Microbiology and Parasitology
Every microorganism the exams ask about, on one page: what it looks like, how it spreads, how it causes disease, how it is diagnosed, which drug class treats it and how it is prevented. With what matters in Colombia and the tropics, and linked to DurgiPedia's conditions.
178 microorganisms in 31 groups
Colombia and the tropics
The microorganisms that weigh most in the exams and in public health in Colombia.
- Ascaris lumbricoides
- Candida albicans
- Chikungunya virus
- Chlamydia trachomatis
- Clostridium tetani
- Cryptococcus neoformans
- Dengue virus
- Entamoeba histolytica
- Enterobius vermicularis
- Escherichia coli
- Giardia duodenalis
- Helicobacter pylori
- Hepatitis A virus
- Hepatitis B virus
- Histoplasma capsulatum
- Human immunodeficiency virus
- Human papillomavirus
- Influenza virus
- Leishmania (Viannia) panamensis, L. braziliensis and L. guyanensis
- Leishmania infantum
- Leptospira interrogans
- Measles virus
- Mycobacterium tuberculosis
- Necator americanus / Ancylostoma duodenale
- Neisseria gonorrhoeae
- Neisseria meningitidis
- Plasmodium falciparum
- Plasmodium vivax
- Rabies virus
- Salmonella Typhi
- Sarcoptes scabiei
- SARS-CoV-2
- Staphylococcus aureus
- Streptococcus pneumoniae
- Streptococcus pyogenes
- Strongyloides stercoralis
- Taenia solium
- Toxoplasma gondii
- Treponema pallidum
- Trichuris trichiura
- Trypanosoma cruzi
- Vibrio cholerae
- Yellow fever virus
- Zika virus
Bacteria
- Other clinically important bacteriaEight bacteria outside the big groups that still show up in exams: anaerobes, bites, seafood, the hospital, Whipple and the non-venereal treponemes.Bacteroides fragilis · Haemophilus ducreyi · Pasteurella multocida · Burkholderia cepacia complex and Burkholderia pseudomallei · Vibrio vulnificus and Vibrio parahaemolyticus · Enterobacter, Serratia and Citrobacter · Tropheryma whipplei · Non-venereal treponemes (yaws, bejel and pinta)
- Gram-negative cocciCoffee-bean diplococci: meningococcus, gonococcus and Moraxella. They cause meningitis, gonorrhea, ear and sinus infections.Neisseria meningitidis · Neisseria gonorrhoeae · Moraxella catarrhalis
- EnterobacteralesGut rods such as E. coli, Salmonella, Shigella, Klebsiella, Proteus and Yersinia: diarrhea, urinary infection and sepsis.Escherichia coli · Salmonella Typhi · Non-typhoidal Salmonella · Shigella · Klebsiella pneumoniae · Proteus mirabilis · Yersinia
- Other Gram-negative rodsCurved rods, coccobacilli and non-fermenters: H. pylori, Vibrio, Pseudomonas, Haemophilus, Bordetella, Legionella and the zoonoses.Helicobacter pylori · Vibrio cholerae · Campylobacter jejuni · Pseudomonas aeruginosa · Acinetobacter baumannii · Haemophilus influenzae · Bordetella pertussis · Legionella pneumophila · Bartonella · Brucella · Francisella tularensis · Gardnerella vaginalis
- StaphylococciGram-positive cocci in clusters that live on skin and in the nose; S. aureus is the most aggressive and MRSA the most feared in hospitals.Staphylococcus aureus · Staphylococcus epidermidis · Staphylococcus saprophyticus
- Streptococci and enterococciGram-positive cocci in chains or pairs that cause anything from sore throat and pneumonia to newborn sepsis and endocarditis.Streptococcus pyogenes · Streptococcus pneumoniae · Streptococcus agalactiae · Viridans streptococci · Enterococcus
- Gram-positive rodsGram-positive rods: spore-forming clostridia and bacilli, corynebacteria, Listeria and the branching Nocardia and Actinomyces.Clostridium tetani · Clostridioides difficile · Clostridium botulinum · Clostridium perfringens · Corynebacterium diphtheriae · Listeria monocytogenes · Bacillus anthracis · Bacillus cereus · Nocardia · Actinomyces israelii
