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

Abstract

Campylobacter 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 C. jejuni and C. coli in Peru. A total of 129 Campylobacter strains (108 C. jejuni and 21 C. coli) were sequenced using Illumina Miseq platform. In silico MLST analysis identified a high genetic diversity among those strains with 30 sequence types (STs), several of them within 11 clonal complexes (CC) for C. jejuni, while the strains of C. coli belonged to a single CC with 8 different STs. Phylogeny analysis showed that Peruvian C. jejuni strains were divided into 2 clades with 5 populations, while C. coli formed a single clade with 4 populations. Furthermore, in silico analyses showed the presence of several genes associated with adherence, colonization and invasion among both species: cadF (83.7%), jlpA (81.4%), racR (100%), dnaJ (83.7%), pebA (83.7%), pldA (82.1%), porA (84.5%), ceuE (82.9%), ciaB (78.3%), iamB (86.8%), and flaC (100%). The majority (82.9%) of the Campylobacter strains carried the cdtABC 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 (tetO, tetW/N/W), beta-lactamases (bla_oxa-61 ), 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 cmeABC 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 Campylobacter 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.

Keywords: Campylobacter; antimicrobial resistance; genomic analysis; virulence genes; whole-genome sequencing.

FIGURE 1

Minimum spanning tree of C. jejuni and C. coli strains sequenced in Peru. The nodes indicate the detected genotypes (STs) and are proportional to the number of strains. Clonal complexes (CC) are indicated with shadows around the corresponding nodes and with bold letters closed to the nodes. The yellow shadow divided Campylobacter spp. into C. jejuni and C. coli. Strains from this study (n = 129) are marked in green, while strains from other studies (n = 62) are indicated in red.

FIGURE 2

Phylogeny of C. jejuni (n = 108) constructed by maximum likelihood using strain NCTC11351 as reference. The strains are represented by circles connected by branches proportional to the phylogenetic distance. The code of each strain is indicated as a label parallel to the corresponding circles. The genotypes (ST) among the studied population are denoted by different colors. The clades are denoted by the numbers I and II. The HierBAPS populations are highlighted by colored boxes and named A–E. The presence of virulence genes is denoted by blocks in color based on six categories: Adhesion (Red), Invasion (Blue), Toxins (Purple), T6SS (Green), T4SS (Light Blue), and LOS (Yellow). The presence of resistance genes is denoted by blocks in color according to the spectrum of action: Fluoroquinolones (green), Multidrug Efflux pump (Red), Macrolides (Blue), Aminoglycosides (Pink), Streptogramins (Orange), Tetracycline (Blue) and Beta-Lactamases (Brown). The names of detected genes are indicated above the blocks. The absence of a gene is indicated by a white block.

FIGURE 3

Phylogeny of C. coli (n = 21) constructed by the maximum likelihood using strain CFSAN054106 as reference. The strains are represented by circles connected by branches proportional to the phylogenetic distance. The code of each strain is indicated as a label parallel to the corresponding circles. The genotypes (ST) among the studied population are denoted by different colors. The clades are denoted by the numbers I and II. The HierBAPS populations lineages found are highlighted by colored boxes and named A–D. The presence of virulence genes is denoted by blocks in color based on six categories: Adhesion (Red), Invasion (Blue), Toxins (Purple), T6SS (Green), T4SS (Light Blue), and LOS (Yellow). The presence of resistance genes is denoted by blocks in color according to the spectrum of action: Fluoroquinolones (green), Multidrug Efflux pump (Red), Macrolides (Blue), Aminoglycosides (Pink), Streptogramins (Orange), Tetracycline (Blue), and Beta-Lactamases (Brown). The names of detected genes are indicated above the blocks. The absence of a gene is indicated by a white block.