Gram Shape Spores Capsule Other virulence Invasion Respiration Motility Culture Colonies Special

stain factors features

Upper respiratory tract infections
Streptococcus Positive Cocci in Non Streptokinase Yes Blood agar β haemolytic Community
pyogenes chains sporing Hyaluronidase pinpoint acquired
DNAse colonies
Haemolysin
(Streptolysin O
& S)
Streptococcus Positive Lanceolate Non Capsulated IgA protease Yes Blood agar α haemolytic Commensal in
pneumoniae diplococci sporing some Draughts- pinpoint Nasopharnyx
serotypes men colonies Optochin
feature sensitive
Moraxella Negative Cocci Non Aerobe Commensal in
catarrhalis sporing Nasopharnyx
Haemophilus Negative Bacilli Non Non No Facultative Chocolate Commensal in
influenzae sporing capsulated aerobe agar Nasopharnyx
Haemophilus Negative Bacilli Non Capsulated IgA protease Yes Facultative Chocolate
influenza b sporing aerobe agar
Bordetella Negative Coccobacilli Non Pertussis toxin No Facultative Bordet -
pertussis sporing aerobe Gengou
medium
Corynebacterium Positive Bacilli Non Diphtheria No
diptheriae sporing toxin
Lower respiratory tract infections
Streptococcus Positive Lanceolate Non Capsulated Yes (some Blood agar α haemolytic Commensal in
pneumoniae diplococci sporing serotypes) Draughts- pinpoint carriers
men colonies Optochin
feature sensitive
Haemophilus Negative Bacilli Non Capsulated Yes Chocolate
influenza b sporing agar
Mycoplasma Negative Pleomorphic Non Non Can’t grow ‘fried egg’ No cell wall
pneumonia (weak) sporing capsulated in culture appearance
Chlamydia Negative Non Cell culture Obligate
pneumoniae (weak sporing intracellular
stain)
Legionella Negative Bacilli Non
pneumophilla sporing
 Gram Shape Spores Capsule Other virulence Invasion Respiration Motility Culture Colonies Special
stain factors features
CNS infections
Neisseria Negative Intracellular Non Capsulated IgA protease Yes Aerobic Commensal in
meningitides Diplococci sporing carriers
Lanceolate
Haemophilus Negative Bacilli Non Capsulated Yes Chocolate
influenza b sporing agar
Streptococcus Positive Lanceolate Non Capsulated Yes Blood agar α haemolytic Commensal in
pneumonia diplococci sporing some pinpoint carriers
serotypes colonies Optochin
sensitive
Escherichia coli Negative Bacilli Non Capsulated VTEC Facultative Motile Blood agar COMMENSAL
(enterobacteria) sporing anaerobe Lactose in GIT
fermenting Oxidase (-)
Indole (+)
Streptococcus Positive Cocci in Non Blood agar β haemolytic Commensal in
agalactiae (group chains sporing pinpoint carriers
B streptococci) colonies
Listeria Positive Bacilli Non Yes
monocytogens sporing
Diarrhoea
Campylobacter Negative Curved/ Non Non Yes Microaerophilic Motile
jejuni spiral rods sporing capsulated (flagella)
S.entertidis / S. Negative Bacilli Non Yes Facultative Non lactose Oxidase (-)
typhimurium sporing anaerobe fermenting
Shigella Negative Bacilli Non Enterotoxin Yes Facultative Motile Non lactose Oxidase (-)
sporing anaerobe fermenting
Vibrio cholera Negative Bacilli or Non Non Exotoxin – No Facultative Motile Oxidase (+)
coma sporing capsulated cholera toxin anaerobe
Escherichia coli Negative Bacilli Non Capsulated Vero cytotoxin
(EIEC & EHEC) sporing
Staphylococcus Positive Cocci in Non Preformed
aureus clusters sporing toxin
Bacillus cereus Positive Bacilli Sporing Preformed
toxin
Listeria Positive Pleomorphic Non
monocytogens bacilli sporing
 Gram Shape Spores Capsule Other virulence Invasion Respiration Motility Culture Colonies Special
stain factors features
Intra-abdominal infections
Clostridium Positive Bacilli Sporing Alpha toxin Anaerobe
perfringens Lecithinase
Hyaluronidase
Collagenase
Proteinase
Clostridium Positive Bacilli Sporing Toxin A, B Anaerobe
difficile Hydrolytic
enzyme
Bacteria Vaginitis
Gardnerella Variable Bacilli Non Facultative Non β haemolytic COMMENSAL
vaginalis sporing anaerobe motile in carriers
Mycoplasma Negative Pleomorphic Non Non Can’t grow ‘fried egg’ No cell wall
hominis (poorly sporing capsulated in culture appearence
staining)
Mobilincus Negative Curved Non Anaerobe Found with G.
Bacilli sporing vaginalis
Sexually Transmitted Diseases
Neisseria Negative Intracellular Non Non IgA protease Aerobic Non Chocolate
gonorrhoea Diplococci sporing capsulated Pili motile agar
Clamydia Negative Non McCoy Cell Obligate
trachomatis sporing culture intracellular
Treponema Negative Spiral Non Non Anaerobe Motile Cannot be Trans
pallidum (poorly sporing capsulated cultured placental
staining) artificially transmission
in the lab
Urinary Tract Infections
Escherichia coli Negative Bacilli Non Capsulated Capsular Facultative Motile Lactose Green sheen COMMENSAL
(enterobacteria) sporing antigen & anaerobe fermenting on EMB agar in GIT
fimbriae Oxidase (-)
Indole (+)
Pseudomonas Negative Bacilli Non Non Obligate Aerobe Motile Non lactose Greenish blue Hospital
aeruginosa sporing capsulated fermenting pigmentation acquired
(pyocyanin) Oxidase (+)
Pyocyanin (+)
 Gram Shape Spores Capsule Other virulence Invasion Respiration Motility Culture Colonies Special
stain factors features
Enterococcus Positive Cocci in Non Facultative Blood agar α, β or Non- COMMENSAL
faecalis chains sporing anaerobe haemolytic in GIT
(group D pin point
streptococci) colonies
Klebsiella Negative Bacilli Non Capsulated Endotoxin Facultative Non Lactose Mucoid COMMENSAL
pneumonia sporing anaerobe motile fermenting colonies in GIT
(enterobacteria) Oxidase (-)
Serratia Negative Bacilli Non DNAse Facultative Motile Red COMMENSAL
marcescens sporing Gelatinase anaerobe pigmentation in GIT
(enterobacteria) Lipase Oxidase (-)
Hospital
acquired
Proteus mirabilis Negative Bacilli Non Facultative Motile Non lactose Swarming COMMENSAL
(enterobacteria) sporing anaerobe fermenting appearance in GIT
Distinct odour
Oxidase (-)
Staphylococcus Positive Cocci in Non Facultative Non- COMMENSAL
saprophyticus clusters sporing anaerobe haemolytic in skin
grey/ white Coagulase (-)
colonies Catalase (+)
Community
acquired
Fever with rash
Rickettisia Negative Pleomorphic Non Cell culture Obligate
Bacilli sporing intracellular
Coxiella burnetti Negative Bacilli Non Cell culture Obligate
sporing intracellular
Fever
Leptospirosis Negative Spiral Non Yes Anaerobe Motile
(poorly sporing
staining)
Salmonella typhi Negative Bacilli Non Capsulated Vi antigen Yes Facultative Motile Non lactose Oxidase (-)
sporing anaerobes fermenting
 Gram Shape Spores Capsule Other virulence Invasion Respiration Motility Culture Colonies Special
stain factors features
Skin infections
Staphylococcus Positive Cocci in Non Coagulase Yes Blood agar β haemolytic Coagulase(+)
aureus clusters sporing Enterotoxin golden yellow
TSST 1 colonies
Epidermolytic T

Staphylococcus Positive Cocci in Non Adherence to Blood agar Large white COMMENSAL
epidermidis clusters sporing medical colonies in skin
equipment via without β Hospital
slime haemolysis acquired
Coagulase (-)
Streptococcus Positive Cocci in Non Streptokinase Yes Blood agar β haemolytic Community
pyogenes chains sporing Hyaluronidase pinpoint acquired
DNAse colonies
Haemolysin
(Streptolysin O
& S)
Mycobacterium
Mycobacterium Acid fast Slender Non Non Lipo- Obligate aerobe Non Lowenstein No carrier
tuberculosis stain straight/ sporing capsulated arabinomanan motile Jensen state
curved Superoxide medium
bacilli dismutase
Mycolic acid
Mycobacterium Acid fast Slender Non Non Obligate aerobe Non Can’t grow Longest
leprae stain straight or sporing capsulated motile in artificial generation
slightly medium, time
curved grown in
bacilli mouse foot
pad or on
armadillo
Toxin mediated infection
Clostridium tetani Positive Bacilli Sporing Exotoxin – No Anaerobe
tetanus
neurotoxin
Clostridium Positive Bacilli Sporing Exotoxin – No Anaerobe
botulinum neurotoxin
Corynebacterium Positive Pleomorphic Non Exotoxin - No Aerobe COMMENSAL
diphtheriae Bacilli sporing cytotoxin in carriers
Vibrio cholerae Negative Coma Non Non Exotoxin - No Facultative
sporing capsulated enterotoxin anaerobe
E. coli (ETEC) Negative Bacilli Non Capsulated Heat labile Facultative Motile Lactose COMMENSAL
sporing and/or heat anaerobe fermenting in GIT
stable Oxidase (-)
enterotoxin

E. coli (EHEC) Shiga toxin

(Verotoxin) –
cytotoxin
Staphylococcus
aureus
Streptococcus
pyogens
Bacillus cereus Positive Bacilli Sporing Exotoxin - Aerobe
enterotoxin