- MycobacteriaRods with a lipid-rich wall that resists acid-alcohol: they cause tuberculosis, leprosy and environmental infections.Mycobacterium tuberculosis · Mycobacterium leprae · Mycobacterium avium complex and other non-tuberculous mycobacteria
- SpirochetesLong, spiral bacteria that move like a corkscrew: syphilis, leptospirosis, Lyme disease and relapsing fever.Treponema pallidum · Leptospira interrogans · Borrelia burgdorferi · Borrelia recurrentis and tick-borne relapsing fever borreliae
- Intracellular and atypical bacteriaBacteria that live inside cells or lack a wall: Chlamydia, Rickettsia, Coxiella, Ehrlichia and Mycoplasma.Chlamydia trachomatis · Mycoplasma pneumoniae · Chlamydia pneumoniae / Chlamydia psittaci · Rickettsia rickettsii / Rickettsia typhi · Mycoplasma genitalium / Ureaplasma · Coxiella burnetii · Ehrlichia / Anaplasma · Orientia tsutsugamushi
Viruses
- Other viruses and prionsChildhood respiratory viruses, haemorrhagic fevers, rodent-borne viruses, mosquito-borne encephalitis and prions, which are not viruses.Parainfluenza virus · Human metapneumovirus · Ebola and Marburg viruses (filoviruses) · Hantavirus · Arenaviruses (Lassa and the South American haemorrhagic fevers) · Equine encephalitis viruses and Mayaro virus · West Nile virus · Prions
- Human herpesvirusesEnveloped DNA viruses that, after the first infection, stay latent for life and can reactivate.Herpes simplex virus 1 · Herpes simplex virus 2 · Varicella-zoster virus · Epstein–Barr virus · Cytomegalovirus · Human herpesviruses 6 and 7 · Human herpesvirus 8
- Other DNA virusesDNA viruses that are not herpesviruses: hepadna-, papilloma-, polyoma-, parvo-, adeno- and poxviruses.Hepatitis B virus · Human papillomavirus · JC polyomavirus · Parvovirus B19 · Adenovirus · Mpox virus · Molluscum contagiosum virus · Variola virus
- RNA arbovirusesViruses spread by the bites of arthropods (mosquitoes, midges). In Colombia they cause dengue, Zika, chikungunya, yellow fever and Oropouche fever.Dengue virus · Zika virus · Chikungunya virus · Yellow fever virus · Oropouche virus
- RNA hepatitis virusesRNA viruses that attack the liver: A and E through water and food; C and D through blood. Hepatitis B, a DNA virus, completes the list.Hepatitis A virus · Hepatitis C virus · Hepatitis D virus · Hepatitis E virus
- Respiratory RNA virusesRNA viruses that enter through the airway: influenza, RSV, SARS-CoV-2, rhinovirus and the rash viruses measles, rubella and mumps.Influenza virus · Respiratory syncytial virus · Measles virus · Mumps virus · Rubella virus · SARS-CoV-2 · Rhinovirus
- Other RNA virusesRetroviruses (HIV, HTLV-1), rabies virus and the enteric viruses: rotavirus, norovirus and enteroviruses such as poliovirus.Human immunodeficiency virus · Human T-lymphotropic virus type 1 · Rabies virus · Rotavirus · Norovirus · Enteroviruses
Fungi
- Yeasts and yeast-like fungiSingle-celled fungi that reproduce by budding: Candida and Cryptococcus cause the most common opportunistic mycoses in hospitals and in HIV.Candida albicans · Cryptococcus neoformans · Pneumocystis jirovecii · Malassezia
- Dimorphic fungiFungi that live as molds in soil and switch to yeasts inside the body; acquired by inhaling spores, they cause the endemic mycoses.Histoplasma capsulatum · Paracoccidioides brasiliensis · Sporothrix schenckii · Coccidioides immitis · Blastomyces dermatitidis
