Quantitative assessment and genomic profiling of Campylobacter dynamics in poultry processing: a case study in the United Arab Emirates integrated abattoir system

In the United Arab Emirates, no previous research has investigated the dynamics of the foodborne pathogen <i>Campylobacter</i> in broiler abattoir processing. This study conducted in one of the largest poultry producers in the UAE, following each key slaughter stage-defeathering, evisceration, and final chilling-five broiler carcasses were collected from 10 slaughter batches over a year. Additionally, one caecum was obtained from 15 chickens in each slaughter batch to evaluate the flock colonization. In total, 300 samples (150 carcasses and 150 caeca) were collected and enumerated for <i>Campylobacter</i> using standard methods. <i>Campylobacter</i> was pervasive in caecal samples from all slaughter batches, with 86% of carcasses post-defeathering and evisceration stages and 94% post-chilling tested positive for <i>Campylobacter</i>. <i>Campylobacter coli</i> predominates in 55.2% of positive samples, followed by <i>Campylobacter jejuni</i> in 21%, with both species co-existing in 23.8% of the samples. <i>Campylobacter</i> counts in caecal contents ranged from 6.7 to 8.5 log₁₀ CFU/g, decreasing post-defeathering and evisceration to 3.5 log₁₀ CFU/g of neck skin and further to 3.2 log₁₀ CFU/g of neck skin post-evisceration. After chilling, 70% of carcasses exceeded 3 log₁₀ CFU/g of neck skin. Whole-genome sequencing (WGS) of 48 isolates unveiled diverse sequence types and clusters, with isolates sharing the same clusters (less than 20 single nucleotide polymorphisms) between different farms, different flocks within the same farm, as well as in consecutive slaughter batches, indicating cross-contamination. Multiple antimicrobial resistance genes and mutations in <i>gyrA</i> T86I (conferring fluoroquinolone resistance) and an RNA mutation (23S r.2075; conferring macrolide resistance) were widespread, with variations between <i>C. coli</i> and <i>C. jejuni</i>. WGS results revealed that selected virulence genes (<i>pglG, pseD, pseI, flaA, flaB, cdtA,</i> and <i>cdtC</i>) were significantly present in <i>C. jejuni</i> compared to <i>C. coli</i> isolates. This study offers the first insights into <i>Campylobacter</i> dynamics in poultry processing in the UAE. This work provides a base for future research to explore additional contributors to <i>Campylobacter</i> contamination in primary production. In conclusion, effective <i>Campylobacter</i> management demands a comprehensive approach addressing potential contamination sources at every production and processing stage, guided by continued microbiological surveillance and genomic analysis to safeguard public health and food safety.