CLINICAL BACTERIOLOGY

CLASSIFICATION OF BACTERIA
AEROBES ANAEROBES
COCCI COCCI
☺ Gram Positive ☺ Gram Positive
Staphylococcus: clusters Anaerobic Streptococci
Streptococcus: chains/pairs Coprococcus
Peptococcus
☺ Gram Negative Peptostreptococcus
Neisseria: pairs Ruminococcus

BACILLI ☺ Gram Negative

☺ Gram Positive Spore Former Acidaminococcus
Bacillus Megasphaera
Veillonella
☺ Gram Negative Non-Spore Formers
Corynebacterium BACILLI
Listeria ☺ Gram Positive Spore Former
Erysipelothrix Clostridium
Lactobacillus
Aerobic Actinomyces ☺ Gram Positive Non-Spore Formers
Kurthia Anaerobic Actinomycetes
Rothia Bifidobacterium
Eubacterium
☺ Gram Negative Glucose Fermenters Anaerobic Lactobacillus
Citrobacter Propionibacterium
Edwardsiella
Escherichia ☺ Gram Negative
Enterobacter Bacteriodes
Hafnia Fusobacterium
Klebsiella Porphorymonas
Pantoea Prevotella
Proteus
Providencia
Salmonella
Serratia
Shigella
Yersinia

☺ Gram Negative Non-Fermenters

Acinetobacter
Alcaligenes
Eikenella
Flavobacterium
Kingella
Moraxella
Oligella
Pseudomonas

☺ Gram Negative Miscellaneous

Aeromonas
Bordetella
Brucella
Campylobacter
Cardiobacterium
Chromobacterium
Francisella
Haemophilus
Helicobacter
Legionella
Pasteurella
Pleismonas
Streptobacillus
Vibrio

