Topnotch Microbiology Supertable UPDATED Jan 2016 by DR - Cocoy Calderon PDF

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MEDICAL BACTERIOLOGY
GRAM-POSITIVE COCCI
TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY SUPERTABLE BY PACIFICO ERIC E. CALDERON, M.D. Page 1 of 75
MICRO- RESERVOIR TRANSMISSION METABOLISM VIRULENCE TOXINS CLINICAL TREATMENT AND DIAGNOSIS NOTES
ORGANISM FACTORS SYNDROMES PREVENTION
Staphylococcus Humans (nasal) Hands Catalase-positive Protein A: binds Exofoliatin: Scaled SKIN and SOFT methicillin- Gram-stain: 95% resistance to
aureus IgG, preventing skin syndrome TISSUE sensitive SA (MSSA) reveals gram- penicillins
Food Coagulase- opsonization and INFECTIONS positive cocci in
positive phagocytosis Enterotoxin: food - Penicillinase- cluster 60% MRSA in the
poisoning - bullous resistant Philippines
Facultative Coagulase: Allows Toxic shock impetigo, penicillins Culture:
anaerobe fibrin formation syndrome toxin folliculitis, (nafcillin, oxacillin, Beta-hemolytic
mecA gene
around organism (TSST-1) furuncles, and dicloxacillin) Produces a golden
carbuncles, yellow pigment.
Hemolysins Panton-Valentine
cellulitis, methicillin- leukocidin
hidradenitis resistant SA
Penicillase suppurativa, (MRSA) Polymerase chain
mastitis, surgical reaction (PCR):
Hyaluronidase: site infections mecA gene for
breaks down - contain altered MRSA
connective tissue PBP; DOC is
ACUTE vancomycin
ENDOCARDITIS
vancomycin-
Staphylokinase: - most common resistant SA (VRSA)
lyses formed cause of acute
endocarditis
- DOC is linezolid
Lipase
- native valve
(tricuspid valve) in
IV drug abusers
PNEUMONIA
- nosocomial,
necrotizing,
complicated by
empyema, abscess
or pneumatocele
- post-viral
OSTEOMYELITIS
and SEPTIC
ARTHRITIS
GASTRO-
ENTERITIS
- acute onset (4
hrs) of vomiting
and diarrhea due
to ingestion of
preformed heat-
stable enterotoxin
- source: salad
made with
mayonnaise
(potato or tuna
salad)
SCALDED SKIN
SYNDROME (Ritter
Disease)
- exfoliatin cleaves
desmoglein in
desmosomes
TOXIC SHOCK
SYNDROME
- fever,
hypotension,
strawberry
tongue,
desquamating
rash and multi-
organ involvement
(>3)
- usually no site of
pyogenic
inflammation;
blood CS negative
-tampon-using
menstruating
women or in
patients with
nasal packing for
epistaxis
Staphylococcus Humans Nosocomial Catalase-positive Polysaccharide Prosthetic device Vancomycin (50% Gram stain: gram-
epidermidis Coagulase- capsule: adheres infections (valves, methicillin positive cocci in
negative to a variety of joints, plates) resistance) clusters
Facultative prosthetic devices.
anaerobe Forms a biofilm. Culture: white
colonies on blood
Highly resistant to agar, non-
antibiotics hemolytic
Metabolism:
NOVOBIOCIN
Catase-positive
SENSITIVE
Coagulase-positive
Staphylococcus Humans Catalase-positive UTI in women Fluoro-quinolones Gram stain: gram- 2nd most common
saphrophyticus Coagulase- TMP-SMX positive cocci in cause of UTI in
negative clusters sexually active
Facultative women
anaerobe Culture: gamma-
hemolytic
NOVOBIOCIN
RESISTANT Metabolism:
Catase-
NO STRES positive
Coagulase-positive
Streptococcus Humans Respiratory Catalase-negative Erythrogenic Hyaluronidase: Impetigo DOC is Penicillin G Gram-positive Disease of poverty
pyogenes droplets toxin: produces degrades contagiosa cocci in chains
scarlet fever hyaluronic acid Patients with a
GABHS (spreading factor) Erysipelas history of Catalase-negative
Streptolysin O rheumatic fever
(oxygen-labile): Streptokinase Cellulitis require long-term Beta-hemolytic
highly antigenic, (fibrinolysin) antibiotic
causes AB prophylaxis to
Necrotizing Bacitracin-
formation DNase prevent
sensitive
(streptodornase): recurrence of the
PHARYNGITIS: disease
Streptolysin S degrades DNA in
most common Lancefield group
(oxygen-stable) exudates or
bacterial cause of A
necrotic tissue
sore throat
Pyogenic exotoxin positive PYR test
A: superantigen C5a peptidase:
SCARLET FEVER
similar to TSST inactivates
complement C5a
STREP-TOCOCCAL
Exotoxin B:
TOXIC SHOCK
protease that
SYNDROME:
rapidly destroys
clinically similar
tissue →
but milder than S.
necrotizing
aureus TSS, due to
fasciitis
pyogenic exotoxin
A, recognizable
site of pyogenic
inflammation,
blood cultures are
often positive
ACUTE
RHEUMATIC
FEVER
APSGN
Streptococcus Vagina Transvaginally UTI in pregnant Gram-positive Most common

agalactiae women cocci in chains cause of neonatal
Trans-placentally sepsis in the world
Neonatal sepsis Beta-hemolytic (the universe,
(meningitis, rather)
pneumonia) Catalase-negative
Endometritis → Bacitracin-
most commonly resistant
polymicrobial;
foul-smelling
Hydrolyzes
lochia
hippurate
CAMP test–
positive
Lancefield group
B
Grows using Lim

broth
Group D Human colon May enter UTIs due to Penicillin plus Gram-positive
streptococci bloodstream indwelling urinary gentamicin cocci in chains
during GIT or GUT catheters and
surgery urinary tract Vancomycin for Catalase-negative
instrumentation penicillin-
resistance Gamma hemolytic
Biliary tract colonies
Urethra and
female genital infections Linezolid for
tract can be vancomycin- Lancefield group
colonized Endocarditis in resistant strains D
patients who
underwent GIT
Bile and optochin-
surgery due to E.
resistant
faecalis
Hydrolyzes
Marantic
esculin in BEA
endocarditis in
patients with
abdominal Positive PYR test
malignancy due to
S. bovis E. faecalis can
grow in 6.5%
NaCl while S.
bovis cannot
Streptococcus Upper respiratory Respiratory Capsule retards PNEUMONIA: Penicillin G Gram-positive polyvalent (23-
pneumoniae tract droplets phagocytosis most common "lancet-shaped" type)
cause of CAP Levofloxacin or cocci in pairs or polysaccharide
IgA protease for Vancomycin chains vaccine
colonization OTITIS MEDIA, combined with
SINUSITIS, Ceftriaxone for Catalase-negative
c-substance reacts MENINGITIS penicillin
with CRP resistance Alpha-hemolytic
- most common
cause
Bile and optochin-

sensitive
SEPTIC SHOCK conjugated
positive Quellung vaccine:
- splenectomy reaction pneumococcal
predisposes to polysaccharide
sepsis coupled with
carrier protein
(diphtheria
toxoid)
viridans Oral flora Enters - glycocalyx - S. mutans, for - Penicillin G with Gram-positive
Streptococci bloodstream enhances adhesion dental caries or without an cocci in chains
during dental to damaged heart aminoglycoside
procedures valves - S. sanguis, for (Gentamicin) - Catalase-negative
subacute bacterial
- protected from endocarditis (SBE) - Vancomycin for - Alpha-hemolytic
host defenses penicillin-
within > most common resistance
- Bile and
vegetations cause of subacute optochin-
and native valve - Linezolid for resistant
endocarditis vancomycin-
resistant strains
- S. intermedius,
for brain abscesses
GRAM-POSITIVE BACILLI
Bacillus Herbivores Endopores Aerobic (but since Protein capsule Exotoxin: 3 Anthrax Ciprofloxacin Gram stain: box- Protein capsule
anthracis (zoonotic): Sheep it can grow (polymer of proteins (DOC) car shaped
Goats without oxygen. It gamma-D- Cutaneous bacteria Medusa head
Cattle is classified as a glutamatic acid): Protective (95%) painless Doxycycline
facultative antiphagocytic antigen (PA) black vesicles; Culture
MCC of death in
anaerobe can be fatal if Vaccine: for high-
woolsorter’s
Non-motile Edema factor untreated risk individuals Serology
disease is
(EF) pulmonary
Pulmonary Vaccine is PCR of nasal swab
hemorrhage
Lethal factor (woolsorter’s composed of the
(LF) disease) protective antigen
(PA) MCC of death is
pulmonary
GI: abdominal
Animal vaccine is hemorrhage in:
pain, vomiting
composed of a live Anthrax,
and bloody
strain, attenuated Leptospirosis
diarrhea
by loss of its (Weil’s syndrome),
protein capsule Congenital syphilis
Infxns result to
permanent
immunity
Bacillus cereus Endospores Aerobic No capsule Enterotoxins Food poisoning: Vancomycin Culture specimen Chinese fried rice
nausea, vomiting Clindamycin from suspected syndrome
Motile heat labile: similar food source
to interotoxin of Resistant to beta-
cholera and E. coli lactam antibiotics
(diarrheal form)
No treatment for
heat stable: food poisoning
produces
syndrome similar
to that of
Staphylococcus
aureus food
poisoning, but
with limited
diarrhea (emetic
form)
Clostridium Soil Endospores (heat Anaerobic Motile: flagella (so Neurotoxins Food-Borne Antitoxin (for Gram stain Flaccid paralysis
botulinum resistant) H-antigen inhibits release of botulism: cranial food-borne and
Stored vegetables: Anaerobes: positive) acetylcholine from nerve palsies, wound botulism) Culture: requires Floppy baby
Home-canned ABC peripheral nerves muscle weakness, anaerobic syndrome
Zip-lock Actinomyces respiratory Human botulism: condition
storage bags Bacteroides Toxin is not paralysis immunoglobulin (thioglycollate-
Botox neurotoxin
Clostridium secreted, rather it (for infant enriched agar)
Smoked fish is released upon Infant botulism: botulism)
the death of the constipation, Patient’s serum
Wild, raw honey: bacterium flaccid paralysis Penicillin injected into mice
associated with (floppy baby results in death
infant botulism syndrome) Supportive
therapy: including
Wound botulism: incubation and
ventilator
similar to food-
assistance
borne except
absence of GI
prodromal
symptoms
Clostridium tetani Soil Endospores: Anaerobic Motile flagella (so Tetanospasmin: Tetanus Tetanus toxoid: Gram stain: gram- Spastic paralysis
introduced H-antigen- inhibits release of vaccination with positive rods,
through wound positive) GABA and glycine muscle spasm formalin- often with an Drumstick, tennis
(both inhibitory inactivated toxin endospore at one racquet, lollipop
neurotransmitters lockjaw (toxoid), part of end, giving them appearance
) from nerve cells, (trismus) the DPT vaccine the appearance of
resulting in a drumstick
sustained muscle risus Antitoxin: human
contraction sardonicus tetanus immnue Requires
globulin (pre- anaerobic
respiratory formed anti- conditions
muscle tetanus
paralysis antibodies)
Clean the wound
Penicillin (DOC)
Supportive
therapy: may
require ventilator
assistance
vaccine DPT:
diphtheria
pertussis
tetanus
Clostridium Ubiquitous: Endospores Anaerobic NON-motile Alpha toxin: Cellulitis/wound Radical surgery Gram stain Double hemolysis
perfringens Soil lecithinase (splits infection (may require Culture: requires on blood agar
G tract of humans lecithin into amputation) anaerobic
and mammals phosphocoline and Clostridial conditions Looks motile, but
diglyceride) myonecrosis: fatal Penicillin not motile on
if untreated blood agar due
11 other tissue Hyperbaric oxygen to avidity for
destructive Watery diarrhea: lecithin in the
enzymes associated with blood membranes
food-borne
ingestion
Clostridium difficile Intestinal tract Fecal-oral: Anaerobic Motile flagella (so Toxin A: diarrhea Pseudomembran Metronidazole Immunoassay for PO vancomycin
ingestion of H-antigen- ous enterocolitis: Oral vancomycin C. difficile toxin because it has
Endospores found endospores positive) Toxin B: cytotoxic antibiotic- poor intestinal
in hospitals and to colonic associated Terminate use of Examine colon absorption, hence,
nursing homes epithelial cells diarrhea the responsilbe with colonoscopy “coats” the lesions
antibiotic with antibiotic
Corynebacterium Throat Respiratory Facultative Pseudo- Exotoxin (coded Diphtheria Antitoxins Gram stain: gram- Obtains exotoxin
diphtheriae droplets from anaerobe membrane forms by a positive from a temperate
carrier in the pharynx, bacteriophage) Mild sore Penicillin or pleomorphic rods bacteriophage by
Catalase-positve which serves as a throat with fever erythromycin (sometimes lysogenic
base from where it Subunit A: blocks initially describe as conversion
secretes its toxin protein synthesis Pseudomem Vaccine DPT looking like
by inactivating brane forms on diphtheria: Chinese letters) Schick test:
EF2 pharynx formalin injection of
Myocarditis inactivated Culture: diphtheria
Subunit B: causing A-V exotoxin, as Potassium exotoxin into the
provides entry conduction block antibodies to the tellurite: dark skin, to determine
into cardiac and and dysrhythmia B-subunit are black colonies whether a person
neural tissue Neural protective is susceptible to
involvement: pertussis Loeffler’s infection by
Exotoxin is like a peripheral nerve tetanus medium: after 12 diphtheriae
human antibiotic palsies, GBS, hours of growth,
(inhibits palatal paralysis stain with Modified Elek
eukaryotic protein and methylene blue. test: for detection
synthesis) neuropathies Reddish (Babes- of toxigenicity
Ernst) granules
can be seen
Listeria Ubiquitous Ingestion of Facultative Motile (via Listeriolysin O Neonatal Ampicillin Gram stain:gram- Facultative
monocytogenes Plants (vegetables) contaminated raw anaerobe flagella): so has H- and meningitis positive rods intracellular
milk or cheese antigen phospholipases: TMP-SMX parasite
from infected cows Catalase-positive tumbling motility allows escape from Meningitis in Culture: can grow
the immune- NOT at temperature as Cell-mediated
Vaginally (during Beta-hemolytic on Hemolysin: (like phagolysosomes of suppressed CEPHALOSPORINS low as 0 C so use immunity is
birth) blood agar streptolysin O) macrophages patients and the : cold enrichment protective
elderly (>50) NONE OF THE technique to
Tranplacental CEPHALOSPORINS isolate from mixed Listeriolysin
infxn of fetus from Septicemia in ARE ACTIVE flora Actin rockets
bacteremic mother pregnant women AGAINST MRSA,
LISTERIA, AND Tumbling motility
ENTEROCOCCI
GRAM-NEGATIVE COCCI
Neisseria Respiratory tract Respiratory Ferments both Antiphagocytic MENINGITIS: Penicillin Culture on Complement
meningitidis droplets maltose and polysaccharide most common chocolate agar deficiencies in the
glucose capsule cause among Ceftriaxone (or late-acting
aged 2-18 yrs cefotaxime) - The Gram-negative, complement
Oxidase-positive Endotoxin (LOS): drug of choice for aerobic, components (C5–
colonies on An LOS can be MENINGO- the treatment of encapsulated C9) predispose to
chocolate agar shed in large COCCEMIA: meningococcal diplococcus that illness
amounts by a dissemination of meningitis and grows best on
process called meningococci into septicemia enriched media,
blebbing, causing the bloodstream; such as Mueller- Most patients with
fever, shock and mmultiorgan Vaccine contains Hinton or meningococcal
other patho- disease, capsular chocolate agar, at meningitis, caused
physiology. This is consumptive polysaccharide of 37°C and in an by the gram-
considered the coagulopathy, strains A, C, Y, and atmosphere of 5- negative
principal factor petechial or W-135 10% carbon diplococcus
that produces the purpuric rash coupled to a dioxide Neisseria
high endotoxin (purpura carrier protein meningitidis,
levels in fulminans) (diphtheria recover
meningococcal toxoid) to enhance completely if
sepsis. immunogenicity appropriate
Meningococcemia
is defined as antibiotic therapy
Meningococcal Currently, is instituted
dissemination of
LOS interacts with vaccinations promptly.
meningococci
human cells, against Nonetheless, the
(Neisseria
producing pro- meningococcus A, disease still is
meningitidis) into
inflammatory C, W, and Y are associated with a
the bloodstream
cytokines and available. The first high mortality rate
(see the image
chemokines, meningococcal and persistent
below). Patients
including with acute vaccine for neurologic defects,
interleukin 1 (IL- serogroup B was particularly among
meningococcemia
1), IL-6, and tumor approved in infants and young
may present with
necrosis factor (1) meningitis (2) October 2014. children.
(TNF). LOS is one
meningitis with
of the important Rifampin
meningococcemia,
structures that chemoprophylaxis
or (3)
mediate to close contacts
meningococcemia
meningococcal
without clinically
attachment to and apparent
invasion into
meningitis.
epithelial cells.
LOS triggers the WATERHOUSE-

