NICU MRSA Outbreak: Whole Genome Sequencing Guides Infection Prevention Investigation

A cluster of hospital-acquired methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections in a Level IV neonatal intensive care unit (NICU) prompted an investigation that identified respiratory colonization and multiple transmission patterns. Following targeted infection prevention measures, no additional hospital-acquired MRSA bacteremias or related respiratory clusters occurred for at least 6 months, according to a poster presented at IDWeek in Washington, DC, held from October 21 to 24, 2026.

The poster, “The Fast and the Curious: Genomic Investigation of MRSA in a level IV NICU at an Academic Medical Center,” describes how investigators combined clinical microbiology findings with whole genome sequencing (WGS). The investigation identified genetically related isolates consistent with horizontal transmission, as well as unrelated isolates indicating independent introductions.

“Targeted infection prevention measures terminated the outbreak, highlighting the importance of respiratory-focused strategies and molecular epidemiology,” the researchers wrote.

Bloodstream Infections Prompt an Investigation

Between August 6 and 22, 2025, investigators identified 3 hospital-acquired MRSA bacteremias in a Level IV NICU. The infections occurred within a short interval and prompted a multidisciplinary outbreak investigation. All affected patients had preceding or concurrent MRSA-positive respiratory cultures, suggesting a respiratory source.

The poster identifies MRSA as a major cause of health care-associated infections in NICUs, where vulnerable patients and frequent respiratory interventions increase transmission risk. In this investigation, the respiratory culture findings became an important part of understanding the bloodstream infection cluster.

Investigators reviewed clinical and surveillance microbiology data to identify MRSA respiratory and blood isolates from preceding months. They also evaluated clustering in time and location across 2 NICUs. Point prevalence screening identified colonized patients, while available isolates underwent WGS to assess genetic relatedness and transmission.

Samples were sent as the outbreak developed. The team also reviewed respiratory care workflows and other infection prevention practices. That review included hand hygiene and equipment cleaning, along with visitor policies.

Respiratory Cultures Help Define the Cluster

The retrospective review identified 13 neonates with positive respiratory cultures. Of these, 8 were related to the same MRSA epidemiological cluster. Cases demonstrated clustering in time and location, suggesting horizontal transmission.

Those findings connected the initial bloodstream infections with a broader group of patients identified through respiratory cultures. The investigation therefore extended beyond the 3 bacteremias that first prompted concern, incorporating earlier microbiology results and screening information to characterize the cluster.

The poster’s isolate-source figure shows 13 sputum isolates and 4 blood isolates. It also includes 1 urine isolate, 1 entry labeled “object”-ETT, and 1 nares PCR entry. The accompanying timeline presents the distribution of first positive MRSA cultures in the NICU.

Sequencing Reveals More Than 1 Pattern

WGS demonstrated several distinct patterns among the available isolates. Four were genetically related, consistent with horizontal transmission. Two formed a second cluster, while 2 were unrelated, indicating independent introductions.

The sequencing findings distinguished related isolates from those representing separate introductions. This added a genetic assessment to the epidemiological investigation, which had already identified cases clustered in time and location. The results did not indicate that every isolate belonged to a single transmission cluster.

A fourth MRSA bloodstream infection was identified in October and linked to the original cluster. The poster’s genetic relatedness figure illustrates the relationships among NICU isolates and was adapted from Mayo Clinic WGS results.

Targeted Prevention Measures Followed

The response included reinforcement of respiratory infection prevention and hand hygiene. Enhanced equipment disinfection and strict visitor hygiene were also implemented. These interventions addressed practices examined during the outbreak investigation.

Following implementation, the researchers reported no additional hospital-acquired MRSA bacteremias or related respiratory clusters for at least 6 months. The reported outcome encompassed both bloodstream infections and related respiratory clustering, reflecting the respiratory findings that had informed the investigation.

“A cluster of hospital-acquired MRSA bacteremias in a Level IV NICU was linked to respiratory colonization and transmission,” the researchers concluded. “WGS demonstrated horizontal transmission and new introductions.”

Their findings emphasize the role of respiratory-focused prevention measures and molecular epidemiology in investigating and responding to this NICU outbreak.

Poster authors: Priscila Fiallo, MD; Ediza Gonzalez, MD, CIC; and Ioana Chirca, MD, MSHQS.

Affiliations: Division of Infectious Diseases and Infection Prevention, Wellstar-MCG/Augusta University, Augusta, Georgia, USA.