Microbiology
Gram Positive Lab Algorithm
Gram-Positive Cocci (GPC)
| Bacteria | Test | S/R |
|---|---|---|
| Staphylococcus epidermidis | Novobiocin | S |
| Staphylococcus saprophyticus | Novobiocin | R |
| Streptococcus pnuemonia | Optochin | S |
| Streptococcus viridans | Optochin | R |
| GAS :: Streptococcus pyogenes | Bacitracin | S |
| GBS :: Streptococcus agalactiae | Bacitracin | R |
| GDS :: Streptococcus bovis | 6.5% NaCl | S |
| GDS :: Enterococcus | 6.5% NaCl | R |
- Streptococcus viridans
- Streptococcus anginosus
- Streptococcus mitis
- Streptococcus sanguinis
- Streptococcus salivarius
- Streptococcus mutans
- Streptococcus bovis
- Streptococcus equinus
- Streptococcus gallolyticus
- Streptococcus infantarius
Gram-Positive Bacilli (GPB)
Non-branching
| Bacteria | Stain | Culture |
|---|---|---|
| Bacillus | - | - |
| Clostridium | - | - |
| Corynebacterium | - | Loffler Tellurite |
| Lactobacillus | - | - |
| Listeria | - | - |
| Mycobacterium | Acid-fast | Lowenstein-Jensen Middlebrook |
| Tropheryma | PAS | - |
Branching
| Bacteria | Stain | Culture |
|---|---|---|
| Actinomyces | - | - |
| Nocardia | Acid-fast | - |
Gram Negative Lab Algorithm
Gram-Negative Cocci (GNC)
| Bacteria | Stain | Culture |
|---|---|---|
| Moraxella | - | - |
| Neisseria | - | Thayer-Martin |
Gram-Negative Bacilli (GNB)
Respiratory
| Bacteria | Stain | Culture |
|---|---|---|
| Acinetobacter | - | - |
| Bordetella | - | Bordet-Gengou Regan-Lowe |
| Haemophilus | - | Chocolate |
| Legionella | Silver | Charcoal yeast |
Enteric {B-SEEK-P-SSPY}
| Bacteria | Stain | Culture | Lactose | Oxidase | H2S |
|---|---|---|---|---|---|
| Bacteroides | - | - | + | ± | - |
| Serratia | - | MacConkey | + | - | - |
| Escherichia | - | MacConkey Eosin-methylene blue (EMB) | + | - | - |
| Enterobacter | - | MacConkey | + | - | - |
| Klebsiella | - | MacConkey | + | - | - |
| Pseudomonas | - | - | - | + | - |
| Salmonella | - | - | - | - | + |
| Shigella | - | - | - | - | - |
| Proteus | - | - | - | - | + |
| Yersinia | - | - | - | - | - |
Zoonotic
| Bacteria | Stain | Culture |
|---|---|---|
| Bartonella | - | - |
| Brucella | - | - |
| Francisella | - | - |
| Pasteurella | - | - |
Curved
| Bacteria | Stain | Culture | Oxidase |
|---|---|---|---|
| Campylobacter | - | - | + |
| Helicobacter | Silver | - | + |
| Vibrio | - | - | + |
Spirochete {BLT}
| Bacteria | Stain | Culture |
|---|---|---|
| Borrelia | Giemsa | - |
| Leptospira | - | - |
| Treponema | - | - |
Intracellular
| Bacteria | Stain | Culture |
|---|---|---|
| Coxiella | - | - |
| Chlamydia | Giemsa | - |
| Rickettsia | Giemsa | - |
| Ehrlichia | Giemsa | - |
Without Cell Wall
| Bacteria | Stain | Culture |
|---|---|---|
| Mycoplasma | - | Eaton |
| Ureaplasma | - | - |
Gram Stain Limitation
| Mnemonic | Bacteria |
|---|---|
| These | Treponema |
| Microbes | Mycobacteria |
| May | Mycoplasma |
| Lack | Legionella |
| Real | Rickettsia |
| Color | Chlamydia |
Microbial Hemolysis Test
β-Hemolytic Bacteria {LABS}
- Listeria monocytogenes
