Where can I find a list of pathogens and disease?

Question

[agata88]

Hi all!

Do you know a database where I can find bacteria pathogens with correlated disease?

Many thanks for help,

Best,

Agata

Answer 1

[Andrzej Zielezinski]

I would use PATRIC database (Bioinformatics Database and Analysis Resource Center). It provides a list of pathogenic bacteria whose genomes have been sequenced (Organisms > All Organisms > Genomes). You can filter the list of organisms according to:

1. Disease (e.g. pneumonia, gastroenteritis, fever etc.)
2. Host name (e.g. human)
3. Antibiotic resistance (i.e. resistant, susceptible, intermediate)

Note: PATRIC articles: 2014, 2017.

[agata88]

Thank you very much for instruction to find this information :). I was searching PATRIC database before but I could not find it, so thanks!, Best, Agata

Answer 2

[Pierre Lindenbaum]

using wikidata:

SELECT ?organism  ?name ?diseaseLabel WHERE {
  ?organism wdt:P225 ?name .  
  ?organism wdt:P31 wd:Q16521. 
  ?organism wdt:P1542 ?disease.

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en" .
  }
}



organism    name    diseaseLabel
http://www.wikidata.org/entity/Q146 Felis silvestris catus  allergy to cats
http://www.wikidata.org/entity/Q808 Virus   viral infectious disease
http://www.wikidata.org/entity/Q808 Virus   viral pneumonia
http://www.wikidata.org/entity/Q1357    Araneae spider bite
http://www.wikidata.org/entity/Q6900    Human herpesvirus 4 Epstein–Barr virus infection
http://www.wikidata.org/entity/Q6929    Human herpesvirus 5 cytomegalia
http://www.wikidata.org/entity/Q6974    Human herpesvirus 6 exanthema subitum
http://www.wikidata.org/entity/Q10876   Bacteria    bacterial infectious disease
http://www.wikidata.org/entity/Q10876   Bacteria    bacterial pneumonia
http://www.wikidata.org/entity/Q12104   Avena sativa    oat sensitivity
http://www.wikidata.org/entity/Q21053   Dicrocoelium dendriticum    lancet liver fluke infection
http://www.wikidata.org/entity/Q127375  Gardnerella vaginalis   bacterial vaginosis
http://www.wikidata.org/entity/Q131027  Entamoeba histolytica   amebiasis
http://www.wikidata.org/entity/Q131065  Chlamydia trachomatis   lymphogranuloma venereum
http://www.wikidata.org/entity/Q131129  Neisseria gonorrhoeae   proctitis
http://www.wikidata.org/entity/Q131271  Streptococcus pyogenes  toxic shock syndrome
http://www.wikidata.org/entity/Q131271  Streptococcus pyogenes  lymphangitis
http://www.wikidata.org/entity/Q131273  Naegleria fowleri   primary amebic meningoencephalitis
http://www.wikidata.org/entity/Q131649  Corynebacterium diphtheriae cutaneous diphtheria
http://www.wikidata.org/entity/Q132592  Klebsiella pneumoniae   klebsiellosis
http://www.wikidata.org/entity/Q134734  Cryptosporidium parvum  cryptosporidiosis
http://www.wikidata.org/entity/Q134745  Treponema   Treponematosis
http://www.wikidata.org/entity/Q137446  Bordetella bronchiseptica   cat flu
http://www.wikidata.org/entity/Q140475  Burkholderia pseudomallei   melioidosis
http://www.wikidata.org/entity/Q140599  Bartonella henselae bacillary angiomatosis
http://www.wikidata.org/entity/Q141236  Balantidium coli    balantidiasis
http://www.wikidata.org/entity/Q145931  Avian leukosis virus    Lymphoid Leucosis
http://www.wikidata.org/entity/Q150946  Klebsiella granulomatis granuloma inguinale
http://www.wikidata.org/entity/Q156007  Treponema pallidum  bejel
http://www.wikidata.org/entity/Q158767  Triticum spelta Gluten related disorders
http://www.wikidata.org/entity/Q158856  West Nile virus West Nile fever
http://www.wikidata.org/entity/Q161098  Triticum aestivum   Gluten related disorders
http://www.wikidata.org/entity/Q195760  African swine fever virus   African swine fever
http://www.wikidata.org/entity/Q202864  Zika virus  Zika fever
http://www.wikidata.org/entity/Q221179  Streptococcus pneumoniae    pneumococcal infection
http://www.wikidata.org/entity/Q221315  Spirochaetales  spirochetal diseases
http://www.wikidata.org/entity/Q292189  Anaplasma phagocytophilum   human granulocytic anaplasmosis
http://www.wikidata.org/entity/Q292297  Demodex demodicosis
http://www.wikidata.org/entity/Q310656  Pasteurella multocida   pasteurellosis
http://www.wikidata.org/entity/Q468771  Ascaris lumbricoides    ascariasis
http://www.wikidata.org/entity/Q500869  Sarcoptes scabiei   fox mange
http://www.wikidata.org/entity/Q618324  Triticum durum  Gluten related disorders

[GenoMax]

That list contains things other than bacteria (e.g. http://www.wikidata.org/entity/Q618324 Triticum durum Gluten related disorders) . If that is a requirement.

[agata88]

I was thinking more about a database with pathogen bacteria species (e.g.. from NCBI) and related disease confirmed in publications. Do you know a database like that? I heard about PATRIC database but I cannot find those information there.