Dowloading the genome sequences of bacterial pathogens
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9.3 years ago
bioinfo ▴ 840

Is there any publicly available database or other resources to download the sequences of full and draft genomes for only pathogenic bacteria?

genome sequence pathogens • 3.6k views
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9.3 years ago
dago ★ 2.8k

This is a really good source http://patricbrc.org/portal/portal/patric/Genomes

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PATRIC didn't really classified or assigned the genomes with a "pathogenic" tag, but in metadata, they added a filtering feature "Disease" (i guess that indicates genomes associated to a disease). Now they have 26750 genomes in total and out of them 3880 are "disease"-related. Still I am not sure how good these metadata are. And downloading these 3880 genomes are not just straight forward though.

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You could look a list of pathogenic bacteria using the meta data and and download them via their FTP (ftp://ftp.patricbrc.org/patric2/LegacyBRC/PATRIC/gff3/). I think It also depends from what you are looking for. If you want all the described pathogenic bacteria available, I think you have to do that manually. I agree that it looks a bit complicated the interface of PATRIC, but it is a really good resource, and integrate many different db types. You could start from http://patricbrc.org/portal/portal/patric/GenomeFinder?cType=taxon&cId=131567&dm= and type "pathogenic" in the keyword field. You will get just around 300 hits.

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9.3 years ago
piet ★ 1.8k

for only pathogenic bacteria

you should first define more clearly and precisely, what you mean by pathogenic bacteria.

Do you mean pathogenic for honey bees or for plants? How precisely do you want to discern commensals from pathogens? Members of the healthy human skin flora like Staphylococcus epidermidis are infrequently found to cause infections, several staphylococcal species are therefore called opportunistic pathogens. Pathogenicity is often not bound to the species. Most E.coli are harmless inhabitants of the intestinal tract, but there also exist some highly pathogenic strains causing hemolytic uremic syndrome (HUSEC outbreak in Germany 2011).

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It is definitely human pathogenic bacteria. I was looking for genomes of bacterial strains that have been reported/shown to have the potential to cause infection in humans (including strains reported in different outbreaks). Hope now it is clear to you. Are you aware of these kinds of resources?

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