Cryptic Escherichia Lurk Among Us!

When I’m not fighting the forces of evil or calling idiots who desperately need my help fucking morons, I’m doing various genomics-related things. One of the things I’m involved with is a project to sequence a bunch of commensal (not associated with disease) E. coli. When most people think of the genus Escherichia, they think of a single species, E. coli. But a recent paper describes five new lineages (clades) of Escherichia that, while found mostly in the environment, are also found in humans (and, yes, we’re sequencing ten of these). Here’s how they’re related to each other:
escherichia phylogeny
UPMGA dendrogram based on the proportion of nucleotide variation at 22 genes

Granted, CI, CII, CIII, CIV, and CV (“C” stands for clade) aren’t the most creative names, but that hides some very interesting biology. With the exception of CIII, these strains are phenotypically indistinguishable from E. coli. If a clinical microbiology lab were to test these, they wouldn’t be able to tell them apart from ‘real’ E. coli. This is surprising since E. coli and its closest relative, CI, diverged between 20-31 million years ago. In fact, the lack of phenotypic diversity is all the more remarkable when we consider that some of these lineages are ten of millions years old:
It also appears that the age of a clade has little to do with its propensity to possess virulence factors (genes implicated in human disease):
While the ‘non-coliEscherichia are disproportionately found in the environment–some are capable of forming lake blooms in pristine habitats, as if they were aquatic bacteria, others live in freshwater beach sands (more about that in a bit)–they do occur in mammals, including humans. We don’t know if they’re implicated in disease: to paraphrase a former Secretary of Defense, the absence of evidence is not evidence of absence (and if you don’t win the first one, you can’t win them all!). But one area where they can cause a problem is water quality monitoring.
If you’ve ever read about a beach closing, you might have heard of “fecal coliform” levels. Water safety officials use the amount of bacteria, including E. coli, to determine if, well, we’re drinking our own shit (that would be a bad thing). However, we might be overestimating contamination, since the tests don’t distinguish between these environmental Escherichia and E. coli (which definitely comes from animal poop).
Still, studying these non-coli Escherichia should tell us a lot about how E. coli survives in other mammals and outside of animals.
Good thing someone thought of sequencing them….
Cited article: Walk, S.T., E.W. Alm, D.M. Gordon, J.L. Ram, G.A. Toranzos, J.M. Tiedje, T.S. Whittam. 2009. Cryptic lineages of the genus Escherichia. Appl Environ Microbiol. 75: 6534-44.

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2 Responses to Cryptic Escherichia Lurk Among Us!

  1. BaldApe says:

    When I took microbiology (many years ago- there were only two kingdoms then) I got irritated with the professor when he used a pathogenic organism as an example of cilliated protists. I went up to him after the lecture and called him on it.
    His reply was that he had to try to keep the pre-meds’ attention. He agreed with me that free living organisms are often much cooler than those that cause disease.
    Anyway, this is way cool. Such lack of phenotypic change in a prokaryotic lineage over such a long time is mind boggling.

  2. llewelly says:

    Since you live in Massachusetts, I thought your readers might appreciate some info about the recent flooding in that area. I will grant it has nothing to do with the topic … except that flooding often leads to water contamination. Sometimes with E. coli.

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