F1F2 Repeat Campaign 2014AL 

 Virus Family Nuclear material Enveloped/ Serotypes
Non Enveloped
Infections of the URT
Influenza Virus ORTHOMYXOVIRUS RNA Enveloped 3
Parainfluenza Virus PARAMYXOVIRUS RNA Enveloped 4
Respiratory Syncytial Virus PARAMYXOVIRUS RNA Enveloped 2
Rhino Virus PICORNAVIRUS SS RNA Non Enveloped >100
Corona Virus PICORNAVIRUS RNA Non Enveloped 4
Adeno Virus ADENOVIRUS DNA Non Enveloped >33
Infections of the CNS
Rabies Virus RHABDOVIRUS SS RNA Enveloped >100
Polio Virus PICORNA VIRUS – RNA Non Enveloped 3
ENTEROVIRUS
Mumps Virus PARAMYXOVIRUS SS RNA Enveloped 1
Enterovirus PICORNA VIRUS RNA Non Enveloped
JE Virus FLAVIVIRUS SS RNA Enveloped
Diarrhoea
Rotavirus REOVIRUS DS RNA Non Enveloped 7
Sexually Transmitted Disease
Human Papilloma Virus (HPV) PAPOVAVIRUS DS DNA Non Enveloped >70
Herpes Simplex Virus HERPESVIRUS DS DNA Enveloped 2
Human Immunodeficiency Virus (HIV) RETROVIRUS RNA Enveloped
Hepatitis
Hepatitis A Virus PICORNAVIRUS SS RNA (+) Non Enveloped 1
Hepatitis B Virus HEPADNAVIRUS DS DNA Enveloped
Hepatitis C Virus FLAVIVIRUS SS RNA (+) Enveloped
Hepatitis D Virus DELTAVIRUS SS RNA (-) Enveloped
Hepatitis E Virus HEPEVIRUS SS RNA (+) Non Enveloped
Fever with rash
Measles Virus PARAMYXOVIRUS SS RNA (-) Enveloped 1
Rubella Virus TOGAVIRUS SS RNA (-) Enveloped 1
Varicella-Zoster Virus HERPESVIRUS DS DNA Enveloped 1
Fever
Influenza Virus ORTHOMYXOVVIRUS RNA Enveloped 3
Dengue Virus FLAVIVIRUS SS RNA Enveloped 4
Chikungunya Virus TOGAVIRUS SS RNA Enveloped
Latent infections
Cyto-Megolo Virus (CMV) HERPESVIRUS DS DNA Enveloped
Epstein Barr Virus (EBV) HERPESVIRUS DS DNA Enveloped
Herpes Simplex Virus (HSV) HERPESVIRUS DS DNA Enveloped 2
Varicella-Zoster Virus (VZV) HERPESVIRUS DS DNA Enveloped
Human Immunodeficiency Virus (HIV) RETROVIRUS RNA Enveloped

F1F2 Repeat Campaign 2014AL 

 Mycobacterium tuberculosis
Disease Tuberculosis
General  Slender,straight/slightly curved
 Cell wall: 60% lipids(mycolic acid)
thus . Cannot be stained by gram
stain
 Resistant to drying
 Beaded bacilli- due to uneven
staingin
 Generation time 18-20 hrs
 Form colonies- 3-8 weeks
 Obligate aerobes
 May be destroyed by phenolic
disinfectants and exposure to UV
light
Pathogenesis Delayed type hypersensitivity reaction
Mainly in the lungs
Reinfections can occour
Mycobacterium leprae
Leprosy
 Straight/slightly curved, slender
 Cigar bundle appearance
 Less strongly acid fast than M.
tuberculsosis
 Stain evenly
 Generation time 21-24 days
(not grown in artificial media- foot pad
of mouse, armadillos)
Delayed type hypersensitivity reaction
Affect shwan cells, resulting in nerve
damage(anesthesia, muscle paralysis)

Two main types based on the immune response

Lepramatous Leprosy Tuberculoid leprosy
Bacilli numerous Infilteration of nerves
Multiply in Macular anesthetic
macrophages patches on skin
Bacilli shed in large Few bacllin in skin
numbers Good CMI response
Granumolatous lesion Almost non infeciots
No immune response

Route of Respiratoy droplets from infected humans Inhalation , skin inoculation though skin
transmission NO CARRIER STATE abrasions
Person to person transmission rare
Diagnosis Specimens Lepromin test – non specif test
Sputum(pulmonary TB) *Commonest Basis : delayed typer hypersentitvity and CMI
CSF (TB meningitis) Prepared from armadillo lepramatous tisye
UFR (renal TB) Usdul for classigign leprosy
Lab tests
Microscopy for AFB
Culture on LJ medium (3-6 weeks)
PCR
st
Management 1 line For adult paucibacilary patients- 6 months with
 Isoneazid Dapsne, Rifampicin
 Rifampicin
 Ethanbutol Adult multibacillary patients – 12 months with
 Pyrazinamide Clofazimine, dapsone, rifampicin
nd
2 line
 Steptomycin
Prevention Early diagnosis and treatment
and Control Contact Tracing
BCG vaccine – Live Attenuated vaccine,
Contains M bovis

F1F2 Repeat Campaign 

 Micro Organism Specimen Gram Stain Culture Antigen PCR- Serology
Detection- pathogenic
Pathogenic DNA,RNA
antigen
Gram Positive Staphylococcal Pus culture for wounds Grape like clusters staph colonies larger than strep,
Cocci Infections blood culture for aureus- golden yellow, B
osteomyelitis hemolytic on blood agar,
midstream urine for UTI epidermidis/saprophyticus- grey
or white, non hemolytic

