Analysis of Antimicrobial Resistance in Non-typhoidal Salmonella Collected From Pork Retail Outlets and Slaughterhouses in Vietnam Using Whole Genome Sequencing

Abstract

Non-typhoidal salmonella (TS) remains a significant health burden worldwide. In Vietnam, pork accounts for 70% of the total meat consumed, and contamination with Salmonella is high. High levels of antimicrobial resistance (AMR) have emerged among porcine NTS and of particular concern is the emergence of colistin resistance, a “last defense” antibioic against multi-drug resistant (MDR) Gram-negative pathogens. This study aimed to investigate the antibiotic susceptibility of 69 NTS isolates collected from the pork retail outlets and slaughterhouses in Vietnam during 2014 a nd 2018/19. Phenotypic testing and whole genome sequencing was used to assess the serotype and AMR gene profiles of the 69 NTS isolates. Seventeen different serotypes were identified, of which S. enterica subsp enterica serotype Typhimurium was the most common followed by S. ser. Rissen, S. ser. London, S. ser. Anatum, and S. ser. Derby. Phenotype AMR was common with 41 (59.4%) isolates deemed MDR. MDR strains were most common in slaughterhouses (83%) and supermarkets (75%) and lowest in traditional markets (38%) and convenience stores (40%). Colistin resistance was identified in 18 strains (15 resistant, three intermediate) with mcr-1 identified in seven isolates (S. ser. Meleagridis, S. Rissen, S. Derby) and mcr-3 in two isolates (S. Typhimurium). This includes the first mcr positive S. Meleagridis to our knowledge. Surprisingly, boutique stores had high levels (60%) of MDR isolates including 5/20 isolates with mcr-1. This study demonstrates that pork from modern retail stores classed as supermarkets or boutique (with pork claiming to be high quality, traceable, environmentally friendly marketed toward higher income consumers) still contained NTS with high levels of AMR.

Colistin resistance and resistance determinants are mobile amongSalmonella entericaisolates from diseased and healthy pigs in Thailand

“…Foodborne infection in humans results in gastroenteritis and is usually self-limiting (Holohan et al, 2022). However, antimicrobial treatment is recommended for infections in children under 5 years of age, elderly people, and immunocompromised patients (Sheen et al, 2022).…”

“…Since 1950, antibiotics such as penicillin, tetracycline, and macrolide have been used in livestock production for increased yield worldwide. Since then, antimicrobial resistance rates have dramatically increased (Holohan et al, 2022). Phenotypic antimicrobial resistance have been linked with veterinary and agricultural use (E.F.S.…”

“…The detection levels of Salmonella in European swine livestock production was 28.5% in 2008, increasing to 66% in 2015 (E.F.S.A, 2017). In south-east Asia, the contamination rates of Salmonella infection on livestock farms are very high (Holohan et al, 2022), with prevalence of NTS in pig farms from the Mekong delta region greater than 80% (Tu et al, 2015). In Thailand, the most common Salmonella enterica serovars identified from pigs are Rissen and Typhimurium (Phongaran et al, 2019).…”

“…Since 1950, antibiotics such as penicillin, tetracycline, and macrolide have been used in livestock production for increased yield worldwide. Since then, antimicrobial resistance rates have dramatically increased (Holohan et al, 2022). Phenotypic antimicrobial resistance have been linked with veterinary and agricultural use (E.F.S.A et al, 2018) and resistance to one or more antimicrobial agents is commonly found in high rate (74%) (Nüesch-Inderbinen et al, 2019) in isolates from food production animals, especially those form the Enterobacteriaceae family (O’Neal et al, 2020).…”

Bactericidal activity of Piper betle L. extract against antibiotic resistant Salmonella spp. isolated from pig farms in Southern Thailand

“…The previous studies have been shown that the Salmonella spp. isolates from pork retail outlets (Holohan et al, 2022), poultry (Vidayanti et al, 2021), and patients (Wu et al, 2021) demonstrate high prevalence of antibiotic resistance. Importantly, the occurrence of multi-drug resistant Salmonella spp.…”