, by analyzing various materials collected in food-producing environments, and spiked with defined mock communities, composed of different bacterial species in various concentrations and carrying AMR and/or virulence genes, taking the specific need of each application into account. Moreover, the short read and long read approaches are being compared to each other, and also to the results obtained with conventional methods.

Results: A commercial kit was selected and optimized for the extraction of sufficient high-molecular weight DNA, to match the needs for long-read sequencing. The analysis of animal and environmental samples collected at a production farm, subsequently spiked with bacterial species present at various concentrations and carrying AMR genes, allowed to identify the spiked species and to make the link with AMR genes detected in the same sample when found on the same reads used for taxonomic identification, except for species present at low concentrations. Comparable results were obtained using short-read sequencing, without being able to link the identified species with the detected AMR genes. Our approach was also successful on artificially contaminated food samples. It allowed the same characterization of the foodborne pathogen (serotyping, virulence genes, relatedness to other cases) as the conventional methods used in reference laboratories, however without isolation and in a shorter time-frame. This could be achieved to the strain level even in samples with several E. coli strains. The method was also used to solve a Salmonella food-borne outbreak that occurred in Belgium in 2019.

Discussion: By applying the shotgun metagenomics approach to specific case studies, we delivered proof-of-concepts and demonstrated its added value compared to the conventional methods. We proved that it can characterize a bacterial pathogen to the strain level in spiked food as well as in the context of a real outbreak, and resolve the investigation in a faster time frame. EFSA called for such proof-of-concepts in a recent opinion about the use of metagenomics for food safety.  Additionally, we showed that the use of long-read sequencing can help to achieve a higher level of resolution by identifying specific bacteria and the AMR genes present in their genomes, with only one analysis. Future studies will explore at the technical level how this new technology can be transferred for fast, easy and direct use on-site, in a food-producing environment. This will open up ample opportunities for future research in the different fields, and even beyond, where the metagenomics approach would then be a well-established tool to be used to address specific public health questions at a more detailed and extended/comprehensive level, contributing to better protection of human health.

%B EFSA One %8 21/06/2022 %G eng %N EFSA %0 Report %D 2022 %T Surveillance épidémiologique des infections invasives à méningocoques - 2021 %A Stéphanie Jacquinet %A Wesley Mattheus %X %P 13 %8 1/08/2022 %G eng %0 Journal Article %J PLoS Negl Trop Dis %D 2022 %T Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo. %A Falay, Dadi %A Liselotte Hardy %A Jacques Tanzito %A Lunguya, Octavie %A Edmonde Bonebe %A Marjan Peeters %A Wesley Mattheus %A Van Geet, Chris %A Verheyen, Erik %A Dudu Akaibe %A Pionus Katuala %A Ngbonda, Dauly %A Weill, François-Xavier %A Maria Pardos de la Gandara %A Jacobs, Jan %K Animals %K Child %K Democratic Republic of the Congo %K Humans %K Multilocus Sequence Typing %K rats %K Salmonella Infections %K Salmonella typhimurium %K Serogroup %X

BACKGROUND: Invasive non-typhoidal Salmonella (iNTS-mainly serotypes Enteritidis and Typhimurium) are major causes of bloodstream infections in children in sub-Saharan Africa, but their reservoir remains unknown. We assessed iNTS carriage in rats in an urban setting endemic for iNTS carriage and compared genetic profiles of iNTS from rats with those isolated from humans.

METHODOLOGY/PRINCIPAL FINDINGS: From April 2016 to December 2018, rats were trapped in five marketplaces and a slaughterhouse in Kisangani, Democratic Republic of the Congo. After euthanasia, blood, liver, spleen, and rectal content were cultured for Salmonella. Genetic relatedness between iNTS from rats and humans-obtained from blood cultures at Kisangani University Hospital-was assessed with multilocus variable-number tandem repeat (VNTR) analysis (MLVA), multilocus sequence typing (MLST) and core-genome MLST (cgMLST). 1650 live-capture traps yielded 566 (34.3%) rats (95.6% Rattus norvegicus, 4.4% Rattus rattus); 46 (8.1%) of them carried Salmonella, of which 13 had more than one serotype. The most common serotypes were II.42:r:- (n = 18 rats), Kapemba (n = 12), Weltevreden and Typhimurium (n = 10, each), and Dublin (n = 8). Salmonella Typhimurium belonged to MLST ST19 (n = 7 rats) and the invasive ST313 (n = 3, isolated from deep organs but not from rectal content). Sixteen human S. Typhimurium isolates (all ST313) were available for comparison: MLVA and cgMLST revealed two distinct rat-human clusters involving both six human isolates, respectively, i.e. in total 12/16 human ST313 isolates. All ST313 Typhimurium isolates from rats and humans clustered with the ST313 Lineage 2 isolates and most were multidrug resistant; the remaining isolates from rats including S. Typhimurium ST19 were pan-susceptible.

CONCLUSION: The present study provides evidence of urban rats as potential reservoirs of S. Typhimurium ST313 in an iNTS endemic area in sub-Saharan Africa.

%B PLoS Negl Trop Dis %V 16 %8 2022 09 %G eng %N 9 %R 10.1371/journal.pntd.0010740 %0 Journal Article %J Microbial Genomics %D 2021 %T Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak %A Florence E Buytaers %A Assia Saltykova %A Wesley Mattheus %A Bavo Verhaegen %A Nancy Roosens %A Kevin Vanneste %A Valeska Laisnez %A Hammami, Naïma %A Pochet, Brigitte %A Vera Cantaert %A Marchal, Kathleen %A Sarah Denayer %A Sigrid C.J. De Keersmaecker %K food surveillance %K Metagenomics %K outbreak %K Salmonella %K SNP analysis %K strain-level %X

Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to more easily obtained isolates from infected people. When no food isolate can be obtained, the source of the outbreak cannot be unambiguously determined. Shotgun metagenomics approaches applied to the food samples could circumvent this need for isolation from the suspected source, but require downstream strain-level data analysis to be able to accurately link to the human isolate. Until now, this approach has not yet been applied outside research settings to analyse real food-borne outbreak samples. In September 2019, a Salmonella outbreak occurred in a hotel school in Bruges, Belgium, affecting over 200 students and teachers. Following standard procedures, the Belgian National Reference Center for human salmonellosis and the National Reference Laboratory for Salmonella in food and feed used conventional analysis based on isolation, serotyping and MLVA (multilocus variable number tandem repeat analysis) comparison, followed by whole-genome sequencing, to confirm the source of the contamination over 2 weeks after receipt of the sample, which was freshly prepared tartar sauce in a meal cooked at the school. Our team used this outbreak as a case study to deliver a proof of concept for a short-read strain-level shotgun metagenomics approach for source tracking. We received two suspect food samples: the full meal and some freshly made tartar sauce served with this meal, requiring the use of raw eggs. After analysis, we could prove, without isolation, that Salmonella was present in both samples, and we obtained an inferred genome of a Salmonella enterica subsp. enterica serovar Enteritidis that could be linked back to the human isolates of the outbreak in a phylogenetic tree. These metagenomics-derived outbreak strains were separated from sporadic cases as well as from another outbreak circulating in Europe at the same time period. This is, to our knowledge, the first Salmonella food-borne outbreak investigation uniquely linking the food source using a metagenomics approach and this in a fast time frame.

%B Microbial Genomics %V 7 %8 Jul-04-2021 %G eng %N 4 %R 10.1099/mgen.0.000547 %0 Report %D 2021 %T Bulletin d’information Méningococcies 2021 (T4) %A Wesley Mattheus %I Sciensano %C Bruxelles, Belgique %G eng %0 Journal Article %J PLoS One %D 2021 %T Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020. %A Nina Van Goethem %A An Van den Bossche %A Pieter-Jan Ceyssens %A Adrien Lajot %A Wim Coucke %A Kris Vernelen %A Nancy Roosens %A Sigrid C.J. De Keersmaecker %A Dieter Van Cauteren %A Wesley Mattheus %K Belgium %K Diagnostic Tests, Routine %K Disease Outbreaks %K Humans %K Public Health Surveillance %K Salmonella %K Salmonella Food Poisoning %K Salmonella Infections %K whole genome sequencing %X

INTRODUCTION: The surveillance of human salmonellosis in Belgium is dependent on the referral of human Salmonella isolates to the National Reference Center (NRC). Knowledge of current diagnostic practices and the coverage of the national Salmonella surveillance system are important to correctly interpret surveillance data and trends over time, to estimate the true burden of salmonellosis in Belgium, and to evaluate the appropriateness of implementing whole-genome sequencing (WGS) at this central level.

METHODS: The coverage of the NRC was defined as the proportion of all diagnosed human Salmonella cases in Belgium reported to the NRC and was assessed for 2019 via a survey among all licensed Belgian medical laboratories in 2019, and for 2016-2020 via a capture-recapture study using the Sentinel Network of Laboratories (SNL) as the external source. In addition, the survey was used to assess the impact of the implementation of culture-independent diagnostic tests (CIDTs) at the level of peripheral laboratory sites, as a potential threat to national public health surveillance programs.

RESULTS: The coverage of the NRC surveillance system was estimated to be 83% and 85%, based on the results of the survey and on the two-source capture-recapture study, respectively. Further, the results of the survey indicated a limited use of CIDTs by peripheral laboratories in 2019.

CONCLUSION: Given the high coverage and the limited impact of CIDTs on the referral of isolates, we may conclude that the NRC can confidently monitor the epidemiological situation and identify outbreaks throughout the country. These findings may guide the decision to implement WGS at the level of the NRC and may improve estimates of the true burden of salmonellosis in Belgium.

%B PLoS One %V 16 %8 2021 %G eng %N 8 %R 10.1371/journal.pone.0256820 %0 Report %D 2021 %T Epidemiologische surveillance van invasieve meningokokkeninfecties - 2019 %A Stéphanie Jacquinet %A Wesley Mattheus %A Adrien Lajot %A Chloé Wyndham-Thomas %A Amber Litzroth %X %P 13 %8 02/2021 %G eng %0 Journal Article %J Journal of Antimicrobial Chemotherapy %D 2021 %T Genomic epidemiology of persistently circulating MDR Shigella sonnei strains associated with men who have sex with men (MSM) in Belgium (2013–19) %A Nathalie Fischer %A Margo Maex %A Wesley Mattheus %A An Van den Bossche %A Dieter Van Cauteren %A Valeska Laisnez %A Hammami, Naïma %A Pieter-Jan Ceyssens %X

OBJECTIVESShigella sonnei resistant to first-line antibiotics azithromycin and ciprofloxacin are on the rise globally. The aim of this study was to describe the epidemiology of MDR S. sonnei in Belgium and to identify origins and circulating clusters through WGS.

METHODS: We undertook demographic, temporal and geographical analysis of 930 S. sonnei isolates submitted to the Belgian National Reference Centre for Salmonella and Shigella between 2017 and 2019. Phylogenetic analysis of WGS data, genotyping and identification of genetic markers of antimicrobial resistance was performed on 372 Belgian isolates submitted between 2013 and 2019.

RESULTSS. sonnei was identified in 75% (930/1253) of Belgian Shigella isolates submitted between 2017 and 2019. Overall, 7% (69/930) of isolates were resistant to ciprofloxacin alone, 6% (57/930) showed reduced susceptibility to azithromycin alone, and 24% (223/930) exhibited both. Men were at higher risk of carrying a double resistant S. sonnei strain, compared with women (risk ratio = 8.6, 95% CI = 5.4-13.9). Phylogenetic analysis revealed four independent Belgian clusters of persistently circulating MDR strains, associated with men who have sex with men (MSM) and of the same genotypes as previously described international MSM-related clades. Belgian isolates carried various incompatibility (Inc)-type plasmids, the SpA plasmid and ESBL genes.

CONCLUSIONS: In Belgium, S. sonnei isolates from men are much more likely to be resistant to important first-line antibiotics than isolates from women. Multiple co-circulating MDR S. sonnei clusters of different genotypes were identified in the MSM community. Further studies on risk groups are needed for targeted prevention, improved clinical and public health management and antimicrobial stewardship in Belgium.

%B Journal of Antimicrobial Chemotherapy %V 77 %8 Sep-10-2022 %G eng %N 1 %R 10.1093/jac/dkab377 %0 Journal Article %J Pathogens %D 2021 %T Identification of the Source for Contamination of Carcasses in a Large Pig Slaughterhouse. %A Zeng, Hang %A Rasschaert, Geertrui %A L. De Zutter %A Wesley Mattheus %A De Reu, Koen %X

To identify the major source of contamination in a pig slaughterhouse, samples were collected from the clean and unclean area and isolates were further typed. Carcasses entering the clean area showed a contamination rate of 96.7% in the oral cavity and 55.0% in the rectum content samples. Evisceration seemed not to be critical as the contamination rate of the carcasses was similar before (16.7%) and after (18.3%) this slaughter step. In the unclean area, a limited number of oral cavity samples were positive after bleeding, while a dramatic increase of positives was observed after dehairing. was detected in up to 0.01 mL of the recycled water collected from the dehairing machine. Genotyping of isolates showed that similar pulsotypes were present in the oral cavity and recycled water. Based on these observations it can be concluded that the recycled water used in the dehairing machine was the major source for the carcass contamination in this slaughterhouse.

%B Pathogens %V 10 %8 2021 Jan 17 %G eng %N 1 %R 10.3390/pathogens10010077 %0 Report %D 2021 %T Infoblad Meningokokkeninfecties 2021 (T4) %A Wesley Mattheus %I Sciensano %C Brussel, België %G eng %0 Journal Article %J Journal of Microbiological Methods %D 2021 %T A molecular assay for rapidly distinguishing the AviPro SALMONELLA VAC T vaccine strain from wild-type field isolates %A Pieter-Jan Ceyssens %A An Van den Bossche %A Lac Kim Phan %A Koenraad Van Hoorde %A Wesley Mattheus %K Luminex-based multiplex test %K Molecular differentiation %K Salmonella typhimurium %K Vac T %K vaccin %X

Rapid differentiation of the AviPro Salmonella VAC T strain from wild-type Salmonella ser. Typhimurium isolates is essential for the monitoring of veterinary isolates and targeted control actions. The distinction between the two strain types is routinely made by phenotypic antimicrobial resistance testing, but this sometime leads to ambiguous results with major economic implications. In this study, we used whole-genome sequencing to identify conserved and specific mutations in resistance and virulence genes which enable to distinguish field and vaccine strains. Based on this information, we developed and validated (n = 199) a Luminex-based assay targeting seven specific single-nucleotide polymorphisms. This molecular test is able to distinguish both Salmonella ser. Typhimurium types with 100% sensitivity and specificity within one working day.

%B Journal of Microbiological Methods %V 184 %8 May-2021 %G eng %R 10.1016/j.mimet.2021.106190 %0 Journal Article %J European Journal of Clinical Microbiology & Infectious Diseases %D 2021 %T Outbreak of Central American born Shigella sonnei in two youth camps in Belgium in the summer of 2019 %A An Van den Bossche %A Pieter-Jan Ceyssens %A Sarah Denayer %A Naïma Hammami %A Maaike van den Beld %A Timothy J Dallman %A Wesley Mattheus %K Cluster analyses %K Next-generation sequencing %K outbreak %K Shigella sonnei %X

In 2019, an outbreak of Shigella sonnei occurred during two youth camps in Belgium. The clustering of isolates from both camps was confirmed by next-generation sequencing, as well as a secondary infection of a technician. The outbreak strain clustered with internationally isolated strains from patients with recent travel history to Central America. This report exemplifies enhanced surveillance and international collaboration between public health institutes by enabling to link local outbreaks to region-specific sublineages circulating abroad. 

