Bacteriology Compilation ● Robert Koch: Learned staining and developed a transparent solid medium by mixing gelatin with

Loeffler’s peptone solution. He later switched to agar.

■ The microorganism must be found in abundance in all organisms suffering from the

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disease, but should not be found in healthy organisms.
HISTORY
■ The microorganism must be isolated from a diseased organism and grown in pure

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● Roger Bacon: Science of Optics first started. culture.
● Galileo Galilei: Invented the telescope and improved the microscope. ■ The cultured microorganism should cause disease when introduced into a healthy

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● Robert Hooke: Micrographia, Used the Compound Microscope, History of Cell Biology. organism.
● Anton van Leeuwenhoek: First to observe live M.O.s (ANIMALCULES), first to use the single-lens ■ The microorganism must be reisolated from the inoculated, diseased experimental
microscope (simple microscope). host and identified as being identical to the original specific causative agent.
● Carolus Linnaeus = Binomial Nomenclature on the basis of genus and specific epithet (Presented in his ● Koch’s Disease = Tuberculosis

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book “Systema Naturae”). ● Hansen’s Disease = Leprosy
● Supporters of Abiogenesis/Spontaneous Generation: ● Edward Jenner: Vaccination, named by Louis Pasteur, from the word vacca meaning cow. (To provide

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● Living organisms come from nonliving things. immunity)
● A vital force forms life. ● Chemotherapy: any chemical agents whether natural or synthetic such as antibiotics. (Quinine = from
● Aristotle: Decaying material by the spontaneous action of nature/air forms living animals. tree bark to treat malaria.)
●

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● Jean Baptista van Helmont: Recipe for mice… (idiot) Paul Ehrlich: Salvarsan, salvation from syphilis and contains arsenic.
● John Needham: Nutrient Broth in covered flask but allowed to cool first. ● Alexander Flemming: Penicillin from Penicillium chrysogenum (fungi).
● Laurent Lavoisier: Discovered Oxygen which strengthened abiogenesis. ● Rebecca Lancefield: Serology to identify bacteria.
● Supporters of Biogenesis: ● Paul Berg: Recombinant DNA.

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● Living organisms arise from preexisting life. ● Bioremediation using Bacillus thuringiensis.
● Francesco Redi: First real experiment to dispute abiogenesis. ● ATCC = American Type Culture Collection.
● Lazarro Spallanzani: Corrected Needham’s experiment. ● Superbugs:

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● Franz Schulze: Passed air through strong acids and then into boiled broth. ● Carbapenem-resistant Klebsiella pneumoniae.
● Rudolf Virchow, Theodor Schwann, Matthias Schleiden: Proponents of the cell theory. (Mostly Virchow) ● Methicillin-resistant Staphylococcus aureus.

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● Cell theory: All living things are composed of cells, The cell is the basic unit of life, All cells come from ● Vancomycin-resistant Staphylococcus aureus.
pre-existing cells. ● Multi-drug resistant Mycobacterium tuberculosis.

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● Louis Pasteur: Nutrient Broth in long-necked flasks, heated then sealed. (COMPLETELY DESTROYED ● Multi-drug resistant Pseudomonas aeruginosa.
ABIOGENESIS) ● Vancomycin-resistant Enterococcus faecalis.
● John Tyndall: Proved that dust carried germs. ● Extended-spectrum beta-lactamase producing Enterobacteriaceae.
● Golden Age of Microbiology (1857-1914): Estimated 60 years
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● Louis Pasteur: Fermentation (By-product is acid) and Spoilage, Pasteurization (Low-heating), Rabies
Vaccine. BACTERIOLOGY BASICS PROPER
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● Oldest known type of fermentation = Alcoholic fermentation (Ethanol from glucose)

● Germ Theory of Disease: Diseases are caused by infectious M.Os and not by demons, wrath of God and ● Microbiology: Study of all microorganisms and encompasses bacteriology, virology, mycology,
evil spirits. phycology, parasitology and also protozoology.
● Agostino Bassi: Silkworm disease caused by fungi. ● Bacteria: Contains both RNA and DNA making it different from viruses.
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● Louis Pasteur: Silkworm disease caused by protozoans. ● Mutualism: Benefit all and is synonymous to Symbiosis.
● Ignaz Semmelweis: Advocated hand washing to eradicate puerperal fever (fever after delivery). ● Commensalism: Benefit one but does not affect the other.
● Joseph Lister: Phenol to prevent surgical wound infection and also perfected the first pure culture ● Parasitism: Benefit of one but harms the other.
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technique using serial dilutions and successfully cultured Lactobacillus lactis. ● Prokaryotes: Unicellular organisms which may be bacteria or archaebacteria.
● Archaebacteria: Difficult to study in the lab and may be a methanogen, halophile or thermoacidophile. ● Lipopolysaccharide: Lipid A (Endotoxin), Core Polysaccharide, O Antigen.
(Lack peptidoglycan cell walls and live in extreme environments) ● Gram Stain: Crystal Violet (1 minute), Gram’s Iodine (1 minute), Acetone Alcohol or Ketone Alcohol (30
● Robert Whittaker: Classified bacteria as Monerans and divided them into Eubacteria and seconds), Safranin (30 seconds).

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Archaebacteria. ● Crystal Violet = Primary Stain, Gram’s Iodine = Mordant (Bridge between primary stain and cell wall),
● Thiomargarita namibiensis: BIGGEST BACTERIA (Sulfur-loving, has pearl luster). Acetone Alcohol = Decolorizer, Safranin = Counterstain.

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● Atypical Bacteria (Mycoplasma, Chlamydia, Rickettsia): SMALLEST BACTERIA. ● Bacteria with Atypical Cell Wall: Mycobacterium and Nocardia as they have cell walls with lipids =
● Bacterial Structures: Mycolic Acids and Cord Factor Wax D.

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● Mitochondria: Similar in size to prokaryotes and contains its own DNA. (Said to have come from ● Some have no cell walls such as Mycoplasma.
prokaryotes) ***Bacteria do not have mitochondria. ● Lysed Gram (+) Bacteria = Protoplast.
● Prokaryotic Cell Structure: Simpler than the eukaryotic cell in every way except its cell envelope and ● Lysed Gram (-) Bacteria = Spheroplast.
flagella.

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● Nucleoid: Bacteria have no true nuclei, instead they have a nucleoid with no nuclear membrane.
(Feulgen positive)

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BACTERIAL CLASSIFICATION AND GROWTH
● Most bacteria have circular chromosomes except Borrelia burgdorferi and Streptomyces coelicolor as
they have linear chromosomes. ● Strain: Descended from a recognized species of an organism. (Represents genetic variability within
● Flagella: Organ of locomotion, its basal body is responsible for initial movement. (Has flagellin which species)

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contains the H Antigen) ● Biovars: Strains differ in biochemical reactions. (Ureaplasma urealyticum: Parvo and T960)
● Endoflagella (Internal Flagella or Axial Filaments): Located in the periplasmic space and provides ● Serovars: Strains differ in antigens. (Salmonella Typhi and Salmonella Paratyphi A)
corkscrew motility to Spirochetes. ● Morphovars: Strains differ in morphology. (Corynebacterium diphtheria and mitis)
● Mesosomes: Projections of cell membrane of bacteria. ● Common name = trivial name. (Example: Mycobacterium tuberculosis = tubercle bacillus)

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● Fimbriae: Common pili for adhesion. (May also be a lectin) ● Traditional Methods of Identification: Gram Stain, Culture, Biochemical Properties.
● Pili: Appendages for mating, made up of pilin and joins bacterial cells for DNA transfer (Conjugation) ● ATCC = American Type Culture Collection. (ATCC BAA1720 = S. aureus)
and also used for adhesion. ● API = Analytical Profile Index. (Used to identify M.Os)

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● Glycocalyx: Made up of sugars or proteins and is found external to the cell wall. (May be either capsule ● BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY: main resource for determining identity of
or slime layer) bacterial species and aids in the identification of unknowns using the DICHOTOMOUS KEY. (Published in

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● Capsule: Highly organized and tightly attached and grants anti-phagocytic ability. 1923)
● All have polysaccharide capsules except Bacillus anthracis which have a protein capsule, ● Photoautotrophs: Requires light as energy source and carbon dioxide as carbon source.

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Poly-D-Glutamic Acid. ● Photoheterotrophs: Requires light as energy source and organic compounds as carbon source.
● Slime Layer: Loosely organized and attached and used for adhesion. ● Chemoautotrophs: Requires chemicals as energy source and carbon dioxide as carbon source.
● Plasmids: Self-replicating DNA that is transferred via pili and encodes for antibiotic resistance. ● Chemolithotrophs: Requires chemical as energy source and inorganic compounds as carbon source.
● Transposons: Jumping genes discovered by Barbara McClintock (1993). ● Chemoorganotrophs/Chemoheterotrophs: Requires chemical as energy source and organic compounds
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● Ribosomes of Bacteria (70S) = Large Ribosome (50S), Small Ribosome (30S). as carbon source.
● S = Svedverg Unit. ● Growth Factors: Essential substances which when lacking a certain fastidious bacteria will not grow.
● Granules: Intracellular storage bodies.
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● Endospores: Resistant to a lot of environmental factors due to Calcium-Dipicolinic Acid-Peptidoglycan
Complex. (Destroyed only through autoclaving)
● Peptidoglycan: May be N-acetylglucosamine (NAG) or N-acetylmuramic acid (NAM) linked by
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● Trace elements: Required in small amounts to grow bacteria but not necessary to add to culture media
as nutrients. (Tap water is used to provide them)
● Fastidious Bacteria: Requires a lot of Growth Factors.
● Toxic Metabolites of Oxygen or Reactive Oxygen Species: Superoxide, Hydrogen Peroxide, Singlet

polypeptide chain. Oxygen.

● Gram (+) Bacteria have thick peptidoglycan allowing them to retain crystal violet and stain purple. ● Obligate Aerobes: Have Superoxide Dismutase and Catalase but no Peroxidase which is why they love
● Gram (-) Bacteria have thin peptidoglycan but with an outer membrane (points of connection within oxygen.
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inner and outer membranes is known as Bayer junctions) with lipopolysaccharide. This allows them to ● Facultative Anaerobes: Can live with or without oxygen as they have Superoxide Dismutase and
lose crystal violet and stain red from safranin. (Has porins) Catalase but no Peroxidase.
 ● Aerotolerant Anaerobes: Have Superoxide Dismutase only. (Tolerates oxygen but does not love it) ● Transduction: Transfer of genetic material from bacteria to bacteria via a virus (bacteriophage).
● Obligate Anaerobes: Lacks the three enzymes which is why they die in the presence of Oxygen. ● Generalized Transduction: Involves lytic phage.
● Microaerophiles: Survive in low Oxygen tension. (Prefers low oxygen) ● Specialized Transduction: Involves lysogenic phage.

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● Capnophiles: Love Carbon Dioxide. ● Lytic phage: Infects bacteria, proliferates and eventually kills the bacteria by lysis to infect other
● Psychrophiles: Loves cold temperatures (0-20C) and responsible for food spoilage. (Listeria bacteria and proliferate.

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monocytogenes, Aeromonas hydrophila, Clostridium botulinum and Yersinia enterocolitica) ● Lysogenic phage: Infects bacteria by placing its RNA or DNA and incorporating it into bacterial DNA. This
● Mesophiles: Loves 20-45 C which is why most pathogenic bacteria are mesophiles since they love the grants the lysogenized bacteria special properties such as unique toxin production. (At some point, lytic

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body temperature. cycle may occur if the environment becomes too dangerous for the lysogenic phage)
● Thermophiles: Loves 45-70C. ● Prophage: Combined genetic material of lysogenic bacteriophage and bacteria through hybridization.
● Water: Critical factor which affects cell growth. (Water Activity, Aw, = the higher the solute (If bacterial cell multiplies, prophage also replicates)
concentration of substance, the lower the Aw) ● Temperate phage: May undergo lytic or lysogenic cycle.

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● ***Aw is the basis of preservation of foods by drying.
● Humidophiles: Loves water, humid, moisture.

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● Xerophiles: Loves dry environment.
IMPORTANT SPECIMEN COLLECTION NOTES
● Halophiles: Requires NaCl for growth. (Loves Salt)
● Halotolerant: Only tolerates salt. ● Recovery of viruses = Done during the acute phase of illness.
●

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Plasmoptysis: Bursting of bacteria due to hypotonic solution. (Equivalent to hemolysis)
● Plasmolysis: Shrinking of bacteria due to hypertonic solution. (Equivalent to crenation)
● Acidophiles, Neutrophiles, Alkaliphile = pH. (Most bacteria = pH 6.5-7.5)
● Bacterial Growth Curve: Lag phase, Log phase, Stationary phase, Death phase.
● Recovery of bacteria = Done before antimicrobial therapy has started.
● 1st week of infection = Blood cultures.
● 2nd week of infection = Stool or Urine cultures.
● 3rd week of infection = Serological Tests. (Most definitive)

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● Lag phase = period where an organism still adapts to the environment and absorbs nutrients to prepare ● Cotton swabs: Toxic to Neisseria gonnorhoeae.
for reproduction. ● Wooden swabs: Toxic to Chlamydia trachomatis.
● Log phase (Exponential phase) = period where bacteria is reproductively active and double with each ● Calcium alginate swabs: Toxic to viruses.