- Molds and dermatophytesFilamentous fungi: environmental molds that attack the immunosuppressed, and dermatophytes that feed on the keratin of skin, hair and nails.Aspergillus fumigatus · Mucorales (Rhizopus, Mucor) · Dermatophytes (Trichophyton, Microsporum, Epidermophyton) · Agents of chromoblastomycosis (Fonsecaea and other pigmented fungi)
- Other fungi of clinical interestThree loose chapters of the textbook: mycetoma of the foot, Talaromyces in AIDS in Asia, and microsporidia, now grouped with the fungi.Mycetoma agents · Talaromyces marneffei · Microsporidia (Enterocytozoon, Encephalitozoon)
Parasites
- NematodesRoundworms: gut worms caught from soil (soil-transmitted helminths), pinworms, and tissue worms such as filariae, Toxocara and Trichinella.Ascaris lumbricoides · Necator americanus / Ancylostoma duodenale · Strongyloides stercoralis · Trichuris trichiura · Enterobius vermicularis · Toxocara canis / Toxocara cati · Ancylostoma braziliense / Ancylostoma caninum · Wuchereria bancrofti / Brugia malayi · Onchocerca volvulus · Trichinella spiralis · Mansonella ozzardi / Mansonella perstans
- Cestodes (tapeworms)Flat, segmented worms with no gut. Humans can host the adult tapeworm in the bowel or, worse, its larva in tissues.Taenia solium · Taenia saginata · Echinococcus granulosus · Hymenolepis nana · Dibothriocephalus latus
- Trematodes (flukes)Leaf-shaped flatworms that need a snail to complete their cycle. They arrive with raw plants, fish or crabs, or through the skin in fresh water.Fasciola hepatica · Schistosoma mansoni / S. haematobium / S. japonicum · Paragonimus spp. · Clonorchis sinensis / Opisthorchis spp.
- EctoparasitesArthropods living on or in the skin: the scabies mite, lice, the chigoe flea and fly larvae that cause myiasis.Sarcoptes scabiei · Pediculus humanus and Pthirus pubis · Tunga penetrans · Dermatobia hominis
- Other parasites of interestSeven parasites that exams ask about even though they are rare: from the harmless trypanosome that mimics Chagas to the Guinea worm.Trypanosoma rangeli · Loa loa · Dracunculus medinensis · Angiostrongylus (A. costaricensis, A. cantonensis) · Gnathostoma and Anisakis · Lagochilascaris minor · Dipylidium caninum
- Arthropod vectorsThe insects that carry dengue, malaria, leishmaniasis and Chagas in Colombia: how they live, how they bite and how they are controlled.Aedes aegypti and Aedes albopictus · Anopheles · Lutzomyia · Triatomines (Rhodnius prolixus, Triatoma dimidiata)
- Hemoflagellates (trypanosomes and Leishmania)Flagellated protozoa with a kinetoplast that live in blood or inside cells, spread by insects: kissing bugs, sand flies and the tsetse fly.Trypanosoma cruzi · Leishmania (Viannia) panamensis, L. braziliensis and L. guyanensis · Leishmania infantum · Trypanosoma brucei gambiense and T. b. rhodesiense
- ApicomplexansIntracellular protozoa with an apical complex for invading cells: Plasmodium, Toxoplasma, Cryptosporidium, Cyclospora, Cystoisospora and Babesia.Plasmodium vivax · Plasmodium falciparum · Plasmodium malariae and Plasmodium ovale · Toxoplasma gondii · Cryptosporidium spp. · Cyclospora cayetanensis and Cystoisospora belli · Babesia spp.
- Intestinal and urogenital protozoaAmoebae, flagellates and ciliates of the gut and genital tract: Entamoeba, Giardia, Blastocystis, Balantioides, commensal amoebae and Trichomonas.Entamoeba histolytica · Giardia duodenalis · Trichomonas vaginalis · Blastocystis spp. · Balantioides coli · Commensal intestinal amoebae (Entamoeba coli, E. dispar, Endolimax nana and others)
- Free-living amoebaeWater and soil amoebae that rarely infect people, but cause severe meningoencephalitis or keratitis when they do.Naegleria fowleri · Acanthamoeba spp.
