摘要
      本研究采用全基因组测序（WGS）技术研究了39株从鸡肉样品中分离的肠炎沙门氏菌的基因型和表型耐药性谱、系统发育相关性、质粒和毒力组成。鉴定出四种不同的血清型；明尼苏达州沙门氏菌（16/39，41%）、婴儿沙门氏杆菌（13/39，33.3%）、肠炎沙门氏菌和一个分离株被检测出肯塔基州沙门氏氏菌（1/39，2.6%），序列类型（ST）分别为：ST548、ST32、ST11和ST198。对四环素（91.2%）、氨苄青霉素（82.4%）、硫异恶唑（64.7%）和萘啶酸（61.6%）的表型耐药性最强。耐药性分析显示存在对氨基糖苷类、β-内酰胺酶、磺酰胺类、甲氧苄啶、氯霉素、林可酰胺类、大环内酯类和四环素类的耐药性基因。质粒组显示在39个基因组中存在8个不相容组，包括IncA/C2、IncFIB（K）_1_Kpn3、Col440I_1、IncR、IncX1、IncI1_1_Alpha、IncFIB（S）/IncFII（S）、IncHI2/IncHI2A、IncX2和ColpVC质粒。三个抗性基因sul2、tetA和blaCMY-2被预测位于明尼苏达分离株的IncA/C2质粒上，而所有婴儿分离株对携带blaCTX-M-65基因的IncFIB（K）_1_Kpn3质粒均呈阳性。在评估的基因组中鉴定出11个沙门氏菌致病岛和多达131个应激和/或毒力基因。系统发育分析显示，四个门组与已鉴定的ST图谱一致，分离株之间具有高度的相互多样性。这是沙特阿拉伯首次使用WGS技术对零售鸡肉中的沙门氏菌分离株进行基因组表征。从包括沙特阿拉伯在内的多个地理位置获得沙门氏菌基因组，将对未来的来源追踪非常有益，特别是在流行病学监测和疫情调查期间。
Abstract
This study investigated genotypic and phenotypic antimicrobial resistance profiles, phylogenic relatedness, plasmid and virulence composition of 39 Salmonella enterica strains isolated from chicken meat samples using whole genome sequencing (WGS) technology. Four distinct serotypes were identified; Salmonella Minnesota (16/39, 41%), Salmonella Infantis (13/39, 33.3%), Salmonella Enteritidis (9/39, 23.1%), and one isolate was detected for Salmonella Kentucky (1/39, 2.6%), with sequence types (STs) as followed: ST548, ST32, ST11, and ST198, respectively. Phenotypic resistance to tetracycline (91.2%), ampicillin (82.4%), sulfisoxazole (64.7%), and nalidixic acid (61.6%) was the most observed. Resistome analysis revealed the presence of resistance genes to aminoglycosides, β-lactamase, sulfonamides, trimethoprim, phenicol, lincosamide, macrolides, and tetracyclines. Plasmidome showed the presence of eight incompatibility groups, including IncA/C2, IncFIB(K)_1_Kpn3, Col440I_1, IncR, IncX1, IncI1_1_Alpha, IncFIB(S)/IncFII(S), IncHI2/IncHI2A, IncX2 and ColpVC plasmids across the 39 genomes. Three resistance genes, sul2, tetA and blaCMY-2, were predicted to be located on IncA/C2 plasmid in S. Minnesota isolates, whereas all S. Infantis isolates were positive to IncFIB(K)_1_Kpn3 plasmid that carries blaCTX-M-65 gene. Eleven Salmonella pathogenicity islands and up to 131 stress and/or virulence genes were identified in the evaluated genomes. Phylogenetic analysis showed four phylogroups that were consistent with the identified ST profiles with a high level of inter-diversity between isolates. This is the first genomic characterization of Salmonella isolates from retail chicken meat in Saudi Arabia using WGS technology. The availability of Salmonella genomes from multiple geographic locations, including Saudi Arabia, would be highly beneficial in future source-tracking, especially during epidemiological surveillance and outbreak investigations.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10100587/