Tag Archives: microbiology

Video Tip of the Week: PATRIC, Pathosystems Resource Integrations Center

PATRIC is a integration portal (as the name implies) of  data concerning disease-causing infectious bacteria. Or to put it in their words:

PATRIC is the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools.

We mentioned PATRIC at the beginning of the year in a SNPpets. Also, recently I was speaking with a threat abatement specialist who was lamenting the lack of coordinated data on infectious bacteria genomes. I was sure there was such a site, so we checked our blog here and voila, sure enough, exactly what they needed.

PATRIC indeed coordinates a lot of different types of data from disease-causing infectious bacteria. This includes data from all NIAID biodefense A/B/C pathogens. This includes hundreds of genomes from many isolation sources. For example, as of this writing there are nearly 500 genomes, including 57 complete, of Escherichia. In addition to genomic data, there are many other types of data including phylogenetic, host-pathogen protein-protein interactions, protein, pathways and more. One interesting feature, of many,  is the disease map (for mycobacterium only right now) that shows local outbreaks and alerts. There are many tools to access and analyze this data from specialized searches to browsers.

To get a good idea of what is available at PATRIC, check out the quick intro video embedded above from the PATRIC developers. They have two other video tutorials on the feature table and identifying novel proteins you also might want to check out. Also, check out the blog for more databases and resources for infectious disease pathogens.

To cite or learn more about PATRIC, see:

Gillespie, J., Wattam, A., Cammer, S., Gabbard, J., Shukla, M., Dalay, O., Driscoll, T., Hix, D., Mane, S., Mao, C., Nordberg, E., Scott, M., Schulman, J., Snyder, E., Sullivan, D., Wang, C., Warren, A., Williams, K., Xue, T., Seung Yoo, H., Zhang, C., Zhang, Y., Will, R., Kenyon, R., & Sobral, B. (2011). PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species Infection and Immunity, 79 (11), 4286-4298 DOI: 10.1128/IAI.00207-11

Genomics Impact on Infectious Disease (with video)

As part of the The Genomics in Medicine Lecture Series from NHGRI, Jonathan Zenilman gave a lecture on various ways that new genome technology has aided in the ways that clinicians can diagnose, manage, and treat infectious disease. This lecture series is delivering a number of videos on various intersections of clinical medical situations and genomics, not just on the basic research in the field.

The opportunities to study previously murky microbial situations–including unculturable organisms, and mixed colonies of microbes that can be invading wounds, was really interesting (but thinking about the community in a brain abscess was…er…not suitable for lunchtime viewing perhaps). But not only were these situations nearly impossible to understand before–but they couldn’t tell whether there were resistant organisms in there. So it seriously affected treatments.

An interesting data point: in brain abscesses, using standard culturing techniques, they identified 22 bugs. Using PCR they found 72! Some were unknown, too. One patient had 16 strains. That’s quite a battle.

One side effect of these new strategies though it that it freaks out hospital administrators. Suddenly because of the increased sensitivity of the tests, there are a lot more organisms reflected on their reports.

The new techniques are really going to help in the treatment of chronic wounds. One important point was that checking the RNA-seq data is key, because it’s important to know which transcriptomes are active. Dead bugs complicate the analysis, so knowing which ones are currently alive and affecting the wound is crucial.

Another important outcome of this work would be getting pointers to more pathogen-directed therapies. Broad-spectrum treatments are causing problems of their own, and having more precise ways to target the bad bugs would really be worthwhile.

I’ve attached a sample of the kinds of data that Zenilman and colleagues have published on the types of work he describes in this lecture, but you can find many more examples. I wanted to choose an open access example though, so this is the one I include.

Reference:

Price, L., Liu, C., Melendez, J., Frankel, Y., Engelthaler, D., Aziz, M., Bowers, J., Rattray, R., Ravel, J., Kingsley, C., Keim, P., Lazarus, G., & Zenilman, J. (2009). Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota PLoS ONE, 4 (7) DOI: 10.1371/journal.pone.0006462

Archaeal Genome Browser from UCSC

Archaeal Genome Browser from UCSCUCSC announced the Archaeal Genome Browser created by the Lowe Lab at UCSC last week. The browser has been accessible for a while, but this is the public ‘unveiling’ and announcement. The interface and use is very similar to the UCSC Genome Browser (free tutorial), though of course modified and geared to the analysis of Archaeal genomes. So add another resource and database to your toolbox, it looks like another good and useful one. As the announcement says:

Currently there are more than 50 completed archaeal genomes, the least studied domain of life. Although archaea and bacteria are both prokaryotes, often co-existing in the same environments, many aspects of archaeal cell biology such as DNA replication, repair, transcription, and translation are homologous to those found in eukaryotes. Some members of archaea are also notable for inhabiting extreme environments, including boiling terrestrial hot springs, black smoker vents at the bottom of the ocean, the ultra briny water of the Dead Sea, and highly acidic drainage water from ore mines, to name a few.

Metagenomics

Just a short post with some information:

Metagenomics is the new genomics :). NIH Roadmap has a new initiative, the Human Microbiome Project with a bit of funding :) . Meanwhile, other projects and databases are developing such as Integrated Microbial Genomes w/ Microbiome Samples (or IMG/M) and Camera. It’s an exciting and fascinating field (my former colleagues at the Bork lab just published interesting research in this field), though some scientists of course have their doubts.