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Utilizing Whole Genome Sequencing to Combat MRSA Infections

Researchers at Jiangsu University in China have demonstrated that whole genome sequencing can be used to confirm findings from traditional bacterial genotyping methods to identify outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) and control nosocomial transmission.
In a study published March 7th in the journal PLOS One, Kong et al analyzed 12 patients affected by a 2012 MRSA outbreak at the Affiliated People’s Hospital of Jiangsu in Zhenjiang, China. They collected 20 clinical isolates overall, including eight environmental isolates (four from bedrails, two from the surface of infusion pumps, one from the uniform of a healthcare worker and one from the hands of a healthcare worker). The isolates were detected via minimum inhibitory concentration of oxacillin and mecA detection by the polymerase chain reaction (PCR). 
The research team extracted genomic DNA from each MRSA isolate using an AxyPrep Bacterial Genomic DNA Miniprep Kit (Axygen Scientific, Inc.), and performed whole genome sequencing using the Illumina MiSeq platform (250 PE, Illumina) with the paired-end mode (2×250) by Shanghai Personalbio Biotechnology. T0131 (NC_017347.1) was used as the reference genome to identify single-nucleotide polymorphisms (SNPs) as well as regions with insertions or deletions.
Among the 20 MRSA isolates, the authors found that 18 had an identical pulsed-field gel electrophoresis (PFGE) profile, while the other two had distinct PFGE patterns with similarity coefficients of 81.1% and 85.7%. They determined that the 20 outbreak isolates were SCCmecIII and belonged to clone ST239 in multilocus sequence typing. The authors then sequenced six isolates from patients and the ward environment, and mapped the genome against the reference sequence for ST239. According to their findings, the SNPs were relatively evenly distributed, “suggesting that the majority of variants were due to point mutations rather than recombination.”
The authors also detected multiple resistance and virulence genes and used whole genome sequencing to determine antimicrobial resistance as well as virulence. They reported that their findings “show an almost complete concordance between the genotypes and phenotypes derived in the antibiogram.”
“We also successfully detected various virulence genes associated with hospital-acquired MRSA based on whole genome sequencing,” the authors write. “Virulence genes, including hlapvlpsmαpsm-mecsasXseasee, and tst-1, were positive in all six isolates.”
The authors of the study did not respond to request for comment. However, in their concluding remarks they write, “We highlight the potential of whole genome sequencing in the analysis of hospital outbreaks and its application in infection control to prevent MRSA transmission, to predict resistance and virulence, and to search for new drugs for therapy. With advances in technology and reduced costs, we believe that whole genome sequencing will be widely used in the analysis of pathogen-based outbreaks.”
Brian P. Dunleavy is a medical writer and editor based in New York. His work has appeared in numerous healthcare-related publications. He is the former editor of Infectious Disease Special Edition.
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