Genomic Characterisation of Campylobacter jejuni Isolates Recovered During Commercial Broiler Production

Abstract

Background:Campylobacter is commonly transmitted to humans from chickens. Campylobacter jejuni is the species most frequently associated with human illness, and the most prevalent species recovered from poultry.Objective: The objective of this study was to analyse a sub-population of C. jejuni from two broiler flocks on the farm and at slaughter using whole-genome sequencing to gain insights into the changes in the Campylobacter population during broiler production, including changes in virulence and antimicrobial resistance profiles.Methods: In this study, ten composite faecal samples (n=10), obtained by pooling ten fresh faecal samples (n=10), were collected in the broiler house on two farms on days 14, 21, 28, and 34 (n=80) and ten composite (n=10) caecal samples were collected at the time of slaughter for each flock (n=20). These were tested for C. jejuni using the ISO 10272-2:2016 method. Seven isolates were randomly selected from each of the nine Campylobacter-positive sampling points (n=63) and were subjected to antimicrobial susceptibility tests. Their genomes were sequenced and the data obtained was used to characterise the population structure, virulence, antimicrobial resistance determinants and inter-strain variation.Results: The Farm 1 isolates had three MLST types (ST257-257, ST814-661 and ST48-48) while those on Farm 2 were ST6209-464 and ST9401. Interestingly, only the MLST types positive for most of the virulence genes tested in this study persisted throughout the production cycle, and the detection of antimicrobial resistance determinants (gyrA T86I and tetO) increased after thinning and at slaughter, with the detection of new strains.Conclusion: The persistence of the most virulent strains detected in this study throughout the production cycle has important implications for the risk to consumers and requires further investigation. The detection of new strains within the population corresponding with the time of thinning and transportation reflects previous reports and provides further evidence that these activities pose a risk of introducing new Campylobacter strains to broiler batches.

Genomic diversity, virulence and source of Campylobacter jejuni contamination in Irish poultry slaughterhouses by whole genome sequencing

“…It has been reported that this gene may have a role in adherence and biofilm formation on food contact surfaces (Emanowicz et al, 2022 ; Lim & Kim, 2017 ) and therefore is potentially of significance for its contribution to cross‐contamination (Bridier et al, 2015 ). Genes associated with capsule synthesis, that is, cj1417c , cj1419c , cj1420c and kpsm were also identified in the present study, and these have previously been reported to be associated with colonization (Truccollo et al, 2021 ).…”

“…This is concerning as C. jejuni isolates carrying the wlaN gene and genes associated with LOS are presumably involved in the expression of ganglioside mimicry which is thought to be a critical factor in the triggering of Guillain-Barre ánd Miller Fisher syndrome after C. jejuni infection in clinical cases (Epping et al, 2019;Gargiulo et al, 2011;Kolehmainen et al, 2019;Linton et al, 2000). A previous study did not detect any of these virulence genes in a subset of 15 Irish poultry C. jejuni genomes mostly isolated in 2008 but did detect them amongst 15 Irish human clinical isolates from 2016 (Truccollo et al, 2021). A more recent study by Emanowicz et al (2022) reported these genes to be present in Campylobacter from an Irish poultry processing plant during 2018 and 2019 which agrees with the results of our study.…”

“…Fasta files for all virulence genes were uploaded to a virulence genes database in BioNumerics. The aim was to remove hits with less than 80% identity and/or coverage (Truccollo et al, 2021 ). Character data was exported from BioNumerics to Excel® where a heat map was generated.…”

Investigation of differences in susceptibility of Campylobacter jejuni strains to UV light-emitting diode (UV-LED) technology

“…Raw sequences were obtained for each strain tested. Raw sequences of the test strains not treated with UV 280 were obtained from a previous study conducted by Truccollo et al 43 and the raw sequence of C. jejuni NCTC 11168 was recovered from the NCBI database (BioProject PRJNA8). Cleaning was a systemic process conducted using Trimmomatic (v0.3.8) after removing adapters, reads containing more than 10% undetermined bases (N > 10%) and low quality reads with a Qscore below or equal to 5 (Qscore ≤ 5) in a 50% of the total bases were removed.…”

Investigation of differences in susceptibility of Campylobacter jejuni strains to UV light-emitting diode (UV-LED) technology

“…Raw sequences were obtained for these isolated strains. Moreover, raw sequences of the 8 C. jejuni strains not treated with UV light were obtained from a previous study conducted by Truccollo, et al 44 and the raw sequence of C. jejuni NCTC 11168 was recovered from the NCBI database (BioProject PRJNA8).…”