Microbiology general

 

Bacterial characteristics and their culture media

Gram Reaction	Pathogenic Bacteria	Special Characteristics	Selective Culture Media
Gram-Positive	Staphylococcus aureus	Produces coagulase	Mannitol Salt Agar
	Streptococcus pneumoniae	Encapsulated, optochin sensitive	Blood Agar, Optochin Agar
	Bacillus anthracis	Produces anthrax toxin, capsule	Blood Agar, MacConkey Agar
	Clostridium difficile	Produces toxins A and B	Cycloserine-cefoxitin fructose agar (CCFA)
	Listeria monocytogenes	Tumbling motility, cold enrichment required	Blood Agar
	Corynebacterium diphtheriae	Produces diphtheria toxin	Loeffler's medium, Tinsdale agar
	Enterococcus faecalis	Group D streptococcus, gamma-hemolytic	Bile Esculin Agar
Gram-Negative	Escherichia coli	Facultative anaerobe, lactose fermenter	MacConkey Agar, Eosin Methylene Blue (EMB)
	Salmonella enterica	Non-lactose fermenter, produces H2S	Xylose Lysine Deoxycholate (XLD) Agar
	Pseudomonas aeruginosa	Oxidase-positive, produces pyocyanin	Cetrimide Agar, Pseudomonas Isolation Agar
	Neisseria gonorrhoeae	Intracellular diplococci, oxidase-positive	Thayer-Martin Agar, New York City Agar
	Klebsiella pneumoniae	Mucoid colonies, lactose fermenter	MacConkey Agar
	Legionella pneumophila	Requires cysteine for growth, intracellular	Buffered Charcoal Yeast Extract (BCYE) Agar
	Helicobacter pylori	Spiral-shaped, urease-positive	Skirrow's Agar, Campylobacter Blood Free Selective Agar (CCDA)
	Vibrio cholerae	Curved, comma-shaped, produces cholera toxin	Thiosulfate Citrate Bile Salts Sucrose (TCBS) Agar
	Shigella spp.	Non-motile, non-lactose fermenter	MacConkey Agar
	Haemophilus influenzae	Requires factors X and V for growth	Chocolate Agar, Haemophilus Test Agar
	Yersinia pestis	Non-motile, produces Yersinia outer proteins	Blood Agar, MacConkey Agar

Protozoal Parasites, their characteristics and identification method

Protozoal Parasite	Detailed Characteristics	Identification
Plasmodium falciparum	Intracellular parasite causing severe malaria; multiple stages in human host	Human blood culture
Plasmodium vivax	Forms hypnozoites (dormant stage) in the liver; relapses can occur	Human blood culture
Plasmodium ovale	Forms dormant liver stage (hypnozoite); similar to P. vivax	Human blood culture
Plasmodium malariae	Causes quartan malaria; distinctive 72-hour replication cycle	Human blood culture
Giardia lamblia	Flagellated parasite causing gastrointestinal infection; forms cysts	Buffered charcoal yeast extract agar (BCYE)
Entamoeba histolytica	Causes amoebic dysentery; forms trophozoites and cysts	Robinson's medium
Trichomonas vaginalis	Causes sexually transmitted infection (trichomoniasis); flagellated parasite	Diamond's medium
Toxoplasma gondii	Intracellular parasite causing toxoplasmosis; can form tissue cysts	Cell culture
Trypanosoma cruzi	Causes Chagas disease; transmitted by triatomine bugs; intracellular parasite	LIT medium
Leishmania spp.	Intracellular parasite causing leishmaniasis; transmitted by sandflies	NNN medium
Cryptosporidium spp.	Intracellular parasite causing cryptosporidiosis; forms oocysts	Modified Ziehl-Neelsen (mZN) staining
Cyclospora cayetanensis	Causes cyclosporiasis; oocyst-forming parasite; associated with contaminated food	Modified acid-fast staining
Isospora belli	Causes isosporiasis; intracellular parasite; forms oocysts	Modified acid-fast staining
Babesia spp.	Intraerythrocytic parasites causing babesiosis; transmitted by ticks	Human blood culture
Naegleria fowleri	Causes primary amoebic meningoencephalitis (PAM); free-living amoeba	Non-selective culture media
Acanthamoeba spp.	Causes Acanthamoeba keratitis and granulomatous encephalitis; free-living amoeba	Non-nutrient agar, Peptone-Yeast-Glucose (PYG) medium
Trichomonas tenax	Found in the oral cavity; non-pathogenic flagellated parasite	Diamond's medium
Blastocystis hominis	Causes gastrointestinal infection; unicellular parasite with diverse forms	Jones' medium
Leishmania donovani	Causes visceral leishmaniasis; intracellular parasite; transmitted by sandflies	NNN medium
Dientamoeba fragilis	Causes gastrointestinal infection; amoeba with no known cyst stage	Non-selective culture media
Balantidium coli	Causes balantidiasis; ciliated parasite; forms cysts and trophozoites	Non-selective culture media
Entamoeba coli	Commensal in the human gastrointestinal tract; non

