Whole-genome analysis of a ST45-SCCmec IVa (2B)-t116 methicillin-resistant Staphylococcus aureus strain isolated from the sputum of a 5-year-old child with pneumonia.

IF 4.8 2区医学 Q2 IMMUNOLOGY Frontiers in Cellular and Infection Microbiology Pub Date : 2025-01-21 eCollection Date: 2024-01-01 DOI:10.3389/fcimb.2024.1413024

Lin Huang, Rui Guo, Jingxian Lin, Xiaowei Li, Zhicong Li, Limei Zhang, Wenting Li, Rui Xue, Cheng Zhang, Xiaosan Feng, Xiaobin Li

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Abstract

Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. In Hainan and Guangzhou of China, the ST45-MRSA was mainly associated with t116.

Methods: The MRSA strain SA2107 was isolated from the sputum of a 5-year-old child with pneumonia. The whole genome of SA2107 was sequence using Illumina (Novaseq 6000) and PacBio (Sequel IIe) sequencers, and the sequences were assembled using hybrid assembly. The carriage of antibiotic resistance genes, virulence genes, and mobile genetic elements were identified using bioinformatics tools. The comparative genomic analyses of MRSA strain SA2107 with other MRSA strains worldwide were performed.

Findings: The genome size of ST45-SCCmec IVa (2B)-t116 MRSA strain SA2107 was ~2.9 Mb. Mobile genetic elements analysis of SA2107 revealed two plasmids (30,064-bp pSA2107-1 and 8,033-bp pSA2107-2), three prophages, two integrative and conjugative elements (ICEs), and two insertion sequences (ISs, IS431 and IS1272). The SCCmec IVa (2B) carried by SA2107 contained the class B mec gene complex (IS431-mecA-ΔmecR1-IS1272) and type 2 ccr gene complex (ccrA2 and ccrB2). Besides mecA, another beta-lactam resistance gene blaZ was found to located on six copies of bla complex (blaZ, blaR1, and blaI) on the chromosome of SA2107. Three kinds of virulence factors were detected on the chromosome of SA2107, including genes encoding toxins, exoenzyme, and immune-modulating protein. Notably, the three prophages harbored by the chromosome of SA2107 all carried virulence genes.

Conclusion: Thus far, only three complete genomes available for ST45-SCCmec IVa (2B)-t116 strain from United States, Germany, and Australia, respectively. The strain SA2107 was the first complete genome data (CP104559) from China for ST45-SCCmec IVa (2B)-t116 MRSA.

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从5岁肺炎患儿痰中分离的ST45-SCCmec IVa (2B)-t116耐甲氧西林金黄色葡萄球菌的全基因组分析

耐甲氧西林金黄色葡萄球菌（MRSA）序列型（ST） 45是全球主要的MRSA谱系，具有巨大的菌株多样性和很高的临床影响。在中国海南和广州，ST45-MRSA主要与t116相关。方法：从1例5岁肺炎患儿痰液中分离MRSA菌株SA2107。采用Illumina （Novaseq 6000）和PacBio （Sequel IIe）测序仪对SA2107进行全基因组测序，并采用杂交组装法对序列进行组装。利用生物信息学工具鉴定了抗生素抗性基因、毒力基因和可移动遗传元件的携带情况。对MRSA菌株SA2107与全球其他MRSA菌株进行比较基因组分析。结果：ST45-SCCmec IVa (2B)-t116 MRSA菌株SA2107的基因组大小约为2.9 Mb。对SA2107进行移动遗传元件分析，发现2个质粒（30,064 bp pSA2107-1和8,033 bp pSA2107-2）、3个噬菌体、2个整合共轭元件（ICEs）和2个插入序列（ISs、IS431和IS1272）。SA2107携带的SCCmec IVa （2B）包含B类mec基因复合体（IS431-mecA-ΔmecR1-IS1272）和2型ccr基因复合体（ccrA2和ccrB2）。除mecA外，在SA2107染色体的bla复合体（blaZ， blaR1和blaI）的6个拷贝上发现了另一个β -内酰胺抗性基因blaZ。在SA2107染色体上检测到三种毒力因子，包括毒素编码基因、外泌酶基因和免疫调节蛋白基因。值得注意的是，SA2107染色体所携带的三个前噬菌体均携带毒力基因。结论：目前仅有来自美国、德国和澳大利亚的ST45-SCCmec IVa (2B)-t116株完整基因组。菌株SA2107是中国首次获得的ST45-SCCmec IVa (2B)-t116 MRSA全基因组数据（CP104559）。

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来源期刊

Frontiers in Cellular and Infection Microbiology IMMUNOLOGY-MICROBIOLOGY

CiteScore

7.90

自引率

7.00%

发文量

1817

审稿时长

14 weeks

期刊介绍： Frontiers in Cellular and Infection Microbiology is a leading specialty journal, publishing rigorously peer-reviewed research across all pathogenic microorganisms and their interaction with their hosts. Chief Editor Yousef Abu Kwaik, University of Louisville is supported by an outstanding Editorial Board of international experts. This multidisciplinary open-access journal is at the forefront of disseminating and communicating scientific knowledge and impactful discoveries to researchers, academics, clinicians and the public worldwide. Frontiers in Cellular and Infection Microbiology includes research on bacteria, fungi, parasites, viruses, endosymbionts, prions and all microbial pathogens as well as the microbiota and its effect on health and disease in various hosts. The research approaches include molecular microbiology, cellular microbiology, gene regulation, proteomics, signal transduction, pathogenic evolution, genomics, structural biology, and virulence factors as well as model hosts. Areas of research to counteract infectious agents by the host include the host innate and adaptive immune responses as well as metabolic restrictions to various pathogenic microorganisms, vaccine design and development against various pathogenic microorganisms, and the mechanisms of antibiotic resistance and its countermeasures.