Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015

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.

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease

“…Contrasting evidence of HGT with quantitative information about the transmission of resistant bacteria between hosts would be extremely useful for understanding the dissemination of AMR among isolates from different habitats. In Campylobacter , studies have attempted to estimate the number of strains excreted into the environment by different animals (Ogden et al ., ) and attribute the source of human infection to livestock (especially poultry) reservoirs (Sheppard et al ., ; Thépault et al ., , ). However, these large‐scale probabilistic studies are utterly underpowered for investigating the almost infinite number of possible transmission events, where the survival and proliferation of a single strain in a new niche could lead to the transfer of AMR genes between hosts and environments.…”

Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon

“…The high prevalence, regular reinfection and prolonged colonization periods in the Peruvian Amazon cohort study (and likely other LMICs) provide greater opportunity for human-to-human spread and adaptation to the host [92,93]. Some studies have attempted to identify signatures of human tropism, or even adaptation [94,95] and it remains possible that the some of the Peruvian STs that are rarely isolated from non-human infections (S7 Table) could provide evidence of human adaptation.…”

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

“…C. jejuni I (Taboada et al, 2012). In a comparison of source-attribution of C. jejuni using 7-loci MLST to source-attribution using presence/ absence of 40 genes belonging to the accessory genome (determined by Taboada et al, 2012) or 15 host segregating markers (determined by (Th epault et al, 2017)), the host segregating markers provided the most accurate predictions, especially with chicken isolates, suggesting that MLST-based source-attribution may underestimate the role of chicken in Campylobacter transmission to humans (Th epault et al, 2018).…”