Strep pyogenus Throat swab in phayringitis, Cocci in chains Pinpoint, beta hemolytic colonies
Group A pus in wounds, impetigo seen among pus
blood culture in sepsis and cells
necrotizing faciatis
Strep agalectae Blood culture and ore CSF In chains Beta hemolytic pinpoint colonies
Group B on blood agar
Strep pneumoniae Blood culture and ore CSF Gram posticive Alpha hemolytic colonies on blood
in meningitis lanceolate agar
Sputum blood culture in diplococcic among Draughtsman feature
pneumonia pus cells
Sinus aspirate in sinusitis
enterococci Mid stream in UTI Gram positive in pinpoint
chains
Gram negative Neisseria gonorrohea Male- urethral swab Many pus cells Chocolate agar
cocci Females- cervical swab Intrecellualr gram
Neonatal conjunct- eye negative kidney
swab shaped diplococci
Neisseria meningitidis CSF and blood Many pus cells Blood agar Meningococcal Meningococcal
Intracellular gram polysaccharide DNA on CSF
negative kidney antigen in CSF
shaped diplococci
Enterobacteria E coli Mid stream urine in UTI, Gram stain Culture- beta hemolysis on blood
Gram negative stools in diarrhea, blood in agar
bacilli septicemia, biliary sepsis,
Oxidase neonatal meningitis
negative Kelbsiella
choliforms Serratia
Proteus
Salmonella B1 Standard agglutination test
S2 for antibodies- widal test
U3 (demonstrate the rising
antibody titre in acute and
convalescent samples)
Shigella feces - Non lactose fermenter Direct slide agglutination test
NLF
Yeresinia
 Micro Organism Specimen Gram Stain Culture Antigen PCR- Serology
Detection- pathogenic
Pathogenic DNA,RNA
antigen
Gram negative H influenza Blood for culture in all invasive Pus cells and gram Difficult to isolate as its fastidious Capsular
bacilli NEVER infections negative bacilli polysaccharide
REFRIGERATE CSF and blood for meningitis detected in CSF in
Sputum in pneumonia meningitis
Synovial fluid in septic arthritis
Bordetell Pernasal swab or Bac culture on special medium PCR for ELISA for IgM
pertussis nasopharyngeal aspirate bacterial DNA
legionella Legionella antigen
in urine
9expensivve0
yersisnia Aspirate from lymph nodes Gram stain culture
sputum or blood
Gardnerallea High vaginal swab Clue
vaginalis cells(epithelial
cells covered in
gram variable
bacilli)
Gram positive Corynebacterium Throat swab Gram stain Culture
bacilli diphtheria
Pseudomonas Oxidase positive Urine in UTI, wound in surgical Gram stain Culture- pyocyanin pigment turns
wounds burn swabs in burn the medium green
infections
Vibrio Feces or rectal swab Culture on special medium Direct agglutination with
monoclonal antibody
camphylobacter feces Culture on special media at 42C
temp
Spore formers Clos botulinum Detection of toxins in food and
blood
Clos difficiale Detection of toxins in feces
Mycobacterium Sputum , urine , CSF Ziehl nelson Culture on LJ medium 3-6 weeks DNA Antibody testing – not very
TB amplification in useful in diagnosis
PCR
leprae Slit skin smears Modifies ziehl Cant in artificial media, inoculation
nelson of the footpad in armadillos
Mycoplasma serum IgM antibody
Chlamydia Eye swabs, endocervical swabs, Cell culture Antigen detection
urethral swabs using ELISa
ricketssiae Ricketsial antibody in serum
spirocheates treponema Scrapings from chancre or other Dark ground Cannot be cultures artificially VDRL- for antibody
skin and mucosal lesions microscopy TPHA
Serum for antibodies
leptos Blood CSF urine Special culture media Serology – IgM
only method used in SL
 Micro Organism Specimen Gram Stain Culture Antigen PCR- Serology
Detection- pathogenic
Pathogenic DNA,RNA
antigen
Respiratory Setection of viral
virus antigen in
nasopharyngeal
aspirate
CNS virus rabies Serum, CSF, skin biopsies, saliva Sellars stain – for Virus antigen
negri bodies in the detection in
hippocampus brian/corneal
smears using
indirect
immunoflorence
poloi stools Tissue culture
rubella Antibodies in patient serum
via ELISA radioimmune
assay…
IgM – recent infection
GI rota Feces transported on ice Wheel shape on Viral antigen
EM detection in feces
arbo JE CSF blood JE AB using HI or ELISA
IgM or 4 fold rise in IgG
between acute and
convalescent
dengue blood AB using HI or ELISA
IgM or 4 fold rise in IgG
between acute and
convalescent
Herpes HSV Fluid from vesicles or scrapings Isolation of virus by tissue culture Antigen detection PCR viral DNA
from ulcers ELISA detection
EBV Blood for serology Paul bunnel or monospot
test- non specific tests fro
heterophile antibodies
IgM for EBV antigens
CMV Urine throat swabs Isolation of virus by tissue culture
HIV Antigen in serum PC for viral antibodies in EISA and
RNA western blot
Candida Gram stained SGA grow in 2 days
budding gram
positive yeast
General Guidelines in the collection and transport of specimens
1. Selection of appropriate specimens
- Coughed up sputum NOT SALIVA in RT infections
- An endocervical swab and not a high vaginal swab to isolate gonococci in
gonorrhea
- In meningitis CSF is an important specimen, also is blood for culture
- Blood culture and stool culture are more important than serology to diagnose
enteric fever
2. Time of collection
- Urine and sputum are best collected early morning when organisms have had
time to multiply at the site over several hours, over night
- Must be done BEFORE ANTIMICROBIAL TREATMENT HAS BEEN STARTED
3. Collection
- Sterile, leak proof, dry containers free from disinfectants
- Containers for stool samples must be clean but not sterile
- Contamination by normal flora must be minimized
4. Labeling and accompanying request form
5. Transport
- If delayed refrigerate
- NEVER REFRIGERATE CSF blood for culture/specimens with Hemophilus
species, strp pneumo, neisseria species
Guidelines for the collection of specific specimens
Throat swab- insert a sterile swab , avoiding lips, tongue and palate and swab the affected
area without contamination of saliva
Nasal Swab- moisten the swab with sterile saline, swab the walls of both anterior nares
Pernasal Swab- a calcium alginate swab on a fine flexible wire is used, gently inserted into
the nostril until it reaches the posterior nares
Sputum early morning expectorated specimen. Wash the mouth thoroughly with water and
make a deep cough. Cough out sputum into a wide mouthed sterile screw capped container
Laryngeal swab is preferred in children as they cannot expectorate
TB – three early morning specimens on 3 consecutive days
Blood for culture
1. Check that the bottle provided for culture are clear and not contaminated(follow
aseptic precautions)
2. Perform the vein puncture using a dry, sterile needle and syringe
3. Remove protective covering from the bottle top and wipe the exposed diaphragm
with an alcohol based disinfectant and allow it to dry
4. Inoculate 5ml of blood into each culture bottles
5. Gently mix the contents of the bottle before labeling
6. Keep at Room Temperature till dispatch to the lab asap
Feces
1. Stools ,
- Defecate into a clean and dry bed pan
- Stools must not be contaminated with urine
- A selected portion of the stool from the watery mucous or blood stained area
is trandfered into a clean wide mouthed disposable container with a lid
2. rectal swabs
- when large number of specimens have to be collected/ patients poor compliance
-Moisten the swab with distilled water before inserting into the rectum, swab
should be rubbed well on the rectal mucosa and should have feces on it
Urine
Midstream urine for UTI
- Wash the genitalia with soap and water, leaving no trace of soap
- Patients hand and genitalia should be dried with a clean towel
- In a female patient separate the labia and collect a clean catch midstream
sample
- In a male pull back the foreskin and collect the urine
- Collect to a side mouthed sterile bottle
- Should be refrigerated at 4C until transported to the lab
In neonates and very young children- supra pubic aspirates of bladder urine is
preferred
If renal TB suspected- all urine passed should be collected, not just mid stream
Purulent material from wounds and abscess
1. Unruptured abscesses -> decontaminate the skin overlying the abscess and aspirate
a needle and syringe and transport in a sterile bottle
2. Infected wounds and open abscesses
- Decontaminate the superficial flora by cleaning with normal saline, remove
the exudates and firmly sample the margin of the lesion with a swab
High vaginal swab
A vaginal speculum is used, 2 swabs are inserted into the upper part of the vagina and
rotated there before withdrawing. One swab is sent for gram stain and bacterial culture the
other for wet mount for trichomonas
Endocervical swab
a vaginal speculum must be used to provide a clear sight of the cervix, and the swab is
inserted into the endocervix and rotated there. Withdraw without contamination of the
vaginal wall. Smear should be made on glass and swab inoculated onto the culture plate at
bed side
F1F2 Repeat Campaign 2014AL 

Orthomyxoviruses – Influenza Paramyxovirus – Parainfluenza, RSV
Rhinoviruses, Enteroviruses, Echovirus, Coxsackie A & B
Adenovirus Coronavirus e.g.- SARS
Source- Human (patient, carrier)
Route- Res. Secretions  via droplets Inhalation
Attaches to receptors and enter cells acute lymphocytic infection
Clinical diagnosis Specimen- Nasopharyngeal aspirate, throat
swab (viral tr. Media , in ice)
Antigen detection (immunofluorescence), PCR
Antibiotics not given
Corynebacterium diphtheriae
Sore throat with formation of a pseudomemebrane
G + aerobic bacilli – Chinese letter arrangement
Source – carriers / patients  spread via respiratory
droplets or exudate from skin lesions
Produces an exotoxin which inhibits protein synthesis
Prominent effect on heart , nerves & kidneys
Diagnosis – Throat swab for PCR. Not cultured
URTI 80% viral
Pharyngitis – All RS viruses, EBV & CMV , Streptococcus pyogenes , Corynebacterium
Epiglottitis – usually bacterial Haemophilus influenzae b
diphtheriae
Noisy breathing Severe life threatening infection
Streptococcus pyogenes ( Group A Streptococcus) – g+ diplococci in grape like clusters.
Beta hemolytic
Droplet transmission from patients and carriers
Source – Humans ( patients, carriers) Route- droplet transmission
NEVER swab Blood for culture in chocolate agar
Causes pharyngitis, tonsillitis, otitis media, sinusitis
Cellulitis, impetigo, erysipelas,necrotising fasciitis
Sinusitis – headache Starts with a viral infection
Often gets superinfected with bacteria Virulence factors – invasion ( enzymes : hyaluronidase, streptolysin O)
Otitis media - Ear ache Starts with a viral infection
Often gets superinfected with bacteria Toxins: erythrogenic toxin  scarlet fever
Streptococcus pneumoniae
Haemophilus influenzae Immunopathology – Rheumatic fever , Acute glomerular nephritis
Moraxella catarrhalis
Specimens. sore throat- throat swab
infected wound – pus necrotising fasciitis – blood
Laboratory tests: Culture – Small, pin-point colonies with beta hemolysis on
Bordetella pertussis  whooping cough G (-) coccobacilli blood agar
A titre of anti streptolysin O can be measured ( ASOT ) – High titre indicates recent
Source – patients / carriers  droplets inhaled infection
Virulence – pertussis toxin , damages the ciliated epi. Of respiratory tract
Clinical features – catarrhal phase ( rhinitis like )  paroxysmal phase ( cough
with inspiratory whoop)  convalescent phase
Complications – sub conjunctival haemorrhage, bronchiectasis , intra cranial
haemorrhage
Lab. Diagnosis – per nasal swab , nasopharyngeal aspirate for culture on F1F2 Repeat Campaign 2014AL 
special media , PCR
Antibiotics only effective in catarrhal phase
Prevention – DPT vaccine – killed pertussis vaccine A cellular vaccine
more effective
 Hospital acquired

LRTI
Community acquired  typical pneumonia

 atypical pneumonia

• Source of infection
Community acquired typical pneumonia Human -Patient
-Carrier (incubation, subclinical or convalescent)
• Acute onset • Route of transmission -Shed in the respiratory secretions
• Productive cough with purulent sputum Droplets are transmitted into the air
• Chest signs are many Inhaled into the respiratory tract
Chest X-ray shows evidence • Infection -Infects the cells of the respiratory tract
of lobar pneumonia Acute inflammation in the alveoli
Consolidation

Streptococcus pneumoniae Haemophilus influenzae

Gram stain – Lanceolate, Gram positive diplococci Small Gram negative bacilli

Culture – Pinpoint colonies. α -hemolytic, draughtsman Require enriched media with heated blood for culture
shaped colonies (chocolate agar)
80+ serotypes
Capsulated strains are very virulent ( b most virulent )
Virulence factors – Invasiveness , pneumolysin , Ig A
protease, Capsule Invasiveness ( capsule protects from phagocytosis)

Diagnosis -Sputum (do not refrigerate) & blood Children LP , Ig A protease

laryngeal swab
Acute pyogenic inflammation
Gram stain and culture in blood agar
Diagnosis – sputum and blood (cold sensitive – not
Acute pyogenic infection refrigerated)

Vaccine – conjugated multivalent Gram stain – Faint staining Gram negative bacilli
Culture – Small colonies on chocolate agar
PNEUMOVAX 23 valent
Conjugated Hib vaccine at 2, 4, 6 & 18 months
 • Insidious onset
• Cough but little sputum
• Chest signs are few
Chest X-ray shows evidence of interstitial pneumonia

Mycoplasma pneumoniae No cell wall. So shape varies (pleomorphic) Cannot be Gram stained

