Cost-Effective Sampling and Sequencing Workflow Identifies ICU Infection Hotspots

Intensive care units face persistent threats from hospital-acquired infections, increasingly driven by drug-resistant bacteria. Rapidly pinpointing environmental reservoirs and transmission hotspots remains a challenge for infection prevention teams and clinical laboratories. Cost and workflow demands can also limit routine sequencing-based surveillance. New findings demonstrate a simple, cost‑effective environmental sampling and sequencing approach that identifies high‑risk sites in real-world ICUs.

Queensland University of Technology (QUT) and collaborators evaluated an environmental surveillance method known as “plate sweeps” in a newly built eight‑bed intensive care unit (ICU) at St Vincent’s Private Hospital Toowoomba. The approach targets the diagnostic gap between routine visual audits and comprehensive genomic monitoring by systematically sampling the built environment. The study, published in Microbial Genomics, underscores how hospital–academic partnerships can operationalize laboratory methods to map transmission pathways within critical care.

Plate sweeps involve swabbing high‑touch hospital surfaces, cultivating the recovered bacteria on culture plates, then scraping the entire plate to extract DNA from the mixed sample for sequencing and organism identification. This cultivation‑plus‑sequencing workflow is designed to capture more bacterial diversity than selecting a single colony, while avoiding the high sequencing costs of more expansive genomic surveys. As described, the method emphasizes practicality for regular environmental microbiology programs.

Investigators sampled 78 locations across the ICU before and after the first patients were admitted, including communal areas such as reception counters, a laundry trolley, and door handles, as well as plumbing‑related sites including sinks, toilets, showers, and drains. After patient introduction, the ICU microbiome “changed completely,” with new species detected—among them Pseudomonas, Klebsiella, and Staphylococcus—and a significant increase in antimicrobial resistance genes. Plumbing emerged as the major source of bacteria, and shared bathrooms were identified as hotspots for ongoing transmission risk. According to the team, implementing this surveillance was cost‑effective and accurate enough for routine use to target intensified cleaning and infection control before outbreaks occur.

The project involved QUT, the University of Southern Queensland, the University of Queensland, and St Vincent’s Private Hospital Toowoomba. The hospital’s opening of its new ICU in November 2023 provided a natural experiment to evaluate how environmental microbiomes evolve with normal clinical activity.

“Hospitals need regular and rigorous surveillance of their environmental microbiome and pathogen transmission, particularly in ICUs where patients are more vulnerable, to help prevent these dangerous infections with improved infection control and cleaning processes,” said Professor Kirsten Spann, School of Biomedical Sciences, Queensland University of Technology.

“Given that it was a new ICU, we thought it was a unique opportunity to have QUT study what happens with the inevitable build-up of environmental microbiomes and pathogens. We know that around the world—and we're no different—that, no matter how diligent a hospital is with its cleaning, ICUs are seeing more infectious disease-causing bacteria which are drug-resistant and can be serious for patients,” said Jeremy Fernando, Director of Intensive Care at St Vincent's Private Hospital Toowoomba. "Ideally, this study will add to the body of knowledge around how ICUs could change their processes and can help to inform how they are managed."

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Queensland University of Technology