Whole-genome sequence of a new sequence type ST-5352 strain of community-acquired methicillin-resistant Staphylococcus aureus from hospital in Pakistan

Abstract Objective Methicillin-resistant Staphylococcus aureus (MRSA) is an important drug-resistant pathogen causing a number of diseases, resulting in increasing rate of mortality. Therefore, whole-genome sequence of MRSA isolate was performed to better characterize the strain and understand the genetic components of antibiotic-resistance and virulence. Methods The MRSA isolate Lr12 was sequenced on the Illumina HiSeq 2500 platform. The genome was assembled with SPAdes and annotated using PGAP; V 4.3. The strain was characterized using spaTyper 1.0, SCCmecFinder; V 1.2 and MLST-2.0 Server. Plasmids, antibiotic-resistance determinants and virulence factors were identified using PlasmidFinder v2.0, CARD, and VFDB, respectively. Results The strain Lr12 has an estimated genome size 2,769,144 bp with 32.7% G + C content, harboring one plasmid, two prophages, eleven antibiotic-resistance determinants, and several virulence factors. The allelic profile of seven housekeeping genes was found unique and the sequence type was classified as unknown hence a new ST number 5352 was assigned. Conclusion The MRSA strain Lr12 has a novel sequence type (ST-5352) and could be used as a reference strain for comparative genomic analysis of other MRSA strains belong to ST-5352.