Classification Of Bacterial Infectious Dieases

Question

[parinitaujoodha]

Hi does anyone know how to classify different bacterial infections according to the host that they infect.

For example, mycobacteria infects human while other strains of mycobacteria infect birds etc... The genbank file of the bacteria does not specify this information. I need to automate this classifcation for a data warehouse.

Does anyone know how to do this or where these information are stored on the web and can be retrieved?

Thank you

Answer 1

[Joseph Hughes]

This sort of thing should be trivial but unfortunately it is not. The best place to get this sort of information is in the host field of GenBank formatted sequences. It is missing for a large number of sequences but if you parse the information for the whole of Genbank you should be able to get a good representation of the known host-pathogen associations.

You might also find this previousl post useful: How To Determine If A Given Species Or Taxon Id Corresponds To A Pathogen Or Not? and Rod Page's blog

[parinitaujoodha]

Hi,I looked into the Genbank files but the information are missing. Thanks

Answer 2

[pld]

You will have to manually curate this information for species and isolates involved. You'll have to deal with zoonotic pathogens, as well as undocumented strains or isolates. Zoonotic pathogens prove to be troublesome because of the sometimes diverse set of hosts. Lastly, you need to catch things where an isolate was only reported in an animal, but the species in general is zoonotic, making it usually a human pathogen as well. This means text mining is especially tricky and could generate a ton of false negatives.

You might be able to find some pathogen databases, but this isn't something that will show up in NCBI and can't be done with sequence data. If you solved the problem of predicting pathogen genetic changes associated with species jumping, you'd revolutionize emerging pathogens research forever.

You might want to check the CDC's Biosafety in Microbiological and Biomedical Laboratories, it will cover a very large array of bacteria. However, the animal only pathogens will be limited to serious agricultural pathogens. So it have a far from complete list.

ABSA has a database you can check, but again this is geared towards infectious disease research and biocontainment, not bacteriology globally. http://www.absa.org/riskgroups/bacteria.html

[parinitaujoodha]

Thank you. That was exactly what I was looking for.