Can be grown in cell free culture media – fried egg colony appearance

 Mycoplasma pneumoniae. Diagnosis – serum ( test for antibodies)

 Mycoplasma hominis
 Ureaplasma urealyticum

Chlamydia pneumoniae Obligate, intracellular parasites Cannot be grown in culture media only in cell culture

Gram (-) weakly staining cannot be seen in gram stain

Elementary bodies – transmissible form Reticulate bodies – intracellular vegetative form

Chlamydia trachomatis : Serotypes A,B,C – trachoma

D-K – genital infections and conjunctivitis
L1, L2, L3 – lymphogranuloma venereum

Chlamydia pneumoniae – respiratory disease in man Chlamydophila

Chlamydia psittaci – zoonotic infection from birds ( psittacosis )

Diagnosis – serology for antibodies

Legionella pneumophila - Legionnaire’s disease

Source: Exogenous pathogens from water ( through air conditioners )

Route of transmission: Inhalation of aerosols into the respiratory tract

Can occur in outbreaks Severe in elderly , mild fever ( pontiac fever ) in the young

Diagnosis – antigen detection in urine

Prevention – proper management of water systems in offices and hotels

 CNS INFECTIONS

CNS infections

Meningitis Encephalitis

Acute pyogenic
Acute septic(viral) Primary
(bacterial)

Acute focal
suppurative Chronic(TB) Post-infectious
(abscess, empyema)

Acute pyogenic meningitis

Neonates Children, adolescents and adults Immunocompromised

•Group B streptococci (S. •S. pneumoniae •Listeria monocytogenes

agalactiae) •Haemophilus influenzae •Cryptococcus
•E.coli (Commenest) •Neisseria meningitidis •Mycobacterium TB
•Listeria monocytogenes •Toxoplasma
•Acanthamoeba

H. influenza
 Capsulated – pathogenic
 Type b most virulent
 Gram - pleomorphic
coccobacilli
 Cold sensitive (Never
refrigerate)
 Cultured in chocolate agar
Source : Infected humans/ Lab diagnosis
carriers in upper respiratory
tracts  CSF gram stain
 CSF culture
Transmission: Via droplet  Blood culture
inhalation  Agglutination kits
Prevention: Hib immunization
(pentavalent vaccine in EPI) and
chemoprophylaxis via Rifampicin
Streptococcus pneumonia
 Commensal in upper
respiratory tract
 Lanceolate diplococcic
 Surrounded by polysaccharide
capsules’
 Sensitive to optochin
 Alpha haemolytic on blood
agar
Neisseria meningitidis
 Gram negative
 Capsulated
 Diplococci, kidney bean shape
 Frequently found
intracellularly
 Serotypes- A B C Y W135
Acute aseptic meningitis
Varicella Enteroviruses
Arbovirus
zoster (Commonest)
Polio virus
 Enterovirus family
 Small RNA virus
 Extremely temperature
sensitive
 3 serotypes,
- Type 1(90% & weekest)
- Type 2 (9% & eliminated)
- Type 3 (1%)
Prediposing factors: Lab diagnosis
 Age <2 and >60  Blood culture
 Respiratory infections,  CSF gram stain
otitis media, mastoiditis  CSF culture
 Head trauma  Immunological methods
 Haemoglobinopathies
Prevention: Pneumococcal
 Immunodeficiency states
vaccination (23 valent)
Source : Human nasopharynx Lab diagnosis :
(asymptomatic carriers)
 CSF gram stain
Transmission : via droplets  CSF culture (chocolate agar)
IP <3d  Antigen detection
Prevention: Immunization
Most common in children <5y
(quadrivalent A C Y W135 and
Clinical: petechial or purparic rash, bivalent A C) no vaccine for B
rapidly progressive fulminant
HSV1 Polio Adenovirus Mumps
 Humans – only source  Highly contagious
 Feco-oral transmission via  Symptoms CNS specific
food and water  Entry into CNS via,
 IP- 7-10 d - Retrograde axonal
 Excretion just before transport
paralysis & within first 2 - Across BBB
weeks of onset - Via infected
macrophages
 Primary encephalitis

Epstein
HSV 2 JE Mumps Rabies
barr

Mumps HSV2

 Paramyxoviridae family  Herpesviridae family

 Rubulavirus genus  Enveloped DNA virus
 Transmission via aerosols and  Transmit from skin, saliva or genital
droplets secretions

Japanese encephalitis

 An arbovirus transmitted by  Common in Western, North-  Amplifying hosts-

Culex mosquito central, North-western and pigs, wading birds,
 Flaviviridae family Sabaragamuwa provinces reptiles and
 Enveloped ssRNA virus  Viral zoonosis amphibians
 Detection of IgM ab in serum  High risk after rainy seasons  Human is incidental
and CSF by ELISA with migratory bird patterns host

Rabies

 Genus Lyssavirus  Zoonotic infection  IP 1-3months

 Family  Can infect all mammals (not  Entry by endocytosis via ACH
Rhabdoviridae domestic rat) receptors in NMJ
 Enveloped  Transmitted by,  Initial replication at port of
 Bullet shaped - Bite of a rabid animal entry 48-72h
 ssRNA virus - Scratches from saliva  3mm/h spread along nerve
contaminated paws  Causes encephalomyelitis
- Thru mucus membranes  Enter salivary glands etc
- Lick on wounds  2 presentations
- Unboiled cow or goat milk -Furious
- Inhalation (Bat caves) -Dumb (paralytic)

Post-Infectious encephalitis
Measls Rubella Varicella zoster Influenza
 CNS Infections

Encephalitis Meningitis

HSV1

Varicella zoster

HSV2

EBV

JE

Rabies

Mumps

Enterovirus

(polio,coxsackie)

Adenovirus

Arbovirus

F1F2 Repeat Campaign 2014AL 

Urinary Tract Infections Urethra-----> Urethritis

Types of Bacteria 1. Colonization & ascending spread

2. Haematogenous spread Bladder----->Cystitis
3. Periurogenital spread
Gram +ve
Gram-ve Kidney----->Pyelonephritis

Enerobacter faecalis oxidase -ve oxidase +ve

Staphylococcus saparophyticus (Enterobacter) (Pseudomonas)

Klebsiella Serratia family features

Lactose fermenting non- Lactose fermenting
• Large polysaccharide capsule causes endotoxins
E. coli Proteus • Characteristic mucoid colony
Klebsiella
Serratia

Enerococcus feacalis Pseudomonas E-coli Klebsiella pneumoniae

•Gram +ve cocci in chains
•facultative anaerobe
•Habitat- human colon
•cause HAI
Staphylococcus
saprophyticus
•Gram +ve clusters
•Facultative anaerobes
•Dwells in skin around GU tract
•Coagulase -ve , Catalase +ve
Candida
•Causes Candiduria ---> presence of
Candida in urine
•Colonization occur not infection
•Risk factors: DM, Indwelling
catheters, Antibiotic use
aeruginosa
•Gram -ve rod/pleomorphic
•produce water soluble greenish
pigment
•occurs through fecal
contamination
•opportunistic in
immunocompromised
comditions
•produce grape like odor
•Typically infects Pulmonary tract,
Urinary tract, Burned wounds
•Naturally resistant to large
amount of antibiotics
•commensal in human colon
•Colonize in vagina and urethra ---
--> ascends and causes UTI
•Virulence factors
•motile
•adherence ------> fimbriae
•capsule
•toxins --------> causes diarrhea
•Klebsiella Serratia family
•found in normal flora- mouth, skin, intestine
•common infections - Pneumonia, UTI, Wound infection
Serratia marcescens
•Klebsiella Serratia family
•Virulence factors
•Motile
•Enzymes -> DNAase, Lipase, Gelatinase
•Causes HAI(Catheter associated), UTI, Bacteremia, Wound
infections
•Red pigmented colonies :Prodigiosin
Proteus mirabilis
•Swarming appearance
•urease--> (Urea--->NH3( distinct odor) ) ---> Alkaline urine---
---> crystals of CaCO3
•Causes Wound infections, Septicemia, Pneumonia
 Suspected in abnormal,

Vaginitis •
•
Discharge
Itching and irritation
• Odor
•
• Risk Factors Diagnosis
• Discharge pH >4.5
• Extremes of age • Presence of clue cells
Candida albicaus • Pregnancy
Commonly found in • +ve Whiff test ; characteristic
• Immunocompromised conditions
• Mouth (Commensal fungi) fishy odor with 10% KOH
• Diabetes mellitus
• Moist skin • Homogenous, white, thin,
• Use of broad spectrum antibiotics
• Lower GIT discharge
• Not a STI
• Vagina ( Amsel Criteria)
Causes Vulvo vaginal Bacterial Vaginosis
•
Candidiasis Also Causes, • Absence of lactobacilli
• Oral thrush
Symptoms of VVC
• Superficial skin infections
• Pruritis
• Nail infections
• Dyspareunia Mobilluncus sp.
• Blood stream infections
• Vaginal soreness & inflamed • Anaerobic
(in immunocompromised people (Polymicrobial
mucosa Diagnosis
infection) • Curved
• External dysuria • Vaginal Swab
• Motile
• Vaginal discharge ( Bivalve speculum)
o Thick curd like o Wet smear : Gram stain +ve • Gram variable
o pH normal pseudo hype
o slight odor o Culture Gardnerella Vaginalis
• Microaerophilic
• Pleomorphic cocco-bacilli
• Non-motile
*Trichomonas vaginalis • Gram variable rods
• Causes Trichomoniasis
• Malodorous yellow green, Frothy discharge
• Women – minimal/ no symptoms Risk factors
• Men – No symptoms
• Virulence factors • Having multiple sex partners
• New sex partners
o Adhesion molecules
• Douching
o Hydrolase
• Absence of Lactobacilli (H2O2
o Cytotoxic molecules
• Diagnosis:
o immediate microscopy on wet smear of vaginal secretions:
Characteristic jerky motility
•
 Fever with Rash

