对从一名5岁肺炎患儿痰液中分离出的ST45-SCC IVa（2B）-t116耐甲氧西林菌株进行全基因组分析。
Whole-genome analysis of a ST45-SCC IVa (2B)-t116 methicillin-resistant strain isolated from the sputum of a 5-year-old child with pneumonia.
作者信息
Huang Lin, Guo Rui, Lin Jingxian, Li Xiaowei, Li Zhicong, Zhang Limei, Li Wenting, Xue Rui, Zhang Cheng, Feng Xiaosan, Li Xiaobin
机构信息
Department of Pediatrics, Zhuhai People's Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, China.
Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, China.
出版信息
Front Cell Infect Microbiol. 2025 Jan 21;14:1413024. doi: 10.3389/fcimb.2024.1413024. eCollection 2024.
INTRODUCTION
Methicillin-resistant (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-SCC 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, IS and IS). The SCC IVa (2B) carried by SA2107 contained the class B gene complex (IS--Δ-IS) and type 2 gene complex ( and ). Besides , another beta-lactam resistance gene was found to located on six copies of complex (, , and ) 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-SCC 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.
引言
耐甲氧西林金黄色葡萄球菌（MRSA）序列类型（ST）45是一种主要的全球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
MRSA菌株SA2107从一名5岁肺炎儿童的痰液中分离得到。使用Illumina（Novaseq 6000）和PacBio（Sequel IIe）测序仪对SA2107的全基因组进行测序，并使用混合组装法对序列进行组装。使用生物信息学工具鉴定抗生素抗性基因、毒力基因和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。
研究结果
ST45-SCC IVa（2B）-t116 MRSA菌株SA2107的基因组大小约为2.9 Mb。对SA2107的移动遗传元件分析揭示了两个质粒（30,064 bp的pSA2107-1和8,033 bp的pSA2107-2）、三个前噬菌体、两个整合和接合元件（ICEs）以及两个插入序列（ISs，IS和IS）。SA2107携带的SCC IVa（2B）包含B类基因复合体（IS--Δ-IS）和2型基因复合体（和）。此外，在SA2107染色体上的六个拷贝的复合体（、和）上发现了另一个β-内酰胺抗性基因。在SA2107的染色体上检测到三种毒力因子，包括编码毒素、外酶和免疫调节蛋白的基因。值得注意的是，SA2107染色体上携带的三个前噬菌体都携带毒力基因。
结论
迄今为止，分别来自美国、德国和澳大利亚的ST45-SCC IVa（2B）-t116菌株仅有三个完整基因组可用。菌株SA2107是来自中国的ST45-SCCmec IVa（2B）-t116 MRSA的首个完整基因组数据（CP104559）。
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