%B European Journal of Clinical Microbiology & Infectious Diseases %8 2021 Feb 11 %G eng %R https://doi.org/10.1007/s10096-021-04164-y %0 Journal Article %J Microorganisms %D 2021 %T Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation. %A Bert Bogaerts %A Raf Winand %A Julien Van Braekel %A Wesley Mattheus %A Sigrid C.J. De Keersmaecker %A Nancy Roosens %A Marchal, Kathleen %A Kevin Vanneste %A Pieter-Jan Ceyssens %X

Shigellosis is an acute enteric infection caused mainly by the species and . Since surveillance of these pathogens indicated an increase in ciprofloxacin-resistant samples collected in Belgium between 2013 and 2018, a subset of 148 samples was analyzed with whole genome sequencing (WGS) to investigate their dispersion and underlying genomic features associated with ciprofloxacin resistance. A comparison between observed phenotypes and WGS-based resistance prediction to ciprofloxacin revealed perfect correspondence for all samples. Core genome multi-locus sequence typing and single nucleotide polymorphism-typing were used for phylogenomic investigation to characterize the spread of these infections within Belgium, supplemented with data from international reference collections to place the Belgian isolates within their global context. For , substantial diversity was observed with ciprofloxacin-resistant isolates assigned to several phylogenetic groups. Besides travel-related imports, several clusters of highly similar Belgian isolates could not be linked directly to international travel suggesting the presence of domestically circulating strains. For , Belgian isolates were all limited to lineage III, and could often be traced back to travel to countries in Asia and Africa, sometimes followed by domestic circulation. For both species, several clusters of isolates obtained exclusively from male patients were observed. Additionally, we illustrated the limitations of conventional serotyping of , which was impacted by serotype switching. This study contributes to a better understanding of the spread of shigellosis within Belgium and internationally, and highlights the added value of WGS for the surveillance of this pathogen.

%B Microorganisms %V 9 %8 2021 Apr 06 %G eng %N 4 %R 10.3390/microorganisms9040767 %0 Journal Article %J Foodborne Pathog Dis %D 2021 %T Prevalence, Antimicrobial Resistance, and Molecular Characterization of in Cattle, Beef, and Diarrheic Patients in Bishoftu, Ethiopia. %A Fanta D Gutema %A Rasschaert, Geertrui %A Getahun E Agga %A Olana Merera %A Addisu B Duguma %A Reta D Abdi %A Duchateau, Luc %A Wesley Mattheus %A Gabriël, Sarah %A de Zutter, Lieven %K Abattoirs %K ADOLESCENT %K Adult %K Aged %K Aged, 80 and over %K Animals %K Anti-Bacterial Agents %K Cattle %K Cattle Diseases %K Child %K Child, Preschool %K Diarrhea %K Drug Resistance, Multiple, Bacterial %K Ethiopia %K Female %K Food Microbiology %K Humans %K Infant %K Male %K Microbial Sensitivity Tests %K middle aged %K prevalence %K Red Meat %K Salmonella %K Salmonella Infections %K Salmonella Infections, Animal %K Serotyping %K Young adult %X

Within Ethiopia, there is a lack of information on the genetic relatedness of from cattle, beef, and diarrheic patients and its potential transmission from cattle to humans through consumption of contaminated beef. The objective of this study was to assess the prevalence and determine the serotypes, genetic relatedness, and antimicrobial resistance of in cattle in two local slaughterhouses, in beef at retail shops, and in diarrheic patients in the only hospital in Bishoftu, Ethiopia. was detected in 2.5% (6/240) of cattle samples, in 8.7% (11/127) of beef samples, and in 2.3% (5/216) of the diarrheic patients. Four serotypes: Typhimurium, Eastbourne, Saintpaul, and Cotham were identified. Typhimurium and Eastbourne were isolated from cattle and beef, whereas Saintpaul and Cotham were isolated only from diarrheic patients. Except for serotype Saintpaul, all isolates were grouped into five pulsotypes, of which two pulsotypes contained isolates from cattle and beef. Isolates from humans represented unique pulsotypes. Among the 22 isolates tested, 95.5% were resistant to at least 1 of the 14 antimicrobials tested. Three isolates originating from cattle were multidrug resistant. One human isolate was susceptible to all antimicrobials tested. More specifically, resistance to ampicillin, sulfamethoxazole, tetracycline, tigecycline, and trimethoprim were observed. The most frequently observed resistance was to sulfamethoxazole (90.9%, 20/22) followed by trimethoprim (22.7%, 5/22). The study revealed considerable contamination of beef at retail shops, antimicrobial resistance to commonly used antimicrobials, and shared genetically similar serotypes between cattle and beef; the link with humans could not be established. Still, the findings of in cattle and beef, the propensity of transfer of from cattle to beef coupled with the common consumption of raw/undercooked beef are likely to pose public health risk in Ethiopia.

%B Foodborne Pathog Dis %V 18 %8 2021 04 %G eng %N 4 %R 10.1089/fpd.2020.2869 %0 Journal Article %J Poult Sci %D 2021 %T Salmonella prevalence and persistence in industrialized poultry slaughterhouses. %A Zeng, Hang %A De Reu, K %A Gabriël, S %A Wesley Mattheus %A De Zutter, L %A Rasschaert, G %K Abattoirs %K Animals %K Chickens %K Food Industry %K Food Microbiology %K Poultry %K prevalence %K Salmonella %X

Salmonella contamination sources and transmission routes were studied in 5 Belgian poultry slaughterhouses. Samples from the slaughter and cutting line after cleaning and disinfection were collected, as well as neck skin samples and thighs during slaughter of the first flock. In total, 680 swab and water samples were taken from the slaughter line before slaughter. In all slaughterhouses, Salmonella was notwithstanding cleaning and disinfection still isolated from the slaughter line before start of activities. The prevalence of Salmonella in the plucking area was 10.4% (38/365) (hanging area: 5.0%, scalding tank: 5.8%, plucking machine: 17.0%); in the evisceration room, 1.5% (2/138); and in the cutting area, 2.0% (3/149). No Salmonella (0/28) was found in samples from the chilling line. On neck skin samples taken from the various lines, Salmonella prevalence was 16.1% (48/299) after plucking, 16.0% (48/300) after evisceration, 23.3% (70/300) after chilling; on thighs, prevalence was 10.0% (24/240). Nine Salmonella serotypes were identified of which Salmonella Infantis was the most common serovar (53.8%), especially in slaughterhouse A. Two contamination causes were identified; first, although all flocks had an official Salmonella negative status, this was in one case incorrect and led to an enormous contamination of the neck skins of the flock and the slaughterline (i.e., cooling water). Second, molecular typing revealed cross-contamination from flocks slaughtered 1 d before sampling. Salmonella was apparently not always eliminated by the cleaning and disinfection process and able to contaminate the carcasses of the first slaughtered flock. In conclusion, the results of this study provided practical insights for poultry production to further improve their Salmonella control, for example, Salmonella status determination closer to the slaughter date, to adapt cleaning and disinfection protocols especially for critical machinery and better hygienic designed equipment.

%B Poult Sci %V 100 %8 2021 Apr %G eng %N 4 %R 10.1016/j.psj.2021.01.014 %0 Report %D 2021 %T Surveillance épidémiologique des infections invasives à méningocoques - 2020 %A Stéphanie Jacquinet %A Wesley Mattheus %A Adrien Lajot %A Chloé Wyndham-Thomas %A Tine Grammens %X %P 12 %8 9/06/2021 %G eng %0 Journal Article %J Preventive Veterinary Medicine %D 2020 %T Bacteriological evaluation of vaccination against Salmonella Typhimurium with an attenuated vaccine in subclinically infected pig herds %A Linda Peeters %A Dewulf, Jeroen %A Boyen, Filip %A Charlotte Brossé %A Tamara Vandersmissen %A G. Rasschaert %A Heyndrickx, Marc %A Mickael Cargnel %A Wesley Mattheus %A Pasmans, Frank %A Haesebrouck, Freddy %A Maes, Dominiek %B Preventive Veterinary Medicine %V 182 %8 Jan-09-2020 %G eng %R 10.1016/j.prevetmed.2019.04.016 %0 Report %D 2020 %T Epidemiologische surveillance van invasieve meningokokkeninfecties - data 2019 %A Stéphanie Jacquinet %A Wesley Mattheus %A Adrien Lajot %A Chloé Wyndham-Thomas %A Amber Litzroth %X %P 13 %8 02/2020 %G eng %0 Journal Article %J Preventive Veterinary Medicine %D 2020 %T Evaluation of group vaccination of sows and gilts against Salmonella Typhimurium with an attenuated vaccine in subclinically infected pig herds %A Linda Peeters %A Dewulf, Jeroen %A Boyen, Filip %A Charlotte Brossé %A Tamara Vandersmissen %A Rasschaert, Geertrui %A Heyndrickx, Marc %A Mickael Cargnel %A Wesley Mattheus %A Pasmans, Frank %A F. Haesebrouck %A Maes, Dominiek %B Preventive Veterinary Medicine %V 182 %8 Jan-09-2020 %G eng %R 10.1016/j.prevetmed.2020.104884 %0 Journal Article %J Food Microbiol %D 2020 %T A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium. %A Mathieu Gand %A Wesley Mattheus %A Nancy Roosens %A Katelijne Dierick %A Marchal, Kathleen %A Sophie Bertrand %A Sigrid C.J. De Keersmaecker %K Salmonella; Genoserotyping; Luminex; Decision support system; Food safety %X

Humans are mostly contaminated by Salmonella through the consumption of pork- and poultry-derived food products. Therefore, a strict monitoring of Salmonella serotypes in food-producing animals is needed to limit the transmission of the pathogen to humans. Additionally, Salmonella can lead to economic loss in the food sector. Previously, a genoserotyping method using the MOL-PCR and Luminex technology was developed for the identification of the 6 Salmonella serotypes, and their variants, subjected to an official control in the Belgian food sector. In this study, 3 additional assays using the same technology were developed for the rapid and cost-effective detection of 13 dangerous highly invasive serotypes or other serotypes frequently isolated from the Belgian poultry and pork sector, i.e. Agona, Anatum, Brandenburg, Choleraesuis, Derby, Enteritidis vaccine strains, Gallinarum var. Gallinarum/Pullorum, Livingstone, Mbandaka, Minnesota, Ohio, Rissen and Senftenberg. Moreover, the previously developed first MOL-PCR assay was improved for S. Paratyphi B and serogroup O:3 detection. Finally, a Decision Support System hosted by a web application was created for an automatic and objective interpretation of the Luminex raw data. The 3 new assays and the modifications of the first assay were validated with a 100% accuracy, using 553 Salmonella and non-Salmonella strains in total.

%B Food Microbiol %V 91 %8 2020 Oct %G eng %R 10.1016/j.fm.2020.103534 %0 Government Document %D 2020 %T Infoblad meningokokkeninfecties 2020 (T1) %A Wesley Mattheus %K Meningococcal Infections %B None %I Sciensano %C Brussels %8 2020 %G eng %0 Report %D 2020 %T Infoblad meningokokkeninfecties 2020 (T4) %A Wesley Mattheus %K Meningitis %I Sciensano %C Brussels, Belgium %P 1 %8 17/02/2021 %G eng %M NA %0 Journal Article %J Food Microbiology %D 2020 %T A multiplex oligonucleotide ligation-PCR method for the genoserotyping of common Salmonella using a liquid bead suspension assay %A Mathieu Gand %A Wesley Mattheus %A Nancy Roosens %A Katelijne Dierick %A Marchal, Kathleen %A Sigrid C.J. De Keersmaecker %A Sophie Bertrand %B Food Microbiology %V 87 %8 Jan-05-2020 %G eng %R 10.1016/j.fm.2019.103394 %0 Report %D 2020 %T Surveillance épidémiologique des infections invasives à méningocoques - données 2019 %A Stéphanie Jacquinet %A Wesley Mattheus %A Adrien Lajot %A Chloé Wyndham-Thomas %A Amber Litzroth %X %P 13 %8 02/2020 %G eng %0 Journal Article %J Front Microbiol %D 2019 %T Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: as a Proof of Concept. %A Assia Saltykova %A Wesley Mattheus %A Sophie Bertrand %A Nancy Roosens %A Marchal, Kathleen %A Sigrid C.J. De Keersmaecker %X

Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized and verified data analysis methods. However, multiple subtyping workflows are now often being used for a single organism, and differences between them are not always well described. Moreover, methodologies for comparison of subtyping workflows, and assessment of their performance are only beginning to emerge. Current work focuses on the detailed comparison of WGS-based subtyping workflows and evaluation of their suitability for the organism and the research context in question. We evaluated the performance of pipelines used for subtyping of , including the currently widely applied cgMLST approach and different SNP-based methods. In addition, the impact of the use of different tools for detection and filtering of recombinant regions and of different reference genomes were tested. Our benchmarking analysis included both assessment of technical performance of the pipelines and functional comparison of the generated genetic distance matrices and phylogenetic trees. It was carried out using replicate sequencing datasets of high- and low-coverage, consisting mainly of isolates belonging to the clonal complex 269. We demonstrated that cgMLST and some of the SNP-based subtyping workflows showed very good performance characteristics and highly similar genetic distance matrices and phylogenetic trees with isolates belonging to the same clonal complex. However, only two of the tested workflows demonstrated reproducible results for a group of more closely related isolates. Additionally, results of the SNP-based subtyping workflows were to some level dependent on the reference genome used. Interestingly, the use of recombination-filtering software generally reduced the similarity between the gene-by-gene and SNP-based methodologies for subtyping of . Our study, where was taken as an example, clearly highlights the need for more benchmarking comparative studies to eventually contribute to a justified use of a specific WGS data analysis workflow within an international public health laboratory context.

%B Front Microbiol %V 10 %8 2019 %G eng %R 10.3389/fmicb.2019.02897 %0 Journal Article %J Appl Microbiol Biotechnol %D 2019 %T Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java. %A Mathieu Gand %A Wesley Mattheus %A Assia Saltykova %A Nancy Roosens %A Katelijne Dierick %A Marchal, Kathleen %A Sigrid C.J. De Keersmaecker %A Sophie Bertrand %X

Discriminating between D-tartrate fermenting and non-fermenting strains of Salmonella enterica subsp. enterica serotype Paratyphi B is of major importance as these two variants have different pathogenic profiles. While D-tartrate non-fermenting S. Paratyphi B isolates are the causative agent of typhoid-like fever, D-tartrate fermenting isolates (also called variant Java) of the same serotype trigger the less dangerous gastroenteritis. The determination of S. Paratyphi B variants requires a time-consuming process and complex biochemical tests. Therefore, a quadruplex real-time PCR method, based on the allelic discrimination of molecular markers selected from the scientific literature and from whole genome sequencing data produced in-house, was developed in this study, to be applied to Salmonella isolates. This method was validated with the analysis of 178 S. Paratyphi B (D-tartrate fermenting and non-fermenting) and other serotypes reaching an accuracy, compared with the classical methods, of 98% for serotyping by slide agglutination and 100% for replacement of the biochemical test. The developed real-time PCR permits to save time and to obtain an accurate identification of a S. Paratyphi B serotype and its D-tartrate fermenting profile, which is needed in routine laboratories for fast and efficient diagnostics.

%B Appl Microbiol Biotechnol %V 103 %8 2019 Jun %G eng %N 12 %R 10.1007/s00253-019-09854-4 %0 Report %D 2019 %T Epidemiologische surveillance van invasieve meningokokkeninfecties - 2018 %A Stéphanie Jacquinet %A Wesley Mattheus %A Adrien Lajot %A Chloé Wyndham-Thomas %I Sciensano %C Brussels %8 2019 %G eng %0 Government Document %D 2019 %T Infoblad meningokokkeninfecties 2019 (T4) %A Wesley Mattheus %K Meningococcal Infections %B None %I Sciensano %C Brussels %8 2019 %G eng %0 Journal Article %J The Lancet Infectious Diseases %D 2019 %T An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study %A Roan Pijnacker %A Timothy J Dallman %A Aloys S L Tijsma %A Gillian Hawkins %A Lesley Larkin %A Kotila, Saara M %A Giusi Amore %A Ettore Amato %A Pamina M Suzuki %A Sarah Denayer %A Sofieke Klamer %A Jacquelyn McCormick %A Hassan Hartman %A Gareth J Hughes %A Lin C T Brandal %A Derek Brown %A Mossong, Joel %A Cecilia Jernberg %A Luise Müller %A Daniel Palm %A Ettore Severi %A Joanna Gołębiowska %A Hunjak, Blaženka %A Slawomir Owczarek %A Le Hello, Simon %A Patricia Garvey %A Kirsten Mooijman %A Ingrid H M Friesema %A Coen van der Weijden %A Menno van der Voort %A Valentina Rizzi %A Eelco Franz %A Sophie Bertrand %A Martine Brennan %A Lynda Browning %A Bruce, Ryan %A Vera Cantaert %A Marie Chattaway %A John Coia %A Sarah Couper %A Tjaša Žohar Čretnik %A Ondřej Daniel %A Anna Maria Dionisi %A Laetitia Fabre %A Ife Fitz-James %A Karolina Florek %A Martina Florianová %A Eithne Fox %A Tatjana Frelih %A Eva Grilc %A Vera Katalinic Jankovic %A Nathalie Jourdan %A Renata Karpíšková %A Hans van den Kerkhof %A Sjoerd Kuiling %A Sanja Kurečić Filipović %A Valeska Laisnez %A Heidi Lange %A Niall deLappes %A Judith Leblanc %A Ida Luzzi %A Georgia Mandilara %A Henry Mather %A Wesley Mattheus %A Mellou, Kassiani %A Deborah Morgan %A Judit Pászti %A de Pinna, Elizabeth %A Ragimbeau, Catherine %A Margrethe Hovda Røed %A Saara Salmenlinna %A Robert Smith %A Alison Smith-Palmer %A Michaela Špačková %A Torpdahl, Mia %A Marija Trkov %A Linda Trönnberg %A Tzani, Myrsini %A Lara Utsi %A Dariusz Wasyl %A Pierre Weicherding %K International %K outbreak %K Salmonella %X

Salmonella spp are a major cause of food-borne outbreaks in Europe. We investigated a large multi-country outbreak of Salmonella enterica serotype Enteritidis in the EU and European Economic Area (EEA).

