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
IntroductionMethicillin-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.MethodsThe MRSA strain SA2107 was isolated from t...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| author | Lin Huang Rui Guo Jingxian Lin Xiaowei Li Zhicong Li Limei Zhang Wenting Li Rui Xue Cheng Zhang Xiaosan Feng Xiaobin Li Xiaobin Li |
| author_facet | Lin Huang Rui Guo Jingxian Lin Xiaowei Li Zhicong Li Limei Zhang Wenting Li Rui Xue Cheng Zhang Xiaosan Feng Xiaobin Li Xiaobin Li |
| author_sort | Lin Huang |
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| description | IntroductionMethicillin-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.MethodsThe 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.FindingsThe 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.ConclusionThus 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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| spelling | doaj-art-cf64ecda3c294a17bed4bf978e9fc4a62025-01-21T05:43:17ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-01-011410.3389/fcimb.2024.14130241413024Whole-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 pneumoniaLin Huang0Rui Guo1Jingxian Lin2Xiaowei Li3Zhicong Li4Limei Zhang5Wenting Li6Rui Xue7Cheng Zhang8Xiaosan Feng9Xiaobin Li10Xiaobin Li11Department of Pediatrics, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, ChinaDepartment of Pediatrics, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, ChinaDepartment of Pediatrics, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, ChinaDepartment of Pediatrics, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, ChinaDepartment of Pediatrics, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, ChinaGuangdong 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, ChinaGuangdong 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, ChinaSchool of Clinical Medicine, Capital Medical University, Beijing, ChinaDepartment of Pediatrics, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, ChinaDepartment of Pediatrics, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, ChinaGuangdong 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, ChinaDepartment of Pulmonary and Critical Care Medicine, Zhuhai People’s Hospital (The Affiliated Hospital of Beijing Institute of Technology, Zhuhai Clinical Medical College of Jinan University), Zhuhai, ChinaIntroductionMethicillin-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.MethodsThe 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.FindingsThe 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.ConclusionThus 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.https://www.frontiersin.org/articles/10.3389/fcimb.2024.1413024/fullmethicillin-resistant Staphylococcus aureus (MRSA)ST45SCCmec IVaprophagevirulence |
| spellingShingle | Lin Huang Rui Guo Jingxian Lin Xiaowei Li Zhicong Li Limei Zhang Wenting Li Rui Xue Cheng Zhang Xiaosan Feng Xiaobin Li Xiaobin Li 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 Frontiers in Cellular and Infection Microbiology methicillin-resistant Staphylococcus aureus (MRSA) ST45 SCCmec IVa prophage virulence |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | methicillin-resistant Staphylococcus aureus (MRSA) ST45 SCCmec IVa prophage virulence |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2024.1413024/full |
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