Tuesday, August 12, 2008

About that contaminant ...

... you know, the Bacillus subtilis contaminant that was found alongside the Bacillus anthracis isolate which was used by the Anthrax Killer?

As other people have noted, B. anthracis is a very clonal organism. What this means is that individual strains are highly similar to each other, there is not a whole lot of diversity. On the other hand, B. subtilis has a high degree of heterogeneity within its genome. What does this mean? It means that B. subtilis is much easier to type (or differentiate) from other strains of B. subtilis.

Yeah, but B. subtilis was a contaminant. What's the big deal? Well, the devil is often in the details. Bruce Ivins worked on B. subtilis. In 2003, Ivins published a paper looking at expression of B. anthracis genes in B. subtilis, and how that effected immune responses in guinea pigs. The link to the paper is above, free of charge as all government publications are considered public domain.

Ok, so what? Well ... since B. subtilis (Bs) has a higher degree of heterogeneity within its genome, it is easier to type. For example: Bs in Lab B, if it didn't receive the strain from Lab A, will most likely hold more differences than Bs in Lab A ... when compared to B. anthracis (Ba) isolates from those two labs. What this means is ... if you have isolates of Ba AND Bs in Lab A, and another set of isolates of Ba and Bs in Lab B, it's easier to type the Bs isolates.

Make sense? So essentially, the FBI probably wasn't as concerned with the Ba in the letters as we might suspect. A goodly portion of the investigation could very well have been focused on the Bs contaminant found in some of the letters. Then, taking multiple Bs isolates from around the world, they probably typed those strains (which would be much easier to do than typing Ba isolates as the Bs isolates have more differences in their genome) to see if Ivins' Bs strain matched the one in the envelopes. I'm not sure if the results have been posted, but I imagine it did. Of course, this probably raises a lot of issues ... like whether or not he gave that Bs strain to anyone ... but it might shed a little more detail on the scientific aspects of this case.


microbiologist xx said...

Thanks for alerting me to your post!
I agree. Knowing the Bs contaminant could provide another link to Ivins' lab...or not. Has any information been posted on the Bs strain?

Tom said...

Nothing has been posted as far as I know. However I wouldn't be surprised if I know who designed the typing test if the FBI did request one.

Philip H. said...

very interesting - would you call this the whorl within the finger print?

Anonymous said...

I haven't seen the subtilis inclusion confirmed; it's not mentioned in this ScienceNOW article, for example. What's your source for that?

Tom said...

Phil, it very well could be. It's not getting much play, and I don't think the FBI will ever truly reveal their entire hand if they don't have to ... and now with Ivins death, they don't.

Tara, back when I was doing my postdoc I was introduced to some individuals from the FBI through a collaborator. They were meeting with that collaborator who, like me at the time, was involved in designing subtyping tests. We never spoke about exactly what they were doing though. Anyways, a few days back, when the entire Ivins case came to light, I wondered if that collaborator had any involvement in the case. Turns out they did, but even they don't know the extent of their final contribution (test development and probability work) ... and their contribution was NOT with Ba.