Moselio Schaechter

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January 12, 2012

That Scary Restroom Microbiota

by Elio Schaechter and Joshua Fierer


Newspapers and other media are reporting with regular frequency that restrooms, ATM machine pads, money bills, and other sites carry many different microbes upon their surfaces including potentially pathogenic bacteria and viruses. Headlines call attention to such scary-sounding news and alarm the general public. We can expect that this practice will engender a widespread concern of the public for their safety. The outcry will encourage the implementation of unreliable, unnecessary, and potentially counterproductive “protective” measures. People may, for example, resort to using soaps with bactericidal compounds that have the potential to alter the generally protective normal flora. Inappropriate or non-essential use of bactericides may well accelerate the development and spread of resistance to microbicides and antibiotics within the microbial community. Resistance capabilities, including the upregulation of efflux pumps, can evolve particularly rapidly, and these same mechanisms may also increase resistance to antibiotics. For a reference to this topic, click here.

Let us suppose, as implied by these reports, that we do often encounter potential pathogens on ‘fomites,’ that is, inanimate objects. This is nothing new.

We have known for over one hundred years that we live in a buggy world, surrounded by actual and potential pathogens, and that we often carry them within us. How often do we get sick from such encounters? Only the most immunosuppressed people must live in an aseptic “bubble” to avoid contact with all environmental microbes. With the exception of some epidemic-type diseases such as the common cold and influenza, most of us living in hygiene-blessed environments lead a life relatively free of externally-acquired infectious disease. In micro classes for medical students, we used to quip that the only people who get sexually transmitted diseases from toilet seats are members of the clergy! The exceptions to such relatively peaceful coexistence are important, viz. the spread of MRSA or Clostridium difficile in hospitals and, of recent, in the community, but these are specific concerns requiring their own focus when epidemiological studies indicate there is a problem.

The studies underpinning these scary headlines commonly involve analysis and/or amplification of the DNA that can be swabbed from surfaces. This methodology does not assess the viability of the organisms nor do these studies necessarily estimate the amount of specific DNA present. It is obvious that not knowing if the agents are alive or dead or if they’re present in amounts that could initiate an infection impacts on conclusions about the danger they may pose. In other words, there is no basis for linking these findings to the realities of public health.

Of particular concern to us, the authors of these scientific articles do not, in general, acknowledge their limitations. Instead, we read such statements as: More generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching of surfaces. This research does provide potentially useful information by listing the vast number of bacterial species that are found in the human environment, many of human origin. However, this merely opens possibilities about their relevance to human health, and, broadly speaking, these facts are far from novel. Do the justifiable conclusions from these studies warrant alarming the public? We think not. We wish that the authors clearly pointed out the limitations of their studies.


Joshua Fierer is Chief of Infectious Diseases at the VA San Diego Health Care System and Professor of Medicine and Pathology, University of California at San Diego.


While I appreciate the comments of the older microbiologists and realize full well that if "you can't grow em, you don't know em". I am happy to embrace the "new" microbiology, for one thing, in teaching a course for non-science majors, it is wonderful to get them excited about the way bacteria interact with us and vice versa.

I wonder: Do the culture-based studies point out their limitations? If you can grow it, it is necessarily important? If you can't grow it (don't know the growth conditions or it died in transit) is it necessarily unimportant?

If the molecular folks still have to point out limitations with every study they publish, even though these are well known by now, I think the culture-based studies should do the same. For instance, they have been culturing Pasteurella out of sheep's noses for decades and still can't decide whether they kill bighorn sheep. Meanwhile, molecular evidence has surfaced that suggests many other microbes are involved. Completely ignored of course.

And in the indoors, should we just stop studying it because some people get freaked out? Is that the fault of the scientists? Should me not learn what is there, what has been there outside of what we can grow? Can we not be interested in how things move around indoors where we spend 90% of our time?

The real nonsense of this blog is the statement that we should ONLY care when an outbreak of something we understand happens (e.g. Clostridium). Well what about the 100,000 deaths per year due to infections acquired in hospital? These are mostly opportunistic. Where did they come from? How can we stop them? Are surfaces involved? Do the bugs come on clothes from the restroom? Do we know this already? Most of the time, these agents are not identified.

DNA work is a wonderful compliment to what is known already in microbiology. It has expanded our understanding 1000-fold over culture methods in the natural world. It has the potential to do the same in the built environment. Please keep this in mind.

Elio replies:

Let’s first agree about the obvious. When it comes to environmental samples, plate counts only detect the bacteria that can be readily cultivated. This widely recognized and is called the “Great Plate Count Anomaly.” Thus, plate counts severely underestimate the number of species in a sample. Plate counts reveal the presence of only some of the living bacteria in the sample and usually tell of their abundance.

On the other hand, metagenomic analysis of a sample tells us what DNA is present and potentially which genes are in attendance. This is indeed valuable information, as it suggests the biological potential in a sample. It is far more inclusive but, generally speaking, is only suggestive. Unless specialized techniques are used, it does not provide quantitative information, nor does it distinguished between live and dead organisms. Relevant to the paper in question is that many human-associated bacteria die rapidly on drying, although the DNA remains in their carcasses.

It would seem obvious that both approaches should be used in concert, being that they yield different kinds of information. Alas, this is seldom done, as many workers favor one of these approaches over the other. They ought to complement each other. To use an imperfect analogy, think of a large library. A metagenomicist may know the titles of the books, usually with a small amount of information about each, the “cultivator” will have read a few of them.

I suspect that Scott may agree with these general points. He says, with plenty of reason, that everyone should be mindful of the limitations of their studies. It’s true that the plate anomaly is seldom spelled out, but I believe that most people are more aware of the limitations of cultivation techniques than of metagenomics.

Finally! I just recieved an email from a colleague with a link pointing me to "11 things germier than toilet seats" - sigh. I never understood if researchers had any control of the media skewing the importance of their findings. I always felt statements should have been made indicating the context in which the data is important to help temper public panic.

I will use this article in my micro class and will also use the analogy.

Is there an email list of hospital administrators to whom this could be mailed?

Curiosity lead me to look at the Minority Opinion in the provided link and it's profound; a one-word position!

Thank you.

This is a great article; I am posting in on the bulletin board outside my office/lab. Sigh. Pasteur introduced the term "germ" meaning "a bit of life," but the word has come to mean something malign to most people.

I tell folks that pathogenic bacteria are like juvenile delinquents: small in overall number, but they get ALL the press, and are used to scare people.

Elio replies: Great analogy. I'll use it too.

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