Category Archives: Genome sequence

Microbial forensics: the science behind the Amerithrax investigation

Nearly a decade after the postal anthrax attacks in the USA that killed 5 individuals and infected more than 20 people, scientists have revealed the measures used to trace the Bacillus anthracis strain used in the bioterror attack in a new paper available online for free from Proceedings of the National Academy of Sciences. A groundbreaking mix of genomics and microbiology were used as part of the criminal investigation  into the 2001 anthrax attacks (called Amerithrax); microbial forensics proved key to identifying the exact flask from which the anthrax spores were taken.

Rasko and colleagues used highly accurate whole-genome sequencing and comparative genomics (against the B. anthracis Ames ancestor, believed to be the progenitor of all Ames lab samples and used as a gold standard reference strain in the USA) to determine the source strain of B. anthracis used in the letter attacks. First, the scientists took spore samples from some of the letters and grew them in the lab. A number of morphological variants were observed in these letter-isolated bacterial samples (yellow or yellow–grey coloured rather than the usual grey–white of wild-type anthrax colonies) and all had diminished abilities to sporulate. These variants were then sequenced and compared with genomes sequences of the gold standard Ames ancestor to identify four distinct loci with genetic mutations (three of which were in B. anthracis sporulation pathways, specifically regulation of a key protein, Spo0F) in the morpholigical variants—features unique to the isolated anthrax variants. None of these variants were found to be prevalent in the environment (even in the areas associated with the Amerithrax investigation).

Ultimately, using comparisons with genomes of repository anthrax sources, the anthrax spores used to lace the letters were found to have a unique genetic fingerprint; anthrax batches were eventually traced back to a source flask (RMR-1029) in the lab of Dr Bruce Ivins (a key suspect in the subsequent criminal investigation who later committed suicide before a criminal case could be brought to trial).

The study authors conclude that the B. anthracis bioterror attack investigations “taught us important lessons about the integration of whole-genome sequencing for forensic applications”, although they do concede that their methods might not applicable to other bioterror agents.

ResearchBlogging.orgRasko, D., Worsham, P., Abshire, T., Stanley, S., Bannan, J., Wilson, M., Langham, R., Decker, R., Jiang, L., Read, T., Phillippy, A., Salzberg, S., Pop, M., Van Ert, M., Kenefic, L., Keim, P., Fraser-Liggett, C., & Ravel, J. (2011). Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1016657108

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Scientists reveal genome sequence for the Irish potato famine pathogen

potato blight Nature coverThe genome of the potato blight mould (Phytophthora infestans) has been successfully sequenced in an international collaboration between scientists. The work, published in Nature last week, also reveals how the potato pathogen has adapted to cause disease.

Phytophthora infestans is a water mould (or oomycete) and the destructive pathogen that causes potato blight (or late blight). Oomycetes are microscopic organisms that form long filaments that look like, but are evolutionarily distinct from, fungi. P. infestans is infamous in human history as the culprit behind the Irish potato famine between 1845 and 1852. 1 million people died in Ireland (reducing the population by 20 – 25%) and 1 million more emigrated as a consequence of the famine. P. infestans is still a significant worldwide agricultural problem; potatoes are the 4th largest agricultural crop and crop losses as a result of potato blight are estimated to cost $6.7 billion. This potato pathogen is incredibly difficult to manage as it can rapidly adapt to control strategies, such as genetically engineering blight resistant potatoes, and still cause disease that rots the leaves and tubers of the potato plant.

The P. infestans genome is the biggest genome, at 240 megabases (Mb), sequenced so far in the chromalveolates (a eukaryote super group that contains water moulds and algae). Interestingly, the genome is so big because it is full of repetitive DNA, which makes up 74% of the genome. This includes a large number of transposons (so called “jumping genes”, DNA sequences that can move around to different positions within the genome). The P. infestans genome was compared to two related genomes, P. sojae (the cause of soy bean root rot) and P. ramorum (the cause of sudden oak death). This revealed that Phytophthora genomes have an unusual organisation; blocks densely packed with conserved (i.e. identical) genes between the genomes, which are separated by regions with high numbers of repeated DNA with few genes present. Interestingly, rapidly evolving virulence genes (which are induced during infection and allow the organism to colonise the potato plant) are present in these gene-sparse areas in P. infestans.

Highly dynamic regions of the Phytophthora genome may be crucial for its rapid adaptability to host plants and how it has evolved as a plant pathogen. The full genome sequence of P. infestans allows scientists to identify essential genes that allow the pathogen to destroy potato crops. This could help researchers devise new ways to protect potato plants from P. infestans, such as breeding new types of resistant potato plants or developing new (hopefully environmentally-friendly) chemicals to kill the potato pathogen.

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Filed under Genome sequence, Science