The Anthrax genome was sequenced in 2003

[Muttocracy]

Why haven't any reporters googled anthrax genome. Full story below, bold is my emphasis. The different strains could have some variation, but this is not a huge genome, and the basic construction of it has been known for years. A particular strain could have a particular plasmid, but given how quickly and easily plasmids are transferred, can you trust them to positively match strains in a criminal case?


http://www.sciam.com/article.cfm?id=anthrax-genome-spills-its
May 1, 2003
Anthrax Genome Spills Its Deadly Secrets

Mutations in just a few genes can turn a benign dirt bacteria into the deadly form of anthrax that was used to kill five people in the fall of 2001, researchers report. Scientists compared the deadly pathogen's genetic makeup with those of its two closest, and less dangerous, relatives. The findings, published today in the journal Nature, should help elucidate how virulence evolved and help researchers mount a better defense against the potential bioterror agent.

Previous research yielded maps of large portions of B. anthracis's genome. In particular, scientists knew that the main differences between B. anthracis and its harmless soil bacteria cousins came from its two plasmids, which are small circles of DNA that lie outside of the chromosome. In B. anthracis, these plasmids (known as pXO1 and pXO2) carry genes that account for much of its toxicity to animals and humans. Now Tim Read of the Institute for Genomic Research (TIGR) and his colleagues have analyzed the five million DNA bases that comprise the entire chromosome of B. anthracis. They also compared the results with the genomes of B. cereus, which can cause food poisoning, and B. thuringiensis, which is employed as a pesticide. The team found only 150 significant differences among the more than 5,000 genes that comprise each of three genomes, including several key changes that could contribute to B. anthracis's harmfulness. Read notes that B. anthracis's virulence "may have come mainly from horizontal gene exchanges, more so than by mutations within the genome."

A second comparison of the B. anthracis genome with that of B. cereus, carried out by Natalia Ivanova of Integrated Genomics and her colleagues, appears in the same issue of Nature. The findings hint that the common ancestor shared by the bacteria favored a carnivorous diet and may have been a parasite or dined on dead flesh. Because the genomes of all three species are so similar, the researchers posit that the ability to cause disease depends mainly on which genes are turned on in each organism. "Deciphering the anthrax genome is important to a wide range of biomedical and biodefense research," Claire M. Fraser of TIGR notes. "The genome sequence will benefit research projects to find targets for new drugs and vaccines as well as to improve anthrax detection and diagnosis."

[Muttocracy]

1. collected more sources: NIH press release

http://www.nih.gov/news/pr/apr2003/niaid-30.htm

The complete genetic blueprint of Bacillus anthracis — the microbe that gained notoriety during the 2001 anthrax mail attacks — is now known, researchers announced today. A formidable bioterrorist threat and the cause of potentially fatal inhalational anthrax, B. anthracis differs very little from the common soil bacterium that is its near relative, the scientists discovered. Those genetic differences are enough to give B. anthracis its disease-causing properties and may also give scientists valuable clues to its vulnerabilities.

The team of researchers supported by the National Institute of Allergy and Infectious Diseases (NIAID) and other federal agencies was led by Claire M. Fraser, Ph.D., and Timothy Read, Ph.D., at The Institute of Genomic Research in Rockville, MD. The complete sequence of the 5.2 million base pairs of the DNA in B. anthracis' single chromosome is published in the May 1 issue of Nature.

"The pace of microbial genomics research continues to be rapid; B. anthracis is just the latest of dozens of important human pathogens to be sequenced," notes NIAID Director Anthony S. Fauci, M.D. "As ever more precise details emerge about the genetic make-up of these organisms, our ability to design effective drugs and vaccines against the diseases they cause is greatly improved," he adds. To date, NIAID has supported sequencing efforts for more than 30 medically important microbes, many of which cause infectious diseases or are potential bioterror agents (see http://www.niaid.nih.gov/dmid/genomes).

Dr. Read and his colleagues compared an isolate of the Ames strain of B. anthracis with two closely related Bacillus bacteria. "There is remarkably little difference among these genomes," says Dr. Read. "In the 5,000 or more genes we analyzed, we found only 150 or so significant differences."

