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

Abstract

<i>Campylobacter</i> is the leading cause of human bacterial gastroenteritis worldwide and has a major impact on global public health. Whole Genome Sequencing (WGS) is a powerful tool applied in the study of foodborne pathogens. The objective of the present study was to apply WGS to determine the genetic diversity, virulence factors and determinants of antimicrobial resistance of the populations of <i>C. jejuni</i> and <i>C. coli</i> in Peru. A total of 129 <i>Campylobacter</i> strains (108 <i>C. jejuni</i> and 21 <i>C. coli</i>) were sequenced using Illumina Miseq platform. <i>In silico</i> MLST analysis identified a high genetic diversity among those strains with 30 sequence types (STs), several of them within 11 clonal complexes (CC) for <i>C. jejuni</i>, while the strains of <i>C. coli</i> belonged to a single CC with 8 different STs. Phylogeny analysis showed that Peruvian <i>C. jejuni</i> strains were divided into 2 clades with 5 populations, while <i>C. coli</i> formed a single clade with 4 populations. Furthermore, <i>in silico</i> analyses showed the presence of several genes associated with adherence, colonization and invasion among both species: <i>cadF</i> (83.7%), <i>jlpA</i> (81.4%), <i>racR</i> (100%), <i>dnaJ</i> (83.7%), <i>pebA</i> (83.7%), <i>pldA</i> (82.1%), <i>porA</i> (84.5%), <i>ceuE</i> (82.9%), <i>ciaB</i> (78.3%), <i>iamB</i> (86.8%), and <i>flaC</i> (100%). The majority (82.9%) of the <i>Campylobacter</i> strains carried the <i>cdtABC</i> operon which code for cytolethal distending toxin (CDT). Half of them (50.4%) carried genes associated with the presence of T6SS, while the frequency of genes associated with T4SS were relatively low (11.6%). Genetic markers associated with resistance to quinolones, tetracycline (<i>tetO, tetW/N/W</i>), beta-lactamases (<i>bla_oxa-61</i> ), macrolides (A2075G in 23S rRNA) were found in 94.5, 21.7, 66.7, 6.2, 69.8, and 18.6% of strains, respectively. The <i>cmeABC</i> multidrug efflux operon was present in 78.3% of strains. This study highlights the importance of using WGS in the surveillance of emerging pathogens associated with foodborne diseases, providing genomic information on genetic diversity, virulence mechanisms and determinants of antimicrobial resistance. The description of several <i>Campylobacter</i> genotypes having many virulence factors and resistance to quinolones and tetracyclines circulating in Peru provides important information which helps in the monitoring, control and prevention strategies of this emerging pathogen in our country.