%B The Lancet Infectious Diseases %V 19 %8 Jan-07-2019 %G eng %N 7 %R 10.1016/S1473-3099(19)30047-7 %0 Generic %D 2019 %T Listeria surveillance in Belgium %A An Van den Bossche %A Wesley Mattheus %K Listeria %K surveillence %X

As is the case in the rest of Europe, the annual incidence of Listeria monocytogenes infections in humans significantly increased over the years. Over the last 18 years, the incidence rates varied between 0.4 and 0.9 cases/100 000 inhabitants, which is relatively high compares to other European countries (average of 0.43/100 000 inhabitants, ECDC report 2016). This increasing trend is mainly due to an increase of non-maternal-neonatal (n-MN) cases, since maternal-neonatal (MN) cases have been decreasing over the years. This latter is a consequence of active prevention campaigns targeting pregnant women. However, in 2018 a relatively high number of 11 MN cases were reported.

In Belgium, listeriosis is a notifiable infectious disease, and strains are voluntarily sent to the National Reference Center (NRC). Identity confirmation is performed using biochemical assays and serotyping by slide agglutination. Since 2018, according to recent evolution in molecular typing, the NRC completely switched to Whole-Genome-Sequencing (WGS) for cluster detection. Therefore, an in-house Galaxy-based bio-informatic pipeline was developed. For the strain collection from 2010 until 2017 both classical data (MLST and PFGE) as cgMLST data are available.

Of all confirmed L. monocytogenes cases in humans, serotypes 1/2a and 4b are most frequently observed. During the period 2000-2018, they comprise 47.1% and 36.2% of the cases, respectively. Notably, the incidence of serotype 4b remains rather stable, while the increase of serotype 1/2a is in relation with the increase of the overall incidence of Listeria cases. The number of sporadic 1/2a cases (unique pulsovars or cgMLST profiles) remained stable, whereas the proportion of cases related to clusters corresponded with the fluctuating annual incidence. Antibiotic resistance to antimicrobials remains a rare event among L. monocytogenes isolates, although a significant increase of MIC50 and MIC90 values for ciprofloxacin resistance were noted recently (Bertrand et al, 2016).

%B ISOPOL %I ISOPOL %C Toronto, Canada %8 09/2019 %G eng %N International Symposium on Problems with Listeria and Listeriosis %0 Journal Article %J Microbiologyopen %D 2019 %T Shifting national surveillance of Shigella infections toward geno-serotyping by the development of a tailored Luminex assay and NGS workflow. %A Eleonora Ventola %A Bert Bogaerts %A Sigrid C.J. De Keersmaecker %A Kevin Vanneste %A Nancy Roosens %A Wesley Mattheus %A Pieter-Jan Ceyssens %K Luminex %K multiplex %K Public Health Surveillance %K sequencing %K Shigella %X

The phylogenetically closely related Shigella species and enteroinvasive Escherichia coli (EIEC) are responsible for millions of episodes of bacterial dysenteriae worldwide. Given its distinct epidemiology and public health relevance, only Shigellae are subject to mandatory reporting and follow-up by public health authorities. However, many clinical laboratories struggle to differentiate non-EIEC, EIEC, and Shigella in their current workflows, leading to inaccuracies in surveillance and rising numbers of misidentified E. coli samples at the National Reference Centre (NRC). In this paper, we describe two novel tools to enhance Shigella surveillance. First, we developed a low-cost Luminex-based multiplex assay combining five genetic markers for species identification with 11 markers for serotype prediction for S. sonnei and S. flexneri isolates. Using a test panel of 254 clinical samples, this assay has a sensitivity of 100% in differentiation of EIEC/Shigella pathotype from non-EIEC strains, and 68.7% success rate in distinction of Shigella and EIEC. A novel, and particularly successful marker was a Shigella-specific deletion in the spermidine acetyltransferase gene speG, reflecting its metabolic decay. For Shigella serotype prediction, the multiplex assay scored a sensitivity and specificity of 96.6% and 98.4%, respectively. All discrepancies were analyzed with whole-genome sequencing and shown to be related to causative mutations (stop codons, indels, and promoter mutations) in glycosyltransferase genes. This observation spurred the development of an in silico workflow which extracts the Shigella serotype from Next-Generation Sequencing (NGS) data, taking into account gene functionality. Both tools will be implemented in the workflow of the NRC, and will play a major role in the shift from phenotypic to genotyping-based surveillance of shigellosis in Belgium.

%B Microbiologyopen %8 2019 Mar 28 %G eng %R 10.1002/mbo3.807 %0 Report %D 2019 %T Surveillance épidémiologique des infections invasives à méningocoques - 2018 %A Stéphanie Jacquinet %A Wesley Mattheus %A Adrien Lajot %A Chloé Wyndham-Thomas %K infections invasives à méningocoques&Surveillance épidémiologique %I Sciensano %C Bruxelles %G eng %0 Report %D 2019 %T Surveillance épidémiologique des infections invasives à méningocoques - 2018 %A Stéphanie Jacquinet %A Wesley Mattheus %A Adrien Lajot %A Chloé Wyndham-Thomas %I Sciensano %C Brussels, Belgium %8 2019 %G eng %0 Journal Article %J Front Microbiol %D 2019 %T Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: as a Proof-of-Concept. %A Bert Bogaerts %A Raf Winand %A Fu, Qiang %A Julien Van Braekel %A Pieter-Jan Ceyssens %A Wesley Mattheus %A Sophie Bertrand %A Sigrid C.J. De Keersmaecker %A Nancy Roosens %A Kevin Vanneste %K national reference center %K Neisseria meningitidis %K public health %K VALIDATION %K whole-genome sequencing %X

Despite being a well-established research method, the use of whole-genome sequencing (WGS) for routine molecular typing and pathogen characterization remains a substantial challenge due to the required bioinformatics resources and/or expertise. Moreover, many national reference laboratories and centers, as well as other laboratories working under a quality system, require extensive validation to demonstrate that employed methods are "fit-for-purpose" and provide high-quality results. A harmonized framework with guidelines for the validation of WGS workflows does currently, however, not exist yet, despite several recent case studies highlighting the urgent need thereof. We present a validation strategy focusing specifically on the exhaustive characterization of the bioinformatics analysis of a WGS workflow designed to replace conventionally employed molecular typing methods for microbial isolates in a representative small-scale laboratory, using the pathogen as a proof-of-concept. We adapted several classically employed performance metrics specifically toward three different bioinformatics assays: resistance gene characterization (based on the ARG-ANNOT, ResFinder, CARD, and NDARO databases), several commonly employed typing schemas (including, among others, core genome multilocus sequence typing), and serogroup determination. We analyzed a core validation dataset of 67 well-characterized samples typed by means of classical genotypic and/or phenotypic methods that were sequenced in-house, allowing to evaluate repeatability, reproducibility, accuracy, precision, sensitivity, and specificity of the different bioinformatics assays. We also analyzed an extended validation dataset composed of publicly available WGS data for 64 samples by comparing results of the different bioinformatics assays against results obtained from commonly used bioinformatics tools. We demonstrate high performance, with values for all performance metrics >87%, >97%, and >90% for the resistance gene characterization, sequence typing, and serogroup determination assays, respectively, for both validation datasets. Our WGS workflow has been made publicly available as a "push-button" pipeline for Illumina data at https://galaxy.sciensano.be to showcase its implementation for non-profit and/or academic usage. Our validation strategy can be adapted to other WGS workflows for other pathogens of interest and demonstrates the added value and feasibility of employing WGS with the aim of being integrated into routine use in an applied public health setting.

%B Front Microbiol %V 10 %8 2019 %G eng %R 10.3389/fmicb.2019.00362 %0 Journal Article %J PLoS One %D 2018 %T Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:. %A Assia Saltykova %A Wuyts, Véronique %A Wesley Mattheus %A Sophie Bertrand %A Nancy Roosens %A Marchal, Kathleen %A Sigrid C.J. De Keersmaecker %K bacterial phylogeny; food-borne; genes; NGS; WGS; computational biology/bioinformatics; disease outbreaks; outbreak; performance evaluation; pipeline; Salmonella; Salmonella enterica; Salmonella typhimurium; SNP; subtyping; whole genome sequencing %X

Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable evolution of the whole genome sequencing data analysis methods. Prior to application of the technology as a routine epidemiological typing tool, however, reliable and efficient data analysis strategies need to be identified among the wide variety of the emerged methodologies. In this work, we have compared three existing SNP-based subtyping workflows using a benchmark dataset of 32 Salmonella enterica subsp. enterica serovar Typhimurium and serovar 1,4,[5],12:i:- isolates including five isolates from a confirmed outbreak and three isolates obtained from the same patient at different time points. The analysis was carried out using the original (high-coverage) and a down-sampled (low-coverage) datasets and two different reference genomes. All three tested workflows, namely CSI Phylogeny-based workflow, CFSAN-based workflow and PHEnix-based workflow, were able to correctly group the confirmed outbreak isolates and isolates from the same patient with all combinations of reference genomes and datasets. However, the workflows differed strongly with respect to the SNP distances between isolates and sensitivity towards sequencing coverage, which could be linked to the specific data analysis strategies used therein. To demonstrate the effect of particular data analysis steps, several modifications of the existing workflows were also tested. This allowed us to propose data analysis schemes most suitable for routine SNP-based subtyping applied to S. Typhimurium and S. 1,4,[5],12:i:-. Results presented in this study illustrate the importance of using correct data analysis strategies and to define benchmark and fine-tune parameters applied within routine data analysis pipelines to obtain optimal results.

%B PLoS One %V 13 %8 2018 %G eng %N 2 %R 10.1371/journal.pone.0192504 %0 Report %D 2018 %T Epidemiologische surveillance van invasieve meningokokkeninfecties - 2017 %A Nele Boon %A Tine Grammens %A Wesley Mattheus %A Chloé Wyndham-Thomas %K Meningococcal Infections %K Meningococcal Vaccines %K Surveillance %X

Het aantal gevallen van invasieve meningokokkeninfecties in België is sterk gedaald sinds de introductie van algemene vaccinatie tegen serogroep C in 2002.

Sinds 2008 is het aantal geconfirmeerde gevallen gerapporteerd door het NRC gestabiliseerd rond een 100-tal gevallen per jaar, met 96 gevallen in 2017 en een geschatte incidentie van 0,85 geconfirmeerde gevallen per 100.000 inwoners.

Serogroep B blijft de meest voorkomende serogroep in 2017 (N=60; 62,5% van de gevallen) .

Het aantal gevallen van serogroep C daalt verder (N=6 gevallen in 2017; 6,3% van de gevallen).

Er is een lichte stijging van het aantal gevallen van serogroep Y sinds 2016 en van serogroep W sinds 2015. Samen vertegenwoordigen deze 2 serotypes 29,2% van de gevallen.

Er werden in 2017 via de verplichte melding 9 sterfgevallen gerapporteerd, waarvan 8 in Vlaanderen. Dit aantal is hoger dan voorgaande jaren.

 

%8 2018 %G eng %0 Generic %D 2018 %T A multiplex oligonucleotide ligation-PCR method using the Luminex technology for the geno-serotyping of the most common Salmonella in Belgium %A Mathieu Gand %A Wesley Mattheus %A Assia Saltykova %A Nancy Roosens %A Katelijne Dierick %A Marchal, Kathleen %A Sigrid C.J. De Keersmaecker %A Sophie Bertrand %K Luminex %K method %K multiplex %K Salmonella %K Serotyping %B ECCMID %I ESCMID %C Madrid, Spain %8 2018 %G eng %0 Report %D 2018 %T Surveillance épidémiologique des infections invasives à méningocoques - 2017 %A Nele Boon %A Tine Grammens %A Wesley Mattheus %A Chloé Wyndham-Thomas %K Meningococcal Infections %K Meningococcal Vaccines %K Surveillance %X

Le nombre de cas d’infections invasives à méningocoques en Belgique a nettement diminué depuis l’introduction de la vaccination contre le sérogroupe C en 2002.

Depuis 2008, le nombre de cas confirmés par le CNR s’est stabilisé autour d’une centaine de cas/an, soit 96 cas en 2017 et une incidence estimée à 0,85 cas confirmés/100.000 habitants.

En 2017, le sérogroupe B reste le plus fréquent (N=60, soit 62.5% des cas).

Le nombre de cas à sérogroupe C continue à diminuer (N=6 en 2017 soit 6.3% des cas)

On observe une tendance à la hausse du nombre de cas à sérogroupe Y depuis 2016 et du sérogroupe W depuis 2015. Ensemble, ces 2 sérotypes représentent 29.2% des cas.

En 2017, 9 décès ont été signalés par les services en charge de la déclaration obligatoire, dont 8 en Flandre. Ce chiffre est plus élevé que les années précédentes.

%8 2018 %G eng %0 Generic %D 2017 %T Development of a real-time PCR test for the geno-serotyping of Salmonella Paratyphi B and its variant Java %A Mathieu Gand %A Wesley Mattheus %A Assia Saltykova %A Nancy Roosens %A Katelijne Dierick %A Marchal, Kathleen %A Sigrid C.J. De Keersmaecker %A Sophie Bertrand %K Luminex %K method %K mutliplex %K Salmonella %K Serotyping %B BSFM conference %I BSFM %C Brussels, Belgium %8 2017 %G eng %0 Journal Article %J Methods Mol Biol %D 2017 %T Molecular Subtyping of Salmonella Typhimurium with Multiplex Oligonucleotide Ligation-PCR (MOL-PCR). %A Wuyts, Véronique %A Wesley Mattheus %A Nancy Roosens %A Marchal, Kathleen %A Sophie Bertrand %A Sigrid C.J. De Keersmaecker %X

A multiplex oligonucleotide ligation-PCR (MOL-PCR) assay is a valuable high-throughput technique for the detection of bacteria and viruses, for characterization of pathogens and for diagnosis of genetic diseases, as it allows one to combine different types of molecular markers in a high-throughput multiplex assay. A MOL-PCR assay starts with a multiplex oligonucleotide ligation reaction for detection of the molecular marker, followed by a singleplex PCR for signal amplification and analysis of the MOL-PCR products on a Luminex platform. This last step occurs through a liquid bead suspension array in which the MOL-PCR products are hybridized to MagPlex-TAG beads.In this chapter, we describe the complete procedure for a MOL-PCR assay for subtyping of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and its monophasic variant S. 1,4[5],12:i:- from DNA isolation through heat lysis up to data interpretation through a Gödel Prime Product. The subtyping assay consists of 50 discriminative molecular markers and two internal positive control markers divided over three MOL-PCR assays.

