基于PATRIC公共数据库不同标本来源的耐碳青霉烯类肺炎克雷伯菌基因组特征比较

 目的 了解不同标本来源的耐碳青霉烯类肺炎克雷伯菌(CRKP)在耐药基因、毒力基因和质粒携带数量等方面是否存在差异,为CRKP感染的预防控制提供参考。方法 从Pathosystems Resource Integration Center(PATRIC)公共数据库中下载2011—2020年不同标本来源CRKP的全基因组测序数据,使用生物信息学分析软件进行耐药基因、毒力基因、质粒等鉴定分析,使用IBM SPSS 23.0和R v4.2.0软件进行比较。结果 共纳入2356个CRKP全基因组数据,CRKP菌株携带耐药基因、质粒和毒力基因数量的中位数(四分位数间距)分别为18(16,20)、4(3,5)、60(57,68),不同标本来源的CRKP携带毒力基因、质粒以及关键毒力基因(iutA、iucA、iucB、iucC、iucD、rmpA、rmpA2、iroB、iroC、iroD、iroN)的数量差异均有统计学意义(均P<0.05)。粪便来源的CRKP菌株携带耐药基因、质粒和毒力基因的数量较多,其中位数(四分位数间距)分别为19(16,21)、5(3,6)、63(61,69);导管附着体液来源的CRKP携带iutA和iuc(iucA、iucB、iucC、iucD)的比率较高(19.0%,4/21);rmpA和rmpA2在肺泡灌洗液来源的CRKP中携带率最高,分别占7.9%(3/38)、15.8%(6/38);无菌体液来源的CRKP携带iro(iroB、iroC、iroD、iroN)基因的比率(6.5%,4/62)高于其他标本类型CRKP(比率范围:0~4.9%)。血标本来源的CRKP比其他标本来源CRKP携带更多的毒力基因(P=0.004)。结论 血标本来源的CRKP菌株携带的毒力基因比其他标本类型来源的CRKP更多,可能与其临床高死亡率有关,建议高度关注血标本中CRKP菌株向高毒力菌株进化,通过加强医院感染控制措施,降低CRKP血流感染的发病率。

Genomic characteristics of carbapenem-resistant Klebsiella pneumoniae from different specimen sources based on PATRIC public database

Objective To understand the differences in the number of drug-resistant genes, virulence genes and plasmids among carbapenem-resistant Klebsiella pneumoniae (CRKP) from different specimen sources, and provide references for the prevention and control of CRKP infection. Methods The whole-genome sequencing data of CRKP from different specimen sources in 2011-2020 were downloaded from public database of Pathsystems Resource Integration Center (PATRIC). Drug-resistant genes, virulence genes, and plasmids were identified and analyzed with bioinformatics analysis software and compared with IBM SPSS 23.0 and R v4.2.0 software. Results A total of 2 356 CRKP whole-genome data was included. The medians (interquartile interval) of drug-resistant genes, plasmids, and virulence genes carried by CRKP strains were 18 (16, 20), 4 (3, 5), and 60 (57, 68) respectively. The number of virulence genes, plasmids, and key virulence genes (iutA, iucA, iucB, iucC, iucD, rmpA, rmpA2, iroB, iroC, iroD, iroN) carried by CRKP strains from different specimen sources was statistically significant (P<0.05). The number of drug-resistant genes, plasmids and virulence genes carried by CRKP strains from fecal specimens was higher, with the medians (interquartile interval) of 19 (16, 21), 5 (3, 6) and 63 (61, 59) respectively. The percentage of CRKP from catheter-attached fluid carrying iutA and iuc (iucA, iucB, iucC, iucD) was higher (19.0%, 4/21). Carrying rates of rmpA and rmpA2 in CRKP from alveolar lavage fluid were the highest, 7.9% (3/38) and 15.8% (6/38) respectively. The percentage of iro (iroB, iroC, iroD, iroN) genes carried by CRKP from sterile body fluids (6.5%, 4/62) was higher than that of CRKP from other specimen types (percentage range: 0-4.9%). CRKP from blood specimen carried more virulence genes than that from other specimen sources (P=0.004). Conclusion CRKP from blood specimen carries more virulence genes than CRKP from other types of specimens, which may relate to the high clinical mortality. It is suggested to pay close attention to the evolution of CRKP strains into high virulence strain in blood specimen, and reduce the incidence of CRKP blood stream infection by strengthening healthcare-associated infection control measures.