Whole-genome characterisation of multidrug resistant monophasic variants ofSalmonellaTyphimurium from pig production in Thailand

Abstract

Background Monophasic Salmonella Typhimurium or S. enterica 1,4,[5],12:i:- is among the top five serotypes reported in Thailand. In this study, nineteen monophasic S. Typhimurium from the pig production chain in Chiang Mai and Lamphun provinces during 2011–2014 were sequenced and compared to a globally disseminated clone. Isolates were probed in silico for the presence of antimicrobial resistance genes and Salmonella virulence factors, including Pathogenicity Islands. Results All isolates were from sequence type 34 (ST-34) and clustered similarly in core and pangenome genealogies. The two closest related isolates showed differences in only eighteen loci from whole-genome multilocus sequence typing analysis. All 19 isolates carried aminoglycoside and beta-lactam class resistance genes and genes for five or more different antibiotic classes. Seven out of 14 known SPIs were detected, including SPI-5, SPI-13 and SPI-14, which were detected in all isolates. Conclusions The multi-drug resistant clone, ST-34 was sampled at all stages of pork production. This clone has infiltrated global agricultural processes and poses a significant public health risk. Differences in the core and accessory genomes of the isolates we collected suggest that strains persist though the pork production process, with evidence of mutation within the core-genome and horizontal acquisition of genes, potentially via sharing of pathogenicity islands and plasmids. This highlights the importance of surveillance and targeted intervention measures to successfully control Salmonella contamination.

Assessing the pathogenic potential of less common Salmonella enterica serotypes circulating in the Thai pork production chain

“…The most common Salmonella serotypes implicated in widespread contamination of the pork production chain in northern Thailand are monophasic Typhimurium and serotype Rissen. Previous genomics studies have focused on these common serotypes, with less common serotypes overlooked (Prasertsri et al, 2019; Patchanee et al, 2020). In this study we focus on these less common serotypes to investigate their genetic diversity and virulence potential.…”

“…All aspects of the production chain have been contaminated, from the farm-slaughterhouse-retail market, which is likely related to the levels of sanitation and hygienic at each step of production (Savall et al, 2016; Chen et al, 2019). Salmonella Rissen and Monophasic Salmonella Typhimurium have been the most common serotypes isolated in Chiang Mai and Lamphun provinces for more than a decade and their epidemiology investigated using molecular typing methods (Prasertsee et al, 2019; Patchanee et al, 2020). In contrast, many of the less common serotypes, such as S. enterica serotypes Anatum, Panama, Stanley and Give have not been studied further.…”

Sequence Analyses and Phenotypic Characterization Revealed Multidrug Resistant Gene Insertions in the Genomic Region Encompassing Phase 2 Flagellin Encoding fljAB Genes in Monophasic Variant Salmonella enterica Serovar 4,5,12:i:- Isolates From Various Sources in Thailand

“…This genotypic profile was most frequently seen in isolates with AmpST phenotype (16 of 20 isolates with this genotype profile) which was also the most prevalent phenotypic AMR pattern in our study. Correlations between AMR phenotype and genotype of tested drugs were calculated from the following formula (Patchanee et al, 2020):…”

“…The emerging monophasic variant S. enterica serovar 4,5,12:i:-(thereafter referred as S. 4,5,12:i:-), regarded as one of the derivatives of S. Typhimurium (STm), which has the antigenic formula 4,5,12:i:1,2, has been substantially increasing in prevalence across many regions around the world (European Food Safety Authority [EFSA], 2008; Centers for Disease Control and Prevention [CDC], 2011; European Food Safety Authority [EFSA] and European Centre for Disease Prevention and Control [ECDC], 2016;Biswas et al, 2019;Sun et al, 2020). In Thailand, S. 4,5,12:i:-has been among the top five most commonly reported Salmonella serovars during the last two decades (Bangtrakulnonth et al, 2004;Thailand Department of Medical Sciences, 2016;Patchanee et al, 2020;Luk-in et al, 2021). It is isolated from several kinds of animal sources, but the tendency of transmission among swine population is relatively high (de la Torre et al, 2003;Mossong et al, 2007;Hauser et al, 2010).…”

Non-serotype 2 isolates from healthy pigs are a potential zoonotic reservoir ofStreptococcus suisgenetic diversity and antimicrobial resistance

“…Imprudent use of colistin in pork production as a growth enhancer (since the 1970s) encouraged the development of resistance in E. coli (and other gram-negative bacteria), which has diminished the effectiveness of antibiotics used in human medicine (Liu et al, 2016; Delannoy et al, 2017; Patchanee et al, 2020a). Furthermore, there is a rising trend in multi-drug resistant (MDR) zoonotic pathogens, such as Salmonella, that pose a significant public health threat (Prasertsee et al, 2019; Patchanee et al, 2020b; Tadee et al, 2021). Regulation of veterinary use of antibiotics is difficult in low- and middle-income countries, which consequently have some of the highest AMR levels (Nguyen et al, 2016).…”