TY - RPRT T1 - Comparative genomics of quinolone-resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP) Y1 - 2018 A1 - Pimlapas Leekitcharoenphon A1 - Cristina Garcia-Graells A1 - N Botteldoorn A1 - Katelijne Dierick A1 - Isabelle Kempf A1 - Satu Olkkola A1 - Mirko Rossi A1 - Suvi Nykäsenoja A1 - Malorny, Burkhard A1 - Kerstin Stingl A1 - Antonio Battisti A1 - Alessia Franco A1 - Mossong, Joel A1 - Kees Veldman A1 - Dik Mevius A1 - Dariusz Wasyl A1 - Kinga Wieczorek A1 - Jacek Osek A1 - Lurdes Clemente A1 - Angela Lacatus A1 - Isabela Nicorescu A1 - Monserrat García Agüero A1 - Escobar, Cristina De Frutos A1 - Manuel Duran Ferrer A1 - Maria Ugarte-Ruiz A1 - Muna F Anjum A1 - Teale, Christopher A1 - Joakim Ågren A1 - Rene S. Hendriksen A1 - Frank M. Aarestrup KW - Campylobacter KW - Europe KW - Genomics KW - Poultry KW - quinolone KW - resistance AB -

A total of 502 Campylobacter jejuni isolates from poultry in 12 different European countries (10 of them the largest poultry production countries in Europe) were whole genome sequenced to examine the genomic diversity of fluoroquinolone resistant (FQ-R) and susceptible (FQ-S) C. jejuni across the poultry producing European countries and to determine whether the emergence of fluoroquinolone resistance among C. jejuni is related to the transmission through countries or to the selection through fluoroquinolone use in the individual countries. A high genomic diversity was observed. The isolates clustered in four main clusters. All trees revealed that the isolates were clustered according to the presence/absence of the gyrA mutations causing fluoroquinolone resistance and ST-types. The cgMLST trees of only FQ-R and FQ-S isolates showed that isolates from the same country of origin were distributed into multiple clusters similarly to the trees combining FQ-R and FQ-S isolates. The different phylogenetic methods, ranging from single nucleotide polymorphisms analysis to gene-by-gene approaches such as rMLST, cgMLST, wgMLST and core genome tree, provided concordant results, but it is not known which is the most accurate method for identifying the country of origin of the isolates. Allele frequency analysis of isolates under this study and a selection of previously published C. jejuni genomes in ENA showed association of geographical origin of poultry C. jejuni populations between Romania-Poland, Italy-Germany-England, Portugal-The Netherlands and USA-Luxemburg. Allele frequency and phylogenetic analysis indicated that the isolates from Finland were genetically different from C. jejuni populations from other European countries included in this study. Trade pattern and antimicrobial use in livestock were not significantly associated with allele frequency or populations of C. jejuni, but data available to investigate these associations were limited.

JF - EFSA Supporting PublicationsEFSA Supporting PublicationsEFSA Supporting Publications VL - 15 SN - 2397-8325 CP - 5 M3 - doi: 10.2903/sp.efsa.2018.EN-1398 ER -