Trying to control the microbial population in settings such as hospitals may have unintended negative consequences. A new study reports that the microbiomes in such highly controlled environments are much less diverse but have a broader arsenal of resistance mechanisms than the microbiomes in less tightly controlled ones (Nat. Commun. 2019, DOI: 10.1038/s41467-019-08864-0). These trends suggest we need to rethink how we manage microbial diversity in hospitals to slow the spread of resistant bacteria.
Alexander Mahnert, a postdoctoral researcher at Graz University of Technology, and coworkers collected samples from surfaces in a variety of buildings. They sequenced bacterial DNA in the samples and used computational methods to reconstruct the genomes of individual microbial species present. The researchers found that more-controlled environments had just as many bacteria as less-controlled environments but fewer species of bacteria.
The cleaner an environment was, the more the microbial population tended toward gram-negative bacteria, the researchers found. Gram-negative bacteria have an outer cell membrane surrounding their cell wall. This extra barrier relative to gram-positive bacteria makes them harder to target with antimicrobial drugs.
The trend toward gram-negative bacteria in cleaner environments “might be related to the strong impact of human-associated microbes in cleaner environments,” says Mahnert, who is now at the Medical University of Graz. “While outdoor environments are rich in gram-positive bacteria, indoor environments show high proportions of gram-negative bacteria, which are very often host associated.”
The researchers analyzed the “resistomes,” to see what antimicrobial resistance mechanisms the various populations had. They found that the microbiomes in controlled environments were equipped with resistance mechanisms such as multidrug efflux pumps that work against a variety of drugs, whereas the microbes in unrestricted environments, such as private houses and open public buildings, had fewer resistance mechanisms that were more targeted at specific antimicrobial compounds.
“Greater diversity of resistance genes implies that these microbes were exposed to diverse antimicrobial substances and could also adapt more easily to such environments,” Mahnert says.
Jack A. Gilbert of the University of California San Diego and coworkers have previously observed similar trends. The new work, Gilbert says, “is a detailed analysis of the phenomenon of increased selection pressure towards gram-negative bacteria with increased antibiotic resistance.”
The work “provides a more in-depth look at the context of antibiotic resistance indoors than previous studies have allowed,” says Erica Marie Hartmann, an environmental engineer at Northwestern University who also studies microbial populations in indoor environments. “Because of the way the samples were pooled, I’m not sure this work yields direct recommendations for how to deal with antibiotic resistance. But it’s certainly an important step in that direction.”
Mahnert says he and his colleagues are working on ways to manipulate the microbiomes of buildings to increase diversity, which is inversely correlated with resistance. Similarly, Gilbert’s group is participating in an international collaboration to make building materials that are impregnated with bacterial spores.
“The time has come to think about ways to preserve microbial diversity in buildings, change microbial maintenance, and guarantee exposure to beneficial microbial communities,” Mahnert says.