- GAS :: Streptococcus pyogenes
- GBS :: Streptococcus agalactiae
- Staphylococcus aureus
Aerobes & Anaerobes
Obligate Aerobes
| Mnemonic | Bacteria |
|---|---|
| Nagging | Nocardia |
| Pests | Pseudomonas |
| Must | Mycobacterium |
| Breathe | Bordetella |
Obligate Anaerobes {ABC}
- Actinomyces
- Bacteroides
- Clostridium
Intracellular Bacteria
Obligate
- Coxiella
- Chlamydia
- Rickettsia
- Ehrlichia
Facultative
| Mnemonic | Bacteria |
|---|---|
| Some | Salmonella typhi |
| Nasty | Neisseria |
| Bugs | Brucella |
| May | Mycobacterium |
| Live | Listeria monocytogenes |
| Facultative | Francisella |
| L | Legionella |
| Y | Yersinia pestis |
Encapsulated Bacteria
- Streptococcus pneumoniae
- Haemophilus influenzae
- Neisseria meningitidis
- Escherichia coli: K capsule
- Klebsiella pneumonia
- Pseudomonas aeruginosa
- Salmonella typhi: Vi capsule
Catalase-Positive Microbes {N-PLACESS}
- Nocardia
- Pseudomonas
- Listeria
- Aspergillus
- Candida
- Escherichia
- Staphylococcus
- Serratia
Oxidase-Positive Microbes {PVNCH}
- Pseudomonas
- Vibrio
- Neisseria
- Campylobacter
- Helicobacter
Urease-Positive Microbes {PUNCH-KS}
- Proteus
- Ureaplasma
- Nocardia
- Cryptococcus
- Helicobacter
- Klebsiella
- Staphylococcus
Spore-forming Bacteria
- Bacillus
- Clostridium
- Coxiella
Bacterial Virulence Factors
Adhesion
| Factor | Bacteria |
|---|---|
| Biofilm | - |
| Fimbria | - |
| Pili | - |
| Teichoic acid | Gram positive bacteria |
Immunoevasion
| Factor | Bacteria |
|---|---|
| Capsule | - |
| A protein | Staphylococcus aureus |
| M protein | Streptococcus pyogenes |
| IgA protease | - |
Destruction
| Factor | Bacteria |
|---|---|
| Hyaluronidase | - |
| Collagenase | - |
Toxins
| Factor | Bacteria |
|---|---|
| Endotoxin | Gram negative bacteria |
| Exotoxin | Gram positive & negative bacteria |
Bacterial Exotoxins
Cell Surface-Active [Type 1]
| Bacteria | Exotoxin |
|---|---|
| Staphylococcus auerus | Toxic shock syndrome toxin-1 (TSST-1) Enterotoxin |
| Streptococcus pyogenes | Erythrogenic toxin |
Membrane Damaging [Type 2]
| Bacteria | Exotoxin |
|---|---|
| Staphylococcus aureus | Leucocidin |
| Streptococcus pyogenes | Streptolysin |
| Clostridium perfringens | α-toxin |
| Listeria monocytogenes | Listeriolysin |
Intracellular [Type 3]
| Bacteria | Exotoxin | Target | Mechanism |
|---|---|---|---|
| Corynebacterium diphtheriae | Diphtheria toxin | Elongation factor (EF-2) | ↓ Protein synthesis |
| Pseudomonas aeruginosa | Exotoxin A | Elongation factor (EF-2) | ↓ Protein synthesis |
| Shigella | Shiga toxin | 60S ribosome | ↓ Protein synthesis |
| EHEC | Shiga-like toxin | 60S ribosome | ↓ Protein synthesis |
| ETEC | Heat-stable toxin (ST) | ↑ GsPCR | ↑ cGMP → ↑ Fluid secretion |
| ETEC | Heat-labile toxin (LT) | ↑ GsPCR | ↑ cAMP → ↑ Fluid secretion |
| Vibrio cholerae | Cholera toxin | ↑ GsPCR | ↑ cAMP → ↑ Fluid secretion |
| Bacillus anthracis | Edema toxin | ↑ GsPCR | ↑ cAMP → ↑ Fluid secretion |
| Bordetella pertussis | Pertussis toxin | ↓ GiPCR | ↑ cAMP → ↓ Phagocytosis |
