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Objectives  We characterized clinical isolates of  Campylobacter  using whole-genome sequencing (WGS) for detection of virulence genes, antimicrobial resistance markers and phylogenetic analysis in order to increase the knowledge on the molecular epidemiology of  Campylobacter  in Ireland, where there are significant gaps due to the widespread in the use of culture independent methods for the diagnosis of campylobacteriosis.    Methods  WGS was applied to 122  Campylobacter  human isolates collected over a 10-years period, from diarrhoeal stool samples submitted for routine enteric screening.    Results  Genes associated with cytotoxin production such as  cdtA ,  cdtB and cdtC  were found in 88%, 89% and 89% isolates, respectively; adherence, colonization and invasion genes such as  cadF ,  dnaJ ,  racR ,  iam ,  virB11  and  ciaB  were found in 99%, 99%, 98%, 99%, 1% and 80% isolates, respectively. Genetic markers associated with resistance to quinolones (C257T in  gyrA ), beta-lactams ( bla  oxa-61 ) and tetracycline ( tet (O)) were present in 43%, 71% and 25% isolates, respectively. The  cmeABC  operon was present in 94% of isolates. No macrolide or aminoglycoside resistance markers were detected. Phylogenetic analysis showed that 112 isolates were assigned to 29 sequence types grouped into 17 clonal complexes. Four clusters previously unidentified were detected. These results shown the similarity of Irish data compared to what has been described globally.    Conclusions  WGS has shown a high discriminatory power for cluster detection, demonstrating that its integration in routine laboratory surveillance could improve the detection and management of outbreaks. In addition we were able to demonstrate that virulence genes in clinical  Campylobacter  infections in Ireland were similar to those known previously. High prevalence of quinolone resistance markers has been found, which has implications for antimicrobial stewardship.

plos one

Molecular characterization of Campylobacter causing human clinical infection using whole-genome sequencing: Virulence, antimicrobial resistance and phylogeny in Ireland