Genomic Characterisation of Isolates Recovered During Commercial Broiler Production.

is commonly transmitted to humans from chickens. is the species most frequently associated with human illness, and the most prevalent species recovered from poultry. The objective of this study was to analyse a sub-population of from two broiler flocks on the farm and at slaughter using whole-genome sequencing to gain insights into the changes in the population during broiler production, including changes in virulence and antimicrobial resistance profiles. In this study, ten composite faecal samples (=10), obtained by pooling ten fresh faecal samples (=10), were collected in the broiler house on two farms on days 14, 21, 28, and 34 (=80) and ten composite (=10) caecal samples were collected at the time of slaughter for each flock (=20). These were tested for using the ISO 10272-2:2016 method. Seven isolates were randomly selected from each of the nine -positive sampling points (=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. 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 ( T86I and ) increased after thinning and at slaughter, with the detection of new strains. 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 strains to broiler batches.