%B Methods Mol Biol %V 1616 %P 39-69 %8 2017 %G eng %1 http://www.ncbi.nlm.nih.gov/pubmed/28600761?dopt=Abstract %R 10.1007/978-1-4939-7037-7_3 %0 Journal Article %J Euro Surveill %D 2017 %T Multi-laboratory validation study of multilocus variable-number tandem repeat analysis (MLVA) for Salmonella enterica serovar Enteritidis, 2015. %A Peters, Tansy %A Sophie Bertrand %A Björkman, Jonas T %A Brandal, Lin T %A Brown, Derek J %A Erdõsi, Tímea %A Heck, Max %A Ibrahem Salha %A Johansson, Karin %A Kornschober, Christian %A Kotila, Saara M %A Le Hello, Simon %A Lienemann, Taru %A Wesley Mattheus %A Nielsen, Eva Møller %A Ragimbeau, Catherine %A Rumore, Jillian %A Sabol, Ashley %A Torpdahl, Mia %A Eija Trees %A Tuohy, Alma %A de Pinna, Elizabeth %K China %K Disease Outbreaks %K Epidemiologic Studies %K Europe %K Humans %K Laboratories %K Minisatellite Repeats %K Molecular Typing %K Multilocus Sequence Typing %K Phylogeny %K Predictive Value of Tests %K Public Health Surveillance %K Reproducibility of Results %K Salmonella enteritidis %K Salmonella Food Poisoning %K Salmonella Infections %K Tandem Repeat Sequences %X

Multilocus variable-number tandem repeat analysis (MLVA) is a rapid and reproducible typing method that is an important tool for investigation, as well as detection, of national and multinational outbreaks of a range of food-borne pathogens. Salmonella enterica serovar Enteritidis is the most common Salmonella serovar associated with human salmonellosis in the European Union/European Economic Area and North America. Fourteen laboratories from 13 countries in Europe and North America participated in a validation study for MLVA of S. Enteritidis targeting five loci. Following normalisation of fragment sizes using a set of reference strains, a blinded set of 24 strains with known allele sizes was analysed by each participant. The S. Enteritidis 5-loci MLVA protocol was shown to produce internationally comparable results as more than 90% of the participants reported less than 5% discrepant MLVA profiles. All 14 participating laboratories performed well, even those where experience with this typing method was limited. The raw fragment length data were consistent throughout, and the inter-laboratory validation helped to standardise the conversion of raw data to repeat numbers with at least two countries updating their internal procedures. However, differences in assigned MLVA profiles remain between well-established protocols and should be taken into account when exchanging data.

%B Euro Surveill %V 22 %8 2017 Mar 02 %G eng %N 9 %1 http://www.ncbi.nlm.nih.gov/pubmed/28277220?dopt=Abstract %R 10.2807/1560-7917.ES.2017.22.9.30477 %0 Government Document %D 2017 %T Salmonella infections: identification techniques for successful investigations %A Sophie Bertrand %A Wesley Mattheus %A Pieter-Jan Ceyssens %A Mathieu Gand %A Raymond Vanhoof %A N Botteldoorn %A Sarah Denayer %A Nancy Roosens %A Sigrid C.J. De Keersmaecker %K identification %K method %K Salmonella %B Labinfo %I AFSCA-FAVV %C Belgium %V 16 %8 2017 %G eng %& 41 %0 Report %D 2016 %T Consumptie-gerelateerde infectieziekten, 2014, België. Epidemiologische trends. %A Toon Braeye %A Sophie Bertrand %A Wesley Mattheus %A Martiny, Delphine %A Piérard, Denis %A De Rauw, Klara %A Jan Verhaegen %A Delmée, Michel %A Laurence Delbrassinne %A Sarah Denayer %A Katelijne Dierick %A Melin,P. %A Van Esbroeck, Marjan %A Vandenberg, Olivier %A N Botteldoorn %A Veronik Hutse %A Sophie Quoilin %K 2014 %K België %K Consumptie-gerelateerde infectieziekten %K trends %I WIV-ISP %C Brussel, België %P 162 %8 feb 2016 %G eng %M D/2016/2505/41 %0 Journal Article %J J Antimicrob Chemother %D 2016 %T Development of a Luminex xTAG® assay for cost-effective multiplex detection of β-lactamases in Gram-negative bacteria. %A Pieter-Jan Ceyssens %A Cristina Garcia-Graells %A Fux, Frédéric %A N Botteldoorn %A Wesley Mattheus %A Wuyts, Véronique %A Sigrid C.J. De Keersmaecker %A Katelijne Dierick %A Sophie Bertrand %K Bacteriological Techniques %K beta-Lactamases %K Cost-Benefit Analysis %K Genotyping Techniques %K Gram-Negative Bacteria %K Humans %K Multiplex Polymerase Chain Reaction %K RNA, Ribosomal, 16S %X

OBJECTIVES: The objective of this study was to design and validate a genotyping method for multiplex identification of ESBLs and carbapenemases in Gram-negative bacilli. This assay had to be (i) superior to traditional (multiplex) PCR/sequencing-based tests in turn-around time, gene coverage and the ability to detect multiple variants of the same allele, and (ii) significantly more cost-effective than commercial microarrays and WGS. The targeted β-lactamases include ESBLs (CTX-M families and subtypes, ESBL and non-ESBL SHV- and TEM-likes, OXA-1/2/7-likes, PER, VEB, GES), plasmid-mediated cephalosporinases (CMY, MOX, FOX, ACC, DHA, MIR/ACT) and carbapenemases (OXA-48, NDM, KPC, VIM, IMP).

METHODS: A modular multiplex oligonucleotide ligation-PCR procedure was used, with read-out on a Luminex MAGPIX(®) platform. We designed 46 xTAG(®)-compatible probes targeting β-lactamase alleles and allele variants, and one probe targeting a conserved 16S rRNA region serving as a DNA extraction control. The assay was optimized using a collection of 48 reference strains and further validated using 105 foodborne ESBL-producing Escherichia coli isolates.

RESULTS: The specificity and selectivity of the test are 100% and 99.4%, respectively. Multiple variants of the same allele were successfully discriminated, as exemplified by five E. coli strains encoding both blaTEM-1 and blaTEM-52 genes. The turn-around time from single colony to result is 5 h and total consumable costs remained <€5 per sample.

CONCLUSIONS: We designed and validated the first Luminex-compatible genotyping assay that reliably and rapidly identifies a broad range of ESBL, pAmpC and carbapenemase producers in culture.

%B J Antimicrob Chemother %V 71 %P 2479-83 %8 2016 Sep %G eng %N 9 %1 http://www.ncbi.nlm.nih.gov/pubmed/27287233?dopt=Abstract %R 10.1093/jac/dkw201 %0 Journal Article %J PLoS One %D 2016 %T Diversity of Listeria monocytogenes Strains of Clinical and Food Chain Origins in Belgium between 1985 and 2014. %A Sophie Bertrand %A Pieter-Jan Ceyssens %A Yde, M %A Katelijne Dierick %A Boyen, F %A Jean Vanderpas %A Vanhoof, R %A Wesley Mattheus %K Adult %K Anti-Infective Agents %K Belgium %K DNA, Bacterial %K Drug Resistance, Bacterial %K Female %K Food Chain %K Food Microbiology %K Foodborne Diseases %K Humans %K Listeria monocytogenes %K Listeriosis %K Male %K Microbial Sensitivity Tests %K Serotyping %X

Listeriosis is a rare but severe disease, mainly caused by Listeria monocytogenes. This study shows the results of the laboratory-based surveillance of Listeriosis in Belgium over the period 1985-2014. Besides the incidence and some demographic data we present also more detailed microbiological and molecular characteristics of human strains isolated since 2000. The strains from the latter period were compared to food and animal strains from the same period. Our study shows that different food matrices were commonly contaminated with L. monocytogenes presenting the same PFGE profile as in patient's isolates. Since 1985, we observed a significant decrease in incidence of the Materno-Neonatal cases (from 0.15 to 0.04 cases /100,000 inhabitants-year), which is probably to be attributed to active prevention campaigns targeting pregnant women. Despite the strengthening of different control measures by the food industry, the incidence of non-Materno-Neonatal listeriosis increased in Belgium (from 0.3 to 0.7 cases /100,000 inhabitants-year), probably due to the rise of highly susceptible patients in an aging population. This significant increase found in non-Materno-Neonatal cases (slope coefficient 7.42%/year, P<0.0001) can be attributed to significant increase in incidence of isolates belonging to serovars 1/2a (n = 393, slope coefficient 6.62%/year, P<0.0001). Although resistance to antimicrobials is rare among L. monocytogenes isolates, a trend to increasing MIC values is evident with chloramphenicol, amoxicillin, tetracycline and ciprofloxacin. We show that fluoroquinolone resistance is not linked to chromosomal mutations, but caused by a variety of efflux pumps. Our study also shows that huge majority of known underlying pathologies (426 out of 785 cases) were cancers (185/426, 43.1%) and haematological malignancies (75/185, 40.5%). Moreover the risk population is susceptible to low levels of contamination in food stressing the need of prevention campaigns specifically targeting these persons.

%B PLoS One %V 11 %P e0164283 %8 2016 %G eng %N 10 %1 http://www.ncbi.nlm.nih.gov/pubmed/27723768?dopt=Abstract %& e0164283 %R 10.1371/journal.pone.0164283 %0 Report %D 2016 %T Infectieziekten bij kinderen, die voorkomen kunnen worden door vaccinatie. Jaarrapport 2015 %A Mendes da Costa,E. %A Tine Grammens %A Amber Litzroth %A Virginie Maes %A Gaetan Muyldermans %A Sophie Quoilin %A Martine Sabbe %A Sophie Bertrand %A Marie-Luce Delforge %A I Desombere %A Veronik Hutse %A Helena Martini %A Martiny, Delphine %A Wesley Mattheus %A S Moreels %A Denis Piérard %A Carole Schirvel %A Béatrice Swennen %A Heidi Theeten %A Geert Top %A Jean-Marie Tremerie %A Viviane Van Casteren %A Steven Van Gucht %A Van Ranst, M %A Jan Verhaegen %K 2015 %K Infectieziekten %K kinderen %K vaccinatie %I WIV-ISP %C Brussel, België %P 108 %8 dec 2016 %@ 2507-0274 %G eng %M D/2016/2505/47 %0 Report %D 2016 %T Infectieziekten bij kinderen die voorkomen kunnen worden door vaccinatie. Jaarrapport 2014 %A Martine Sabbe %A Mendes da Costa,E. %A Sophie Quoilin %A Sophie Bertrand %A Dediste,A. %A Marie-Luce Delforge %A Heymans,C. %A K Huygen %A Veronik Hutse %A Stéphanie Jacquinet %A Mak,R. %A Wesley Mattheus %A S Moreels %A Muyldermans,C. %A Denis Piérard %A Carole Schirvel %A Béatrice Swennen %A Heidi Theeten %A Geert Top %A Jean-Marie Tremerie %A Viviane Van Casteren %A Marc Van Ranst %A Jan Verhaegen %A Zinnen,V. %K Infectieziekten %K kinderen %K vaccinatie %I Johan Peeters/WIV-ISP %C Bruxelles %P . %8 0/0/2016 %@ D/2015/2505/75 %G eng %1 37182 %0 Report %D 2016 %T Maladies infectieuses pédiatriques à prévention vaccinale. Rapport annuel 2015 %A Mendes da Costa,E. %A Tine Grammens %A Amber Litzroth %A Virginie Maes %A Gaetan Muyldermans %A Sophie Quoilin %A Martine Sabbe %A Sophie Bertrand %A Marie-Luce Delforge %A I Desombere %A Veronik Hutse %A Helena Martini %A Martiny, Delphine %A Wesley Mattheus %A S Moreels %A Denis Piérard %A Carole Schirvel %A Béatrice Swennen %A Heidi Theeten %A Geert Top %A Jean-Marie Tremerie %A Viviane Van Casteren %A Steven Van Gucht %A Van Ranst, M %A Jan Verhaegen %K 2015 %K Maladies infectieuses pédiatriques %K Vaccination %I WIV-ISP %C Bruxelles, Belgique %P 108 %8 12/2016 %@ 2507-0266 %G eng %M D/2016/2505/46 %0 Journal Article %J BMC Infect Dis %D 2016 %T Microbiological, clinical and molecular findings of non-typhoidal Salmonella bloodstream infections associated with malaria, Oriental Province, Democratic Republic of the Congo. %A Falay, Dadi %A Kuijpers, Laura Maria Francisca %A Phoba, Marie-France %A De Boeck, Hilde %A Lunguya, Octavie %A Vakaniaki, Emmanuel %A Sophie Bertrand %A Wesley Mattheus %A Pieter-Jan Ceyssens %A Vanhoof, Raymond %A Devlieger, Hugo %A Van Geet, Chris %A Verheyen, Erik %A Ngbonda, Dauly %A Jacobs, Jan %K ADOLESCENT %K Adult %K Anti-Bacterial Agents %K Asian Continental Ancestry Group %K Azithromycin %K Bacteremia %K Ceftriaxone %K Child %K Child, Preschool %K Coinfection %K Democratic Republic of the Congo %K Disease Outbreaks %K Drug Resistance, Multiple, Bacterial %K Female %K Hospitalization %K Humans %K Infant %K Infant, Newborn %K Malaria %K Malaria, Falciparum %K Male %K Salmonella enteritidis %K Salmonella Infections %K Salmonella typhimurium %K Serogroup %K Tandem Repeat Sequences %X

BACKGROUND: In sub-Saharan Africa, non-typhoidal Salmonella (NTS) can cause bloodstream infections, referred to as invasive non-typhoidal Salmonella disease (iNTS disease); it can occur in outbreaks and is often preceded by malaria. Data from Central Africa is limited.

METHODS: Clinical, microbiological and molecular findings of NTS recovered in a blood culture surveillance project (2009-2014) were analyzed.

RESULTS: In March-July 2012 there was an epidemic increase in malaria infections in the Oriental Province of the Democratic Republic of the Congo (DRC). In one referral hospital, overall hospital admissions in June 2012 were 2.6 times higher as compared to the same period in the years before and after (336 versus an average of 128 respectively); numbers of malaria cases and blood transfusions were nearly three- and five-fold higher respectively (317 versus 112 and 250 versus 55). Case fatality rates (in-hospital deaths versus all admissions) peaked at 14.6 %. Salmonella Typhimurium and Salmonella Enteritidis together accounted for 88.9 % of pathogens isolated from blood cultures collected during an outreach visit to the affected districts in June 2012. Children infected with Salmonella Enteritidis (33 patient files available) tended to be co-infected with Plasmodium falciparum more often than children infected with Salmonella Typhimurium (40 patients files available) (81.8 % versus 62.5 %). Through the microbiological surveillance project (May 2009-May 2014) 113 unique NTS isolates were collected (28.5 % (113/396) of pathogens); most (95.3 %) were recovered from children < 15 years. Salmonella Typhimurium (n = 54) and Salmonella Enteritidis (n = 56) accounted for 47.8 % and of 49.6 % NTS isolates respectively. Multilocus variable-number tandem-repeat analysis (MLVA) revealed more heterogeneity for Salmonella Typhimurium than for Salmonella Enteritidis. Most (82/96, 85.4 %) NTS isolates that were available for antibiotic susceptibility testing were multidrug resistant. All isolates were susceptible to ceftriaxone and azithromycin.

CONCLUSION: During the peak of an epidemic increase in malaria in the DRC in 2012, a high proportion of multidrug resistant Salmonella Typhimurium and Salmonella Enteritidis were isolated from blood cultures. Overall, the two serovars showed subtle differences in clinical presentation and genetic diversity.

