Genomic diversity of Salmonella enterica serovar Typhimurium isolated from chicken processing facilities in New South Wales, Australia

Abstract

Contamination of poultry products by Salmonella enterica serovar Typhimurium (STm) is a major cause of foodborne infections and outbreaks. This study aimed to assess the diversity and antimicrobial resistance (AMR) carriage of STm in three chicken processing plants using genomic sequencing. It also aimed to investigate whether any particular strain types were associated with cases of human illness. Multilevel genome typing (MGT) was used to analyze 379 STm isolates from processed chicken carcasses. The diversity of chicken STm sequence types (STs) increased from MGT1 (2 STs) to MGT9 (257 STs). STs at MGT5 to MGT9 levels that were unique to one processing plant and shared among the processing plants were identified, likely reflecting the diversity of STm at their farm source. Fifteen medium resolution MGT5 STs matched those from human infections in Australia and globally. However, no STs matched between the chicken and human isolates at high resolution levels (MGT8 or MGT9), indicating the two STm populations were phylogenetically related but were unlikely to be directly epidemiologically linked. AMR genes were rare, with only a blaTEM-1 gene carried by a 95 kb IncI1 Alpha plasmid being identified in 20 isolates. In conclusion, subpopulations that were widespread in processing plants and had caused human infections were described using MGT5 STs. In this STM population, AMR was rare with only sporadic resistance to a single drug class observed. The genomic analysis of STm from chicken processing plants in this study provided insights into STm that contaminate meat chickens early in the food production chain.