Rafei Rayane, Koong Jonathan, Osman Marwan, Al Atrouni Ahmad, Hamze Monzer, Hamidian Mehrad
Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon.
Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo NSW 2007, Australia.
FEMS Microbes. 2022 Nov 18;3:xtac027. doi: 10.1093/femsmc/xtac027. eCollection 2022.
has successfully spread during the last decades as one of the main critically important pathogens. However, many aspects including plasmids, are still under-investigated. Here, we report the complete sequence of an strain, belonging to the ST25 (Institut Pasteur) sequence type recovered in 2012 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. This strain (Cl107) carries a 198 kb plasmid called pCl107 that encodes the MPF conjugative transfer system. The plasmid carries the , , and (B) antibiotic resistance genes. pCl107 region encompassing the , , (B) is closely related to AbGRI1 chromosomal resistance islands, which are widespread in strains belonging to Global Clone 2. The resistance region found in pCl107 is one of the missing links in the evolutionary history of the AbGRI1 islands. pCl107 also contains a BREX Type 1 region and represents one of the two main evolution patterns observed in BREX clusters found in plasmids related to pCl107. pCl107 also harbours a phosphonate metabolism module, which plays an ancestral structure compared to other large plasmids in ST25 strains. While the uric acid metabolic module found in pCl107 is incomplete, we identified possible ancestors from plasmids and chromosomes of spp. Our analyses indicate a complex evolutionary history of plasmids related to pCl107 with many links to multiple antibiotic resistance and metabolic pathways.
在过去几十年中，作为主要的关键重要病原体之一已成功传播。然而，包括质粒在内的许多方面仍研究不足。在此，我们报告一株菌株的完整序列，该菌株属于2012年在黎巴嫩分离出的ST25（巴斯德研究所）序列型，采用了Illumina MiSeq和牛津纳米孔测序相结合的方法以及混合组装策略。该菌株（Cl107）携带一个198 kb的质粒，名为pCl107，其编码MPF接合转移系统。该质粒携带了、和（B）抗生素抗性基因。包含、、（B）的pCl107区域与AbGRI1染色体抗性岛密切相关，这些抗性岛在属于全球克隆2的菌株中广泛存在。在pCl107中发现的抗性区域是AbGRI1岛进化历史中缺失的环节之一。pCl107还包含一个BREX 1型区域，代表了在与pCl107相关的质粒中发现的BREX簇中观察到的两种主要进化模式之一。pCl107还含有一个膦酸盐代谢模块，与ST25菌株中的其他大质粒相比，它具有祖先结构。虽然在pCl107中发现的尿酸代谢模块不完整，但我们从物种的质粒和染色体中鉴定出了可能的祖先。我们的分析表明，与pCl107相关的质粒具有复杂的进化历史，与多种抗生素抗性和代谢途径有许多联系。