Virus classification 

          

Classification	Envelop	Number of Strands	Family	Species	Shape	Size (nm)	Diseases Caused
DNA Viruses
Adenoviridae	No	Double-stranded	Adenovirus	Human adenovirus (HAdV)	Icosahedral	70-90	Respiratory infections, Conjunctivitis
Herpesviridae	Yes	Double-stranded	Herpesvirus	Herpes simplex virus (HSV-1,   HSV-2)	Icosahedral	150-200	Cold sores, Genital herpes
Herpesviridae	Yes	Double-stranded	Herpesvirus	Varicella-zoster virus (VZV)	Icosahedral	150-200	Chickenpox, Shingles
Herpesviridae	Yes	Double-stranded	Herpesvirus	Epstein-Barr virus (EBV)	Icosahedral	150-200	Infectious mononucleosis, Burkitt's lymphoma
Papillomaviridae	No	Double-stranded	Papillomavirus	Human papillomavirus (HPV)	Non-enveloped	45-55	Cervical cancer, Genital warts
Polyomaviridae	No	Double-stranded	Polyomavirus	JC virus	Non-enveloped	40-45	Progressive multifocal leukoencephalopathy (PML)
Polyomaviridae	No	Double-stranded	Polyomavirus	BK virus	Non-enveloped	40-45	Kidney disease, Transplant complications
Parvoviridae	No	Single-stranded	Parvovirus	Parvovirus B19	Non-enveloped	18-26	Fifth disease (Erythema infectiosum)
RNA Viruses
Picornaviridae	No	Single-stranded	Enterovirus	Poliovirus	Icosahedral	22-30	Polio
Picornaviridae	No	Single-stranded	Enterovirus	Coxsackievirus	Icosahedral	22-30	Hand, Foot, and Mouth Disease
Picornaviridae	No	Single-stranded	Enterovirus	Echovirus	Icosahedral	22-30	Meningitis, Myocarditis
Picornaviridae	No	Single-stranded	Rhinovirus	Rhinovirus	Icosahedral	22-30	Common cold
Flaviviridae	Yes	Single-stranded	Flavivirus	Dengue virus	Icosahedral	40-60	Deng

 

