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The current SARS-CoV-2 pandemic has highlighted a critical need for genomic surveillance of emerging viral strains. Through genomic analysis of variants we can understand the epidemiology of emerging strains and define the predominant routes by which SARS-CoV-2 infection is transmitted both in the community and within healthcare institutions so that better approaches can be developed to prevent these infections. In partnership with the Massachusetts Department of Public Health and the Broad Institute we are sequencing and analyzing SARS-CoV-2 virus from positive samples to contribute to this effort.

Genomics surveillance of hospital infections

The nares of approximately one-third of the population are colonized by SA and, among hospital patients, about 5% are colonized with MRSA. SA is responsible for about 12% of all adult, and 15% of all pediatric, healthcare-associated infections (HAI). The opioid epidemic is associated with an increase in MRSA infection rates (from 4% to 9%) among persons who inject drugs. At UMass Medical Center, ~ 45% of all inpatient SA infections are MRSA, consistent with national estimates. We apply genomic surveillance to identify potential transmission events in the hospital and to determine whether nasal colonization predicts subsequent infection, specifically if the nasal strain is the same as the clinical infecting strain.

Outbreak investigation

Transplant patients are susceptible to life threatening hospital acquired infections. The actual source of the infecting strain can be the hospital environment or even the patient's own microbiome. Suspect infection about breaks among susceptible populations are investigated genomically to determine their origin to isolate outbreaks and inform infection control measures.