Abstract
Pathogen source attribution studies are a useful tool for identifying reservoirs of human infection. Based on Multilocus Sequence Typing (MLST) data, such studies have identified chicken as a major source of C. jejuni human infection. The use of whole genome sequence-based typing methods offers potential to improve the precision of attribution beyond that which is possible from 7 MLST loci. Using published data and 156 novel C. jejuni genomes sequenced in this study, we performed probabilistic host source attribution of clinical C. jejuni isolates from France using three types of genotype data: comparative genomic fingerprints; MLST genes; 15 host segregating genes previously identified by whole genome sequencing. Consistent with previous studies, chicken was an important source of campylobacteriosis in France (31–63% of clinical isolates assigned). There was also evidence that ruminants are a source (22–55% of clinical isolates assigned), suggesting that further investigation of potential transmission routes from ruminants to human would be useful. Additionally, we found evidence of environmental and pet sources. However, the relative importance as sources varied according to the year of isolation and the genotyping technique used. Annual variations in attribution emphasize the dynamic nature of zoonotic transmission and the need to perform source attribution regularly.
Highlights
Campylobacter spp. are regarded as the most common foodborne bacterial zoonosis in Europe[1], despite potential underestimation due to underreporting of cases[2]
C. jejuni clinical isolates from 2009 appeared to be highly diverse with 85 CGF40 clusters based on 100% of similarity between isolates, and 62 STs29
A total of 1,618 animal and environmental C. jejuni isolates from putative sources of human infection constituted the comparison data set of CGF40 genotypes, while the comparison data sets of Multilocus Sequence Typing (MLST) and host-segregating markers profiles comprised respectively 857 and 740 isolates characterized in previous studies (Supplementary Table S1)
Summary
Campylobacter spp. are regarded as the most common foodborne bacterial zoonosis in Europe[1], despite potential underestimation due to underreporting of cases[2]. Principally based upon Multilocus sequence typing (MLST) data[18] which consists in the sequencing and the allele designation of 7 housekeeping genes of C. jejuni, have identified chicken as a major source of human infection worldwide, while ruminants, pets and environmental sources are implicated[19,20,21,22]. We assessed the accuracy of attributions of C. jejuni isolates to their source based on MLST, CGF40 profiles and the 15 host segregating markers, and used the most accurate methods to identify the most likely origin of French campylobacteriosis from 2009 and 2015. Isolates originating from chicken, ruminant, pets, environmental waters and wild birds were considered as potential sources of human infection in the analysis
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