Dr. Read and his coworkers found a number of genes encoding proteins that B. anthracis may need to enter its host's cells. These could provide targets for drugs designed against the organism, says Dr. Read.

Unlike its near relatives, B. anthracis possesses genes that give it the ability to thrive on protein-rich matter such as the decaying animal bodies it frequently grows on, the scientists discovered. Their analysis also found that B. anthracis has an enhanced capacity to scavenge iron, which it may use to survive in its host.

Using techniques of comparative genomics, the investigators gleaned several clues about the possible evolutionary pathway taken by B. anthracis ancestors. The similarities between certain B. anthracis genes and those of microbes that infect insects, for example, suggest that a recent ancestor of B. anthracis may have infected insects. Of note is a similarity between one gene of Yersinia pestis, which causes plague in mammals and can also infect insects, and a gene in B. anthracis, which infects only mammals.

NIAID supported the anthrax sequencing through the pathogen functional genomics resource center at TIGR. This initiative, launched by NIAID in 2001, trains researchers in the latest techniques in functional genomics. It also serves as a reagent repository. The center's resources are available to the scientific community through online and other services. Besides NIAID, support for the anthrax sequencing effort came from the United States Office of Naval Research, the Department of Energy and the United Kingdom's Defense Sciences Technology Laboratory.

NIAID is a component of the National Institutes of Health (NIH), which is an agency of the Department of Health and Human Services. NIAID supports basic and applied research to prevent, diagnose, and treat infectious and immune-mediated illnesses, including HIV/AIDS and other sexually transmitted diseases, illness from potential agents of bioterrorism, tuberculosis, malaria, autoimmune disorders, asthma and allergies.

The teleconference on Wednesday April 30 will include investigator Timothy Read, Ph.D., of TIGR; TIGR President Claire M. Fraser, Ph.D.; and Maria Y. Giovanni, Ph.D., assistant director for microbial genomics and related technology development at NIAID.

[Junkdrawer]

2. Look, today was Prosecution Wet Dream Day...

Want the suspects narrowed down to a single lab?

*Poof* Here's a NEW TEST that proves exactly that.

Want the suspect to have a suspicious work pattern?

*Poof* Here's the proof and no one's there to refute it.

Having problems explaining how he weaponized the anthrax?

*Poof* There's an FBI study showing the anthrax in question wasn't weaponized at all.

Prosecution is EASY when there's no defense.

[Muttocracy]

3. Summary in Nature

Nature (despite its simple name, one of the top scientific journals) adds a more general summary of important research articles near the front of the issue.

Nature 423, 23-25 (1 May 2003)
Genomics: Relative pathogenic values
Julian Parkhill and Colin Berry

excerpts:

Particular notoriety has been accorded to Bacillus anthracis of late. As the causative agent of anthrax, this bacterium was used in the 2001 postal attacks in the United States1, and it has reportedly been 'weaponized' as a warfare agent on at least one occasion2. On pages 81 and 87 of this issue, Read et al.3 and Ivanova et al.4 bring the power of genomics to bear on efforts to understand this pathogen and its close relatives.

Bacillus anthracis is a member of a group of closely related organisms that includes B. cereus, an opportunistic pathogen of humans, and B. thuringiensis, an insect pathogen that has been used worldwide as a pesticide for over 40 years. Read et al.3 describe the genome sequence of a strain of B. anthracis that was isolated from a Texan cow and subsequently used as a standard laboratory strain around the world. The same group has previously shown that this strain is virtually identical to that used in the US postal attacks5 and is, therefore, still representative of a fully virulent strain. Read et al.3 also generated an incomplete sequence of a strain of B. cereus for comparative purposes, and manufactured a microarray to extend this comparison to further strains of B. cereus. Ivanova et al.4 have completed the sequence of a different strain of B. cereus, and compared it to the unfinished sequence of the postal bioterror strain generated by Read et al. in their earlier work.

...

In contrast, B. anthracis isolates represent a group that is closely related genetically, probably indicating a recent evolutionary origin7. The unanswered questions around these certainties concern exactly how closely these organisms are related. Are they really separate species or, as has been suggested, the same species carrying different plasmids8?