%B BMC Infect Dis %V 16 %P 271 %8 2016 Jun 10 %G eng %N 1 %1 http://www.ncbi.nlm.nih.gov/pubmed/27286886?dopt=Abstract %& 271 %R 10.1186/s12879-016-1604-1 %0 Journal Article %J PLoS One %D 2016 %T Molecular Analysis of Rising Fluoroquinolone Resistance in Belgian Non-Invasive Streptococcus pneumoniae Isolates (1995-2014). %A Pieter-Jan Ceyssens %A Van Bambeke, Françoise %A Wesley Mattheus %A Sophie Bertrand %A Fux, Frédéric %A Van Bossuyt, Eddie %A Damée, Sabrina %A Nyssen, Henry-Jean %A Stéphane De Craeye %A Verhaegen, Jan %A Tulkens, Paul M %A Vanhoof, Raymond %K Amino Acid Substitution %K ATP-Binding Cassette Transporters %K Bacterial Proteins %K Belgium %K DNA Gyrase %K Drug Resistance, Bacterial %K Female %K Fluoroquinolones %K Humans %K Longitudinal Studies %K Male %K Mutation, Missense %K Pneumococcal Infections %K Streptococcus pneumoniae %X

We present the results of a longitudinal surveillance study (1995-2014) on fluoroquinolone resistance (FQ-R) among Belgian non-invasive Streptococcus pneumoniae isolates (n = 5,602). For many years, the switch to respiratory fluoroquinolones for the treatment of (a)typical pneumonia had no impact on FQ-R levels. However, since 2011 we observed a significant decrease in susceptibility towards ciprofloxacin, ofloxacin and levofloxacin with peaks of 9.0%, 6.6% and 3.1% resistant isolates, respectively. Resistance to moxifloxacin arised sporadically, and remained <1% throughout the entire study period. We observed classical topoisomerase mutations in gyrA (n = 25), parC (n = 46) and parE (n = 3) in varying combinations, arguing against clonal expansion of FQ-R. The impact of recombination with co-habiting commensal streptococci on FQ-R remains marginal (10.4%). Notably, we observed that a rare combination of DNA Gyrase mutations (GyrA_S81L/GyrB_P454S) suffices for high-level moxifloxacin resistance, contrasting current model. Interestingly, 85/422 pneumococcal strains display MICCIP values which were lowered by at least four dilutions by reserpine, pointing at involvement of efflux pumps in FQ-R. In contrast to susceptible strains, isolates resistant to ciprofloxacin significantly overexpressed the ABC pump PatAB in comparison to reference strain S. pneumoniae ATCC 49619, but this could only be linked to disruptive terminator mutations in a fraction of these. Conversely, no difference in expression of the Major Facilitator PmrA, unaffected by reserpine, was noted between susceptible and resistant S. pneumoniae strains. Finally, we observed that four isolates displayed intermediate to high-level ciprofloxacin resistance without any known molecular resistance mechanism. Focusing future molecular studies on these isolates, which are also commonly found in other studies, might greatly assist in the battle against rising pneumococcal drug resistance.

%B PLoS One %V 11 %P e0154816 %8 2016 %G eng %N 5 %1 http://www.ncbi.nlm.nih.gov/pubmed/27227336?dopt=Abstract %& e0154816 %R 10.1371/journal.pone.0154816 %0 Book %B Diagnostic Bacteriology Protocols %D 2016 %T Molecular subtyping of Salmonella Typhimurium with multiplex oligonucleotide ligation-PCR (MOL-PCR) %A Wuyts,V. %A Wesley Mattheus %A Nancy Roosens %A Marchal,K. %A Sophie Bertrand %A Sigrid C.J. De Keersmaecker %E Bishop-Lilly,K. %K a %K analysi %K analysis %K AS %K bacteria %K bead suspension array %K Biology %K Control %K data %K detection %K Diagnosis %K disease %K Diseases %K Dna %K Genetic %K Gödel Prime Product %K high-throughput assay %K IS %K Isolation %K IT %K Luminex %K lysis %K Marker %K Markers %K method %K methods %K MOL-PCR %K Molecular %K Molecular biology %K molecular markers %K molecular subtyping %K Multiplex assay %K ON %K pathogen %K PCR %K PRODUCTS %K protocol %K S %K Salmonella %K Salmonella enterica %K Salmonella typhimurium %K Subtyping %K Technique %K Type %K Viruses %X A multiplex oligonucleotide ligation-PCR (MOL-PCR) assay is a valuable high-throughput technique for the detection of bacteria and viruses, for characterization of pathogens and for diagnosis of genetic diseases, as it allows to combine different types of molecular markers in a high-throughput multiplex assay. A MOL-PCR assay starts with a multiplex oligonucleotide ligation reaction for detection of the molecular marker, followed by a singleplex PCR for signal amplification and analysis of the MOL-PCR products on a Luminex platform. This last step occurs through a liquid bead suspension array in which the MOL-PCR products are hybridized to MagPlex-TAG beads.In this chapter, we describe the complete procedure for a MOL-PCR assay for subtyping of %B Diagnostic Bacteriology Protocols %7 - %I Humana Press %C Totowa, New Jersey %P - %8 0/0/2016 %@ 978-1-58829-594-1 %G eng %9 Methods in Molecular Biology %1 568 %& submitted %0 Report %D 2016 %T Rapport thématique. Maladies infectieuses liées à la consommation, 2014, Belgique. Tendances épidémiologiques. %A Toon Braeye %A Sophie Bertrand %A Wesley Mattheus %A Martiny, Delphine %A Denis Piérard %A De Rauw, Klara %A Jan Verhaegen %A Delmée, Michel %A Laurence Delbrassinne %A Sarah Denayer %A Katelijne Dierick %A Melin,P. %A Van Esbroeck, Marjan %A Vandenberg, Olivier %A N Botteldoorn %A Veronik Hutse %A Sophie Quoilin %K 2014 %K Belgique %K Maladies infectieuses liées à la consommation %K tendances %I WIV-ISP %C Bruxelles, Belgique %P 164 %8 sep 2016 %G eng %M D/21016/2505/42 %0 Generic %D 2015 %T Antimicrobial resistance testing in 2020: Will we still be looking at the phenotype? %A Pieter-Jan Ceyssens %A Wesley Mattheus %A Vanessa Mathys %A R. Vanhoof %A Michael Kalai %A Sophie Bertrand %E Institut Pasteur %K Antimicrobial %K Antimicrobial resistance %K at %K Phenotype %K resistance %K Still %K TESTING %B RIIP Meeting %8 0/0/2015 %G eng %N Institut Pasteur %1 37023 %2 04/2015 %0 Generic %D 2015 %T Blueprint of serotype distribution and antimicrobial resistance in human salmonellosis in Belgium (2009-2013) %A Pieter-Jan Ceyssens %A Wesley Mattheus %A R. Vanhoof %A Sophie Bertrand %K Antimicrobial %K Antimicrobial resistance %K Belgium %K conference %K distribution %K Human %K International %K ON %K Research %K resistance %B International Conference on Antimicrobial Research %I ICAR %C Madrid, Spain %V 4 %8 17/5/2015 %G eng %N ICAR %1

37037

%2 1/10/2014 ; 3/10/2014 %6 4 %R 10.1128/AAC.04203-14 %0 Journal Article %J PLoS One %D 2015 %T Changes in Meningococcal Strains in the Era of a Serogroup C Vaccination Campaign: Trends and Evolution in Belgium during the Period 1997-2012. %A Wesley Mattheus %A Hanquet, Germaine %A J-M Collard %A Vanhoof, Raymond %A Sophie Bertrand %K ADOLESCENT %K Adult %K Belgium %K Biological Evolution %K Child %K Child, Preschool %K DNA, Bacterial %K Female %K Humans %K Infant %K Male %K Meningococcal Infections %K Meningococcal Vaccines %K Multilocus Sequence Typing %K Neisseria meningitidis, Serogroup C %K Phenotype %K Prognosis %K Serogroup %K Survival Rate %K Time Factors %K Vaccination %K Young adult %X

BACKGROUND: Invasive meningococcal disease (IMD) is a major cause of bacterial meningitides and septicaemia. This study shows the results of the laboratory-based surveillance of IMD in Belgium over the period 1997-2012.

METHODS: The results are based on microbiological and molecular laboratory surveillance of 2997 clinical isolates of N. meningitides received by the Belgian Meningococcal Reference Centre (BMRC) over the period 1997-2012.

RESULTS: Serogroup B has always been a major cause of meningococcal disease in Belgium, with P3.4 as most frequent serotype till 2008, while an increase in non-serotypable strains has been observed in the last few years. Clonal complexes cc-41/44 and cc-269 are most frequently observed in serogroup B strains. In the late nineties, the incidence of serogroup C disease increased considerably and peaked in 2001, mainly associated with phenotypes C:2a:P1.5,2, C:2a:P1.5 and C:2a:P1.2 (ST-11/ET-37 clonal complex). The introduction of the meningococcal C conjugate vaccine has been followed by an 88% significant decrease in serogroup C disease from 2001 to 2004 nationally, yet sharper in Flanders (92%) compared to Wallonia (77%). Since 2008 a difference in incidence of serogroup C was observed in Flanders (0-0.1/100,000) versus Wallonia (0.1-0.3/100,000).

CONCLUSION: This study showed the change in epidemiology and strain population over a 16 years period spanning an exhaustive vaccination campaign and highlights the influence of regional vaccination policies with different cohorts sizes on short and long-term IMD incidences.

%B PLoS One %V 10 %P e0139615 %8 2015 %G eng %N 10 %1 http://www.ncbi.nlm.nih.gov/pubmed/26425857?dopt=Abstract %R 10.1371/journal.pone.0139615 %0 Report %D 2015 %T CNR Listeria. Rapport annuel 2014. Souches de Listeria %A Sophie Bertrand %A R. Vanhoof %A Wesley Mattheus %K Belgique %K de %K EN %K Listeria %K rapport %K rapport annuel %I ISP %C Bruxelles %P 26 %8 0/9/2015 %@ D/2015/2505/49 %G eng %1 37010 %& 1 %0 Report %D 2015 %T CNR Neisseria meningitidis. Rapport annuel 2014. Souches de Neisseria meningitidis %A Sophie Bertrand %A R. Vanhoof %A Wesley Mattheus %K Belgique %K de %K EN %K Neisseria %K Neisseria meningitidis %K rapport %K rapport annuel %I ISP %C Bruxelles %P 26 %8 0/9/2015 %@ D/2015/2505/47 %G eng %1 38060 %& 1 %0 Report %D 2015 %T CNR Salmonella & Shigella. %A Sophie Bertrand %A R. Vanhoof %A Wesley Mattheus %K Belgique %K de %K EN %K rapport %K rapport annuel %K Salmonella %K Shigella %I ISP %C Bruxelles %P 42 %8 0/9/2015 %@ D/2015/2505/51 %G eng %1 37012 %& 1 %0 Generic %D 2015 %T Development of xTAG®-based assays as a tailor-made solution in the genotyping of antimicrobial resistance in Enterobacteriaceae. %A Pieter-Jan Ceyssens %A Wesley Mattheus %A Sophie Bertrand %K a %K Antimicrobial %K Antimicrobial resistance %K AS %K Development %K Enterobacteriaceae %K resistance %B xMAP connect meeting %I NA %C NA %8 0/0/2015 %G eng %N xMAP connect %1 39152 %2 11/2015 %0 Generic %D 2015 %T Evaluation of whole genome sequencing for routine subtyping of Salmonella Typhimurium for surveillance and outbreak investigation %A Wuyts,V. %A Sophie Bertrand %A Wesley Mattheus %A Nancy Roosens %A Marchal,K. %A Sigrid C.J. De Keersmaecker %K a %K additional %K an %K analysi %K analysis %K Antibiotic %K Antibiotic resistance %K AS %K aspects %K at %K Belgian %K Case %K data %K Diagnosis %K disease %K Diseases %K Electrophoresis %K epidemiology %K Evaluating %K EVALUATION %K Genome %K Genotype %K Human %K identify %K INFECTION %K Infectious %K Infectious diseases %K investigation %K IS %K LEVEL %K method %K national %K Next-generation sequencing %K NGS %K ORIGIN %K outbreak %K Phenotype %K resistance %K routine %K S %K Salmonella %K Salmonella enterica %K Salmonella typhimurium %K Shigella %K situation %K Species %K study %K Subtyping %K Surveillance %K Technique %K technology %K whole genome %K whole genome sequencing %X

Characterisation of bacterial isolates beyond the species and subspecies level, i.e. subtyping, is necessary for surveillance of infectious diseases and is crucial to identify a link between the origin of an infection and the human isolate in case of outbreak situations.At the Belgian National Reference Centre (NRC) for

%B Revolutionizing Next-Generation Sequencing: Tools and Technologies %I NA %C NA %8 15/1/2015 %G eng %N VIB %1 5086 %2 15-16/01/2015 %0 Generic %D 2015 %T Evolution of beta-lactam resistance in non-invasive clinical isolates of Streptococcus pneumoniae collected in Belgium in a 20 year survey (1995 to 2014). %A R. Vanhoof %A Sophie Bertrand %A Pieter-Jan Ceyssens %A Damee,S. %A Fux,F. %A Wesley Mattheus %A Nyssen,H.J. %A Van Bossuyt,E. %A Van Eldere,J. %A Jan Verhaegen %A The Belgian Streptococcus pneumoniae study group %K a %K Belgium %K beta-Lactam Resistance %K Clinical %K de %K Evolution %K non-invasive %K resistance %K Streptococcus pneumoniae %K survey %B 35 e Réunion Interdisciplinaire de chimiothérapie anti-infectieuse. %I RICAI %C Paris, France %8 0/0/2015 %G eng %N XX %1

39226

%2 14/12/2015;15/12/2015 %0 Journal Article %J Appl Environ Microbiol %D 2015 %T Extensive genetic variability linked to IS26 insertions in the fljB promoter region of atypical monophasic variants of Salmonella enterica serovar Typhimurium. %A Cécile Boland %A Sophie Bertrand %A Wesley Mattheus %A Katelijne Dierick %A Vicky Jasson %A Rosseel, Toon %A Steven Van Borm %A Mahillon, Jacques %A P Wattiau %K Animals %K Belgium %K DNA Transposable Elements %K DNA, Bacterial %K Flagellin %K Genetic Variation %K Meat %K Molecular Sequence Data %K Mutagenesis, Insertional %K polymerase chain reaction %K Promoter Regions, Genetic %K Salmonella Infections %K Salmonella Infections, Animal %K Salmonella typhimurium %K Sequence Analysis, DNA %K Swine %X

Fifty-nine monophasic Salmonella enterica serovar Typhimurium isolates, collected in Belgium during the period from 2008 to 2011, have been serotyped as 4,[5]:i:- and shown to harbor an fljB coding sequence. The genetic differences between these strains and phenotypically biphasic Salmonella Typhimurium were analyzed through PCR and DNA sequencing. Genetic alterations in the fljB promoter region affecting expression of the phase 2 flagellin were observed in 53 isolates. Other genetic events in the invertible region carrying the fljB promoter were observed in 2 isolates. For the remaining 4 isolates, no molecular differences with a reference biphasic Salmonella Typhimurium strain could be observed. Next-generation sequencing of one representative isolate affected in the fljB promoter region revealed a 26-kb IS26 composite transposon insertion along with a local genomic rearrangement. Several other IS26 element-mediated alterations of this genomic region were observed. This group of monophasic Salmonella Typhimurium isolates was genetically heterogeneous, as revealed by multilocus variable-number tandem-repeat analysis (MLVA), PCR, and sequencing. Pigs and pork represented a major source of such monophasic isolates in Belgium, as reported in other countries. Three out of 5 isolates of human origin presented genetic profiles identical to those of food isolates, demonstrating the pathogenic potential of the newly characterized variants and potential dissemination along the food chain. This study highlighted the key role played by IS26 insertions in the loss of phase 2 flagellin expression and the subsequent generation of multiple monophasic variant lineages from biphasic Salmonella Typhimurium ancestors.

