Abstract：
OBJECTIVE: The emergence of carbapenem-resistant Klebsiella pneumoniae presents significant health challenges. Here, we present the structural genome sequence of an NDM-5-producing K. pneumoniae (HZKP2) in China.
METHODS: Antimicrobial susceptibility tests were conducted via broth microdilution. Whole-genome sequencing was performed for genomic analysis. Wzi and capsular polysaccharide (KL) were analysed using Kaptive. Resistance genes, virulence factors, and comparative genomics analyses were also conducted. Multilocus sequence typing (MLST), replicons type, and core genome MLST analysis were further conducted using BacWGSTdb server.
RESULTS: HZKP2 was resistant to cefepime, ceftazidime, ciprofloxacin, ciprofloxacin, meropenem, and ertapenem. It harboured fosA, blaSHV-187, oqxA, oqxB, sul1, dfrA1, tet(A), floR, aph(6)-Id, aph(3\'\')-Ib, sul2, blaCTX-M-55, and blaNDM-5. Based on the RAST results, 5563 genes that belonged to 398 subsystems were annotated. The complete genome sequence of HZKP2 was characterized as ST1, wzi 19, and KL19, 5 five contigs totalling 5 654 446 bp, including one chromosome and four plasmids. Further analysis found that blaNDM-5 was located in a 46 161 bp IncX3 plasmid (pHZKP2-3). The genetic structure of blaNDM-5 gene was ISKox3-IS26-bleMBL-blaNDM-5-IS5-ISAb125-IS3000. Further analysis revealed that insertion sequences mediated the dissemination of blaNDM-5 from other species of Enterobacterales. Phylogenetic analysis showed that the closest relative was from a human stool specimen in China, which differed by 53 core genome MLST alleles.
CONCLUSIONS: Our study provides the first structural perspective of the ST1 K. pneumoniae isolate producing NDM-5 in China. These results could provide valuable insights into the genetic characteristics, antimicrobial resistance mechanisms, and transmission dynamics of carbapenem-resistant K. pneumoniae in clinical settings.
METHODS: Antimicrobial susceptibility tests were conducted via broth microdilution. Whole-genome sequencing was performed for genomic analysis. Wzi and capsular polysaccharide (KL) were analysed using Kaptive. Resistance genes, virulence factors, and comparative genomics analyses were also conducted. Multilocus sequence typing (MLST), replicons type, and core genome MLST analysis were further conducted using BacWGSTdb server.
RESULTS: HZKP2 was resistant to cefepime, ceftazidime, ciprofloxacin, ciprofloxacin, meropenem, and ertapenem. It harboured fosA, blaSHV-187, oqxA, oqxB, sul1, dfrA1, tet(A), floR, aph(6)-Id, aph(3\'\')-Ib, sul2, blaCTX-M-55, and blaNDM-5. Based on the RAST results, 5563 genes that belonged to 398 subsystems were annotated. The complete genome sequence of HZKP2 was characterized as ST1, wzi 19, and KL19, 5 five contigs totalling 5 654 446 bp, including one chromosome and four plasmids. Further analysis found that blaNDM-5 was located in a 46 161 bp IncX3 plasmid (pHZKP2-3). The genetic structure of blaNDM-5 gene was ISKox3-IS26-bleMBL-blaNDM-5-IS5-ISAb125-IS3000. Further analysis revealed that insertion sequences mediated the dissemination of blaNDM-5 from other species of Enterobacterales. Phylogenetic analysis showed that the closest relative was from a human stool specimen in China, which differed by 53 core genome MLST alleles.
CONCLUSIONS: Our study provides the first structural perspective of the ST1 K. pneumoniae isolate producing NDM-5 in China. These results could provide valuable insights into the genetic characteristics, antimicrobial resistance mechanisms, and transmission dynamics of carbapenem-resistant K. pneumoniae in clinical settings.
摘要：
目的：耐碳青霉烯类肺炎克雷伯菌（CRKP）的出现带来了重大的健康挑战。这里,我们介绍了中国产NDM-5的肺炎克雷伯菌（HZKP2）的结构基因组序列。
方法：通过肉汤微量稀释进行抗菌药物敏感性试验。进行全基因组测序(WGS)用于基因组分析。使用Kaptive分析Wzi和荚膜多糖(KL)。抗性基因，毒力因子，并进行了比较基因组学分析。多位点序列分型(MLST),replicons类型,使用BacWGSTdb服务器进一步进行核心基因组多位点序列分型（cgMLST）分析。
结果：HZKP2对头孢吡肟具有抗性，头孢他啶,环丙沙星,环丙沙星,美罗培南,和ertapenem.它藏有FosA，blaSHV-187,oqxA,OQXB,sul1,dfrA1,tet(A),floR,aph(6)-Id,aph(3\'\')-Ib,sul2、blaCTX-M-55和blaNDM-5。根据RAST结果,注释了属于398个子系统的5563个基因。HZKP2的完整基因组序列的特征为ST1，wzi19和KL19，具有五个重叠群，总计5,654,446bp，包括一条染色体和四个质粒.进一步分析发现blaNDM-5位于46,161bp的IncX3质粒(pHZKP2-3)中。blaNDM-5基因的遗传结构为ISKox3-IS26-bleMBL-blaNDM-5-IS5-ISAb125-IS3000。进一步的分析表明，插入序列介导了blaNDM-5从其他肠杆菌物种的传播。系统发育分析表明，最接近的亲属来自中国的人类粪便标本，差异有53个cgMLST等位基因。
结论：我们的研究提供了在中国产生NDM-5的ST1肺炎克雷伯菌分离株的第一个结构观点。这些结果可以为遗传特征提供有价值的见解，抗菌素耐药机制，和CRKP在临床环境中的传播动力学。
方法：通过肉汤微量稀释进行抗菌药物敏感性试验。进行全基因组测序(WGS)用于基因组分析。使用Kaptive分析Wzi和荚膜多糖(KL)。抗性基因，毒力因子，并进行了比较基因组学分析。多位点序列分型(MLST),replicons类型,使用BacWGSTdb服务器进一步进行核心基因组多位点序列分型（cgMLST）分析。
结果：HZKP2对头孢吡肟具有抗性，头孢他啶,环丙沙星,环丙沙星,美罗培南,和ertapenem.它藏有FosA，blaSHV-187,oqxA,OQXB,sul1,dfrA1,tet(A),floR,aph(6)-Id,aph(3\'\')-Ib,sul2、blaCTX-M-55和blaNDM-5。根据RAST结果,注释了属于398个子系统的5563个基因。HZKP2的完整基因组序列的特征为ST1，wzi19和KL19，具有五个重叠群，总计5,654,446bp，包括一条染色体和四个质粒.进一步分析发现blaNDM-5位于46,161bp的IncX3质粒(pHZKP2-3)中。blaNDM-5基因的遗传结构为ISKox3-IS26-bleMBL-blaNDM-5-IS5-ISAb125-IS3000。进一步的分析表明，插入序列介导了blaNDM-5从其他肠杆菌物种的传播。系统发育分析表明，最接近的亲属来自中国的人类粪便标本，差异有53个cgMLST等位基因。
结论：我们的研究提供了在中国产生NDM-5的ST1肺炎克雷伯菌分离株的第一个结构观点。这些结果可以为遗传特征提供有价值的见解，抗菌素耐药机制，和CRKP在临床环境中的传播动力学。
