Basic Microbiology

 

• Taxonomy

  Example: Enterobacteriaceae is the family, Eschericia is the genus, E. coli is the species, and E. coli O157 is the serotype.

• Classification of bacteria

  Gram positive bacteria

  Thick peptidoglycan layer retains the blue-purple crystal violet stain.

  Cocci

  • Staphylococcus
  • Streptococcus
  • Enterococcus
  • Viridans streptococci
  • Peptococcus (anaerobe)
  • Peptostreptococcus (anaerobe)

  Bacilli

  • Clostridioides (anaerobe)
  • Listeria monocytogenes
  • Corynebacterium diphtheriae
  • Bacillus anthracis
  • Bacillus cereus
  • Actinomyces (anaerobe)

  Gram negative bacteria

  Thin peptidoglycan layer cannot retain crystal violet, so coloured red-pink by safranin counterstain. However, they have a second outer membrane of lipids, lipoproteins, and lipopolysaccharides (LPS), the latter containing an important endotoxin.

  Cocci

  • Neisseria
  • Moraxella
  • Bordetella

  Bacilli

  Enterobacteriaceae family:

  • Coliforms: E. coli, Klebsiella, Enterobacter.
  • Non-coliforms: Shigella, Salmonella, Proteus, Yersinia.

  Many others:

  • GI: Campylobacter jejuni, Vibrio cholera, Helicobacter pylori (helix-shaped curved rod).
  • Respiratory: Pseudomonas, Haemophilus influenzae, Legionella.
  • Others: Burkholderia, Brucella, Bacteroides (anaerobe), Fusobacterium (anaerobe).

  Spirochetes

  • Weakly Gram negative, though their small size means they are hard to visualise with traditional microscopy.
  • Pathogens: Treponema, Leptospira, Borrelia.

  Atypical bacteria

  Definition

  • Atypical bacteria lack a cell wall so don't stain Gram positive or negative.
  • Does not include mycobacteria, as they do have a cell wall, though it doesn't stain due to it's thick and oily nature.

  Pathogens

  • Intracellular: Chlamydia, Rickettsia.
  • Extracellular: Mycoplasma, Ureaplasma.

  Mnemonics

  • Gram positive cocci have coccus in the genus name (they're positive about being cocci): Staphylococcus, Streptococcus, and Enterococcus. Note that gonococcus is not a genus name, but short for the species Neisseria gonorrhoeae, which is Gram negative.
  • Gram positive bacilli are ABCD+L: Actinomyces, Bacillus, Clostridium, Diphtheria, and Listeria.
  • GraM Negative cocci are Moraxella and Neisseria.
  • Spirochetes are like little BULLETS: Borrelia, Leptosira, Treponema.
  • Bacteria without a cell wall might CRUMble: Chlamydia, Rickettsia, Ureaplasma, Mycoplasma.
  • Everything else is a Gram negative bacillus.

• Viruses

  Infectious agent composed of nucleic acid and proteins, which uses the cellular machinery of living organisms to replicate.

  DNA viruses

  • Double-stranded (dsDNA): herpesviruses (HSV1-2, VZV, EBV, CMV, HHV6-8), adenoviruses, poxviruses.
  • Single-stranded (ssDNA): parvovirus.
  • dsDNA with RNA intermediate (retrovirus): HBV.

  RNA viruses

  • Single-stranded sense RNA ((+)ssRNA): enteroviruses (enterovirus, poliovirus, Coxsackie, echovirus), flaviviruses (yellow fever, dengue, Zika, West Nile), coronavirus, hepatitis A/C/E.
  • Single-stranded antisense RNA ((-)ssRNA): many respiratory viruses (influenza, parainfluenza, RSV, metapneumovirus), measles, mumps, VHF viruses (Lassa, Ebola, Marburg, hantavirus), rabies.
  • Double-stranded RNA (dsRNA): rotavirus.
  • ssRNA with DNA intermediate (retrovirus): HIV, HTLV.

• Protozoa

  Motile, unicellular eukaryotic parasites.

  GI pathogens

  • Giardia
  • Entamoeba
  • Cryptosporidium
  • Cyclosporidium

  Systemic pathogens

  • Plasmodium
  • Trypanosoma
  • Leishmania
  • Toxoplasma

• Helminths

  Aka parasitic worms.

  Flatworms (platyhelminths)

  • Trematodes (aka flukes): Schistosoma (blood fluke).
  • Cestodes (aka tapeworms): Echinococcus granulosus (dog tapeworm), Echinococcus multilocularis, Taenia saginata (beef tapeworm), Taenia solium (pork tapeworm).

  Roundworms (nematodes)

  • Strongyloides (threadworm).
  • Ascaris (roundworm).
  • Dracunculus medinensis (Guinea worm).
  • Ancylostoma and Necator (hookworm).
  • Enterobius (pinworm).

• Fungi

  A eukaryotic kingdom. Their cell walls contain both glucans and chitin.

  Yeasts

  • Unicellular.
  • Pathogens: Candida, Cryptococcus.

  Molds

  • Multicellular, with filaments known as hyphae.
  • Pathogens: Aspergillus, Histoplasma, Pneumocystis, Stachybotrys.

• Lab findings by pathogen type

  • Bacterial: ↑neutrophils, pus (i.e. neutrophils), ↑CRP, ↑procalcitonin.
  • Viral: ↑lymphocytes, sometimes ↓lymphocytes.
  • Parasite: ↑eosinophils.