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
  • 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