引言抗菌素耐药性(AMR)已成为一种威胁,在全球细菌物种中传播。AMR现在被认为是导致治疗失败的无声大流行。因此,有必要建立有效的监测机制,以了解从人体临床标本中分离出的细菌种类.本研究采用下一代测序(NGS)或全基因组测序(WGS)来鉴定抗性和毒力基因,序列类型,和血清型。方法本研究包括18例多药耐药(MDR)肺炎克雷伯菌(K。肺炎)从患有不同感染的患者中获得的分离株,这些患者参加了Prathima医学科学研究所,Karimnagar,印度。所有分离物均已鉴定,和抗菌药物敏感性曲线通过常规微生物技术确定,并通过自动化系统确认。使用NGS或WGS对所有分离株进行了研究,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。进行多位点序列分型(MLST)以鉴定序列类型,进行了Kleborate分析以确认该物种,AMR的基因,和毒力,并评估分离株携带的荚膜多糖(KL)和细胞壁/脂多糖(O)血清型。结果患者平均年龄为46.11±20.35岁。在包括的患者中,男性12例(66.66%),女性6例(33.33%)。观察到高百分比(>50%)的具有编码AMR的基因的高毒力肺炎克雷伯氏菌(hvKp)菌株和具有携带blaNDM和抗性基因的潜力的质粒。在分离物中,16(88.88%)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。blaSHV(17/18;94.44%)和blaCTX-M-15(16/18;88.88%)AMR基因的患病率较高。鉴定的其他AMR基因包括blaTEM(83.33%;15/18)和blaOXA(14/18;77.77%)。两个(11.11%)菌株各自显示blaNDM-1和blaNDM-5基因的存在。鉴定的毒力基因包括gapA,infb,mdh,PGI,phoE,rpoB,tonB,还有ybt.最常见的肺炎克雷伯菌血清型是KL51:O1v2(3/18,16.66%),KL17:O1v1(3/18,16.66%),和KL64:O2v1(3/18,16.66%)。KL64(4/18;22.22%)是分离株中最常见的荚膜血清型。最常见的基于MLST的序列类型(ST)包括ST-147(5/18,27.77%),其次是ST-231(3/18,16.66%)和ST-101(2/18,11.11%)。结论肺炎克雷伯菌分离株的分子分析显示存在多种AMR,质粒,和毒力基因。此外,MLST注意到了许多全球ST。结果注意到hvKp菌株的高流行率。使用NGS/WGS进行细菌菌株的分子表征对于了解细菌菌株的流行病学以及它们可能携带的抗生素抗性和毒力基因很重要。从这项研究中获得的数据可用于设计谨慎的抗生素处方方法并改善患者管理实践。
Introduction Antimicrobial resistance (AMR) has become a menace, spreading among bacterial species globally. AMR is now recognized as a silent pandemic responsible for treatment failures. Therefore, an effective surveillance mechanism is warranted to understand the bacterial species isolated from human clinical specimens. The present study employed next-generation sequencing (NGS) or whole-genome sequencing (WGS) to identify the resistance and virulence genes, sequence type, and serotypes. Methods This study included 18 multidrug-resistant (MDR) Klebsiella pneumoniae (K. pneumoniae) isolates obtained from patients suffering from different infections attending the Prathima Institute of Medical Sciences, Karimnagar, India. All isolates were identified, and antimicrobial susceptibility profiles were determined through conventional microbiological techniques and confirmed by automated systems. All the isolates were investigated using NGS or WGS to identify the genes coding for resistance, such as extended-spectrum beta-lactamases (ESBLs), metallo-beta-lactamases, and virulence genes. Multilocus sequence typing (MLST) was conducted to identify the sequence types, and Kleborate analysis was performed to confirm the species, genes for AMR, and virulence and evaluate the capsular polysaccharide (KL) and cell wall/lipopolysaccharide (O) serotypes carried by the isolates. Results The mean age of the patients was 46.11±20.35 years. Among the patients included, 12 (66.66%) were males and 6 (33.33%) were females. A high percentage (>50%) of hypervirulent K. pneumoniae (hvKp) strains that had genes coding for AMR and plasmids having the potential to carry blaNDM and resistance genes were observed. Among the isolates, 16 (88.88%) 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 blaSHV (17/18; 94.44%) and blaCTX-M-15 (16/18; 88.88%) AMR genes. Other AMR genes identified included blaTEM (83.33%; 15/18) and blaOXA (14/18; 77.77%). Two (11.11%) strains each showed the presence of blaNDM-1 and blaNDM-5 genes. The virulence genes identified included gapA, infB, mdh, pgi, phoE, rpoB, tonB, and ybt. The most frequent K. pneumoniae serotypes found were KL51:O1v2 (3/18, 16.66%), KL17:O1v1 (3/18, 16.66%), and KL64:O2v1 (3/18, 16.66%). KL64 (4/18; 22.22%) was the most common capsular serotype identified among the isolates. The most frequent MLST-based sequence type (ST) identified included ST-147 (5/18, 27.77%), followed by ST-231 (3/18, 16.66%) and ST-101 (2/18, 11.11%). Conclusions The molecular analysis of K. pneumoniae isolates revealed multiple AMR, plasmid, and virulence genes. Additionally, many global STs were noticed by MLST. The results noted a high prevalence of hvKp strains. Molecular characterization of bacterial strains using NGS/WGS is important to understand the epidemiology of bacterial strains and the antibiotic resistance and virulence genes they are potentially carrying. The data obtained from this study may be utilized to devise careful antibiotic-prescribing approaches and improve patient management practices.