Basic Microbiology

Table 1-1: Characteristics of medically important microorganisms.

Characteristics Viruses Bacteria Fungi Parasites
Cells N Y Y Y
Approximate 0.02-0.2 1-5 3-10 (yeast) 15-25
diameter (um) (tropozoites)
Nucleic acid Either DNA or RNA Both DNA and Both DNA and Both DNA and
RNA RNA RNA
Type of nucleus -- Prokaryote Eukaryote Eukaryote
Ribosomes -- 70S (50S + 30S) 80S (60S+40S) 80S (60S+40S)
Mitochondria -- -- + +
Outer surface Capsid (Protein); Cell wall Cell wall (chitin) Flexible
Envelope(Lipoprotein) (Peptidoglycan) membrane
EXCEPT
Mycoplasma
Manner of -- Binary fission Budding/ Mitosis
replication Mitosis
Number of -- One >1 >1
chromosomes

Table 1-2: Prokaryotes vs. Eukaryotes

Characteristics Prokaryote Eukaryote
Example Bacteria Fungi; Parasites; Plants;
Animals
Nucleus -- +
Membrane-bound organelles -- +
Mitochondria -- +
Nuclear membrane -- +
Golgi apparatus -- +
Endoplasmic reticulum -- +
Lysosomes -- +
Mitosis -- +
Ribosomes 70S 80S
Cell wall (Peptidoglycan) + -
Unicellular Multicellular
Number of chromosomes One (1) >1

Bacterial cell morphology

3 Basic shapes: Arrangements:

 Cocci - In pairs
 Bacilli - In chains
 Spirochetes - In clusters
– In singly

*Pleomorphic  variation in shape (many-shaped)

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Table 1-3: Gram stain
Reagents Gram-positive Gram-negative
Crystal Violet Blue/ Purple Blue/ Purple
Gram’s Iodine Blue/ Purple Blue/ Purple
Alcohol/ Acetone Blue/ Purple Colorless
Safranin Blue/ Purple Red/ Pink

Table 1-4: Bacterial structure

Envelope structure Gram + or - Chemical composition Functions
Capsule Polysaccharide EXCEPT Anti-phagocytic; Immunogenic;
Bacillus anthracis, in Virulence/Pathogenicity factor;
which it is a Adherence to host cell
polypeptide of D-
glutamic acid
Outer membrane * Phospholipids/proteins:
Lipopolysaccharide(LPS)
Lipid A Toxic component of endotoxin
Polysaccharide Immunogenic

OM proteins Attachment

Protein proteins Passive transport

Cell wall* = Peptidoglycan-open-3- Rigid support; Cell shape;
Peptidoglycan D net of: NAM & NAG Protection from osmotic damage;
Present to all bacteria Synthesis (-) by penicillins and
EXCEPT Mycoplasma cephalosporins ; Confers Gram
reaction; Degraded by lysosome
Immunogenic; Attachment;

Teichoic acid: Induces TNF-α and IL-1

polymers of ribitol or
glycerol, bound to cell
membrane or
peptidoglycan
Acid-fast Acid fastness; Resistance to drying
organism Mycolic acid and chemicals
Periplasmic space* “Storage space” Enzymes to break down large
between the inner and molecules,  lactamases ; Aids
outer membrane regulation of osmolarity
Cytoplasmic Phospholipid bilayer Hydrophobic cell “sack” Selective
membrane* with many embedded permeability and active transport;
proteins Carrier for enzymes for: Oxidative
metabolism; Phosphorylation
Phospholipid synthesis; DNA
replication; Peptidoglycan cross
linkage; Penicillin Binding Proteins
(PBPs)
Mesosomes* Invagination of plasma Participates in cell division and
membrane secretion

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Table 1-5: Bacterial surface structure
Surface structure Gram + or - Chemical composition Functions
Pilus or Fimbria Glycoprotein Two types:
1.) Common – mediates
attachment to surfaces
2.) sex pilus mediates attachment
of two bacteria during conjugation
Flagellum Protein Motility
Axial filaments Spriochetes Protein Motility
(internal flagellum)