☺ Gram Variable
Gardnerella

☺ Acid Fast Bacilli

Mycobacterium

☺ Partially Acid Fast Bacilli

Nocardia

SPIROCHETES
Borrelia
Treponema
Leptospira
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1. Bacteria -Are larger and more complex than viruses,
smaller than fungi  CLASS III BSC
-Unicellular organisms (singled-cell) -Provide the highest level of safety
-Are true living organisms that belong to Kingdom -All air entering and leaving the cabinet is sterilized with
Prokaryotes HEPA filter
-can REPRODUCE by an asexual process (BINARY FISSION) -System is entirely close, and all infectious material are
-MOST bacteria are visible under the light microscopy handled with rubber gloves that are sealed to the cabinet
-MOST bacteria possess both DNA and RNA -Consists of 2 HEPA filters
-MOST PATHOGENIC BACTERIA are capable of independent
growth  CLASS IV BSC
-Level 3 practices plus entrance through a separate room
2. ROBERT KOCH (1843-1910) where separate clothing is changed and replaced with
-a German physician; known as the “Father of Bacteriologic laboratory clothing
Techniques” -Primarily used in research facilities
-he formulated the “Germ Theory”, also known as cause &
effect phenomenon 11. POST-EXPOSURE CONTROL
-1st proof that bacteria actually cause a disease for every  All laboratory accidents and potential exposures
disease, a living organism is responsible must be reported to the SUPERVISOR and SAFETY
-discovered rod-shaped bacteria: Mycobacterium OFFICER
tuberculosis  Immediate medical care must be given
 PROPHYLAXIS
3. LOUIS PASTEUR- “Father of Medical Microbiology” 1. Hepatitis B virus immunoglobulin (HBIg)
2. Hepatitis B virus booster immunization
4. PILI 3. Follow-up treatment should be assessed such as drawing
-hair-like extensions of the cell of sera for HIV testing (6 weeks-3 months-6 months
-synonyms: fimbrae interval)
-Adherence factor
Types of pili: 12. BLOOD CULTURE
1. Ordinary pili- adherence of the bacteria to the host cell  Antiseptic: alcohol – iodine – alcohol
2. Sex pili- bacterial conjugation  Anticoagulant: 0.025%-0.030% SPS
o Neutralizes bactericidal effect of human
5. CHANGES IN TEMPERATURE serum
»MESOPHILIC BACTERIA- grows best at 200C-400C o Prevents Phagocytosis
»THERMOPHILIC BACTERIA-grows best at 500C-600C
»PSYCHROPHILIC BACTERIA-grows best at 00C-100C 13. THROAT AND NASOPHARYNGEAL CULTURES
»Campylobacter spp.-grows best at 420C  Most abundant normal flora- ALPHA-HEMOLYTIC
STREP (S. pneumoniae)
6. MOIST HEAT (Bacillus stearothermophilus)  Most common pathogen- GRP A STREP (S.
a. boiling/flowing steam-kills pathogen within 10 minutes pyogenes)
b. autoclaving-15 psi pressure at 1210C for 15 minutes
14. Nasopharyngeal swab
7. DRY HEAT (Bacillus subtilis) o H. influenzae
a. direct flaming-burning contaminants to ashes o N. meningitidis
b. incinerations-burning to ashes o B. pertussis
c. hot-air sterilization-oxidation (1700C for about 2 hours)
15. SPUTUM CULTURES
8. DISINFECTION- destruction of vegetative pathogens  Deep cough and examine immediately
(1:10 bleach/sodium hypochlorite)  Examine wet mount before culturing
 BARTLETT’S CLASSIFICATION
9. Nosocomial infection/Hospital acquired infection  <10 Epithelial cells/LPF
-An infection that is NOT present before the patient entered  >PMNs/LPF
the hospital or even before an antibiotic was given, the
infection was acquired in the hospital 16. URINE CULTURES
- Most often associated nosocomial pathogens: E. coli, S.  Midstream clean-catch urine: least invasive
aureus, Enterococcus, P. aeruginosa  Suprapubic urine: most ideal
 Preservative: boric acid
10. BIOLOGICAL SAFETY CABINETS (BSC)  Colony count: 105 BACTERIA/mL or 100,000
-Is a device that encloses a workspace in such a way as to colonies/mL (UTI)
protect workers from an aerosol exposure to infectious
disease agents 17. CSF
-HEPA filter- removes particle larger than 0.3 um in diameter  Examine immediately or hold in incubator for no
longer than 1 hour
 CLASS I BSC  Centrifuge, use sediment for:
-Open-fronted, negative pressure, ventilated cabinets o Smears, Gram stain, India ink
-Unsterilized room air enters and circulates within the o Culture- H. influenzae, N. meningitidis, S.
cabinet pneumoniae
-Exhaust air from the cabinet is filtered by HEPA filter
18. STD include infections caused by:
 CLASS II BSC  T. pallidum
-Sterilize both the air entering and circulating the cabinet  N. gonorrhoeae
and exhaust air  C. trachomatis
-Used by most hospital microbiology laboratories  G. vaginalis
-Also known as LAMINAR FLOW BSCs  T. vaginalis
-Class IIa-FIXED OPENING  C. albicans
-Class IIb-SASH OPENING  HSV
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19. CALCIUM AGITATE should be avoided for viral culture
 COTTON-TIPPED SWAB have excessive FATTY