%B Appl Environ Microbiol %V 81 %P 3169-75 %8 2015 May 01 %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/25724958?dopt=Abstract %& 3169 %R 10.1128/AEM.00270-15 %0 Report %D 2015 %T Infectieziekten bij kinderen, die voorkomen kunnen worden door vaccinatie. Jaaroverzicht 2014 %A Martine Sabbe %A Tine Grammens %A Toon Braeye %A Corinne Bleyenheuft %A Mendes da Costa, Elise %A Sophie Quoilin %A Sophie Bertrand %A Dediste, Anne %A Delforge, Marie-Luce %A Heymans,C. %A Huygen, Kris %A Veronik Hutse %A Stéphanie Jacquinet %A Mak, Ruud %A Wesley Mattheus %A S Moreels %A Gaetan Muyldermans %A Denis Piérard %A Carole Schirvel %A Béatrice Swennen %A Heidi Theeten %A Top, Geert %A Jean-Marie Tremerie %A Viviane Van Casteren %A Van Ranst, M %A Verhaegen, J. %A Zinnen,V. %K 2014 %K Infectieziekten %K kinderen %K vaccinatie %I WIV-ISP %C Brussel, België %P 62 %8 dec 2015 %G eng %M D/2015/2505/75 %0 Report %D 2015 %T Infectieziekten bij kinderen die voorkomen kunnen worden door vaccinatie. Jaarrapport 2013 %A Tine Grammens %A Toon Braeye %A Corinne Bleyenheuft %A Sophie Quoilin %A Sophie Bertrand %A Dediste,A. %A Detemmerman,L. %A K. De Schrijver %A Goubert,P. %A Heymans,C. %A K Huygen %A Veronik Hutse %A Stéphanie Jacquinet %A Mak,R. %A Wesley Mattheus %A S Moreels %A Gaetan Muyldermans %A Denis Piérard %A Carole Schirvel %A Béatrice Swennen %A Heidi Theeten %A Geert Top %A Jean-Marie Tremerie %A Viviane Van Casteren %A Steven Van Gucht %A Marc Van Ranst %A Jan Verhaegen %A Waegenaere,J. %A Zinnen,V. %K Infectieziekten %K kinderen %I WIV-ISP %C Brussel %P 156 %8 0/0/2015 %@ D/2015/2505/05 %G eng %1 39200 %0 Generic %D 2015 %T Infections invasives à Neisseria meningitidis: Tendances récentes en Belgique %A Sophie Bertrand %A Wesley Mattheus %A Hanquet,G. %A R. Vanhoof %E Institut Bordet %K de %K EN %K INFECTION %K infections %K Neisseria %K Neisseria meningitidis %B Séminaire de l'Institut Bordet %8 0/0/2015 %G eng %N Institut Bordet %1 39135 %2 3/06/2015 %0 Journal Article %J Clin Infect Dis %D 2015 %T Invasive Salmonella Infections at Multiple Surveillance Sites in the Democratic Republic of the Congo, 2011-2014. %A Lisette Mbuyi Kalonji %A Post, Annelies %A Phoba, Marie-France %A Falay, Dadi %A Ngbonda, Dauly %A Muyembe, Jean-Jacques %A Sophie Bertrand %A Pieter-Jan Ceyssens %A Wesley Mattheus %A Verhaegen, Jan %A Barbé, Barbara %A Kuijpers, Laura %A Van Geet, Chris %A Lunguya, Octavie %A Jacobs, Jan %K ADOLESCENT %K Adult %K Aged %K Anti-Bacterial Agents %K Azithromycin %K Bacteremia %K beta-Lactamases %K Child %K Child, Preschool %K Ciprofloxacin %K Democratic Republic of the Congo %K Drug Resistance, Multiple, Bacterial %K Epidemiological Monitoring %K Female %K Humans %K Infant %K Male %K Microbial Sensitivity Tests %K middle aged %K Salmonella %K Salmonella enteritidis %K Salmonella Infections %K Salmonella typhi %K Salmonella typhimurium %K Seasons %K Young adult %X

BACKGROUND: This study reports the microbiological landscape of Salmonella Typhi and invasive nontyphoidal Salmonella (iNTS) in the Democratic Republic of the Congo (DRC).

METHODS: Blood cultures obtained from hospital-admitted patients suspected of bloodstream infection (BSI) in 4 of 11 provinces in DRC (Kinshasa, Bas-Congo, Equateur, and Orientale) were processed. Sampling had started in 2007; the results for the period 2011-2014 are reported.

RESULTS: Salmonella Typhi and iNTS were cultured from 194 (1.4%) and 840 (5.9%), respectively, of 14,110 BSI episodes and ranked first among BSI pathogens in adults (65/300 [21.7%]) and children (783/1901 [41.2%]), respectively. A total of 948 of 1034 (91.7%) isolates were available for analysis (164 Salmonella Typhi and 784 iNTS). Salmonella Typhimurium and Salmonella Enteritidis represented 386 (49.2%) and 391 (49.9%), respectively, of iNTS isolates, fluctuating over time and geography and increasing during the rainy season. Adults accounted for <5% of iNTS BSI episodes. Children <5 years accounted for 20.3% of Salmonella Typhi BSI episodes. Among Salmonella Typhi, rates of multidrug resistance and decreased ciprofloxacin susceptibility (DCS) were 37.8% and 37.2%, respectively, and 18.3% displayed combined multidrug resistance and DCS; rates of azithromycin and ceftriaxone resistance were 0.6% and absent, respectively. Among NTS isolates, ≥80% (79.7% of Salmonella Enteritidis and 90.2% of Salmonella Typhimurium isolates) showed multidrug resistance, and <2.5% showed DCS. Combined extended-spectrum β-lactamase production (blaTEM-1 gene) and azithromycin resistance was noted in 12.7% of Salmonella Typhimurium isolates, appearing in Bas-Congo from 2013 onward.

CONCLUSIONS: Salmonella Typhi and NTS are major causes of BSI in DRC; their antimicrobial resistance is increasing.

%B Clin Infect Dis %V 61 Suppl 4 %P S346-53 %8 2015 Nov 01 %G eng %1 http://www.ncbi.nlm.nih.gov/pubmed/26449951?dopt=Abstract %R 10.1093/cid/civ713 %0 Generic %D 2015 %T Macrolide and tetracycline resistance and the presence of mef A, erm B and tet M genes in non-invasive clinical isolates of Streptococcus pneumoniae collected in Belgium in a 20 year survey (1995 to 2014). %A R. Vanhoof %A Sophie Bertrand %A Pieter-Jan Ceyssens %A Damee,S. %A Fux,F. %A Wesley Mattheus %A Nyssen,H.J. %A Van Bossuyt,E. %A Van Eldere,J. %A Jan Verhaegen %A The Belgian Streptococcus pneumoniae study group %K non-invasive %K resistance %K Streptococcus pneumoniae %K survey %B 35 e Réunion Interdisciplinaire de chimiothérapie anti-infectieuse. %I RICAI 2015 %C Paris, France %8 0/0/2015 %G eng %N XX %1

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%2 14/12/2015;15/12/2015 %0 Report %D 2015 %T Maladies infectieuses pédiatriques à prévention vaccinale. Synthèse annuelle 2014 %A Martine Sabbe %A Tine Grammens %A Toon Braeye %A Corinne Bleyenheuft %A Mendes da Costa,E. %A Sophie Quoilin %A Sophie Bertrand %A Dediste,A. %A Marie-Luce Delforge %A Heymans,C. %A K Huygen %A Veronik Hutse %A Stéphanie Jacquinet %A Mak,R. %A Wesley Mattheus %A S Moreels %A Gaetan Muyldermans %A Denis Piérard %A Carole Schirvel %A Béatrice Swennen %A Heidi Theeten %A Geert Top %A Jean-Marie Tremerie %A Viviane Van Casteren %A Van Ranst, M %A Jan Verhaegen %A Zinnen,V. %K 2014 %K Maladies infectieuses pédiatriques %K Vaccination %I WIV-ISP %C Bruxelles, Belgique %P 63 %8 12/2015 %G eng %M D/2015/2505/76 %0 Journal Article %J Plos One %D 2015 %T Molecular surveillance of rising fluoroquinolone resistance in non-invasive S. pneumoniae isolates in Belgium collected in a survey (1995-2014) %A Pieter-Jan Ceyssens %A F. Van Bambeke %A Sophie Bertrand %A Damee,S. %A Fux,F. %A Wesley Mattheus %A Nyssen,H.J. %A Van Bossuyt,E. %A Jan Verhaegen %A The Belgian Streptococcus pneumoniae study group %A Tulkens,P.M. %A R. Vanhoof %K fluoroquinolone %K longitudinal study %K non-invasive infections %K Pat A/B %K Streptococcus pneumoniae %X

We present the results of a longitudinal surveillance study (1995-2014) on fluoroquinolone resistance (FQ-R) among Belgian non-invasive Streptococcus pneumoniae isolates (n = 5,602). For many years, the switch to respiratory fluoroquinolones for the treatment of (a)typical pneumonia had no impact on FQ-R levels. However, since 2011 we observed a significant decrease in susceptibility towards ciprofloxacin, ofloxacin and levofloxacin with peaks of 9.0%, 6.6% and 3.1% resistant isolates, respectively. Resistance to moxifloxacin arised sporadically, and remained <1% throughout the entire study period. We observed classical topoisomerase mutations in gyrA (n = 25), parC (n = 46) and parE (n = 3) in varying combinations, arguing against clonal expansion of FQ-R. The impact of recombination with co-habiting commensal streptococci on FQ-R remains marginal (10.4%). Notably, we observed that a rare combination of DNA Gyrase mutations (GyrA_S81L/GyrB_P454S) suffices for high-level moxifloxacin resistance, contrasting current model. Interestingly, 85/422 pneumococcal strains display MICCIP values which were lowered by at least four dilutions by reserpine, pointing at involvement of efflux pumps in FQ-R. In contrast to susceptible strains, isolates resistant to ciprofloxacin significantly overexpressed the ABC pump PatAB in comparison to reference strain S. pneumoniae ATCC 49619, but this could only be linked to disruptive terminator mutations in a fraction of these. Conversely, no difference in expression of the Major Facilitator PmrA, unaffected by reserpine, was noted between susceptible and resistant S. pneumoniae strains. Finally, we observed that four isolates displayed intermediate to high-level ciprofloxacin resistance without any known molecular resistance mechanism. Focusing future molecular studies on these isolates, which are also commonly found in other studies, might greatly assist in the battle against rising pneumococcal drug resistance.

%B Plos One %V 11 %8 26/05/2016 %G eng %N 5 %1

37042

%2 14/12/2015;15/12/2015 %& e0154816 %R 10.1371/journal.pone.0154816 %0 Journal Article %J PLoS One %D 2015 %T Multi locus variable-number tandem repeat (MLVA) typing tools improved the surveillance of Salmonella enteritidis: a 6 years retrospective study. %A Sophie Bertrand %A De Lamine de Bex, Guillaume %A Wildemauwe, Christa %A Lunguya, Octavie %A Phoba, Marie France %A Ley, Benedikt %A Jacobs, Jan %A Vanhoof, Raymond %A Wesley Mattheus %K Anti-Bacterial Agents %K Bacterial Typing Techniques %K Disease Outbreaks %K Genetic Loci %K Humans %K Minisatellite Repeats %K Public Health Surveillance %K Retrospective Studies %K Salmonella enteritidis %K Salmonella Infections %X

Surveillance of Salmonella enterica subsp. enterica serovar Enteritidis is generally considered to benefit from molecular techniques like multiple-locus variable-number of tandem repeats analysis (MLVA), which allow early detection and confinement of outbreaks. Here, a surveillance study, including phage typing, antimicrobial susceptibility testing and MLVA on 1,535 S. Enteritidis isolates collected between 2007 and 2012, was used to evaluate the added value of MLVA for public health surveillance in Belgium. Phage types PT4, PT8, PT21, PT1, PT6, PT14b, PT28 and PT13 dominate the Belgian S. Enteritidis population. The isolates of S. Enteritidis were most frequently susceptible to all antibiotics tested. 172 different MLVA profiles were detected, of which 9 frequent profiles included 67.2% of the S. Enteritidis population. During a serial passage experiment on selected isolates to investigate the in vitro stability of the 5 MLVA loci, no variations over time were observed indicating that the MLVA profiles were stable. The MLVA profile of isolates originating from different outbreaks in the Democratic Republic of the Congo (DRC) between 2010 and 2011 were distinct from any of the MLVA profiles found in Belgian isolates throughout the six year observational period and demonstrates that MLVA improves public health surveillance of S. Enteritidis. However, MLVA should be complemented with other subtyping methods when investigating outbreaks is caused by the most common MLVA profile.

%B PLoS One %V 10 %P e0117950 %8 2015 %G eng %N 2 %1 http://www.ncbi.nlm.nih.gov/pubmed/25693200?dopt=Abstract %R 10.1371/journal.pone.0117950 %0 Journal Article %J Appl Microbiol Biotechnol %D 2015 %T A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium %A Wuyts,V. %A Wesley Mattheus %A Nancy Roosens %A Marchal,K. %A Sophie Bertrand %A Sigrid C.J. De Keersmaecker %K analysis %K Antibiotic %K Antibiotic resistance %K AS %K cause %K causes %K Concordance %K data %K detection %K EPIDEMIOLOGICAL %K gene %K Genes %K genomic %K INFECTION %K infections %K International %K investigation %K IS %K IT %K Laboratories %K LEVEL %K Luminex %K Marker %K Markers %K method %K microsphere array %K MOL-PCR %K Molecular %K molecular markers %K Network %K Objective %K observed %K ON %K outbreak %K outbreaks %K resistance %K result %K results %K S %K Salmonella %K Salmonella enterica %K Salmonella typhimurium %K stability %K Subtyping %K Surveillance %K Technique %K Type %K use %K VALIDATION %X

Subtyping below the serovar level is essential for surveillance and outbreak detection and investigation of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and its monophasic variant 1,4,[5],12:i:- (S. 1,4,[5],12:i:-), frequent causes of foodborne infections. In an attempt to overcome the intrinsic shortcomings of currently used subtyping techniques, a multiplex oligonucleotide ligation-PCR (MOL-PCR) assay was developed which combines different types of molecular markers in a high-throughput microsphere suspension array. The 52 molecular markers include prophage genes, amplified fragment length polymorphism (AFLP) elements, Salmonella genomic island 1 (SGI1), allantoinase gene allB, MLVA locus STTR10, antibiotic resistance genes, single nucleotide polymorphisms (SNPs) and phase 2 flagellar gene fljB. The in vitro stability of these markers was confirmed in a serial passage experiment. The validation of the MOL-PCR assay for subtyping of S. Typhimurium and S. 1,4,[5],12:i:- on 519 isolates shows that the method is rapid, reproducible, flexible, accessible, easy to use and relatively inexpensive. Additionally, a 100 % typeability and a discriminatory power equivalent to that of phage typing were observed, and epidemiological concordance was assessed on isolates of 2 different outbreaks. Furthermore, a data analysis method is provided so that the MOL-PCR assay allows for objective, computerised data analysis and data interpretation of which the results can be easily exchanged between different laboratories in an international surveillance network.

%B Appl Microbiol Biotechnol %V 99 %P 8137 - 8149 %8 0/10/2015 %@ 0175-7598 %G eng %N 19 %1 5212 %& 8137 %R 10.1007/s00253-015-6831-7 %0 Report %D 2015 %T NRL Listeria. Jaarverslag 2014. Listeria %A Sophie Bertrand %A R. Vanhoof %A Wesley Mattheus %K België %K Listeria %I ISP %C Bruxelles %P 42 %8 0/9/2015 %@ D/2015/2505/50 %G eng %1 38063 %& 1 %0 Report %D 2015 %T NRL Neisseria meningitidis. Jaarverslag 2014. Neisseria meningitidis %A Sophie Bertrand %A R. Vanhoof %A Wesley Mattheus %K België %K Neisseria %K Neisseria meningitidis %I ISP %C Bruxelles %P 22 %8 0/9/2015 %@ D/2015/2505/48 %G eng %1 38061 %& 1 %0 Report %D 2015 %T NRL Salmonella & Shigella %A Sophie Bertrand %A R. Vanhoof %A Wesley Mattheus %K België %K Salmonella %K Shigella %I ISP %C Bruxelles %P 22 %8 0/9/2015 %@ D/2015/2505/52 %G eng %1 37013 %& 1 %0 Generic %D 2015 %T Results of the 16 th Belgian Survey on antimicrobial resistance in non-invasive clinical isolates of Streptococcus pneumoniae collected in winter 2013-2014 with special attention to Penicillin non-susceptibility. %A R. Vanhoof %A Sophie Bertrand %A Fux,F. %A Wesley Mattheus %A Van Eldere,J. %A Jan Verhaegen %K Antimicrobial %K Antimicrobial resistance %K Attention %K Belgian %K Clinical %K de %K non-invasive %K ON %K resistance %K result %K results %K Streptococcus pneumoniae %K survey %K Winter %B 34 e réunion Interdisciplinaire de chimiothérapie anti-infectieuse. %8 0/0/2015 %G eng %N XX %1 39225 %2 27/11/2014; 28/11/2014 %0 Journal Article %J Antimicrob Agents Chemother %D 2015 %T Trends in serotype distribution and antimicrobial susceptibility in Salmonella enterica isolates from humans in Belgium, 2009 to 2013. %A Pieter-Jan Ceyssens %A Wesley Mattheus %A Vanhoof, Raymond %A Sophie Bertrand %K Bacterial Proteins %K Belgium %K beta-Lactam Resistance %K beta-Lactamases %K Cefotaxime %K Ciprofloxacin %K DNA Gyrase %K DNA Topoisomerase IV %K Drug Resistance, Bacterial %K Humans %K Microbial Sensitivity Tests %K Salmonella enterica %K Salmonella Infections %K Serogroup %X

The Belgian National Reference Centre for Salmonella received 16,544 human isolates of Salmonella enterica between January 2009 and December 2013. Although 377 different serotypes were identified, the landscape is dominated by S. enterica serovars Typhimurium (55%) and Enteritidis (19%) in a ratio which is inverse to European Union averages. With outbreaks of Salmonella serotypes Ohio, Stanley, and Paratyphi B variant Java as prime examples, 20 serotypes displayed significant fluctuations in this 5-year period. Typhoid strains account for 1.2% of Belgian salmonellosis cases. Large-scale antibiotic susceptibility analyses (n = 4,561; panel of 12 antibiotics) showed declining resistance levels in S. Enteritis and Typhimurium isolates for 8 and 3 tested agents, respectively. Despite low overall resistance to ciprofloxacin (4.4%) and cefotaxime (1.6%), we identified clonal lineages of Salmonella serotypes Kentucky and Infantis displaying rising resistance against these clinically important drugs. Quinolone resistance is mainly mediated by serotype-specific mutations in GyrA residues Ser83 and Asp87 (92.2% not wild type), while an additional ParC_Ser80Ile mutation leads to ciprofloxacin resistance in 95.5% S. Kentucky isolates, which exceeds European averages. Plasmid-mediated quinolone resistance (PMQR) alleles qnrA1 (n = 1), qnrS (n = 9), qnrD1 (n = 4), and qnrB (n = 4) were found in only 3.0% of 533 isolates resistant to nalidixic acid. In cefotaxime-resistant isolates, we identified a broad range of Ambler class A and C β-lactamase genes (e.g., bla(SHV-12), blaTEM-52, bla(CTX-M-14), and bla(CTX-M-15)) commonly associated with members of the family Enterobacteriaceae. In conclusion, resistance to fluoroquinolones and cefotaxime remains rare in human S. enterica, but clonal resistant serotypes arise, and continued (inter)national surveillance is mandatory to understand the origin and routes of dissemination thereof.

