Use of Genomic Surveillance Helps Identify Hidden MRSA Outbreak

Once an uncommon resistant infection, methicillin-resistant Staphylococcus aureus (MRSA) is now widespread throughout the community and the world. In health care, it is so common that the efficacy of actually isolating those patients has increasingly been a topic of debate. While other resistant organisms have taken the spotlight, the truth is that MRSA is still a dangerous and formidable microbe.

In infection prevention and control, we track outbreaks of resistant organisms, like MRSA, when they occur in health care facilities. Unfortunately, MRSA outbreaks aren’t isolated to a particular environment or population. An article in Proceedings of the National Academy of Sciences describes an outbreak of MRSA in a Brooklyn religious enclave in which investigators tested a new approach to tracking diseases in the community, and explains how hospital-based genomic surveillance can play a critical role in identifying disease clusters.

Investigators from the NYU School of Medicine began noticing an increase in community-acquired MRSA (CA-MRSA) in infants and young children in Brooklyn’s Orthodox Jewish communities over an 18-month period in 2015 and 2016. Health officials identified 4368 children who were admitted for CA-MRSA complications. The infection rate per 1000 admissions was 10-fold higher than those from other zip codes. Through nasal and throat swabs of 451 patients, they found that the rate of MRSA colonization was doubled in children from the Brooklyn community than in children admitted from other zip codes.

During the study time, investigators collected single-patient isolates of MRSA from infected Brooklyn community members. Of the 92 isolates obtained, 84 were from children. The use of molecular typing found that all isolates were a direct clone of the epidemic CA-MRSA USA300. This strain is frequently associated with skin infections, but further genomic sequencing found that the strain was USA300_FPR3757.

A total of 93% of the isolates from Brooklyn community patients were clustered within a unique clade of MRSA and consistent with that of the clone. Further genomic analysis found that the specific strain of CA-MRSA had acquired genes that allowed for increased virulence and conferred resistance to mupirocin and chlorhexidine, which are topical treatments for decolonization to help reduce the spread of the bacteria.

Investigators also observed that the majority of infections in the children were skin infections in the groin/buttock area likely related to skin breakdown due to wet or soiled diapers. The potential for enteric (i.e. gastrointestinal tract) carriage is vital for prevention and de-colonization efforts.

The investigators noted that “it is known that community-associated MRSA frequently colonizes the gastrointestinal tract of infants and that broken skin can serve as a nidus for infection.” Those children with CA-MRSA skin infections had colonization in the rectum and perianal skin areas, meaning that further assessment of gastrointestinal colonization is highly needed.

Overall, the use of genomic sequencing to identify the unique USA300 clone of CA-MRSA spreading through the Orthodox Jewish community in Brooklyn identified not only an at-risk population, but a new strategy for identifying community outbreaks with methods typically used for hospital outbreak investigation.

Genomic surveillance is commonly used to identify health care outbreaks and identify a source, but its application for community infection surveillance and control has great potential. As this study has shown, the use of genomic surveillance can help uncover outbreak and pathogenic reservoirs that might be ignored or undetected.