ACIDS which may be toxic to certain bacteria like
NEISSERIA GONORRHOEAE
 WOODEN SHAFT SWABS are toxic to CHLAMYDIA
TRACHOMATIS
20. Quellung: “capsular swelling” reaction -identified with
different capsular types of Streptococcus pneumoniae and
Haemophilus influenzae
21. Plating Media
 Bile esculin agar (BEA)- Differential isolation and
presumptive identification of Group D Streptococci
and Enterococci
 Buffered charcoal-yeast extract (BCYE) agar-
Enrichment for Legionella spp.
 Cefoperazone, vancomycin, amphotericin (CVA)
medium- Selective medium for isolation of
Campylobacter spp.
 Cefsulodin-irgasan-novobiocin (CIN) agar- Selective
for Yersinia spp.; may be useful for isolation of
Aeromonas spp.
 Chocolate agar- Cultivation of Haemophilus spp. and
pathogenic Neisseria spp.
 Cystine-tellurite blood agar- Isolation of
Corynebacterium diphtheria
 Hektoen enteric (HE) agar- Differential, selective
medium for isolation and differentiation of
Salmonella and Shigella spp. from other gram-
negative enteric bacilli
 Mac Conkey sorbitol agar- For the selection and
differentiation of E. coli O157:H7 in stool specimens
 Phenylethyl alcohol (PEA) agar- Inhibits growth of
gram-negative organisms
 Schaedler agar- Selective for Campylobacter and
Helicobacter spp.
 Selenite broth- Enrichment of isolation of Salmonella
spp.
 Skirrow agar- Selective for Campylobacter spp.
 Thayer-Martin agar- Selective for N. gonorrhoeae
and N. meningitides
 Thiosulfate citrate-bile salt sucrose (TCBS) agar-
Selective and differential for Vibrio spp.
 Xylose lysine desoxycholate (XLD) agar- Isolation
and differentiation of Salmonella and Shigella spp.
from other gram-negative enteric bacilli
22. Indicators
 CIN: neutral red and crystal violet
 EMB: Eosin & methylene blue
 HEA: Acid fuchsin & bromthymol blue
 MAC: Neutral red
 SSA: Neutral red
 TCBS: Bromthymol blue
 XLD: Phenol red
23. Acetamide Test- is used to isolate and grow P.
aeuroginosa (+: blue color)
24. CAP can be grown by Hemophilus, Streptococcus,
Neisseria
25. Staphylococcus aureus- predominant pathogen in
joint infection among adults
 produces golden yellow colonies due to the pigment
(lipochrome)
Staphylococcus epidermidis- Porcelain white in color
Staphylococcus saprophyticus- Common cause of UTI in
young women
Staphylococcus cereus- rarely found and grown in agar;
produces lemon-yellow colonies
26. Streptococcus pneumoniae (pneumococcus)-
Lancet shaped, encapsulated, non-motile, non-spore forming
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Streptococcus pyogenes- Scarlet fever-“strawberry tongue”
- Tonsillitis (“strep throat”)
- May be associated with: ACUTE RHEUMATIC FEVER (ARF)
& ACUTE GLOMERULAR NEPHRITIS (AGN)
Viridans Streptococci
 Most common cause of dental caries (S. mutans)
 Most common cause of subacute infectious
endocarditis (“endocarditis lenta”: caused by ALL
species of S. Viridans)
 Cerebral abscesses and hepatic abscesses (S.
intermedius)
 Septicemia (caused by ALL species of S. Viridans)
Streptococcus agalactiae- associated with neonatal
infections (pneumonia, meningitis, and bacteremia)
27. Corynebacterium diphtheriae- Kleb-Leoffler’s
bacillus; Clubbed-shaped bacillus Greek work: “KORY-
CLUB” shape (irregular swelling at one end); Banded or
beaded appearance due to their metachromatic granules
(BABE-ERNST GRANULES), which are stained red when
methylene blue is applied
Media used for isolation
-Pai’s coagulated egg medium
-Leoffler’s coagulated serum medium
-Potassium Tellurite medium
-Colonies are brown to black with a brown black halo
because the tellurite is reduced intracellularly (Staph and
Strep can also produce black colonies)
Types
1. Tinsdale- contain potassium tellurite
2. Cystine Tellurite medium
TOXIGENECITY TEST
1. In vivo: Animal inoculation Guinea pig/White rabbit
2. In vitro: Elek’s test/Gel diffusion test/ Forbischer’s test
SCHICK’ TEST
-Susceptibility Test for Corynebacterium diphtheriae
-injection of:
o Test arm: 0.1 mL toxin
o Control arm: toxin and anti-toxin (0.1mL)
o Read results: 24-48 hours and after 6 days
MALONEY TEST
-Test to determine if the patient is allergic to diphtheria
toxoid
-0.1 mL of 1:10 dilution of diphtheria toxoid is introduced
28. Corynebacterium jeikeium (formerly group JK)
-Associated with endocarditis, pneumonia and peritonitis
-Can cause disease in immunocompromised patients
-Clearly associated with infections of implanted prosthetic
materials (e.g. heart valves, CSF, and joints)
C. pseudodiphthericum (C. hoffmani)- CN: Hoffman’s
bacillus; Normal inhabitat of the pharynx and recovered from
blood of patients with SBE (sub-acute bacterial endocarditis)
29. Genus Bacillus
 BAP:
-OPAQUE, LARGE, RAISED with comma-shaped
outgrowths (MEDUSA HEAD colonies)
-Ground Glass appearance
