Chen Sheng Lin, Kang Yu Tong, Liang Yi He, Qiu Xiao Tong, Li Zhen Jun
School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China;State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
Biomed Environ Sci. 2023 Apr 20;36(4):343-352. doi: 10.3967/bes2023.040.
A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in .
In this work, we propose a publicly available cgMLST scheme for using chewBBACA. In total 72 complete genomes, representing the diversity of this species, were used to set up a cgMLST scheme targeting 1,842 genes, 635 unfinished (contig, chromosome, and scaffold) genomes were used for its validation.
We identified a total of 205 CGs from 695 strains with regional distribution characteristics. Of these, 159 unique CGs were distributed in 16 countries. CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes. Nine virulence genes ( , , , , , , , , and ) related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20. These CGs require attention due to potential risks.
This research innovatively performs high-resolution molecular typing of using whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We found that the CGs of showed regional distribution differences. We expect that our research will contribute to the establishment of cgMLST for .
一种用于对[具体物种]进行基因分型并识别潜在风险克隆群（CGs）的核心基因组多位点序列分型（cgMLST）方案。
在本研究中，我们提出了一种利用chewBBACA软件针对[具体物种]的公开可用的cgMLST方案。总共72个代表该物种多样性的完整基因组被用于建立一个针对1842个基因的cgMLST方案，635个未完成的（重叠群、染色体和支架）基因组被用于验证该方案。
我们从695株[具体物种]菌株中总共鉴定出205个具有区域分布特征的CGs。其中，159个独特的CGs分布在16个国家。CG20和CG3携带大量共享和独特的抗生素抗性基因。与导致严重尿路感染的P菌毛操纵子相关的9个毒力基因（[具体基因名称1]、[具体基因名称2]、[具体基因名称3]、[具体基因名称4]、[具体基因名称5]、[具体基因名称6]、[具体基因名称7]、[具体基因名称8]和[具体基因名称9]）仅在CG20中发现。由于潜在风险，这些CGs需要引起关注。
本研究创新性地利用全基因组测序技术结合生物信息学流程（chewBBACA）对[具体物种]进行高分辨率分子分型。我们发现[具体物种]的CGs存在区域分布差异。我们期望我们的研究将有助于为[具体物种]建立cgMLST。