A to Z
- Acanthamoeba spp.Free-living amoebae
- Acinetobacter baumanniiOther Gram-negative rods
- Gram-negative
- Contact
- Actinomyces israeliiGram-positive rods
- Gram-positive
- AdenovirusOther DNA viruses
- Non-enveloped (naked)
- Contact
- Droplet
- Aedes aegypti and Aedes albopictusArthropod vectors
- Agents of chromoblastomycosis (Fonsecaea and other pigmented fungi)Molds and dermatophytes
- Ancylostoma braziliense / Ancylostoma caninumNematodes
- Angiostrongylus (A. costaricensis, A. cantonensis)Other parasites of interest
- AnophelesArthropod vectors
- Arenaviruses (Lassa and the South American haemorrhagic fevers)Other viruses and prions
- Enveloped
- Contact
- Droplet
- Ascaris lumbricoidesNematodes
- Aspergillus fumigatusMolds and dermatophytes
- Babesia spp.Apicomplexans
- Bacillus anthracisGram-positive rods
- Gram-positive
- Bacillus cereusGram-positive rods
- Gram-positive
- Bacteroides fragilisOther clinically important bacteria
- Gram-negative
- Balantioides coliIntestinal and urogenital protozoa
- BartonellaOther Gram-negative rods
- Gram-negative
- Blastocystis spp.Intestinal and urogenital protozoa
- Blastomyces dermatitidisDimorphic fungi
- Bordetella pertussisOther Gram-negative rods
- Gram-negative
- Droplet
- Borrelia burgdorferiSpirochetes
- Does not Gram-stain
- Borrelia recurrentis and tick-borne relapsing fever borreliaeSpirochetes
- Does not Gram-stain
- BrucellaOther Gram-negative rods
- Gram-negative
- Burkholderia cepacia complex and Burkholderia pseudomalleiOther clinically important bacteria
- Gram-negative
- Contact
- Campylobacter jejuniOther Gram-negative rods
- Gram-negative
- Contact
- Candida albicansYeasts and yeast-like fungi
- Chikungunya virusRNA arboviruses
- Enveloped
- Chlamydia pneumoniae / Chlamydia psittaciIntracellular and atypical bacteria
- Gram-negative
- Chlamydia trachomatisIntracellular and atypical bacteria
- Gram-negative
- Clonorchis sinensis / Opisthorchis spp.Trematodes (flukes)
- Clostridioides difficileGram-positive rods
- Gram-positive
- Contact
- Clostridium botulinumGram-positive rods
- Gram-positive
- Clostridium perfringensGram-positive rods
- Gram-positive
- Clostridium tetaniGram-positive rods
- Gram-positive
- Coccidioides immitisDimorphic fungi
- Commensal intestinal amoebae (Entamoeba coli, E. dispar, Endolimax nana and others)Intestinal and urogenital protozoa
- Corynebacterium diphtheriaeGram-positive rods
- Gram-positive
- Droplet
- Contact
- Coxiella burnetiiIntracellular and atypical bacteria
- Gram-negative
- Cryptococcus neoformansYeasts and yeast-like fungi
- Cryptosporidium spp.Apicomplexans
- Cyclospora cayetanensis and Cystoisospora belliApicomplexans
- CytomegalovirusHuman herpesviruses
- Enveloped
- Dengue virusRNA arboviruses
- Enveloped
- Dermatobia hominisEctoparasites
- Dermatophytes (Trichophyton, Microsporum, Epidermophyton)Molds and dermatophytes
- Dibothriocephalus latusCestodes (tapeworms)
- Dipylidium caninumOther parasites of interest
- Dracunculus medinensisOther parasites of interest
- Ebola and Marburg viruses (filoviruses)Other viruses and prions
- Enveloped
- Contact
- Droplet
- Airborne
- Echinococcus granulosusCestodes (tapeworms)
- Ehrlichia / AnaplasmaIntracellular and atypical bacteria
- Gram-negative
- Entamoeba histolyticaIntestinal and urogenital protozoa
- Enterobacter, Serratia and CitrobacterOther clinically important bacteria
- Gram-negative
- Contact
- Enterobius vermicularisNematodes
- EnterococcusStreptococci and enterococci
- Gram-positive
- Contact
- EnterovirusesOther RNA viruses
- Non-enveloped (naked)
- Contact
- Epstein–Barr virusHuman herpesviruses
- Enveloped