-consistency of “beaten egg white”
 PLET medium (polymyxin lysozyme EDTA thallous
acetate)
 PEA (phenylethyl alcohol agar medium)- growth
almost inhibited
 CH (chloral hydrate)- growth completely inhibited
 Gelatin medium- slow liquefaction; “INVERTED PINE
TREE” growth
rfgeronimo2018
B. anthracis: is the most virulent pathogen; agent of
anthrax
-Cutaneous anthrax; Woolsorter’s disease or pulmonary
anthrax; Gastrointestinal anthrax
 Virulence factors: capsule (poly-D-glutamic acid);
polysaccharide; anthrax toxin (primary VF)
 ASCOLI test: “precipitin test”, is used to the
diagnosis of anthrax in dead animals and to
determine whether hide for industrial use has been
removed from infected animals
 Culture: “bamboo pole arrangement”
 String of pearls (MHA with penicillin)- susceptibility
test for penicillin; it will still grow but will assume a
spherical shape due to swelling of cells and produce
morphology similar with “string of pearl”
B. cereus: associated with food poisoning isolated from
several foods: rice, other cereals, vegetables and milk
-Motile; Produces a wide zone of beta-hemolysis; Produces
acid from dextrose, maltose, and salicin; Produces
phospholipase and beta-lactamase
 Pathogenecity: food poisoning eating
contaminated fried rice
30. CHO fermentation:
 (-) sucrose except C. perfringens
 (-) lactose except C. perfringens
and C. septicum
 (+) glucose except C. tetani and C.
histolyticum
31. C. perfringens/ C. welchii (CN: Welch’s bacillus)-
Cause of myonecrosis (gas gangrene) and food poisoning;
spore: center or eccentric “BOX CAR” appearance
-Lecithinase positive
-Reverse CAMP test positive
-Nagler’s reaction/Lecithovitelline reaction (presumptive
test)- uses egg yolk medium (e.g. Lombard Dowell)
containing 20% bile and egg yolk
ACTION ON LITMUS MILK/STORMY CLOT TEST
-Clot with gas
-C. perfringens
32. C. botulinum
 Agent of food and wound botulism, as well as infant
botulism
 Common Name: “canned good bacillus”
 Botulism results from the liberation of botulism
toxin, a powerful neurotoxin
 Gram positive bacilli; non-encapsulated; spore; oval
sub-terminal spores
 “SNOW SHOE appearance”
 Classical/Food-Borne: FLACCID PARALYSIS- no
contraction (Blocks the release of acetyl choline at
the synapses)
33. C. tetani
 Etiologic agent of tetanus, which results from entry
of the organism or spores into a puncture wound
 CN: drumstick bacillus, tackhead, lollipop
 Spore: round, terminal swollen sporangium
 Gram-positive bacilli; Motile and encapsulated
 Produces tetanospasmin (neurotoxin), associated
with spastic contractions/lock jaw
 Biochemical Tests:
o BAP: beta-hemolytic
o Colonies: round, small with fimbriated
edges
o CHO fermentation: negative
o Gelatinase and Indole: positive
o Lecithinase and Lipase: negative
 Reservoir of spores: SOIL Muscular spasms
(SPASTIC paralysis); Neurotoxin blocks the release
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of inhibitory mediators GLYCINE and GAMMA-
AMINOBUTYRIC ACID
34. C. difficile
 Important cause of antibiotic – associated
pseudomembranous colitis
 TOXIN A (enterotoxin); TOXIN B (cytotoxin)
 Biochemical Tests:
o Ferments glucose and fructose
o Lecithinase, Lipase, and Indole negative
o Gelatinase positive
 Spores: bulge terminal end
 Cultured on CCFA (Cycloserine Cefoxitin Fructose
Agar) -“horse manure-like odor”
 Antibiotics: Clindamycin and Ampicillin
 Pseudomembrane: yellow plaques on the colonic
mucosa
35. Listeria monocytogenes (Gram-positive small
coccobacilli; non-spore forming, non-motile, non-
encapsulated)
 Found in the environment in soil, water, sewage,
and decaying vegetation and in feces of humans,
swine and poultry
 Major source of infection is contaminated food
(cabbage, fruit, dairy products)
 Only pathogenic Listeria spp.
General Characteristics and Morphology
 Chinese letter arrangement
 MOTILE: 25OC (tumbling motility or head
over heels motility)
 NON-MOTILE at 37OC
 Perinatal Human Listeriosis (granulomatosis
infanseptica)
 Hanging drop: tumbling/head over wheels
 Semisolid medium: umbrella growth
 Cultured on Mac Bride medium (Selective
medium)
o Colonies are smooth, translucent,
slightly raised with blue-green
color
o Semi-solid: “umbrella-like growth”
 Virulence test: ocular test
 ANTON TEST
o Specimen: CSF or blood
o Instillation of 24 hours broth culture into
the conjunctival sac of rabbit or guinea pigs
o Result: (+) purulent conjunctivitis within
24-36 hours
36. Erysipelothrix rhusiopathiae (E. insidiosa)
 Cutaneous inflammation of hand or fingers (seal
finger or whale finger)
 Veterinary infection and occupational hazard for
those handling meat, poultry and fish
 Gelatin stab: “bottle brush”/ “pipe
cleaner appearance”
37. Lactobacillus acidophilus
 Normal flora of the mouth, gastrointestinal tract and
