Microbiome: In the pipeline

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  • Published: Mar 15, 2016
  • Author: David Bradley
  • Channels: Chemometrics & Informatics
thumbnail image: Microbiome: In the pipeline

Hospital showers

Georgia Tech Doctoral Student Maria Juliana Soto-Girón and School of Civil and Environmental Engineering Professor Kostas Konstantinidis are shown with images of bacteria. Research done with scientists from the U.S. Environmental Protection Agency documented bacteria in shower hoses taken from hospital patient rooms.

New metagenomics techniques have revealed the telltale signs of potentially harmful bacteria growing in pipework in a hospital shower facility, according to work published in the journal Applied and Environmental Microbiology. The approach allows strains to be detected that would be invisible to conventional culture-based assays.

The human microbiome is a term that encompasses the diverse "flora and fauna" that live within us and our skin. The impact on human health of this biodiversity is only now being unravelled. Important clues about diseases that pivot on the rise and fall of different microbial species, in our guts, on our teeth and skin and in every nook and cranny of our bodies, are now beginning to emerge as considerable effort is focused on the role of these microbes. However, a new and intriguing perspective is also emerging that discusses the microbiome of the built environment too. One particular niche that is of particular interest is the community of putatively pathogenic microbes that might dwell within water supply pipes.

Researchers from the US Environmental Protection Agency (EPA) and the Georgia Institute of Technology have investigated the microbiome that exists as bacterial biofilm communities within the shower hoses of a major hospital. What they cannot yet say is whether or not these microbes pose any threat to patients or staff at the hospital. The work documented bacteria and related genes. Some of those genes are known to have pathogenic characteristics, as well as resistance to antibiotics so the researchers urgently need to learn more to calculate whether there is a problem to address.

A question of culture

The team cultured bacteria from 40 shower hoses removed from individual hospital rooms by EPA researchers. They extracted nucleic acid from five of the shower hoses and processed using next-generation sequencing technology. The sequencing data were then sent to Georgia Tech, where Maria Juliana Soto-Girón matched the sequences against known bacteria and highlighted genes that have known effects, such as virulence and antibiotic resistance.

The data revealed the presence of previously unknown "mycobacterium-like" strains that are apparently related to Mycobacterium rhodesiae and M. tusciae. The conventional culture-based methods identified organisms associated with Proteobacteria, among them Sphingomonas, Blastomonas and Porphyrobacter, as the most abundant. There were genes harboured in these shower hose ecosystems associated with tolerance to some disinfectants as well as other genes associated with resistance to drugs such as beta-lactam, aminoglycoside, amphenicol and quinolone antibiotics. When the data were compared to those from the freshwater Lake Lanier, a natural ecosystem studied by the team those genes were not seen in the same abundance, which they suggest warrants a closer inspection of water supply pipes.

Genetic acquisition

EPA microbial ecologist Jorge Santo Domingo points out that well-known pathogens were not seen, just worrying genes in other strains. "If they have a core of genes, they may be receptive to acquiring other genes that will render these microorganisms more problematic," he says. "These organisms are very good at living in difficult environmental conditions with limited carbon sources, so fighting them could become a challenging proposition. We don't know if they constitute a problem, but we certainly want to find out." One implication is that water disinfection in hospitals is not sufficiently strong. The sequencing data and bioinformatics analyses will help identify genetic markers that could be used to monitor these genes and determine their public health relevance and the impact of changing the disinfectant regime.

"Metagenomics gives you a more complete and quantitative picture of what microorganisms are there and how abundant they are," explains Kostas Konstantinidis who is associate professor in the School of Civil and Environmental Engineering at Georgia Tech. "This shows that traditional culture methods are limited in what they can detect, and that they can often provide a biased look at what is there." He adds that, "We can say confidently that if pathogens are in there, they are not there in very high abundance, but the organisms that we detected as abundant in these biofilms appear to have characteristics that could be of interest because they are related to some bacteria that are opportunistic pathogens that could pose a threat, especially to immunocompromised hospital patients."

Related Links

Appl Environ Microbiol 2016, online: "Characterization of biofilms developing on hospital shower hoses and implications for nosocomial infections"

Article by David Bradley

The views represented in this article are solely those of the author and do not necessarily represent those of John Wiley and Sons, Ltd.

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