A pilot study revealing host‐associated genetic signatures for source attribution of sporadic Campylobacter jejuni infection in Egypt

Abstract

Campylobacter jejuni (C. jejuni), is considered among the most common bacterial causes of human bacterial gastroenteritis worldwide. The epidemiology and the transmission dynamics of campylobacteriosis in Egypt remain poorly defined due to the limited use of high-resolution typing methods. In this pilot study, we evaluated the discriminatory power of multiple typing 'gene-by-gene based' techniques to characterize C. jejuni obtained from different sources and estimate the relative contribution of different potential sources of C. jejuni infection in Egypt. Whole genome sequencing (WGS) was performed on 90 C. jejuni isolates recovered from clinical samples, retail chicken, and dairy products in Egypt from 2017 to 2018. Comparative genomic analysis was performed using conventional seven-locus multilocus sequence typing (MLST), ribosomal MLST (rMLST), core genome MLST (cgMLST), allelic variation in 15 host-segregating (HS) markers, and comparative genomic fingerprinting (CGF40).The probabilistic source attribution was performed via STRUCTURE software using MLST, CGF40, cgMLST and allelic variation in HS markers. Comparison of the discriminatory power of the aforementioned genotyping methods revealed cgMLST to be the most discriminative method, followed by HS markers. The source attribution analysis showed the role of retail chicken as a source of infection among clinical cases in Egypt when HS and cgMLST were used (64.2% and 52.3% of clinical isolates were assigned to this source, respectively). Interestingly, the cattle reservoir was also identified as a contributor to C. jejuni infection in Egypt; 35.8% and 47.7% of clinical isolates were assigned to this source by HS and cgMLST, respectively. Here, we provided evidence of the importance of using WGS typing methods to facilitate source tracking of C. jejuni.Our findings suggest the importance of non-poultry sources, together with the previously reported role of retail chicken in human campylobacteriosis in Egypt that can provide insights to inform national control measures.

Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance

“…In Egypt, farming practices often lack adequate biosecurity and regulation. Only limited studies have reported the prevalence and distribution of Campylobacter in Egyptian campylobacteriosis cases [4], and little is known about the dominant source reservoirs driving infection and transmission [20]. In Europe, potential source reservoirs have been identified through source attribution studies, with poultry products regarded as the primary source of infection [6, 21–23].…”

Circulation of thermophilic Campylobacter in pigeons, turkeys, and humans at live bird markets in Egypt

“…In relation to the rate of Campylobacter infections in human population in Egypt, several previous studies documented that Campylobacterios is an important cause of diarrhea in children in the country (39)(40)(41). In this respect, up to 85% of children in Egypt were found infected with Campylobacter sp.…”

A Review on Microbiological Source Attribution Methods of Human Salmonellosis: From Subtyping to Whole-Genome Sequencing

“…Another population genetic method for source attribution is STRUCTURE (Jehanne et al, 2020 ; Mughini-Gras et al, 2021 ; Mulder et al, 2020 ; Saif et al, 2022 ). STRUCTURE uses model-based clustering, which assigns a cluster (population) to each sample, while simultaneously estimating the allele frequency in each population (Pritchard et al, 2000 ).…”