背景:多重耐药肺炎克雷伯菌(MDR-KP)的出现代表了严重的临床健康问题。抗生素耐药性和毒力相互作用在肺炎克雷伯菌感染的发病机制中起着重要作用。因此,通过使用计算分析工具监测细菌基因组中的抗生素抗性基因(ARG)和毒力因子来追踪临床抗性组和病毒组对于预测下一次流行至关重要.
方法:在目前的研究中,从曼苏拉大学医院收集了一百个产生超广谱β-内酰胺酶(ESBL)的临床分离株,埃及,在2022年1月至6月的六个月内。由于高抗性表型,选择了一个分离株,并调查了住院患者MDR-KP的遗传特征。否则,使用DL抗菌药物敏感性测试(AST)系统确定了对25种抗菌药物的敏感性。采用使用IlluminaNovaSeq6000的全基因组测序(WGS)来提供对肺炎克雷伯菌WSF99临床分离株的基因组见解。
结果:分离的肺炎克雷伯菌WSF99对通过抗生素药敏试验研究的抗生素具有表型耐药性。WGS分析显示,WSF99的总基因组长度为5.7Mb,估计有5,718个蛋白质编码基因,GC含量为56.98mol%。此外,WSF99分离株的等位基因谱被分配给高风险克隆ST147.此外,在基因组中确定了多种抗生素抗性基因,这些基因解释了高水平的抗性表型。几个β-内酰胺酶基因,在WSF99分离物中检测到blaCTX-M-15、blaTEM-1、blaTEM-12、blaSHV-11、blaSHV-67和blaOXA-9。此外,一个碳青霉烯酶基因,blaNDM-5,在基因组中预测,位于移动卡带内。此外,在基因组中预测了其他抗性基因,包括,aac(6\')-Ib,aph(3')-VI,sul1,sul2,fosA,aadA,arr-2、qnrS1、tetA和tetC。四个质粒复制子CoIRNAI,IncFIB(K),IncFIB(pQil),和IncR在基因组中预测。基因组分析草案揭示了位于ARG周围的遗传移动元件的出现,表明通过水平基因转移容易传播。
结论:本研究报告了从住院患者中分离出的MDR-KP的全面致病基因组分析。这些发现可能与未来研究埃及抗生素耐药性和毒力多样性的研究有关。
BACKGROUND: The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K. pneumoniae infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic.
METHODS: In the current study, one hundred extended spectrum β-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into K. pneumoniae WSF99 clinical isolate.
RESULTS: The isolate K. pneumoniae WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7 Mb with an estimated 5,718 protein-coding genes and a G + C content of 56.98 mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several β-lactamase genes, including blaCTX-M-15, blaTEM-1, blaTEM-12, blaSHV-11, blaSHV-67, and blaOXA-9, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, blaNDM-5, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, aac(6\')-Ib, aph(3\')-VI, sul1, sul2, fosA, aadA, arr-2, qnrS1, tetA and tetC. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer.
CONCLUSIONS: This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.