巴基斯坦一家医院分离的社区获得性耐甲氧西林金黄色葡萄球菌新序列型（ST5352）菌株的全基因组测序。
Whole-genome sequencing of a new sequence type (ST5352) strain of community-acquired methicillin-resistant Staphylococcus aureus from a hospital in Pakistan.
机构信息
Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Sector H-12, Islamabad 44000, Pakistan.
Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Sector H-12, Islamabad 44000, Pakistan.
出版信息
J Glob Antimicrob Resist. 2019 Dec;19:161-163. doi: 10.1016/j.jgar.2019.09.015. Epub 2019 Sep 23.
OBJECTIVES
Methicillin-resistant Staphylococcus aureus (MRSA) is an important drug-resistant pathogen causing a number of diseases, resulting in increased mortality. Therefore, whole-genome sequencing of an MRSA strain isolated from a patient admitted to a hospital in Lahore, Pakistan, was performed to better characterise the strain and to understand the genetic components of antimicrobial resistance and virulence.
METHODS
MRSA isolate Lr12 was sequenced on an Illumina HiSeq 2500 platform. The genome was assembled with SPAdes and was annotated using PGAP v.4.3. The strain was characterised using spaTyper 1.0, SCCmecFinder v.1.2 and MLST 2.0 server. Plasmids, antimicrobial resistance determinants and virulence factors were identified using PlasmidFinder v.2.0, CARD and VFDB, respectively.
RESULTS
MRSA strain Lr12 has an estimated genome size of 2 769 144bp with a GC content of 32.7% and harbours 1 plasmid, 2 prophages, 11 antimicrobial resistance determinants and several virulence factors. The allelic profile of seven housekeeping genes was unique and the sequence type (ST) was classified as unknown, hence a novel sequence type (ST5352) was assigned.
CONCLUSION
MRSA strain Lr12 has a novel sequence type (ST5352) and could be used as a reference strain for comparative genomic analysis of other MRSA strains belong to ST5352.
目的
耐甲氧西林金黄色葡萄球菌（MRSA）是一种重要的耐药病原体，可引起多种疾病，导致死亡率增加。因此，对从巴基斯坦拉合尔一家医院收治的患者中分离出的一株 MRSA 菌株进行全基因组测序，以更好地对该菌株进行特征描述，并了解其抗微生物药物耐药性和毒力的遗传成分。
方法
在 Illumina HiSeq 2500 平台上对 MRSA 分离株 Lr12 进行测序。使用 SPAdes 进行基因组组装，并使用 PGAP v.4.3 进行注释。使用 spaTyper 1.0、SCCmecFinder v.1.2 和 MLST 2.0 服务器对菌株进行特征描述。使用 PlasmidFinder v.2.0、CARD 和 VFDB 分别识别质粒、抗微生物药物耐药决定因子和毒力因子。
结果
MRSA 菌株 Lr12 的估计基因组大小为 2 769 144bp，GC 含量为 32.7%，包含 1 个质粒、2 个前噬菌体、11 个抗微生物药物耐药决定因子和多个毒力因子。7 个看家基因的等位基因谱是独特的，序列类型（ST）被归类为未知，因此分配了一个新的序列类型（ST5352）。
结论
MRSA 菌株 Lr12 具有新的序列类型（ST5352），可作为其他属于 ST5352 的 MRSA 菌株的比较基因组分析的参考菌株。
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