innate immune FRIDERICHSEN
system by SYNDROME: most
activating the Toll- severe form of
like receptor meningococcemia;
4MD2 cell surface high fever, shock,
receptor complex widespread
and myeloid in purpura,
non-myeloid disseminated
human sounds. intravascular
coagulation,
The degree of thrombocytopenia,

activation of and adrenal
complement then insufficiency
coagulation bilateral
system is directly hemorrhagic
related to the destruction of the
bacterial load. adrenal glands
IgA protease
At least 13
serogroups have
been described: A,
B, C, D, E, H, I, K, L,
W-135, X, Y, and Z.
Serogroups B and
C have caused
most cases of
meningococcal
meningitis in the
United States since
the end of World
War II; before that,
group A was more
prevalent. More
than 99% of
meningococcal
infections are
caused by
serogroups A, B, C,
29E, or W-135.
Neisseria Humans only (no Sexually Facultative- Pili: Endotoxin: Asymptomatic Antibiotic of Gram-stain of Kidney bean
gonorhoeae immunity to anaerobe Adherence to lipooligosaccharid (but still choice: third urethral plus shaped with
repeated Birth epithelial cells e (LOS) infectious) generation reveals the tiny concave sides
infections) Grows best in high Antigenic variation cephalosporin gram-negative facing each other
CO2 environment Antiphagocytic, No exotoxins Men: urethritis such as doughnut-shaped forming the
binds bacteria ceftriaxone (Add diplococci within appearance of
Ferments only tightly to host cell Women: cervical doxycycline to white blood cells doughnut
glucose (not protecting it from gonorrhea, which cover incubating Gram-negative
maltose)- easy to phagocytosis can progress to Chlamydia Culture: diplococci
remember, since pelvic trachomatis and Specimen on
there is only a “g” IgA protease inflammatory syphilis) chocolate agar Reinfection
(no “m”) in disease (PID) Selective media: because there is no
gonorrhoeae Outer membrane complications of The Centers for prevents growth of immunity to
proteins: Protein I: PID Disease Control other bacteria previous infections
porin protein II (CDC) Thayer Martin
(opacity protein): Lower abdominal recommends that with VCN
presence pain: Most all patients with Fitz-Hugh-Curtis
associated with consistent gonorrheal Cell wall contains syndrome
dark, opaque symptom of PID infection also be cytochrome
colonies treated for oxidase which
Septic arthritis in
Both men and presumed co- oxidizes dye
sexually active
For adherence: women: infection with tetramethylphenyl
patients
Has unique Gonococcal Chlamydia ene diamine from
protein that bacteremia trachomatis colorless to deep
can extract Septic (2015) pink. Used to ID Well-characterized
iron from arthritis: colonies plasmids
transferrrin, gonococcal Second line, but commonly carry
lactoferrin and arthritis is the not effective PCR in bacterial antibiotic-
hemoglobin most common against syphilis: DNA in clinical resistance genes,
cause of septic Flouro-quinolones specimens most notably
arthritis in Spectinomycin penicillinase.
sexually active Plasmid and
individuals For opthalmia nonplasmid genes
Neonates: neonatorum: are transmitted
Ophthalmia Erythromycin eye freely between
neonatorum drops should be different subtypes.
conjunctivitis in given immediately The ensuing
newborns N. following birth, for exchange of
gonorrhoeae is prophylaxis surface protein
acquired during against both N. genes results in
passage through gonorrhoeae and high host
an infected birth Chlamydia susceptibility to
canal; trachomatis reinfection. The
conjunctivitis conjunctivitis exchange of
usually erupts antibiotic
within the first 5 Infants with resistance genes
days ophthalmia has led to
neonatorum extremely high
require systemic levels of resistance
treatment with to beta-lactam
ceftriaxone. antibiotics.
Erythromycin
syrup should also
be provided to
cover for possible
concurrent
chlamydial disease
(this is important,
as failure to treat
neonatal
Chlamydia
conjunctivitis can
lead to chlamydial
pneumonia)
Moraxella Part of the Otitis media in Azithromycin or Resistant to
(Branhamella normal flora children clarithromycin penicilins
catarrhalis)
Can cause other Amoxicillin with
respiratory tract clavulanate
infections, such as
sinusitis, Oral second or
bronchitis and third generation
pneumonia cephalosporin
COPD TMP-SMX
exacerbation
GRAM-NEGATIVE BACILLI
Haemophilus Man only (obligate Transmitted via Haemophilus Some strains of H. Hib meningitis: Second or third Gram stain NTHi strains form
influenzae human parasite) respiratory route influenzae requires influenzae possess Most serious generation biofilm in vitro
two factors for a polysaccharide manifestation of cephalosporins Culture specimen and ex vivo and
The NTHi strains growth (both capsule, and these Hib infection; (since H. on blood agar that have been
colonize the found in blood): strains are antecedent upper influenzae can has been heated to implicated in
nasopharynx in up serotyped into 6 respiratory tract acquire ampicillin 80oC for 15 chronic infection
to 80% of X factor: different types (a- infections are resistance by minutes (now such as otitis
individuals Hematin f) based on their common; Hib plasmids) called chocolate media, sinusitis,
V factor: biochemically meningitis agar). This high and bronchitis.
NAD+ different capsules. manifestations Hib vaccine: H. temperature lyses NTHi biofilm
indistinguish-able influenzae the red blood cells formation was
The most virulent from other polysaccharide releasing both found in patients
strain is H. bacterial capsule of type b hematin (called X with CF on the
Satellite growth
influenzae type b meningitis causes strain (Hib) is factor) and NAD+ apical surface of
around
(Hib). conjugated to (called V factor). airway epithelia
Staphylococcus
Cellulitis: Most diphtheria toxoid Like the Neisseria, with decreased
aureus
commonly H. influenzae antibiotic
Some H. influenzae
involves the buccal grows best when susceptibility.
strains have no Passive
and periorbital the chocolate agar
capsule and are Immunization:
termed non- regions; usually mother is is placed in a high Approximately 6%
associated with CO2 environment of individuals with
encapsulated H immunized during
fever at 37oC Hib meningitis
influenzae or 8th month of
nontypeable H pregnancy to experience
Epiglottitis: Fever, permanent
influenzae (NTHi). increase passive Fluorescently
sore throat, sensorineural
antibody transfer labeled antibodies
dysphagia, hearing loss.
in breast milk (ELISA and latex
drooling, and particle
difficulty
The Centers for agglunation)
breathing
Disease Control
Hib pneumonia: and Prevention
Clinically (CDC) Advisory
indistinguish-able Committee on
from other Immunization has
bacterial released updated
pneumonias— 2014 vaccination
except for its recommendations
for adults aged 19 4. Positive
insidious onset Quellung test: due
and a history of years and older.
Key changes in the to its capsule,
fever, cough, and similar to
purulent sputum recommendations
include the Streptococcus
production pneumoniae
following:
Hib pericarditis:
Fever, respiratory Hib vaccine:
distress, and Vaccination is
tachycardia recommended for
(1) certain adults
Septic arthritis: at increased risk
Joint pain, for Hib who have

swelling, and not previously
decreased mobility received the
vaccine—except
Occult bacteremia: for individuals
Fever, anorexia, with human
and lethargy immunodeficiency
(HIV) infection,
NTHi infections: who have a low
Commonly causes risk for Hib
various mucosal infection; and (2)
infections, adults who have
including otitis undergone a
media and successful
conjunctivitis hematopoietic
stem cell
transplant (HSCT).
(Administer a 3-
dose series of Hib
vaccine 6-12 mo
post-
ransplantation,
regardless of Hib
vaccination
status.)
Haemophilis Sexually Small, gram- Chancroid: Azithromycin or Gram stain and A sexually
ducreyi transmitted negative, painful genital erythromycin culture of ulcer transmitted
disease facultative ulcer, often exudate and pus disease
anaerobic bacillus associated with Ceftriaxone(IM) released from
that is highly unilateral swollen swollen lymph Requires X factor
infective lymph nodes that node (hematin) only.
Ciprofloxacin
can rupture,
releasing pus
Chancroid is most
commonly
observed in
nonwhite men
who are
uncircumcised.
Women represent
only 10% of
known cases
because they are
more likely to be
asymptomatic
carriers.
Gardnerella Normal flora Shift in vaginal Bacterial Metronidazole Clue cells: vaginal Does not require X
vaginalis flora vaginosis: foul Therapy with epithelial cells that factor or V factor
smelling vaginal metro-nidazole contain tiny for growth
discharge (with or clindamycin pleomorphic
fishy odor), may alter the gram-negative Demonstration of
vaginal pruritus, vaginal flora bacilli within the clue cells on a
and often dysuria and predispose cytoplasm saline smear (the
the patient to most specific
Gray, thin, and development of diagnostic
homogeneous vaginal criterion)
vaginal discharge, candidiasis
which adheres to
the vaginal mucosa
(milk-splattered)
Bordetella Man: highly Transmitted via Capsule Pertussis toxins: Whooping Cough Erythromycin Bordet-Gengou The diagnosis of
pertussis contagious respiratory route activates G (most effective agar: potatoes, pertussis is made
Beta-lactamase proteins that 1. Catarrhal phase: when given in blood and glycerol by isolation of B
increases cAMP patient is highly catarrhal stage) agar, with pertussis in
resulting in: contagious (1-2 penicillin added culture. A
Filamentrous
weeks) Vaccine: DaPT polymerase chain
hemagglutinin
Increased Rapid serologic reaction (PCR) test
(FHA): A pili rod
sensitivity to tests: (ELISA) can also be
that extends from 2. Paroxysmal Pertussis
histamine performed.
the surface of B. phase (2-10 vaccination during
pertussis, enabling weeks) pregnancy is safe Collect specimen
the bacteria to Increased insulin from posterior The culture
bind to ciliated release pharynx on a specimen should
Whoop (burst of Treat household
epithelial cells of calcium alginate be obtained during
non-productive contacts with
the bronchi swab since B. the first 2 weeks of
Increased number coughs) erythromycin.
pertussis will not cough by using
of lymphocytes in
grow on cotton deep
blood Increased number nasopharyngeal
of lymphocytes in aspiration
2. Extra- blood smear
cytoplasmic
For PCR testing,
adenylate cyclase: Antibiotics Direct fluorescein-
nasopharyngeal
”weakens” ineffective during labeled antibodies
specimens should
neutrophils this stage applied to
be taken at 0-3
lymphocytes and nasopharyngeal
weeks following
monocytes specimens for
3. Convalescent cough onset
rapid diagnosis
stage
3. Filamentous
The CDC
hemagglutinin: PCR detection of
recommends a
allows binding to bacterial DNA in
combination of
ciliated epithelial respiratory
culture and PCR
cells seceretions
assay if a Pt’s
cough >3 wks
4. Tracheal
cytotoxin: kills
Early serial
ciliated epithelial
cells monitoring of
white blood cell
(WBC) counts is
warranted
Legionella Ubiquitous in man No person-to- Aerobic, motile, Facultative Cytotoxins: kill Pontiac fever: Azithromycin Culture on Facultative
pneumophila and natural water person and nutritionally intracellular hamster ovary headache, fever, buffered charcoal intracellular
environments (air transmission fastidious parasite: inhibits cells muscle aches and Levofloxacin yeasts extract parasite: inside
conditioning pleomorphic macrophage fatigue, self- agar (L-cysteine is alveolar
systems; cooling gram-negative phagosome/endo/ timing: recovery in a critical macrophages
Doxycycline
towers) rods. lysosome fusion a week is common ingredient)
Persons with
Growth depends Cu-Zn superoxide Legionnaires’ Serology (IFA and compromised
Freshwater on the presence of dismutase and Disease: ELISA) immune systems
amoebae appear to L-cysteine and catalase- pneumonia: fever are especially
be the natural iron in special peroxidase and non- Urinary antigen susceptible
reservoir for the media. protects bacteria productive cough can be detected by
organisms. from macrophage radioimmunoassa Atypical
The organism has superoxide and y with high pneumonia +
been isolated in hydroperoxide sensitivity and diarrhea +
natural aquatic oxidative burst specify and will hyponatremia
habitats remain positive for
(freshwater 3. Pili and flagella months after Legionnaires
streams and lakes, promote infection. Urine disease (LD) was
water reservoirs) attachment and antigen test only recognized in
and artificial invasion detects L. 1976 after an
sources (cooling pneumophilia outbreak of
towers, potable 4. Secretion of serogroup 1, but pneumonia at an
water distribution protein toxins like this accounts for American Legion
systems). RNAase, 90% of cases. convention in
phospholipase A Philadelphia.
Optimal growth and phospholipase
temperature is 28- C
40°C; organisms
are dormant below
20°C and are killed
at temperatures
above 60°C.
GRAM-NEGATIVE BACILLI: GASTROINTESTINAL AND GENITOURINARY INFECTIONS
Escherichia coli Humans: Fecal-oral Indole-positive Fimbriae (pili): Enterotoxins Neonatal Penicillins Gram-negative
GI and urinary attachment/ meningitis
tract Ascending Beta-hemolytic colonization factor 1. LT (heat-labile): Amino-glycosides Culture (specimen
infection to the increases cAMP UTI may be urine,
urethra Ferments lactose Siderophore (same as cholera 2nd and 3rd gen sputum, CSF or
toxin) Nosocomial sepsis cephalosporins blood); can grow
Colonization of Adhesins at 45.5 C
catheters in 2. ST (heat-stable) Nosocomial Fluoro-quinolones
hospitalized Capsule (K- Increases cGMP pneumonia Pathogenic strains
patients antigen) may be isolated
3. Shiga-like toxin from stool
Diarrhea
Aspiration Flagella (H- (verotoxin):
antigen) inhibits protein E. coli ferments
ETEC: releases LT
synthesis by lactose, so colonies
and ST toxins,
inactivating the appear purple to
traveler’s diarrhea
60S subunit of black on EMB agar
eukaryotic cells (E. and pink to purple
coli O157:H7, EHEC/STEC on MacConkey
STEC, EHEC) (Shiga-like toxic agar
producing E. coli):
no fever, no pus in
stool; secretes
shiga-like toxin
(verotoxin):
causes
hemorrhagic
colitis and
hemolytic uremic
syndrome (E. coli
strain O157:H7)
EIEC: with pus in

