背景:伤寒,由伤寒沙门氏菌引起,由于抗菌素耐药性(AMR)的不断升级,这是一个重大的公共卫生问题,广泛耐药(XDR)伤寒沙门氏菌菌株的治疗选择有限,对疾病管理和控制构成严重威胁.本研究旨在探讨基因组特征,巴基斯坦伤寒患者XDR伤寒S.Typhi菌株的流行病学和AMR基因。
方法:我们评估了200例有肠热症状的患者,通过培养和生化试验确认65例伤寒沙门氏菌。随后的抗菌药物敏感性测试显示40例广泛耐药(XDR)和25例多药耐药(MDR)。选择13株XDR菌株进行全基因组测序,分析它们的序列类型,系统发育学,抗性基因,致病性岛,和使用各种数据分析资源的质粒序列。对140株XDR菌株进行了全基因组分析,包括13个内部菌株和来自巴基斯坦其他地区的127个菌株,评估它们的遗传多样性和功能注释。
结果:MLST分析将所有分离株分类为4.3.1.1的序列类型1(ST-1)。P1基因型表征。噬菌体和沙门氏菌致病性岛(SPI)分析鉴定出完整的噬菌体和8个参与沙门氏菌在宿主细胞内入侵和复制的SPI。基因组数据分析显示了许多AMR基因,包括dfrA7,sul1,qnrS1,TEM-1,Cat1和CTX-M-15,以及与抗生素抗性相关的SNP。IncY,IncQ1,pMAC,和pAbTS2质粒,赋予抗菌素耐药性,在一些伤寒沙门氏菌XDR菌株中检测到。系统发育分析推断来自巴基斯坦不同地区的XDR菌株之间存在密切的流行病学联系。注意到Pangenome在这些菌株中处于封闭状态,并且功能注释突出了与代谢和发病机理相关的基因。
结论:这项研究揭示了巴基斯坦XDR伤寒S.表示一个单一的持续传输,具有高度抗生素抗性的克隆.观察到的封闭的泛基因组强调了有限的遗传多样性,并强调了基因组监测对对抗抗药性伤寒感染的重要性。
BACKGROUND: Typhoid fever, caused by Salmonella enterica serovar Typhi, is a significant public health concern due to the escalating of antimicrobial resistance (AMR), with limited treatment options for extensively drug-resistant (XDR) S. Typhi strains pose a serious threat to disease management and control. This study aimed to investigate the genomic characteristics, epidemiology and AMR genes of XDR S. Typhi strains from typhoid fever patients in Pakistan.
METHODS: We assessed 200 patients with enteric fever symptoms, confirming 65 S. Typhi cases through culturing and biochemical tests. Subsequent antimicrobial susceptibility testing revealed 40 cases of extensively drug-resistant (XDR) and 25 cases of multi-drug resistance (MDR). Thirteen XDR strains were selected for whole-genome sequencing, to analyze their sequence type, phylogenetics, resistance genes, pathogenicity islands, and plasmid sequences using variety of data analysis resources. Pangenome analysis was conducted for 140 XDR strains, including thirteen in-house and 127 strains reported from other regions of Pakistan, to assess their genetic diversity and functional annotation.
RESULTS: MLST analysis classified all isolates as sequence type 1 (ST-1) with 4.3.1.1. P1 genotype characterization. Prophage and Salmonella Pathogenicity Island (SPI) analysis identified intact prophages and eight SPIs involved in Salmonella\'s invasion and replication within host cells. Genome data analysis revealed numerous AMR genes including dfrA7, sul1, qnrS1, TEM-1, Cat1, and CTX-M-15, and SNPs associated with antibiotics resistance. IncY, IncQ1, pMAC, and pAbTS2 plasmids, conferring antimicrobial resistance, were detected in a few XDR S. Typhi strains. Phylogenetic analysis inferred a close epidemiological linkage among XDR strains from different regions of Pakistan. Pangenome was noted closed among these strains and functional annotation highlighted genes related to metabolism and pathogenesis.
CONCLUSIONS: This study revealed a uniform genotypic background among XDR S. Typhi strains in Pakistan, signifying a persistence transmission of a single, highly antibiotic-resistant clone. The closed pan-genome observed underscores limited genetic diversity and highlights the importance of genomic surveillance for combating drug-resistant typhoid infections.