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generation time. ● Specimen Collection: Collect at sites with minimal contamination and label is very important.
● Stationary phase (Plateau phase) = period where bacteria maintains greatest population density. ● CSF and Blood MUST NOT be refrigerated but can be incubated as refrigeration kills potential Neisseria

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(Growth rate = Death rate) gonnorhoeae in the sample.
● Death phase (Decline phase) = period where there is rapid decline in growth due to accumulation of ● Blood is used to detect blood-borne pathogens and is collected before antibiotic therapy has started

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toxins, waste product and exhaustion of nutrients. (Involution happens where bacteria changes its and preferably at the onset of chills and fever.
morphology upon death) ● Fever, Hypothermia, Leukocytosis (with a left shift), Granulocytopenia and Hypotension often indicates
● Generation time (Doubling time): Time it takes for bacteria to double its number. bacterial infection.
● Staphylococcus epidermidis: common contaminant of blood cultures since it is a normal flora of the
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skin. (Other contaminants: CoNS and Viridans Streptococci)
BACTERIAL GENETICS ● For blood cultures, clean the site with 70-90% alcohol then with 1-2% iodine then clean again with
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alcohol.
● Vertical Gene Transfer: Mother cell to offspring. (Binary fission) ● 20-30 mL of 2-3 blood samples over a period of 24 hours for blood culture.
● Horizontal Gene Transfer: Acquisition of genes from other microbes of the same generation through pili ● 1-5 mL of blood per culture bottle.
or plasmids or transposons. ● Transient Bacteremia (Nasaag ra), Intermittent Bacteremia (Pabalik-balik due to abscess), Continuous
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● Conjugation: For Gram (-) bacteria only as they are the only ones with pili that mediate conjugation. It Bacteremia (The Real Deal)
involves the transfer of plasmids from one bacterial cell to another bridged by pili. ● In the Laboratory: Gram Stain is done first. Followed by Culture, Biochemical Tests, Serological Tests and
● Transformation: Direct uptake of exogenous DNA by a competent bacteria. (Proved by Frederick Griffith Antimicrobial Susceptibility Tests. (Genetic identification is the most sensitive)
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using S. pneumoniae with capsule which was killed and S. pneumoniae without capsule which acquired ● Reject any specimens for blood cultures that are preserved in formalin as it alters antigenic properties.
the capsule upon transformation with the DNA of the dead encapsulated S. pneumoniae. ● Observe Universal Precautions (refer to Clinical Chemistry).
 ● Referral Testing: Refer sample to other hospitals for confirmation. ● Special stains are used to stain special structures such as endospores, flagella and granules.
● Sodium Polyanethol Sulfonate (Found in yellow top tubes): Inhibits phagocytosis, coagulation and ● Capsule Stains: Welch, Anthony’s, India Ink/Nigrosin, Hiss, Tyler’s. (Fungi stained by capsular staining =
complement activation in order to preserve bacteria in blood cultures. It is 0.02-0.05% and is mixed Cryptococcus neoformans)

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with blood in a 1:10 ratio. ● Cell Wall Stain: Dyar’s
● Growth is indicated by: Turbidity, Pellicle Formation, Hemolysis or Gas Production. ● Granule Stain: Loeffler’s Alkaline Methylene Blue Stain and Albert’s.

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● Biphasic Blood Culture System: Has both liquid and solid media where colonies grown are subjected ● Flagella Stain: Hugh and Leifson’s Flagella Stain
directly to Antimicrobial Susceptibility Tests. ● Endospore: Dorner’s, Schaeffer and Fulton, Wirtz-Conklin.

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● ***In blood transfusions, platelets are the blood component with most contaminants especially with ● Gram (-) = Neisseria, Branhamella, Moraxella and Veilonella.
Yersinia enterocolitica. (Has shelf-life of 5 days) ● Gram (+) = Mycobacterium, Nocardia, Corynebacterium, Lactobacillus, Listeria, Clostridium, Bacillus,
● CSF: Neisseria meningitidis, Haemophilus influenzae type b and Streptococcus pneumoniae. (DO NOT Erysipelothrix.
REFRIGERATE AND VIABLE ONLY FOR 1 HOUR) ● All spirals are Gram (-).

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● 1st tube of CSF: CSF Chemistries (Protein, Glucose, Lactate, Glutamate) ● MgRNA Theory = MgRNA + Crystal violet-iodine complex forms an insoluble compound.
● 2nd tube of CSF: Gram Stain and Culture. (India Ink is also performed to assess Cryptococcus ● Benian Theory = Gram (+) bacteria have less permeable cell walls.

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neoformans in the CSF) ● Stearn and Stearn Theory = Gram (+) bacteria have low isoelectric point making them acidic and easily
● 3rd tube of CSF: Hematology stained with a basic dye, crystal violet.
● 4th tube of CSF: Serology ● Lipid content = Gram (-) cell walls have high lipid content.
● ●

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Throat swabs: Used to culture for Streptococcus pyogenes, causative agent of strep throat.
● M.Os of LRT: S. pneumoniae, S. aureus, H. influenzae, M. catarrhalis, Legionella, Mycobacterium,
Mycoplasma, Klebsiella, Enterobacteriaceae
● M.Os of Urine: Enterobacteriaceae, S. saprophyticus, S. aureus, Enterococcus, Yeast (>100,000 CFU/mL
Most significant problem in Gram Stains = Overdecolorization.
● L-alanine-4-nitroanilitie (LANA) turns yellow when touched to Gram (-) colonies.
● 3% KOH test forms string-like material indicating Gram (-) bacteria.
● Acid Fast Stain: Ziehl-Neelsen (Hot Method), Kinyoun (Cold Method), Pappenheim, Baumgarten.

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indicates infection) ● Ziehl-Neelsen = Carbolfuchsin (Basic fuchsin + phenol), Heat, Acid Alcohol and Methylene blue. (Used
● ***ONLY SPECIMEN NOT GRAM-STAINED IS STOOL. (Assume Gram (-) rods are present) for staining sputum samples)
● 1st Day of Stool: Inoculate specimens on EMB, Mac, XLD, SSA, HEA and BAP. ● Kinyoun = Carbolfuchsin, Tergitol, Acid Alcohol and Brilliant Green or Malachite Green. (Used for

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● 2nd Day of Stool: Check for lactose fermentation, subculture and biochemical tests. staining Mycobacteria in tissues)
● 3rd Day of Stool: Note biochemical patterns, Serological typing if Salmonella, Shigella and Vibro, Perform ● Pappenheim = Differentiates Mycobacterium tuberculosis (red) from Mycobacterium smegmatis (blue).

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AST ● Baumgarten = Differentiates Mycobacterium tuberculosis (blue) from Mycobacterium leprae (red).
● 4th Day of Stool: Release results. ● Wayson’s stain is used to stain bipolar bodies red.

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● 1% Gelatin = enhances growth of Neisseria gonnorhoeae. ● Stains for spirochetes: Fontana Tribondeau = spirochetes are dark brown or black, Levaditi Silver
● 0.01% Bacto-agar = enhances growth of anaerobic bacteria. Impregnation = spirochetes are black, India ink negative stain = spirochetes are unstained, background
● Sputum: Yellow, cheesy, mucopurulent (desired sputum characteristics) subject to Gram Stain and Acid is black.
Fast Stain. (Digestion and Concentration technique using NaOH is used to free bacteria by dissolving ● Cultures:
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fats and mucus) ● Provides nutrients for bacterial growth.
● Inoculum: Microbes introduced to a medium.
● Agar: Solidifying agent.
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● Colony: Macroscopic visible masses of bacterial growth.

