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

Abstract

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.

Campylobacteriosis Agents in Meat Carcasses Collected from Two District Municipalities in the Eastern Cape Province, South Africa

“…From the PCR results of the virulence gene assessed, most Campylobacter species were detected to harbour a high proportion of cadF, flaA, and iam genes responsible for colonisation, invasion, and adherence, and our results corroborate the report of Abu-Madi et al [75]. The iam gene had the highest occurrence rate of 43.14% (Table 3) among the various virulence genes screened, and our results also corroborate the report of Redondo et al [76].…”

Occurrence, Virulence and Antimicrobial Resistance-Associated Markers in Campylobacter Species Isolated from Retail Fresh Milk and Water Samples in Two District Municipalities in the Eastern Cape Province, South Africa

“…The presence of one or more virulence genes in the Campylobacter genome give rise to the incidence of human infection (Abu-Madi et al [ 80 ]). In our study, some Campylobacter species were observed to harbor multiple virulence genes and several studies including the studies of Aslantaş [ 81 ], Redondo et al [ 82 ], Samad et al [ 83 ] and Wei et al [ 84 ] have also detected multiple virulence genes in Campylobacter species and our finding also corroborate with their reports. Detection of these virulence genes in Campylobacter isolates recovered from retail milk and water samples position them a risk to human health and continuous consumption of raw milk in the study area may put people at high risk of ill-health.…”

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

“…This mutation is the most frequently reported mutation worldwide and confers high levels of resistance to fluoroquinolones [48,49]. To determine the virulence gene content of the C. jejuni and C. coli strains, we first assembled a list of 220 potential virulence genes, including genes described in the Virulence Factor Database [59] and genes reported to contribute to the virulence of Campylobacter in the literature [38,[60][61][62][63]. These genes were grouped into five distinct categories (adhesion and colonization, invasion, motility, secretion systems and toxins) and were used to screen each of the 81 genomes using BLASTn.…”

“…To date, there is only one T6SS cluster described in Campylobacter [60], and it has been linked to a wide variety of phenotypes, including host cell adherence, cellular invasion and resistance to bile salt, and oxidative stress [67][68][69]. In addition,…”