印度肺炎克雷伯菌分离株的序列型、抗菌药物耐药性和毒力基因的相关性：比较基因组学研究。

Association of sequence types, antimicrobial resistance and virulence genes in Indian isolates of Klebsiella pneumoniae: A comparative genomics study.

机构信息

Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India.

出版信息

J Glob Antimicrob Resist. 2022 Sep;30:431-441. doi: 10.1016/j.jgar.2022.05.006. Epub 2022 May 13.

DOI:10.1016/j.jgar.2022.05.006

PMID:35569758

Abstract

OBJECTIVES

Klebsiella pneumoniae genomic surveillance in India was performed to understand the spread of antimicrobial resistant genes across the country over 10 years and to delineate environment and clinical K. pneumoniae through comparative genomics approach.

METHODS

The genomic data of 153 strains were retrieved from PATRIC. To compare the presence of AMR genes, virulence genes, episomes and their evolutionary relationship in 153 K. pneumoniae genomes, ResFinder, Virulence Factor Database, Plasmid Finder and CSI phylogeny tools were used, respectively.

RESULTS

Diverse serotypes were found among the 153 K. pneumoniae isolates, of which K51 (28%) and K64 (21.56%) were majorly found. Most of the K51 isolates belong to ST231 (93.02 %). The number of associated virulence genes (rmpA, magA, entB, ybtS, iutA, allS) appeared to be higher in ST231-KL51 and ST23-KL1 isolates. More than 97% of clinical strains have yersiniabactin, aerobactin genes. Importantly, 98% and 62% of the ESBL and carbapenemase-producing isolates harboured ybtS, iutA, and rmpA, magA genes, respectively. The IncF conjugative plasmids are predominant in K. pneumoniae. The phylogenetic analysis clearly separates the environmental strains from clinical and characterised by uncommon STs and serotypes.

CONCLUSION

Our study illustrates K. pneumoniae genomic surveillance in India representing the phylogenetic evolution, STs, AMR, virulence, serotype to provide more attention for immediate treatment and preventing the dissemination of K. pneumoniae.

摘要

目的

对印度的肺炎克雷伯菌进行基因组监测，以了解该国 10 年来抗微生物药物耐药基因的传播情况，并通过比较基因组学方法对环境和临床肺炎克雷伯菌进行描绘。

方法

从 PATRIC 中检索了 153 株菌株的基因组数据。为了比较 153 株肺炎克雷伯菌基因组中 AMR 基因、毒力基因、附加体及其进化关系的存在情况，分别使用了 ResFinder、毒力因子数据库、质粒查找器和 CSI 系统发育工具。

结果

在 153 株肺炎克雷伯菌分离株中发现了不同的血清型，其中 K51（28%）和 K64（21.56%）是主要的血清型。大多数 K51 分离株属于 ST231（93.02%）。与 ST231-KL51 和 ST23-KL1 分离株相关的毒力基因（rmpA、magA、entB、ybtS、iutA、allS）数量似乎更高。超过 97%的临床菌株具有耶尔森菌素、aerobactin 基因。重要的是，98%和 62%的产 ESBL 和碳青霉烯酶的分离株分别携带 ybtS、iutA 和 rmpA、magA 基因。IncF 型接合质粒在肺炎克雷伯菌中占优势。系统发育分析清楚地将环境株与临床株分离，并具有不常见的 ST 和血清型。