Whole Genome Sequencing for Cluster Detection of USA300 MRSA in an Urban Community
Background: USA300 MRSA is endemic in certain communities but risk and geographic distribution vary. In the hospital, whole genome sequencing (WGS) has been used to infer transmission between individuals by identifying genetically similar MRSA strains with recent ancestry. The objective of this study was to use WGS to determine if clusters of highly similar USA300 strains exist in an urban community where USA300 MRSA is endemic.
Methods: WGS was performed on colonizing USA300 MRSA isolates from 74 individuals (53 HIV-infected & 21 HIV-negative) within 72 hours of admission to a public hospital in Chicago, IL. We identified single nucleotide variants (SNVs) in strains and used phylogenetic analysis to examine ancestry. In hospitals, a limit of <40 SNV differences has been used to infer recent transmission. Isolates were categorized as clustered if they were within 40 or 80 SNV differences and were supported by bootstrap analysis (neighbor-joining and maximum likelihood) and/or Bayesian analysis (posterior probability >95%). Epidemiologic data were compared to WGS results.
Results: The genomic sequences of our isolates differed from the reference USA300 MRSA genome (median SNV difference 95, range 54-146). A total of 4,033 synonymous, non-synonymous, and non-coding SNV positions were identified. At <40 SNVs and <80 SNVs, 5 and 9 clusters were identified, respectively (Figure). Most clusters included 2 individuals, although Cluster A (<80 SNVs) included 6 individuals. There were a total of 10 (14% of population) and 18 (24%) individuals in clusters at the <40 and <80 SNV limits, respectively. Individuals in various clusters were more likely to be current or former illicit drug users compared to those not in a cluster, but the difference did not reach statistical significance (67% vs 43%, p=0.08). All individuals in Cluster A were African-American and HIV-infected; 4 (67%) were current or former drug users and 2 (33%) had resided in the same homeless shelter in the prior year.
Conclusion: Using WGS, we found that clusters of highly similar USA300 MRSA strains with recent common ancestry exist in a Chicago community where USA300 is endemic. Determination of epidemiologic exposures that lead to clustering will allow optimal targeting of community prevention efforts.
B. Hota, None
A. Aroutcheva, None
M. K. Hayden, None
R. A. Weinstein, None
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