| Clostridium botulinum | Botulinum toxin | SNARE | ↓ ACh release |
| Clostridium tetani | Tetanus toxin | SNARE | ↓ GABA & Glycine release |
Microbes Producing Shiga Toxin
- Shigella dysenteriae serotype 1
- Shiga-toxin-producing Escherichia coli (STEC)
Microbes with Toxins Carried on Lysogenic Phages {ABCDE}
| Toxin | Bacteria |
|---|---|
| Shiga-like toxin | EHEC |
| Botulinum toxin | Clostridium botulinum |
| Cholera toxin | Vibrio cholera |
| Diphtheria toxin | Corynebacterium diphtheria |
| Erythrogenic toxin | Streptococcus pyogenes |
Classification of Fungi
Yeast
- Cryptococcus
- Candida
- Pneumocystis
Dimorphic
- Blastomyces
- Coccidioides
- Histoplasma
- Paracoccidioides
- Sporothrix
Mold
- Aspergillus
- Mucor & Rhizopus
- Malassezia
- Dermatophytes
- Epidermophyton
- Microsporum
- Trichophyton
Classification of Parasites
Protozoan Parasites
Amoebae
- Acanthamoeba
- Entamoeba
- Naegleria
Flagellates
- Giardia
- Leishmania
- Trichomonas
- Trypanosoma
Ciliates
Sporozoans
- Babesia
- Cryptosporidium
- Plasmodium
- Toxoplasma
Animalian Parasites
Cestodes [Tapeworms]
- Taenia
- Taenia solium
- Taenia saginata
- Echinococcus
- Diphyllobothrium
Trematodes [Flukes]
- Clonorchis
- Paragonimus
- Schistosoma
- Schistosoma haematobium
- Schistosoma mansoni
- Schistosoma japonicum
Nematodes [Roundworms]
- Enterobius vermicularis
- Ascaris lumbricoides
- Trichuris trichiura
- Trichinella spiralis
- Toxocara
- Toxocara canis
- Toxocara catis
- Strongyloides stercoralis
- Ancylostoma duodenale
- Necator americanus
- Wucheria bancrofti
- Onchocerca volvulus
- Loa loa
- Dracunculus medinensis
Characteristics of Parasites
Autoinfection
- Cryptosporidium parvum
- Enterobius vermicularis
- Strongyloides stercoralis
- Capillaria philippinensis
- Teania solium
- Hymenolepis nana
Absent Cyst Stage
- Trichomona vaginalis
- Dientamoeba fragilis
Life Cycle of Viruses {APUSAR}
- Attachment
- Penetration
- Uncoating
- Synthesis
- Assembly
- Release
Viral Replication
| Species | Replication | Enzymes |
|---|---|---|
| dsDNA | dsDNA → dsDNA | DNA polymerase |
| dsDNA :: hepadnavirus | dsDNA → RNA → dsDNA | RNA polymerase Reverse transcriptase |
| +ssRNA | +ssRNA → -ssRNA → +ssRNA | RNA polymerase |
| +ssRNA :: retrovirus | +ssRNA → dsDNA → +ssRNA | Reverse transcriptase RNA polymerase |
| -ssRNA | -ssRNA → +ssRNA → -ssRNA | RNA polymerase |
Viral Transcription
| Species | Transcription | Enzymes |
|---|---|---|
| dsDNA | dsDNA → +mRNA | RNA polymerase |
| dsDNA :: hepadnavirus | dsDNA → +mRNA | RNA polymerase |
| +ssRNA | +ssRNA → -ssRNA → +mRNA | RNA polymerase |
| +ssRNA :: retrovirus | +ssRNA → dsDNA → +mRNA | Reverse transcriptase RNA polymerase |
| -ssRNA | -ssRNA → +mRNA | RNA polymerase |
Classification of DNA Viruses
| Virus | Strand | Nucleic Acid | Capsid | Envelope |
|---|---|---|---|---|
| Adenovirus | 2 | Linear | Icosahedral | - |
| Hepadnavirus | 2 | Circular | Icosahedral | + |
| Herpesvirus | 2 | Linear | Icosahedral | + |
| Parvovirus | 1 | Linear | Icosahedral | - |