the stool and fever
Proteus mirabilis Urease: hydrolyzes Swarming motility No toxins UTI: high urine pH Ampicilin Culture: Colonies Weil-Felix
ureas into NH3 due to urease swarm over entire reaction: a test
and CO2 production TMP-SMX culture plate that uses
struvite calculi antibodies against
Indole-negative formation; Alkaline urine certain strains of
staghorn calculi (high pH) Proteus to
(tx with surgery) diagnose
Does not ferment
rickettsial disease
lactose
Sepsis (as certain
rickettsiae share
similar antigens)
See also: Rickettsia
species
Shigella Humans Fecal-oral No H2S production Invades Shiga toxin MOA: Bloody diarrhea Fluoro-quinolones Stool culture: IgA is best for
dysenteriae submucosa of inactivates the 60S with mucus and because Shigella is immunity
Does not ferment intestinal trac, but ribosome, pus (similar to Azithromycin never a part of the
lactose not the lamina inhibiting protein enteroinvasive E. normal intestinal Shigella is more
propria ulcers synthesis and coli) flora toxic and invasive
TMP-SMX
bledding killing intestinal than Salmonella
epithelial cells
Shiga toxin,
therefore, is a
NON-motile: No H-
protein synthesis
antigen (since they
inhibitor of
have no flagella)
EUKARYOTES
Salmonella typhi S. typhi is found S. typhi is Produces H2S Motile (H-antigen) Enteric fever Ciprofloxacin Culture: blood A. Facultative
only in humans transmitted via stool or urine may intracellular
fecal-oral route Does not ferment Capsule (called the Typhoid Ceftriaxone contain S. typhi parasite:
Zoonotic: lactose Vi antigen): fever
1. Pet turtles protects from Never part of the 1. Lives within
Non-typhoidal TMP-SMX
intracellular killing intestinal flora macrophages in
groups of Parathypoid -
Salmonella 2. Chickens fever (similar to lymph nodes
Azithromycin
Siderophores typhoid fever, but
3. Uncooked eggs caused by non- 2. Can live in gall
*Salmonella
typhoidal bladder for years
gastroenteritis:
Salmonella) (carriers secrete S.
there is little
typhi in stool)
benefit from
Chronic carrier antibiotic
state in the gall treatment; it may B. Persons who are
bladder prolong carrier asplenic or have
state non-functioning
Gastroentritis spleens (sickle cell
anemia) are at
In the Philippines,
Sepsis first line drug for increased risk of
infection by this
typhoid:
Osteomyelitis: Amoxicillin, TMP-
Especially in sickle SMX, organism

cell patients Chloramphenicol
(Salmonella Gastric acid is
choleraesuis) protetive against
salmonellosis,
hence,
gastrectomy/antac
ids increase the
risk
Yersinia Zoonotic: can be Ingestion of Non-lactose V and W antigens Enterotoxin Pseudo- Antibiotics do not Stool or blood Survives
enterocolitica found in pigs contaminated food fermenter similar to the heat appendicitis (RLQ alter the course of cultures mat be refrigeration
or water Motile stable toxin of E. pain) the diarrhea. positive
Virulence factors coli increases mesenteric However, patients Closely related to
Unpasteurized are temperature cGMP levels lymphadenitis with positive Examination of the Yersinia pestis
milk sensitive blood culture terminal ilium
expressed at 37oC Acute should be treated with colonoscopy Mesenteric
enterocolitis, with with antibiotics will reveal lymphadenitis in
fever, diarrhea and mucosal ulceration children
abdominal pain
pseudo-
appendicitis
Diarrhea - The
most common
clinical
manifestation of
this infection;
diarrhea may be
bloody in severe
cases
Low-grade fever
Abdominal pain -
May localize to the
right lower
quadrant
Vomiting - Present
in approximately
15-40% of cases
Vibrio cholerae Humans only Fecal-oral Oxidase-positive Motile (H-antigen) Choleragen Cholera: severe Fluid and Dark field Death by
transmiision Shooting star (enterotoxin): like diarrhea with rice electrolyte microscopy of dehydration:
Ferments sugar motility LT of E. coli, water stools. No replacement stool reveals children affected
Morphology: (except lactose) increases levels of pus in stools motile organism in endemic areas
Short, comma cAMP, causing Doxycycline that are 1991: Latin
shaped, with a secretion of immobilized with America epidemic
single polar electrolytes from antiserum
Flouro-quinolones
flagellum the intestinal 1993: Epidemic in
epithelium. This Bangladesh and
Digest mucous results in secretion India
layer so V. cholera of fluid into the
can attach to cells Grows as flat
intestinal tract.
yellow colonies Washer woman’s
secretory diarrhea
on selective media: hands sign
3. Fimbrae: helps
thiosulfate- wirnkled skin due
with attachment to
citrate-bile-salts- to loss of skin
cells
sucrose (TCBS) turgor due to
agar dehydration
4. Non-invasive
Vibrio para- Fish, seafood Consumption of Halophilic (likes Motile (H-antigen) Hemolytic Cause of 25% of Doxycycline TCBS Diarrhea after
haemolyticus raw fish salt) cytotoxins food poisoning in ingestion of raw
Capsule Japan (diarrhea for Fluoroquinolone seafood; also
Morphology: short, 3 days) because consider Norwalk
comma shaped, Japanese love virus; important to
Unclear if
with a single polar seafood distinguish viral
antibiotics change
flagellum from bacterial
clinical course of
the disease
Campylobacter Zoonotic: wild and Uncooked meat Microaerophilic Motile (H-antigen) Enterotoxin: Secretory or Fluoroquinolone Microscopic exam One of the three
jejuni domestic animal (especially similar to cholera bloody diarrhea of stool reveals most common
and poultry; poultry) Oxidase Positive Invasive toxin and the LT of Erythromycin motile, curved causes of diarrhea
undercooked E. coli Associated with gram-negative in the world
chicken Unpasteurized Guillain-Barre rods
Optimum
milk Cytotoxins: syndrome Most common
temperature is
destroy mucosal Selective media cause of bacterial
42oC – to inhibit
cells with antibiotic at gastroenteritis
Fecal-oral the growth of
other fecal species 42oC
Morphology:
curved gram- Skirrow’s agar
negative rods with
a single polar Campy’s agar
flagellum
Helicobacter pylori Morphology: Microaerophilic No toxin Duodenal ulcers Bismuth, Peptic ulcer
curved gram- ampicillin, disease
negative rods with Urease-positive Chronic gastritis metronidazole and
a tuft of polar tetracycline Gastric carcinoma
flagella
Clarithromycin MALT lymphoma
and omeprazole
Both regimens
reduce duodenal
ulcer relapse
Bacteriodes fragilis Colon Part of the normal Anaerobic (O2 Does not contain Abscesses in the Metronidazole – Gram-stain Infection occurs
flora of the inhibits its lipid A gastrointestinal DOC for anaerobic when the
intestine growth) tract, pelvis and infections Anaerobic culture organism enters
lungs the peritoneal
Most common Gram-negative rod Clindamycin cavity
colonic flora Brain abscesses
(chloramphenicol Hence, if the
Non-spore former Chloram-phenicol
is ideal because it anatomy of the GI
is lipophilic) tract is altered
Polysaccharide Chloram-phenicol (surgery, trauma,
capsule is static, but cidal perforation)
to the following:
Neisseria
meningitidis
Bacteroides fragilis
Streptococcus
pneumonia
Haemophilus
influenza
NBSH – No
Boyfriend Since
Highschool
Pseudomonas Soil, Water, Plants, Medical devices Obligate aerobe Motile (polar Exotoxin A Burn infections MDR, XDR strains Culture: greenish, Common etiology
aeruginosa Animals, Intestinal (does not ferment) flagella) (similar to metallic colonies for infection in
Flora, Skin Hands of diphtheria toxin): Endocarditis in IV SEE on blood agar, neutropenic
healthcare 2.Non-lactose Hemolysins inhibits protein drug users ANTIPSEUDOMON with fruity odor patients.
workers fermenter synthesis by AL LIST GIVEN BY (grape-like odor)
blocking EF2 DR. CALDERON Produces pigments
Collagenase Necrotizing
3. Oxidase-positive pneumonia – fleur Cetrimide medium when cultured:
Elastase de lys morphology Antimicrobials are
on histopath the mainstay of a. pyocyanin (blue
therapy. pigment)
Fibrinolysin
Sepsis (in the
immunocompromi Meningitis: b. pyoverdin
Phopholipase C
sed); ecthyma Ceftazidime is the (green pigment)
gangrenosum antibiotic of
DNAse choice
Malignant otitis
Antiphagocytic externa Eye infections: Nosocomial
capsule Treat small organisms similar
UTI (catheter- superficial ulcers to Pseudomonas:
related) with topical
therapy (eg,
Acinetobacter
ophthalmic
Diabetic baumannii
aminoglycoside
osteomyelitis
solution rather
than an ointment) Elizabethkingia
Typhlitis, Shanghai every 30-60 meningo-septicum
fever minutes; when
perforation is Burkholderia
It is the most imminent, cepacia
common subconjunctival
pathogen (or subtenon)
isolated from administration is
patients who preferred;
have been management of
hospitalized endophthalmitis
longer than 1 requires
week, and it is a aggressive
frequent cause of antibiotic therapy
nosocomial (parenteral,
infections. topical,
subconjunctival
[or subtenon], and,
often, intraocular)
GRAM-NEGATIVE BACILLI: ZOONOTIC INFECTIONS
Yersinia pestis Wild rodents Flea bite Facultative Fraction 1 (F1): Pesticins: kills Bubonic plague: Streptomycin or Gram strain will Facultative
anaerobe this capsular other bacteria rRegional lymph gentamicin reveal gram- intracellular
City rats Contact with antigen is (including E. coli) nodes ( usually negative rods with parasite
infected animal Virulence factors antiphagocytic groin) swell, and Doxycycline bipolar staining:
tissue are temperature Intracellular become red, hot the ends of these Yersinia can accept
Squirrels and
sensitive: only V and W proteins murine toxin: and tender (called rod shaped plasmids in E. coli,
prairie dogs in the Killed vaccine is
expressed at 37oC lethal to mice a bubo); high bacteria take up and shares many
U.S Inhaled effective only for a
(temperature fever; stain more than antigens with
aerosolized Non-motile few months
inside conjunctivitis the center (closed enteric bacteria
organisms: human (attenuated
macrophages) safety pin
to human Requires calcium vaccine is more
Septicemic appearance)
transmission at 37oC. If effective but also Subcutaneuos
occurs during Virulence is plague: bacteria has more side hemorrhage result
insufficient
epidemics plasmid-mediated survive in effects) Blood culture in a blackish skin
calcium, Y. pestis
macrophages, and discoloration,
alters its
spread to blood Culture bubo giving the name
metabolism and
and organs. Death aspirate “Black Death”
protein
occurs in 75% in
production. This
untreated
trait assists with Serology Yersinia is named
its intracellular in honor of
state Pneumonic Alexander Yersin,
Rapid diagnositic
plague: during who successfully
test: antibody
epidemics, isolated the
The virulence of against F1
pneumonia occurs, bacteria in 1894
this bacterium (capsular antigen)
as bacteria are during the
results from the 32
spread from pandemic that
Y pestis
person to person began in China in
chromosomal
by aerosolized the 1860s.
genes and two Y
respiratory
pestis –specific
secretion: 100% in
plasmids, Plague was first
untreated
constituting the described in the
only new genetic Old Testament and
material acquired has persisted into
since its evolution the modern era.
from its Plague has caused
predecessor. large-scale
These acquired epidemics, thereby
genetic changes changing the
have allowed the course of history
pathogen to in many nations.
colonize fleas and The first pandemic
to use them as was believed to
vectors for have started in
transmission. Africa and killed
100 million people
The bacteria over a span of 60
elaborate a years. In the
lipopolysaccharide Middle Ages,

endotoxin, plague killed
coagulase, and a approximately one
fibrinolysin, which fourth of Europe's
are the principal population. The
factors in the pandemic that
pathogenesis of began in China in
plague. the 1860s spread
to Hong Kong in
the 1890s and was
subsequently
spread by rats
transported on
ships to Africa,
Asia, California,
and port cities of
South America. In
the early twentieth
century, plague
epidemics
accounted for
about 10 million
deaths in India. As
reported in
National
Geographic, mass
graves of plague
victims were
recently
discovered in an
area of Venice
called "Quarantine
Island."
Francisella Rabbits and Bite of tick, deerfly Obligate aerobe Capsule Tularemia Gentamicin or Culture (but very The diagnosis of
tularensis squirrels or infected antiphagocytic streptomycin dangerous due to tularemia is
animals Requires cysteine Ulceroglandular: (DOC) its high infectivity, usually based on
Ticks can serve as Non-motile at the site of tick requires addition serology results.
a reservoir Direct contact with bite or direct Doxycycline of cysteineto blood Tests vary from
infected animal contact with agar media antibody detection
The ability of F
tissue (usually contaminated (using latex
tularensis to Attenuated
rabbit) rabbit, an ulcer Skin test agglutination or
impair phagocyte vaccine: onlfor
devcelops ,with enzyme-linked
function and high-risk
swelling of focal immunosorbent
Inhaled survive in infected individuals Measure rise in
lymph nodes assay [ELISA]
aerosolized cells is central to IgG antibody titer
testing) to the
organisms its virulence. This (IgM is not very
Pneumonic: examination of a
intracellular life good)
range of
Ingestion of cycle has been inhalation, or
polymerase chain
contaminated shown to be through the blood
reaction (PCR)
meat or water related to the
assay products.
tightly regulated Oculoglandular:
expression of a direct inoculation
5. Easily An agglutination
series of genes. into eyes
transmitted to lab titer greater than
personnel 1:160 is
Typhoidal: considered
ingestion results in presumptively
gastrointestinal positive, and
symptoms treatment may be
(abdominal pain) started if this
and fever result is obtained.
A second titer,
demonstrating a 4-
fold increase after
2 weeks, confirms
the diagnosis.
Brucella Goats (meeee!) Direct contact with Obligate aerobe Capsule Brucellosis: Pasteurization of Culture blood, Brucella ovis –
contaminated milk bone marrow nonpathogenic to
Brucella livestock or Brucellae are Non-motile Undulating fever (best yield), liver, man
meltitensis aborted placentas aerobic gram- (fever peaks in the 2Treat with or lymph nodes
(highest negative evening, and combination of Although Brucella
Tropism for
pathogenicity) Ingestion of coccobacilli that returns to normal doxyxycline and Serologic tests infection is
erythritol, a
infected milk possess a unique by morning) one other drug primarily
Cattle sugar found in
products ability to invade (gentamicin, controlled through
animal placentas Skin test: Indicates
both phagocytic Weakness streptomycin, or cell-mediated
exposure only
and nonphagocytic rifampin). immunity rather
Brucella abortus Aerozolization in Erythritol is a four-
cells and to Loss of appetite than antibody
laboratory or carbon sugar
Pigs survive in the activity, some
possibly due to preferentially All cattle are
intracellular immunity to
bioterrorism utilized by Brucella immunized with a
environment by reinfection is
spp. The presence Includes abortions living attenuated
Brucella suis finding ways to
in animals strain of Brucella provided by serum
avoid the immune of erythritol in the
Dogs placentas of goats, abortus immunoglobulin
system. (Ig). Initially, IgM
cows, and pigs has
been used to levels rise,
Brucella canis: explain the followed by IgG
titers. IgM may
localization of
remain in the
Brucella to these
serum in low
sites and the
subsequent levels for several
months, whereas
accumulation of
large amounts of IgG eventually
bacteria, declines.
eventually leading Persistently
elevated IgG titers
to abortion.
[Microbes Infect. or second rises in
IgG usually
2013 Jun;15(6-
7):440-9] indicate chronic or
relapsed infection.
IgA antibodies are
elaborated late
and also may
persist for very
long intervals.
Pasteurella Part of the normal Bite from dog or Facultative Capsule Wound infections Penicillin G Culture specimen Not a faculatative
multocida flora of domestic cat anaerobe (following dog or on standard intracellular
and wild animals Non-motile cat bites): may Doxycycline laboratory media organism
progress to
infection of Human bite
Third generation
nearby bones and infection- Eikenella
cephalosporin
joints corrodens
MISCELLANEOUS BACTERIA
MICROORGANISM RESERVOIR TRANSMISSION METABOLISM VIRULENCE CLINICAL TREATMENT DIAGNOSIS NOTES