Pathogens and their characteristics

Group	Pathogen	Typical Characteristics
Bacteria	Escherichia coli	Gram-negative, facultative anaerobe, commonly found in the intestinal tract, can cause gastrointestinal infections, produces toxins
Bacteria	Staphylococcus aureus	Gram-positive, facultative anaerobe, forms clusters, commonly found on the skin and mucous membranes, can cause skin infections, produces various toxins
Bacteria	Streptococcus pyogenes	Gram-positive, facultative anaerobe, forms chains, commonly found in the throat and skin, can cause strep throat, skin infections, produces toxins
Bacteria	Salmonella enterica	Gram-negative, facultative anaerobe, commonly found in contaminated food and water, can cause gastrointestinal infections, produces toxins
Bacteria	Mycobacterium tuberculosis	Acid-fast staining, slow-growing, intracellular pathogen, causes tuberculosis, has a waxy cell wall, requires specialized media for culture and long incubation periods
Bacteria	Clostridium difficile	Gram-positive, anaerobic, forms spores, commonly found in the gastrointestinal tract, can cause severe diarrhea and colitis, associated with antibiotic use, produces toxins
Bacteria	Neisseria gonorrhoeae	Gram-negative, aerobic, diplococci, sexually transmitted pathogen, causes gonorrhea, can infect the urogenital tract and other mucous membranes, can develop resistance to antibiotics
Bacteria	Vibrio cholerae	Gram-negative, curved rod, facultative anaerobe, commonly found in contaminated water, causes cholera, produces cholera toxin
Bacteria	Helicobacter pylori	Gram-negative, microaerophilic, spiral-shaped, commonly found in the stomach, causes gastric ulcers and gastritis, has the ability to survive in the acidic environment of the stomach
Bacteria	Pseudomonas aeruginosa	Gram-negative, aerobic, opportunistic pathogen, commonly found in moist environments, can cause infections in the respiratory tract, urinary tract, and wounds, produces various virulence factors
Protozoa	Plasmodium falciparum	Intracellular parasite, causes severe malaria, undergoes complex life cycle involving human and mosquito hosts, forms different stages (merozoites, trophozoites, gametocytes) in the human host
Protozoa	Giardia lamblia	Flagellated parasite, causes gastrointestinal infection (giardiasis), forms cysts that can survive in the environment, transmitted through contaminated water and food
Protozoa	Entamoeba histolytica	Amoeboid parasite, causes amoebic dysentery, forms trophozoites and cysts, can invade the intestinal wall and other organs, transmitted through contaminated food and water
Protozoa	Trichomonas vaginalis	Flagellated parasite, sexually transmitted pathogen, causes trichomoniasis, infects the urogenital tract, motile and does not form cysts
Protozoa	Toxoplasma gondii	Intracellular parasite, causes toxoplasmosis, can form tissue cysts in various organs, transmitted through ingestion of contaminated food, can be transmitted from mother to fetus during pregnancy

Modes of transmission of pathogens

Mode of Transmission	Parasites
Vector-borne	Plasmodium spp. (malaria), Trypanosoma spp. (African trypanosomiasis, Chagas disease), Leishmania spp. (leishmaniasis), Borrelia burgdorferi (Lyme disease), Rickettsia spp. (Rocky Mountain spotted fever)
Fecal-oral	Giardia lamblia, Entamoeba histolytica, Cryptosporidium spp., Cyclospora cayetanensis, Ascaris lumbricoides (ascariasis), Enterobius vermicularis (pinworm), Taenia spp. (taeniasis), Echinococcus spp. (echinococcosis)
Sexual transmission	Trichomonas vaginalis, Human papillomavirus (HPV), Treponema pallidum (syphilis), Neisseria gonorrhoeae (gonorrhea), Chlamydia trachomatis (chlamydia)
Direct contact	Sarcoptes scabiei (scabies), Pediculus humanus (lice infestation), Tinea spp. (ringworm), Candida spp. (yeast infection)
Inhalation	Histoplasma capsulatum (histoplasmosis), Coccidioides spp. (coccidioidomycosis), Mycobacterium tuberculosis (tuberculosis)
Blood transfusion	Plasmodium spp. (malaria), Trypanosoma spp. (African trypanosomiasis, Chagas disease), Babesia spp. (babesiosis), Hepatitis B virus, Hepatitis C virus, Human immunodeficiency virus (HIV)
Organ transplantation	Trypanosoma cruzi (Chagas disease), Toxoplasma gondii, Strongyloides stercoralis (strongyloidiasis)
Congenital transmission	Toxoplasma gondii, Treponema pallidum (syphilis), Parvovirus B19 (fifth disease), Rubella virus, Cytomegalovirus (CMV)
Foodborne	Taenia spp. (taeniasis), Echinococcus spp. (echinococcosis), Trichinella spp. (trichinellosis), Salmonella spp., Escherichia coli (E. coli), Hepatitis A virus, Norovirus
Waterborne	Cryptosporidium spp., Giardia lamblia, Entamoeba histolytica, Cyclospora cayetanensis, Vibrio cholerae, Salmonella spp., Leptospira spp.
Animal bites	Rabies virus, Pasteurella multocida (from dog/cat bites)