- Equine encephalitis viruses and Mayaro virusOther viruses and prions
- Enveloped
- Escherichia coliEnterobacterales
- Gram-negative
- Contact
- Fasciola hepaticaTrematodes (flukes)
- Francisella tularensisOther Gram-negative rods
- Gram-negative
- Gardnerella vaginalisOther Gram-negative rods
- Gram-variable
- Giardia duodenalisIntestinal and urogenital protozoa
- Gnathostoma and AnisakisOther parasites of interest
- Haemophilus ducreyiOther clinically important bacteria
- Gram-negative
- Haemophilus influenzaeOther Gram-negative rods
- Gram-negative
- Droplet
- HantavirusOther viruses and prions
- Enveloped
- Helicobacter pyloriOther Gram-negative rods
- Gram-negative
- Hepatitis A virusRNA hepatitis viruses
- Non-enveloped (naked)
- Contact
- Hepatitis B virusOther DNA viruses
- Enveloped
- Hepatitis C virusRNA hepatitis viruses
- Enveloped
- Hepatitis D virusRNA hepatitis viruses
- Enveloped
- Hepatitis E virusRNA hepatitis viruses
- Non-enveloped (naked)
- Contact
- Herpes simplex virus 1Human herpesviruses
- Enveloped
- Herpes simplex virus 2Human herpesviruses
- Enveloped
- Contact
- Histoplasma capsulatumDimorphic fungi
- Human herpesvirus 8Human herpesviruses
- Enveloped
- Human herpesviruses 6 and 7Human herpesviruses
- Enveloped
- Human immunodeficiency virusOther RNA viruses
- Enveloped
- Human metapneumovirusOther viruses and prions
- Enveloped
- Contact
- Human papillomavirusOther DNA viruses
- Non-enveloped (naked)
- Human T-lymphotropic virus type 1Other RNA viruses
- Enveloped
- Hymenolepis nanaCestodes (tapeworms)
- Influenza virusRespiratory RNA viruses
- Enveloped
- Droplet
- JC polyomavirusOther DNA viruses
- Non-enveloped (naked)
- Klebsiella pneumoniaeEnterobacterales
- Gram-negative
- Contact
- Lagochilascaris minorOther parasites of interest
- Legionella pneumophilaOther Gram-negative rods
- Gram-negative
- Leishmania (Viannia) panamensis, L. braziliensis and L. guyanensisHemoflagellates (trypanosomes and Leishmania)
- Leishmania infantumHemoflagellates (trypanosomes and Leishmania)
- Leptospira interrogansSpirochetes
- Does not Gram-stain
- Listeria monocytogenesGram-positive rods
- Gram-positive
- Loa loaOther parasites of interest
- LutzomyiaArthropod vectors
- MalasseziaYeasts and yeast-like fungi
- Mansonella ozzardi / Mansonella perstansNematodes
- Measles virusRespiratory RNA viruses
- Enveloped
- Airborne
- Microsporidia (Enterocytozoon, Encephalitozoon)Other fungi of clinical interest
- Molluscum contagiosum virusOther DNA viruses
- Enveloped
- Moraxella catarrhalisGram-negative cocci
- Gram-negative
- Mpox virusOther DNA viruses
- Enveloped
- Contact
- Airborne
- Mucorales (Rhizopus, Mucor)Molds and dermatophytes
- Mumps virusRespiratory RNA viruses
- Enveloped
- Droplet
- Mycetoma agentsOther fungi of clinical interest
- Mycobacterium avium complex and other non-tuberculous mycobacteriaMycobacteria
- Acid-fast
- Mycobacterium lepraeMycobacteria
- Acid-fast
- Mycobacterium tuberculosisMycobacteria
- Acid-fast
- Airborne
- Mycoplasma genitalium / UreaplasmaIntracellular and atypical bacteria
- Does not Gram-stain
- Mycoplasma pneumoniaeIntracellular and atypical bacteria
- Does not Gram-stain
- Droplet
- Naegleria fowleriFree-living amoebae
- Necator americanus / Ancylostoma duodenaleNematodes
- Neisseria gonorrhoeaeGram-negative cocci
- Gram-negative
- Neisseria meningitidisGram-negative cocci
- Gram-negative
- Droplet
- NocardiaGram-positive rods
- Gram-positive
- Non-typhoidal SalmonellaEnterobacterales
- Gram-negative
- Contact
- Non-venereal treponemes (yaws, bejel and pinta)Other clinically important bacteria
- Does not Gram-stain
- NorovirusOther RNA viruses