FACTORS SYNDROMES
Chlamydia Humans Direct contact LIFE CYCLE Resistant to lysozyme Serotypes A, B, & C Genital and eye Can NOT be grown Gram-negative, but
trachomatis (since their cell wall Trachoma: causes infections: artificial media. Can lacks peptidoglycan
Primarily affects the Elementary body lacks muramic acid) scarring of the inside classically be grown layer and muramic
A-C: trachoma eyes, genitals, lungs (EB): dense spherule of the eyelid, in chick yolk sacs: acid
that infects cells Prevents phagosome resulting in Doxycycline (use only More commonly
– lysosome fusion redirection of the for adults) chlamydia is cultured Trachoma is seen in
D-K: genital, neonatal Poor hygiene for
eyelashes onto the in certain cell lines underdeveloped
trachoma Initial (reticulate)
corneal surface (McCoy cells for countries, and
L1-3: LGV body: After EB enters Non-motile Erythromycin
corneal scarring and example) transmission occurs
cell, it transforms (especially for infants
blindness due to poor hygiene
into an initial body; No pili and pregnant
larger, osmotically women) For inclusion
fragile; can produce Serotypes D through K conjunctivitis Presence of
No exotoxins Inclusion (ophthalmia
via binary fission; Azithromycin chlamydial
requires ATP from conjunctivitis neonatorum): inclusions or
the host (opthalmia Scraping from the elementary bodies
neonatorum) surface of the on Giemsa-stained
conjunctiva will show smears of the
The initial body
Infant pneumonia intracytoplasmic conjunctivae or
transform back into
inclusion bodies nasopharynx
EB, which leaves the
within conjunctival confirms the
cell to infect the other Urethritis, cervicitis
epithelial cells diagnosis
cells and pelvic
(Halberstaedter-
inflammatory disease
Prowazek
(PID) in women Interesting risk
inclusions). The
factors:
inclusion bodies
Nongonococcal contain glycogen and
urethritis, thus, stain of iodine Certain cytokine
epididymitis and or Giemsa polymorphisms –
prostatitis in men These have been
associated with
Gram-stain of genital
Complications of severe disease and
secretions will not
chlamydial genital risk of tubal factor
show gram-negative
tract infection: infertility
organisms
Sterility, ectopic Certain variants in

Urethritis: most
pregnancy and Toll-like receptor 1
commonly diagnosed
chronic pain may and 4 genes – These
by polymerase chain
occur after pelvic predispose to
reaction of urethral infection
inflammatory disease swab or urine sample
Reiter’s syndrome: Having been a foster

Immuno-fluorescent child (males only)
triad of conjunctivitis, slide test place
urethritis, and infected genital or
arthritis ocular secretions on a
slide and stain with
Fitz-Hugh-Curtis fluorescein-
Syndrome: conjugated anti-

perihepatitis chlamydial antibody
Serotypes L1, L2 & L3 Serologic: Examine

Lymphogranuloma blood for elevated
venereum (LGV) titers of
antichlamydial
antibodies with
compliment fixation
and
immunofluorescence
tests.
Lymphogranuloma
venereum: Serologic
test
Frei test, which is

rarely used, is similar
to the PPD skin test
for tuberculosis
Chlamydophila Birds, poultry Bird feces dry out, Life cycle is similar to Psittacosis: a viral- Doxycycline Serologic: Examine History of
psittaci fecal particles are Chlamydia like atypical blood for elevated occupational
inhaled, infecting the trachomatis pneumonia, with Erythromycin titers of antibodies exposure to birds
lungs fever and dry, non- compliment fixation
productive cough and immune- This bacterium can
An occupational (similar to fluorescence tests infect parrots,
disease of zoo and Mycoplasma parakeets, canaries,
pet-shop employees, pneumonia) According to case and other avian
poultry farmers, and definitions from the species (eg, turkeys,
ranchers. Human-to- CDC (2000), a pigeons, ducks).
human transmission confirmed case Another term for this
is rare. involves one of the infection is
following criteria: ornithosis, which
describes the
Isolation of the infection caused by
organism by culture nonpsittacine birds.
Compatible clinical
illness with a 4-fold
rise (to a reciprocal Psittacosis is found
titer of 32 or greater worldwide. The
by paired sera incidence seems to be
collected at least 2 increasing in
weeks apart) in CF or developed countries,
MIF antibodies which is correlated to
against C psittaci the import of exotic
birds.
Detection of an IgM
titer of 16 or greater
against C psittaci by
MIF
Chlamydophila Humans (spread Respiratory route Life cycle is similar to Atypical pneumonia: Macrolides are the Serologic: Examine Accelerated
pneumoniae from human to Chlamydia viral like atypical first-line antibiotics blood for elevated atherosclerosis
human) trachomatis pneumonia ( similar for the treatment of C titers of antibodies
to Mycoplasma) in pneumoniae with compliment Culture for C.
young adults pneumonia fixation and pneumoniae is
immunofluorescence technically complex
Doxycycline test. Criteria for and time consuming.
infection include a When compared to
Erthromycin single IgM titer ≥1:16 serology and PCR, it
or a 4-fold increase in also has low
IgG titer. sensitivity and is
mainly used in
Intracytoplasmic research labs
inclusion bodies do
not stain with iodine The FilmArray
Respiratory Panel is a
The Infectious multiplex PCR which
Diseases Society of detects common
America and respiratory
American Society of pathogens in
Microbiology nasopharyngeal
currently recommend specimens. In 2012,
serologic testing or the US Food and Drug
polymerase chain Administration (FDA)
reaction (PCR) for the approved the
diagnosis of C addition of 2 corona
pneumoniae. Despite viruses and 3
evident drawbacks, bacteria to the Panel,
serology is still including C
considered the gold pneumoniae,
standard Bordetella pertussis,
and Mycoplasma
Real-time PCR assays pneumonia. The
of pharyngeal swab, FilmArray Panel can
bronchoalveolar now detect 17
lavage, sputum or viruses and 3
tissue can be used to bacteria from a single
detect C pneumoniae- sample. Reported
specific DNA. Because sensitivity and
of the complexity of specificity were both
these tests, 100% for C
widespread pneumoniae but the
implementation had sample size was
been limited until small and fewer than
recent years. 10 samples were
positive in the study.
Rickettsia rickettsii Dogs, rabbits & wild Wood tick: In Rocky mountain Doxycycline Clinical exam
rodents western U.S spotted fever:
Dermacentor 1. Fever Chloramphenicol Direct immune-
andersoni fluorescent exam of
2. Conjunctival skin biopsy from rash
Dog tick: In Eastern injection (redness) site
U.S Dermacentor
variabilis 3. Severe headache Serology
4. Rash on wrists, Well-Felix reaction

ankles, soles and
palms initially, Positive OX-19
become
generalized later
Positive OX-2
Rickettsia akari House mice Mites (which live on Rickettsial Pox: Doxycycline Well-Felix reaction
the house mice) Vesicular rash similar negative
to chicken pox. It Chloramphenicol
resolves over 2
weeks
Rickettsia prowazekii Humans Human body louse 1, Epidemic Louse- Doxycycline Well-Felix reaction: Epidemic typhus is
(Pediculus humanus borne typhus positive OX-19 caused by Rickettsia
Flying squirrels var. corporis) Chloramphenicol prowazekii and
A. Abrupt onset of Serology transmitted by
fever and headache human body lice. For
Eradicate human lice
centuries, it has been
associated with
B. Rash, which spares
overcrowding, cold
the palms, soles, and
weather, and poor
face
hygiene.
C. Delirium/stupor
Brill-Zinsser
disease is a
D. Gangrene of hands recurrent form of
or feet epidemic typhus that
is unrelated to louse
2. Brill-Zinsser infestation and
Disease: develops sporadically
years after the
A. Reactivation of primary illness.
Rickettsia prowazekii Clinical features are
similar to, but milder
B. Mild symptoms than, those of
epidemic typhus
C. NO rash
Rickettsia Rats Rat flea (Xenosylla Endemic (or murine) Doxycycline Well-Felix reaction:
cheopsis) typhus: fever, positive OX-19
typhi Small Rodents headache and rash Chloramphenicol
Orientia Rats Mite larvae Scrub typhus: Doxycycline Well-Felix reaction:

tsutsugamushi (chiggers) Fever and headache positive OX-K
Shrew Chloramphenicol
Eschar (scab) at bite
Mongooses site
Birds Followed by a rash
Bartonella quintana Humans Body louse Not an obligate 1. Trench Fever: fever, Doxycycline Serology
intracellular parasite headache and back
pain. It last for 5days Chloramphericol PCR
recurs at 5 day
interval
Azithromycin
2. Bacteremia,
endocarditis, and
baciliary
angiomatosis
Bartonella henselae Cats Cat bite or scratch Not an obligate Cat-scratch disease Azithromycin Serology Bacillary
intracellular parasite angiomatosis is a
Baciliary Doxycycline PCR differential
angiomatosis diagnosis for
Kaposi’s sarcoma
Bacteremia
Endocarditis, “culture
negative”
Coxiella burnetii Cattle,sheep, goats No anthropod vector Can grow at pH 4.5 Q fever. Fever, Doxycycline Complement fixation This is the only
required. Direct within headache & viral-like test demonstrating a rickettsial disease
airborne phagolysosomes pneumonia. No rash! Erythromycin rise in antibody without a skin rash.
transmission of
endospore from cow Has an endospore Complications: PCR
Pasteurize milk at
hide or dried form 60oC
placenta, or via
1. Hepatitis
consumption of
endospore-
contaminated 2. Endocarditis
unpasteurized
cowmilk
Ehrlichia chaffeensis Deer, dogs, coyotes Ticks Clusters of Ehrlichia Human ehrlichiosis: Doxycycline Rise in acute and Ehrlichiosis is an
multiply in host similar to rocky convalescent infection of white
Anaplasma monocyte vacuoles mountain spotted Rifampin antibody liters blood cells that
phogocytophilum (phagosomes) to fever, but rash is affects various
Deer, white-footed form large, mulberry- rare Characteristic mammals, including
Resistant to
mouse shaped aggregates ehrlichial inclusion mice, cattle, dogs,
Ehrlichia ewingii chloramphericol
called morulae bodies are deer, horses, sheep,
sometimes seen in goats, and humans
leukocytes on blood
smears
PCR The primary target

cell for human
monocytic erlochiosis
(HME) is the
macrophage, and the
primary target for
human granulocytic
anaplasmosis (HGA)
is the granulocyte.
Intracellular infection
is established within
phagosomes, most
often found in
macrophages in the
liver, spleen, lymph
nodes, bone marrow,
lung, kidney, and
CNS.
Treponema pallidum Humans only Sexual Microaerophilic Motile Syphilis Penicillin G Cultaneuos lesions Jarisch-Herxheimer
pallidum examined by dark reaction: acute
Morphology: thick A. Primary: painless Erythromycin field microscopy, worsening of
Between 1905 and rigid spirals chancre immunofluorescence. symptoms after
1910, Schaudinn and ELISA, or silverstain Penicillin is started
Doxycycline
Hoffman identified T Highly sensitive to B. Second stage: Rash
pallidum as the cause elevated on palms and soles Non-specific
of syphilis, and temperatures treponemal tests:
Wasserman VDRL; RPR
Condylomata lata:
described a
painless, wart-like
diagnostic test for the Specific treponemal
lesion which occurs
long-recognized test : FTA-ABS, MHA-
in warm, moist places
infection. Pathogenic TP
(vulva or scrotum)
treponemes are
associated with the
CNS, eyes, bones, VDRL and FTA-ABS
following 4 diseases:
kidneys and/or joints are positive
can be involved
Venereal syphilis,
caused by T pallidum
pallidum C. Latent: 25% may
relapse back to the
Yaws, caused by T secondary stage
pallidum pertenue
D. Tertiary (33%):
Endemic syphilis
(bejel), caused by T Gummas of skin and
pallidum endemicum bone
Pinta, caused by T Cardiovascular

carateum syphilis (aortitis)
Neurosyphilis:
Agryll-Robertson
pupil
E. Congenital
syphilis: contacted
transplacentally
(MCC of death is
pulmonary
hemorrhage)
According to a
Centers for Disease
Control and
Prevention report,
untreated syphilis,
especially early
syphilis, during
pregnancy can lead to
deafness, neurologic
impairment, bone
deformities, stillbirth,
and neonatal death
Borrelia burgdorferi White-footed mouse Vector = Ixodes ticks Microaerophilic LYME DISEASE Doxycycline (DOC) Elevated levels of Largest medically
antibodies against important bacterium
White-tailed deer A. Early localized Amoxicilin Borellia burgdorferi (size)
Ixodes scapularis: stage (stage 1): ban be detected by
East & Midwest Erythema chronicum ELISA
Ceftriaxone for
migrans (ECM) neurologic disease
Ixodes pacificus: Western
West coast B. Early disseminated immunoblotting
stage (stage 2):
Together with
Babesia microti Multiple smaller ECM
Neurologic: aseptic
meningitis, cranial
nerve palsies (Bell’s
palsy), and
peripheral
neuropathy
Cardiac: transient
heart block or
myocarditis
Brief attacks of
arthritis of large
joints (knee)
C. Late stage (stage

3):
Chronic arthritis
Acrodermatitis
chronica atrophicans
Encephalopathy
Leptospira Zoonotic (dogs, cats, Direct contact with AEROBIC – the other Leptospiremic phase: Penicillin G First week: culture The traditional
interorgans livestock, and wild infected urine or spirochetes are organisms in blood blood or cerebral system divided the
animals) animal tissue: microaerophiles and CSF causes high Doxycycline for spinal fluid (on lab genus into 2 species:
23 serogroups, 250 Organism penetrate spiking temperature, chemoprophylaxis media, or by the pathogenic
serovars History of wading in broken skin (i.e. on Spiral shaped, with headache and severe inoculation into Leptospira
flood water (in 3rd feet) and mucous hooks on both ends muscle aches (thighs animals interrogans and the
world setting) membranes (“ice tongs”) and lower back) nonpathogenic
(swallowing urine- Shepherd’s crook Second week to Leptospira biflexa.
History of exposure contaminated water) appearance Immune phase: months: culture urine These species were
to animals (butcher) correlates with divided further into
emergence of IgM serogroups, serovars,
Two axial flagella Rarely, dark field
and involves and strains based on
wrap around and run microscopy is
recurrence of the shared antigens. L
along the length of successful (not
above symptoms, interrogans included
the organism under recommended)
often with more than 250
the outer membrane
meningismus (neck serovars.
(oeriplasmic flagella) Antibody based
pain)
ELISA to detect
Leptospira antigens
WEIL’S DISEASE: in the urine
most severe case of
leptospirosis with Polymerase Chain
renal failure ,
Reaction (PCR) to
hepatitis (and
detect bacterial DNA
jaundice), mental
in serum, CSF and
status changes, and
urine
hemorrhage in many
organs. ECG
abnormalities are Microscopic
common during the agglutination
leptospiremic phase testing (MAT; the
of Weil syndrome. In criterion standard for
severe cases, serologic
congestive heart identification of
failure and leptospires, available
cardiogenic shock only at reference
may occur. laboratories)
Mycobactrium 40% of total cell dry Aerobic Mycosides No exotoxin nor Tuberculosis First line drugs: Acid-fast stain of Mycolic acids are also
tuberculosis weight is lipid endotoxin specimen found in Nocardia
Catalase-positive Cord factor: only A. Primary Isoniazid (INH) (carbolfuchsin (which also is acid
Composed of mycolic found in virulent tuberculosis: primary stain; fast)
acids strain (May be methylene blue
Slow growth rate Rifampin
responsible for secondary stain) Purified Protein
Asymptomatic
Thin rods release of tumor Derivative (PPD) Test
Pyrazinamide
necrosis factor RAPID CULTURE:
Overt disease,
Non-motile involving the lungs 1. Measure zone of
Ethambutol
Sulfatides: inhibit or other organs Bactec radiometric unduration:
phagosome-lysosome culture: a liquid
Facultative Streptomycin
fusion broth in a bottle, with Positive reaction:
intracellular growth: B. Reactivation or
radioactive palmitate > 5mm (immune-
M. tuberculosis can secondary
Wax D: acts as an as a carbon source. compromised
survive and multiply tuberculosis:
adjuvant Mycobacteria grow host)
in macrophages
and use the carbon,
1. Pulmonary allowing early
Iron siderophore 2> 10 mm (have
detection (in 1-2
(mycobactin) chronic disease or
2. Pleural or weeks) even before
risk factors for
pericardial colonies can be seen.
exposure to TB)
3. Lymph node PPD skin test
>15mm (all
infection
others)
Chest X-ray
4. Kidney
2. A positive reaction
PCR and DNA probes does not mean active
5. Sketetal disease.
Mycobacterium Tb
6. Joints Direct Test (MTDT): 3. Can get false
amplifies ribosomal negative in patients
7. Central nervous RNA in respiratory with AIDS or
system secretions, allowing malnourished
rapid identification of individuals
8. Miliary M. tuberculosis
tuberculosis
QuantiFERON-TB -
blood test that
measures interferon
gamma levels
produced in whole
blood in response to
addition of specific
tuberculosis antigens
has been approved
by the FDA. An
advantage of this test
is the relative
specificity for
Mycobacterium
tuberculosis; it is not
positive in patient in
previous BCG
vaccination, (MMWR,
Recommendation
and Reports, 2005)
Luciferase Reporter
Mycobacteriophage
(LRP) Assays - can
detect
Mycobacterium
tuberculosis and
characterize
mycobacterial drug
susceptibility
patterns within 24 to
48 h in positive
cultures (luciferase is
an enzyme obtained
from fireflies)
Mycobacterium Humans Catalase-positive Non-motile Leprosy - the most Rifampin Can NOT be grown on Lepromin skin test -
leprae common cause of artificial lab media: Although not useful
Armadillos Grows best at low Facultative crippling of the hand Dapsone can only be cultured for diagnosis, it
temperature intracellular growth in certain animals, allows positioning of
A. Lepromatous such as mice foot patients on the
Clofazimine
leprosy (LL): pads, armadillos or immunologic
Phenolase-positve:
monkeys spectrum
converts DOPA into a
pigmented product 1. Low cell-mediated
(used for diagnosis) immunity Skin or nerve biopsy Also known as
will reveal acid-fast Hansen disease,
bacilli (lepromatous) named after G.A.
2. Organisms found
or granulomas Hansen, who is
everywhere (organs
(tubercoloid) credited with the
and blood)
1873 discovery of M
leprae.
3. Skin, nerves, eyes
and testes involved
bilaterally: multiple
skin lumps and
bumps, leonine Classification of
facies, saddle nose, leprosy: Leprosy has
peripheral 2 classification
neuropathy, digit schemas: the 5-
absorption, blindness category Ridley-
and infertility in men Jopling system and
(from testicular the simpler and more
damage) commonly used WHO
standard.
B. Tubercoloid
leprosy (TL): Ridley-Jopling:
Depending on the
host response to the
1. Intact-cell
mediated immunity organism, leprosy

