Today in “where’s the pathogen?” Can you find Burkholderia on 500 acres with 50 samples?

Well, this story is a wee bit disturbing: Deadly bacteria release sparks concern at Louisiana lab. Summary from USA Today:

Officials are investigating how a deadly type of bacteria was released from a high-security laboratory at the Tulane National Primate Center in Louisiana. Officials say there is no risk to the public.

Many parts of the story are disconcerting.  But here I would like to focus on the details of how the EPA and others are trying to detect the pathogen – Burkholderia pseudomallei – in specific locations.

Key details:

  • Tulane was working on Burkholderia pseudomallei in a secure lab.
  • at least four monkey-like rhesus macaques – that were never used in the experiments and were kept in large outdoor cages in another part of the 500-acre facility – have been exposed to the bacteria, initial tests have found” (quote from USA Today story)
  • in other words – these macaques should NOT HAVE ENCOUNTERED THIS BUG BUT DID
  • one person has show evidence for having been exposed to this pathogen though the source is not known.

Health officials, at least some of them, are saying things like “There has never been a public health threat,” Lackner said.”

Yet, as far as I can tell from the story – the EPA, CDC and Tulane University do not really know how the macaques got infected by this pathogen (though they have some ideas).

To back up the claims of a lack of a health threat the officials are citing:

  • “Tests of 39 soil and 13 water samples from the center’s grounds have not detected the presence of the bacteria.”

Umm.  Well, this is a 500 acre facility.  And they have no idea how the infectious agent was transmitted to the macaques (or if it was transmitted to the person).  So how can 39 soil and 12 water sample tests from such a large facility with no clear model for the mode of transmission, be used as evidence of “no health threat“?  I don’t  think it can.  Mind you, I think it is incredibly unlikely for there to be any health threat at this time.  But for the officials to think that these tests are much help, is disconcerting.

I note – the USA Today reporter also picks up on this noting:

However, it appears that far too few soil tests were taken to draw any conclusions. Studies have found that that Burkholderia pseudomallei is difficult to detect in contaminated soil without taking a large number of samples because the bacteria form colonies that are like invisible ant hills. They also aren’t evenly distributed across an area. So unless a shovel is put in the right spot, the test will yield a false-negative result.

(Kudos by the way to the reporter Alison Young for her story).

Read the story for more details.  Anyway – this is a good case study in how one needs to really think about sampling strategies carefully when trying to study microbial ecology and dispersal …


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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.