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

Natalia Redondo,Anne Carroll,Eleanor Mcnamara,Tiago J Zilch

doi:10.1371/journal.pone.0219088

Natalia Redondo, Anne Carroll + Show 2 more

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https://doi.org/10.1371/journal.pone.0219088

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Abstract

ObjectivesWe 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.MethodsWGS was applied to 122 Campylobacter human isolates collected over a 10-years period, from diarrhoeal stool samples submitted for routine enteric screening.ResultsGenes 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 (blaoxa-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.ConclusionsWGS 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.

Highlights

Campylobacter is a leading cause of bacterial foodborne illnesses worldwide
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 and tetracycline (tet(O)) were present in 43%, 71% and 25% isolates, respectively

Summary

Introduction

Campylobacter is a leading cause of bacterial foodborne illnesses worldwide. In 2015, Campylobacter was the most commonly reported gastrointestinal bacterial pathogen in human in the European Union (EU) [1]. The species Campylobacter jejuni is responsible for 80–90% of cases, while Campylobacter coli accounts for 10–20% of human infections. The clinical manifestations caused by C. jejuni and C. coli infections are indistinguishable and comprise diarrhoea, abdominal pain and cramps as the most typical symptoms. Complications such as pancreatitis, cholecystitis, peritonitis and gastointestinal haemorrhage arise in less than 1% of cases and mostly in immunocompromised, the very young or very elderly individuals [2]

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