City microbes survive on disinfectants, study finds

New research shows that the microbes in our cities are evolving to resist the cleaners we use to kill them. It also identifies new strains living in Hong Kong that were previously only found in Antarctic desert soil.

After the recent pandemic, the use of disinfectants has increased, but are efforts to create sterile urban environments backfiring?

A study published in the journal Microbiota identified new strains of microbes that have adapted to use the limited resources available in cities and showed that our daily behavior changes the composition of microorganisms in indoor environments.

“Built environments provide distinct conditions that distinguish them from natural and artificial habitats,” says Dr. Xinzhao Tong, assistant professor at Xi’an Jiaotong-Liverpool University (XJTLU), China, and lead author of the study. .

“Areas with many buildings are low in traditional nutrients and essential resources that microbes need to survive, so these built environments have a unique microbiome.

“Our use of cleaning products and other manufactured products creates a unique environment that places selective pressures on microbes, to which they must adapt or be eliminated, but the mechanisms by which microbes adapt and survive in built environments are poorly understood,” says Dr Tong. .

The townspeople

Researchers collected 738 samples from various built environments, including subways, residences, public facilities, piers and human skin in Hong Kong. They then used metagenomic sequencing to analyze the genomic content of microbes and understand how they adapted to harsh urban conditions.

The team identified 363 previously unidentified microbial strains that live on the skin and in the environment. The genome of some of these strains contained genes for metabolizing manufactured goods found in cities and using them as sources of carbon and energy. This includes the discovery of a strain of the phylum Candidatus Eremiobacterota, previously reported only in Antarctic desert soil.

Dr Tong says: “The genome of this new strain of Eremiobacterota allows it to metabolize ammonium ions found in cleaning products. The strain also has genes for alcohol and aldehyde dehydrogenases to break down residual alcohol found in common disinfectants.

“Microbes with enhanced abilities to use limited resources and tolerate manufactured products, such as disinfectants and metals, outcompete non-resistant strains, thereby improving their survival and even evolution within built environments. They could therefore present health risks if they are pathogenic.

The team identified 11 unique and uncharacterized strains of Micrococcus luteus, generally non-pathogenic but capable of causing opportunistic infections in immunocompromised individuals.

“The question of their adaptation to our behavior becomes particularly critical in clinical settings where hospitals serve as hotspots for various pathogens causing hospital-acquired infections (HAIs). HAIs pose a significant threat, particularly in healthcare units intensive care where mortality rates can reach 30%,” explains Dr Tong.

A balancing act

The researchers also characterized two new strains of Patescibacteria, known as “nanobacteria,” because they have tiny genomes that don’t contain many of the genes needed to produce their own resources.

Dr Tong says: “Some strains of Patescibacteria are considered parasitic because they rely on bacterial hosts to provide their nutrients. However, in this study, researchers found that one of the nanobacteria strains, recovered from human skin, contains genes for biosynthesis. carotenoids and ubiquinone.

“These antioxidant compounds are vital to humans, and we typically acquire them, particularly carotenoids, through our diet, suggesting a possible mutualistic relationship between the bacteria and us as hosts.”

This improved understanding of microbial metabolic functions in built environments helps develop strategies to create a healthy indoor ecosystem of microbes that we can live with.

The team is currently studying the transmission and evolution of resistance of pathogenic microbes in intensive care units exposed to strict and extensive disinfection practices. They hope to improve infection control practices and increase the safety of clinical environments for healthcare workers and patients.