Punchihewage-Don Anuradha J, Chen Zhao, Meng Jianghong, Parveen Salina
Food Microbiology and Safety Laboratory, Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA.
Joint Institute for Food Safety and Applied Nutrition, and Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20740, USA.
Food Res Int. 2025 Jun;211:116349. doi: 10.1016/j.foodres.2025.116349. Epub 2025 Apr 17.
Multidrug-resistant Salmonella is becoming a public health hazard. This study aimed to investigate the genomic diversity of the selected Salmonella serovars isolated from organic and non-organic chickens using whole-genome sequencing (WGS). A total of 94 Salmonella isolates [Infantis (n = 71), Enteritidis (n = 13), Typhimurium (n = 10)] recovered from organic and non-organic retail chickens were subjected to WGS using Illumina MiSeq. All Salmonella isolates contained at least one antibiotic resistance (AR) gene (ARG). All S. Typhimurium and S. Enteritidis isolates, and 98.6 % of S. Infantis isolates possessed aac(6')-Iaa which predicted resistant to aminoglycosides. Most isolates harbored ARGs for sulfonamides, β-lactamase inhibitors, tetracyclines, and fluoroquinolone/quinolone resistance regardless of chicken types. Fisher's exact test indicated a significantly higher prevalence of ARGs in Salmonella isolated from organic chickens. The virulence genes that stimulate Salmonella pathogenicity island 1 (SPI1) encoding, type three secretion system 1 (TTSS-1) translocated effectors, SPI2 encoding, TTSS-2 translocated effectors, fimbrial adherence determinants, serum resistance, stress adaptation and Mg uptake were observed in every serovar regardless of chicken types. Seven plasmids were detected in Salmonella isolates from non-organic chicken, including IncFIB(pN55391), IncFIB(S), Col(BS512), IncFII(S), IncX1, IncC, and ColpVC, whereas Salmonella isolates from organic chicken carried only three plasmids [IncFIB(pN55391), Col(BS512), and IncC]. Phylogenetic analysis confirmed that a significant portion of the isolates had single nucleotide polymorphism (SNP) distances greater than the threshold (SNP ≤ 20), indicating genetic distance among them. These results suggest that the Salmonella isolates from organic and non-organic chickens possessed various AR and virulence genes and thus have the potential to cause salmonellosis.
多重耐药性沙门氏菌正成为一种公共卫生危害。本研究旨在通过全基因组测序（WGS）调查从有机鸡和非有机鸡中分离出的选定沙门氏菌血清型的基因组多样性。从有机和非有机零售鸡中回收的总共94株沙门氏菌分离株[婴儿沙门氏菌（n = 71）、肠炎沙门氏菌（n = 13）、鼠伤寒沙门氏菌（n = 10）]使用Illumina MiSeq进行全基因组测序。所有沙门氏菌分离株都至少含有一个抗生素抗性（AR）基因（ARG）。所有鼠伤寒沙门氏菌和肠炎沙门氏菌分离株，以及98.6%的婴儿沙门氏菌分离株都拥有预测对氨基糖苷类耐药的aac(6')-Iaa。无论鸡的类型如何，大多数分离株都携带磺胺类、β-内酰胺酶抑制剂、四环素类以及氟喹诺酮/喹诺酮耐药的ARGs。费舍尔精确检验表明，从有机鸡中分离出的沙门氏菌中ARG的流行率显著更高。无论鸡的类型如何，在每个血清型中都观察到了刺激沙门氏菌致病岛1（SPI1）编码、三型分泌系统1（TTSS-1）易位效应蛋白、SPI2编码、TTSS-2易位效应蛋白、菌毛黏附决定因素、血清抗性、应激适应和镁摄取的毒力基因。在非有机鸡的沙门氏菌分离株中检测到7种质粒，包括IncFIB(pN55391)、IncFIB(S)、Col(BS512)、IncFII(S)、IncX1、IncC和ColpVC，而有机鸡的沙门氏菌分离株仅携带3种质粒[IncFIB(pN55391)、Col(BS512)和IncC]。系统发育分析证实，很大一部分分离株的单核苷酸多态性（SNP）距离大于阈值（SNP≤20），表明它们之间存在遗传距离。这些结果表明，从有机鸡和非有机鸡中分离出的沙门氏菌分离株拥有各种AR和毒力基因，因此有可能导致沙门氏菌病。