Prevention &
Disease Organism causing Pathogenesis Rash Clinical features Diagnosis
Control
Measels Paramyxoviridae Only via humans 4th day High fever, malaise, Clinically & Vaccine
Morbilivirus Droplets/ Direct contact Face-large swollen anorexia, irritability, epidemiologically 1st dose- 9 months
Single serotype Multiplication in RS→ blotches resp.disease, coryza, IgM ELISA in 2nd dose- 3 years
RNA virus RES→VIremia→ Trunk & limbs- cough, conjunctivitis, koplik blood/saliva (along with rubella)
(dissemination maculopapular spots IgG-fourfold rise
throughout the body) Lasts 4-7 days

Rubella Toga virus Human reservoir 2nd/3rd day Mild systemic viral infction Antbody (serology) Live attenuated
ssRNA RS → multiply in Fine macular rash Low grade fever and IgM/IgG vaccine
single serotype nasopharynxand lymph Fades without malaise, lymphadenopathy In pregnancy All females 14-40
enveloped nodes desquamation Pregnancy- pass through Confirm years in MOH clinics
Patients may be placenta up to 4 months exposure→check for
subclinical Congenital rubella syndrme immunity→IgM

Chicken Herpes Zoster virus Humans In trunk and face mainly Systemic viral infection Mainly clinical Acyclovir/valacyclovir
pox DNA virus Infected ones Central oval vesicles (fever,malaise,anorexia) In rare types IgM Orally
Enveloped Airborne spread/ direct Clear oval vesicles → Exanthem/ Enanthem rash from vesical fluid Within 48 hours of
contact with vesicle fluid opaque pustules → dry first lesion
crust
Mucosal lesions

Herpes Latent inn sensory Pain in dermatome 24 hours of the first

Zoster ganglia followed by vesicles lesion with strong
Reactivation due to Pain, fever, malaise analgesics
stress, malignancy, age, Unilateral, pruritic
intercurrent illness

Herpes DNA virus HSV1 Asymptomatic Skin mucus Acyclovir

Enveloped Shed in saliva Acute gingivostomatitis membranes Valacyclovir
HSV1 & HSV2 Oral to oral ☻ Cold sores due to Scrapings Famcyclovir
Inoculation in to skin/ recurrence Test ELISA
mucous membranes

F1F2 Repeat Campaign 2014AL 

 ORGANISMS CAUSING FEVER
Leptospirosis

Spirochetes Chief pathogen : Leptospira interrogans

icterohaemorrhagica
 Resemble a spiral/helix Clinical features:
 Motile  Endemic Zoonosis
Biphasic
 Not stain/poorly stain except  Source : Primarily rats, exctreted in
Borrelia (Gram -) urine and survive in stagnant water 1. Bacteraemic:
 Dark ground microscopy, Staining (Other mammals can be sources too) Fever, severe
with heavy metals,  MOT : Thru intact mucous membranes myalgia,
Immunoflorescent antibody and abraded skin prostration,
detection  High risk: Farmers, sewer workers Conjunctival
 Incubation: 4-14d suffusion
Spirochetes
 Diagnosis : Serology (Ab) or culture 2. Immune:
from blood Meningitis,
Treponema Leptospira Borrelia
 Treatment : Penicillin/ Doxycycline Liver, Kidney
and Lungs

Typhoid (Enteric) Fever

Pathogen: Salmonella typhi, paratyphi Source : Human patients and

A/B/C chronic carriers Clinical :
MOT : Faeco oral 1st w- Low fever, bradycardia, malaise,
 Enterobacteria
Incubation : 5-21 d headache, cough, leukopenia
 Motile Diagnosis : 1st week – Blood 2nd w- High step ladder fever,
 Gram – culture Diarrhoea or constipation, Rose spots,
 Facultative anaerobe 2nd week – Stool culture hepatosplenomegaly
 Non lactose fermenting in Mc 3rd week – Urine culture 3rd w- Intestinal haemorrhage,
konkey Widal test – detect Ab against H & perforation leading to sepsis and
 Exclusively human pathogens O Ags peritonitis, Encephalitis, Abcesses,
Colecystitis, Endocarditis, Osteitis

Typhus

Athropode Vector born Tick bite or scratch, inoculate faeces causing Local Lab diagnosis: Weil Felix
zoonosis inflammation forms painless Eschar test (Lack sensitivity n
Scrub T.- Orientia Ricketsaemia leading to multiorgan vasculitis specificity), Newer tests
tsutsugamushi Clinical: Acute
Treatment: Tetracycline
Endemic T. – Rickettsia typhi high fever, Myalgia, Conjunctival infection, end of 1st
(dramatic response) or
Ricketsiae: week: Lymphadenopathy, meningism, rash,
Chloramphenicol or
- Small pleomorphic cocobacilli hepatosplenomegaly Complications:
Fluoroquinolones
- Obligate intracellular Lungs, CNS, liver involvement
 Influenza

- Orthomyxoviridae family Antigenic shit – Clinical – Fever, sore throat,

- Influenza A,B,C  Abrupt, major change myalgia, headache, fatigue,
in HA/ NA in In.A nasal discharge, Cough etc
- Enveloped RNA virus
resulting in new Avian influenza – H5N1 A
- Influenza A has subtypes based on surface
subtypes potential threat to humans as
haemaglutinin and neuraminidase
 Causes pandemics they are genetically unstable,
A – A. Shift + Drift
Antigenic drift – and in a continuous genetic
B – Drift only, found in humans flux. High fatality. Human to
 Minor changes
C – Drift only, humans & swine human transmition is less.
occurring in HA/NA

Dengue

Dengue virus Primary infection Lab diagnosis:

 Arbovirus Reinfection by a different  NS1 antigen detection-
 Flaviviridae family serotype early (2-3d)
 ssRNA  Antibody detection-
 4 serotypes (1-4) Antibody dependant
IgM, IgG
 Same serotype>90% homology, enhancement
 Haemaglutinin
different serotype 65% homology Clinical: Fever, headache, retro- Inhibition Test (HAI)
 Transmitted by Aedes aegypti and orbital pain, arthralgia, myalgia, Considered as gold
Aedis albopictus. rash, anorexia standard
 Incubation 4 d  PCR

Chikungunya Fever

 Alpha virus Clinical: Lab diagnosis

 Same mosquito as dengue Fever, petechial or maculopapular  ELISA
 ssRNA rash involving limbs and trunks,  PCR
 Main reservoirs are monekys, arthralgia or arthritis, headache,
primates, mammals and birds photophobia, conjunctival infection

F1F2 Repeat Campaign 

 Infective Causes Of Diarrhoea

Osmotic Secretory Invasive

Inability to absorb osmotically active Secretion of Cl- Inflammation of bowel Virus
particles in the gut lumen due to NaCl Pump failure wall and education with
destruction of absorptive loud mucus WBC Rota Virus
enterocytes and replacement by Reoviridae Family,Cartwheel/Double shell capsid
secretory cells. appearance*
Rota Virus EPEC EHEC Leading single cause of severe infant and childhood
ETEC Shigella diarrhoea.Good hygiene and water supply has no effect on
Vibrio Cholerae Campylobacter transmission.
Amoebic dysentery Infects cells of small intestine(secretory type)-Lactose
intolerance may follow due loss of brush border enzymes.

Calcivirus/Norvovirus
RNA virus with different genotypes
Prevalent in all ages
Causes acute gastroenteritis with disease outbreaks in
closed communities
Adeno Virus – DNA Virus SI

Sapovirus,Astrovirus- RNA Virus SI

Non Enveloped Viruses (Gl)

Rota virus
Hepatitis A Virus
Poliomyelitis Virus

F1F2 Repeat Campaign 2014AL 

Bacteria

E Coli Campylobacter jejunai Salmonella Shigella Yersenia Vibrio cholerae

enterocolitica
S.dysenteriae,S.fleneri,S.boydii,
S.sonnei
Facultative anaerobic Microaerophilic Facultative anaerobes Gram negative Gram Gram negative
Gram negative* Gram negative Gram negative* Non motile,non capsulated negative Comma shaped
Motile Single flagellum or on both Motile Non Lactose fermenting * Facultative Aerobic bacilli
Lactose fermenting ends Non Lactose fermenting* anaerobes Antigenic structures contain flagella H
(Macconkey agar)* Seagull shaped* O and H antigens present * Non Lactose antigen somatic O antigen
Flagellum(H),capsule(k),LPS(O) Several environmental fermenting O for pathogenicity*
antigens* resovoirs Motile at
0
Chicken GI tract,contaminated 25 C
poultry,contaminated drinking Non
water hemolytic

Watery SI
ETEC-Enterotoxigenic-
Travellers
EPEC-Enteropathogenic-
childhood
Invasive
EIEC-Enteroinvasive-Shigella
like dysentery in LI,shiva like
toxin produced
EHEC-Causes HUS(O157)
Invade the small and large
intestine epithelial layer
resulting in blood and mucous
diarrhea
Do not multiply in food
Enteric fever/typhoid causing Exclusively human pathogen Sporadic Source
(exclusively human pathogen) A very small number of episodes Faeces of infected
S.paratyphi A,B,C organisms needed(low Commonly natural aquatic reservoir
S.typhi innoculum) affects young Virulence
Virulence persons Cholera toxin(Rice water diarrhea)
Non typhoid Salmonella Invasion-LI Infected Secretory type diarrhea by irreversible
Food poisoning and Shiga toxin-inhibition of animals are a activation of cAMP
diarrhea(gastroenteritis) protein synthesis source Inhibition of NaCl pump
Commensals of animals(poultry) HUS+ extraintestinal Invades SI Hypersecretion of Cl-
S.typhimurium manifestations lymphoid Blocks water uptake
S.enteriditis Blood and mucous diarrhea as tissue
a specimen not rectal swabs* Toxins+ ORF supportive therapy given
Invade enterocytes and produce Capsule+ Antibiotics are secondary
toxins
Multiply in foods Stool specimens taken for culture

Probiotics-
Oral administration of living organisms to promote health by competition with other bacteria and stimulation of non specific immunity.

