Background: USA300 MRSA causes many clinical syndromes, most often skin and soft tissue infections (SSTIs), in the healthcare setting and in the community. Recurrent infections with USA300 are common yet understudied and little is known regarding intra-host evolutionary dynamics.
Methods: Prospective collection of all MRSA isolates from the Clinical Microbiology Laboratory at the University of Chicago was performed. Patients with >1 episode of MRSA infection from Nov 2003 - Apr 2009 were identified. For a 20% sample of these subjects, the first isolate from each MRSA episode underwent multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec) typing and PCR for Panton-Valentine leukocidin (PVL). Every typed isolate from the 4 patients who had the greatest number of recurrent episodes caused by USA300 (SCCmec IV, ST8, PVL+) underwent whole genome sequencing (WGS) (n=19). Single nucleotide polymorphisms (SNP) were annotated and evolutionary rates compared. Patients A - D had 6, 6, 4, and 3 isolates respectively. All but 2 of the 19 infections were SSTIs.
Results: The average duration of recurrent episodes was 706.8 days (range: 222-1278). WGS revealed patients B and D had strain replacement after 4 and 2 infections, 424 and 104 days after their index infections, respectively (Fig 1). SNP differences between these periods were 75 and 78 for patients B and D, respectively, compared to an overall between-patient mean difference of 60. Intra-patient SNP differences for 6 infection periods ranged from 6-15 (mean: 7.7). SNP were more often in coding regions with significantly more non-synonymous mutations than synonymous (p=0.03) (Fig 2). The substitution rate was 7.82 SNP/genome/year.
Conclusion: We demonstrated the ability of WGS to investigate intra-host microevolution of MRSA. Interestingly, we found strain replacement in 2 patients with recurrent infections, an observation missed by traditional typing. We also provided an estimate of intra-host evolutionary rates, which may provide context for inter-host studies. The greater number of non-synonymous mutations requires further investigation to determine the potential role of selective advantage.
Fig 1 Time-scaled phylogeny of isolates.
Fig 2 Timeline and minimum spanning tree with SNP annotations.
Z. Yin, None
S. Boyle-Vavra, None
M. Salemi, None
R. S. Daum, None
M. Z. David, None
J. L. Steinbeck, None