引言从人临床样本中分离的细菌中的抗微生物耐药性(AMR)的巨大增加导致治疗失败。通过下一代测序(NGS)或全基因组测序(WGS)增加监测可以促进耐药菌株的流行病学研究,抗性基因,以及它们可能携带的其他毒力决定因素。方法本研究包括30个大肠杆菌(E.大肠杆菌)从Prathima医学科学研究所的尿路感染(UTI)患者中获得的分离株,Karimnagar,印度。鉴定了所有细菌分离株,和抗菌药物敏感性模式通过常规微生物技术确定,并通过自动化系统确认。使用NGS对所有分离株进行了调查,以鉴定编码抗性的基因,如超广谱β-内酰胺酶(ESBLs),金属-β-内酰胺酶,和毒力基因。多位点序列分型(MLST)用于了解流行的菌株类型,并进行血清分型以评估分离物携带的O(细胞壁抗原)和H(鞭毛抗原)血清型。结果常规药敏试验发现15株(50%)对亚胺培南(IPM)耐药,10例(33.33%)对阿米卡星(AK)耐药,13例(43.33%)对哌拉西林他唑巴坦(PTZ)耐药,17例(56.66%)对头孢菌素耐药,14例(46.66%)对呋喃妥因(NIT)耐药。在分离物中,26(86.66%)揭示了多种抗生素抗性基因的存在,证据表明至少有一种基因编码β-内酰胺酶抗性。blaCTX-M(19/30,63.33%)基因患病率较高,其次是blaTEM和blaOXA-1。在三个分离物中发现了blaNDM-5基因(3/30,10%)。本研究中鉴定的毒力基因是iutA,sat,ISS,还有爸爸,在其他人中。大肠杆菌血清型主要属于O25:H4(5,16.66%),其次是O102:H6(4,13.33%)。在所检查的样品中鉴定出总共16个MLST变体。在识别的基于MLST的序列类型(ST)中,以ST-131(7,23.33%)为主,其次是ST-167(3,10%)和ST-12(3,10%)。结论本研究结果表明,从UTI患者中分离的大肠杆菌菌株具有潜在的耐药性和毒力基因,属于基于MLST的不同菌株类型。使用分子分析(如NGS)仔细评估细菌菌株可以促进对细菌抗生素抗性及其毒力潜力的更好理解。这可以使医生选择合适的抗菌药物,并有助于更好的患者管理,从而防止耐药细菌的出现和传播。
Introduction An enormous increase in antimicrobial resistance (AMR) among bacteria isolated from human clinical specimens contributed to treatment failures. Increased surveillance through next-generation sequencing (NGS) or whole genome sequencing (WGS) could facilitate the study of the epidemiology of drug-resistant bacterial strains, resistance genes, and other virulence determinants they are potentially carrying. Methods This study included 30 Escherichia coli (E. coli) isolates obtained from patients suffering from urinary tract infections (UTIs) attending Prathima Institute of Medical Sciences, Karimnagar, India. All bacterial isolates were identified, and antimicrobial susceptibility patterns were determined through conventional microbiological techniques and confirmed by automated systems. All the isolates were investigated using NGS to identify genes coding for resistance, such as extended-spectrum beta-lactamases (ESBLs), metallo-beta-lactamases, and virulence genes. Multilocus sequence typing (MLST) was used to understand the prevalent strain types, and serotyping was carried out to evaluate the type of O (cell wall antigen) and H (flagellar antigen) serotypes carried by the isolates. Results The conventional antimicrobial susceptibility testing revealed that 15 (50%) isolates were resistant to imipenem (IPM), 10 (33.33%) were resistant to amikacin (AK), 13 (43.33%) were resistant to piperacillin-tazobactam (PTZ), 17 (56.66%) were resistant to cephalosporins, and 14 (46.66%) were resistant to nitrofurantoin (NIT). Among the isolates, 26 (86.66%) had revealed the presence of multiple antibiotic-resistant genes with evidence of at least one gene coding for beta-lactamase resistance. There was a high prevalence of blaCTX-M (19/30, 63.33%) genes, followed by blaTEM and blaOXA-1. The blaNDM-5 gene was found in three isolates (3/30, 10%). The virulence genes identified in the present study were iutA, sat, iss, and papC, among others. The E. coli serotype found predominantly belonged to O25:H4 (5, 16.66%), followed by O102:H6 (4, 13.33%). A total of 16 MLST variants were identified among the examined samples. Of the MLST-based sequence types (STs) identified, ST-131 (7, 23.33%) was the predominant one, followed by ST-167 (3, 10%) and ST-12 (3, 10%). Conclusions The study results demonstrated that the E. coli strains isolated from patients suffering from UTIs potentially carried antimicrobial resistance and virulence genes and belonged to different strain types based on MLST. Careful evaluation of bacterial strains using molecular analyses such as NGS could facilitate an improved understanding of bacterial antibiotic resistance and its virulence potential. This could enable physicians to choose appropriate antimicrobial agents and contribute to better patient management, thereby preventing the emergence and spread of drug-resistant bacteria.