%B Antimicrob Agents Chemother %V 59 %P 544-52 %8 2015 Jan %G eng %N 1 %1 http://www.ncbi.nlm.nih.gov/pubmed/25385108?dopt=Abstract %& 544 %R 10.1128/AAC.04203-14 %0 Government Document %D 2015 %T The usefulness of whole genome sequencing for outbreak investigation of food pathogens, Salmonella Enteritidis as a case study %A Wuyts,V. %A Sarah Denayer %A Nancy Roosens %A Wesley Mattheus %A Sophie Bertrand %A Marchal,K. %A Katelijne Dierick %A Sigrid C.J. De Keersmaecker %K a %K abstract %K AS %K Case %K case studies %K Case study %K case-study %K food %K Genome %K investigation %K outbreak %K pathogen %K Salmonella %K Salmonella enteritidis %K study %K whole genome %K whole genome sequencing %X

No abstract

%B LabInfo %V submitted %8 0/0/2015 %G eng %1 5211 %0 Generic %D 2015 %T User-friendly WGS analysis of Salmonella Enteritidis PT4 outbreaks %A Wuyts,V. %A Sarah Denayer %A Nancy Roosens %A Wesley Mattheus %A Sophie Bertrand %A Marchal,K. %A Katelijne Dierick %A Sigrid C.J. De Keersmaecker %E BSFM %K analysi %K analysis %K conference %K food %K Food Microbiology %K microbiology %K ON %K outbreak %K outbreaks %K Salmonella %K Salmonella enteritidis %K WGS %K whole genome sequencing %8 2015/10/08/ %G eng %1 5222 %0 Journal Article %J PLoS Curr %D 2015 %T Whole Genome Sequence Analysis of Salmonella Enteritidis PT4 Outbreaks from a National Reference Laboratory's Viewpoint. %A Wuyts, Véronique %A Sarah Denayer %A Nancy Roosens %A Wesley Mattheus %A Sophie Bertrand %A Marchal, Kathleen %A Katelijne Dierick %A Sigrid C.J. De Keersmaecker %K a %K additional %K ALL %K an %K analysi %K analysis %K Antibiotic %K Antibiotic resistance %K Antimicrobial %K article %K AS %K at %K Belgian %K Belgium %K bioinformatics %K Biology %K Biotechnology %K Brussels %K Case %K case studies %K Case study %K case-study %K Common %K data %K Discussion %K disease %K Diseases %K electronic %K epidemiology %K expertise %K food %K foodborne outbreaks %K future %K gene %K Genetic %K genetics %K Genome %K genomic %K Genomics %K health %K Human %K Infectious %K Infectious diseases %K INFORMATION %K Institute %K investigation %K IS %K IT %K journal %K Laboratories %K method %K methods %K Molecular %K Molecular biology %K national %K ON %K ORIGIN %K outbreak %K outbreaks %K pathogen %K period %K Phage type %K plant %K profile %K public %K public health %K Public-health %K Questionnaire %K resistance %K result %K results %K routine %K routine laboratory %K S %K Salmonella %K Salmonella enterica %K Salmonella enteritidis %K Sequence Analysis %K Serotyping %K Service %K Shigella %K SOFTWARE %K STANDARD %K study %K Subtyping %K System %K Systems %K technology %K TESTING %K time %K Type %K Universities %K university %K whole %K whole genome %X

INTRODUCTION: In April and May 2014, two suspected egg-related outbreaks of Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) were investigated by the Belgian National Reference Laboratory of Foodborne Outbreaks. Both the suspected food and human isolates being available, and this for both outbreaks, made these the ideal case study for a retrospective whole genome sequencing (WGS) analysis with the goal to investigate the feasibility of this technology for outbreak investigation by a National Reference Laboratory or National Reference Centre without thorough bioinformatics expertise.

METHODS: The two outbreaks were originally investigated epidemiologically with a standard questionnaire and with serotyping, phage typing, multiple-locus variable-number of tandem repeats analysis (MLVA) and antimicrobial susceptibility testing as classical microbiological methods. Retrospectively, WGS of six outbreak isolates was done on an Illumina HiSeq. Analysis of the WGS data was performed with currently available, user-friendly software and tools, namely CLC Genomics Workbench, the tools available on the server of the Center for Genomic Epidemiology and BLAST Ring Image Generator (BRIG).

RESULTS: To all collected human and food outbreak isolates, classical microbiological investigation assigned phage type PT4 (variant phage type PT4a for one human isolate) and MLVA profile 3-10-5-4-1, both of which are common for human isolates in Belgium. The WGS analysis confirmed the link between food and human isolates for each of the outbreaks and clearly discriminated between the two outbreaks occurring in a same time period, thereby suggesting a non-common source of contamination. Also, an additional plasmid carrying an antibiotic resistance gene was discovered in the human isolate with the variant phage type PT4a.

DISCUSSION: For the two investigated outbreaks occurring at geographically separated locations, the gold standard classical microbiological subtyping methods were not sufficiently discriminative to distinguish between or assign a common origin of contamination for the two outbreaks, while WGS analysis could do so. This case study demonstrated the added value of WGS for outbreak investigations by confirming and/or discriminating food and human isolates between and within outbreaks. It also proved the feasibility of WGS as complementary or even future replacing (sub)typing method for the average routine laboratory.

%B PLoS Curr %V 7 %8 2015 Sep 11 %G eng %1 http://www.ncbi.nlm.nih.gov/pubmed/26468422?dopt=Abstract %R 10.1371/currents.outbreaks.aa5372d90826e6cb0136ff66bb7a62fc %0 Generic %D 2014 %T Evaluation of whole genome sequencing for routine subtyping of Salmonella Typhimurium for surveillance and outbreak investigation %A Wuyts,V. %A Sophie Bertrand %A Wesley Mattheus %A Nancy Roosens %A Marchal,K. %A Sigrid C.J. De Keersmaecker %E WIV-ISP %K application %K applications %K EVALUATION %K Genome %K health %K investigation %K NGS %K outbreak %K public %K public health %K Public-health %K routine %K Salmonella %K Salmonella typhimurium %K Subtyping %K Surveillance %K whole genome %K whole genome sequencing %B Applications of Next Generation Sequencing for public health %8 10/10/2014 %G eng %N WIV-ISP %1 39123 %2 10/10/2014 %0 Journal Article %J Vet Microbiol %D 2014 %T Molecular typing of monophasic Salmonella 4,[5]:i:- strains isolated in Belgium (2008-2011). %A Cécile Boland %A Sophie Bertrand %A Wesley Mattheus %A Katelijne Dierick %A P Wattiau %K Animals %K Bacteriophage Typing %K Belgium %K Flagellin %K Food Safety %K Humans %K Molecular Typing %K polymerase chain reaction %K Salmonella %K Salmonella Food Poisoning %K Salmonella Infections %K Salmonella typhimurium %K Tandem Repeat Sequences %X

To assess the distribution of Salmonella 4,[5]:i:- subtypes in the Belgian food chain and compare it to the subtypes associated with human infections, a molecular assessment was initiated. Two hundred fifty-three Salmonella isolates serotyped as 4,[5]:i:- during the period 2008-2011 in Belgium and originating from animal productions, food or human clinical samples were analysed by a specific duplex PCR. One hundred ninety-four isolates (76.7%) fit the profile of a S. Typhimurium monophasic variant as defined by the European Food Safety Authority. The other isolates possessed but did not express the phase II flagellin gene (23.3%). Multiple Locus Variable Number of Tandem Repeats Analysis (MLVA) revealed many but closely related profiles in the fljB-negative S. Typhimurium monophasic variant isolates. Some MLVA types were associated with both human and animal isolates but no unique source of human contamination could be demonstrated.

%B Vet Microbiol %V 168 %P 447-50 %8 2014 Jan 31 %G eng %N 2-4 %1 http://www.ncbi.nlm.nih.gov/pubmed/24398228?dopt=Abstract %R 10.1016/j.vetmic.2013.11.040 %0 Journal Article %J Euro.Surveill %D 2014 %T Multidisciplinary investigation of a multicountry outbreak of Salmonella Stanley infections associated with turkey meat in the European Union, August 2011 to January 201334078 %A Kinross,P. %A L. van Alphen %A J. Martinez Urtaza %A M. Struelens %A Takkinen,J. %A Coulombier,D. %A Makela,P. %A Sophie Bertrand %A Wesley Mattheus %A Schmid,D. %A Kanitz,E. %A Rucker,V. %A Krisztalovics,K. %A Paszti,J. %A Szogyenyi,Z. %A Lancz,Z. %A Rabsch,W. %A Pfefferkorn,B. %A Hiller,P. %A Mooijman,K. %A Gossner,C. %K 2012 %K a %K Adult %K an %K analysi %K analysis %K Animal %K Animals %K article %K AS %K Case %K classification %K Cluster Analysis %K Communicable Disease Control %K Control %K Countries %K disease %K Disease Outbreaks %K Diseases %K ecdc %K electronic %K Electrophoresis %K environmental %K epidemic %K EPIDEMIOLOGICAL %K epidemiology %K EU %K Europe %K European %K European Union %K evidence %K feed %K Female %K food %K Food Microbiology %K Food Safety %K health %K Human %K Humans %K im %K incidence %K INFECTION %K infections %K INFORMATION %K Information system %K International %K investigation %K IS %K isolation & purification %K journal %K Male %K Meat %K microbiology %K Molecular Typing %K Monitoring %K national %K ON %K ORIGIN %K outbreak %K Population Surveillance %K prevention %K prevention & control %K production %K profile %K public %K public health %K Public-health %K routine %K S %K SAFETY %K Salmonella %K Salmonella enterica %K Salmonella Infections %K sampling %K SB - IM %K Serotyping %K Sweden %K System %K Transmission %K Turkey %K Turkeys %K veterinary %X Between August 2011 and January 2013, an outbreak of Salmonella enterica serovar Stanley (S. Stanley) infections affected 10 European Union (EU) countries, with a total of 710 cases recorded. Following an urgent inquiry in the Epidemic Intelligence Information System for food- and waterborne diseases (EPIS-FWD) on 29 June 2012, an international investigation was initiated including EU and national agencies for public health, veterinary health and food safety. Two of three local outbreak investigations undertaken by affected countries in 2012 identified turkey meat as a vehicle of infection. Furthermore, routine EU monitoring of animal sources showed that over 95% (n=298) of the 311 S. Stanley isolates reported from animal sampling in 2011 originated from the turkey food production chain. In 2004-10, none had this origin. Pulsed-field gel electrophoresis (PFGE) profile analysis of outbreak isolates and historical S. Stanley human isolates revealed that the outbreak isolates had a novel PFGE profile that emerged in Europe in 2011. An indistinguishable PFGE profile was identified in 346 of 464 human, food, feed, environmental and animal isolates from 16 EU countries: 102 of 112 non-human isolates tested were from the turkey production chain. On the basis of epidemiological and microbiological evidence, turkey meat was considered the primary source of human infection, following contamination early in the animal production chain %B Euro.Surveill %V 19 %8 15/5/2014 %G eng %N 19 %1 34078 %0 Generic %D 2014 %T NeXSplorer.iph: Development of next generation sequencing data analysis tools in support of a fast response for public health and food chain safety %A Sigrid C.J. De Keersmaecker %A Sophie Bertrand %A Wesley Mattheus %A Philippe Herman %A Katelijne Dierick %A N Botteldoorn %A Sarah Denayer %A Steven Van Gucht %A Isabelle Thomas %A Deforce,D. %A Marchal,K. %A Nancy Roosens %K a %K analysi %K analysis %K application %K applications %K bioinformatics %K data %K Development %K food %K Food Chain %K GMO %K health %K NGS %K public %K public health %K Public-health %B Applications of Next Generation Sequencing for public health %I NA %C NA %8 0/0/2014 %G eng %N =WIV-ISP %1 38637 %2 10/10/2014 %0 Government Document %D 2013 %T Bilan épidémiologique: le nombre de cas d'infections invasives à méningocoques est stable depuis 2008. %A Tine Grammens %A Sophie Bertrand %A Wesley Mattheus %K 2008 %K de %K epidemiology %K LE %K Meningococcal Infections %K Meningococcal Vaccines %K vaccines %X NA %B VAX Info Magazine %V Dec 2013 %8 5/12/2013 %G eng %N NA %1 30415 %0 Journal Article %J PLoS One %D 2013 %T MLVA as a tool for public health surveillance of human Salmonella Typhimurium: prospective study in Belgium and evaluation of MLVA loci stability. %A Wuyts, Véronique %A Wesley Mattheus %A Guillaume De Laminne de Bex %A Wildemauwe, Christa %A Nancy Roosens %A Marchal, Kathleen %A Sigrid C.J. De Keersmaecker %A Sophie Bertrand %K Bacterial Typing Techniques %K Belgium %K Disease Outbreaks %K Humans %K Minisatellite Repeats %K Prospective Studies %K Public Health Surveillance %K Salmonella Infections %K Salmonella typhimurium %X

Surveillance of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is generally considered to benefit from molecular techniques like multiple-locus variable-number of tandem repeats analysis (MLVA), which allow earlier detection and confinement of outbreaks. Here, a surveillance study, including phage typing, antimicrobial susceptibility testing and the in Europe most commonly used 5-loci MLVA on 1,420 S. Typhimurium isolates collected between 2010 and 2012 in Belgium, was used to evaluate the added value of MLVA for public health surveillance. Phage types DT193, DT195, DT120, DT104, DT12 and U302 dominate the Belgian S. Typhimurium population. A combined resistance to ampicillin, streptomycin, sulphonamides and tetracycline (ASSuT) with or without additional resistances was observed for 42.5% of the isolates. 414 different MLVA profiles were detected, of which 14 frequent profiles included 44.4% of the S. Typhimurium population. During a serial passage experiment on selected isolates to investigate the in vitro stability of the 5 MLVA loci, variations over time were observed for loci STTR6, STTR10, STTR5 and STTR9. This study demonstrates that MLVA improves public health surveillance of S. Typhimurium. However, the 5-loci MLVA should be complemented with other subtyping methods for investigation of possible outbreaks with frequent MLVA profiles. Also, variability in these MLVA loci should be taken into account when investigating extended outbreaks and studying dynamics over longer periods.