vaginal canal: Doderlain’s bacilli
 Non-pathogenic and has little clinical significance
 Cultured on Rogosa’s selective tomato
juice agar
38. Mycobacterium tuberculosis
 Koch’s bacillus
o 0.2- 0.6 micron in diameter and 1-4 micra
in length
o Remain in putrifying sputum for weeks and
in dried sputum for 6-8 months
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 o Droplets of dried sputum in the air may be 42. Genus Neisseria (gram negative cocci)
infectious for 8-10 days 1. N. gonorrheae- causes gonorrhea
 Cells form granulomatous lesions called tubercles, 2. N. meningitides- causes meningitis and
which can be seen on chest X-rays. The lesions meningococcemia
calcify, at which point they are called “GHON  Gram-negative diplococci resembling coffee beans
COMPLEXES’’ or kidney beans except N. elongata (rod-shaped)
 Skin test for TB: PPD (Purified Protein Derivative)-  Catalase positive except N. elongata
heat killed ammonium sulfate – precipitated
organism is injected intradermally (+ redness after Selective Media:
48 hours)  Thayer-Martin Medium- composed of CAM added
with antibiotics: Vancomycin (inhibits gram +);
Media Colistin (inhibits gram -); Nystatin (inhibits fungi)
1. Lowenstein-Jensen  Modified Thayer-Martin Medium-uses hemoglobin
2. Petragnani solution + supplements commercially available:
3. American Thoracic Society o Vancomycin; Colistin; Nystatin; Trimethoprim
4. Middlebrook 7H10 and 7H11 c lactate: inhibits spreading of Proteus (g – bacilli
hypermotile); Isovitalex (supplements)
Stains  New York City agar (VCA): Vancomycin; Colistin;
1. Ziehl-Neelsen Amphotericin B
2. Kinyoun  Martin Lewis Agar (VCT): Vancomycin; Colistin;
3. Fite-Faraco’s Trimethoprim lactate
4. Auramine-rhodamine stain (Truant’s)
-Fluorescent organisms on black background 43. N. gonorrhoeae
 A leading cause of STD. Genital infections include
CDC Method to Report AFB purulent urethritis in males and cervicitis in females
Number of AFB Seen Report  Other localized infections include pharyngitis,
0……………………………….. - (negative) anorectal infections and conjunctivitis (e.g.
1-2/300 fields……………. +/-, Repeated on second slide ophthalmia neonatorium of newborns acquired
1-9/100 fields…………… 1+ during birth from the infected mother)
1-9/10 fields……………... 2+  Virulence factors:
1-9/field…………………... 3+ *pili: adherence factor; the primary virulence factor
>9/field……………………. 4+ *protein M: present in the outer membrane of the cell,
adherence factor
National Tuberculosis Association Method *lipopolysaccharides: site of endotoxins
Number of Report *beta-lactamase: penicillin resistance
Organism Seen *IgA protease: degrades immunoglobulin A
1 to 2 per slide Report number
and request 44. N. meningitides
another specimen -Common Name: Meningococcus
3 to 9 per slide Rare (1+) -Life-threatening, acute, purulent meningitis
10 or more per Few (2+) -MOT: respiratory droplets
slide  -JEMBEC: James E. Martin Biological Environmental
1 or more per OIF Numerous (3+) Chamber- transport media
NATIONAL STANDARD REPORTING SCALE - Waterhouse-Friedrichsen syndrome (massive hemorrhage
0 No AFB seen in 300 visual fields into the adrenal gland)
+n 1-9 AFB / 100 visual fields
1+ 10-99 AFB / 100 visual fields 44. VITEK-Micro Automation
2+ 1-10 AFB / OIF in at least 50 visual -used for sensitivity
fields
3+ More than 10 AFB / OIF in at least 45. Escherichia (E.coli)
20 visual fields  UTI – 90%; Sepsis; Meningitis – (also Group B
Strep) causes meningitis in infants; Diarrheal
39. Mycobacterium leprae diseases
 Hansen’s disease or leprosy  IMVIC: ++--
 Acid fast rod in nasal mucosa of patients with nodular  E.coli 0157:H7 on SMAC: sorbitol substituted MAC
variety of Hansen’s disease (pink)
 Transmission occurs person to person through inhalation  Hemolytic Uremic Syndrome (HUS) – most severe
or contact with infected skin manifestation of EHEC; thrombosis following
 Armadillo is susceptible to Hansen’s disease and has thrombocytopenia
been used experimentally
***Smears of tissue juice, AF stain for Lepra cells: large 46. Enterobacteriaceae
mononuclear phagocytes  Gram negative rods
 Motile with peritrichous flagella except Klebsiella
40. Actinomyces and Shigella (non-motile)
 Gram positive but neither acid fast nor stained with  Facultative anaerobes
fungus stain, anaerobic  Ferments glucose
 Causes chronic suppurative granulomatous disease  Often with gas production
 Agent of A. israelli  Catalase positive
 Colonies: compact colonies: sulfur granules  Oxidase negative: diff. from vibrio
 Reduce nitrate to nitrite except for Erwinia and
Pantoea agglomerans
41. Nocardia  Some Salmonellae have capsular (K) antigens,
 Gram positive, PARTIALLY ACID FAST, aerobic referred to as Vi
 N. asteroids is the most clinically relevant species