The new work3, 4 goes a long way towards answering these questions. It is clear from the results that the genomes sequenced are highly conserved, and that even many of the B. anthracis plasmid genes are present in other strains of the B. cereus group. The only significant and consistent differences between B. anthracis and B. cereus are the genes encoding toxin components, which are carried on an apparently recent insert (a pathogenicity island) within the B. anthracis pXO1 plasmid, and a loss by mutation in the B. anthracis genome of a regulator (PlcR) of the expression of a wide range of genes, many associated with virulence9. It is also clear from these analyses that factors involved in virulence are not restricted to the plasmid. Instead, the chromosome itself, which is often considered to be a relatively inert background for the virulence-determining plasmids, carries many genes that seem to be involved in virulence.

...

All of this serves to underline the point that, whatever crude attempts are made by human beings, the true biowarfare experts are the bacteria themselves — they are constantly ready and exquisitely able to adapt to, and exploit, any environmental or pathogenic niche that presents itself. We can only hope that the availability of these sequences will assist those who are working to protect us against these agents of disease.

References
------------------
1. Jernigan, D. B. et al. Emerg. Infect. Dis. 8, 1019-1028 (2002).
2. Seelos, C. Nature 398, 187-188 (1999).
3. Read, T. D. et al. Nature 423, 81-86 (2003).
4. Ivanova, N. et al. Nature 423, 87-91 (2003).
5. Read, T. D. et al. Science 296, 2028-2033 (2002).
6. Carlson, C. R. & Kolsto, A.-B Mol. Microbiol. 13, 161-169 (1994).
7. Keim, P. et al. J. Bacteriol. 179, 818-824 (1997).
8. Helgason, E. et al. J. Bacteriol. 66, 2627-2630 (2000).
9. Mignot, T. et al. Mol. Microbiol. 42, 1189-1198 (2001).
10. Margulis, L. et al. Proc. Natl Acad. Sci. USA 95, 1236-1241 (1998).

[Supersedeas]

4. and yet it took nearly 7 years to confront their leading suspect

[Muttocracy]

5. The research article in Nature - coauthors at USAMRIID (not Ivins), UK Defense, others in Maryland

The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria

This won't copy and paste well; many coauthors from Institute for Genomic Research, Rockville, MD., others from Univ. of MD, George Wash Univ., Johns Hopkins, Univ. of Oslo, Defence Science Technology Laboratory, Porton Down, UK, Univ. of Mich., Univ. of TX.

oh look - there are genetic repositories (not this would not be exact match for the strain used)
"The B. anthracis genome sequence has been deposited at GenBank under accession number AE016879; the microarray data have been deposited at Gene Expression Omnibus (GEO) under accession number GSE341."

Final sentence of abstratct "The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis."

...

The B. anthracis Ames chromosome sequenced in this work (5,227,293 base pairs, bp) derives from an isolate taken from a dead cow in Texas (Methods). This sequence differs in only 11 confirmed single nucleotide polymorphisms5 (SNPs) from the 2001 Florida attack Ames isolate, verifying that the chromosome sequenced to completion is essentially identical to a virulent strain. The chromosome encodes 5,508 predicted protein-coding sequences (Table 1) with a pronounced bias for genes on the replication leading strand (Fig. 1), as has been seen in other low G + C Gram-positive replicons6.





more to come as I keep reading...

[Junkdrawer]

6. Weren't the reference strains destroyed by the FBI shortly after the attacks?

I can't find a reference, but I remember reading it in a reputable place.

[Muttocracy]

7. so then how did some new technology in 2005/2006 change the identification?

[Muttocracy]

8. From a Science article - tree of Anthrax strains

http://www.sciencemag.org/cgi/content/full/296/5575/2028
Has sequence detail down to single nucleotides in many regions; getting beyond what I can interpret.



Figure 1. Suggested relationship of Ames isolates. Known direct transfers of the isolates (and hence generations of growth) are shown as solid arrows. Diamond boxes are the sources of DNA for genomic sequencing. Hypothetical lines of descent are shown as dashed arrows. Porton1 and Porton2 are different cultures of the Porton Ames isolate (5).

[Muttocracy]

9. if there are any molecular biologists reading:

Bacillus anthracis Ames Genome Page
http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?org=gba