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.

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

Essential oils were proposed as natural additives to ensure food safety and quality in a more sustainable approach. The chemical composition of Thymus vulgaris essential oil (TV-EO) collected from Morocco, its antioxidant and antimicrobial activity against different serotypes of Salmonella enterica subsp. enterica was investigated. A mathematical model was implemented to predict the Salmonella behavior when exposed to TV-EO. In situ antimicrobial activity and sensory influence were tested in minced poultry meat experimentally contaminated with Salmonella and treated with TV-EO. Hydrodistillation was used to extract TV-EO, and gas chromatography-mass spectrometry (GC-MS) analysis found thymol as the most representative compound. Results of the antioxidant activity showed an IC50 of 0.29 ± 0.04 mg/mL, EC50 of 0.74 ± 0.08 mg/mL, and RC50 of 0.59 ± 0.06 mg/mL. All the Salmonella strains were susceptible to TV-EO with performing results for the disc diffusion method (inhibition diameters ranged between 24 ± 0.4 mm and 32 ± 0.6 mm), determination of minimum inhibitory concentration (MIC; 0.5%) and minimum bactericidal concentration (MBC; 1%), sublethal-injured cells (7.99 ± 0.08%), in situ activity (growth inhibition after 3 days), and meat sensory preservation (up to 1 week). The implemented mathematical model well fitted the Salmonella growth curve. TV-EO with significant antioxidant and antibacterial activities was suitable to ensure food safety and quality consistent with the new sustainable trends in the food field.

Comprehensive Evaluation on the Use of Thymus vulgaris Essential Oil as Natural Additive against Different Serotypes of Salmonella enterica

Probiotic bacteria exhibit beneficial effects on human and/or animal health, and have been widely used in foods and fermented products for decades. Most probiotics consist of lactic acid bacteria (LAB), which are used in the production of various food products but have also been shown to have the ability to prevent certain diseases. With the expansion of applications for probiotic LAB, there is an increasing concern with regard to safety, as cases with adverse effects, i.e., severe infections, transfer of antimicrobial resistance genes, etc., can occur. Currently, in vitro assays remain the primary way to assess the properties of LAB. However, such methodologies are not meeting the needs of strain risk assessment on a high-throughput scale, in the context of the evolving concept of food safety. Analyzing the complete genetic information, including potential virulence genes and other determinants with a negative impact on health, allows for assessing the safe use of the product, for which whole-genome sequencing (WGS) of individual LAB strains can be employed. Genomic data can also be used to understand subtle differences in the strain level important for beneficial effects, or protect patents. Here, we propose that WGS-based bioinformatics analyses are an ideal and cost-effective approach for the initial in silico microbial risk evaluation, while the technique may also increase our understanding of LAB strains for food safety and probiotic property evaluation.

Whole genome sequencing for the risk assessment of probiotic lactic acid bacteria.

Salmonella spp. is recognized as an important zoonotic pathogen. The emergence of antimicrobial resistance in Salmonella enterica poses a great public health concern worldwide. While the knowledge on the incidence and the characterization of different S. enterica serovars causing chick embryo death remains obscure in China. In this study, we obtained 45 S. enterica isolates from 2,139 dead chick embryo samples collected from 28 breeding chicken hatcheries in Henan province. The antimicrobial susceptibility assay was performed by the broth microdilution method and the results showed that 31/45 (68.8%) isolates were multidrug-resistant (≥3 antimicrobial classes). Besides the highest resistance rate was observed in the aminoglycoside class, all the isolates were susceptible to chloramphenicol, azithromycin, and imipenem. Furthermore, genomic characterization revealed that S. Enteritidis (33.33%; 15/45) was a frequent serovar that harbored a higher number of virulence factors compared to other serovars. Importantly, genes encoding β-lactamases were identified in three serovars (Thompson, Enteritidis, and Kottbus), whereas plasmid-mediated quinolone resistance genes (qnrB4) were detected in certain isolates of S. Thompson and the two S. Kottbus isolates. All the examined isolates harbored the typical virulence factors from Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2). Additionally, a correlation analysis between the antimicrobial resistance genes, phenotype, and plasmids was conducted among Salmonella isolates. It showed strong positive correlations (r -0.6) with IncHI2 and IncHI2A plasmids. Together, our study demonstrated antimicrobial-resistant S. enterica circulating in breeding chicken hatcheries in Henan province, highlighting the advanced approach, by using genomic characterization and statistical analysis, in conducting the routine monitoring of the emerging antimicrobial-resistant pathogens. Our findings also proposed that the day-old breeder chicks trading could be one of the potential pathways for the dissemination of multidrug-resistant S. enterica serovars.

/pdf/genomic-investigation-of-antimicrobial-resistant-salmonella-4rx5vz1hnk.pdf

Genomic Investigation of Antimicrobial-Resistant Salmonella enterica Isolates From Dead Chick Embryos in China.

Foodborne pathogens are the main factors causing food safety incidents. Rapid and accurate detection of foodborne pathogens is of great significance to the protection of human life and health. Food omics have been widely used in food safety detection, traceability, and other fields. While the CRISPR-based technologies have a broad application prospect in the detection of foodborne pathogens. Future food detection, which is expected to develop a more effective and convenient platform with the combination of big data produced by omics-based technologies and high sensitivity of CRISPR-based technologies. Here, we highlight the application of food omics in foodborne pathogens, the detection and gene editing of foodborne pathogens based on CRISPR, and discuss how this integrated approach enables effective detection of foodborne pathogens, hence developing novel gene-editing techniques and killing foodborne pathogens in the food matrix. 

Yingyu Liu

Papers

Prevalence and genomic investigation of Salmonella isolates recovered from animal food-chain in Xinjiang, China.