METHODS OF IDENTIFICATION
● Colony: May be mucoid or slimy (presence of capsule), rough (presence of granules) and smooth.
● Microscopy and Staining: ● On the basis of consistency: Liquid Media (growth is indicated by turbidity or particulate appearance),
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● Smear of living state to assess motility or fixed state. Semi-solid Media (Agar 0.3-0.5% or Gelatin 1.5-3%) has a clot-like appearance and is used to asses
● Fixing a smear may be through the usage of heat or 75% methanol. (Adheres smear to slide) bacterial motility, Solid Media (Agar 1-5% or Gelatin 10-15%)
● Refractive index of microorganisms = water. (When viewed under a microscope, they look like water. ● On the basis of distribution: Tubed Media (Butt/Slant) or Plated Media.
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This is the reason why we stain.) ● On the basis of chemical composition: Synthetic (All components are defined) or Non-synthetic (One of
● Staining may be simple (only one dye), differential (two dyes) and special staining. its components are not defined).
● On the basis of function: General Purpose (to grow non-fastidious bacteria), Enriched (solid media for
growth of fastidious organisms), Enrichment (liquid media for growth of fastidious organisms), Selective
(selects to grow only a type of bacteria), Differential (allow the differentiation of different bacterial
species in the media)
● Beta-hemolysis (clear zone), alpha-hemolysis (green discoloration), gamma-hemolysis and alpha-prime
hemolysis (combination of beta and alpha).
● Chocolate Agar Plate is brown due to overcooking of blood at 80C.
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● Multiple Overlap (3+1 lawn technique) is the streaking technique used in Antimicrobial Susceptibility
Tests.
● Multiple Interrupted streak is the most commonly used in the laboratory. (Quadrant 1, 2, 3 and 4)
● Preserving cultures: Deep-freezing (-50C to -95C) or Lyophilization (Frozen at -54 to -72C and
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dehydrated on vacuum to form powder)
● Powder to liquid = Reconstitution.
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● Methods of Pure Culture: Streak Plate, Pour Plate (growth is within the agar and is measured in
CFU/mL), Animal Inoculation, Selective Media.
● Biochemical Characteristics:
● ●
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On the basis of enzymes.
● Carbohydrate Fermentation Test: Checks for an organism’s ability to ferment carbohydrates. Media
used: Triple Sugar Iron Agar, Kligler’s Iron Agar, Russell’s Double Agar.
● TSI has 3 carbohydrates: glucose (butt), sucrose (slant), lactose (slant)
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● TSI has phenol red as pH indicator turning yellow when carbohydrate is fermented and acid is produced
and also has ferrous ammonium sulphate to detect H2S. (H2S production = black color in TSI) ***STAB,
STREAK
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● K/A = Glucose is fermented, K/K, = No sugars fermented, A/A = 2-3 sugars are fermented.
● A/A with gas = E. coli, K/A with H2S = Salmonella typhi, K/A without H2S = Shigella, K/K = Pseudomonas
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aeruginosa.
● IMViC = Indole, Methyl Red, Voges-Proskauer, Citrate
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CONTROL OF MICROBIAL GROWTH AND ANTIBIOTICS
● Indole Test checks for the enzyme tryptophanase which will degrade tryptophan to form an indole. The
presence of indole is indicated by a pink to wine-colored ring on top of the tube. (Tube used: SIM, QC +
is E. coli, QC – is K. pneumoniae)
● Indole Test utilizes Kovac’s Reagent which is basically para-dimethylaminobenzaldehyde (PDAB) and
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may also use Ehrlich’s Reagent (more sensitive) which uses PDAB and Ether or Xylene while Spot Indole
Test uses para-dimethylaminocinnamaldehyde (PDAC).
● Methyl Red Test checks if the bacteria will utilize carbohydrates to form mixed acids such as lactic acid,
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succinic acid, propionic acid and formic acid. The indicator used is methyl red which turns red in the
presence of acid at pH 4.5 or below. (QC + is E. coli, QC – is Enterobacter cloacae)
● Voges-Proskauer Test checks if the bacteria will utilize carbohydrates to form acetoin
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(acetylmethylcarbinol). This is indicated by the addition of KOH and Alpha-naphthol to form a pink or
red color or pink-cherry red color (pink-burgundy). (QC + is Enterobacter cloacae, QC – is E. coli)
● MRVP Medium is used.
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● Citrate Test checks if the bacteria can utilize citrate as a sole carbon source with ammonia and
carbonate as by-products which are both basic. The medium used is Simmon’s Citrate Agar and its
indicator is bromothymol blue. In basic pH (+), the color of the indicator is blue. (QC + is Klebsiella
pneumoniae, QC – is E. coli)
● The Catalase Test checks for the enzyme catalase which if present will break down H2O2 to form water
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and oxygen (indicated by bubbles or effervescence). (QC + is Staphylococcus aureus, QC – is
Streptococcus pyogenes)
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● For Neisseria gonnorhoeae, 30% H2O2 is used to detect in catalase tests.
● Oxidase Test checks for the enzyme cytochrome oxidase which will act on the reagent tetra-methyl
para-phenylenediamine dihydrochloride (TMPDD) to form indophenol which is purple/dark-blue in
color. (QC + is Neisseria gonnorhoeae, QC – is Escherichia coli)
● Phenylalanine deaminase checks if a bacteria can deaminate amino acids. Phenylalanine upon the
action of a deaminase and reacted with 10% Ferric Chloride will produce a green color. (QC + is Proteus
vulgaris, QC – is Escherichia coli)
● Urease Test checks for the enzyme urease which will cleave urea into ammonia which is basic. The pH
indicator used is phenol red and a positive color is indicated by magenta at pH 8.1 while a negative
result is light-orange at pH 6.8. (The medium used is Christensen’s Urea Agar, QC + is Proteus vulgaris,
QC – is E. coli)
Lysine Iron Agar checks if a bacteria can decarboxylate and deaminate lysine. Decarboxylating lysine
happens at the butt which will yield to cadaverine that is basic. The pH indicator used in the agar is
bromcresol purple which turns purple in basic pH or yellow in acidic pH thus allowing it to also detect
for glucose fermentation. Deaminating lysine will form flavin mononucleotide which is red in color. H2S
production may also be assessed since it has ferric ammonium citrate. (Deamination only occurs in
Proteus, Providencia, Morganella)
● Original colors: TSI = brown, LIA = violet, SCA = green, SIM = yellow, Urease = light orange.
● If not SIM, Motility Indole Ornithine (MIO) may be used.
● Penicillin: Inhibits peptidoglycan synthesis.
● Isoniazid: Inhibits mycolic acid synthesis.
● Chloramphenicol: Inhibits protein synthesis at 50S subunit. (It is known as the drug of last resort as it
has nitrobenzene in its structure which may cause aplastic anemia leading to Gray Man Syndrome)
● Tetracycline: Inhibits protein synthesis by interfering with tRNA attachment.
● Aminoglycosides: Gentamicin and Streptomycin (inhibits protein synthesis at 30S subunit) while
Erythromycin inhibits protein synthesis at the 50S subunit.
● Rifampin: Inhibits synthesis of RNA.
● Polymyxin B: Disrupts microbial cell membrane.
● Trimethoprim-Sulfamethoxazole: Inhibits successive steps in folate synthesis which is required for DNA
synthesis. (May cause Steven-Johnson Syndrome which is a type of toxic epidermal necrolysis)
● Vancomycin: Inhibits proper cell wall synthesis of Gram (+) bacteria but does not do much
against Gram (-) bacteria. (May cause Red Man Syndrome due to excessive bleeding)
 ● Multiple Drug Therapy is used to minimize the risk of resistance occurring in organisms, to immediately
kill a bacteria, to fight against polymicrobial infections.
● Antimicrobial Susceptibility Tests: Measures ability of antibiotics to inhibit bacterial growth in vitro.
● Mueller-Hinton Agar is used for AST.
● First, standardize the inoculum to a 0.5 McFarland Turbidity Standard which contains 1.5 x 10^8
organisms.
● Most common method used is the Disk Diffusion Method or Kirby-Bauer technique. (Measure zone of
inhibition)
● Tube Dilution Methods measure Minimum Inhibitory Concentration (MIC) or Minimum Bactericidal
Concentration (MBC).
● The E-test is the most sophisticated and can detect both zones of inhibitions and MIC/MBC.
● AUTOCLAVE: 121C for 15 mins. At 15 psi to destroy bacterial endospores and most bacteria. (PSI =
Pounds per Square Inch)
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● Commercial Sterilization: Autoclaving used to destroy the spores of Clostridium botulinum.
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PATHOGENESIS OF DISEASE
● Pathology: Scientific study of disease and concerned with the structural and functional changes
brought about by disease and their final effects on the body.
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● Etiology: Study of the cause of disease.
● Pathogenesis: The manner in which a disease develops.
● Pathognomic: Characteristic w/c denotes “distinctive for a specific disease.”
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● Infection: Invasion or colonization of the body by pathogenic MOs.
● Disease: Occurs when infection results in any change from a state of health.
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● Normal Microbiota: Colonize the body but do not produce disease under normal conditions.
● ***E. coli synthesizes Vitamin B and K in the intestines of humans and also secretes colicins to prevent
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other bacteria from growing.
● Probiotics: Live microbial cultures ingested to exert a beneficial effect.
● Prebiotics: Chemicals that selectively promote growth of beneficial bacteria.
● Symptoms: Subjective changes in body function such as pain and malaise.
O
● Signs: Objective changes the physician can observe and measure. (Lesions, swelling, fever, paralysis...)
● Syndrome: Specific signs and symptoms accompanying a disease.
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● Acute disease: Develops rapidly but lasts only a short time.
● Chronic disease: Develops slowly and is less severe but lasts for a long time.
● Subacute disease: Intermediate between acute and chronic.
● Latent disease: Causative agent remains inactive for a time then becomes active to produce symptoms
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of disease.
● Local Infection: Limited to a small area in the body.
● Systemic Infection: Spread throughout the body in either blood or lymph. (Measles)
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● Focal Infection: Local infection then systemic.
● Bacteremia – bacteria in blood. Toxemia – toxins in blood. Viremia – virus in blood.
● Sepsis: Toxic inflammatory condition arising from spread of bacteria and their toxins from a focus of
infection.
● Septicemia/Blood Poisoning: Systemic infection arising from multiplication of pathogens in blood.
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● Primary Infection: Acute infection w/c causes initial illness.
● Secondary Infection: Caused by opportunistic pathogens after the host has been weakened.
M
● Incubation Period: Time interval between initial infection and first appearance of any signs or
symptoms. (Depends on specific microorganism, its virulence, number and resistance of host)
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● Prodromal Period: Relatively short period characterized by early, mild symptoms of disease such as
general aches and malaise.
● Period of Illness: Disease is most severe. Person exhibits signs and symptoms specific to the disease.
(Death may occur in this period)
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● Period of Decline: Signs and symptoms subside but the patient is vulnerable to secondary infections.
● Period of Convalescence: Person regains strength and body returns to prediseased state.
● Mechanical Vector Transmission: Passive transport of pathogens on insect’s feet or body parts.
● Biological Vector Transmission: Active process where an arthropod bites a host which transmits the
pathogen through the bloodstream.
●
Compromised Host: One whose resistance to infection is impaired by disease, therapy or burns.
● Most common site of nosocomial infection = UTIs.
● Handwashing: Most important means to prevent spread of infection. (CDC)
● Pathogenicity: Ability of MO to cause disease by overcoming host defenses.
● Virulence: The degree of pathogenicity and ability to cause severe disease.
● Toxigenicity: Capacity of microbes to produce toxins.
● Exotoxins: Enzymatic in nature w/c makes them harmful because they can act over and over again.
(Botulism and Staphylococcal food poisoning = intoxication)
● Antitoxins: Provide immunity to exotoxins.
● Toxoids: Inactivated toxins but still stimulate the body to produce antitoxins. They are used as vaccines
to produce immunity. (Diphtheria and tetanus shots)
● A-B Toxins: First toxins studied and most common exotoxin. (A = active enzyme component, B = binding
component)
● Membrane Disrupting Toxins: Causes lysis of host cells by disrupting their plasma membranes.
● Superantigens: Antigens (bacterial proteins) that provoke a very intense immune response. They
stimulate proliferation of T cells w/c release cytokines that regulate immune responses and mediate
cell to cell communication.
● Exotoxin vs. Endotoxin
● Exotoxin = extracellular, Endotoxin = intracellular (Lipid A).
● Exotoxin = no fever, Endotoxin = fever.
● Exotoxin = released by bacteria any time, Endotoxin = released by bacteria upon death.
STAPHYLOCOCCUS (Cocci means berry in Greek, Staphyle = bunch of grapes)
● Medically relevant: S. aureus, S. epidermidis, S. saprophyticus
● Facultatively anaerobic, halophilic (7.5-10% NaCl), Lipochrome (Staphyloxanthin)
● Comes from the family Micrococcaceae.
● Differentiated from Micrococcus using Modified Oxidase Test. (S. aureus is Modified Oxidase Negative)
● Susceptible to Lysostaphin but resistant to Bacitracin (0.04 units).
● Culture media used: BAP (Beta-hemolytic with golden yellow pigments), Phenylethanol Agar (Inhibits
Gram negative bacteria), Colistin Nalidixic Acid Agar (CNA is selective for Staph), Mannitol Salt Agar
(MSA has salt which selects for Staph and mannitol fermentation differentiates SAU from other Staph)
● Catalase (+)
STREPTOCOCCUS PYOGENES (Group A Strep)
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● Staphylococcus aureus is Catalase (+), Coagulase (+) and DNase (+).
● Micrococcus pyogenes var aureus / Golden Staph / Oro Staphira.
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● Major virulence factor is Coagulase.
● Other virulence factors: Protein A (binds to Fc region of IgG), Clumping Factor (causes bacterial
aggregation), Hyaluronidase (Spreading Factor), Leukocidin (Panton-Valentine Factor), Exfoliative Toxin
(Scalded Skin Syndrome and attacks stratum granulosum of skin), TSST-1 (Toxic Shock Syndrome),
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Staphylococcal Enterotoxin (Gastroenteritis) and Peptidoglycan (Fever).
● TSST-1 = prototype superantigen,
● Protein A = utilized in coagglutination.
● S. aureus is responsible for Toxic Shock Syndrome (associated with tampons), Scalded Skin Syndrome
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(Ritter-Lyell Disease), Gastroenteritis, Most common cause of arthritis in adults, furuncles and
carbuncles and Sepsis.
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● S. epidermidis is a normal flora of the skin and frequent contaminant of blood cultures. (Catalase +,
Coagulase - , MSA -)
N
● S. epidermidis colonizes prosthetic devices such as catheters, prosthetic heart valves and joints.
● Both S. aureus and S. epidermidis are novobiocin susceptible. (No growth if there is novobiocin)
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● Both S. epidermidis and S. saprophyticus are gamma-hemolytic on BAP while SAU is beta-hemolytic.
● S. saprophyticus is the 2nd most common cause of UTIs next to E. coli.
● S. saprophyticus is Catalase (+), Coagulase (-), MSA (-), Resistant to novobiocin.
● In order to treat Staphylococcal infections: Methicillin, nafcillin, cloxacillin, vancomycin. (Last line is
Vancomycin = causes Red Man Syndrome, erythematous rash after administration of vancomycin)
O
● If Staphylococcus produces beta-lactamases, penicillins are ineffective and vancomycin is the only drug
to treat.
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● Interleukin-1 = endogenous pyrogen.
● Protein A = belongs to the group MSCRAMMS (Microbial Surface Components Recognizing Adhesive
Matrix Molecules).
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C
MICROCOCCUS (Micrococcus luteus)
● Comes from the family Micrococcaceae.
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● Has a tetrad or sarcinae formation.
● Differentiated from Staphylococcus using Modified Oxidase Test. (Utilizes TMPDD and Dimethyl
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Sulfoxide)
● Micrococcus = Modified Oxidase (+), Staphylococcus = Modified Oxidase (-).
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● Micrococcus = Resistant to Lysostaphin but susceptible to Bacitracin.
● Gram (+) cocci in chains.
● Primary plating media is BAP but may also grow on Phenylethanol Agar.
● Requires 5-10% CO2 with glassy, matte, discoid colonies
● Streptococcus are classified according to Smith and Brown Classification (according to hemolysis),
Serological Specificity of Cell Wall Group-Specific Substances (Lancefield Classification) and Bergey’s or
Academic Classification (according to physiologic and thermal requirements.
● Pyogenic Strep = grows at neither 45C nor 10C, Viridans Strep = grows at 45C but not at 10C,
Enterococcus = grows at both 45C and 10C, Lactic Group = grows at 10C but not at 45C.
● Prototype human pathogen.
● PYR = Pyrrolidonyl arylamidase (Bright cherry red color)
● Catalase (-), Beta-hemolytic, Susceptible to Bacitracin (Taxo A), PYR (+) and LAP (+).
● Called as pyogenes as it is pus-producing.
● It is resistant to SXT thus making the antibiotic selective for S. pyogenes.
● Major virulence factor is M Protein. (Inhibits phagocytosis, chemotaxis, complement activation and also
clumps platelets and leukocytes.
● Other virulence factors: Capsule, IgG and IgA Binding Proteins and C5a Protease (inhibits chemotaxis),
Streptokinase, Streptodornase, Hyaluronidase, Diphosphopyridine Nucleotidase, Pyrogenic Exotoxin
(Erythrogenic Toxin) are superantigens which causes TSLS, Scarlet Fever and Necrotizing Fasciitis.
● Streptolysin S = Oxygen-stable, Responsible for surface hemolysis and is non-antigenic.
●
Streptolysin O = Oxygen-labile, Responsible for subsurface hemolysis (deep into BAP since it will be
deactivated in presence of oxygen), Antigenic (elicits production of Anti-Streptolysin O which is used for
serological testing for S. pyogenes.
● Diseases: Strep Throat (most common infection due to S. pyogenes), Erysipelas, Cellulitis, Impetigo,
Puerperal Fever (most common cause of puerperal fever), Sepsis, Necrotizing Fasciitis (S. pyogenes
causing this is termed as flesh-eating bacteria), Toxic Shock Like Syndrome and Scarlet Fever
(strawberry tongue appearance and erythematous rash).
● Sequelae infections of Strep: Acute Glomerulonephritis and Acute Rheumatic Fever. (Caused by
complications that arise from the primary infection and is due to antibodies accidentally attacking the
body) = Autoimmune
● Anti-streptolysin O is used to diagnose serologically.
 ● Treatment for Streptococcus pyogenes is Penicillin G. ● Quellung Test (Newfeldt Reaction) utilizes an antisera against the capsule of Streptococcus
● Scarlet Fever Susceptibility Tests: Dick’s Test (Redness in test arm) and Schultz-Charlton (Blanching pneumoniae. A positive test is indicated by a swollen capsule due to an inflammatory reaction.
phenomenon due to administration of antitoxin). ● Phadebact Test may also be used. (Coagglutination Slide Test)

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STREPTOCOCCUS AGALACTIAE (Group B Strep) VIRIDANS STREP

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● Beta-hemolytic, Christie, Atkins, Munch-Peterson or CAMP (+), Sodium hippurate hydrolysis (+), ● Not grouped under Lancefield Classification yet.
Resistant to Bacitracin ● Exhibits alpha-hemolysis on BAP.
● Has polysaccharide capsule with sialic acid capable of host mimicry. ● Bile solubility and Optochin Resistant.
● Most common cause of neonatal meningitis. ● Causes subacute bacterial endocarditis (any Viridans Strep) and commonly causes dental caries

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● Arrowhead zone of hemolysis in CAMP = Positive Test. (Streptococcus mutans).
● Deep purple color in Sodium Hippurate Hydrolysis = Positive Test.

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● IMPORTANT PATHOGEN OF NEONATES OR CHILDREN.
● ENTEROCOCCUS (Group D Strep)
NUTRITIONALLY VARIANT STREP (Group C Strep)
● Streptococcus bovis is of most importance to human disease within the group.

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● Generally weakly Catalase (+) and most are non-hemolytic.
● Generally grows on Bile Esculin Agar which is indicated by blackening of the agar due to the hydrolysis
of esculin while bile salts inhibit other bacteria.
● Divided into Enterococcal and Non-enterococcal groups.
● Requires other nutrients such as cysteine and pyridoxal (Vitamin B6).
● AKA Pyridoxal-requiring Strep, Thiol-requiring Strep, Satelliting Strep (Because they grow on sides of S.
aureus colonies as SAU provides pyridoxal for Group C Strep)
● From the genus Abiotrophia.

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● One of the causes of nosocomial infections and is associated with UTI. ● Includes Streptococcus defectivus and Streptococcus adjacens.
● Enterococcal group = Growth at 6.5% NaCl, Penicillin Resistant, PYR (+), LAP (+). (Enterococcus faecalis, ● Group C Strep includes Streptococcus dysagalactiae, Streptococcus zooepidemicus, Streptococcus
Enterococcus faecium, Streptococcus durans, S. avium) equisimitis.

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● Non-enterococcal group = Without Growth at 6.5% NaCl, Penicillin Susceptible, PYR (-), LAP (-).
(Streptococcus bovis and Streptococcus equinus)

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MILLERI GROUP

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STREPTOCOCCUS PNEUMONIAE ● Streptococcus constelatum, intermedius and anginosus.
● Voges-Proskauer (+).
● Formerly Diplococcus pneumoniae. ● Distinct caramel odor.
● Gram (+) lancet-shaped or bullet-shaped diplococci.
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● Capnophilic (5-10% CO2), always alpha-hemolytic.
● Virulence factors include: Capsule and Pneumolysin (responsible for alpha-hemolysis)
LACTIC GROUP (Group N)
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● Most common cause of Community-acquired Pneumonia or Lobar Pneumonia, Otitis Media and
Sinusitis. ● Causes souring of milk.
● Rusty Red Sputum is diagnostic of Streptococcus pneumoniae. ● Streptococcus lactis and Streptococcus cremoris.
● Mucoid colonies due to abundant capsule formation that are dome-shaped which later develops to a
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crater-like appearance.
● Optochin (Taxo P) Susceptible, Bile Solubility Test (+), Quellung Test.
● Optochin utilizes ethylhydrocupreine hydrochloride which is a 6mm disk; susceptibility is indicated by a
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zone of inhibition of 14mm or greater.

