Genomic Epidemiology of USA300 Methicillin-Resistant Staphylococcus aureus in an Urban Community.
BACKGROUND
In a community, it is unknown what factors account for transmission of methicillin-resistant Staphylococcus aureus (MRSA). We integrated whole genome sequencing (WGS) and epidemiologic data to identify factors associated with MRSA transmission networks in an urban community.


METHODS
WGS was performed on colonizing USA300 MRSA isolates from 74 individuals within 72 hours of admission to a public hospital in Chicago, IL. Single nucleotide variants (SNVs) were used to reconstruct the phylogeny of sequenced isolates, and epidemiologic data was overlaid to identify factors associated with transmission networks.


RESULTS
The maximum within-patient SNV difference for an individual with multisite colonization was 41 SNVs, with no systematic divergence among body sites. We observed a minimum of 7 SNVs and maximum of 153 SNVs between isolates from different individuals. We identified 4 pairs of individuals whose isolates were within 40 SNVs of each other. Putting our isolates in the context of previously sequenced USA300 isolates from other communities, we identified a 13-member group and two 4-member groups that represent samples from putative local transmission networks. Individuals in these groups were more likely to be African American, to be human immunodeficiency virus-infected, to reside in high detainee release areas, and to be current users of illicit drugs.


CONCLUSIONS
Using WGS, we observed potential transmission networks in an urban community and that certain epidemiologic factors were associated with inclusion in these networks. Future work with contact tracing and advanced molecular diagnostics may allow for identification of MRSA "epicenters" in the community where interventions can be targeted.
Rush University Medical Center/Stroger Hospital of Cook County, Chicago, Illinois.
Kyle J
KJ
Popovich
University of Michigan, Ann Arbor.
Evan
E
Snitkin
University of Illinois at Chicago.
Stefan J
SJ
Green
Rush University Medical Center/Stroger Hospital of Cook County, Chicago, Illinois.
Alla
A
Aroutcheva
Rush University Medical Center, Chicago, Illinois.
Mary K
MK
Hayden
Rush University Medical Center/Stroger Hospital of Cook County, Chicago, Illinois.
Bala
B
Hota
Rush University Medical Center/Stroger Hospital of Cook County, Chicago, Illinois.
Robert A
RA
Weinstein
D002641:Chicago / Q000453:epidemiology; D005260:Female; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D006801:Humans; D008297:Male; D055624:Methicillin-Resistant Staphylococcus aureus / Q000145:classification* / Q000235:genetics*; D017720:Molecular Epidemiology; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013203:Staphylococcal Infections / Q000453:epidemiology* / Q000382:microbiology*
MRSA; whole genome sequencing