Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2024

Comparative genomic analysis of Salmonella Typhimurium isolated from meat chicken production chain in New South Wales, Australia (#74)

Michael Payne 1 , Samitha Bandaranayake 1 , Sarah Williamson 2 , Jack Stewart 1 2 , Sandeep Kaur 1 , Anthony Pavic 2 , Ruiting Lan 1
  1. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
  2. Birling Laboratories, Bringelly, NSW, Australia

Salmonella enterica serovar Typhimurium (STm) is a globally prevalent pathogen, causing foodborne illnesses in humans through contaminated poultry products. In Australia, meat chickens are reservoirs of STm. In this study, we performed a comparative genomic analysis of STm isolates from different stages of the Australian meat chicken production chain in New South Wales (NSW). In particular, we used Multilevel genome typing (MGT) to investigate genomic diversity of STm from different production stages of meat chickens, to identify prevalent sequence types (STs), assess their distribution and investigate pathogen transmission pathways across the production chain. 

We sequenced a total of 895 STm isolates obtained from hatcheries, tier 1 breeder farms, tier 2 breeder farms, processing plants, value-added products, and feed ingredients and analyzed them using MGT. At the lowest resolution level, MGT1 (equal to the classic seven-gene multilocus sequence typing), the isolates were divided into 2 STs with 664 isolates in ST19 and 247 isolates in ST2066. At the highest resolution level, MGT9, the isolates were divided into 547 STs with the largest, ST27886, comprising 58 isolates. STs transmitting down the meat chicken production chain and STs unique to each category were identified from MGT5 to MGT9. MGT5 ST46 comprised 52 isolates and was transmitted across all the six stages of the production chain. At MGT9 more than 30 STs were identified across multiple stages of the production chain.  The two most frequent MGT9 STs (ST27886 and ST27876) were transmitted across five stages of the production chain. Beta-lactamase (blaTEM-1) was the only antimicrobial resistant (AMR) gene identified and found in 4.9% of the isolates. The blaTEM-1 gene was carried by 95 kb IncI1 Alpha plasmid and was sporadically carried across 10 different MGT5 STs.

In conclusion, we identified both MGT5 STs prevalent in all stages of the meat chicken production chain, and MGT9 STs demonstrating direct transmission across multiple stages. These findings provide insights into STm transmission and will facilitate the implementation of intervention strategies to decrease the transmission of STm throughout the chicken production chain.

Key words: Meat chicken farms, processing plants, Multilevel genome typing, Salmonella Typhimurium, genomic diversity.