College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China.
Department of Veterinary Medicine & Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China.
Food Res Int. 2021 Apr;142:110198. doi: 10.1016/j.foodres.2021.110198. Epub 2021 Feb 5.
Salmonella is a major foodborne pathogen worldwide, causing serious cases of morbidity and mortality due to the consumption of contaminated foods. Animal-borne foods were considered the main source of transferring Salmonella to humans; however, route surveillance by genomic platforms along the food-chain is limited in China. Here, we proceeded to the application of whole genome sequencing in the epidemiological analysis of Salmonella isolated along the food-chain in Xinjiang, China. A total of 2408 samples were collected from farms, slaughterhouses, and markets, and subjected to the isolation of Salmonella strains. 314 (13.04%) of the samples were positive for Salmonella. Phenotypic antimicrobial resistance was conducted by the broth dilution method using 14 antimicrobial agents belonging to ten classes for all 314 isolates. A selection of representative 103 isolates was subjected to whole-genome sequencing for understanding the Salmonella diversity, including serovars, antimicrobial and virulence genes, plasmid types, multi-locus sequence types, and allelic types. We found that S. Agona was the dominant serovar and O:4(B) was the dominant serogroup. The dominant genotype was ST13 and each serovar has a unique MLST pattern. Plasmids prediction reported Col(MGD2)_1 and Col(Ye4449)_1 as the dominant plasmids, in addition to the detection of IncFII(S)_1 and IncFIB(S)_1 carried by all S. Enteritidis isolates. Importantly, virulence genes prediction showed the presence of cdtB gene encoding typhoid toxins, spv genes, and pef gene cluster encoding fimbriae in the genomes of S. Indiana and S. Enteritidis. Phenotypic antimicrobial resistance identified 92.04% of the sampled isolates as multi-drug resistance (MDR), with high resistance to tetracycline (78.03%; 245/314), amoxicillin/ clavulanic acid (75.80%; 238/314), and ampicillin (70.70%; 222/314). Together, we firstly reported the prevalence of MDR Salmonella isolates harboring critical virulence factors transmission via animal-borne food-chain in Xinjiang, hence route surveillance by whole-genome sequencing platform could facilitate recognition and project early warning for the emerging MDR clones along the food-chain.
沙门氏菌是一种全球性的主要食源性病原体，由于食用受污染的食物，导致严重的发病和死亡病例。动物源性食品被认为是将沙门氏菌转移给人类的主要来源；然而，中国沿食物链进行基于基因组的监测的途径有限。在这里，我们着手将全基因组测序应用于中国新疆沿食物链分离的沙门氏菌的流行病学分析。从农场、屠宰场和市场采集了 2408 个样本，并对沙门氏菌菌株进行了分离。314 个（13.04%）样本对沙门氏菌呈阳性。对 314 株分离株进行了 14 种抗生素的肉汤稀释法表型药敏试验，抗生素属于十个类别。选择了 103 个有代表性的分离株进行全基因组测序，以了解沙门氏菌的多样性，包括血清型、抗生素和毒力基因、质粒类型、多位点序列类型和等位基因类型。我们发现，肠炎沙门氏菌是主要血清型，O:4(B)是主要血清群。优势基因型为 ST13，每种血清型都有独特的 MLST 模式。质粒预测报告 Col(MGD2)_1 和 Col(Ye4449)_1 为主要质粒，此外，所有肠炎沙门氏菌分离株均携带 IncFII(S)_1 和 IncFIB(S)_1。重要的是，毒力基因预测显示伤寒毒素编码基因 cdtB、spv 基因和编码菌毛的 pef 基因簇存在于印第安纳沙门氏菌和肠炎沙门氏菌的基因组中。表型药敏试验确定 92.04%的采样分离株为多药耐药（MDR），对四环素（78.03%；245/314）、阿莫西林/克拉维酸（75.80%；238/314）和氨苄西林（70.70%；222/314）的耐药性很高。总的来说，我们首次报道了新疆动物源性食物链中携带重要毒力因子的 MDR 沙门氏菌分离株的流行情况，因此全基因组测序平台的监测途径可以促进对食物链中新兴 MDR 克隆的识别和项目预警。