Table 1-6: Bacterial internal structure

Internal structure Gram + or - Chemical composition Functions
Nucleoid region* DNA; RNA; Proteins Genetic material (all essential
genes); Primers; mRNA linker
proteins; polymerases
Plasmids DNA Non-essential genetic material;
Roles in conjugation; Drug
resistance; Toxin production
Ribosomes* 70S (CHON/RNA) Protein synthesis

30S (16s RNA)

50S (23 & 5 s)

Granules Glycogen Storage: polymerization of
molecules present in high numbers
in cells reduces osmotic pressure
Endospores Keratin coat; Calcium Resistance to heat, chemical and
dipicolinate dehydration
Note: All marked ( *) are essential components of a bacterial cell

Table 1-7: Comparison of Bacterial cell envelope

Component Gram-positive Gram-negative
Capsule Y Y
Surface CHON Y Y
Surface CHO Y Y
Peptidoglycan Y (Thick 85%) Y (Thin 15%)
Teichoic acid Y N
Outer membrane N Y
Porin channels N Y
Periplasmic space N Y
Spheroplast N Y
Protoplast Y N

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GRAM STAINING REACTIONS
(†Marked organisms have high numbers of questions in the pool.)

Table I-9. Gram-Negative Bacteria

Table I-8. Gram-Positive Bacteria Aerobic
Cocci Cocci Neisseria†
†
Staphylococcus Moraxella
Streptococcus†
Rods Rods
Aerobic or facultative anaerobic
Pseudomonas
Bacillus Legionella
Listeria Brucella
Corynebacterium† Bordetella†
Nocardia Francisella
†
Mycobacterium
Helical (and microaerophilic)
Anaerobic
Clostridium
† Campylobacter
Facultative anaerobic rods
Actinomyces Helicobacter
Eubacterium Enteobacteriaceae†
Propionibacterium Escherichia†
Lactobacillus Shigella
†
Salmonella
*Spore formers are Bacillus and Clostridium.
Citrobacter
Klebsiella
Table I-10. Non-Gram-staining Bacteria*
Enterobacter
Mycoplasmataceae Serratia
Mycoplasma†
Proteus
Ureaplasma
Yersinia†
Vibrionaceae
Vibrio
*Note also:
Pasteurellaceae
Pasteurella
Poorly visible on traditional Gram stain:
Mycobacterium does not stain well with the Haemophilus †
Gram stain due to its waxy cell wall. It is
Anaerobic straight to helical rods
considered Gram-positive.
Most spirochetes, Chlamydiae, and rickettsias
Bacteriodes/Prevotella
are so thin that the color of the Gram stain Fusobacterium
cannot be seen. All have Gram-negative cell
Spirochetes
walls.
Treponema†
Legionella (Gram-negative) also does not stain Borrelia
†
well with the traditional Gram stain unless Leptospira
counterstain time is increased.
Rickettsiaceae Rickettsia†
and relatives Bartonella (Rochalimea)
Coxiella
Ehrlichia
Chlamydiaceae
Chlamydia†

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Classifications of bacteria:

A. According to Carbon requirement:

I. Heterotrophs/ Organotrophs *
II. Lithotrophs/ Autotrophs
B. According to Energy requirement:
I. Chemotrophs *
II. Phototrophs
C. According to Oxygen requirement:
I. Obligate aerobes
II. Obligate anaerobes
III. Aerotolerant
IV. Microaerophilic
V. Facultative anaerobes
D. According to pH requirement:
I. Acidophiles
II. Neutrophiles *
III. Alkalophiles/ Basophiles

Figure 1-1 Bacterial growth curve

STERILIZATION AND DISINFECTION

Table 2-1 :Definition of terms.

