Salmonella enterica serovar Typhimurium (STM) is a significant causative pathogen of gastrointestinal disease in humans resulting in many hospitalizations and occasional deaths each year worldwide. Poultry products are a common source of outbreaks of STM. Proper surveillance tools to monitor Salmonella contamination in the food production chain are essential. The objective of this study was to assess the diversity of STMs collected from three chicken processing plants in NSW, Australia, using a whole genome-based typing method and to explore the possibility that specific strain types, if any, were linked to the human disease.
We sequenced 122 chicken STM isolates and analyzed them using multilevel genome typing (MGT). Phylogenetic analysis was used to assess relatedness within different STM populations. The gradient of resolutions produced by MGT was evident in the 122 isolates with only two STs at MGT1 and 90 STs at MGT9. MGT5, comprising 24 STs, was selected as it best described lineages identified using phylogenetic analysis. Specific STs were identified in each processing plant as well as four STs common to all plants. Ten of the 25 MGT5 STs were found in the public MGT database. Among those, 8 contained isolates from human infections, two of those were identified from previous outbreaks. Nine isolates (in four MGT5 STs) contained one AMR gene (blaTEM-1; broad-spectrum class A beta-lactamase TEM-1).
In summary, MGT performed well to describe poultry STM isolates from NSW. MGT5 STs, allowed the description of STM subpopulations that were widespread in processing plants and those which had caused human infections. In addition, AMR was rare in this STM population with only sporadic resistance to a single drug class observed, which warrants further investigation.