● Bile Solubility Test is indicated by a clear solution due to S. pneumoniae’s autolytic properties.
NEISSERIA
● Discovered by Albert Neisser.
● Gram (-) diplococci that are kidney-shaped or coffee-bean shaped except Neisseria elongata as it is
rod-shaped.
● Normally resides inside neutrophils because they are intracellular.
● Neisseria flavescens, Neisseria cinerea, Neisseria lactamica, Neisseria subflava have yellow pigmented
colonies.
● Neisseria sicca produces brittle, wrinkled colonies.
● Moraxella catarrhalis produces pinkish-gray opaque colonies.
● Culture for Neisseria gonnorhoeae is CAP while other Neisseria spp. and M. catarrhalis may be cultured
on BAP.
● Requires 3-10% CO2.
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● Transgrow and JEMBEC (John E. Martin Biological Environmental System) are the transport media used.
● Modified Thayer-Martin = CAP as base with vancomycin, colistin, nystatin and trimethoprim.
● Martin-Lewis = CAP as base with vancomycin, colistin, anisomycin and trimethoprim.
● New York City Agar = Clear peptone or cornstarch base with vancomycin, colistin, Amphotericin B and
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trimethoprim.
● GC-Lect = Specific for Neisseria gonnorhoeae.
● Oxidase (+) = dark purple color due to the formation of an indophenol. (Aerobic organisms)
● Cystine Trypticase Soy Agar = Carbohydrate Oxidation Tests for Neisseria.
N
● GC = Glucose only, MGC = Maltose and Glucose, N. lactamica = Glucose, maltose and lactose while
Moraxella catarrhalis = cannot oxidize any sugars but is DNase (+).
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● Virulence factors include: Pilin (for adhesion), Opa Protein (AKA Protein II which induces endocytic
uptake into neutrophils), Por Protein (AKA Protein I which prevents phagosome-lysosome fusion and
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serve as channels for entry of nutrients), Rmp Protein (AKA Protein III which associates with Por protein
in the formation of pores), IgA1 Protease and Lipooligosaccharide (Endotoxin).
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● Causes acute urethritis, pharyngitis, proctitis, Pelvic Inflammatory Disease (Salpingitis, Oophoritis,
Endometritis), Ectopic Pregnancy, Infertility and Perihepatitis (Fitz-Hugh-Curtis Syndrome).
● It may also cause Ophthalmia Neonatorum (infant conjunctivitis) and Disseminated Gonococcal
Infection leading to endocarditis, meningitis and most often septic arthritis. (Ophthalmia neonatorum
is treated with Silver nitrate, Erythromycin or Tetracycline Eye Drops)
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● Penicillin is the drug of choice.
● PPNG = Penicillinase-producing Gonococci. (Resistant to penicillin)
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NEISSERIA MENINGITIDIS
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● Disease causing strains are A, B, C, X, Y, W-135.
● Has pili, Opc Protein (for attachment and invasion), Lipooligosaccharide, Outer Membrane Proteins,
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Opa Protein and Rmp Protein.
● Most common cause of endemic and epidemic meningitis.
● May be a normal flora of the nasopharynx in carrier states.
● Causes fulminant meningococcemia or meningitis.
● Petechial rash (small hemorrhages) is the hallmark of Meningococcal Infections.
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● Fulminant meningococcemia is characterized by Disseminated Intravascular Coagulopathy (abnormal
clotting of the body leading to loss of clotting factors which promotes hemorrhages).
M
● When haemorrhage in DIC reaches the adrenal glands, it is termed as Waterhouse-Friderichsen
Syndrome (generalized shock and toxaemia).
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● Important symptoms of meningitis are stiffness of the neck and back. (Patients dies due to cerebral
hyperemia which is the flooding of blood in the brain)
● Penicillin G is the drug of choice.
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MORAXELLA CATARRHALIS
● Significant cause of otitis media and maxillary sinusitis in children and causes pneumonia and
bronchitis in immunocompromised patients.
● DNase (+), does not oxidize any sugars.
BACILLUS ANTHRACIS
● Bacillus and Clostridium are spore-forming Gram (+) bacilli.
● Bacillus is differentiated from Clostridium in terms of Catalase test as Bacillus is Catalase (+) and is
aerobic while Clostridium is Catalase (-) and anaerobic.
●
Large, square-ended, non-motile Gram (-) bacilli which has a characteristic Chinese bamboo fishing rod
appearance.
●
Central or Subterminal endospore.
● Its virulence factors include capsule, poly-D-glutamic acid (a polypeptide), and Anthrax Toxin.
● The major virulence factor of Bacillus anthracis is Anthrax Toxin which is composed of protective
antigen (binds to cell receptors and allows entry of Lethal Factor or Edema Factor into cells), lethal
factor (blocks intracellular signalling pathways of macrophages resulting to inability to signal other
WBCs) and edema factor or adenylyl cyclase toxin (which triggers increased cAMP production leading
to edema and lysis).
● Capable of causing Cutaneous Anthrax (characterized by black eschars and is the most common form of
anthrax), Pulmonary Anthrax or Woolsorter’s Disease (inhalation of spores) and Gastrointestinal
Anthrax or Violent Enteritis (ingestion of spores and is the most severe form of anthrax).
● Agent of bioterrorism and biological warfare.
● Gram Stain, India Ink and Fluorescence Antibody Test is used in microscopy.
● Serological test involves the use of gamma bacteriophage as B. anthracis is susceptible.
● Medusa head or Lion head colonies on BAP (gamma-hemolytic). Beaten egg white appearance on
Polymyxin B – Lysozyme – EDTA – Thallous Acetate (PLET) Agar.
● Inverted Fig Tree on Gelatin media.
 ● Pearls of String appearance on Mueller-Hinton Agar with Penicillin. ● Symptoms of Botulism start with double vision, dysphagia and speech difficulty. Descending flaccid
● Ascoli Test is a precipitation test for detection of the anthrax bacilli. paralysis also occurs.
● Treatment is with antitoxins.

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M
BACILLUS CEREUS
CLOSTRIDIUM TETANI
● Similar to Bacillus anthracis but motile.

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● Exhibits beta-hemolytic, large, feathery and spreading colonies.
● Causes food poisoning due to its enterotoxin or emetic toxin which may be classified as: Emetic Type or
Diarrheal Type.
● The emetic type is usually associated with ingestion of fried rice and is characterized by nausea and
● Tack Head Bacillus due to its terminal spore. (Tennis racket/Drumstick appearance)
● Virulence factors include Tetanolysin (cleaves tetanospasmin into two) and Tetanospasmin (major
virulence factor).
● Tetanospasmin inhibits both glycine and Gamma-aminobutyric acid (GABA) which are inhibitory

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vomiting while the diarrheal type is characterized with diarrhea. neurotransmitters leading to no inhibition of motor neurons resulting to SPASTIC PARALYSIS.
● Comparison and Contrast of B. cereus and B. anthracis: ● Causative agent of tetanus.

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● Bacillus cereus – motile, encapsulated, beta-hemolytic, grows at 45C, gray to lavender colonies, Salicin ● Starting symptoms include trismus/lockjaw, risus sardonicus (sardonic grin) and opisthotonus (arching
Fermentation (+), Penicillin resistant, Gamma bacteriophage resistant. of the back). Death occurs when paralysis reaches the diaphragm.
● Bacillus anthracis – nonmotile, encapsulated, gamma-hemolytic, does not grow at 45C, gray-white ● Unique characteristic: DOES NOT FERMENT ANY CARBOHYDRATES.

AS
colonies, Salicin Fermentation (-), Penicillin susceptible, Gamma bacteriophage susceptible. ● Treatment is antitoxin.

BACILLUS SUBTILIS CLOSTRIDIUM PERFRINGENS

N
● Hay Bacillus or Grass Bacillus. ● Formerly Clostridium welchii, Bacillus welchii and Bacillus aerogenes capsulatus.
● Considered as the best studied Gram (+) bacteria. ● Non-motile Clostridium that are Box-car shaped. (DOES NOT PRODUCE SPORES IN ORDINARY MEDIA)

T
● Used for a lot of tests such as the Guthrie Inhibition Test (refer to Clin Chem). ● Gas Gangrene Bacillus.
●

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Major virulence factor is Lecithinase (Alpha Toxin).
● Lecithinase splits lecithin which is a component of cell membranes.
●

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Other virulence factors are theta toxin (has similar haemolytic and necrotizing effects but not as potent
CLOSTRIDIUM
as the alpha toxin), hyaluronidase and collagenase and a powerful enterotoxin are also produced.
● Most have peritrichous flagella. ● Causes gas gangrene (Clostridial myonecrosis). Called as gas gangrene due to its highly fermentative
● Beta-hemolytic on BAP and are obligate anaerobic organisms (Catalase negative). unique characteristic. (Opposite to Clostridium tetani)
● Causes food poisoning and also Necrotizing Enteritis (Pigbel or Darmbraid).
O
● Treatment includes early amputation, antibiotic administration, antitoxins and Hyperbaric Oxygen
Chamber.
CLOSTRIDIUM BOTULINUM
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● Chopped Meat-Glucose Medium

● Alkaline Glucose Gelatin. ● Has a characteristic Target Zone of Hemolysis or Double Zone of Beta-hemolysis.
● Major virulence factor is botulinum toxin which is one of the most potent toxins in the world. (4 kg of ● In Milk Media, it exhibits stormy fermentation. (Confirmatory Test for C. perfringens)
the toxin can kill the human race) ● Lecithinase Test (Nagler’s Reaction) exhibits an opaque halo (opalescence) which is usually yellow in
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● Botulinum toxin inhibits release of acetylcholine causing FLACCID PARALYSIS. color surrounding the colony in an Egg Yolk Agar is a positive test.
● Causes food-borne botulism, Infant Botulism (where honey is the most frequent vehicle of infection ● Reverse CAMP (+): First culture Streptococcus agalactiae then culture Clostridium perfringens which
and causes Floppy Baby Syndrome and Sudden Infant Death Syndrome) and Wound Botulism. will exhibit an arrowhead zone of hemolysis or bowtie zone of hemolysis.
C
CLOSTRIDIUM DIFFICILE ● Var belfanti = ONLY BIOVAR THAT IS NEGATIVE IN NITRATE.
● Treatment is Penicillin G and Antitoxin.
● Produces Toxin A which is a potent enterotoxin and Toxin B which is a potent cytotoxin. ● Corynebacterium minutissimum = causative agent of erythrasma.

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● It causes antibiotic-associated diarrhea and pseudomembranous colitis. (Happens as a result of ● Corynebacterium ulcerans = diphtheria-like infection.
prolonged intake of antibiotics which leads to the death of normal flora in the body). ● Corynebacterium pseudotuberculosis (C. ovis) = equine and human lymphadenitis.

M
● Pseudomembrane is formed in an attempt to heal the ulceration. ● Corynebacterium bovis = CNS shunt infections with nephritis.
● Cycloserine Cefoxitin Fructose Agar = selective for C. difficile. ● Rhodococcus equi (Corynebacterium equi) = mycobacterial or nocardial-like infections.

,R
● Has a characteristic “horse manure” odor. ● Corynebacterium jeikeium = has a characteristic metallic sheen on BAP, multi-drug resistant but
● Additionally, it is Gelatinase (+). susceptible to vancomycin, may cause subacute bacterial endocarditis and bacteremia in
immunocompromised patients. (Group JK)
● Corynebacterium urealyticum (Group D2) exhibits multi-drug resistance and is the only

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CLOSTRIDIUM SORDELII Corynebacterium that is Urease (+).

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● Causes Toxic Shock Syndrome after abortions.
LISTERIA MONOCYTOGENES

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CORYNEBACTERIUM DIPHTHERIAE ● Obligately intracellular parasite and non-fastidious.
● Exhibits tumbling end-over-end motility in any liquid media (by means of 4 peritrichous flagella) and
● Klebs-Loeffler Bacillus. has a characteristic umbrella-shaped growth or inverted Christmas tree appearance in semisolid media.
● Palisade, Chinese-character, Picket Fence appearance in Gram Stain caused its “snapping movement” ● Grows best at 25-35C but is able to grow slowly at 4C allowing it to survive at refrigerator temperatures

N
when two cells divide. (V and L formations) which is the basis for the cold enrichment technique.
● Club-shaped due to irregular swellings at one end of the cell. ● Catalase (+), Esculin Hydrolysis (+), CHO Fermentation (+) with no gas.
● Contains characteristic metachromatic granules (Volutin granules or Babes-Ernst Granules) which stain ● Major virulence factor is Listeriolysin O which lyses the phagosomal membrane allowing the bacteria to

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red with blue dyes. escape into the cytoplasm and be intracellular.
● Small zones of beta-hemolysis on BAP. ● Other virulence factors are Adhesins, Internalin A (promote phagocytosis into epithelial cells), ActA

N
● Brown to black with brown-black halo on Mueller’s tellurite due to the reduction of potassium tellurite. (Actin Activation Protein which propels Listeria to other cells using actin polymerization) and
(Potassium tellurite and Tinsdale’s Medium) Siderophores (steals iron).

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● Major virulence factor is the Diphtheria toxin which inactivates Elongation Factor-2 that is required for ● Infections out of the bacteria = Listeriosis.
protein synthesis. (Results to necrosis) ● Causes Early-onset Syndrome = Granulomatosis Infantiseptica and Late-onset Syndrome = Neonatal
● The diphtheria toxin is acquired by C. diphtheria only after a lysogenic conversion with a bacteriophage. meningitis, Meningoencephalitis and Bacteremia.
(Non-lysogenized C. diphtheria are nontoxigenic) ● Most common cause of meningitis in immunocompromised patients.
O
● Causative agent of diphtheria which causes necrosis and pseudomembrane formation in the respiratory ● Blue-green colonies on Trypticase Soy Agar.
tract. The toxin may also disseminate to the blood and cause nerve damage. ● McBride Agar is a selective and enriched media for Listeria monocytogenes. (Crushed glass appearance)
●
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Very weakly acid-fast due to its short chain of mycolic acid.
● Catalase (+), Urease (-), Pyrazinamidase (-), Glucose and maltose fermentation (+) but sucrose
fermentation (-)
● Toxigenicity Test: Elek Test (formation of white precipitin band at 45 degree angle)
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● In BAP, colonies are somewhat similar to Streptococcus spp.
● Catalase (+), Ferments glucose, trehalose and salicin.
● Treatment is ampicillin.