Terms Definition
Sterilization Is the killing / removal of all microorganisms, including bacterial spores.
Disinfection Is the killing of pathogenic microorganisms
Disinfectant Antimicrobial agent that are applied to non-living objects to destroy
microorganisms, the process of which is known as disinfection.
Antiseptic Antimicrobial substances that are applied to living tissue/skin to reduce
the possibility of infection, sepsis, or putrefaction.

2 FORMS: 1.) Physical agents 2.) Chemical agents

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 I. Physical agents:

i. Heat
a. Moist Heat
i. Boiling – 100 °C
ii. Autoclaving- 121 ºC x 15-20 minutes at 15 psi
- Sporocidal
b. Dry heat - 180°C x 2 hrs

ii. Radiation
a. Ultraviolet (UV) light - 250 -260 nm
b. X-rays - Used in sterilization of heat-sensitive items, such as sutures and
surgical gloves, and plastic items, such as syringes

iii. Filtration - work by physically trapping particles larger than the pore size and by
retaining somewhat smaller particles via electrostatic attraction of the particles
to the filters

II. Chemical agents

Table 2-2: Chemical agents

Mechanism of action
Disruption of cell membrane
Modification of proteins
Modification of nucleic acids
Example of chemical agent
Alcohols; Detergents; Phenols
Chlorine; Iodine; Heavy metals; Hydrogen Peroxide;
Formaldehyde & Glutaraldehyde ; Ethylene Oxide
Acids & Alkalis
Dyes

ANTIBACTERIALS

Table 2-3: Definition of terms.

Terms Definition
Selective toxicity Is the ability of an antimicrobial agent to act an infecting organism
without toxic effects on host cells
Bactericidal drug Antimicrobial agent that kills bacteria
Bacteriostatic agent Antimicrobial agent that inhibits the growth of bacteria

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Table 2-4: Mechanism of action of important antibacterial drugs.
Mechanism of action Drugs
Inhibition of cell wall synthesis Penicillins, Cephalosporins, Carbapenems,
Monobactams, Vancomycin, Bacitracin
Inhibition of protein synthesis Aminoglycosides, Chloramphenicol, Macrolides,
Tetracyclines, Streptogramins, Linezolid ,
Clindamycins
Inhibition of nucleic acid synthesis Fluoroquinolones, rifampin
Inhibition of folic acid synthesis Sulfonamides, Trimethoprim, Pyrimethamine

Table 2-5: Inhibitors of cell wall synthesis

Drugs
β-lactam Penicillins; Cephalosporins; Carbapenems; Monobactams
Other antibiotics Vancomycin, Bacitracin

Table 2-6 Examples of β-lactam antibiotics

Example of β-lactam antibiotics Drugs
Penicillins Penicillin G, Penicillin V, Methicillin, Nafcillin, Oxacillin.
Cloxacillin, Dicloxacillin, Ampicillin, Amoxicillin, Carbenicillin,
Ticarcillin, Piperacillin, Mezlocilin, Azlocillin
Cephalosporins
 1st generation Cephalothin , Cephapirin , Cephradine , Cephalexin , Cefazolin ,
Cefadroxil
 2nd generation Cefamandole , Cefuroxime , Cefonicid , Ceforanide , Cefaclor,
Cefoxitin , Cefotetan , Cefprozil , Cefuroxime , Cefmetazole
 3 generation
rd
Ceftzoxime , Ceftriaxone , Ceftazidime , Ceftibuten ,
Cefotaxime , Cefixime , Cefpodoxime , Cefoperazone , Cefdinir
 4th generation Cefepime
Carbapenems Imepenem, Cilastatins
Monobactam Aztreonam

Table 2-7 Mechanism of action of protein inhibitors.