5 | Page MICROBIOLOGY FINAL COACHING NOTES rfgeronimo2018

47. Klebsiella
-Second most common cause of lobar pneumonia;
pulmonary abscesses; cystitis; second most common cause
of septicaemia
 K. pneumoniae- Friedlander’s bacillus,
encapsulated and appears as mucoid colonies
that tend to string
 K. ozaenae – Purulent sinus infection
 K. rhinoscleromatis – Granuloma of the nose
and oropharynx
48. Enterobacter- gram negative rods/bacilli;
encapsulated; motile
-skin infections (folliculitis, cellulitis and impetigo); skin
abscesses; bronchopneumonia and pulmonary abscesses;
cystitis and renal abscesses (primarily if urinary catheters)
 Opportunistic infections: UTI, RT and
wound infections
 Most predominant isolate is E. cloacae
 Produces yellow pigmentation that
intensifies at 25 oC: Enterobacter sakazakii
49. Serratia
 S. marcescens and S. rubidea produce a red pigment
 S. odorifera produces a rancid potato-like odor
 Common opportunistic pathogen in hospitalized patients
50. Salmonella
 Sources of infection: water, milk and dairy products,
shellfish (from contaminated water), dried or frozen
eggs, meat and meat products and household pets
 Cause enteritis, systemic infection and enteric fever
(typhoid fever)
 Cause enteric fever:
o S. paratyphi A (serogroup A)
o S. paratyphi B (serogroup B)
o S. cholerasuis (serogroup C)- Bacteremia
o S. typhi (serogroup D)
o S. typhi (most important cause)
 Enterocolitis/gastroenteritis – most common
manifestation of Salmonella infection – S. typhimurium
(most common)
51. Pseudomonas aeruginosa
-Pigments: PYOCYANIN (water-soluble blue pigment);
FLUORESCEIN/PYOVERDIN (yellow fluorescing pigment that
results in the typical blue-green color of P. aeruginosa)
- Colonies have a feathered, ground (frosted) glass
appearance
-Corn tortilla odor (some prefer to describe it as a grape-like
odor)
-Grows between 4◦C and 42◦C
52. Pseudomonads are found in moist environments
-Unusual habitats: cosmetics, swimming pools, hot tubs,
inner soles of sneakers
53. P. fluorescens and P. putida are in the fluorescent
Pseudomonas group, but are differentiated from P.
aeruginosa as neither produces pyocyanin or grows at 42◦C
54. P. fluorescens
-Is found in the soil and water as an environmental
contaminant
-Associated with food spoilage and plant infections
-Rare cases seen in UTI and wound infections
P. putida
-Associated with isolated cases of septicaemia and infections
of the arms and legs
-Isolated from hospital environmental sources (sinks)
6 | Page MICROBIOLOGY FINAL COACHING NOTES
55. P. mallei
☺ It causes “Glanders” (infection derived from horses,
goats, sheep, and monkey)
☺ MOA: direct contact, trauma, inhalation
☺ ONLY NON-MOTILE PSEUDOMONAD & RESISTANT
TO POLYMYXIN B
☺ Colonies on BAP: smooth, creamy-white
☺ Weakly Oxidase positive; Fails to grow at 42OC
56. P. pseudomallei
☺ Agent of “Melioidosis” (a glanders-like disease found
in humans and animals in Southeast Asia and
Australia)
☺ Found in soil, water, fruit, vegetables; Aerosolized
organism
☺ Commonly infections of American soldiers during
the Vietnam conflict
☺ Associated by an acute and severe pneumonia that
can lead to septicaemia
☺ Colonies on BAP: cream to tan and wrinkled
☺ Oxidase and ADH: positive; Motile: multi-trichous
flagella
57. P. cepacia
☺ Found in water sources and in intravenous fluids,
detergents, and disinfectants
☺ The cause of onion bulb rot in plants and foot rot in
humans
☺ Opportunistic and nosocomial infection
☺ Clinical manifestations: pneumonia, UTIs,
septicaemia, endocarditis (contaminated with heart
valves)
☺ Frequently seen in cystic fibrosis
☺ Resistant to aminoglycosides
☺ It produces yellow, serrated colonies that are
weakly oxidase positive
☺ LDC positive; ADH negative
58. Stenotrophomonas (Xanthomonas) maltophilia
-Is found in the environment and causes a wide
range of nosocomial infections
59. Acinetobacter spp.
* A. baumannii
-BAP: produces large, gummy, translucent, gray to white,
convex, entire colonies
-MAC: bluish or peach to pink tint; ammonia-like odor
-EMB: cornflower blue color
-Resistant to penicillin
-Negative lysine decarboxylase; ferments glucose rapidly,
rapidly assimilated with lactose
* A. lwoffii
-Second most common Acinetobacter isolate
-Non-motile
-Negative lysine decarboxylase & lactose; Asaccharolytic
bacterium
60. Chryseobacterium (Flavobacterium)
meningosepticum
-Is a cause of neonatal meningitis or septicemia,
especially in premature infants
-Can cause pneumonia, endocarditis, bacteremia,
and meningitis in adults
-Isolated with water sources: ice machines, water
fountains, sinks, incubator, water bath
-OF glucose and mannitol tubes: delayed positive
reactions
-Indole, Esculin hydrolysis positive
-Pinpoint & glistening pale yellow pigments
-Resistant to penicillin and aminoglycosides
61. Eikenella corrodens
-Is found as normal mouth and nasopharyngeal flora
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-The name is derived from the corroding or pitting of the
agar by the colonies
-The organism is a facultative aerobe and requires hemin for
growth (CAP)
-Non-saccharolytic, oxidase positive, catalase negative, non-
motile
 Infective agent of chancroid (soft chancre venereal
disease)
 Ragged painful ulcer on the genitalia
 Found in Asia, North America and Europe
 Direct examination of the genital ulcer: resembles to
“schools of fish”

