Isolation, Genomic Analyses and Antimicrobial Resistance Profiling of Salmonella and Campylobacter Isolated from Different Stages of No-Antibiotic-Ever (NAE) and Conventional Broiler Complexes

Abstract

Salmonella and Campylobacter are the leading bacterial foodborne pathogens that are often associated with the consumption or handling of raw poultry meat and products. At present, the major challenges of the poultry industry are how to minimize the risk of introduction or spread of such bacteria in broiler flocks, to minimize the persistence of such bacteria along broiler production chain, and how to achieve the USDA FSIS product performance standards at the processing plants. Salmonella can survive desiccation and can persist in dry environments for years, while Campylobacter can multiply up to 109 CFU/mL in birds’ cecal crypts and rapidly spread to the entire flock within a week. To determine the prevalence status, critical entry points and movement patterns of such bacteria along the poultry food chain, two different longitudinal studies were conducted in commercial no-antibiotic-ever (NAE) and conventional broiler complexes. Indoor and outdoor environmental samples were collected from the surroundings of production farms (pullet, breeder and broiler) and facilities (hatchery, transport and processing plant). Samples were screened with 3M-Molecular Detection System and suspect positive samples were further processed for confirmation of results and identification. In addition, whole genome sequencing and phylogenetic analyses were conducted to determine the genetic relatedness between bacterial strains. Moreover, antimicrobial resistance phenotypic and genotypic characteristics were studied in these isolates. Odds ratio and 95% confidence limits were calculated for different complexes, stages of broiler production and sample types (α= 0.05) using a multivariable model. From the NAE broiler complex, 2% (16/856) and 4% (19/531) of total samples were positive for Salmonella and Campylobacter respectively. The Salmonella serovars identified were Typhimurium, Barranquilla, Liverpool, Kentucky, Enteritidis, Luciana, and Rough_O:r:1,5. Similarly, from conventional broiler complex, 18% (192/1071) and 17% (135/790) of total samples were positive for Salmonella and Campylobacter respectively. The Salmonella serovars identified were Kentucky, Enteritidis, Typhimurium, Johannesburg, Montevideo, Mbandaka, Newport, Senftenberg, Inverness, Ohio, Uganda, and N/A (9:z29:-). The species of Campylobacter identified were C. jejuni and C. coli in both complexes. Interestingly, the odds of Salmonella detection were more likely (p<0.05) in the surroundings of the facilities compared to the production farms, while the odds of Campylobacter detection in broiler farms’ surroundings were more likely (p<0.05) as compared to parent pullets and breeder farms’ surroundings. Among different sample types from production farms’ surroundings, boot swabs and sponge-stick swabs were useful (p<0.05) for detection of Campylobacter. In the processing plant, the chilling step was effective (p<0.05) for reducing Salmonella and Campylobacter in chicken carcasses. Phylogeny results show close genetic relatedness among bacterial strains isolated from different locations within the same stage and between different stages. It also suggests a diverse movement pattern of bacterial strains and the possibility of multiple critical entry points into the complex. In addition, 57.65% (49/85) of Salmonella isolates showed phenotypic resistance to at least one antibiotic with 5.88% (5/85) of isolates being multi-drug resistant. Similarly, 25% (14/57) of Campylobacter isolates showed phenotypic resistance to at least one antibiotic while 7% (4/57) of the isolates were multi-drug resistant. The results indicate potential risks to consumers from ingestion of contaminated raw or under-cooked poultry meat with antibiotic resistant foodborne bacteria. It suggests the need for a multifaceted comprehensive control strategy with strict biosecurity measures and best management practices to minimize contamination of such pathogens from broiler production chain. Keywords: Salmonella, Campylobacter, no-antibiotic-ever, conventional, antimicrobial resistance