Events Drugs Mechanisms
1. Formation of Aminoglycosides (30S) Interfere with initiation codon functions–
initiation complex block association of 50S ribosomal
subunit with mRNA – 30S (static);
misreading of code – incorporation of
wrong AA (-cidal)
2. Amino-acid Tetracyclines (30S) Block the attachment of aminoacyl tRNA
incorporation to acceptor site (-static)
3. Formation of Chloramphenicol (50S) Inhibit the activity of peptidyltranferase
peptide bond (-static)
4.Translocation Macrolides & Clindamycin (50S) Inhibit translocation of peptidyl-tRNA
from acceptor to donor site (-static)

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Table 2-8: Examples of Nucleic acid inhibitors
Nucleic acid inhibitors Example Drugs
Fluoroquinolones
 1st generation Nalidixic acid, Conoxacin, Oxonilic acid
 2 generation
nd
Ciprofloxacin, Lomefloxacin, Ofloxacin, Enoxacin
 3 generation
rd
Clinafloxacin , Gatifloxacin , Gemifloxacin , Levofloxacin ,
Moxifloxacin , Sparfloxacin

Table 2-9: Anti-tubercular drugs.

Drug MOA/ MOR
Isoniazid (INH) (-) Mycolic acid synthesis; high level
resistance – deletion in katG gene
(encodes catalase needed for INH
bioactivation); low level resistance –
deletions in inhA gene (encodes acyl
carrier protein, the “target”)
Rifampicin Inhibits DNA-dependent RNA
polymerase. Resistance via change in
enzyme
Ethambutol Inhibits synthesis of arabinogalactan
(cell-wall component)
Pyrazinamide (PZA) Unknown, but metabolically activated
by bacteria – strains lacking the
bioactivating enzyme are resistant
Streptomycin Protein synthesis inhibition
Adverse Effect
Hepatitis (age-dependent), older
peripheral neuritis (use Vitamin B6),
hemolysis in G6PD deficiency, SLE in
slow acetylators (rare)
Proteinuria, hepatitis, “flu-like”
syndrome, induction of P450,
thrombocytopenia, red-orange
metabolites
Dose-dependent retrobulbar
neuritis  visual acuity and red-
green discrimination
Polyarthralgia, myalgia, hepatitis,
rash, hyperuricemia, phototoxicity,
porphyrin synthesis
Deafness, vestibular dysfunction,
nephrotoxicity

NORMAL FLORA
 Is the tern used to describe the various bacteria and fungi that are permanent residents of
certain body sites, especially the skin, oropharynx, colon and vagina.

Table 3-1: Medically important normal flora.

Location Most common flora Less common flora
Skin Staphylococcus epidermidis Staphylococcus aureus, Corynebacterium
(diphtheroids), various streptococci, Pseudomonas
aeruginosa, anaerobes (Propionibacterium), yeast
(Candida)
Nose Staphylococcus aureus S. epidermidis, Corynebacterium (diphtheroids),
various streptococci
Mouth Viridans Streptococci Various streptococci, Eikenella corrodens
Throat Viridans Streptococci Various streptococci, Neisseria sp. Haemophilus
influenzae, S.epidermidis
Dental plaque Streptococcus mutans Prevotella, Porphyromonas
Gingival Various anaerobes, eg.
crevices Bacteroides, Fusobacterium
Streptpcocci, Actinomyces

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Table 3-1: Medically important normal flora.
Location Most common flora Less common flora
Colon Bacteroides fragilis, Bifidobacterium, Eubacterium, Fusobacterium,
Escherichia coli Lactobacillus, various aerobic gram-negative rods,
Enterococcus faecalis and other streptococci,
Clostridium
Vagina Lactobacillus, E. coli, Various streptococci, various gram-negative rods,
Group B strep B. fragilis, Corynebacterium, C. albicans
Urethra S. epidermidis, Corynebacterium, various strep,

Table 3-2: Comparison of Exotoxin vs. Endotoxins

Property Exotoxin Endotoxin
Source Gram-positive & Gram-negative Gram-negative only
Chemistry Polypeptide LPS
Toxicity HIGH (fatal dose 1 ug) LOW (fatal dose 100 ug)
Vaccines Toxoids No Toxoids available
Heat stability Labile Stable
Typical diseases Tetanus, Botulism, Diphtheria Meningococcemia, sepsis from
gram-negative rods

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