Genomic epidemiology and genetic characteristics of clinical Campylobacter species cocirculating in West Bengal, India, 2019, using whole genome analysis

Abstract

Campylobacter species are the most common pathogens responsible for foodborne gastroenteritis worldwide. India is a region with frequent diarrheal infections and a high level of Campylobacter infection incidence, but the detailed genomic information is limited. This study aimed to characterize 112 isolates of Campylobacter from diarrhea patients at two hospitals in Kolkata, West Bengal, by whole genome analysis. The Campylobacter isolates consisted of 90 C. jejuni, 20 C. coli, and 2 C. lari isolates. Multilocus sequence typing analysis revealed that the largest sequence type (ST) populations were ST-2131 in C. jejuni and ST-830 in C. coli and seven novel STs were found in C. jejuni and one in C. coli. Notably, ST-2131, which is rarely seen elsewhere, was positive for a sialylated LOS-related gene (wlaN +neuA + cstIII) associated with Guillain-Barré syndrome. Antibiotic resistance factors predicted from the genome sequence included blaOXA variants (58.9%), tet(O) (54.5%), tet(W) (0.9%), ant(6)-Ia (0.9%), mutation in GyrA (T86I, T86I+D90N, T86I+P104S, T86I+D90N+P104S) (79.5%), and mutation in 23S rRNA (A2075G) (12.5%). In addition to the high drug resistance of Campylobacter in Kolkata, Campylobacter pathogens were circulating that may be associated with Guillain-Barré syndrome. This study indicates the importance of genomic analysis in the surveillance of pathogens, which provides genomic information on genetic diversity, virulence mechanisms, and determinants of antimicrobial resistance.

Keywords: Campylobacter jejuni/coli; phylogenetic analysis; plasmid structure; whole genome sequencing.

Fig 1

Core genome phylogenetic tree of C. jejuni (A) and C. coli (B). The phylogenomic analysis is based on core genome comparison using Panaroo. The maximum likelihood tree was generated by IQ-TREE. Bootstrap support values were calculated from 1,000 replicates, and only values above 95% are shown as circles. Right fields indicate sequence type, clonal complex, in silico Penner typing, resistance genes, and important virulence genes. In the blaOXA61-like family, filled boxes indicate the presence of promoter mutations, and blank boxes indicate no promoter mutations; in tet(O) and tet(W), filled boxes indicate acquisition in the genome, and blank boxes indicate acquisition in the plasmid; in cstIII, neuABC, and wlaN, filled boxes indicates the presence of a gene (80% or more sequence identity), and a blank box indicates the presence of a gene with low identity (less than 80% sequence identity). A comprehensive list of all virulence genes identified in each strain is given in Table S3.

Fig 2

Minimum spanning tree of C. jejuni and C. coli. The nodes indicate the detected sequence types and are proportional to the number of strains. For nodes with more than two strains, the number of strains is indicated in [ ]. Clonal complexes are colored with the corresponding node indicated in the legend.

Fig 3

Comparison of resistance gene prevalence between C. jejuni (A) and C. coli (B). The percentages of genes detected in the RefSeq genome are represented by blue bars, and the percentages of genes detected in this study are represented by red bars. ^*P < 0.05 according to the chi-squared test.