Genomic Investigation of Salmonella Isolates Recovered From a Pig Slaughtering Process in Hangzhou, China

Abstract

The pig industry is the principal source of meat products in China, and the presence of pathogens in pig-borne meat is a crucial threat to public health. Salmonella is the major pathogen associated with pig-borne diseases. However, route surveillance by genomic platforms along the food chain is still limited in China. Here, we conducted a study to evaluate the dynamic prevalence of Salmonella in a pig slaughtering process in Hangzhou, Zhejiang Province, China. Fifty-five of 226 (24.37%) samples were positive for Salmonella; from them, 78 different isolates were selected and subjected to whole genome sequencing followed by bioinformatics analyses to determine serovar distribution, MLST patterns, antimicrobial resistance genes, plasmid replicons, and virulence factors. Moreover, phenotypic antimicrobial resistance was performed using the broth dilution method against 14 antimicrobial agents belonging to 10 antimicrobial classes. Our results showed that samples collected from the dehairing area (66.66%) and the splitting area (57.14%) were the most contaminated. Phenotypic antimicrobial resistance classified 67 of 78 isolates (85.90%) as having multidrug resistance (MDR), while the highest resistance was observed in tetracycline (85.90%; 67/78) followed by ampicillin (84.62%; 66/78), chloramphenicol (71.80%; 56/78), and nalidixic acid (61.54%; 48/78). Additionally, serovar prediction showed the dominance of Salmonella Typhimurium ST19 (51.28%; 40/78) among the 78 studied isolates, while plasmid prediction reported the dominance of IncHI2A_1 (20.51%; 16/78), followed by IncX1_1 (17.95%; 14/78) and IncHI2_1 (11.54%; 9/78). Virulence factor prediction showed the detection of cdtB gene encoding typhoid toxins in two Salmonella Goldcoast ST358 and one Salmonella Typhimurium ST19, while one isolate of Salmonella London ST155 was positive for genes encoding for the siderophore “yersiniabactin” and the gene senB encoding for enterotoxin production. From this study, we conclude that pig slaughterhouses are critical points for the dissemination of virulent and multidrug-resistant Salmonella isolates along the food chain which require the implementation of management systems to control the critical points. Moreover, there is an urgent need for the implementation of the whole genome sequencing platform to monitor the emergence of virulent and multidrug-resistant clones along the food chain.

Discerning the Antimicrobial Resistance, Virulence, and Phylogenetic Relatedness of Salmonella Isolates Across the Human, Poultry, and Food Materials Sources in Malaysia

“…According to studies sanctioned by the Department of Veterinary Services Malaysia under the Livestock Farm Practices Scheme (SALT) program, for Salmonella species isolated from chicken cloacal swabs revealed that 13.5% of the Salmonella isolates were resistant to tetracycline, 5.4% to polymyxin and erythromycin. This is similar to the investigation conducted in China where tetracycline resistance was found to predominate among Salmonella isolates obtained from slaughtered pigs ( Wu et al, 2021 ). In comparison, 2.7% were resistant to chloramphenicol and trimethoprim ( Azmi et al, 2018 ).…”

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

“…Comparison of the AMR genotypes with AST data showed many inconsistencies with some isolates demonstrating resistance but without obvious genotypes and sensitive isolates having identifiable AMR genes within their genomes. Similar results of incoherence between AMR phenotype and genotype in Salmonella have been reported in China ( 73 , 74 ). In this study, for example, the presence of TEM-1 was strongly linked to ampicillin resistance, although some bla TEM−1 positive strains were still sensitive.…”

Genomic Investigation Reveals a Community Typhoid Outbreak Caused by Contaminated Drinking Water in China, 2016

“…To test the antimicrobial susceptibility of the isolates, their minimal inhibitory concentrations (MICs) of 20 antibiotics were tested by the broth microdilution method using Mueller-Hinton broth. The MIC assay was conducted according to the guideline of the Clinical Laboratory Standards Institute (CLSI 2019) ( 21 ). The antibiotics used in the MIC assay contain Ampicillin (Amp), Cefotaxime (Ctx), Ceftazidime (Ctz), Cefepime (Cfp), Cefoxitin (Cxt), Imipenem (Imp), Aztreonam (Azt), Meropenem (Mer), Amoxicillin/Clavulanic acid (Amo/Cla), Chloramphenicol (Chl), Sulfamethoxazole/Trimethoprim (Sul/Tri), Nalidixic acid (Nal), Ciprofloxacin (Cip), Levofloxacin (Lev), Amikacin (Ami), Gentamicin (Gen), Kanamycin (Kan), Azithromycin (Azi), Doxycycline (Dox), and Tetracycline (Tet).…”