Prebiotic
Non digestible food that stimulate growth of microbiota(bifidobacter and lactobacteria)
Eg- soluble carbohydrate fibres

Staphylococcus aureus causes food poisoning diarrhea by a heat stable enterotoxin.

Bacillus cereus(gram positive) heat stable enterotoxin causes food poisoning diarrhea.

F1F2 Repeat Campaign 2014AL 

Viral Hepatitis
Hep A virus Hep B virus Hep C virus Hep D virus Hep E virus

Virus family Piconaviridae Hepadnaviridae Flaviviridae Deltaviridae Calicivirus

Structure ss RNA Ds DNA Ss RNA Ss RNA Ss RNA

Enveloped Enveloped Enveloped Non-enveloped
Onset Usually abrupt Usually insidious Insidious Usually abrupt Usually abrupt
IP 3-5 weeks 2-6 months 2 weeks -6 months 3-13 weeks 15-60 days
Route of transmission Faeco-oral Parenteral – Needle stick Parenteral- IV narcotic use, Same as Hep B Faeco-oral
injuries, HD, Piercing , HD, Regular blood
Tattooing , Iv drug use, transfusion etc.
Blood transfusion, Sexual and vertical -
transplant etc. minimal
Mucosal- Sexually
Vertically
Horizontally- e.g.
Contaminated toothbrushes
Diagnosis Ig M antibodies HBsAg , anti HBc , and HBV Anti HBc , HCV RNA Anti HDV antibodies ELISA based antibody
(4 fold rise in paired sera if DNA PCR testing
Ig G is used)
Mortality About 0.3% 0.5-1.0% 0.2-0.4% 2-30% with coinfection, About 1-2%,
up to 30% with 15-20% in pregnant
superinfection women
Chronicity None 10 – 15% - cirrhosis 85% -10 – 20% cirrhosis 6% Unknown
-primary liver -1 – 5% carcinoma
cancer
Vaccine Killed vaccine Plasma derived No active or passive HBV vaccine No vaccine or Ig
Ig Genetically engineered immunization
(recombinant DNA vaccine
in SL)
Ig

F1F2 Repeat Campaign 2014AL 

 SEXUALLY TRANSMITTED DIESEASES Latency
HPV – Human Papilloma Virus – ds DNA Enveloped Herpes Virus – ds DNA

 Viral warts on the skin. (Planter warts,

Condyloma acuminata) child  Asymptomatic
 Can be direct digital or perinatal.  Gingivostomatitis, Cold sores
HSV 1  Keratoconjunctivitis,Dendritic ulcer
Hyper keratinization of epithelial cells.  Whitlow, Encephalitis
 Kaposi Varicelliform eruption –IC
 In malignancy – integrated into chromosomes . In saliva
Vertical trans. ,Oral-Oral, Oral-hand
 Tx - cryotherapy, electro cautery, excision
 Can even regress spontaneously
 1ry genital herpes
Precautions Adult
 Recurrent genital herpes
1.Barrier methods 2.HPV vaccine
 Neonatal herpes
(cervical Ca. precaution) HSV 2
(by contact, not via placenta)

Sexual, vertical transmission

Chlamydia (Obligate intracellular pathogen) In genital secretions

C. trachomatis Shallow, painful, multiple ulcers

Chlamydia
A B C – Trachoma  Scraping from lesions ELISA,Viral cell
culture, PCR
D-K - Genital , Conjunctivitis
Tx – Acyclovir, valacyclovir, Famiciclovir
L1,L2,L3 - LGV
Prevention – Cracarean section when mother having
primary herpes, + Gloves, Condoms
C.pneumoniae
Chlamydophila Atypical
C.psittaci pneumonia
LGV – sexually transmission
 Causes suppurative inguinal adenitis
Elementary body Trachoma (not a STD)
Dx – Urethral swab
Fibrosis,entropion,tricchiasis,
Endocervical swab (not high vaginal)
Reticulate body Blindness Tx – Tetracyclin oin.

McCoy cell culture

Genital chlamydia Antigen detection
Non
gonococcal Inoculation into eye - Conjunctivitis PCR
urethritis,
prostatitis Conjunctival swab
,Epididimytis
In Male During birth Ophthalmia neonatarum Tx – Tetracycline – 3 weeks
Cervicitis,salphingitis Azithro – 1 dose
Tx – Oral erythromycin
,infertility,ectopic
pregnancy F1F2 Repeat Campaign 2014AL 
In Female Also causes neonatal pneumonia
 spirochetes
Syphilis capsule Gonorrhoea G (-)

se Treponema pallidum Neisseria gonorrhoeae

en G (-) , Motile
 Pili, IgA protease, Penicillinases for virulence
 Dark ground microscopy
 Heavy metal stain
 Immunofluorescence
 Gonococcal Urethritis

Male
Primary syphilis
Dysuria, purulent discharge
Chancre – painless, indurated, single ulcer Acute epididimytis symptomatic
(on glans penis, perianal, mouth, tongue)

6 – 10 weeks
Female
Secondary syphilis
Asymptomatic carriers or symptomatic
 Maculo-papular rash in palms & soles
 Snail track ulcers  Vaginal discharge, Dyspareunia
 Condylomata lata in the perineum @endocervix  Lower abdominal pain PID
 Enlarged lymph nodes  Acute perihepatitis
Latent, Subclinical,
20yrs

Tertiary Syphilis Ophthalmia neonatarum

Bilateral conjunctivitis following vaginal delivery
 Gummatous Syphilis

Granulomatous lesions on skin, mucus

membranes, Bones Disseminated Gonococcal infection(DGI)
 Cardiovascular Syphilis Bacteria enter blood stream

Lesions like aortic incompetence

Narrowing coronary Ostia
Arthritis , Rash
 Neurosyphilis Meningovascular syphilis May be
Tabes dorsalis permanent
disability Can lead to,

Gonococcal meningitis, endocarditis

Dx
Scrapings  VRDL – antibody test
from
(false positives common) Tx ( for urethritis)
chancre

 TPHA – Heamagglutination
Cefuroxime oral
(TPPA) – Portical Agglutination Ceftriaxone IM – single dose
 FTA – Ab –fluorescent tripo. antibody

Tx – Penicilins Pregnant mothers F1F2 Repeat Campaign 2014AL 

Prevention – safe sex, screening Donor blood
 Transmission AIDS indicative diseases Pathogenesis

 Sexual Intercourse 1. Pneumocystis jiroveci pneumonia

 Mother to child – intrauterine,
intrapartum, perinatally, breast feeding
 Contaminated blood, blood products
and organ donations
 Contaminated needles
- Fungus, commensal in lung
2. Oesophageal candidaisis
3. Disseminated candidaisis
Cryptococcus, Aspergillus, Histoplasmosis, toxoplasmosis,
cryptosporidiosis, leishmaniasis, CMV, Kaposis sarcoma…

Post exposure prophylaxis Hallmark : profound immunodeficiency

resulting primarily from progressive qualitative
Squeeze the site of needle prick
and quantitative deficiency of the subset of T
Clean with soap and water
Helper cells
Anti retro viral therapy for 4 weeks
CD4 molecules on T helper cells are the primary
receptors
Prevention and Control
Co receptors also must be present: CCR5 and
Screening of all donated blood for HIV prior to CXCR4
transfusion
Depletion of T helper cells occur due to :
Strict adherence to universal precautions
Policy of handling and disposal of sharps 1. Direct cytopathic effect
Screening of all tissues before transplantation 2. Cytotoxic killing by activated CD8 T cells
Counseling of IVDU on needle sharing 3. Syncytial formation
Health education on safer sex 4. Activation of the apoptosis pathway
Treatment of STD 5. Autoantibody formation
Anti retroviral drugs
Incubation -> 2-4 weeks

Primary illness -> 6-8 weeks after exposure

Treatment Lab diagnosis
Clinical latency -> Median time of 10 years from
Anti retroviral drugs IgG Ab to gp 120 and its subunits
infection to AIDS
P24 antigen
Highly active anti retroviral drugs HAART- at least 3 du=rugs Isolation of virus
used in combo PCR
F1F2 Repeat Campaign 2014AL 
NRTI, NNRTI, protease inhibitor, CCR5 inhibitor Western blot
 • Like pseudomonas
- Gram negative any infection caused by this
- Oxidase positive organism is called
- Non fermenting
• Soil saprophyte Burkholderia pseudomallei
(The Great Mimicker)
• Transmission- accidental
pathogen: occupational, Lab diagnosis
recreation, lifestyle
• Culture (gold
standard)
• Gram stain : Safety pin
From soil or water appearance
• Antibody test ( indirect
High risk Co-Morbidities haemagglutination assay)
 Diabetes
 Liver disease Ingestion
 Lung disease Inhalation Inoculation
(Droplets)
 Renal disease
 Alcoholism
 Thalassemia
Variable
incubation
period Acute fulminant
Localized infections septicemia
with abscesses
• Variable clinical
features
• At any site in theMight
body

Relapse months
or years later

Reduce Early diagnosis

Potentially fatal and effective
disease therapy
F1F2 Repeat Campaign 2014AL 
 Portal
Mode of
Organism Source of Latent in Clinical features Complications Lab diagnosis Special features
Transmission
entry

