Algorism to define epidemic methicillin-resistant Staphylococcus aureus (MRSA) in community using whole genome sequencing (WGS) has not been established. ST834-MRSA has been isolated intermittently from the pediatric outpatients of Saitama City Hospital in Saitama, Japan, from June 2011 to November 2014. The aim of this study is to compare the conventional molecular typing with the WGS-based typing in community-associated MRSA to assess the regional epidemic.
Eleven ST834-MRSA (including three single-locus variants) were analyzed. Antimicrobial susceptibility tests, detection of toxin genes by PCR, SCCmec typing, spa typing, and pulsed-field gel electrophoresis (PFGE) were performed for these strains. WGS was performed using Illumina MiSeq (Illumina), followed by de novoassembly using CLC Genomics Workbench (CLC bio). The contigs were submitted to the websites for molecular analysis: ResFinder-2.1 for genes responsible for antimicrobial resistance, VirulenceFinder 1.2 for virulence genes, and snpTree 1.1 to investigate single nucleotide polymorphisms (SNPs).
All ST834-MRSA strains in the present study were susceptible to levofloxacin and minocycline, and typed as SCCmec IVc. Ten strains had tst and sec. Spa typing differentiated 8 spa-1381 (t9624) and 3 spa-1152 (t1379) strains. Antimicrobial resistant genes found by WGS were consistent with the results of antimicrobial susceptibility except erythromycin. WGS revealed sel was possessed by the ten strains with tst and sec, supporting these strains could have a same genomic island. Defining the strain Saitama2 as a reference, PFGE found other 7 indistinguishable, 2 closely related and 1 possibly related strains. The number of SNPs ranged from 49 to 151, and the 3 spa-1152 (t1379) strains constructed a cluster in the phylogenetic tree.
Levofloxacin and minocycline were not approved for children, suggesting this ST834-MRSA clone could be endemic to Japanese children. WGS had advantage to detect multiple kinds of toxin genes than PCR methods. The number of SNPs around 150 could be a threshold to define regional epidemic compared with PFGE definition, and spa typing could detect differences among the strains more sensitively than PFGE.
St Luke's Life Science Institute:
M. Kawada, None
M. Furuichi, None
E. Imajo, None
Y. Sato, None
S. Tanno, None
K. Hiramatsu, Japan Agency for Medical Research and Development: Investigator , Research grant
Japanese Ministry of Education, Culture, Sports, Science and Technology: Investigator , Research grant