● Schick test used to detect if a person is susceptible to diphtheria.

● Var gravis = EXHIBITS LARGE COLONIES ON BAP AND GAMMA-HEMOLYTIC.
ERYSIPELOTHRIX RHUSIOPATHIAE (Formerly Erysipelothrix insidiosa)
● Var mitis = EXHIBITS FRIED EGG APPEARANCE AND HAS A BLEACH-LIKE ODOR IN ANY MEDIUM USING
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TELLURITE ● Microaerophilic Gram (+) Bacteria which has a tendency to switch from S form to the R form.
● Var intermedius ● Exhibits alpha-hemolysis on BAP. (In BAP, similar looking to Viridans Strep)
 ● Catalase (-), Oxidase (-), Indole (-), H2S in TSI (+), Urease (-) and Nitrate (-).
● Causes Erysipeloid in humans and erysipelas in swine.
● Erysipeloid (whale finger or seal finger) occurs at the site of cut or abrasion where severe pain and
swelling occurs with a violaceous lesion. (It may produce a bacteremia leading to a more diffuse
cutaneous infection)
● People at risk = Butchers.
● Has a characteristic test tube brush appearance in Gelatin media.
● Produces black colonies on tellurite media.
● Erysipelothrix rhusiopathiae’s resistance to neomycin differentiates it from Listeria monocytogenes
(sensitive).
● Treatment is penicillin.
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NOCARDIA (Nocardia asteroides and Nocardia brasiliensis)
● Gram (+), Catalase (+), Urease (+), Partially Acid Fast.
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● Has aerial filaments and branching colonies resembling fungus.
● Aerobic bacilli.
● Heaped, irregular, waxy colonies in a wide variety of culture media. (Nonfastidious organisms)
● Partially acid fast due to mycolic acids and Cord Factor.
N
● 1-4% H2SO4 is used in acid fast stains for Nocardia as Acid Alcohol is too strong.
● Causative agent of Nocardiosis (characterized as a chronic lobar pneumonia that mimics tuberculosis
and is opportunistic).
T
● It is also the causative agent of Actinomycetoma (Madura Foot).
● Urease (+), Growth in Milk Media/Middlebrook 7H10 enhances acid-fastness.
N
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ACTINOMYCES (Actinomyces israelii and Actinomyces gerencseriae)
● Facultative anaerobic Gram (+) Bacilli.
● Colonies form fungus-like branched networks of aerial hyphae.
O
● Most common cause of infection in dental procedures and oral abscesses.
● Causative agent of actinomycosis which may be cervicofacial (causes Lumpy Jaw), thoracic or
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abdominal.
● Characterized by pyogenic lesions with interconnecting sinus tracts.
● Exhibits characteristic molar tooth colonies.
● Treatment is prolonged administration of penicillin for 6-12 months.
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PROPIONIBACTERIUM (Propionibacterium acnes)
● Capable of converting lactic acid to propionic acid and CO2.
T
● Causative agent of acne vulgaris (acne in the face).
● Major virulence factor is Lipase.
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● Beta-hemolytic on BAP.
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MYCOBACTERIUM TUBERCULOSIS
● Philippines ranked 2nd to Cambodia in cases of TB.
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● NTP = National Tuberculosis Program.
● Weakly Gram (+) and may be considered as Gram Ghost.
● Strongly acid-fast due to mycolic acids and Cord Factor.
● Obligate aerobic bacilli.
● Major virulence factor is Cord Factor which only those with Cord Factor are virulent strains and is
responsible for serpentine cord or parallel growth or banding appearance of M. tuberculosis. (Cord
Factor damages mitochondria by releasing Tumor Necrotic Factor or Cachectin causing cell wasting)
● Other virulence factors are Mycoside (mycolic acids), Wax D (acts as an adjuvant which enjances
antibody formation and triggers cell-mediated immunity of macrophage) and Sulfatides (inhibit
phagosome-lysosome fusion).
● Exudative Type = acute inflammatory reaction which resembles bacterial pneumonia and where
tuberculin test (PPD or Purified Protein Derivative test) is positive.
● Productive Type = fully developed chronic granuloma with 3 zones: Central area with giant cells,
Midzone with pale epitheloid cells, Peripheral zone with lymphocytes and other cells and Very Outer
End is Scar or Fibrosis.
● Some granuloma may undergo caseation necrosis which is the liquefaction of the midzone and central
regions resulting in a cheesy-like appearance (caseating granuloma.
● Primary TB, Latent TB, Secondary/Reactivated TB.
● MTB usually starts infecting the middle lower part of the lung but later goes to the upper lobe due to
high oxygen pressure. (It will form consolidations in the upper lobe which will never heal known as the
Ghon lesion)
● Miliary tuberculosis = MTB in the bloodstream.
● Pott’s Disease = MTB in spine.
● Signs and Symptoms: Hemoptysis, Dyspnea, Weight Loss, Night Sweats.
● PPD (through intradermal infection), Mantoux (through intracutaneous injection), Von Pirquet (through
scratch) and Volmer (through patching) = Skin Tests that rely on Delayed Hypersensitivity.
● Fresh morning sputum
● N-acetyl-L-cysteine (nALC) is commonly used to concentrate and 2% NaOH is commonly used to
decontaminate sputum samples of MTB.
● Ziehl-Neelsen (Hot Method) for sputum, Kinyoun (Cold Method) for tissues and utilizes tergitol as
mordant. (Decolorizer is Acid Alcohol: 95% Ethanol in 3% HCl)
 ● Most sensitive test to diagnose MTB is fluorochrome stains: Auramine O-rhodamine (Truant’s Method) MOTT
= yellow-orange fluorescence.
● Spengler’s = MTB staining for the color blind. (MTB is black) ● Mycobacterium kansasii = Yellow Bacillus.

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● Culture is not useful since it takes 2 months to grow MTB. ● Mycobacterium marinum = Swimming Pool Granuloma.
● Non-selective culture media used: Lowenstein-Jensen, Petragnani and American Thoracic Society ● Mycobacterium ulcerans = Rough domed, lemon yellow colonies. (Inert Bacillus and causes Buruli

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(Egg-based with malachite green as inhibitory agent) Ulcers)
● Seaweed-based = Middlebrook 7H10, 7H11, 7H9. ● Mycobacterium gordonae = Tap Water Bacillus.

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● Among non-selective, Petragnani is best.
● Tan to buff-colored, irregular grainy, bumpy, cauliflower (or warty) appearance in colonies.
● Runyoun Classification to separate MTB from MOTT (Mycobacteria Other Than Tuberculosis).
● MTB Complex, Runyoun Group I (Photochromogens), Runyoun Group II (Scotochromogens), Runyoun
● Mycobacterium xenopi = Bird’s Nest Colonies on Cornmeal Agar.
● Mycobacterium terrae = Raddish Bacillus.
● Mycobacterium avium-intracellulare = Battey Bacillus. (Pulmonary disease in AIDS patients)

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Group III (Nonchromogens), Runyoun Group IV (Rapid Growers)
● Antibiotics against TB: Isoniazid (H), Rifampicin (R), Pyrazinamide (Z), Ethambutol (E), Streptomycin (S) TREPONEMA PALLIDUM (Treponema means turning thread)

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RIPES
● Rifampicin causes red secretions, Ethambutol causes color blindness to green. ● Helically coiled, spiral or corkscrew-shaped Gram (-) bacilli.
● DOTS = Directly Observed Treatment Short Course (To eliminate TB). ● Replicate by transverse fission.
● ● Has an outer sheath of glycosaminoglycan coating.

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BOILING FOR 10 MINUTES IS USED TO KILL.
● IT IS ALSO KILLED WITHIN 2 HOURS IN DIRECT SUNLIGHT. ● Has an endoflagella (axial filaments) in periplasmic space conferring a corkscrew motility.
● Has a tapered end for adhesion.
● Not easily stained by aniline dyes. Instead Iron stains, Immunofluorescence Stains and Dark Field

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Illumination is used to view the organism microscopically.
MYCOBACTERIUM LEPRAE (MOST FASTIDIOUS)
● In tissues, Warthin-Starry Silver Impregnation Stain may be used.
● Grown and inoculated into foot pads of armadillos. (Reservoir host) ● Treponema pallidum subspecies pallidum causes syphilis.

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● Specific skin test = Lepromin Test (tuberculoid form) ● Treponema pallidum subspecies pertenue causes yaws or frambesia (ulcerative skin lesions).
● Fite-Faraco Stain is used to stain biopsy of M. leprae. (Lepromatous form) ● Treponema pallidum subspecies endemicum causes endemic syphilis characterized by oral mucosal

N
● Leprosy causes lion face appearance of the infected. lesions (bejel).
● Tuberculoid Leprosy = patches of anesthesia (sensory loss), few or no acid-fast bacilli in tissues, low ● Treponema pallidum subspecies carateum causes pinta characterized by red lesions.

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infectivity, reactive to lepromin. ● It is unique as it has never been cultured continuously on artificial media.
● Lepromatous Leprosy = extensive tissue damage, numerous acid-fast bacilli in tissues, infectivity is high, ● It may grow on tissue culture but only for very short periods of time.
non-reactivity to lepromin, Erythema nodosum leprosum is present. ● Microaerophilic (requires 1-4% O2).
● Causes leprosy or Hansen’s Disease. ● Bacteriological techniques are of no use to diagnose the organism. Serology is used to diagnose.
●
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Non Pathogenic treponemes = Reiter strains. (Pathogenic strains = Nichols strain)
● Spirochetes are easily killed by drying and temperature of 42C. They are also rapidly killed by trivalent
arsenic, mercury and bismuth (contained in drugs such as Salvarsan).
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MYCOBACTERIUM BOVIS ● Penicillin is the drug of choice.

● Cardiolipin is also an important component of the treponemal antigens.
● Primary cause of TB in cattles.
● Treponema pallidum also has Reagin or Wasserman antibodies which is an antibody-like substance
● Acquired through drinking unpasteurized milk of cow.
that gives a positive CF and flocculation tests.
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● Susceptible to Thiophene-2-Carboxylic Acid Hydrozide.

● A disease transmitted by the New World (America) to the Old World (Europe).
● Niacin Test is used to differentiate it from MTB (Niacin positive).
● Causative agent of Syphilis: Primary Stage (Hard Chancre that is painless and Regional
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Lymphadenopathy), Secondary Stage (Condyloma lata or papules in soles and palms with Alopecia or
hair loss and General Lymphadenopathy), Latent Stage (No symptoms but serological tests are positive),
 Tertiary Stage (Gummas or granulomatous lesions in organs, Neurosyphilis, Syphilitic meningitis, LEPTOSPIRA INTERROGANS
hepatitis and etc may occur)
● It is known as the GREAT IMITATOR. ● Tightly coiled, flexible spirochete with one end forming a HOOK.

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● Dark-Field Microscopy is used to diagnose Primary and Secondary Stage while Serology for Latent and ● Grows best under aerobic conditions at 28-30 C in semisolid medium (EMJH medium –
Tertiary Stage. Ellinghausen-McCullough-Johnson-Harris)

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● Congenital Syphilis: Saddlenose, Hutchinson’s Teeth, Interstitial Keratitis… ● It also grows on Fletcher’s Medium which is semi-solid. When you hear Fletcher’s Medium, it is
● Nontreponemal test: USR (Unheated Serum Reagin), RPR (Rapid Plasma Reagin and is the routinely always for Leptospira.

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used), TRUST (Toluidine Red Unheated Serum Test) and VDRL (Venereal Disease Research Laboratory
and is the reference method for Neurosyphilis)
● Treponemal test: TP-PA (Treponema pallidum Particle Agglutination and is the most widely used in the
USA), TPHA (T. pallidum Hemagglutination), TP-MHA (T. pallidum Microhemagglutination), EIA (Enzyme
● Grows well on Tween 80 Albumin media.
● After 1-2 weeks of culture, the leptospires produce a diffuse zone of growth near the top of the tube
and later a ring of growth at a level in the tube corresponding to the level of optimal oxygen tension
for the organisms.

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Immunoassay) and FTA-ABS (Fluorescent Treponemal Antibody Absorbance and is the routine ● Able to survive for weeks in water, particularly at alkaline pH.
treponemal test). ● Causative agent of Leptospirosis or Weil’s Disease.

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● Penicillin is used to treat yet Jarisch-Herxheimer Reaction may occur when T. pallidum releases ● Incubation period is 1-2 weeks.
endotoxins faster than the body can remove them. ● Characterized by haemorrhage and jaundice of the parenchymatous organs.
● Acquired from urine of rats.

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BORRELIA RECURRENTIS
SPIRILLUM MINOR (SPIRILLUM MORSUS MURIS)
● Causative agent of relapsing fever.

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● Loosely coiled Gram (-) spiral organism. ● Causes one form of rat-bite fever (Sodoku).
● Stained readily with Giemsa and Wright’s Stain as it is a blood pathogen. ● Carried by rats all over the world and is inoculated into humans through the bite of a rat resulting in a
● Exhibits great antigenic variation which is why it is relapsing. local lesion, regional gland swelling, skin rashes and fever of the relapsing type.

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● Ultimate recovery occurs only after 3-10 relapses.

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MYCOPLASMA SPP. (PLEUROPNEUMONIA ORGANISMS)

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BORRELIA BURGDORFERI
● Atypical organisms as they do not have cell walls thus making them the smallest bacteria. (125-250 nm
● Causative agent of Lyme Disease, Erythema chronicum migrans, Lyme arthritis, Bannwarth’s Syndrome. in size)
● Transmitted by the bite of the deer tick Ixodes. ● Since they do not have cell walls, their cellular structure is maintained by sterols.
● Lyme Disease presents with a characteristic bulls-eye lesion known as erythema chronicum migrans in ● RESISTANT TO PENICILLIN SINCE IT DOES NOT HAVE A CELL WALL IN THE FIRST PLACE.
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Stage 1. Stage 2 is characterized by arthralgias and arthritis. Stage 3 is characterized with CNS ● Mycoplasmas use glucose as an energy source while Ureaplasma uses urea.
involvement such as Bell’s Palsy. ● Have flask-like or filamentous shapes and specialized polar tip structure that mediate adherence to host
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● Arthritis is the most common complication of Lyme Disease. cells.