Childhood- common (70-100%) Specimen- Blood(serum)

Usually asymptomatic
Young adults- infectious Tests-
saliva mononucleosis 1. Blood picture - Sore throat with
Cancers atypical Exudate
EBV Infected humans - contaminated - fever, malaise, tiredness
- lymphocytosis ( ( pus in pharyngitis
( The shed in saliva -hands Mouth
B
- Burkitt's lymphoma
blue cells with large is usually seen in
Sore throat
kissing (from time to
- Lymphocytes - Nasopharyngeal nuclei) and very bacterial infections,
disease) time) Toys - Generalized lymphadenopathy carcinoma high lymphocytic this is an
-Food Kissing - Hepatomegaly counts exception)
2. IgM antibodies
- Hepatitis 3. Paul Bunnel test (
Recurrence is usually asymptomatic not done now)

Childhood & adulthood - very

common (70-100%)
Usually asymptomatic
- recurrence is asymptomatic
Specimen
Oro-pharyngeal swab,
Brain damage in
- Infectious mononucleosis like fetus- can be Urine, blood, histological
- Contact with
- Monocytes illness damaged at any specimens
secretions & - Endothelial
- Hepatitis trimester , Primary
Tests
CMV excretions of In immune compromised infection will cause
cells -Microscopy-
(Infectious Infected humans- body fluids - pneumonia significant damage Screen all
Mononucleo shed in saliva and
mucus - Smooth (More dangerous than cytomegalic inclusion pregnant mothers
s-is like urine
- Transplacental membranes
muscle
- retinitis rubella as this is cells ( owl's eye cells) for CMV IgM
illness) (ToRCHeS) cells - Transplant rejection asymptomatic) -viral antigen
- Blood - Some - CMV colitis
- cell culture
Life and sight
transfusion CD8+ Congenital threatening illness in
- ELISA for IgM/ IgG
- jaundice, hepatomegaly, immunocompromised - Quantitative PCR- to
thrombocytopenia, anaemia monitor treatment
- Mental retardation
- Deafness

F1F2 Repeat Campaign 2014AL 

 LATENT INFECTIONS
Epstein Barr Hep C
Virus
( covered in hepatitis)

Hep B
Cytomegalovirus
All Herpes Viruses Human
(Covered in Hepatitis)
HIV
Papilloma
• HSV Virus (Covered in
HIV/AIDS)
(Covered in
• VZV
STD)

(Covered in STD &

Fever with rash)

• An asymptomatic infection (dormant or minimally replicating) capable of manifesting symptoms under

particular circumstances or if activated (reactivation).

• More common with DNA viruses than RNA viruses.

Latency Reactivation
Primary infection
Virus lies dormant/
slowly multiplying
asymptomatically

Pictures to look at before the OSCE

1. EBV- pharyngitis (with exudate), lymphadenopathy

2. CMV- CMV inclusion cells (owls eye cells)

F1F2 Repeat Campaign 2014AL 

 Superficial mycoses
Malassezia furfur
Human-human direct contact
Chronic mild infection of the skin
Hyper-pigmented patches
Pityriasis versicolor/tinea versicolor alu han
• Skin scrapings direct microscopy
(Spaghetti meatball appearance)
Candida
Candida albicans normal flora endogenous
infections
✓ Mouth - oral thrush
✓ Vagina - vaginal thrush
✓ Moist area of skin -intertrigo
✓ Nails
✓ Systemic inf. in immunocompromised
Skin/mucosa becomes red and inflamed.
Mucosa shows white adherent patches & thick
white discharge like curd.
Lesions are very itchy and sore
• Skin scrapings/nails/high vaginal swab
direct microscopy
Gram + budding yeast
• Culture - Sabroud glucose agar
Risks-extremes of age, pregnancy, antibiotics,
DM, immunocompromised
Dermatophytes
Infect keratinized tissue (nail,hair,skin)
Tinea corporis -circular scaling lesion with
central healing & active raised inflammatory
edge.
Tinea capitis - area of baldness with broken hair
stumps & scaling of the scalp
Tinea unguium - discolored, thickened, brittle &
distorted nails
Tinea cruris – inguinal area
• Specimen like skin scrapings, nail
clippings, debris under the nails & hair
with root intact are sent for KOH mount
microscopy or SGA fungal culture.
Candida sp. and other saprophytic fungi cause
skin and nail infections called onchomycoses
Subcutaneous mycoses
Fungi implanted into skin through trauma →
Lead to chronic infection with tissue destruction
and sinus formation (Mycetoma)
✓ Eg: Madura foot ( a fungal infection that
looks like an infection due to
filamentous bacteria such as nocardia)
Systemic Mycoses
Serious and often fatal
Opportunistic fungal infections in
immunocompromised
• Cryptococcal meningitis
Caused by Cryptococcus neoformans (a yeast)
in pigeon droppings. It is negatively stained.
• Disseminated candida infections
• Disseminated aspergillus infections
Dimorphic fungi
✓ Histoplasmosis
✓ Coccidiomycosis
✓ Blastomycosis
Get inhaled from soil in to lungs and
disseminated to many organs to cause systemis
infections.
They cause chronic granulomatous infections.
 Fungal infections

Filamentous fungi / moulds

✓ Fungi are eukaryotic cells Fungi Yeasts

Dimorphic fungi

❖ Filamentous fungi grow hyphae that intertwine to form mycelium

Eg:- Dermatophyes

▪ Epidermophyton
▪ Tricophyton
▪ Microsporum

❖ Yeasts are round or oval shaped. Reproduce by budding.

❖ Dimorphic fungi grows as filamentous fungi in environment but as yeast in body temperature.
 Toxin mediated disease

Exotoxins – proteins that bind to specific receptors → endocytosis → specific action

❖ Neurotoxins ❖ Enterotoxins

Clostridium tetani, Vibrio cholera,

• a gram - anaerobic bacilli found in soil • Gram – bacteria

• form very resistant spores that can survive
for yaers in the soil
• makes tetanoplasmin
tetanoplasmin → binds to nerve endings →
inhibit release of GABA → muscle spasms
• Causes rice water diarrhea. Not seen in Sri
Lanka.
Stimulate production of adenylyl cyclase →
↑ synthesis of cAMP → ↑ Na+ & water
secretion

Clostridium botulinum,
Staphylococcus aureus,
• Found in non-sterilized canned food
• Produces a heat table toxin
• Makes botulinum toxin – food botulism,
• Causes vomiting and diarrhea (food
wound botulism, infant botulism
poisoning)
• Spores resistant to boiling, germinate in
anaerobic environment

Botulinum → inhibit neurotransmitters (Ach) → Bacillus cereus,

paralysis → dyspnea, dysphagia
• Causes food poisoning by a heat stable
enterotoxin (usually in rice)

❖ Cytotoxins
Escherichia coli (ETEC)

Corynebacterium diphtheria, • Produces heat sable and heat labile toxins

• Childhood diarrhea, Travelers’ diarrhea
• Gram + aerobic non sporing bacilli with
Chinese letter appearance
• Via respiratory droplets
Escherichia coli (EHEC)
Diphtheria toxin → enters cells → inhibit
❖ Produces shiga-like toxin/verotoxin
protein synthesis → pseudo membrane
❖ Blood and mucus diarrhea
formation
❖ Streptococcus pyogens produces an erythrogenic exotoxin that gives a red rash called Scarlet fever

Toxic shock syndrome

Exotoxin stimulate T helper cells

Cytokine production in large amounts

Disseminated intravascular coagulation and vasodilation

Shock

eg:-

▪ Erythrogenic toxin and Streptococcal pyrogenic exotoxin (SPE) produced by Streptococcus pyogens.
▪ Staphylococcal toxic shock syndrome toxin (TSST) produced by Staphylococcus aureus.

❖ Inactivated toxins are given as toxoid vaccines

❖ They give good immunity by stimulating antibody production as they are proteins.
eg:- DPT vaccine

❖ Sometimes preformed antibodies can be given to patients to neutralize toxins. No long term
immunity.

eg:- equine anti-tetanus serum

Endotoxins – lipopolysaccharides that are part of the cell wall of gram – bacteria.

➢ Released when bacteria are destroyed.

➢ Pyrogenic. Releases inflammatory mediators in large amounts.
➢ Can cause endotoxic shock
➢ Poorly antigenic. Body cannot make effective antibodies.
eg:- Neisseria meningitidis
 Some respiratory viruses are
Parainfluenza virus 1-4 [PRECIA]
Rhinoviruses
Enteroviruses
Coronaviruses
Influenza virus A, B, C
Adeno virus

 Causative viruses of common cold [Common PRAthiyava]

Coronaviruses
Parainfluenza virus
RSV
Adenovirus
*In addition to above viruses, Rhinoviruses also cause common cold

 Causative agents of pharyngitis [PARIngitis]

Parainfluenza viruses
Adeno viruses
Rhino viruses
Influenza viruses

 Acute laryngotracheobronchitis (croup) [PIA]

Parainfluenza viruses
Influenza viruses
Adeno viruses

 Tracheitis and tracheobronchitis

Influenza viruses (When we look at trachea in front of it, it takes the shape of letter “I”

 Causative viruses of viral pneumonia

Corona viruses
Influenza viruses In Adults (CIA)
Adenoviruses

Parainfluenza
RSV
Influenza In Children ( PRIMary)
Measles virus

 Influenza type C virus DOESN’T appear to causes diseases IN HUMAN

 Influenza virus surface is covered by HA (Haemagglutitin) and NA ( Neuraminidase) spikes.
 Antigenic drift – Relatively minor changes in the HA and NA antigens due to point mutations in the gene.
 Antigenic shift - Occurs only in influenza A viruses due to the acquisition of new gene segments encoding HA
and NA.
 Main method of diagnosing respiratory tract infections caused by respiratory viruses is DETECTING VIRAL
ANTIGENS in the nasopharyngeal aspirate.
 RSV is the COMMENEST cause of fatal acute respiratory infection in infants and young children.
 Rhinovirus is the MOST IMPORTANT cause of COMMON COLD and UTI.