%B PLoS One %V 8 %P e84055 %8 2013 %G eng %N 12 %1 http://www.ncbi.nlm.nih.gov/pubmed/24391880?dopt=Abstract %R 10.1371/journal.pone.0084055 %0 Journal Article %J Foodborne.Pathog.Dis. %D 2012 %T Trend analysis of antimicrobial resistance in Campylobacter jejuni and Campylobacter coli isolated from Belgian pork and poultry meat products using surveillance data of 2004-2009234 %A Wesley Mattheus %A N Botteldoorn %A Kim Heylen %A Pochet,B. %A Katelijne Dierick %K 0 %K 2004 %K 2007 %K 2009 %K a %K Abattoirs %K acid %K Agent %K Agents %K ALL %K Ampicillin %K Ampicillin Resistance %K an %K analysi %K analysis %K Animals %K Anti-Bacterial Agents %K Antimicrobial %K Antimicrobial resistance %K Antimicrobials %K article %K at %K Belgian %K Belgium %K Brussels %K Campylobacter %K Campylobacter coli %K Campylobacter jejuni %K Chickens %K Ciprofloxacin %K Combination %K Comparative Study %K data %K Dna %K DNA Gyrase %K drug effects %K Drug Resistance,Bacterial %K Drug Resistance,Multiple,Bacterial %K electronic %K Erythromycin %K Food Handling %K Food Microbiology %K genetics %K health %K husbandry %K im %K Increase %K Institute %K IS %K isolation & purification %K journal %K LEVEL %K Meat %K Meat Products %K metabolism %K methods %K Microbial Sensitivity Tests %K microbiology %K Nalidixic Acid %K pathogen %K period %K pharmacology %K Point Mutation %K Population Surveillance %K Pork %K Poultry %K Poultry Products %K PRODUCTS %K public %K public health %K Public-health %K resistance %K SB - IM %K Service %K study %K Surveillance %K Sus scrofa %K Tetracycline %K Time Factors %K trend %K Turkeys %K use %X The purpose of this study was to analyze and compare antimicrobial resistance in Campylobacter spp. isolated from pork and poultry carcasses, and pork and poultry meat (at slaughterhouse level, during meat cutting, and at retail) in Belgium, using available surveillance data over the period 2004-2009. The susceptibilities of 1724 Campylobacter isolates for ampicillin, ciprofloxacin, nalidixic acid, tetracycline, erythromycin, and gentamicin were tested by E-test. Gentamicin resistance was low (near 0%) until 2007, with an increase to over 20% by 2009 for all species-matrix combinations. Resistance to tetracycline fluctuated around the same level during the entire study period and was significantly higher (p-value of <0.05) in C. coli than in C. jejuni. Erythromycin resistance was low and showed a slight decrease between 2004 and 2007, but increased from 2007 until 2009. Fluoroquinolone and ampicillin resistance was significantly higher in isolates derived from poultry, compared to pork-related isolates. This correlates with the higher use of these antimicrobials in poultry husbandry. A total of 25% of C. coli isolates from poultry showed the most apparent multiresistance (resistance to four or more antimicrobials). Approximately 1% of the poultry-derived isolates (both C. coli and C. jejuni) showed resistance to all tested antimicrobials, while none was found in pork products %B Foodborne.Pathog.Dis. %V 9 %P 465 - 472 %8 0/5/2012 %G eng %N 5 %1 234 %& 465 %R http://dx.doi.org/10.1089/fpd.2011.1042 %0 Journal Article %J Euro Surveill %D 2012 %T Usefulness of the European Epidemic Intelligence Information System in the management of an outbreak of listeriosis, Belgium, 2011. %A Yde, M %A Naranjo, M %A Wesley Mattheus %A Stragier, P %A Pochet, B %A Beulens, K %A De Schrijver, K %A Van den Branden, D %A Valeska Laisnez %A Flipse, W %A A. Leclercq %A Lecuit, M %A Katelijne Dierick %A Sophie Bertrand %K Aged %K Aged, 80 and over %K Arsenites %K Bacterial Typing Techniques %K Belgium %K Cadmium Chloride %K Cluster Analysis %K Disease Outbreaks %K Drug Resistance, Microbial %K Electrophoresis, Gel, Pulsed-Field %K Europe %K Female %K Foodborne Diseases %K Geographic Information Systems %K Hospitalization %K Humans %K Information Dissemination %K Listeria monocytogenes %K Listeriosis %K Male %K Microbial Sensitivity Tests %K middle aged %K Molecular Sequence Data %K Population Surveillance %X

A cluster of time-linked cases and the identification of a clonal strain suggest the occurrence of an outbreak of listeriosis in Belgium in 2011, presumably due to the consumption of hard cheese made with pasteurised milk and produced by a Belgium manufacturer. The outbreak clone was identified as Listeria monocytogenes serovar 1/2a, sensitive to arsenic and cadmium and of multilocus sequence typing MLST-type 37. Food investigation of this outbreak was facilitated by the European Epidemic Intelligence Information System and data exchanged between French and Belgium listeriosis surveillance systems.

%B Euro Surveill %V 17 %8 2012 Sep 20 %G eng %N 38 %1 http://www.ncbi.nlm.nih.gov/pubmed/23040965?dopt=Abstract %R NA %0 Journal Article %J PLoS One %D 2011 %T Microbiological and molecular assessment of bacteriophage ISP for the control of Staphylococcus aureus %A Vandersteegen,K. %A Wesley Mattheus %A Pieter-Jan Ceyssens %A Bilocq,F. %A De Vos,D. %A Pirnay,J.P. %A J.P. Noben %A Merabishvili,M. %A Lipinska,U. %A Hermans,K. %A Lavigne,R. %K Antibiotic resistance %K phage %K phage therapy %K Staphylococcus aureus %X

The increasing antibiotic resistance in bacterial populations requires alternatives for classical treatment of infectious diseases and therefore drives the renewed interest in phage therapy. Methicillin resistant Staphylococcus aureus (MRSA) is a major problem in health care settings and live-stock breeding across the world. This research aims at a thorough microbiological, genomic, and proteomic characterization of S. aureus phage ISP, required for therapeutic applications. Host range screening of a large batch of S. aureus isolates and subsequent fingerprint and DNA microarray analysis of the isolates revealed a substantial activity of ISP against 86% of the isolates, including relevant MRSA strains. From a phage therapy perspective, the infection parameters and the frequency of bacterial mutations conferring ISP resistance were determined. Further, ISP was proven to be stable in relevant in vivo conditions and subcutaneous as well as nasal and oral ISP administration to rabbits appeared to cause no adverse effects. ISP encodes 215 gene products on its 138,339 bp genome, 22 of which were confirmed as structural proteins using tandem electrospray ionization-mass spectrometry (ESI-MS/MS), and shares strong sequence homology with the 'Twort-like viruses'. No toxic or virulence-associated proteins were observed. The microbiological and molecular characterization of ISP supports its application in a phage cocktail for therapeutic purposes

%B PLoS One %V 6 %P e24418 %8 0/0/2011 %G eng %N 9 %1

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%& e24418 %R http://dx.doi.org/10.1371/journal.pone.0024418 %0 Report %D 2011 %T Nationaal referentielaboratorium voedseltoxi-infecties, antimicrobiële resistentie voan zoönotische kiemen levensmiddelenmicrobiologie en tweekleppige weekdieren, jaarverslag 2010 %A N Botteldoorn %A Katelijne Dierick %A Sarah Denayer %A Marie Polet %A Wesley Mattheus %K 2010 %K EN %K food %K foodborne outbreaks %K ISO methods %K meetings %I WIV-ISP %C Brussels, Belgium %P 36 %8 1/3/2011 %G eng %1 38082 %0 Journal Article %J Chem.Biol. %D 2010 %T Isolation and purification of a new kalimantacin/batumin-related polyketide antibiotic and elucidation of its biosynthesis gene cluster %A Wesley Mattheus %A Gao,L.J. %A Herdewijn,P. %A Landuyt,B. %A Jan Verhaegen %A Masschelein,J. %A Volckaert,G. %A Lavigne,R. %K 0 %K Activity %K Agent %K Agents %K an %K Anti-Bacterial Agents %K Antibiotic %K antibiotics %K article %K Base Sequence %K Belgium %K biosynthesis %K chemicals %K Clinical %K Cluster %K Design %K electronic %K Engineering %K function %K functions %K gene %K Gene Knockdown Techniques %K Genes,Bacterial %K Genetic %K genetics %K genomic %K Group %K Hydroxymethylglutaryl-CoA Synthase %K im %K inactivation %K INFECTION %K infections %K IS %K isolation & purification %K IT %K journal %K Laboratories %K mechanism %K metabolism %K MODEL %K Molecular Sequence Data %K Multigene Family %K observed %K Open Reading Frames %K organic %K Organic Chemicals %K Peptide Synthases %K pharmacology %K Polyketide Synthases %K production %K Pseudomonas %K Pseudomonas fluorescens %K purification %K region %K Research %K Research Support %K resistance %K SB - IM %K staphylococcus %K strain %K structure %K study %K System %K technology %X Kal/bat, a polyketide, isolated to high purity (>95%) is characterized by strong and selective antibacterial activity against Staphylococcus species (minimum inhibitory concentration, 0.05 microg/mL), and no resistance was observed in strains already resistant to commonly used antibiotics. The kal/bat biosynthesis gene cluster was determined to a 62 kb genomic region of Pseudomonas fluorescens BCCM_ID9359. The kal/bat gene cluster consists of 16 open reading frames (ORF), encoding a hybrid PKS-NRPS system, extended with trans-acting tailoring functions. A full model for kal/bat biosynthesis is postulated and experimentally tested by gene inactivation, structural confirmation (using NMR spectroscopy), and complementation. The structural and microbiological study of biosynthetic kal/bat analogs revealed the importance of the carbamoyl group and 17-keto group for antibacterial activity. The mechanism of self-resistance lies within the production of an inactive intermediate, which is activated in a one-step enzymatic oxidation upon export. The genetic basis and biochemical elucidation of the biosynthesis pathway of this antibiotic will facilitate rational engineering for the design of novel structures with improved activities. This makes it a promising new therapeutic option to cope with multidrug-resistant clinical infections %B Chem.Biol. %V 17 %P 149 - 159 %8 26/2/2010 %G eng %N 2 %1 34022 %& 149 %R http://dx.doi.org/10.1016/j.chembiol.2010.01.014 %0 Journal Article %J PLoS One %D 2009 %T Quality-controlled small-scale production of a well-defined bacteriophage cocktail for use in human clinical trials. %A Merabishvili, Maya %A Pirnay, Jean-Paul %A Verbeken, Gilbert %A Chanishvili, Nina %A Tediashvili, Marina %A Lashkhi, Nino %A Glonti, Thea %A Krylov, Victor %A Jan Mast %A Van Parys, Luc %A Lavigne, Rob %A Volckaert, Guido %A Wesley Mattheus %A Verween, Gunther %A De Corte, Peter %A Rose, Thomas %A Jennes, Serge %A Zizi, Martin %A De Vos, Daniel %A Vaneechoutte, Mario %K Bacteriophages %K Burns %K Clinical Trials as Topic %K Genome, Viral %K Humans %K Proteome %K Pseudomonas aeruginosa %K Pseudomonas Infections %K Staphylococcal Infections %K Staphylococcus aureus %K wound infection %X

We describe the small-scale, laboratory-based, production and quality control of a cocktail, consisting of exclusively lytic bacteriophages, designed for the treatment of Pseudomonas aeruginosa and Staphylococcus aureus infections in burn wound patients. Based on successive selection rounds three bacteriophages were retained from an initial pool of 82 P. aeruginosa and 8 S. aureus bacteriophages, specific for prevalent P. aeruginosa and S. aureus strains in the Burn Centre of the Queen Astrid Military Hospital in Brussels, Belgium. This cocktail, consisting of P. aeruginosa phages 14/1 (Myoviridae) and PNM (Podoviridae) and S. aureus phage ISP (Myoviridae) was produced and purified of endotoxin. Quality control included Stability (shelf life), determination of pyrogenicity, sterility and cytotoxicity, confirmation of the absence of temperate bacteriophages and transmission electron microscopy-based confirmation of the presence of the expected virion morphologic particles as well as of their specific interaction with the target bacteria. Bacteriophage genome and proteome analysis confirmed the lytic nature of the bacteriophages, the absence of toxin-coding genes and showed that the selected phages 14/1, PNM and ISP are close relatives of respectively F8, phiKMV and phage G1. The bacteriophage cocktail is currently being evaluated in a pilot clinical study cleared by a leading Medical Ethical Committee.

%B PLoS One %V 4 %8 2009 %G eng %N 3 %R 10.1371/journal.pone.0004944 %0 Journal Article %J J Bacteriol %D 2006 %T Genomic analysis of Pseudomonas aeruginosa phages LKD16 and LKA1: establishment of the phiKMV subgroup within the T7 supergroup. %A Pieter-Jan Ceyssens %A Lavigne, Rob %A Wesley Mattheus %A Chibeu, Andrew %A Hertveldt, Kirsten %A Jan Mast %A Robben, Johan %A Volckaert, Guido %K Dna %K Electron %K Gene Order %K Mass Spectrometry %K Microscopy %K Molecular Sequence Data %K Nucleic Acid %K Podoviridae %K Pseudomonas aeruginosa %K Pseudomonas Phages %K Repetitive Sequences %K Sequence Analysis %K Sequence Homology %K Terminal Repeat Sequences %K Transmission %K Viral %K Viral Genes %K Viral Genome %K Viral Proteins %X

Lytic Pseudomonas aeruginosa phages LKD16 and LKA1 were locally isolated and morphologically classified as Podoviridae. While LKD16 adsorbs weakly to its host, LKA1 shows efficient adsorption (ka = 3.9 x 10(-9) ml min(-1)). LKA1, however, displays a narrow host range on clinical P. aeruginosa strains compared to LKD16. Genome analysis of LKD16 (43,200 bp) and LKA1 (41,593 bp) revealed that both phages have linear double-stranded DNA genomes with direct terminal repeats of 428 and 298 bp and encode 54 and 56 genes, respectively. The majority of the predicted structural proteins were experimentally confirmed as part of the phage particle using mass spectrometry. Phage LKD16 is closely related to bacteriophage phiKMV (83% overall DNA homology), allowing a more thoughtful gene annotation of both genomes. In contrast, LKA1 is more distantly related, lacking significant DNA homology and showing protein similarity to phiKMV in 48% of its gene products. The early region of the LKA1 genome has diverged strongly from phiKMV and LKD16, and intriguing differences in tail fiber genes of LKD16 and LKA1 likely reflect the observed discrepancy in infection-related properties. Nonetheless, general genome organization is clearly conserved among phiKMV, LKD16, and LKA1. The three phages carry a single-subunit RNA polymerase gene adjacent to the structural genome region, a feature which distinguishes them from other members of the T7 supergroup. Therefore, we propose that phiKMV represents an independent and widespread group of lytic P. aeruginosa phages within the T7 supergroup.

%B J Bacteriol %V 188 %8 2006 Oct %G eng %N 19 %R 10.1128/JB.00831-06 %0 Report %D 0 %T Epidemiologische surveillance van invasieve meningokokkeninfecties - 2020 %A Stéphanie Jacquinet %A Wesley Mattheus %A Adrien Lajot %A Tine Grammens %A Chloé Wyndham-Thomas %X %P 13 %8 09/06/2021 %G eng %0 Report %D 0 %T Infoblad meningokokkeninfecties 2019 (T4) %A Wesley Mattheus %G eng %U www.sciensano.be %0 Government Document %D 0 %T Infoblad meningokokkeninfecties 2020 (T2) %A Wesley Mattheus %G eng %0 Report %D 0 %T Infoblad Meningokokkeninfecties 2020 (T3) %A Wesley Mattheus %G eng %0 Government Document %D 0 %T Infoblad Meningokokkeninfecties 2020 (T3) %A Wesley Mattheus %G eng %0 Report %D 0 %T méningocoque: rapport épidémiologique 2018 %A Stéphanie Jacquinet %A Wesley Mattheus %A Adrien Lajot %G eng %0 Report %D 0 %T Surveillance épidémiologique des infections invasives à méningocoques - 2019 %A Stéphanie Jacquinet %A Wesley Mattheus %A Chloé Wyndham-Thomas %A Adrien Lajot %G eng