can manifest
2. Difficult to isolate clinically along a
M. leprae from skin or spectrum bounded by
blood the tuberculoid and
lepromatous forms of
the disease. Most
patients fall into the
intermediate
classifications, which
include borderline
3. Skin and nerves tuberculoid leprosy,
involved: 1 or 2 midborderline
superficial unilateral leprosy, and
lesions borderline
lepromatous leprosy.
Damage in the The classification of
following nerves is the disease typically
associated with changes as it evolves
characteristic during its
impairments in progression or
leprosy: management. The
Ridley-Jopling system
Ulnar and median - is used globally and
Clawed hand forms the basis of
clinical studies of
leprosy. It may also
Posterior tibial -
be more useful in
Plantar insensitivity
guiding treatment
and clawed toes
regimens and
assessing risk of
Common peroneal - acute complications.
Foot drop Physical findings in
each subtype are
Radial cutaneous, presented in the
facial, and greater Clinical section.
auricular nerves
(may also be WHO system: The
involved) WHO recommends
classifying leprosy
according to the
number of lesions
and the presence of
bacilli on a skin
smear. This method
is useful in countries
where biopsy
analysis in
unavailable.
Paucibacillary
leprosy is
characterized by 5 or
fewer lesions with
absence of organisms
on smear.
Paucibacillary
leprosy generally
includes the
tuberculoid and
borderline
lepromatous
categories from the
Ridley-Jopling
system.
Multibacillary
leprosy is marked by
6 or more lesions
with possible
visualization of bacilli
on smear.
Lepromatous leprosy,
borderline
lepromatous leprosy,
and midborderline
leprosy on the
Ridley-Jopling scale
are included in the
multibacillary
leprosy category.
Mycoplasma No cell wall Requires STEROL for Protein P1 adhsesin: Recently, M Tracheobronchitis Macrolides Cold agglutinins Chest X-ray will show
pneumoniae membrane formation adheres to epithelial pneumoniae has been (azithromycin, patchy infiltrates that
Pleomorphic: can bacteria do not cells of the shown to produce an Walking pneumonia clarithromycin) Complement fixation look worse than
The smallest free- appear round to normally contain respiratory tract; exotoxin that is also (also called atypical test physical examples
living organisms. oblong shaped sterols mediates attachment, believed to play a pneumonia): fever Tetracyclines and clinical
followed by induction major role in the with a dry, non- (doxycycline) symptoms suggest
Culture: takes 2-3
Aerobic (the other of ciliostasis, local damage to the productive hacking
Although scientists Smallest bacteria weeks (Eaton’s
mycoplasmas are inflammation that respiratory cough Disease usually
have isolated at least capable of growth & Quinolones agent)
17 species of reproduction outside facultative consists primarily of epithelium that (ciprofloxacin, occurs in children,
anaerobes) perivascular and occurs during acute adolescents and
Mycoplasma from a living cell (smaller levofloxacin) Requires cholesterol
peribronchial infection. This toxin, young adults
humans, 4 types of that some viruses: 1- and nucleic acids
infiltration of named the
organisms are 2 microns) Penicillin and
mononuclear community-
responsible for most cephalosporins do CHILD 5-15 YEARS
leukocytes, and tissue acquired Add penicillin to
clinically significant Motile (glides) NOT work as OLD WITH
destruction that may respiratory disease inhibit growth of
infections that may mycoplasma does not PNEUMONIA?
be mediated by toxin (CARDS) is an contaminating
come to the attention have a cell wall THINK
liberation of ADP-ribosylating and bacteria
of practicing MYCOPLASMA!
hydrogen peroxide vacuolating cytotoxin
physicians. These
similar to pertussis Dome-shape colonies
species are Children with sickle
toxin. [Infect Immun. with “fried egg”
Mycoplasma cell disease and
2005 May.] appearance or
pneumoniae, functional asplenia
Mycoplasma hominis, “mulberry”
may be at greater risk
Mycoplasma Evidence from animal appearance (in the
for severe
genitalium, and models of M case of Mycoplasma
respiratory tract
Ureaplasma species. pneumoniae infection pneumoniae)
disease
have proven that
recombinant CARDS Rapid identification
toxin results in Test:
significant
pulmonary Sputum can be tested
inflammation, release with DNA probes
of proinflammatory (nucleic acid
cytokines, and airway hybridization). PCR
dysfunction. [PLoS sputum samples.
One. 2009.
4(10):e7562]
Actinomyces israelii Normal flora of the Gram-positive rod; Actinomycosis is a Penicillin G Examine tissue or Yellow “sulfur
mouth and GI tract filamentous subacute, chronic, pus from infection granules”:
bacterium cellulitic invasion of Surgery site, and look for microcolonies of
the soft tissues that “sulfur granules” Actinomyces and
Anaerobic bacteria causes the formation cellular debris
(ABC!) of external sinus Anaerobic culture All species of
tracts that discharge Actinomyces are
sulfur granules. This normal commensal
Grow as branching
chains or beaded process spreads inhabitants of the
unimpeded by oral and buccal
filaments
traditional anatomic cavities in humans
barriers after the and certain other
endogenous oral mammals. They
commensal cannot be classified
organisms invade the as symbiotic
tissues of the face organisms because
and neck. they do not have a
Actinomycosis may mutually beneficial
also spread to the relationship with
pulmonary and GI their host. They are
systems. not true parasites
because they usually
Eroding abscesses of do not cause harm to
the mouth, lung or the host; however,
gastrointestinal tract, they definitely
classified as: assume a parasitic
1. Cervicofacial role when they result
actinomycosis in an infection with
an inflammatory
2. Thoracic tissue response.
actinomycosis Does not appear to
be an opportunistic
infection because
3. Abdominal
actinomycosis is not
actinomycosis
common in patients
who are
immunosuppressed
or in patients with
AIDS
Nocardia asteroides Never part of the Gram-positive rods Pneumonia Thrimethoprim/sulfa Gram-stain Nocardia infection
normal flora methozole usually occurs in
Partially acid-fast: Formation of Modified acid-fast immunocompromis
Respiratory due to mycolic acids abscesses in the lung, SNAP= stain: Decolorized ed patients
transmission in the cell wall kidney, and central Sulfa Nocardia with 1%sulfuric acid
nervous system Actinomyces instead of acid
Penicillin alcohol. Nocardia are
Members of the Aerobic
genus Nocardia are typically weakly acid-
aerobic fast after traditional
Grow as branching
actinomycetes that chains or beaded staining and positive
are ubiquitous on modified acid-fast
filaments
saprophytes in soil, staining, but this is
decaying organic not invariable.
matter, and fresh and
salt water. Aerobic culture
MEDICAL VIROLOGY
HEPATITIDES
VIRUS TAXONOMY/MORPHOLOGY TRANSMISION CLINICAL TREATMENT SEROLOGY
Hepatitis A Picornaviridae Fecal-oral Acute viral hepatitis Pooled immune serum Anti-HAV IgM - Active disease
fever, jaundice and a globulin
painful enlarged liver Anti-HAV IgG – old: No active disease against repeated infection
Positive (+) single-stranded Supportive care
RNA
HAV vaccine
No envelope (naked)
Icosahedal capsid
Hepatitis B Hepadnaviridae Blood transfusion Acute viral hepatitis Prevention: Hepatitis B HBsAg – Disease (acute or chronic)
recombinant vaccine
Needlestick injury Fulminant haepatitis: Anti-HbsAg – immunity provides protection against repeated infection
Double-stranded circular DNA severe acute hepatitis Screen blood to remove
and rapid destruction of HBV contaminated IgM anti-HBcAg – New infection
Sexual
Enveloped liver blood to the donor pool
HBeAg – high infectivity
Across the placenta
Icosahedal capsid Treatment options:
Anti- HBeAg – Low infectivity
interferons (alfa and
Perinatally
Chronic hepatitis (10%) pegylated-interfron
Dane particle (intact virus) Hepatitis B antigen (HBeAg): soluble component of the core, which
alfa) or nucleoside
includes: envelope, capsid- is marker for active disease
analogs (Iamivudine,
associated proteins, capsid, A. Asymptomatic carrier
adefovir, entecavir and
core (DNA+protein enzymes), INTERPRETING HBV SEROLOGY
telbivudine
hepatis B surface antigen B. Chonic persistent
(HBsAg), envelope, capsid- hepatitis
associated proteins, heptitis Lamivudine –
B core antigen (HBcAg) antiretroviral drug; also
C. Chronic active used in HIV; a reverse
hepatitis transcriptase inhibitor
Double-stranded DNA
because HBV also
Coinfection or expresses reverse
DNA polymerase enzyme superinfection with transcriptase
hepatitis Delta virus
Capsid (HDV)
Complications: primary
hepatocellular carcinoma,
cirrhosis
VIRUS TAXONOMY/MORPHOLOGY TRANSMISION CLINICAL TREATMENT SEROLOGY
Hepatitis C Flavivirus Blood transfusion Acute viral hepatitis Treatment: combination Screening anti-HCV antibodies
therapy with interferon
Single-stranded RNA Needlestick injury Up to 85% develop and ribavirin
chronic hepatitis
Enveloped icosachedral capsid Sexually
20% will develop
cirrhosis
Across the placenta
Increased risk of
developing primary
hepatocellular carcinoma
(especially with
alcoholism)
Hepatitis D Incomplete RNA virus-only Blood transfusion Coinfection: HBV and Control of HBV infection Serology is not very helpful, since detectable titers of IgM and IgG anti-
infective with the help of HDV are acquired at the is currently the only HDV are present only fleetingly
Complementation with hepatitis B virus Needlestick injury same time, and caused an way to protect against
HBV acute hepatitis. HDV
Helical nucleocapsid that Sexual
requires the hepatitis B Anti-HBV antibodies help
envelope (HBsAg) to be cure infections
Across the placenta
infectious
Superinfection: HDV
infects a patient with
chronic hepatitis B who
can not manufacture
Anti-HBsAg antibodies
Complications:
A. Fulminany hepatitis
B. Cirrhosis
Hepatitis E Hepeviridae Fecal-oral Hepatitis (like hepatitis

A)
Single-stranded RNA
High mortality in
pregnant women
No envelope (naked)
DNA VIRUSES
VIRUS MORPHOLOGY VIRULENCE FACTORS CLINICAL SYNDROMES TREATMENT & PREVENTION DIAGNOSIS
Herpesviridae: Double-stranded DNA Direct contact of mucous Gingivostomatitis Acyclovir Tzanck smear reveals
membranes multinucleated giant cells with
HSV 1 and 2 Enveloped Reactivation of Gingivostomatitis Valacyclovir intranuclear inclusions
Viral shedding usually occurs in occurs immunocompromised
Icosahedral symmetry the presence of obvious individuals Famciclovir Viral culture
herpetic lesions, but viral
shedding can also occur when Herpetic keratitis Polymerase chain reaction
Trifluridine eye drops: for corneal
there no visible lesions
infection
Serology
Sexually transmitted
TEMPORAL lobe encephalitis: Direct Fluorescent Antibodies

HSV travels up sensory nerve infection (most cases are (DFA) Ulcer base scrapings can be
fibers to the sensory nerve reactivation of latent HSV-1) of the tested with antibodies will latch
ganglia, where it replicates then brain results in cell death and onto HSV if present, & will
returns along the sensory nerve brain tissue swelling , manifested
fibers to produce skin lesions as fever, headache and neurologic fluoresce

(NEUROTROPISM, LATENCY) abnormalities
Genital herpes: painful group

local vesicles on the cervix, or on
the external genitalia of men and
women. Often associated with
fever and viral symptoms. These
vesicles usually do not scar.
Reactivation of genital herpes

similar eruption of vesicles, but
less painful and vesicles last for
few more days
Neonatal herpes: acquired

during the passage of a fetus
through an infected birth canal.
The risk of transmission is highest
when a primary genital infection
is present during delivery (One of
the TORCHES Organism)
Herpetic whitlow
Disseminated herpes infection of

organs
Aerosolized respiratory secretions
Contact with ruptured vesicles

Varicella-Zoster Virus Acyclovir Vesicles are described as few
Zoster: reactivation of VZV from drops on the top of a rose petal: a
dorsal root ganglion Valacyclovir red base with fluid filled vesicle on
Varicella (chicken pox) top
Risk factors for severe varicella in Famciclovir
neonates are as follows: 2 week incubation period
Varicella vaccine
The first month of life: A neonate’s Fever and headache Lesions appear in all stages of
first month of life is a susceptible development (erupting papules,
Zoster immune globulin
period for severe varicella, Rashes: vesicles first erupts on active vesicles, crusting lesions) at
especially if the mother is the trunk and face, and spread to a single time differentiates
seronegative. involve the entire body (including varicella from other pediatric
mucous membranes). Vesicles rashes
Early delivery: Delivery before 28 erupt in crops, so one crop forms
weeks’ gestation also renders a as another crop scabs over. Tzanck smear reveals
baby susceptible because Patients are infectious until all
transplacental transfer of their lesions scab over. multinucleated giant cells

immunoglobulin G (IgG)
antibodies occurs after this time Pneumonia or encephalitis can
occur in immunocompromised
patients
Zoster (shingles): painful

eruption of vesicles isolated to a
single dermatome distribution.
The vesicles dry up and form
crusts, which disappear in about 3
weeks. Pain in the dermatomal
distribution can last for months in
the elderly.
Herpes zoster ophthalmicus:

vesicles on one side of the
forehead and on tip of the nose
(the dermatomal distribution of
the first division of cranial nerve
V) may be associated with severe
corneal involvement that (similar
to HSV) can lead to blindness
Although most varicella infection

confers life-long immunity,
varicella clinical reinfections
among healthy children have been
described [Pediatrics. 2002 Jun.
109(6):1068-73.]
Cytomegalovirus (CMV) Double-stranded linear DNA Virus present in milk, saliva, urine Asymptomatic infection (latent Ganciclovir CMV shell viral culture: Blood
& tears phase) buffy coat (WBC) is cultured
Enveloped Foscarnet overnight. The cells are then
Transmission occurs with Congenital disease (TORCHES) centrifuged. This breaks up the
prolonged exposure, such as white blood cells, releasing CMV
Icoshedral symmetry Cidofovir
between children in households or antigens, which are detected with
CMV mononucleosis (heterophil-
day care center monoclonal antibodies
negative) Formivirsen
Sexual transmission Reactivation in MV has been detected via culture

