Healthcare crises like the ongoing COVID-19 pandemic are a reminder of just how easily infections can spread. Given that hospital environments are a central battleground for the rising threat of antibiotic resistance, characterizing the pathogens present in hospitals can provide crucial information for managing outbreaks.
To survey microbes in hospital environments, they are first isolated and cultured before the functional and genetic characteristics of individual strains can be identified. However, culturing is laborious, prone to isolation bias, and ineffective for isolating a large proportion of pathogens.
In collaboration with local and international partners, a Singapore-based research team turned to metagenomics, a scalable, high-throughput method that can be used to profile the overall community structure and characteristics of microbes, without the need for isolation.
“A large baseline survey such as the one conducted in this study provides vital information to hospitals for infection control, by highlighting high-risk areas and the opportunity to tailor cleaning practices,” said study corresponding author Niranjan Nagarajan, Associate Director and Senior Group Leader at A*STAR’s Genome Institute of Singapore (GIS).
Over 1.5 years, the researchers took swab samples from 179 sites within Tan Tock Seng Hospital, a major tertiary-care hospital in Singapore. By combining metagenomics with culturing in the presence of various antibiotics, they were able to enrich for antibiotic-resistant pathogens present at low levels and ultimately produce a database of genetic elements related to antibiotic resistance found in hospital environments.
“Our findings suggest that hospital environments harbor distinct microbial communities, such as biofilm-forming and human-skin-associated bacteria, which persist despite extensive cleaning, and appear to be enriched for multi-antibiotic resistance,” said Nagarajan.
Phylogenetic analysis and comparisons with samples taken from patients more than eight years prior revealed just how persistent some microbial strains can be despite extensive cleaning. It highlights the possible existence of stable reservoirs in the hospital, such as plumbing, drainage and air-conditioning systems, which are not eliminated by standard cleaning protocols.
These reservoirs of microbiome diversity can be the origin of new opportunistic infections and serve as fertile ground for the evolution of multidrug-resistant superbugs, Nagarajan noted. “It raises a plausible concern that aggressive cleaning measures may be selecting for them, and suggests that alternative avenues to ‘rebalance’ environmental microflora with other species could be worth exploring.”
The methods adopted in this study may also be useful for understanding how RNA viruses like SARS-CoV-2 can persist in hospital environments, Nagarajan suggested. “With the ongoing COVID-19 outbreak, it would be both interesting and relevant to utilize the technology and approach developed in this study to understand the distribution and persistence of SARS-CoV-2 in hospital environments.”
The A*STAR-affiliated researchers contributing to this research are from the Genome Institute of Singapore (GIS).