Genome-based analysis of infrequent Salmonella serotypes through the Thai pork production chain

Abstract

Salmonella is a prevalent zoonotic foodborne pathogen. Swine and pork are implicated as important sources of salmonellosis in humans. In Chiang Mai and Lamphun Provinces in northern Thailand, there has been a high prevalence of Salmonella persistence for over a decade. Infection is usually with dominant S. enterica serotypes, including serotypes Rissen and 1,4,[5],12:i:-. However, other serotypes also contribute to disease but are less well characterized. The whole genome sequencing data of 43 S. enterica serotypes isolated from pork production chain through 2011-2014, were used to evaluate genetic diversity and ascertain the possible source of Salmonella contamination based on Core Genome Multilocus Sequence Typing (cgMLST) approach. The Salmonella serotypes recovered from farms and slaughterhouses were re-circulating by swine environmental contamination. Conversely, the Salmonella contamination in the retail market represents cross-contamination from multiple sources, including contaminated foodstuffs. Salmonella contamination in the pork production chain has the competency for host cell adhesion, host cell invasion, and intracellular survival, which is enough for the pathogenicity of salmonellosis. In addition, all of these isolates were multi-drug resistant Salmonella, which contained at least 10 antimicrobial resistance genes. This result indicated that these S. enterica serotypes also pose a significant public health risk. Our findings support the need for appropriate surveillance of food-animal products going to market to reduce public exposure to highly pathogenic, multi-drug resistant Salmonella. Acquiring information would motivate all stakeholders to reinforce sanitation standards throughout the pork production chain in order to eradicate Salmonella contamination and reduce the risk of salmonellosis in humans.

Keywords: Salmonella; antimicrobial resistance genes (ARG); core genome MLST (cgMLST); pork production chain; virulence genes; whole genome sequencing.

FIGURE 1

The minimum spanning tree (MST) analysis of Salmonella isolates recovered from the pork production chain. Each isolate was grouped according to the loci different of EnteroBase Salmonella database’s cgMLST scheme, which considers a total of 3,002 loci (Pearce et al., 2020). The number on the branch represent the number of loci different between each isolate. Node color coding: green color, yellow color and pink color represent the Salmonella isolates recovered from farm, slaughterhouse and retail market, respectively. Outer border color represents each serotype of Salmonella isolates.

FIGURE 2

The minimum spanning tree (MST) analysis of 43 Salmonella isolates recovered from pork production chain (striped nodes) and additional 61 Salmonella isolates circulating in Thailand. Each isolate was grouped according to the loci different of EnteroBase Salmonella database’s cgMLST scheme, which considers a total of 3,002 loci (Pearce et al., 2020). The number on the branch represent the number of loci different between each isolate. Node color coding were representing the sources of the Salmonella isolates. Outer border color represents each serotype of Salmonella isolates.

FIGURE 3

Binary heatmap analysis of virulence genes harbored in the Salmonella isolates recovered from pork production chain circulating in Chiang Mai and Lamphun municipality area during the period 2011–2014.

FIGURE 4

Binary heatmap analysis of antimicrobial resistance genes harbored in the Salmonella isolates recovered from pork production chain circulating in Chiang Mai and Lamphun municipality area during the period 2011–2014.