A UCLA microbiology lab used whole-genome sequencing to trace a carbapenem-resistant Pseudomonas outbreak to a single ICU sink, revealing how biofilm and plumbing can silently harbor superbugs.
A routine culture from an ICU patient at UCLA Health sparked an investigation that ultimately uncovered a silent, domestic outbreak of a highly resistant strain of Pseudomonas aeruginosa. The discovery was led by the Molecular Microbiology and Pathogen Genomics Laboratory and highlights the critical role clinical laboratories play in outbreak detection, antimicrobial resistance surveillance, and environmental tracking.
The findings were recently published in the American Journal of Infection Control.
The initial isolate appeared typical: P. aeruginosa, a common hospital-associated pathogen. But further analysis revealed something more troubling, the presence of NDM-1 (New Delhi metallo-β-lactamase), an enzyme that breaks down carbapenems and other powerful beta-lactam antibiotics, rendering them ineffective.
“This was the first time we’d ever seen an NDM-1-producing Pseudomonas strain in our hospital—and in a patient with no international travel,” said Shangxin Yang, PhD, director of UCLA Health’s Molecular Microbiology and Pathogen Genomics Laboratory.
Shangxin Yang, PhD, director of UCLA Health’s Molecular Microbiology and Pathogen Genomics Laboratory noted, “While NDM-1 is prevalent in Asia, Europe and the Middle East, it remains rare in the United States. That’s when we knew this wasn’t imported. This was something domestic—and very concerning.” (Photo credit: UCLA)
Sporadic Cases, Elusive Source
Over the next 18 months, seven additional patients were identified with the same rare resistance pattern. The cases were sporadic—spread across time and units—and did not follow conventional outbreak patterns, complicating source identification.
In collaboration with UCLA Health’s infection prevention team, the lab launched a detailed investigation. Routine epidemiologic methods failed to identify commonalities between the cases. Shared equipment, staffing patterns, and care protocols were ruled out. With limited leads, the microbiology team turned to whole-genome sequencing (WGS).
Whole-Genome Sequencing Connects the Dots
WGS became the turning point. By sequencing all eight patient isolates and comparing them to environmental samples, Yang’s lab determined that seven of the eight clinical isolates and two environmental strains shared an almost identical genomic profile. Only one isolate, from a patient previously treated in Iran, was genetically distinct.
“Whole-genome sequencing gave us the clarity we needed,” said Yang. “It allowed us to move from hypothesis to high-resolution confirmation—pinpointing the genetic relatedness of these organisms with certainty.”
The team had uncovered a clonal outbreak of NDM-1-producing P. aeruginosa, likely stemming from a single environmental reservoir.
Unexpected Reservoir: An ICU Sink
During a third round of environmental testing, the lab isolated the same NDM-1-producing strain from a contaminated sink drain and P-trap in one ICU room. Notably, two of the eight patients had been admitted to that room more than a year apart.
The persistence of the organism was attributed to biofilm formation in the sink plumbing. Pseudomonas is known for forming robust biofilms that adhere to moist surfaces and resist standard disinfection methods.
“This wasn’t just about surface contamination,” said Yang. “This was a deeply embedded reservoir that conventional cleaning protocols couldn’t touch.”
Lab-Driven Response and Mitigation
Once the lab identified the environmental source, targeted interventions were put in place:
- Weekly disinfection of ICU sinks using Virasept, a biofilm-effective agent
- Plumbing replacement, including P-trap components known to harbor persistent biofilms
- Engineering modifications to faucet angles to reduce splash-back and droplet spread
- Expanded environmental surveillance to monitor other sinks for colonization
The lab continued to monitor the situation post-intervention, and no further cases of NDM-1-producing P. aeruginosa have been identified since the changes were implemented.
Lessons Learned
This case reinforces the value of whole-genome sequencing in resolving complex outbreaks, linking patient isolates to an environmental source that traditional methods missed. It highlights the need to include plumbing and other biofilm-prone areas in environmental sampling. Most importantly, it shows how microbiology labs through genomic, phenotypic, and molecular tools can lead outbreak investigations, especially when paired with strong cross-department collaboration.
“This is a clear example of the power of the clinical lab when genomic tools and environmental surveillance are used strategically,” said Yang. “Without WGS, this would have remained an unsolved mystery.”
—Janette Wider