Healthy people who are infected (human fibroblast), serologies,
immunocompromised patients with CMV but who have no antigen assays, polymerase chain
symptoms usually do not require reaction (PCR), and cytopathology.
A. Pneumonia medical treatment. In the transplant population,
antigen assays or PCR is used
B. Retinitis (MCC of blindness in Antiviral treatment is used for (sometimes in conjunction with
HIV) immunocompromised individuals cytopathology) for diagnosis and
who have eye infections or life- treatment determinations.
C. Esophagitis threatening illnesses due to CMV.
Histology: reveals enlarged
D. Disseminated disease DOC for prevention of CMV (Cytomegalic) cells with
disease in solid-organ transplant intranuclear and cytoplasmic
patients is valganciclovir [Lancet. inclusion bodies. The pathologic
2005 Jun 18-24. 365(9477):2105- hallmark of CMV infection is an
15] enlarged cell with viral
inclusion bodies. CMV early
Currently, no vaccine available antigens can be detected in WBCs.
These antigens are an early
marker for infection in bone
marrow transplant patients
PCR testing for CMV DNA
Epstein-Barr virus (EBV) Double-stranded linear DNA Intimate contact from Infectious mononucleosis: fever, Supportive Elevated heterophileantibodies
asymptomatic shedders of EBV sore throat, severe lethargy,
Enveloped enlarged lymph nodes and spleen Differential white blood cells
Infects human B-cells (generalized) count will show elevated “atypical
Icoshedral symmetry transforms them (Receptor: CD lymphocytes” Downey cells
21) Infectious mononucleosis was first
described by Sprunt and Evans in Serology: IgM against the viral
Immune response to EBV infection the Bulletin of the Johns Hopkins capsids antigens (VCA)
is fever occurs because of Hospital in 1920.
cytokine release consequent to B-
lymphocyte invasion by EBV. Associated with Burkitt’s B-cell
Lymphocytosis observed in the lymphoma (MCC lymphoma in
RES is caused by a proliferation of children)
EBV-infected B lymphocytes.
Pharyngitis observed in EBV

infectious mononucleosis is
caused by the proliferation of
EBV-infected B lymphocytes in the
lymphatic tissue of the
oropharynx.
Human Herpesvirus 6 Double-stranded linear DNA Transmitted by saliva Roseola (exanthum subitum): Supportive Clinical diagnosis
(HHV-6) Enveloped
High fever lasting 3-5 days, which
Icoshedral resolves, and is followed by a …
Rash: located mostly on trunk,

which lasts just a day or two
HHV-8 Double-stranded linear DNA Sexual transmission, especially Appears to be the cause of HAART is an integral part of CD4 lymphocyte counts and
with MSM practice Kaposi’s sarcoma successful Kaposi sarcoma plasma HIV viral-load studies
Enveloped therapy. HAART may be tried as should be performed for patients
Kaposi’s sarcoma - a spindle-cell the sole modality in nonvisceral with HIV infection.
tumor thought to be derived from disease. For visceral disease,
Icoshedral
endothelial cell lineage; carries a chemotherapy may be added.
variable clinical course ranging
from minimal mucocutaneous The following local therapies can
disease to extensive organ be used for palliation of locally
involvement. advanced symptomatic disease or
in individuals who have
Categorized into 4 types: cosmetically unacceptable lesions:
• Epidemic of AIDS- • Radiation therapy

related
• Cryotherapy
• Immunocompromised
• Laser therapy
• Classic, or sporadic
• Surgical excision
• Endemic (African)
• Intralesional vinca
AIDS-related Kaposi sarcoma, alkaloid therapy
unlike other forms of the disease,
tends to have an aggressive • Topical retinoids
clinical course. It is the most
common presentation of Kaposi
Immunomodulation with
sarcoma.
interferon-alfa has clinical activity
in Kaposi sarcoma that may be
mediated by its antiangiogenic,
antiviral, and immunomodulatory
properties.
Poxviridae Complex coat: large, brick-shaped Smallpox is a high-priority Smallpox: causes skin lesions and Vaccine: an avirulent pox vaccine No animal reservoirs: Virologists
virus (making it cytoplasmic in (category A) agent for death. This disease has been was developed that included have speculated that it evolved
location) bioterrorism, defined as follows eradicated from the earth. immunity to virulent pox virus from an African rodent poxvirus
by the CDC: Histopathology: Guarnieri bodies 10 millennia ago. Because of the
Double-stranded linear DNA absence of an animal vector,
• Easily disseminated or Molluscum contagiosum: small communities had to reach a
transmitted from white bumps with a central critical population (estimated at
The only DNA virus to replicate
person to person dimple (like a wart). Often found 200,000 around 3000 B.C.) before
in cytoplasm
in the genital region. endemic smallpox could be
Histopathology: Henderson- established.
• High mortality rate
and potential for Peterson bodies
significant public Codes for DNA and RNA
health effect polymerase
• Probable instigator of
panic and social
disruption
Special actions required for public

health preparedness
Papovaviridae Naked icosahedral Human papilloma virus (HPV) Methods of wart removal Second smallest DNA virus
causes warts (over 50 viral
Double-stranded circular DNA strains) Liquid nitrogen (freeze them off) - HPV is oncogenic because of E6
best method and E7 genes that code for
A. Common warts (types 1, 2, 4 & suppressors of human tumor
Replicates in nucleus
7) suppressor genes.
Surgical
Condylomata lata – syphilis
B. Genital warts (types 6, 11, 16, Electrosurgery (laser ablation) Condylomata acuminate – genital
18 and others) – condylomata
warts, okay?
acuminata
Podophyllin: for genital warts
C. Laryngeal warts (6, 11) In genital intraepithelial

Many warts resolves
spontaneously in 1-2 years neoplasia, it is essential to
D. Penile, vulvar, cervical, anal determine the extent of disease
cancer (type 16, 18, 31, 33) Relapses are common after through careful inspection and
treatment, because HPV DNA is colposcopy.
About 50% of men who are found in normal appearing tissue
homosexual and have anal around the wart Laboratory studies that may be
squamous cell carcinoma have considered include the following:
anorectal warts
Cervical cytologic testing with the
BK Polyomavirus: causes kidney Papanicolaou (Pap) test to screen
disease in renal transplant for cervical neoplasia (guidelines
patients, hemorrhagic cystitis in for cervical cancer screening now
bone marrow transplant patients, include a delay in the initiation of
and mild respiratory illness in screening and longer intervals
children between subsequent screens
JC polyomavirus: Progressive HPV DNA testing (eg, with

multifocal leukoencephalopathy, Hybrid Capture II or polymerase

characterized by degenerative chain reaction [PCR] assay) for
central nervous system white detection of HPV and
matter disease posttreatment follow-up of
cervical intraepithelial neoplasia
The acetic acid test: This test can

be used in conjunction with
colposcopy to examine cervical
lesions; however, it is reserved for
suspicious lesions and should not
be used for routine screening
Adenoviridae Naked icosahedral Childhood upper respiratory tract Illness is self-limited Pharyngo-conjunctival fevel
infections
Double-stranded circular DNA
A. Rhinitis
B. Sore throat
C. Fever
D. Conjunctivitis
2. Epidemic keratoconjunctivitis
(pink eye)
3. Epidemic diarrheal illness in

infants and children
Parvoviridae Naked icosahedral Erythema infectiosum (fifth Illness is self-limited Smallest DNA virus
disease): affects children between
Parvovirus B-19 Double-stranded linear DNA the ages of 4 to 12 I.V. immunoglobulin can be used
virus (negative stranded) with aplastic crisis
Fever + “Slapped cheek” rash
Transient aplastic anemia
crisis: occurs when the
Parvovirus stops the production of
red blood cells in the boone
marrow
RNA VIRUSES
Orthomyxoviridae Negative (-) single-stranded RNA Hemagglutinin (HA) Influenza Vaccine contraindicated in egg Antigenic drift, small mutations,
glycoprotein: binds to red blood • Fever allergies (vaccine grown in eggs) resulting in minor changes in the
Influenza A: human and animal Segmented (7-8) genome cells. Also binds to cells of the antigenicity of HA or NA. This
strain upper respiratory tract. The HA is • Sore throat Prevention of influenza is the results in epidemics of the
then cleaved into pieces (HA1 & most effective management common flu
Lipid containing envelope
HA2) by host cell proteases, which strategy. Influenza A and B
Influenza B: human only strain • Myalgias
allows HA to activate fusion. The vaccine is administered each year Antigenic shift (occurs with
Helical symmetry viral RNA in then dumped into before flu season. The CDC Influenza A): genomic
Influenza C: human only strain these cells • Frontal or retro-
orbital headache analyzes the vaccine subtypes reassortment. Major changes of
Replicates in the nucleus each year and makes any the HA or NA (including
(Retroviruses are the only other Neuraminidase (NA) necessary changes on the basis of acquisition of animal HA or NA).
type of RNA viruses that replicate glycoprotein: breaks down • Nasal discharge worldwide trends. This results in devastating
in the nucleus) neuraminic acid, an important influenza pandemics
component of mucin • Weakness and severe Traditionally, the vaccine is
fatigue trivalent (ie, designed to provide New avian influenza H5N1 has
The hemagglutinin and protection against 3 viral infected hundreds of people and
neuraminidase variants are used • Cough and other subtypes, generally an A-H1, an A- represents a great risk of starting
to identify influenza A virus respiratory symptoms H3, and a B). The first a human pandemic.
subtypes. For example, influenza A quadrivalent vaccines, which also
subtype H3N2 expresses • Tachycardia provide coverage against a second Mortality is highest in infants and
hemagglutinin 3 and influenza B subtype, were the elderly. The 2012-2013 season
neuraminidase 2. The most Red, watery eyes approved in 2012 and were made was notable for widespread
common subtypes of human available for the 2013-2014 flu disease and a higher death rate
influenza virus identified to date Complications season. than was reported in previous
contain only hemagglutinins 1, 2, years. In addition, the
and 3 and neuraminidases 1 and 2. Amantadine and Rimantidine predominant influenza virus
H3N2 and H1N1 are the most (used in parkinsonism) prevent subtype was an H3N2, in contrast
Secondary bacterial pneumonias
common prevailing influenza A viral uncoating of influenza A to dominance by H1N1 subtypes
in the elderly
subtypes that infect humans. Each in recent past years.
year, the trivalent vaccine used
Reye’s syndrome in children who Zanamivir (inhaled) & Oseltamivir
worldwide contains influenza A
use aspirin, get liver and brain (oral) are neuraminidase Year 1918 - the Spanish flu
strains from H1N1 and H3N2,
disease inhibitors. Can shorten course of (though cases appeared earlier in
along with an influenza B strain.
influenza A and B the United States and elsewhere in
Europe), this pandemic killed an
Because the viral RNA Increased mortality in the elderly
estimated 20-50 million persons
polymerase lacks error- and in those underlying
[Emerg Infect Dis. 2006 Jan.
checking mechanisms, the year- pulmonary and cardiac disease
12(1):9-14.]
to-year antigenic drift is
sufficient to ensure that there is
a significant susceptible host
population each year. However,
the segmented genome also has
the potential to allow
reassortment of genome segments
from different strains of influenza
in a coinfected host.
Paramyxoviridae Negative (-) single stranded RNA HA, but no NA Measles - one of the most Treatment of measles is Although the diagnosis of measles
contagious infectious diseases, essentially supportive care, as is usually determined from the
Measles (Rubeola) Unsegmented F-protein (fusion protein) – with at least a 90% secondary follows: classic clinical picture, laboratory
leads to formations of infection rate in susceptible identification and confirmation of
multinucleated giant cells domestic contacts. Despite being -Maintenance of good hydration the diagnosis are necessary for
considered primarily a childhood and replacement of fluids lost public health and outbreak
illness, measles can affect people through diarrhea or emesis control. Laboratory confirmation
Helical symmetry of all ages. is achieved by means of the
-IV rehydration may be necessary following:
Replicates in cytoplasm Prodrome: high fever, hacking if dehydration is severe
cough and conjunctivitis • Serologic testing for
measles-specific IgM
-Vitamin A supplementation
Koplik’s spots: small red-based or IgG titers
should be considered
blue-white centered lesions in the
mouth • Isolation of the virus
Postexposure prophylaxis should
be considered in unvaccinated
Rash: from head, then to neck and contacts; timely tracing of Reverse-transcriptase polymerase
torso, then to feet. As the rash contacts should be a priority. chain reaction (RT-PCR)
spreads, it coaleces Patients should receive regular evaluation
follow-up care with a primary care
Complications: physician for surveillance of Biopsy of rash or Koplik’s spots
complications arising from the reveals multinucleated giant cells
Pneumonia, eye damage, infection.
Warthin-Finkeldey bodies
myocarditis and encephalitis
(multinucleated giant cells in
WHO recommends vitamin A
measles)
20% risk of fetal death if acquired supplementation for all
by a pregnant women early in her children diagnosed with
pregnancy measles, regardless of their
country of residence, based on
their age, as follows:
Subacute Sclerosing
Panencephalitis: slow form of
encephalitis that occurs many -Infants younger than 6 months:
years after a measles infection 50,000 IU/day PO for 2 doses
(Damson disease)
-Age 6-11 months: 100,000
IU/day PO for 2 doses
-Older than 1 year: 200,000

IU/day PO for 2 doses
Children with clinical signs of

vitamin A deficiency : The first 2
doses as appropriate for age, then
a third age-specific dose given 2-4
weeks later
Prevention: MMR vaccine:
Parainfluenza 1 and 2 Negative (-) single stranded RNA Glycoproteins with combined HA Upper respiratory tract infection Supportive: racemic epinephrine Isolation and identification of the
and NA activity in adults: bronchitis, pharyngitis, virus in cell culture or direct
Unsegmented rhinitis Antiviral agents are of uncertain detection of the virus in
F-protein (Fusion protein): benefit; antibiotics are used only if respiratory secretions by means of
results in multinucleated giant Viral pneumonia in children bacterial complications (eg, otitis immunofluorescent assay,
cells (called syncytial cells) elderly and immunocompromised and sinusitis) develop. enzyme-linked immunosorbent
assay (ELISA), or polymerase
Helical symmetry chain reaction (PCR) assay
Human PIVs are common Croup. Children develop a barking
community-acquired respiratory cough due to infection and
Replicates in cytoplasm Demonstration of a significant rise
pathogens without ethnic, swelling (narrowing) of the larynx
socioeconomic, gender, age, or steeple sign in specific immunoglobulin G
geographic boundaries. Many (IgG) antibodies between
factors have been found that appropriately collected paired
Human PIV-1 is most commonly
predispose individuals to these serum specimens or in specific
associated with croup.
infections, including the following: immunoglobulin M (IgM)
antibodies in a single serum
Human PIV-2 is also associated specimen
• Malnutrition with croup.
• Overcrowding Human PIV-3 is second only to