● The major cause of arthritis in adults is S. aureus while the disease that will most commonly lead to ● Have a predilection (preference) for mesothelial cells.
arthritis is Lyme disease caused by Borrelia burgdorferi. ● Mycoplasma pneumoniae is the causative agent of WALKING PNEUMONIA, ATYPICAL PNEUMONIA AND
● Grows most readily in a complex liquid medium, Barbour-Stoenner-Kelly (BSK II) medium. IS KNOWN AS THE EATON’S AGENT (first isolated from hamster).
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● Ureaplasma urealyticum causes non-gonococcal urethritis in men. It is known as a T FORM

MYCOPLASMA due to its tiny colonies.
● Cultures of Mycoplasma and Ureaplasma require 2-3 weeks under microaerophilic conditions with
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CHOLESTEROL in a Nutrient Agar. (Dome-shaped colonies)

 ● Edward’s Agar may also be used where Mycoplasma exhibits a characteristic FRIED EGG ● Queensland tick typhus is caused by Rickettsia australis. Its vector is the tick.
APPEARANCE. ● Siberian Tick Typhus or North Asian Tick Typhus is caused by Rickettsia sibrica. Its vector is the tick
● DIENE’S STAIN is used to stain Mycoplasma blue. while its animal reservoir is the rodents.

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● Serological tests used are Cold hemagglutinins or Complement Fixation Tests. ● Q Fever is caused by Coxiella burnetii. Its vector is airborn fomites. (Transmission is through inhalation
of dust contaminated with rickettsiae)

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● Trench Fever is caused by Rochalimaea quintana. (Formerly Bartonella quintana)
● Ehrlichia chaffeensis and Neorickettsia sennetsu cause Human Monocyte Ehrlichiosis. (Characteristic
CHLAMYDIA TRACHOMATIS

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atypical white blood cells)
● Obligately intracellular and energy parasites. ● Ehrlichia ewingii causes Human Granulocytic Ehrlichiosis.
● Has a complex life cycle. ● Anaplasma phagocytophilum causes Human Granulocytic Anaplasmosis.
● Its infective stage is the elementary bodies which will trigger endocytosis to the inside of the cell and ● All Rickettsiae and Ehrlichiae are treated with TETRACYCLINES.

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will form reticulate bodies inside the host cells. These reticulate bodies are also known as
agglomerated bodies due to the fusion of many elementary bodies. They will then undergo binary

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fission to produce more elementary bodies which will leave the host cell and infect other cells. ENTEROBACTERIACEAE
● Gram Stain is useless in staining the bacteria and Giemsa Stain is used.
● Grow in cell lines (tissue cultures): McCoy, HL (Hela cells), HEp-2 cells. ● Shigella and Klebsiella are nonmotile organisms while Yersinia is usually motile but is non motile at 37

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● Sulfonamide susceptibility is used to differentiate Chlamydia species. (Chlamydia pneumoniae = C. (SKY)
Sulfonamide resistant, Chlamydia trachomatis = Sulfonamide susceptible) ● Among the stated genus of the family Enterobacteriaceae, only Shigella, Salmonella, Yersinia and
● Chlamydia trachomatis serogroup A-C causes TRACHOMA (leading cause of blindness in the world). certain E. coli strains are considered as true pathogens.
● Chlamydia trachomatis serogroup D-K causes STDs such as Lymphogranuloma venereum. (It is also the ● Facultative anaerobes or aerobes.

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cause of inclusion conjunctivitis of newborn, similar to ophthalmia neonatorum, and is the most ● Most common group of Gram (-) rods cultured in the clinical laboratory.
common cause of neonatal pneumonia) ● Along with Staphylococci and Streptococci, they are among the most common bacteria that cause
● Chlamydia pneumoniae serogroup TWAR = Taiwan Acute Respiratory Syndrome. disease.

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● Chlamydia psittaci causes PSITTACOSIS OR ORNITHOSIS. ● When the Enterobacteriaceae are motile, they usually have a peritrichous flagella.
● All Enterobacteriaceae ferment glucose and often with resulting gas production.

N
● Enterobacteriaceae that ferments CHO with resulting gas production are called AEROGENIC while those
that do not are ANAEROGENIC.

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RICKETTSIAE
● Enterobacteriaceae possess the enzyme nitroreductase which is why it is nitrate reduction (+). (With
● Grows readily on yolk sacs of embryonated eggs. the exception of Erwinia and Pantoea spp.)
● Obligate intracellular parasites with special affinity to infect endothelial cells. ● They are generally NONFASTIDIOUS organisms and may be grown on a variety of culture media.
● All are transmitted via arthropods except Coxiella burnetii which is transmitted via dust. ● They lack Cytochrome Oxidase which is why it is Oxidase (-).
O
● The Typhus group is located within the cytoplasm while the Spotted Fever Group is located within the ● They are capable of producing colicins. (Bacteriocins)
nucleus. ● Common culture media used are MacConkey Agar (Primary Plating Media), Eosin Methylene Blue Agar,
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● Epidemic typhus or Brill-Zinnser Disease (louse-borne typhus) is caused by Rickettsia prowazekii. Its Thiosulfate-Citrate-Bile Salt-Sucrose Agar, Hektoen Enteric Agar, Salmonella Shigella Agar, Xylose Lysine
vector is the louse. Deoxycholate Agar and Blood Agar Plate.
● Endemic typhus or Murine typhus (flea-borne typhus) is caused by Rickettsia typhi. Its vector is the ● May exhibit blue-black colonies with green metallic sheen (E. coli), mucoid (Klebsiella), swarming
flea. (Proteus), pigments (Serratia) on culture.
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● Scrub typhus is caused by Orientia tsutsugamushi. Its vector is the mite. ● Lactose Fermented Rapidly (EKE group): Escherichia coli, Klebsiella pneumoniae and Enterobacter
● Rocky Mountain Spotted Fever (RMSF) is caused by Rickettsia rickettsiae. Its vector is the tick. (It is aerogenes. (Possesses the two enzymes for lactose fermentation: Lactose Permease and
the most fatal and most frequent rickettsial disease and also known as blue disease) Beta-galactosidase)
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● Rickettsial pox is caused by Rickettsia akari. Its vector is the mite. (Has a characteristic vesicular rash ● Lactose Fermented Slowly or the Late Lactose Fermenters (ESCAPE): Edwardsiella, Serratia, Citrobacter,
or eschars) Arizona, Providencia, Erwinia. (They only possess the enzyme Beta-galactosidase)
 ● Lactose Not Fermented or Non-lactose Fermenters (SSPP): Shigella, Salmonella, Proteus, Pseudomonas. ● Gastroenteritis: ETEC (LT AND ST), EAEC (BIOFILM FORMATION AND ST-LIKE TOXIN), EHEC (SHIGA-TYPE
● O Antigens (Associated with Lipopolysaccharide) and is aka Somatic Antigen or Body Antigen. It is TOXIN), EPEC (PEDESTAL FORMATION), EIEC (TYPE III SECRETION SYSTEM)
resistant to heat and alcohol and antibodies against the O antigen are usually IgM. ● Enteroinvasive Escherichia coli = Shigella-like infection (due to intracellular invasion and bloody

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● K Antigens (Associated with Capsules) and is aka Envelope or Capsular Antigen. It is heat-labile and may diarrhea).
interfere with agglutination by O antisera. (In order to avoid interference with O antisera, boil for 15 ● Enteroaggregative Escherichia coli = Produces biofilm.

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minutes) ● Enteropathogenic Escherichia coli = Pedestal causes effacement of microvilli.
● Salmonella typhi’s K antigen is known as the Vi Antigen. ● Enterotoxigenic Escherichia coli = Increased cAMP and cGMP leading to watery diarrhea. (Causes

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● H Antigens (Associated with Flagella) and is denatured or removed by heat or alcohol. Antibodies
against the H antigen are usually IgG.
● Bacteriocins are virus-like bactericidal substances which are responsible for lytic activities of certain
normal flora against other pathogenic bacteria. Colicins for E. coli, Marcescens by Serratia, Proticines by
Traveller’s Diarrhea, Montezuma’s Revenge or Turista)
● Enterohemorrhagic Escherichia coli = Shiga-type toxin which inhibits protein synthesis causing bloody
diarrhea and Hemolytic-Uremic Syndrome. (E. coli O157:H7)
● Hemolytic-Uremic Syndrome (Thrombocytopenia, Hemolytic Anemia, Renal Failure) = Microangiopathic

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Proteus and Pyocins by Pseudomonas. Hemolytic Anemia.
● Bacteriocin-producing strains are resistant to their own bacteriocin which is why bacteriocins may also ● Sorbitol MacConkey Agar = E. coli O157:H7 (As this strain cannot ferment sorbitol within 48 hours).

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be used for typing the organism. ● Treatment is with ciprofloxacin. (Previously, it was SXT).
● Ortho-nitrophenyl-Beta-Galactopyranoside (ONPG) is a test for late lactose fermenters and checks if
bacteria can degrade ONPG to nitrophenyl which is yellow in color.

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KLEBSIELLA PNEUMONIAE

ESCHERICHIA COLI ● AKA Friedlander’s Bacillus.

● TSI A/A, Gas (+), LIA K/K, Citrate (+), Urease (+), Sulfide (-), Indole (-), Non-motile.

N
● It is the prototype facultative anaerobic or aerobic microbial intestinal flora. ● Causes Permanent Lung Damage due to Necrotizing Pneumonia and subsequent bloody sputum.
● Most significant species in the genus. ● Capable of causing UTI with a characteristic purple urine.
● Has a green metallic sheen or iridescent sheen on EMB because as it ferments lactose, it also ● Mucoid colonies due to large amounts of capsule.

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precipitates the eosin and methylene blue stains used in the culture media resulting in a greenish
discoloration.

N
● Pink colonies on MacConkey Agar since it is a lactose fermenter.
KLEBSIELLA OZAENAE
● May be haemolytic on BAP. (This is more commonly observed in pathogenic strains from urine isolates)

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● Exhibits TSI A/A, Gas (+), LIA K/K (meaning decarboxylase positive), Citrate (-), Urease (-), Sulfide (-), ● Causes ozena which is characterized by the progressive atrophy of the nasal mucosa. The condition is
Indole (+), Motile with peritrichous flagella. also called Chronic Atrophic Rhinitis.
● Beta-glucuronidase (+); the test utilizes the substrate 4-methylumbelliferyl-Beta-glucuronide or MUG ● Differs from Klebsiella pneumoniae in Urease as K. ozaenae is Urease (-).
and is therefore MUG (+).
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● IMViC ++--
● Virulence factors include: Lipid A (endotoxin, associated with septic shock), K1 Antigen (associated with
OTHER KLEBSIELLA
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neonatal meningitis), Enterotoxins: LT and ST (associated with ETEC watery diarrhea), Shiga toxin or
Verotoxin (inhibits protein synthesis at the 60S subunit and associated with EHEC bloody diarrhea),
Enteroaggregative ST-like Toxin (associated with EAEC watery diarrhea), Type III Secretion System
(associated with EIEC invasive properties), Type III Secretion System (associated with EPEC pedestal
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● Klebsiella oxytoca is the only Klebsiella species that is Indole (+).
● Klebsiella rhinoscleromatis (Frisch Bacillus) causes rhinoscleroma which is a destructive granuloma in
the nose and oropharynx.

formation), Adhesins, Capsules, Enterochelin and Outer Membrane Proteins. ● Klebsiella granulomatis (formerly known as Calymmatobacterium granulomatis) causes chronic genital
● Causes UTIs (due to uropathogenic strains and biofilm producing strains such as EAEC), Cystitis ulcerative disease or granuloma inguinale.
(infection reaches the bladder), Pyelonephritis (infection reaches the kidneys and is diagnosed when ● Most Klebsiella spp. often exhibit ESBL (Extended Spectrum Beta-Lactamases) which confers to it an
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hematuria and pyuria, WBCs in urine, occurs), Neonatal Meningitis (K1 Antigen), Septicemia (Lipid A), extended resistance to various drugs.
Gastroenteritis, Hemolytic-Uremic Syndrome.
ENTEROBACTER SPP. PROTEUS

● TSI A/A, Gas (+), LIA K/K, Citrate (+), Urease (-), Sulfide (-), Indole (-), Motile with peritrichous flagella. ● Among the PPM, only Proteus exhibits swarming colonies and are Non-Lactose Fermenters.

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(Enterobacter aerogenes) ● In order to inhibit the swarming of Proteus, we use Phenylethyl Alcohol Agar and Cystine Lactose
● Mucoid colonies however are lesser compared to that of Klebsiella as it has smaller capsules. Electrolyte Deficient Agar.

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● Enterobacter gergoviae is similar to E. aerogenes but has strong urease activity, Urease (+). ● Two Proteus spp. that are swarming will not join together and they will form a demarcation between
● Enterobacter cloacae are Arginine Dehydrogenase (+) and Ornithine Decarboxylase (+). their colonies in order to separate them from one another. This phenomenon is known as Dienes’

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● Enterobacter sakazakii is Arginine Dehydrogenase (+), Ornithine Decarboxylase (+) and has a Phenomenon.
characteristic yellow pigment. ● TSI A/A, Gas (+), LIA R/A, Citrate (+), Urease (+), Sulfide (+), Indole (+) for Proteus vulgaris, Indole (-) for
● Enterobacter taylorae is Arginine Dehydrogenase (+), Ornithine Decarboxylase, Lactose (-). (AKA Proteus mirabilis, Motile.
Enterobacter cancerogenus) ● H2S (+) sets it apart from other PPM.

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● Pantoea agglomerans is Indole (+), Lysine Decarboxylase, Ornithine Decarboxylase, Arginine ● Indole sets Proteus mirabilis and vulgaris apart.
Dehydrogenase (-) ● Proteus spp. have a characteristic “Burned Chocolate Odor.”

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● Enterobacter cloacae, Enterobacter aerogenes, Enterobacter agglomerans and Enterobacter sakazakii ● 2 Clinically Significant spp. are P. mirabilis and P. vulgaris.
are now classified into the genus Cronobacter. ● Major virulence factor is Urease.
● Causes UTIs, Bacteremia and Stone Formation (Lithiasis).
● Proteus mirabilis is susceptible to ampicillin and cephalosporin while Proteus vulgaris is resistant to the

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two drugs.
SERRATIA MARSESCENS

● Voges-Proskauer (+), Lipase (+), Gelatinase (+), DNase (+).

N
● Produces a red pigment prodigiosin. (Red colonies) MORGANELLA MORGANII
● Produces a bacteriocin called Marsescens.
● Recently, it is called the most common cause of nosocomial infections along with Pseudomonas ● Also deaminase (+) similar to other PPM.

