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

Abstract

<jats:title>ABSTRACT</jats:title><jats:p><jats:italic>Campylobacter jejuni</jats:italic> and <jats:italic>Campylobacter coli</jats:italic> are the leading causes of human gastroenteritis in the developed world and an emerging threat in developing countries. There is increasing evidence that the incidence of campylobacteriosis in Chile and other South American countries is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from these countries, leaving an important knowledge gap in our understanding of the population structure, virulence potential, and antimicrobial resistance profiles of clinical <jats:italic>Campylobacter</jats:italic> strains. We recently published the whole-genome sequences of a collection of 68 <jats:italic>C. jejuni</jats:italic> and 12 <jats:italic>C. coli</jats:italic> strains isolated from patients with enteric infections during a 2-year period (2017-2019) attending Clinica Alemana in Santiago, Chile. In the present study, we sequenced an additional <jats:italic>C. jejuni</jats:italic> genome and performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance potential of these 81 strains. cgMLST analysis identified a high genetic diversity of <jats:italic>C. jejuni</jats:italic> as well as 13 novel STs and alleles in both <jats:italic>C. jejuni</jats:italic> and <jats:italic>C. coli</jats:italic>. 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 a low rate of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for larger genomic epidemiology studies to better understand the genetic diversity, virulence potential and antimicrobial resistance of human clinical <jats:italic>Campylobacter</jats:italic> strains in South America.</jats:p><jats:sec><jats:title>DATA SUMMARY</jats:title><jats:list list-type="order"><jats:list-item><jats:p>Genome sequences and assemblies of all <jats:italic>C. jejuni</jats:italic> and <jats:italic>C. coli</jats:italic> used in this study have been deposited in public databases (<jats:bold>Table S1</jats:bold>) and most strains have also been published as genome resource announcements [1,2].</jats:p></jats:list-item><jats:list-item><jats:p>Bacterial draft genome sequence reannotations and nucleotide sequence fasta files used for virulome and plasmid screening analysis are available as a supplementary dataset on Zenodo (DOI: 10.5281/zenodo.3925206) <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://doi.org/10.5281/zenodo.3925206">https://doi.org/10.5281/zenodo.3925206</jats:ext-link>.</jats:p></jats:list-item><jats:list-item><jats:p>The reconstructed phylogenetic trees and associated metadata of clinical strains from Chile in the global context of <jats:italic>C. jejuni</jats:italic> and <jats:italic>C. coli</jats:italic> sequenced strains can be interactively visualized on Microreact at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://microreact.org/project/VbEQsZtQD">https://microreact.org/project/VbEQsZtQD</jats:ext-link>.</jats:p></jats:list-item></jats:list></jats:sec>

Campylobacter jejuni and other emerging Campylobacteraceae in retail beef liver – an underestimated potential source?

“…For the current study, four clonal lineages (CC-21, CC-42, CC-48 and CC-52) were found in common between the strains isolated from beef liver and the clinical strains previously reported in Chile (Collado et al 2018;Bravo et al 2021), which suggests a zoonotic transmission.…”

“…Recently, Bravo et al . (2021) also reported finding the operon encoding for this pump, in all the Chilean clinical strains they analysed.…”

“…2018; Bravo et al . 2021). Out of the 29 C. jejuni isolates, 13 different genotypes were defined by the flagellin gene restriction fragment length polymorphism ( flaA ‐RFLP) method (Figure S1).…”

“…These genes were found in all C. jejuni strains that exhibited antibiotic resistance in this study. Recently, Bravo et al (2021) also reported finding the operon encoding for this pump, in all the Chilean clinical strains they analysed.…”

“…Genotyping was assessed only for C. jejuni isolates, due to their clinical importance and the availability of data on genotypes of clinical strains in Chile from previous studies (Collado et al 2018;Bravo et al 2021). Out of the 29 C. jejuni isolates, 13 different genotypes were defined by the flagellin gene restriction fragment length polymorphism (flaA-RFLP) method (Figure S1).…”