62. Moraxella species H. hemolyticus

-Are normal flora of mucous membranes  Occasional normal flora of the upper respiratory
-Conjunctivitis is caused by M. lacunata cavity
-M. catarrhalis is normal oral flora of the respiratory tract  Mistaken for Group A Streptococcus on BAP
and may cause otitis media, sinusitis, and respiratory
infections H. parahemolyticus
-Tiny gram negative diplococci/diplobacilli  Normal flora of the upper respiratory tract
-Free living in soil and water  Rarely infectious
-Very susceptible to low levels to penicillin
-Confused with Neisseria spp. (M: will grow in BAP; N: will H. aphrophilus and H. paraphrophilus
not grow on BAP)  Normal flora of the oral cavity
 Found in dental plaque
63. Alcaligenes and Achromobacter are divided into  Very rarely associated with endocarditis
asaccharolytic and sacchrolytic species
69. Pasteurella multocida
-These opportunists are found in water and are resistant to
disinfectants  Most common isolated specie
-The asaccharolytic Alcaligenes faecalis is most often seen in  Agent of “shipping fever” in cattle
clinical specimens and has been isolated from urine, sputum,  “Pasteurella infection”/”Pasteurellosis”
wound, and blood o Characterized by pain, redness, swelling,
-OPPORTUNISTIC pathogen cellulitis, purulent discharge
-Grows flat, dull colonies with an irregular edge on BAP  Culture characteristics
-The strain (A. odorans): fruity odor of apples or pears o Growth on 5% blood or chocolate shows
-Motile; Oxidase, Nitrite to nitrogen gas, Growth in 6.5% small, smooth, grayish, convex colonies
NaCl: Positive o Non-hemolytic
o “Musty” or “Earthy” odor
64. Vibrio cholerae o No growth on MAC agar
-Gram negative, comma–shaped bacteria; Do not form  Microscopic examination
spores o Very small gram-negative rods
-Actively motile, exhibiting a darting motility and they o Bipolar staining with Giemsa or Methylene
possess a polar flagellum blue
-Grow cell on thiosulfate citrate bile salt sucrose agar (TCBS) o “Safety-pin” appearance
on which it produces a yellow colonies  Identification
-Grow at a very high pH (8.5 – 9.5) and are rapidly killed by o Oxidase positive
acid o Indole positive
-Rice watery stool o Non-motile
o Catalase positive
65. Fastidious group of gram-negative bacilli o Glucose fermenter
HACEK (Haemophilus, Actinobacillus, Cardiobacteria, o Nitrate positive
Eikenella & Kingella) o Urease negative
o Starch hydrolysis negative
66. Hemophilus spp. o Acid not produced from maltose and lactose
-Haemophilus = “blood loving” o Acid but no gas produced from glucose,
-Require either heme (X factor) or NAD (V factor) sucrose, mannose
-Haemophilus is facultative and can grow anaerobically
-Organism is sensitive to drying and extremes in 70. Brucella spp.
temperature
-Distinctive “mousy” or “bleach-like” odor  Causes infection in cattle (zoonosis)
 Acquired through aerosol, percutaneous and oral
67. Hemophilus influenzae routes of exposure
-Most frequently clinically isolated Hemophilus  Brucellosis
-Formerly known as the “Pfeiffer’s bacillus”  Primarily seen with animal handlers and those who
-Six serotypes: a,b,c,d,e,f handle animal products
-Serotype b: encountered most frequently in infections  Febrile agglutinins: “Gold standard” for Brucella
-Serotyping is based on the characteristics of the capsule identification
-Eight biotypes: I, II, III, IV, V, VI, VII, VIII  Causative agent for “Malta” or “Undulant fever” or
-Biotype I: meningitis and septicaemia; Biotypes II & III: “Brucellosis” (Chronic and Recurring fever)
found in eye and respiratory tract; Biotypes IV & V: ear and o Weight loss and anorexia
respiratory tract o Severe form: Granulomatous infections
(RES & Bone)
68. Miscellaneous Hemophilus Species
H. aegypticus 71. FRANCISELLA TULARENSIS
 Formerly known as “Koch Weeks Bacillus”  Small, non-motile, pleomorphic gram negative
 Closely resembles H. influenza biotype III bacillus
 Causes “pink eye” conjunctivitis  Highly infectious Type 3 biohazard – can be
transmitted through unbroken skin, bite from an
H. ducreyi insect, direct contact with infected animals or
 Tiny gram negative bacilli (intracellular inhalation of aerosols
polymorphonuclear neutrophils)  Easily acquired laboratory infection