RSV as a cause of pneumonia and
• Vitamin A deficiency bronchiolitis in infants and young
children.
• Lack of breastfeeding
Human PIV-4 is detected in
• Environmental smoke patients less often, perhaps
or toxins because HPIV-4 causes less severe
disease.
Bronchiolitis in children
Respiratory syncytial virus (RSV) Negative (-) single stranded RNA F-protein Most common cause of pneumonia Palivizumab: a monoclonal Specific diagnostic tests for
in infants less 6 months of age antibody against RSV that is confirming RSV infection include
The leading cause of lower Unsegmented NO HA nor NA glycoproteins produced a recombinant DNA. It is the following:
respiratory tract infections Acute otitis media occurs in up to given intramuscularly.
(LRTIs) in infants and young Lipid containing envelope 33% of children with RSV illness -Culture, Antigen-revealing
children. The American Academy of techniques, PCR, Molecular probes
Pediatrics has released updated
Helical symmetry
guidelines addressing palivizumab
prophylaxis for RSV
Replicates in cytoplasm
According to the updated
recommendations, palivizumab
prophylaxis for RSV should be
limited to infants born before 29
weeks' gestation and to infants
with chronic illness such as
congenital heart disease or
chronic lung disease. Other
recommendations include the
following:
-Give infants who qualify for

prophylaxis in the first year of life
no more than five monthly doses
of palivizumab (15 mg/kg per
dose) during the RSV season
-In the second year of life,

palivizumab prophylaxis is
recommended only for children
who needed supplemental oxygen
for 28 days or more after birth
and who continue to need medical
intervention (supplemental
oxygen, chronic corticosteroid, or
diuretic therapy).
-Clinicians may consider

prophylaxis for children younger
than 24 months if they will be
profoundly immunocompromised
during the RSV
Ribavirin - primarily reserved for

patients with significant
underlying risk factors and severe
acute RSV disease (eg, transplant
recipients)
Mumps (Rubulavirus) Negative (-) single stranded RNA Glycoproteins with combined HA Mumps - acute, self-limited, Conservative, supportive medical Mumps is a clinical diagnosis.
systemic viral illness care is indicated for patients with
Unsegmented and NA activity characterized by the swelling of mumps. No antiviral agent is Only one antigenic type.
one or more of the salivary glands, indicated for viral illness, as Therefore, the vaccine is
Lipid containing envelope F-protein typically the parotid glands. The mumps is a self-limited disease. protective.
illness is caused by the RNA virus,
Rubulavirus Current evidence suggests that
Helical symmetry
patients diagnosed with mumps
Parotid gland swelling (painful) should be isolated for 5 days from
Replicates in cytoplasm the onset of symptoms.
Testicular inflammation (very
Prevention: MMR vaccine :
painful)
MeningitisEncephalitis
Togaviridae Enveloped virus with an The virus attaches to and invades Rubella: ( Geman mesles/3 day Prevention: MMR vaccine A clinical diagnosis of rubella may
icosahedral nucleocapsid and one the respiratory epithelium. It then measles) be difficult to make because many
Rubella ss-positive-RNA spreads hematogenously (primary exanthematic diseases may mimic
viremia) to regional and distant rubella infection. In addition, as
lymphatics and replicates in the Fever, lymphadenopathy and mild many as 50% of rubella infections
Derived from a Latin term
reticuloendothelial system. This is flu-like symptoms may be subclinical; therefore,
meaning "little red."
followed by a secondary viremia laboratory studies are important
that occurs 6-20 days after to confirm the diagnosis of acute
Rash: from forehead to face to
infection. rubella infection.The laboratory
torso to extremities (lasts 3 days)
diagnosis of rubella can be made
either though serologic testing or
The major complication of rubella by viral culture. The serologic
is its teratogenic effects when diagnosis consists of
pregnant women contract the demonstrating the presence of
disease, especially in the early rubella-specific immunoglobulin
weeks of gestation. M (IgM) antibody in a single
serum sample or observation of a
Congenital defects: occurs when a significant (>4-fold) rise in
women in her first trimester of rubella-specific immunoglobulin G
pregnancy gets exposed. The fetus (IgG) antibody titer between the
may develop defects of the heart, acute and convalescent serum
eyes, or central nervous system specimens drawn 2-3 weeks apart.
False-positive rubella IgM test
results have been reported in
persons with other viral infections
(eg, acute EBV, CMV, parvovirus
B19 infection) and in the presence
of rheumatoid factor (RF).
Flaviviridae Positive (+) single-stranded RNA Yellow fever: hepatitis Prevention: mosquito control Viral culture
with(jaundice), Fever, Backache
Yellow fever virus Nonsegmented RNA Vaccination required when Serology
Dengue fever: “Break bone fever” travelling to and from endemic
countries
Dengue virus Icosahedral symmetry With repeat infections, individuals
“Painful fever”: High fever along are at higher risk of developing
with the hemorrhagic form of dengue
St. Louis encephalitis Replicates the cytoplasm 1. Headaches fever
Japanese B encephalitis Enveloped 2. Muscle aches West Nile: Serology is much more
sensitive that PCR, although
Hepatitis C virus Vector = mosquito 3. Joint aches because of cross-reactions with
other flaviviruses, it is less specific
West Nile Virus Aedes: yellow fever and 4. backache
dengue fever
Dengue hemorrhagic fever:
Culex: St. Louis, Japanese, hemorrhage, thrombocytopenia
and West Nile and septic shock
encephalitis
St. Louis, Japanese, West Nile
encephalitis: encephalitis and
fever
Hepatitis C virus – see Hepatitides
West Nile: fever and encephalitis

or myelitis that produces flaccid
paralysis
Picornaviridae Positive (+) single-stranded RNA Inapparent, asymptomatic Vaccine: Transmission: Fecal-oral
infection
Poliovirus Naked icosahedral symmetry The chance of developing
Abortive poliomyelitis – most Salk vaccine formalinkilied polio paralytic poliomyelitis increase as
Replication occurs in the common clinical form; mild, virus that is injected one gets older.
cytoplasm febrile illness with headache, sore subcutaneously
throat, nausea, and vomiting. Since the World Health Assembly
Oral polio vaccine (developed by in May 1988 resolved to eradicate
Nonparalytic poliomyelitis – Sabin): Attenuated (non-virulent) poliomyelitis, the estimated global

aseptic meningitis polio virus is ingested incidence of polio has decreased
by more than 99%, and 3 World
Paralytic poliomyelitis – virus Health Organization (WHO)
destroys the anterior horn cells in regions (the Americas, the
the spinal cord flaccid Western Pacific, and Europe) have
paralysis; permanent motor nerve been certified as polio-free.
damage
Coxsackie A
“Cold” rashes, viral meningitis
Herpangina: Fever, sore throat

and small red- based vesicle over
the back of the patient’s throat
Hand Foot and Mouth Disease:

Occurs in children less than 5,
Vesicles erupt on hands, foot and
mouth, which are highly
contagious
Viral meningitis
Coxsackie B Myocarditis/pericarditis:
arrhythmia, cardiomyopathy,
heart failure
Pleurodynia: fever and sharp

pleuritic chest pain
“Cold”, rashes, viral meningitis

ECHOviruses (Enteric, Cytopathic,
Human Orphan) Pericarditis
Common colds
Rhinovirus
Replicates better at 33°C than at
37°C they affect primarily the
113 serotypes
nose and conjunctiva rather than
the lower respiratory tract.
Acid-labile killed by gastric acid

when swallowed à they do not
infect the gastrointestinal tract,
unlike the enteroviruses.
Host range is limited to humans

and chimpanzees
Caliciviridae Positive (+) single stranded RNA Noroviruses are highly contagious, Viral gastroenteritis: (explosive, Supportive Immune electron microscopy:
with infection requiring fever than but self-limited): Immune serum is used to
Norwalk virus ; Naked icosahedral symmetry 10 virions (ID50 = 10 virions), Fever, Abdominal pain, Vomiting, aggregate virus in stool samples to
leading to disease in 50% of Diarrhea aid detection
inoculated individuals.
New name: NOROVIRUS Replication occurs in the
cytoplasm Antigen detection immunoassay:
The virus is extremely stable in the Has high sensitivity but low
The most common cause of
environment and resists freezing specificity because of reactivity
epidemic nonbacterial Fecal-oral transmission
temperatures, heat (up to 60°C), with antigenic variants and
gastroenteritis in the world
disinfection with chlorine, acidic homologous viruses
conditions, vinegar, alcohol,
antiseptic hand solutions, and high Nucleic acid amplification: Highly
sugar concentrations. sensitive and specific
The incubation period is Serum antibody titers can be

approximately 1-2 days, and detected within 2 weeks of illness.
symptoms typically last 1-3 days During norovirus infection,
(or longer in immunoglobulin M (IgM) to
immunocompromised norovirus has been found to be
individuals). Viral shedding occurs more specific than IgG.
for up to 3 weeks following
infection.
Reoviridae Double-stranded RNA Viral gastroenteritis: causes Intravenous fluids Rotavirus may be identified by the
profound dehydaration following means:
Rotavirus Segmented (11 segments) genome New oral rotavirus vaccine
Hyperactive bowel sounds: Most appears safe and effective in - Enzyme immunoassay (most
common finding infants common)
Naked icosahedral symmetry
Especially in infants. Fever,
Fecal-oral tranmission There are currently 2 FDA- - Latex agglutination
abdominal pain, vomiting and
approved rotavirus vaccines to
diarrhea
protect against rotavirus - Electron microscopy
gastroenteritis (ie, RotaTeq and
No blood, No pus in diarrhea Rotarix). These vaccines are - Culture

indicated in infants aged 6-32
A major cause of infant death in weeks (RotaTeq) and those aged
underdeveloped countries and the 6-24 weeks (Rotarix)
most common cause of diarrhea in
infants less than 3 years of age
Coronaviridae Positive (+) single-stranded RNA After establishment of infection, Upper respiratory tract infection Supportive According to guidelines from the
SARS-CoV causes tissue damage by (“common cold”) Centers for Disease Control and
Coronavirus Nonsegmented (1) direct lytic effects on host cells Prevention (CDC), the laboratory
and (2) indirect consequences Severe acute respiratory diagnosis of SARS-CoV infection is
resulting from the host immune syndrome (SARS) is a serious, established on the basis of
Helical symmetry
response. Autopsies demonstrated potentially life-threatening viral detection of any of the following
changes that were confined mostly infection caused by a previously with a validated test, with
Enveloped to pulmonary tissue, where diffuse confirmation in a reference
unrecognized virus from the
alveolar damage was the most Coronaviridae family, the SARS- laboratory:
Replication in prominent feature. associated coronavirus (SARS-
CoV) • Serum antibodies to
the cytoplasm The other mechanism was thought SARS-CoV in a single
to be the induction of apoptosis. The clinical course of SARS serum specimen
The SARS-CoV–3a and –7a generally follows a typical pattern.
proteins have been demonstrated • A 4-fold or greater
to be inducers of apoptosis in increase in SARS-CoV
Stage 1 is a flulike prodrome that
various cell lines antibody titer
begins 2-7 days after incubation,
lasts 3-7 days, and is between acute- and
characterized by the following: convalescent-phase
serum specimens
tested in parallel
-Fever (>100.4°F [38°C])
• Negative SARS-CoV
-Fatigue
antibody test result on
acute-phase serum
-Headaches and positive SARS-
CoV antibody test
-Chills result on
convalescent-phase
-Myalgias serum tested in
parallel
-Malaise
• Isolation in cell
-Anorexia culture of SARS-CoV
from a clinical
No vaccine currently exists for specimen, with
Middle East respiratory MERS, and no specific treatment confirmation using a
syndrome (MERS) is a has been recommended. test validated by the
respiratory disease caused by a Management is currently CDC
newly recognized coronavirus supportive.
(MERS-CoV). It was first reported
in 2012 in Saudi Arabia and is
thus far linked to countries in or
near the Arabian Peninsula • Detection of SARS-CoV
(United Arab Emirates [UAE], RNA via reverse

Qatar, Oman, Jordan, Kuwait, transcriptase
Yemen, and Lebanon). As of May polymerase chain
2014, two cases had been reaction (RT-PCR)
reported in the United States, both assay validated by the
in men who had recently returned CDC, with
from Saudi Arabia. [MMWR Morb confirmation in a
Mortal Wkly Rep. 2015 Jan 30. 64 reference laboratory,
(3):61-2] from (1) two clinical
specimens from
different sources or
(2) two clinical
specimens collected
from the same source
on 2 different days
The recommended algorithm for

detection of MERS-CoV includes
testing using rRT-PCR.
Serologic testing is available for

the evaluation of MERS-CoV
infection or exposure
Rhabdoviridae Bullet shaped Rabies is a highly neurotropic Incubation period: asymptomatic NO TREATMENT Diagnosis: Microscopic
virus that evades immune examination of the central
Rabies virus Negative (-) single-stranded RNA surveillance by its sequestration in Prodromal period: The virus Vaccination of animals nervous system reveals Negri
the nervous system. Upon enters the CNS. The duration of bodies. These are collections of
Nonsegmented inoculation, it enters the this period is 2-10 days. If bitten by possible rabid animal, virions in the cytoplasm where
peripheral nerves. A prolonged Nonspecific symptoms and signs replication occurs
there are three possibilities:
incubation follows, the length of develop. Paresthesia, pain, or
Helical nucleocapsid is coiled into which depends on the size of the intense itching at the inoculation Viral cultures and PCR
a bullet shape inoculum and its proximity to the Capture animal: observe for 10
site is pathognomonic for rabies
CNS. Amplification occurs until and occurs in 50% of cases during -Saliva - Results of saliva culture
Replication in the cytoplasm bare nucleocapsids spill into the this phase; this may be the days for rabies virus are positive in low
myoneural junction and enter individual’s only presenting sign. yield within 2 weeks of illness
Zoonotic (all warm blooded motor and sensory axons. At this Destroy animal: examine for Negri onset
animals): dogs, cats, skunks, point, prophylactic therapy Acute neurologic period: bodies
coyotes, foxes, raccoons, and bats becomes futile, and rabies can be associated with objective signs of -Cerebrospinal fluid - After the
are reservoirs in the U.S. expected to follow its fatal course, developing CNS disease. first week of illness, 80%
Treat immediately (if you can not
with a mortality rate of 100%. monocytosis is observed; protein
capture the animal, or the animal
Transmitted via an animal bite Furious rabies may develop is found to have a rabies): and glucose test results are
The rabies virus travels along during this period: patients normal
these axons at a rate of 12-24 develop agitation, hyperactivity, 1. Clean wound
mm/d to enter the spinal ganglion. restlessness, thrashing, biting, -Brain tissue - Often postmortem;
Its multiplication in the ganglion is confusion, or hallucinations. staining with
heralded by the onset of pain or 2. Passive immunization with
immunohistochemical or
paresthesia at the site of the rabies immune globulin
Paralytic rabies (dumb rabies or florescent antibody staining is
inoculum, which is the first clinical definitive. Negri bodies are
apathetic rabies) patient is
symptom and a hallmark finding. 3. Active immunization pathognomonic (cytoplasmic
relatively quiet compared with a
From here, the rabies virus inclusion bodies reflective of
person with the furious form
spreads quickly, at a rate of 200- With killed rabies virus vaccine accumulated virions within
400 mm/d, into the CNS, and rabies-infected neurons). They are
spread is marked by rapidly Comma
found in the horn of Ammon of the
progressive encephalitis. hippocampus and cerebral cortex
Thereafter, the virus spreads to
the periphery and salivary glands.
Retroviridae Enveloped virus with two copies PHASE 0 – INFECTION: HIV highly active antiretroviral Presumptive diagnosis
(diploid) of a single-stranded, acquired through sexual therapy (HAART): two nucleoside detection of antibodies by ELISA.
HIV positive-polarity RNA genome intercourse, blood, or perinatally inhibitors (zidovudine and There are some false-positive
lamivudine) and protease results with this test
Most complex of the known PHASE 1 - WINDOW PERIOD: inhibitor (indinavir)
retroviruses rapid viral replication but HIV test Definitive diagnosis Western
is negative blot analysis
Many serotypes
PHASE 2 – SEROCONVERSION: Grown in culture from clinical
peak of viral load, positive HIV specimens
test, mild flu-like illness, lasting 1-
2 weeks Polymerase chain reaction (PCR)
very sensitive and specific: To
PHASE 3 - LATENT PERIOD: detect HIV DNA within infected
asymptomatic, CD4 goes down, cells. Some individuals who do not
lasts 1-15 years have detectable antibodies have
been shown by this test to be
PHASE 4 - EARLY infected. Amount of viral RNA in
SYMPTOMATIC: CD4 500 to 200, the plasma (i.e., the viral load) can
Transmembrane protein, TM
lasts 5 years, mild mucocutaneous, also be determined using PCR-
(fusion protein, also called gp41),
dermatologic and hematologic based assays.
which is linked to a surface
protein, and SU (attachment illnesses
protein, gp120)
PHASE 5 – AIDS: CD4 <200, lasts
Cone-shaped, icosahedral core 2 years, AIDS-defining illnesses
containing the major capsid develop
protein (CA also called p24)
MA (p17)-- directs entry of the

