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DNA Sequencing: The Next Generation

​By J. David Miller

I have a bias, but I think that one of the great sessions at AIHce EXP 2017 was “Microbiomes of the Built Environment.” Typically, settled dust contains outdoor air particulate pollution, soil, a lot of fibers of various fabrics, and a surprising amount of skin scales. Aside from that, there are thousands of species of bacteria and fungi. Particularly in the last decade, new tools have been developed that allow large regions of DNA to be extracted from dust collected on surfaces.

Professor James Scott of the University of Toronto opened the session with a stellar explanation of the technology. The “old” methods (PCR) looked for the barcodes unique to a modest number of organisms with available barcodes in the sample. The next-generation methods detect everything with DNA present in the sample. Large regions of the extracted DNA are sequenced, which can be recognized in the sequence database. DNA in house dust includes everything from dogs to the fungi that colonize building materials to a vast array of bacteria to occupants. These technologies used to be expensive, but now they are inexpensive.

Rachel Adams, PhD, a project scientist at the University of California Berkeley Indoor Microbial Ecology Research Consortium, demonstrated how these methods can be used to detect changes in the indoor air bacterial and fungal bioburdens with the multiple unique signatures of the bacteria from occupants and the fungi introduced on clothes from home. In one case, she was able to demonstrate that someone visiting the home had introduced spores of a generally uncommon fungus from their particular environment. Using size-selective samplers, Adams showed that the fungi in outdoor air were in larger particle sizes and the numerous species detected indoors were present in smaller particle sizes. While the phenomenon is now well known, the new methods provided high-resolution data on the species present in each size fraction.

Continuing the fungal theme, Lan Chi Nguyen-Weekes of InAir Environmental illuminated situations where fungal contamination is really hard to detect until it is too late—for example, contamination in inaccessible HVAC ducts. The use of the next-generation methods will allow quicker resolution of these difficult situations.

William Rhoads, PhD, of Virginia Tech, brought the next-generation sequencing technology to the world of the bacteria in premise piping. Reducing water use in buildings has had a large effect on the resident community of bacteria present. Lower water use generally means the water gets warmer, the disinfection residuals decay, and the oxygen concentrations decrease. In turn, bacteria that cause corrosion thrive, typically changing the water chemistry (for example, releasing lead and copper). Rhoads has been a key member of the Virginia Tech team leading the investigation of lead poisoning in Flint, Mich., where changing the water chemistry (and not adding corrosion inhibitors) increased corrosion, releasing lead from the service lines. As shown by blood lead concentrations, this lead ended up in the children of Flint. Much of the press has been about lead, the change in water chemistry, and resulting changes in the resident microbiome, which led to a significant increase in Legionella cases. 

Finally, Erica Stewart of Kaiser Permanente introduced the potential of using “good” bacteria as an alternative to disinfectants. In hospitals, chemical disinfectants are associated with a large burden of workplace asthma in essentially all occupational groups. This idea has emerged from next-generation studies of the populations of bacterial pathogens in hospitals. These have shown just how rapidly pathogens colonize the surfaces in hospital rooms with each patient. The use of microbial biocides is under trial in a number of locations in Europe, and the early results demonstrate effectiveness. 

J. David Miller, PhD, FAIHA, is a professor in the Department of Chemistry at Carleton University in Ottawa, Ont. He was a presenter at “Microbiomes of the Built Environment” at AIHce 2017.​​


careful about unintended consequences of "good bacteria"

The last presentation Dr. Miller describes suggests an idea popular with a lot of research microbial ecologist. think what a boon it would be for funding their work if it gains some traction!

But biology is complex and the battle for survival of the fittest will result in mutations and evolution that are not easy to predict in advance.

The hospital environment is full of susceptible humans, so experimenting there is ill-advised.

Viruses are not adequately studied yet by microbial ecologist because their methods are not aimed at them. But viruses use bacteria as part of their own evolution and the outcomes are unpredictable. Experience to date is that evolution will go in the direction of antibiotic resistance, but it might also go toward sterilizing chemical resistance. Once colonized, a hospital could be beyond repair given our limited knowledge and control over the microbes that inhabit them.
 on 7/11/2017 3:23 PM by Hal Levin | Flag comment for inappropriate content

my thought

Hello Hal

I would say that the specific risk you emphasize is unlikely.

That said, Ms Stewart  explained what it would take for a hospital to consider this approach to augment their disinfection program. The first thing is to wait for actual data which are being generated in Europe and then a lot of legal questions would need to be addressed. 

Aside from finding better ways to control infections and manage the development of resistance to disinfection agents, an important issue to factor in is the really large burden of occupational disease resulting from current disinfection methods.
 on 7/12/2017 9:27 AM by J. David Miller | Flag comment for inappropriate content

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