摘要

目的建立一种核心基因组多点序列分型（cgMLST）方案，对奇异变形杆菌进行基因分型和潜在风险克隆群的鉴定。方法在这项工作中，我们提出了一个公开可用的奇异紫外藻cgMLST方案，使用咀嚼BBACA。在总共72个代表该物种多样性的完整奇异紫茉莉基因组中，建立了一个针对1842个基因的cgMLST方案，635个未完成的（重叠群、染色体和支架）基因组用于其验证。
结果我们从695株奇异紫外菌株中共鉴定出205个具有区域分布特征的CGs。其中，159个独特的CG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。与引起严重尿路感染的P菌毛操纵子相关的9个毒力基因（papC、papD、papE、papF、papG、papH、papI、papJ和papK）仅在CG20中发现。由于存在潜在风险，这些CG需要引起注意。结论本研究创新性地利用全基因组测序技术结合生物信息学管道（chewBBACA）对奇异紫外藻进行了高分辨率分子分型。我们发现奇异紫茉莉的CGs表现出区域分布差异。我们希望我们的研究将有助于建立奇异紫外藻的cgMLST
Abstract
Objective A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify
potential risk clonal groups (CGs) in Proteus mirabilis.
Methods In this work, we propose a publicly available cgMLST scheme for P. mirabilis using
chewBBACA. In total 72 complete P. mirabilis 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.
Results We identified a total of 205 CGs from 695 P. mirabilis 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 (papC, papD, papE,
papF, papG, papH, papI, papJ, and papK) 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.
Conclusion This research innovatively performs high-resolution molecular typing of P. mirabilis using
whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We
found that the CGs of P. mirabilis showed regional distribution differences. We expect that our research
will contribute to the establishment of cgMLST for P. mirabilis

https://www.besjournal.com/fileSWYXYHJKX/journal/article/swyxyhjkx/2023/4/PDF/22263.pdf