Sci. report, recommendat°, guidance doc., directive, monograph
English
SCIENSANO
Abstract:
Abstract
In Belgium, the FASFC monitors the evolution of antimicrobial resistance (AMR) in food and foodproducing animals (primary production). Resistance in the zoonotic bacteria Salmonella and Campylobacter and in methicillin-resistant Staphylococcus aureus (MRSA) as well as resistance in indicator bacteria Escherichia coli, Enterococcus faecalis and Enterococcus faecium was monitored in 2022. Moreover, a specific monitoring of presumptive extended spectrum betalactamases/AmpC/carbapenemase producing E.coli is done on strains isolated from food-producing animals and meat derived thereof. Microbiological resistance was assessed using epidemiological cutoff values (ECOFF) according to EUCAST (European Committee on Antimicrobial Susceptibility Testing). In 2022, the European Commission Implementing Decision 2020/1729 of the 17th of November 2020 was applicable for the determination of the epidemiological cut-off values as well as for the selection of antimicrobial panels (EUVSEC3/EUCAMP3). In Campylobacter jejuni isolated from poultry meat, the predominant resistance profiles included ciprofloxacin combined with tetracycline. An increase in resistance to these antibiotics as well as to ertapenem and erythromycin was seen in 2022. Multidrug resistance in C. jejuni also increased in 2022 up to 13% compared to 4,4% in 2021. In Campylobacter coli from poultry meat, while ciprofloxacin resistance increased in 2022, resistance to erythromycin, ertapenem and tetracycline slightly decreased, thus lowering the multidrug resistance rate as well from 43,48% in 2021 to 39,13%. In primary production, the monitoring of Campylobacter coli in fattening pigs showed overall stable resistance levels except for an increased resistance to erythromycin and a first detection of low chloramphenicol resistance. In 2022, 20% of the isolates were resistant to the macrolide erythromycin compared to 9% observed in 2021. However, in C. coli isolated from veal calves, resistances to erythromycin, ertapenem and chloramphenicol were lower in 2022 than in 2021 but resistances to ciprofloxacin and gentamicin were higher. In C. jejuni, resistances to erythromycin, ertapenem, gentamicin and chloramphenicol increased but resistances to ciprofloxacin and tetracycline remained stable. Overall, as seen in previous reports, antimicrobial resistance levels are lower in C. jejuni than in C. coli. In 2022, considering all Salmonella spp. recovered from food matrices, the most prevalent serotypes were S. Infantis recovered mainly from fresh meat from poultry and S. Monophasic Typhimurium from fattening pigs and veal calves. Resistance levels increased for 6 out of the 15 tested antimicrobials in Salmonella isolated from food matrices, resistance to amikacin was also detected for the first time in processed meat (cold cuts) but resistance to (fluoro)quinolones decreased compared to 2021. In foodproducing animals however, resistance to (fluoro)quinolones increased in 2022, especially in poultry. Resistance to third generation cephalosporins was only found in one isolate of S. Paratyphi B var L(+) tartrate(+) from poultry cutted meat and one S. Dublin recovered from veal calves. Overall, resistance to colistin is very low, only two isolates of S. Dublin recovered one from poultry cutted meat and another from veal calves were resistant to colistin. The specific monitoring of ESBL, AmpC or carbapenemase producing E.coli was carried out in broilers, turkeys, fattening pigs and veal calves and in meat derived from these 4 categories of animals. As it has been the case in the previous years, the highest prevalence of ESBL E.coli was found in broilers (75%) followed by turkeys (64%), veal calves (64%) and fattening pigs (35%). In fresh meat from foodproducing animals as well, the prevalence was the highest in fresh meat from broilers (58%) followed by fresh meat from turkeys (24%). The prevalence was much lower in fresh meat from veal calves (2%) and fresh meat from fattening pigs (2%). No meropenem-resistant isolates were detected in 2022. However, ESBL E.coli isolated from these matrices showed extremely high levels of multidrug resistance (>80%). 2 In indicator E.coli, in comparison with 2021 an overall increased resistance was detected in most categories of food-producing animals, especially in isolates from faeces samples of laying hens, breeding hens and bovines at the farm level. (Fluoro)quinolones resistance also increased in isolates from caecal samples of broilers, veal calves, and fattening pigs taken at the slaughterhouse. However, resistance to critical antimicrobials such as colistin, tigecycline, cephalosporins and meropenem remains very low or non-existant in the different matrices in 2022. Also, in E.coli isolated from caecal samples of fattening turkeys, the levels of resistance to most antimicrobials were lower in 2022 than in 2021. Monitoring of methicillin-resistant Staphylococcus aureus (MRSA) was carried out in fattening pigs and sows on farm in 2022. The bovines and poultry were monitored in 2021 and 2020, respectively (3 yearsrotation). The aim of this monitoring is to assess the MRSA prevalence in these animal categories and determine the genotypes (STs and spa-types) of 170 of collected MRSA isolates together with their AMR and virulence genes. Several changes in the methodology used for the monitoring of MRSA have been made in 2022, including a new isolation method and the study of AMR through NGS rather than phenotypic susceptibility testings. The 2022 data will now serve as a new baseline for analyzing future trends. The extremely high prevalence (87.9%) observed in fattening pigs and, in a lesser extent, the very high prevalence observed in sows (52.6%), in 2022 with the new isolation method is a matter of concern. In 2022, all but one isolate were genotyped as LA-MRSA according to their STs/spa-types combinations. The latter isolate is likely to belong to LA-MRSA as well, according to our investigation. All MRSA isolated were harboring the mecA gene and at least one tetracycline resistance genes, which are also characteristic of LA-MRSA. Several other resistance genes were observed. Of particular concern is the carriage of the cfr gene, encoding a.o. resistance to the critically important antibiotic linezolid, observed again in 2022 in 3 isolates (n=1 sows and n=2 fattening pigs). In addition to AMR genes, qac (precisely, qacG and qacJ) genes mediating resistance to quaternary ammonium compounds were observed in some MRSA isolates in 2022. Moreover, several virulence genes associated with the immune evasion cluster (sak, scn), toxins (hlgA, hlgB, hlgC, seb and selw) and exoenzymes (aur) were detected. One sow isolate belonging to the ST398-t034 LA-MRSA type carried the sak and scn genes associated with the human immune evasion cluster and several genes associated with toxins (hlgA, hlgB, hlgC and selw) and exoenzyme (aur). This isolate did not carry critically antimicrobial resistance gene (no cfr gene), neither qac disinfectant resistance gene. The genes associated with the immune evasion cluster were not observed in the other isolates. The detection of the seb gene encoding an exotoxin known to be the source for multiple pathologies in humans in an isolate from fattening pigs highlights the importance of monitoring these different virulence factors in the future. The presence of MRSA in foodproducing animals and their carriage of several AMR and virulence genes represents a public health risk. The monitoring of Enterococcus faecalis and Enterococcus faecium, organized in Belgium in foodproducing animals between 2011 and 2013, and resumed in 2019, continued. Investigation of the AMR prevalence in these commensal indicator bacteria was assessed in order to complete the picture of the situation of antimicrobial resistance within our farms and slaughterhouses,. Enterococci are also considered to be reservoirs of antibiotic resistance genes, present in both humans and animals. In 2022, the prevalences of enterococci species by animal category were similar to those observed in previous years. Indeed, Enterococcus faecium was more frequently isolated than Enterococcus faecalis within the samples of breeding hens (85.6%), laying hens (69.9%), veal calves (64.0%) and pigs (66.4%). Conversely, E. faecalis was isolated more frequently than E. faecium in broiler (65.4%) and turkey (92.0%) samples. The antimicrobial susceptibility tests carried out this year showed that, in general, the resistance rates observed in Enterococcus faecalis and Enterococcus faecium within the various animal matrices studied have remained stable since 2019, with a few exceptions (significant decreases). Significant decreases in antimicrobial resistance were observed for chloramphenicol in E. faecalis isolated from veal calves, and for ampicillin in E. faecium isolated from broilers in 2022. Resistance to tetracycline, erythromycin and to quinupristin/dalfopristin were still the most observed resistances, both in E. faecalis and E. 3 faecium. Resistance to linezolid (n=18), a critical antibiotic for human health, was also observed in 2022, in 13 E. faecalis isolated from veal calves (n=11), pigs (n=2) and in 5 E. faecium isolated from pigs (n=2), veal calves (n=2) and breeding hens (n=1). No resistance to teicoplanin or vancomycin was observed in 2022. Daptomycin resistance was very low in 2022 but it could be related to the modification of its threshold in 2021. Tigecycline resistance was observed for the first time since 2019 (n=2). Multidrug resistance (resistance to at least 3 antimicrobial classes) was mainly observed in broilers and veal calves with 60.3% of multi-resistant E. faecium and 60.2% of multi-resistant E. faecalis, respectively. In addition, strains accumulating the higher number of different antimicrobial resistances were isolated from veal calves, with a maximum of 6 different resistances observed in E. faecalis and E. faecium. In 2022, some enterococci were completely sequenced by Next-generation sequencing (NGS). This report also presents these NGS results and the detailed characterization of these strains, including the detection of optrA and poxtA genes encoding linezolid resistance.