| Papillomavirus | 2 | Circular | Icosahedral | - |
| Polyomavirus | 2 | Circular | Icosahedral | - |
| Poxvirus | 2 | Linear | Complex | + |
Classification of RNA Viruses
| Virus | Strand | Nucleic Acid | Capsid | Envelope |
|---|---|---|---|---|
| Hepevirus | + | Linear | Icosahedral | - |
| Calicivirus | + | Linear | Icosahedral | - |
| Picornavirus | + | Linear | Icosahedral | - |
| Reovirus | 2 | Linear | Icosahedral | - |
| Coronavirus | + | Linear | Helical | + |
| Flavivirus | + | Linear | Icosahedral | + |
| Togavirus | + | Linear | Icosahedral | + |
| Retrovirus | + | Linear | Icosahedral | + |
| Arenavirus | - | Circular | Helical | + |
| Bunyavirus | - | Circular | Helical | + |
| Deltavirus | - | Circular | Helical | + |
| Paramyxovirus | - | Linear | Helical | + |
| Orthomyxovirus | - | Linear | Helical | + |
| Filovirus | - | Linear | Helical | + |
| Rhabdovirus | - | Linear | Helical | + |
Segmented RNA Viruses {BOAR}
- Bunyavirus
- Orthomyxovirus
- Arenavirus
- Reovirus
Subspecies of Herpesvirus
| Subspecies | Virus |
|---|---|
| HHV1 | Herpes simplex virus 1 (HSV1) |
| HHV2 | Herpes simplex virus 2 (HSV2) |
| HHV3 | Varicella zoster virus (VZV) |
| HHV4 | Epstein-Barr virus (EBV) |
| HHV5 | Cytomegalovirus (CMV) |
| HHV6 | Roseolovirus |
| HHV7 | Roseolovirus |
| HHV8 | Kaposi sarcoma-associated herpesvirus (KSHV) |
Subspecies of Picornavirus {PERCH}
- Poliovirus
- Echovirus
- Rhinovirus
- Coxsackievirus
- HAV
Microbe Detection Techniques
Special Stain
| Stain | Microbes |
|---|---|
| PAS | Tropheryma |
| Giemsa | Chlamydia Borrelia Rickettsia Trypanosoma Plasmodium |
| Acid-fast | Mycobacterium Nocardia |
| Silver | Helicobacter Legionella Fungi |
| India ink | Encapsulated bacteria Cryptococcus |
Special Culture
| Agar | Microbes |
|---|---|
| Loffler Tellurite | Corynebacterium |
| Lowenstein-Jensen Middlebrook | Mycobacterium |
| Thayer-Martin | Neisseria |
| Bordet-Gengou Regan-Lowe | Bordetella |
| Chocolate | Haemophilus |
| Charcoal yeast | Legionella |
| MacConkey | Serratia Escherichia Enterobacter Klebsiella |
| Eosin-methylene blue (EMB) | Escherichia |
| Eaton | Mycoplasma |
Special Laboratory Tests
| Test | Microbes |
|---|---|
| Amine whiff test | Gardnerella vaginalis |
| CAMP test | GBS :: Streptococcus agalactiae |
| Cold agglutinin test | Mycoplasma HCV & EBV & CMV |
| ELISA Western blot | Borrelia burgdorferi HIV |
| Elek test | Corynebacterium diphtheriae |
| Germ tube test | Candida albicans |
| Latex agglutination test | Cryptococcus neoformans EBV |
| Heterophile antibody test Monospot test | EBV |
| Nitrite test | Gram negative bacteria |
| PCR | Neisseria gonorrhoeae Chlamydia trachomatis |
| Quellung reaction | Encapsulated bacteria |
| Strep test | GAS :: Streptococcus pyogenes |
| Tzanck test | HSV & VZV |
| Urea breath test Fecal antigen test | Helicobacter pylori |
| Urine antigen test | Streptococcus pneumoniae Legionella Histoplasma |
| Dark-field VDRL/RPR FTA-ABS | Treponema pallidum |
| Weil-Felix test | Rickettsia |