- Non-enveloped (naked)
- Contact
- Onchocerca volvulusNematodes
- Orientia tsutsugamushiIntracellular and atypical bacteria
- Gram-negative
- Oropouche virusRNA arboviruses
- Enveloped
- Paracoccidioides brasiliensisDimorphic fungi
- Paragonimus spp.Trematodes (flukes)
- Parainfluenza virusOther viruses and prions
- Enveloped
- Contact
- Parvovirus B19Other DNA viruses
- Non-enveloped (naked)
- Droplet
- Pasteurella multocidaOther clinically important bacteria
- Gram-negative
- Pediculus humanus and Pthirus pubisEctoparasites
- Contact
- Plasmodium falciparumApicomplexans
- Plasmodium malariae and Plasmodium ovaleApicomplexans
- Plasmodium vivaxApicomplexans
- Pneumocystis jiroveciiYeasts and yeast-like fungi
- PrionsOther viruses and prions
- Non-enveloped (naked)
- Proteus mirabilisEnterobacterales
- Gram-negative
- Pseudomonas aeruginosaOther Gram-negative rods
- Gram-negative
- Contact
- Rabies virusOther RNA viruses
- Enveloped
- Respiratory syncytial virusRespiratory RNA viruses
- Enveloped
- Contact
- RhinovirusRespiratory RNA viruses
- Non-enveloped (naked)
- Droplet
- Rickettsia rickettsii / Rickettsia typhiIntracellular and atypical bacteria
- Gram-negative
- RotavirusOther RNA viruses
- Non-enveloped (naked)
- Contact
- Rubella virusRespiratory RNA viruses
- Enveloped
- Droplet
- Salmonella TyphiEnterobacterales
- Gram-negative
- Contact
- Sarcoptes scabieiEctoparasites
- Contact
- SARS-CoV-2Respiratory RNA viruses
- Enveloped
- Contact
- Airborne
- Schistosoma mansoni / S. haematobium / S. japonicumTrematodes (flukes)
- ShigellaEnterobacterales
- Gram-negative
- Contact
- Sporothrix schenckiiDimorphic fungi
- Staphylococcus aureusStaphylococci
- Gram-positive
- Contact
- Staphylococcus epidermidisStaphylococci
- Gram-positive
- Staphylococcus saprophyticusStaphylococci
- Gram-positive
- Streptococcus agalactiaeStreptococci and enterococci
- Gram-positive
- Streptococcus pneumoniaeStreptococci and enterococci
- Gram-positive
- Streptococcus pyogenesStreptococci and enterococci
- Gram-positive
- Droplet
- Contact
- Strongyloides stercoralisNematodes
- Taenia saginataCestodes (tapeworms)
- Taenia soliumCestodes (tapeworms)
- Talaromyces marneffeiOther fungi of clinical interest
- Toxocara canis / Toxocara catiNematodes
- Toxoplasma gondiiApicomplexans
- Treponema pallidumSpirochetes
- Does not Gram-stain
- Triatomines (Rhodnius prolixus, Triatoma dimidiata)Arthropod vectors
- Trichinella spiralisNematodes
- Trichomonas vaginalisIntestinal and urogenital protozoa
- Trichuris trichiuraNematodes
- Tropheryma whippleiOther clinically important bacteria
- Gram-positive
- Trypanosoma brucei gambiense and T. b. rhodesienseHemoflagellates (trypanosomes and Leishmania)
- Trypanosoma cruziHemoflagellates (trypanosomes and Leishmania)
- Trypanosoma rangeliOther parasites of interest
- Tunga penetransEctoparasites
- Varicella-zoster virusHuman herpesviruses
- Enveloped
- Contact
- Airborne
- Variola virusOther DNA viruses
- Enveloped
- Contact
- Airborne
- Vibrio choleraeOther Gram-negative rods
- Gram-negative
- Contact
- Vibrio vulnificus and Vibrio parahaemolyticusOther clinically important bacteria
- Gram-negative
- Viridans streptococciStreptococci and enterococci
- Gram-positive
- West Nile virusOther viruses and prions
- Enveloped
- Wuchereria bancrofti / Brugia malayiNematodes
- Yellow fever virusRNA arboviruses
- Enveloped
- YersiniaEnterobacterales
- Gram-negative
- Droplet
- Zika virusRNA arboviruses
- Enveloped
Educational content on microorganisms; not a treatment guide and no substitute for a health professional's advice. No doses are given.
Representative model, for educational purposes only.