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

Abstract

Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n = 81), collected in 2017–2019 in Santiago, Chile. This culture collection accounts for more than one third of the available genome sequences from South American clinical strains. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.

Genomic Analysis and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli in Peru

“…In the case of the C. coli strains, the in silico MLST analysis revealed that 67% (14/21) belonged to CC-828, while 33% (7/21) presented MLST profiles that were novel and not previously reported in the MLST database. The high prevalence of CC-828 strains in this study is consistent with its wide distribution throughout the world ( Sheppard and Maiden, 2015 ; Bravo et al, 2021 ), being sometimes the unique CC detected by investigators ( Noormohamed and Fakhr, 2014 ). The MST and phylogenetic analysis revealed the same composition; strains belonged to the same ST and/or CC grouped together into single clusters ( Ramos et al, 2021 ).…”

“…Strains belonging to CC-21 are widely distributed in the world, representing 18.9% of all strains logged to the PubMLST database. Our study reported the presence of strains in Peru belonging to CC-353, 607, and 464, which have also been found in several countries (Bravo et al, 2021;Zbrun et al, 2021), showing the transmission of these strains across very distant geographical countries, but in general, STs diversity is variable among countries, especially when comparing developed and developing countries (Noormohamed and Fakhr, 2014). Also, in this study,14 strains of C. jejuni that have a novel allelic profile or ST which were not previously reported in the MLST database were identified, an information corroborated by other diversity studies using MSLT, which detected usually strains that were not assigned STs (Noormohamed and Fakhr, 2014).…”

“…The cdtABC operon, responsible for the presence of the cytolethal distending cytotoxin (CDT) in Campylobacter , was also present in most of the Peruvian strains from this study. Previous studies in Chile, Brazil, Korea, Poland and Ireland ( Redondo et al, 2019 ; Ramires et al, 2020 ; Wysok et al, 2020 ; Bravo et al, 2021 ) have reported a high prevalence of CDT in Campylobacter strains isolated from patients with life-threatening diarrhea.…”

“…Additionally, cst-II/cst-III, cgtA , and cgtB genes involved in sialic acid production are associated with the synthesis of lipo-oligosaccharides (LOS) of human ganglioside type that can induce Guillain Barré syndrome ( Zhang et al, 2015 ). Two different type IV secretion systems (T4SS) have been described in Campylobacter , one codified by the plasmid pVir , associated with the adherence and invasion ( Bravo et al, 2021 ), and the second present on the plasmids pTet and pCC31, which contribute to bacterial conjugation ( Batchelor et al, 2004 ). Moreover, a type VI secretion system (T6SS) probably involved in virulence in Campylobacter is poorly understood despite its increasing prevalence in Campylobacter jejuni isolates ( Wieczorek and Osek, 2013 ).…”

The Distribution of Campylobacter jejuni Virulence Genes in Genomes Worldwide Derived from the NCBI Pathogen Detection Database

“…It has a similar or higher discriminatory power than MLST, especially in short-term and localized epidemiological investigations [58][59][60][61]. Punctual studies from multiple places worldwide have reported a high prevalence of flagellin A and B in C. jejuni [62][63][64][65][66][67][68][69][70][71].…”