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aeruginosa. (Commonly causing pneumonia and septicaemia in immunosuppressed patients) ● It is unique as it is the only PPM that is Citrate (-).
● It is one of the causes of COMMUNITY-ACQUIRED ENDOCARDITIS. ● May cause UTIs.

N
● Serratia odorifera has a characteristic rancid, potato-like odor.

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PROVIDENCIA SPP.
HAFNIA ALVEI
● PPM is H2S (-) but Citrate (+) is most likely Providencia.
● It is biochemically similar to the Enterobacter spp. ● Providencia rettgeri are pathogens of the urinary tract and are common in nosocomial outbreaks and
O
● It is responsible for the scent of human feces since it produces the skatole found in feces. may also be found in burn unit cases in the hospital.
● Its most notable characteristic is a DELAYED CITRATE REACTION. ● P. rettgeri ferments adonitol but not trehalose.
● ●
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It was previously called Enterobacter alvei. Providencia stuartii have been isolated in urine and are responsible for nosocomial outbreaks in burn
● It is capable of causing gastroenteritis because the bacteria is capable of adhesion to epithelial cells but units and are more common in burn units than P. rettgeri.
the exact mechanism of its ability to cause gastroenteritis is not well understood. ● Providencia stuartii ferments trehalose but not adonitol.
● Providencia alcalifaciens is the only PPM that is Urease (-).
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CITROBACTER FREUNDII ● Salmonella typhi has a special capsular antigen called the Vi antigen.
● Salmonella enterica subsp. enterica has 4 serovars: A = Paratyphi A, B = Paratyphi B, C1 = Cholerasuis
● TSI K/A or A/A with H2S (+), LIA K/A, Citrate (+). and D = Typhi.

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● Biochemically similar to Salmonella since both are highly H2S (+). ● TSI K/A with No Gas Production but H2S (+). (Salmonella typhi)
● EDWARDSIELLA TARDA ● Has a characteristic moustache H2S in TSI and causes black centered colonies when cultured due to

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● TSI K/A with Gas Production and H2S Production, LIA K/K with H2S Production. abundant H2S production. (Salmonella typhi)
● Biochemically similar to Escherichia coli except that it is H2S (+). ● Salmonella paratyphi A produces no H2S and is Lysine Decarboxylase (-).

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● It is associated with infections of cold-blooded animals and infections acquired from aquatic ● One genus from the Enterobacteriaceae is biochemically similar to Salmonella and that is Shewanella.
environments. The only difference between the two is that Shewanella is Sucrose (+) while Salmonella is Sucrose (-).
● Widal Test or the Tube Dilution Agglutination is used to check for antibodies against Salmonella. High
titer of O antigen (Greater than 1:320) against H antigen titer of greater than 1:640 is considered

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SHIGELLA SPP. positive for Salmonella. High titer of only H antigen suggests past vaccination or past infection of
Salmonella. High titer of the Vi Antigen suggests a carrier state of the Salmonella bacteria.

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● TSI K/A with No Gas Production and no H2S production, LIA K/A, Citrate (-), Urease (-), Sulfide (-), Indole ● Typhidot is also used for the rapid detection of specific IgM and IgG antibodies to the Outer Membrane
(-), Non-motile. Proteins of Salmonella typhi. If IgM antibody is increased or IgG and IgM is increased, it would indicate
● Generally Non-Lactose fermenters however, S. sonnei may show delayed lactose fermentation. acute typhoid fever. If only IgG is increased, it indicates persistent, relapsing, recurring, previous
(Meaning S. sonnei is ONPG positive)

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● 4 Pathogenic species under the genus Shigella are Shigella dysenteriae (A), Shigella flexneri (B), Shigella
boydii (C) and Shigella sonnei (D). (Most infective is dysenteriae, then flexneri then sonnei then boydii)
● The A, B, C and D grouping of the species are based on the O antigen serotyping.
infection with typhoid fever or carrier state of Salmonella typhi. If IgM and IgG titer is not increased,
there is no typhoid fever.
● Both Widal and Typhidot are only (+) after the 3rd week of infection where serological tests may
already be performed.

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● Its O antigen is similar to E. coli which is why it is important to identify the organism first as Shigella ● Same virulence factors with that of Escherichia coli and Shigella. (No LT, ST, Shiga Toxin and Biofilm)
before serotyping. ● Causative agent of Typhoid Fever or Enteric Fever. (Characterized by lymphoid hyperplasia and
● Virulence factors include endotoxin, Shiga Toxin (inhibits protein synthesis at 60S subunit) and Outer hypertrophy, hepatosplenomegaly and bloody diarrhea)

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Membrane and Secreted Proteins. ● ROSE SPOTS ON CHESTS IS SUGGESTIVE OF TYPHOID FEVER.
● Shiga Toxin may also cause meningismus which is similar to meningitis with only no actual ● Salmonella Cholerasuis is capable of causing septicaemia.

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inflammation of meninges. ● Capable of causing enterocolitis which is the least virulent manifestation. (Self-limiting)
● Causes Shigellosis or Bacillary Dysentery with bloody diarrhea due to intracellular nature of the ● Carrier state may happen if bacteria gets trapped in the gallbladder.

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bacteria and actin polymerization in a manner similar to Listeria monocytogenes. (One notable ● One of the most famous carriers of Salmonella was Mary Mallon, the first person in the US to be
symptom is tenesmus) identified as an asymptomatic carrier.
● Septicemia is very rare. ● 1st week = Blood cultures, 2nd week = Stool/Urine cultures, 3rd week = Serology.
● Ingestion of only 10-100 organisms are required to cause an infection. ● Cholecystectomy may be required to treat carrier states.
O
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SALMONELLA PSEUDOMONAS AERUGINOSA

● There are only 3 species under the genus Salmonella but only 1 of them is clinically significant which is ● Obligate aerobes and are therefore Oxidase (+).
Salmonella enterica. ● It is invasive and toxigenic and causes infection among people with abnormal host defences (weak
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● Salmonella enterica has 5 subspecies: I – enterica, II – salamae, IIIa – arizonae, IIIb – diarizonae, IV – immune system).
houtenae, VI – indica. ● It is the traditional #1 cause of nosocomial infections and they thrive in moist environments.
● Among the 5 subspecies, only Salmonella enterica subsp. enterica is associated with human infections. ● Motile with Monotrichous Flagella. (Monotrichous is faster while Peritrichous is tumbling)
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● The subspecies were reported out as serotypes based on the Kauffman-White scheme of classification. ● Has a characteristic sweet or grape-like or corn taco-like odor in BAP due to the production of
● The Kauffman-White scheme is based on Somatic and Flagellar Antigens. 2-aminoacetophenone and smooth, round with fluorescent greenish colony in ordinary culture media.
 ● Culture from patients with cystic fibrosis will yield Pseudomonas aeruginosa that form mucoid colonies STENOTROPHOMONAS MALTOPHILIA (Xanthomonas maltophilia)
due to alginate slime overproduction which is responsible for biofilm formation. (STRONGLY
ASSOCIATED WITH CYSTIC FIBROSIS TOGETHER WITH BURKHOLDERIA CEPACIA) ● Loves maltose.

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● It contains pigments: pyocyanin (blue), pyoverdine (green), pyorubin (red), pyomelanin (black). ● Oxidase (-), Grows at 42C.
● Has a characteristic fluorescent greenish colony on any culture media due to pyoverdine. ● Large colonies with yellow tan pigment in Trypticase Soy Agar.

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● Capable of Growth at 42C. ● Lavender-green colonies on Sheep Blood Agar Plate.
● Oxidation-Fermentation Test using Hugh and Leifson’s Oxidative Fermentative Medium with 0.02% ● Has a characteristic ammonia-like odor.

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Peptone is used.
● Indicator of O-F Test is Bromthymol blue.
● Tube 1 = Yellow and Tube 2 = Green : OXIDIZER. (Pseudomonas aeruginosa) HACEK GROUP OF BACTERIA
● Tube 1 = Yellow and Tube 2 = Yellow : FERMENTER. (Escherichia coli)

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● Tube 1 = Green and Tube 2 = Green : NONOXIDIZER OR NONSACCHAROLYTIC. (Alcaligenes faecalis) ● Haemophilus, Aggregatibacter, Chromobacterium, Eikenella, Kingella.
● Virulence factors include N-methyl-phenylalanine pili, Alginate Slime (responsible for biofilm in cystic ● Aggregatibacter actinomycetemcomitans = STAR-SHAPED COLONIES.

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fibrosis patients), Exotoxin A (blocks protein synthesis), Endotoxin and Flagella. ● Chromobacterium violaceum = DARK VIOLET METALLIC SHEEN COLONIES. (This is due to a pigment
● Has characteristic blue-green pus in wound and burn infections. violacein which is also used as a natural antibiotic)
● Causes Mild Otitis Externa (Swimmer’s Ear) as Pseudomonas aeruginosa thrives in moist environments. ● Cardiobacterium hominis = Causes endocarditis.
● ● Eikenella corrodens (CORRODING BACILLUS) = Requires hemin for growth (CAP), may cause

AS
Causes Ecthyma Gangrenosum which is Pseudomonal sepsis.
● Multiple drug therapy must be used as the bacteria rapidly develops resistance. culture-negative endocarditis, CORRODES AGAR, CHARACTERISTIC BLEACH-LIKE OR SEMEN ODOR.
(Associated with human bites)
● Kingella kingae = PITS INTO THE AGAR and is BETA-HEMOLYTIC but does not grow on MacConkey.

N
(Significant cause of infection in children and causes Spondylodiscitis)
BURKHOLDERIA MALLEI

● Causes glanders in horses which is characterized by broken skin with multiple abscesses.

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● Weakly Oxidase (+) and does not grow at 42C. ESKAPE PATHOGENS

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● Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii,
Pseudomonas aeruginosa and Enterobacter.

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BURKHOLDERIA PSEUDOMALLEI
● Exhibits a high rate of antibiotic resistance.
● Causes melioidosis which is a primary pneumonitis that will always lead to septicaemia. ● Acinetobacter baumannii is also known as Iraqibacter due to its sudden appearance during the Iraq
● AKA Vietnamese Time Bomb Disease, Glander’s-Like Disease and Vietnamese Tuberculosis. War.
● Has a characteristic cornflower appearance on Ashdown’s Agar with an earthy odor.
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● Oxidase (+) and grows at 42C.
VIBRIO CHOLERAE
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● Serogroup O1 and O139 = Epidemic cholera.

BURKHOLDERIA CEPACIA (Formerly EO-1)
● Serogroup non-O1 and non-O139 = Cholera-like disease.
● Onion bulbs rot in plants and feet rot in animals. ● Comma-shaped, aerobic rods that are Oxidase (+).
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● Causes severe pneumonia in cystic fibrosis patients. (STRONGLY ASSOCIATED WITH CYSTIC FIBROSIS ● Oxidase (+), grows best at 37C on TCBS with yellow colonies. (Oxidase test will set apart its difference
PATIENTS) from Enterobacteriaceae)
● Characteristic yellow, serrated (feathery) colonies. ● Indicator in TCBS: BROMOTHYMOL BLUE.
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● Grows at a very high pH (8.5-9.5) and is killed by acid.

● TCBS is used as the selective medium while APW is the enrichment medium.
 ● Vibrios are susceptible to 2,4-diamino-6,7-diisopropylpteridine phosphate (compound O/129) which ● Unique characteristic of its gastroenteritis is the presence of RBCs AND WBCs in the stool.
differentiates it from Aeromonas spp. which are resistant to the compound. ● Campylobacter fetus has S Protein (virulence factor) and causes abortion in cattles. (Differentiated
● Growth in 6% NaCl differentiates Vibrio from Aeromonas spp. from C. jejuni and C. coli due to its inability to grow at 42C and susceptibility to cephalotin)

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● Vibrio cholerae is only halotolerant while the rest (Vibrio parahemolyticus and Vibrio vulnificus) are
halophilic.

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● Vibrio cholerae serogroup O1 has determinants for further subtyping such as Ogawa (India), Inaba
HELICOBACTER PYLORI
(Philippines), Hikojima (Japan).

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● Vibrio cholerae exhibits 2 biotypes: El Tor which agglutinates Chicken RBC, is haemolytic, is
Voges-Proskauer (+) and is Polymyxin resistant; Classical which is the exact opposite of El Tor.
● Vibrio cholerae produces heat-labile enterotoxin (Choleragen) which has 2 Fragments: Fragment A and
Fragment B, acting in a manner similar to the LT toxin of ETEC strains and is also antigenically related to
● Causative agent of antral gastritis, duodenal peptic ulcer, gastric ulcer and gastric carcinoma.
● The ONLY bacteria capable of causing cancer is Helicobacter pylori.
● It is a spiral-shaped or helical-shaped, microaerophilic, Gram (-) rod containing 4-6 multiple flagella at
one pole. (Lophotrichous)

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it. (Causes severe watery diarrhea expelling 20-30 liters of water per day) ● Strong producer of urease and has protease.
● Since it is inactivated by acid, it requires greater than 10^10 or more organisms to cause infection if ● Grows at a pH of 6.0-7.0.

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coming from water but requires only less than 10^2-10^4 organisms if coming from food as food has ● Since it is a spiral organism, a special silver stain (Warthin-Starry Silver Stain) or Modified Giemsa
a buffering capacity. stain is used to view the bacteria in a microscope.
● Cholera is typically a non-invasive infection and will never affect the bloodstream. ● Determination of serum antibodies in the blood, Stool Antigen Tests, Carbon Urea Breath Test (due to
●

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Cholera infections lead to watery diarrhea with characteristic RICE WATER STOOLS. its strong urease activity) and Endoscopy (to provide a biopsy sample for rapid urease test, histology
● Vibrio parahaemolyticus causes gastroenteritis, acquired through ingestion of seafoods, green and microbial culture).
colonies on TCBS and KANAGAWA TEST (+). ● MICROAEROPHILIC and may grow on Skirrow’s Medium.
● Kanagawa Test is a test for hemolysin. ● Harms the stomach due to ammonia production via urease.

N
● Vibrio vulnificus causes wound infections, acquired through eating infected oysters, blue-green ● Proton pump inhibitors may also be given to directly inhibit Helicobacter pylori and inhibit its strong
colonies on TCBS, and is commonly associated after typhoons. urease production.

