Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg 2131, South Africa.
Acta Trop. 2022 Oct;234:106620. doi: 10.1016/j.actatropica.2022.106620. Epub 2022 Jul 27.
Salmonella enterica is a zoonotic pathogen of worldwide public health importance. We characterised Salmonella isolates from poultry along the farm-to-fork continuum using whole genome sequencing (WGS) and bioinformatic analyses. Three multilocus sequence types (MLSTs), i.e., ST15 (1.9%), ST152 (5.9%) and ST1316 (92.2%) and three serotypes, i.e., S. Heidelberg (1.9%), Kentucky (5.9%) and Yoruba (92.2%) were detected. The rare serotype, S. Yoruba, was detected among the farm and abattoir isolates and contained resistance and virulence determinants. Resistome analysis revealed the presence of the aac(6')-Iaa gene associated with aminoglycoside resistance, a single point mutation in the parC gene associated with fluoroquinolone and quinolone resistance, and a single isolate contained the fosA7 gene responsible for fosfomycin resistance. No antibiotic resistance genes (ARGs) were identified for isolates phenotypically non-susceptible to azithromycin, cephalosporins, chloramphenicol and nitrofurantoin and resistance was thought to be attributable to other resistance mechanisms. The fully susceptible profiles observed for the wastewater isolates suggest that the poultry environment may receive antibiotic-resistant strains and resistance determinants from poultry with the potential of becoming a pathway of Salmonella transmission along the continuum. Six plasmids were identified and were only carried by 92.2% of the S. Yoruba isolates in varying combinations. Four plasmids were common to all S. Yoruba isolates along the continuum; isolates from the litter and feces on the farm contained two additional plasmids. Ten Salmonella pathogenicity islands (SPIs) and 177 virulence genes were identified; some were serotype-specific. Phylogenetic analysis of S. Heidelberg and Kentucky showed that isolates were related to animal and human isolates from other countries. Phylogenetic analysis among the S. Yoruba isolates revealed four clades based on the isolate sources along the farm-to-fork continuum. Although the transmission of Salmonella strains along the farm-to-fork continuum was not evident, pathogenic, resistant Salmonella present in the poultry production chain poses a food safety risk. WGS analysis can provide important information on the spread, resistance, pathogenicity, and epidemiology of isolates and new, rare or emerging Salmonella strains to develop intervention strategies to improve food safety.
肠炎沙门氏菌是一种具有世界公共卫生重要性的人畜共患病病原体。我们使用全基因组测序（WGS）和生物信息学分析方法，对从农场到餐桌连续体中的家禽分离株进行了沙门氏菌的特征描述。共检测到 3 种多位点序列类型（MLST），即 ST15（1.9%）、ST152（5.9%）和 ST1316（92.2%），3 种血清型，即 S. Heidelberg（1.9%）、Kentucky（5.9%）和 Yoruba（92.2%）。在农场和屠宰场的分离株中检测到罕见血清型 S. Yoruba，其中含有耐药性和毒力决定因子。耐药组分析显示存在与氨基糖苷类耐药相关的 aac(6')-Iaa 基因、与氟喹诺酮类和喹诺酮类耐药相关的 parC 基因中的单个点突变，以及单个分离株含有负责磷霉素耐药的 fosA7 基因。表型上对阿奇霉素、头孢菌素、氯霉素和呋喃妥因不敏感的分离株未发现抗生素耐药基因（ARGs），耐药性被认为归因于其他耐药机制。废水分离株的完全敏感谱表明，家禽环境可能会从具有沿连续体传播沙门氏菌潜力的家禽中接收抗生素耐药菌株和耐药决定因子。鉴定出 6 个质粒，它们仅以不同组合存在于 92.2%的 S. Yoruba 分离株中。4 个质粒存在于整个连续体中的所有 S. Yoruba 分离株中；来自农场的垫料和粪便中的分离株含有另外 2 个质粒。鉴定出 10 个沙门氏菌致病性岛（SPIs）和 177 个毒力基因；其中一些是血清型特异性的。对 S. Heidelberg 和 Kentucky 的系统发育分析表明，分离株与来自其他国家的动物和人类分离株有关。对 S. Yoruba 分离株的系统发育分析显示，根据沿农场到餐桌连续体的分离株来源，有 4 个进化枝。尽管沿农场到餐桌连续体传播沙门氏菌菌株并不明显，但存在于家禽生产链中的致病性、耐药性沙门氏菌构成了食品安全风险。WGS 分析可为分离株的传播、耐药性、致病性和流行病学以及新的、罕见的或新兴的沙门氏菌菌株提供重要信息，以制定干预策略来改善食品安全。