double-stranded DNA provirus
into the nucleus, and is later
essential for the process of virus
assembly. There are two identical
copies of the positive sense, single-
stranded RNA genome in the
capsid (that is, unlike other
viruses, retroviruses are diploid).
The RNA is tightly complexed with

a basic protein, NC (p7), in a
nucleocapsid structure that differs
in morphology among the different
retrovirus genera.
MEDICAL MYCOLOGY
NAME RESERVOIR MORPHOLOGY CLINICAL SYNDROME TREATMENT DIAGNOSIS NOTES ANATOMIC LOCATION
Malassezia furfur Naturally found on the “Spaghetti and meat Tinea/Pityriasis Dandruff shampoo Potassium hydroxide SUPERFICIAL (SKIN)
skin surfaces of many balls” versicolor - a common, (containing selenium (KOH) prep: reveals
AN-AN animals, including benign, superficial sulfide) short, curved,
humans. Dimorphic, lipophilic cutaneous fungal unbranched hyphae with
fungi infection usually Topical imidazole spherical yeast cells (
AP-AP
Isolated in 18% of characterized by look like “spaghetti and
infants and 90-100% of hypopigmented or meatballs”)
adults. hyperpigmented
macules and patches on Malassezia is extremely
the chest and the back. difficult to propagate in
In patients with a laboratory culture and is
predisposition, tinea culturable only in media
versicolor may enriched with C12- to
chronically recur. The C14-sized fatty acids.
fungal infection is
localized to the stratum
corneum.
DERMATOPHYTES Depending on the Dermatophytosis Topical imidazole KOH: branched hyphae Secretes the enzyme CUTANEOUS
particular species keratinase, which
Microsporum Tinea corporis (body): Oral griseofuivin is used Wood’s lamp: ceratin digests keratin
“ringworm” for tinea unguium and species of Microsporum
Soil (geophilic) tinea capitis will fluoresce under For atypical
Trichopyton
ultraviolet light presentations of tinea
Tinea cruRis (groin):
corporis, further
Epidermophyton Animals (zoophilic) “jock itch” Oral terbinafine
evaluation for HIV
floccosum A fungal culture, which
infection and/or an
Human (anthropophilic) Tinea pedis (feet): is often used as an
immunocompromised
“athlete’s foot” adjunct to KOH for
state should be
diagnosis, is more
Infections due to considered.
zoophilic or geophilic Tinea capitis (scalp) specific than KOH for
detecting a
dermatophytes may
produce a more intense dermatophyte infection.
Tinea unguium (nail): Therefore, if the clinical
inflammatory response Onychomycosis suspicion is high yet the
than those caused by
KOH result is negative, a
anthropophilic microbes
fungal culture should be
obtained.
If the above clinical

evaluations are
inconclusive, a
polymerase chain
reaction (PCR) assay for
fungal deoxyribonucleic
acid (DNA) identification
can be used.
Sporothrix schenkii Found on rose thorns Suppurating Itraconazole Dimorphic Primary pulmonary SUBCUTANEOUS
subcutaneous nodules infection (pulmonary
that progress proximally Fluconazole Culture at 25oC will grow sporotrichosis) is rare,
along lymphatic branching hyphae as is direct inoculation
channels into tendons, bursae, or
Oral potassium iodide
(lymphocutaneous joints.
Culture at 37oC will grow
sporotrichosis)
yeast cells
Osteoarticular
sporotrichosis is caused
Definitive diagnosis of
by direct inoculation or
sporotrichosis at any site
hematogenous seeding.
requires the isolation of
S schenckii in a specimen
culture from a normally In rare cases,
sterile body site. disseminated S schenckii
infection (disseminated
sporotrichosis) occurs,
The organism can be
characterized by
recovered with fungal
disseminated cutaneous
culture from sputum,
lesions and involvement
pus, subcutaneous tissue
of multiple visceral
biopsy, synovial fluid,
synovial biopsy, bone organs; this occurs most

drainage or biopsy, and commonly in persons
cerebrospinal fluid with AIDS.
(CSF).
Coccidioides immitis Desert areas of the Dimorphic: Coccidiodomycosis Amphotericin B Biopsy of affected tissue: Common oppurtunisitc SYSTEMIC
southwestern United lung biopsy, skin biopsy, infection in AIDS
States and northern Mycelial forms with Asymtomatic (in most Itraconazole etc. patients from the
Mexico spores at 25oC persons) southwest United States
Fluconazole Silver stain or KOH prep
Respiratory Yeast forms at 37oC Pneumonia SPHERULES WITH
transmission Culture on Sabouraud’s ENDOSPORES
Disseminated: can affect agar
the lungs, skin , bones
and meninges Serology
Skin test
Histoplasma capsulatum Mississippi valley Dimorphic: Histoplasmosis Itraconazole Lung biopsy Can survive SYSTEMIC
intracellularly within
Present in bird and bat Mycelial forms with Asymptomatic (in most Amphotericin B (in Silver stain specimen macrophages
droppings spores at 25oC persons) immunocompromised
patients YEASTS WITHIN
Culture on Sabouraud’s
MACROPHAGES
Respiratory Yeast forms at 37oC Pneumonia: lessions agar will reveal hyphae
transmission calcify, which can be at 25oC and yeast at 37oC
seen on chest X-ray (may
look similar to PTB) Serology
Disseminated: can occur Skin test (test for

in almost any organ, exposure only)
especially in lung,
spleen, or liver
Urine antigen test
Blastomyces dermatitidis Dimorphic: Blastomycosis Itraconazole Biopsy of affected tissue: BROAD-BASED BUD SYSTEMIC
Asymptomatic lung biopsy, skin biopsy,
Mycelial forms with (uncommon) Ketoconazole etc.
spores at 25oC Pneumonia: lesion rarely Amphotericin B Silver stain specimen

calcifies
Yeast forms at 37oC Culture on Sabouraud’s
Disseminated (MC): agar
weight loss, night
sweats, lung Serology
involvement, skin ulcers
Cutaneous: skin ulcer

Skin test (test for
Blastomycosis is usually exposure only)
localized to the lungs
and may present with:
Sputum specimens
processed with 10%
A self-limited flulike potassium hydroxide,
illness with fever, chills, cytology smears, or a
myalgia, headache, and a fungal stain
nonproductive cough
Enzyme immunoassay
An acute illness (EIA) techniques on
resembling bacterial sputum, tissue, or
pneumonia, with high bronchoscopic
fever, chills, a productive specimens
cough, and pleuritic
chest pain;
mucopurulent or
purulent sputum
Chronic illness, with

low-grade fever, a
productive cough,
fatigue, night sweats,
and weight loss
Rapidly progressive, and

severe disease, eg,
multilobar pneumonia
or ARDS, with fever,
shortness of breath,
tachypnea, hypoxemia,
and finally
hemodynamic collapse
Cryptococcus neoformans Pigeon droppings Polysaccharide capsule Cryptococcus Amphotericin B and India-ink stain of Most cases occur in SYSTEMIC
flucytosine (is superior cerebrospinal fluid immunocompromised
Yeast form only (Not Subacute or chronic to amphotericin B alone) (CSF): observe person
dimorphic) meningitis encapsulated yeast
MCC of
Cryptococcal antigen meningoencephalitis in
Pneumonia: usually self-
limited and test of CSF: detects HIV

asymptomatic polysaccharide antigens
YEAST WITH A HALO
Skin lesions: look like Fungal culture
acne
Candida albicans Normal flora of the skin, Pseudohyphae and yeast Candidiasis in a The choice of antifungal KOH stain of specimen YEAST WITH CUTANEOUS or
mouth and normal host agent depends on the PSEUDOHYPHAE SYSTEMIC (normal host,
gastrointrointestinal area involved and its Silver stain of specimen or opportunistic)
tract Oral thrush severity.
Blood culture: growth
Vulvovaginal candidiasis must be respected
Cutaneous Blood assay for beta-D-

glucan
Diaper rash
Rash in the skin folds of

obese individuals
Candidiasis in an
immunocompromised
host
Thrush, vaginitis and/or

cutaneous, plus:
Esophageal
Disseminated
candidiasis: acquired by
very sick hospitalized
patients, resulting in
multi-organ system
failure
Chronic mucocutaneous
candidiasis
Aspergillius fumigatus Ubiquitous Branching septated Aspergillosis Allergic Allergic Rarely found in OPPORTUNISTIC
hyphae (acute angles, bronchopulmonary brochopulmonary individuals who are
Aspergillius flavus Aspergillus may cause a 45O) Allergic aspergillosis treat aspergillosis: immunocompetent
broad spectrum of bronchopulmonary with corticosteroids
disease in the human aspergillosis (IgE High level of IgE (IgE The FDA has approved
Aspergillius niger
host, ranging from mediated): asthma type Aspergilloma: removal level > 1000 IU/dL) an intravenous
hypersensitivity asthma type reaction via thoracic surgery formulation of the
reactions to direct with shortness of breath Sputum culture triazole antifungal
angioinvasion. and high fever posaconazole (Noxafil),
Invasive aspergillosis:
Aspergillus primarily which is indicated for
treat with voriconazole, Wheezing patient and
affects the lungs, causing the prophylaxis of
Asperigilloma (Fungus possibly caspofungin. chest X-ray with fleeting
the following four main invasive Aspergillus and
ball): associated with (very high mortality) infiltrates
syndromes: Candida infections in
hemoptysis (blood
severely
cough)
Increased level of immunocompromised
-Allergic
eosinophils adults who are at high
bronchopulmonary Invasive aspergillosis: risk of developing these
aspergillosis (ABPA) necrotizing pneumonia.
Skin test: immediate infections.
May disseminate to
hypersensitivity reaction
-Chronic necrotizing other organs in immune- Aflatoxins contaminate
Aspergillus pneumonia compromised patients peanuts, grains, and rice
(or chronic necrotizing Aspergilloma: diagnose
pulmonary aspergillosis with chest X-ray or CT
[CNPA]) scan
-Aspergilloma Invasive aspergillosis:

sputum examination and
-Invasive aspergillosis Aflatoxin consumption culture
(produced by Aspergillus
flavus ) can cause liver
damage and live cancer
Rhizopus Saprophytic molds Broad, non-septated, Mucormycosis Amphotericin B and Biopsy The disease is rapidly OPPORTUNISTIC
branching hyphae (right surgery fatal
Rhizomucor angles, 90o) Rhinocerebral Black nasal discharge
(associated with
Mucor diabetes): starts on nasal
mucosa and invades the
sinus and orbit
Pulmonary
mucormycosis
Pneumocystis jirovecii Unicellular fungi found The organism is found in PJP – Pneumocystis TMP-SMX A lactic dehydrogenase The taxonomic
in the respiratory tracts 3 distinct morphologic jirovecii pneumonia (LDH) study is classification of the
of many mammals and stages, as follows: occurs when both performed as part of the Pneumocystis genus was
humans cellular immunity and initial workup.LDH debated for some time. It
humoral immunity are levels are usually was initially mistaken
The trophozoite (trophic defective. elevated (>220 U/L) in for a trypanosome and
form), in which it often patients with P jiroveci then later for a
exists in clusters Once inhaled, the trophic pneumonia (PJP). They protozoan. In the 1980s,
form of Pneumocystis are elevated in 90% of biochemical analysis of
The sporozoite organisms attach to the patients with PJP who the nucleic acid
alveoli. Multiple host are infected with HIV. composition of
(precystic form)
immune defects allow The study has a high Pneumocystis rRNA and
for uncontrolled sensitivity (78%-100%); mitochondrial DNA
The cyst, which contains replication of its specificity is much identified the organism
several intracystic Pneumocystis organisms lower because other as a unicellular fungus
bodies (spores) and development of disease processes can rather than a protozoan.
illness. Activated result in an elevated Subsequent genomic
alveolar macrophages LDH level. [Clin Invest sequence analysis of
without CD4+ cells are Med. 1992 Aug. multiple genes including
unable to eradicate 15(4):309-17.] elongation factor 3, a
Pneumocystis organisms. component of fungi
Increased alveolar- Quantitative PCR for protein synthesis not
capillary permeability is pneumocystis may found in protozoa,
visible on electron become useful in further supported this

microscopy. distinguishing between notion.
colonization and active
infection, but these
assays are not yet
available for routine
clinical use.
SOURCExS:
• Jawetz Melnick and Adelbergs Medical Microbiology 26e, by Brooks, Carroll, Butel, and Morse
• Medical Microbiology 8e, by Murray, Rosenthal, and Pfaller
• Textbook of Diagnostic Microbiology 2e, by Lehman, Mahon, and Manuselis
• Bailey & Scott's Diagnostic Microbiology 13e, by Tille

“Always trust a microbiologist because they have
• USMLE Step 1 First Aid the best chance of predicting when the world will
end.”
• Various evidence-based literature (journal references as cited in the text)
― Teddie O. Rahube
• Major internet sources: www.medscape.com and www.cdc.gov

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Streptococcus Vagina Transvaginally UTI in pregnant Gram-positive Most common

Grows using Lim

Bile and optochin-

Clean the wound

LOS triggers the WATERHOUSE-

The degree of thrombocytopenia,

Joint pain, for Hib who have

GRAM-NEGATIVE BACILLI: GASTROINTESTINAL AND GENITOURINARY INFECTIONS

EIEC: with pus in

the stool and fever

Especially in sickle SMX, organism

GRAM-NEGATIVE BACILLI: ZOONOTIC INFECTIONS

lipopolysaccharide Middle Ages,

MICROORGANISM RESERVOIR TRANSMISSION METABOLISM VIRULENCE CLINICAL TREATMENT DIAGNOSIS NOTES

Sterility, ectopic Certain variants in

Reiter’s syndrome: Having been a foster

Syndrome: conjugated anti-

Serotypes L1, L2 & L3 Serologic: Examine

Frei test, which is

4. Rash on wrists, Well-Felix reaction

Orientia Rats Mite larvae Scrub typhus: Doxycycline Well-Felix reaction:

Birds Followed by a rash

PCR The primary target

Pinta, caused by T Cardiovascular

C. Late stage (stage

mediated immunity organism, leprosy

VIRUS TAXONOMY/MORPHOLOGY TRANSMISION CLINICAL TREATMENT SEROLOGY

VIRUS TAXONOMY/MORPHOLOGY TRANSMISION CLINICAL TREATMENT SEROLOGY

Hepatitis E Hepeviridae Fecal-oral Hepatitis (like hepatitis

TEMPORAL lobe encephalitis: Direct Fluorescent Antibodies

fibers to produce skin lesions as fever, headache and neurologic fluoresce

Genital herpes: painful group

Reactivation of genital herpes

Neonatal herpes: acquired

Disseminated herpes infection of

Aerosolized respiratory secretions

Contact with ruptured vesicles

transplacental transfer of their lesions scab over. multinucleated giant cells

Zoster (shingles): painful

Herpes zoster ophthalmicus:

Although most varicella infection

Sexual transmission Reactivation in MV has been detected via culture

PCR testing for CMV DNA

Pharyngitis observed in EBV

Rash: located mostly on trunk,

• Epidemic of AIDS- • Radiation therapy

Special actions required for public

C. Laryngeal warts (6, 11) In genital intraepithelial

JC polyomavirus: Progressive HPV DNA testing (eg, with

multifocal leukoencephalopathy, Hybrid Capture II or polymerase

The acetic acid test: This test can

3. Epidemic diarrheal illness in

-Older than 1 year: 200,000

Children with clinical signs of

Prevention: MMR vaccine:

• Overcrowding Human PIV-3 is second only to

-Give infants who qualify for

-In the second year of life,

-Clinicians may consider

Ribavirin - primarily reserved for

St. Louis encephalitis Replicates the cytoplasm 1. Headaches fever