T
N
AEROMONAS HYDROPHILA HAEMOPHILUS INFLUENZAE (PARVOBACTERIA: Haemophilus, Bordetella, Brucella, Francisella)
● Similar to Vibrio except it is resistant to Compound O/129 and does not grow in 6% NaCl. ●

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Pleomorphic, Gram (-) coccobacilli.
● CAPABLE OF GROWTH UP TO 4C. ● Requires enriched media with blood or blood products. (Blood Loving)
● ONPG (+) ● Requires X Factor (Hemin) which is heat-stable and V Factor (NAD) which is heat-labile.
● Capable of causing dysenteric gastroenteritis or cholera-like disease. ● The 2 Clinically Significant species are Haemophilus influenza type b and Haemophilus ducreyi.
● The best media to isolate Haemophilus spp. is with the use of Horse or Rabbit Blood in a Chocolate
O
Agar Plate as these two do not contain NADases in their RBC. It requires heating the blood to at least
CAMPYLOBACTER JEJUNI AND COLI 80 C to release the hematin.
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● There are 5 ways of isolating Haemophilus spp.: Staphylococcus Streak (Satellitism), Horse
● Clinically indistinguishable Blood-Bacitracin Agar (Differentiate Hemolysis), Levinthal Agar (Differentiate Encapsulated Strains), Use
● GULL WING SHAPED RODS. (Or S-shaped rods). of the X and V Factors and Delta-aminolevullinic acid test (Check for Hemin Requirement).
● Hard to stain using Gram stain. (Replace safranin with carbolfuchsin to better stain the organism) ● Porphyrin is detected in Delta-aminolevullinic acid Test which has an absorbance at 340 nm.
IC

● Skirrow’s Medium, CAMPY Blood Agar, Cefoperazone Vancomycin Amphotericin (CVA) Medium and ● Pfeiffer’s Bacillus
Campylobacter thioglycollate broth. ● It is the most important pathogenic species of the genus as it causes meningitis in children and
● GROWS AT 42-43C. respiratory tract infections in both children and adults.
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● NONSACCHAROLYTIC and MICROAEROPHILIC. (Requires 5% O2, 10% CO2, 85% Nitrogen) ● It requires both X and V Factors for growth on Nutrient Agar.
● Virulence factors include: Endotoxin, Cytopathic toxin and Enterotoxin.
 ● Encapsulated strains consist of 6 serotypes on the basis of the polysaccharide capsule it has: a,b,c,d,e,f that since it is bacterial there is also neutrophilia; lymphocytosis is present but is generally not
which are identified through typing. elevated as to the total number of lymphocytes or absolute lymphocytes)
● Infections out of Haemophilus influenzae are usually accompanied with bacteremia and is usually ● Polymerase Chain Reaction is the most sensitive method to diagnose pertussis.

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caused by serotype B. ● Erythromycin is the drug of choice for whooping cough and is very effective in the catarrhal stage.
● Its major virulence factor is its polysaccharide capsule. (For type b strains, the capsular ● Usually in combination with toxoids of diphtheria and tetanus injected intramuscularly. (DPT)

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polysaccharide is a Polyribose-ribitol Phosphate) ● Bordetella bronchiseptica is the only Bordetella species that is motile (has peritrichous flagella) and
● It commonly affects children between 5 months to 5 years while infants under 3 months of age do not is a rapid urease producer. It is also the only one associated with septicaemia.

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contract the infection as they contain IgG antibodies from their mothers. (MOST COMMON CAUSE OF
MENINGITIS IN CHILDREN AGED 5 MONTHS TO 5 YEARS)
● Ampicillin (Amoxicillin) is used to treat if the organism is not a Beta-lactamase producer.
BRUCELLA
● Haemophilus aegyptius causes conjunctivitis and Brazilian purpuric fever. It is formerly called the

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Koch-Weeks Bacillus and also Haemophilus influenzae biotype III. ● Obligate human and animal parasites and are located intracellularly.
● Haemophilus aphrophilus causes infective endocarditis and pneumonia. It is now reclassified as ● Relatively inactive metabolically.

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Aggregatibacter aphrophilus. ● Brucella melitensis typically infects goats, Brucella suis infects swine, Brucella abortus infects cattle
● Haemophilus ducreyi causes soft chancre (chancroid) and requires X Factor only. Isovitalex is used to and Brucella canis infects dogs.
grow this organism. ● Brucella abortus (Bang’s Bacillus) causes abortion in cattle due to its affinity for ERYTHRITOL.
●

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Haemophilus haemolyticus is non-pathogenic which requires the X and V Factors and exhibits ● Very Fastidious.
beta-hemolysis. ● Differentiation among Brucella species or biovars is through their sensitivity to dyes and H2S
● Haemophilus parainfluenzae requires the V Factor only and causes infective endocarditis and urethritis. production.
(In immunocompromised individuals) ● Has cell wall antigens: A and M. (Antigen A is found in Brucella abortus and Antigen M is found in

N
● Haemophilus suis causes diseases in hogs. It also resembles H. influenzae bacteriologically. Brucella melitensis)
● Haemophilus haemoglobinophilus requires the X Factor and is only found in dogs and never in ● Causes BRUCELLOSIS (Undulant fever, Malta fever and Bang Disease) which is characterized by
humans. granulomatous nodules in parenchymatous organs, general lymphadenopathy and splenomegaly.

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● Among the 4 species, Brucella melitensis infection is the most acute and severe.
● The most common vehicle of infection is cheese from unpasteurized goats’ milk. (Ingestion of infected

N
BORDETELLA PERTUSSIS (Generally non-motile) milk)
● Castaneda Medium and Brucella Agar.

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● Small Gram (-) coccobacilli which has bipolar metachromatic granules seen using toluidine blue stains ● Brucella abortus = Thionine (S), Fuchsin (R).
and is encapsulated. ● Brucella suis = Thionine (R), Fuchsin (S)
● Bordet-Gengou Agar (Potato-Glycerol Base), Jones-Kendrich Charcoal Agar, Regan-Lowe (MOST ● Brucella canis = Thionine (R), Fuchsin (S)
PREFERRED), Steiner-Scholte Agar. ● Brucella melitensis = Thionine (R), Fuchsin (R)
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● Exhibits MERCURY DROPLETS in Bordet-Gengou Agar. (Bordetella parapertussis exhibits brown ● Serum agglutination tests are performed with IgG agglutinin titers above 1:80 indicate active infection.
pigments in Bordet-Gengou Agar) ● Those who test negative with strong clinical evidence of Brucellosis must be subjected to a test for
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● Causative agent of the whooping cough. “blocking antibodies.”

● The disease consists of 3 stages: Catarrhal, Paroxysmal and Convalescent.
● It possess a heat-stable endotoxin (LPS) and exotoxins such as filamentous hemagglutinin, Pertussis
toxin or Adenylate Cyclase toxin, Tracheal Cytotoxin and Dermonecrotic toxin.
FRANCISELLA TULARENSIS
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● The filamentous hemagglutinin mediates adhesion to the ciliated epithelial cells. Pertussis toxin
promotes lymphocytosis because it blocks the re-entry of all lymphocytes into lymph glands or ● Associated with rabbits since it is the animal reservoir and is most infectious in rabbits.
lymphoid tissue and promotes sensitivity to histamine. The Adenylate Cyclase Toxin functions to ● Its clinical presentation depends on the route of infection with six major syndromes.
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increase cAMP levels which leads to inhibition of immune effector cell functions. The Tracheal (Ulceroglandular Tularemia is characterized by an ulcerating papule and regional lymphadenopathy,
Cytotoxin inhibits DNA synthesis in ciliated cells and functions for ciliostasis. (It is important to note
 Pneumonic/Peribronchial Tularemia. Oculoglandular Tularemia, Glandular Tularemia, Oropharyngeal YERSINIA ENTEROCOLITICA
Tularemia and Typhoidal Tularemia (Septicemia).
● Biochemically inactive. ● Non-lactose fermenting, Gram (-) rods that are Oxidase (-), Urease (+) and Motile as opposed to

T
● It is one of the organisms that may be used as a biological weapon: since it is extremely invasive and Yersinia pestis which are Urease (-) and Non-motile.
very infective. (Easily spread via aerosols) ● They grow best and are motile at 25C but non-motile at 37C.

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● It is a Biohazard 3 organism and must not be cultured in normal laboratories. ● It mimics APPENDICITIS.
● Consists of two major biovars: Jellison type A and Jellison type B. ● Has characteristic bull’s-eye colonies on Cefsulodin-Irgasan-Novobiocin (CIN) Agar.

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● Jellison type A is lethal for rabbits, produces severe illness in humans while Jellison type B is not lethal ● PASTEURELLA MULTOCIDA
for rabbits and produces milder disease in humans. ● Causes cellulitis and Shipping Fever.
● Since it is highly infectious in nature, it is a potential agent of bioterrorism. (Only 50 organisms are
needed to cause disease)

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● It may be cultured on Glucose Cysteine Blood Agar with Thiamine where it exhibits metallic gray LEGIONELLA PNEUMOPHILA
colonies.

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● May also grow on BCYE and Supplemented Charcoal Yeast Agar. (Cysteine is the growth requirement ● It was a bacteria named after an outbreak of pneumonia in persons attending the American Legion
of bacteria) Convention in Philadelphia thus earning the name Legionella.
● Single serum titer of 1:160 is highly suggestive of tularemia. ● Causative agent of Legionnaire’s Disease and Pontiac Fever (serogroups 1 and 6).
● It stains poorly using the Gram stains because of its unique lipopolysaccharide content and are not seen

AS
in stains of clinical specimens. (Replace safranin with 0.1% basic fuchsin to better stain the organism)
● Giemsa stain may also be used.
YERSINIA PESTIS
● Grown on complex media such as BCYE with alpha-ketoglutarate, cysteine and iron. (BCYE contains

N
● Pleomorphic Gram (-) rods that exhibit striking bipolar staining (safety pin appearance) with Wayson’s alpha-ketoglutarate which enhances the growth of L. pneumophila)
stain. ● Opal-like colonies on BCYE.
● It is typically Catalase (+), Oxidase (-), Indole (-) and Urease (-). ● Catalase (+), Oxidase (+), Hippurate Hydrolysis (+), Gelatinase (+) and has a beta-lactamase.

T
● It grows better at 28C than at 37C. ● Other Legionella species are Catalase (+), exhibits variable oxidase activity, Hippurate Hydrolysis (-),
● Has a bacteriocin called pesticin. mostly produces gelatinase and beta-lactamase with the exception of Legionella micdadei.

N
● Virulent Yersinia pestis produce V and W Antigens which yields the growth requirement for calcium for ● Legionella micdadei is the causative agent of Pittsburgh Pneumonia.
growth at 37C. (V and W Antigens are essential for its virulence) ● Legionella bozemanii is the Wiga Agent.

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● It also has a capsular protein which is produced at 37C and confers antiphagocytic properties. ● Characteristic Coiling Phagocytosis is exhibited by the bacteria during its pathophysiology.
● It has an iron-scavenging siderophore called yersiniabactin. ● Sputum is not used as a specimen since it contains a lot of normal flora which may overgrow Legionella
● Yersinia pestis is the causative agent of the plague which is an infection of wild rodents and is pneumophila in BCYE.
transferred to humans by the bite of the flea, Xenopsylla cheopis.
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● ASSOCIATED WITH RATS AS IT IS A ZOONOSIS.
● It produced the pandemic known as the “Black Death” in previous centuries resulting in millions of BARTONELLA SPP.
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fatalities. (Black due to black hemorrhages upon autopsies of bodies)

● It may also cause pneumonic plague because it can be transmitted by aerosol making it a potential ● Bartonella bacilliformis causes Oroya fever (initial stage) which is a serious infectious anemia and
biological weapon. Verruga peruana (eruptive stage) which is characterized by vascular skin lesions that occur in CROPS.
● Hemorrhagic and necrotic lesions develop in all organs when a person acquires the plaque. ● Transmitted by the sandfly Lutzomyia.
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● Primary pneumonic plague also results from inhalation of infective droplets (usually from a coughing ● Bartonella henselae causes cat-scratch disease (Teeny’s disease).
patient) with hemorrhagic consolidations, sepsis and death. ● The most common ocular manifestation of Cat-Scratch Fever is Parinaud’s oculoglandular syndrome
● Convalescent serum titer of 1:16 or greater is presumptive for Yersinia pestis infection. (lymphadenopathy in the ears with granulomatous conjunctivitis).
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 ● Both Bartonella henselae and Bartonella quintana are capable of causing Bacillary Angiomatosis PLESIOMONAS SHIGELLOIDES
which is characterized by an enlarging, red (cranberry-like) papule often with surrounding scale and
erythema. ● Common cause of gastritis in Japan

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● The clinical appearance of Bacillary Angiomatosis is similar to that of Kaposi’s sarcoma (cancer of the
nerves) in AIDS patients.

M
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GARDNERELLA VAGINALIS

● Gardnerella vaginalis yields clue cells which are vaginal epithelial cells covered with many
gram-variable bacilli.

R
● No inflammatory cells are present in its vaginosis but with lots of anaerobic bacteria such as
Mobiluncus spp.

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● Causative agent of bacterial vaginosis.
● Its vaginal discharge often has a distinct fishy odor or fishy amine odor (especially through KOH/Whiff
Test).

AS
● The pH of vaginal secretions of women infected with the bacteria is over 4.5 when infected with
Gardnerella vaginalis.
● Culture media used may be HBT (Human Blood Bilayer Tween) or Columbia Agar.
● The drug of choice for the bacteria is metronidazole which suggests its association with anaerobes.

N
T
STREPTOBACILLUS MONILIFORMIS

N
Normal flora of the throat of rats and humans acquire the infection through rat bite.
● The disease it causes is known as Rat-Bite Fever and is characterized by septic fever, blotchy and

KE
petechial rashes and very painful polyarthritis. (Sodoku caused by Spirillum minor is similar to Rat-bite
fever but of different clinical appearance only)
● It is also capable of causing infection after ingestion of milk and causes Haverhill fever if infection is in
this manner.
● Penicillin is the drug of choice.
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TROPHERYMA WHIPPLEI

● Causes Whipple’s disease which is characterized by fever, abdominal pain, diarrhea, weight loss and
migratory polyarthralgia.
IC

● Characteristic vacuoles within the macrophage that stain with Periodic Acid Schiff (PAS) are
pathognomonic of the disease.
C