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  Category A Biological agent-it can be spread from
person to person or disseminated, high mortality
rates
 Infection in rabbits, sheep, squirrels and ticks
 Zoonotic infection in humans
o “Tularemia” (agent disease of
rodents/rabbits)
 Blood cysteine glucose agar (BCGA) with thiamine:
special medium
 Modified Charcoal yeast agar and CAP with
IsoVitaleX: alternative medium (requires 2-4 days to
grow; strict aerobe)
 Colony Morphology
o BAP = No growth
o MAC = No growth
o CAP = Small, smooth, gray gram- negative
coccobacillus at 2-5 days
o Requires special media
o Oxidase: negative
o Catalase: negative- weak positive
o Ferments glucose
o X and V negative
 NOTE: Usually identified by DFA or
direct agglutination tests due to
risk of lab acquired infection
72. Legionella
 General characteristics
 Habitat
o Aquatic sources
o Cooling towers, condensers
 Ubiquitous gram-negative rods
 Acquired by humans primarily through inhalation of
aerosols
 Legionnaire’s disease
o Disease with pneumonia and
extrapulmonary involvement
o Malaise, rapid onset of dry cough and fever
o Illness is fatal in 15-30% of cases not
treated
 Pontiac fever
o Influenza-like
o Fever, headache, malaise
o Not fatal- short lived (2-5 days)
73. Legionella spp.
Legionella micdadei
 Pittsburgh pneumonia agent
 Isolated from respiratory care equipment and
cooling towers
 Associated with severe pulmonary infections in
patients with leukemia, following renal transplant
Legionella bozemanii
 “Wiga” agent
 Isolated agent of pneumonia
74. Vibrio cholera (“Komma bacillus”)
Cultural characteristics
 Tellurite Taurocholate Gelatin Agar (TTGA) &
Thiosulfate Citrate Salt Sucrose Agar (TCBS)
o pH: 8.4
o Smooth, yellow colonies (due to sucrose
fermentation) with opaque centers, thin
edge and transparent peripheries
 TSI: A/A
 LIA: K/K
 Enrichment medium: Alkaline Peptone Water (APW)
 Vibrio cholera O1: cause of cholera
75. Biotypes (Biovars) & Pathogenicity
 El Tor
o causative agent of cholera
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o the most severe form of
gastroenteritis from infected
seafood
o localized in the intestinal tract.
The stool is characterized by the
presence of mucus, epithelial cells
and large number of vibrios
 Classical
o Responsible for pandemics in the
past
76. Serological types of Vibrio cholera based on the
development of agglutinating antibodies:
1. Original J or Inaba type – causing diarrhea in the
Philippines
2. Middle Intermediate or Hikojima type – found in Japan
3. Variant F or Ogawa type – found in India
77. Vibrio parahaemolyticus
-halophilic organisms (high salt concentration) causing
gastroenteritis and food poisoning associated with the
consumption of contaminated seafood
-Enteritis subside spontaneously in 1 – 4 days with no
treatment other than restoration of water and electrolyte
-Most common cause of diarrhea during summer in Japan
because of eating SUSHI (rice roll topped with raw fish)
-There is no defined enterotoxin has been discovered but
hemolysis on Wagatsuma agar has been used to identify
pathogenic strains (Kanagawa phenomenon)
78. Campylobacter jejuni
-gram negative rods with comma, “S” or “gull wing” shapes -
motile with single polar flagellum
-grow well in an atmosphere containing 10% CO 2
-Selective medium: Skirrow’s medium incorporated with
vancomycin, polymyxin B and trimethoprim (colonies tend to
be colorless or gray)
-exhibit darting or cork screw motility under phase contrast
or darkfield microscopy
79. Enteric Campylobacter: grows best at 42-43OC;
capnophilic environment: 85% nitrogen, 5% oxygen, 10%
CO2
80. Helicobacter pylori
 It is formerly identified as a Campylobacter pylori
 Natural habitat: Human stomach
 It is involved in chronic gastritis and
peptic/duodenal ulcers
 It grows best at 35-37oC
 Are rod–like, bizarre, U–shaped gram negative
bacterium
 Microaerophilic with a tuft of polar flagella with cork
screw motility
 Positive: Urease, Oxidase, Catalase
 Histological staining and culture biopsies obtained
from the stomach and duodenum are recommended
for identification
81. Biochemical reactions are similar to
Pseudomonas except that Aeromonas are gelatinase
(+) and mannitol fermenters while Pseudomonas are
gelatinase (–) and mannitol fermenters
82. Aeromonas hydrophilia (“water-loving”) - most
common human isolate (associated with gastrointestinal
disease)
*It produces a heat labile enterotoxin and a heat stable
cytotoxic enterotoxin A
83. Plesiomonas shigelloides
-Formerly known as “Aeromonas shigelloides”
-Imitates Shigella but motile
-Grow on media used for enteric bacteria
-Oxidase (+) and DNAse (+)
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84. Bacteroides fragilis
-Most frequently isolated from clinical infections
-Predominant organism of the normal human intestinal tract
-More resistant to antimicrobial agents
-White to gray, non–hemolytic, translucent, glistening
colonies; pale rods
-Bile is stimulatory, catalase production is positive
85. Fusobacterium nucleatum
-Appears in pairs end to end
-Important pathogen in head, neck and lower respiratory
infections
-Alpha hemolytic colonies with flecked internal structures or
breadcrumb like colonies
-Indole (+) and Levulose (+)
-Bile inhibit its growth
-Major metabolic product: butyric acid
86. Bordetella pertussis
-Aerobic, oxidative obligate organism
-Most important human specie
-B. parapertussis: non-toxigenic strain of B. pertussis
-Motility: non-motile
-Sheep BAP: no growth
-MAC: no growth
-Bordet Gengou agar/ Regan-Lowe medium in increased CO2
at 35-37OC: convex, shiny, silver, “mercury-like” droplets or
“pearls” in 7 days
-Catalase: positive
-Citrate: negative
-Indole: negative
-DPT (diphtheria-pertussis-tetanus) vaccine: 2-4-6 months;
boosters at 12 & 15 months and 4 & 6 years
-STAGES:
-Incubation period: 7-10 days; Flu-like symptoms
(runny nose, infrequent coughing, low-grade fever)
-Catarrhal stage: bacteria multiply, spread to
contagious area (respiratory tract)
-Convalescent phase: lasts for 4-8 weeks
accompanied by coughing; secondary to bacterial infections
-Associated with “Whooping cough” symptoms
87. Family Mycoplasmataceae organisms
 Are small, free-living organisms that lack a cell
wall
*M. pneumoniae
 Is the causative agent of “atypical or walking
pneumonia”
 This organism is not normal flora, and isolation is
always significant
*U. urealyticum and M. hominis
 Colonize the lower genitourinary tract
 Cause opportunistic infections such as non-
gonococcal urethritis in males and post-partum
infections in females
*The organisms can be cultured on special enriched media
*Mycoplasma colonies: very small, requiring a dissecting
microscope for observation
*A characteristic “fried egg” appearance (raised center with
flat edges)
*Colonies of Ureaplasma are much smaller
*Dienes or methylene blue stains can be used to visualize
the colonies on agar media
88. Chlamydia spp.
C. trachomatis
 Is the causative agent of trachoma,
lymphogranuloma venereum, and various other
sexually transmitted diseases
 Trachoma is a leading cause of blindness worldwide
 C. trachomatis: most common sexually transmitted
bacterial pathogen in the United States
C. pneumoniae
 Is an important cause of pneumonia and pharyngitis
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C. psittaci
 Is the cause of psittacosis (“ornithosis” or “parrot
fever”)
o A respiratory tract disease seen in patients
exposed to birds
Laboratory diagnosis
 Shell vial tissue cultures are used for detection of
Chlamydia
o Fluorescein-labeled monoclonal antibodies
can also be used to detect the chlamydial
inclusions in Shell vial cultures
 Cell lines, usually McCoy cells, can be inoculated
with specimens suspected of harboring Chlamydia
o After 72 hours, staining with iodine shows
darkly stained inclusion bodies within the
cells
89. Borrelia
 Microaerophilic; helically coiled bacteria
 Stained well with Giemsa/Wright (Borrelia:
blue)
 Diagnostic tool: PBS
 Media: Modified Kelly’s medium/Barbour-
Stoenner-Kelly medium (BSK-II) 7-14 days at
30-35OC
 Is the cause of :
o Relapsing fever (B. recurrentis)
o Lyme disease (B. burgdorferi)
 Spread by Ixodes ticks
 Ixodes dammini &
Ixodes pacificus: USA
 Ixodes ricinus: Europe
 Relapsing fever is also associated with louse-
borne transmission
 Erythema chronicum migrans (EMC)
o Is characterized by classic skin lesions
and rashes at the site of the tick bite
o Relapsing febrile episodes are caused
by antigenic variation in the spirochete
and are characteristic of infections
caused by B. recurrentis
o Laboratory diagnosis of relapsing fever
is achieved by observation of
spirochetes in blood smears stained
with the Giemsa or Wright stain
 Diagnosis of Lyme’s disease: serologic tests
o Antibody in the patient’s serum may be
detected after the third week of the illness
90. Leptospira interrogans
 Causative agent of Leptospirosis or Weil’s disease
 Animals reservoirs: dogs, rats, rodents
 Transmitted via exposure to the urine of carriers or
urine-contaminated soil or water
 Culture media: Fletcher medium/ Stuart liquid
medium
o A semi-solid tubed medium
o Growth occurs in a ring just beneath the
medium surface
 Diagnosis may be made from microscopy (dark-
field/ phase-contrast/ immunofluorescent
microscopy)
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