 Rhinovirus is HIGHLY INFECTIOUS. (Very small infective dose)

 Adenoviruses are DNA viruses.

 Adenoviruses are the SECOND COMMENEST cause of DIARRHOEA in children. COMMONEST cause is Rotavirus.

 Rabies viruses slowly spread along the nerves to the CNS.

 Specimen for the diagnosis of Rabies

Rabid animal – Impression smears are made from the hippocampus area.
Human – Corneal impressions and skin from the nape of the neck.

 Laboratory tests for the diagnosis of Rabies are demonstration of ,

-Rabies virus inclusion bodies ( Negri bodies ) in the hippocampus using the Sellar’s stain.(Negro & Stellar)
-Rabies virus antigen in the brain or corneal impression using indirect immunofluorescence.

 RABIES IS ALWAYS FATAL.

 Polio virus is an ENTEROVIRUS.

 Humans are the ONLY SOURCE of polio virus – otherwise to eradicate – must vaccinate animals as well.

 Polio virus enters the next source through the faeco-oral route,

 In poliomyelitis,
-few patients develop aseptic meningitis without paralysis.
-small proportion develops acute flaccid paralysis.

 Polio virus is SENSITIVE to drying and high temperature.

 The salk vaccine is a killed type vaccine.

 Mumps and Measles viruses are paramyxoviruses.

 Meningitis , Mumps orchitis, Pancreatitis may occur as complications in Mumps.(MOP)

 Humans are the ONLY KNOWN HOST OF MUMPS, MEASLES AND RUBELLA viruses.

 A live attenuated vaccine is available as a trivalent Measles-Mumps-Rubella (MMR) vaccine.

 Measles is a major cause of preventable blindness in the world.

 Measles, Rubella and CRS are NORTIFIABLE diseases.

 Live attenuated Measles vaccine is given at 9 month of age and in combination with the Rubella vaccine (MR) at
3 years of age as a part of EPI.

 Measles during early pregnancy may cause fetal death or congenital rubella syndrome (CRS) in the baby.
 Rubella is transmitted by RESPIRATORY DROPLETS.

 The live attenuated rubella vaccine is given in combined with measles vaccine of EPI.

Arboviruses are viruses which transmitted by a blood sucking arthropds

Dengue virus. JE virus

It isn’t a zoonosis. It is a zoonosis.
There is man to man transmission. There is no man to man transmission.
The man is an END HOST.
The animals are the only source.
Pigs act as reservoirs.

Mosquito – Aedis aegypti, Aedis albopictus Mosquito – Culex tritaeniorhynchus, Culex gelidus
Breeds in small collections of water. Breeds in larger collections of clean water
Indoor biters. Outdoor biters

Common in urban areas. Common in rural areas.

 Hepatitis A virus transmitted predominantly through faeco-oral route.

 Hepatitis caused by Hepatitis A virus. It can rarely lead to fulminant hepatitis and liver necrosis.
 Hepatitis B virus is a DNA virus.
 Complications of HBV vaccines,
-Fulminant Hepatitis
-10% become chronic carriers. Some of these carriers develop chronic hepatitis which sometimes end in
cirrhosis and primary liver cancer.
 Hepatitis C infection can lead to chronic liver diseases and its complications such as cirrhosis and hepatocellular
carcinoma.
 Hepatitis D virus is detective as it can only replicate only in concurrence with replication of HBV to
1. Co – infection
2. Super infection

 Hepatitis E virus transmitted through the faeco-oral route.

 Herpes viruses are DNA viruses.
 After the PRIMARY INFECTION, herpes viruses remain LATENT in the host and may REACTIVATE from time to
time.
 Many animal herpes viruses are proven causes of CANCERS.
 HSV – 2 the main course of genital herpes. Sometimes HSV -1 too can cause genital herpes.
 HSV – 1 is usually excreted in the saliva of latent carriers and is spread by direct contact with oral secretions.
 HSV – 2 is shed in the genital secretions and is usually spread by sexual contact.
Mycoplasma DO NOT have cell walls and cannot be gram stained
Mycoplasma CAN BE GROWN in cell free culture media BUT Chlamydiae and Rickettsiae CANNOT BE GROWN in cell free
culture media.
Chlamydiae and Rickettsiae are OBLIGATE INTRACELLULAR parasites.
Chlamydia trachomatis D-K transit from mother to baby during passage through the birth canal BUT NOT through the
placenta.
Chlamydia is NOT an exclusive human pathogen.
Group A streptococcus aetiology.
C (see) The NIPPLES:
 Cellulitis
 Tonsillitis & peritonsillar abscess
 Necrotizing fasciitis
 Impetigo
 Pharyngitis
 Puerperal Sepsis
 Lymphangitis
 Erysipelas
 Streptococcal TSS
Meningitis causing bacteria NHS:
 N eisseria meningitidis
 H aemophilus influenzae
 S treptococcus pneumoniae
Note: NHS is an acronym for National Health Service in several countries.
Streptococcus pneumoniae infections - COMPS
 C-Exacerbations of Chronic bronchitis
 O-Ottis media
 M- Meningitis
 P- Pneumonia
 S - Sinusitis
UTI causing organisms - KEEPS
 K- Klebsiella
 E- E. coli
 E- Enterococci (Group D streptococci)
 P- Pseudomonas aeruginosa
 S- Staphylococcus saprophyticus
 Mycobacteria are ACID FAST BACILLI but not either gram positive or gram-negative bacilli. Mycobacteria are
SLOW GROWERS. Mycobacteria are NON-CAPSULATED, NON-MOTILE, NON-SPORING bacteria.
 Mycobacterium tuberculosis is more resistant to disinfectants than other bacteria but may be destroyed by
phenolic disinfectants and EXPOSURE TO UV LIGHT.
 There are no carrier states in Mycobacterium tuberculosis infections.

 Mycobacterium tuberculosis is resistant to drying.

 BCG vaccine is given to prevent TB.
 Mycobacterium leprae cannot be grown in artificial media.
 Treponema pallidum CANNOT be cultured artificially in the laboratory.
 Mycobacterium leprae is NOT VERY INFECTIOUS. Prolonged contact is necessary for transmission.
 Spirochaetes (note the spelling) enter in to the body by penetrating intact mucosae or through abraded skin
(and not through intact skin)
 Treponema pallidum causes congenital syphilis by crossing the placenta (and not during birth that’s why there
can be even abortions). (During primary, secondary, and latent syphilis)
 An VDRL test is not enough to confirm the presence of syphilis.
 Leptospirosis is an important cause endemic ZOONOSIS in Sri Lanka.
 If an article is rendered completely free of organisms including spores, the article is STERILE.
 If only the pathogenic bacteria are removed it is called DISINFECECTION.
 Disinfectants are used on articles and human waist. Antiseptics are used on body surfaces.
 NEVER REFRIGERATE CSF, blood for culture or specimens for isolation of Haemophilus species,
 Streptococcal pneumoniae or Neisseria species.
 Specimens for viral isolation should be transported in ICE and processed quickly or frozen at - 70°C.
 Specimens for anaerobic culture should be submitted in an appropriate transport medium or collected and
transported under anaerobic conditions.
 Adults - an EARLY MORNING EXPECTORATED specimen is preferable. If there is a delay in transport the specimen
should be held at ROOM TEMPERATURE as Haemophilus influenzae is cold sensitive.
 Children-A LARYNGEAL SWAB is preferable as they cannot expectorate.
 In TB THREE EARLY MORNING specimens should be collected on THREE CONSECUTIVE days. They may be
refrigerated and submitted together.
 While collecting CSF strict ASEPTIC TECHNIQUE should be used.
 For the diagnosis of renal TB THREE EARLY MORNING specimen of urine, collected on THREE consecutive days
should be sent. ALL URINE passed should be collected.
 Urine specimens should be held at 4°C in the refrigerator until it is transported.
 HIGH VAGINAL swabs NOT endocervical swabs are used in the diagnosis of VAGINOSIS, VAGINITIS, and UTERINE
SEPSIS.
 ENDOCERVICAL SWAB is used for the diagnosis of GONOCOCCAL and NON-GONOCOCCAL cervicitis
Classification based on mode of transmission

Syphilis-Treponema Pallidum
Gonorrhoea-Neisseria Gonorrhoea
Lymphogranuloma venereum-Chlamydia trachomatia D-K
AIDS-HIV
Chancrold-Haemophilus ducreyi
Genital Herpes-HSV2(mainly)
-HSV1
Hepatitis- hepatitis B,D (no C)
Warts-Human papilloma virus

Vertical transmission -during birth

Neonatal conjunctivitis-Neisseria gonorrhoea
Neonatal conjunctivitis & neonatal pneumonia- Chlamydia trachomatis D-K
Neonatal herpes- HSV2
AIDS-HIV

Blood and blood products

AIDS-HIV
Hepatitis-Hepatitis B,C
Syphilis- Treponema pallidum

Faeco-oral route
Typhoid fever-Salmonella typhi
Shigella dysentery-shigella
Polio-polio virus
Viral gastroenteritis- rotavirus,adenovirus
Hepatitis-hepatitis A,E

Vertical Transmission-via placenta

Listeria monocytogenes
Congenital syphilis-Treponema pallidum
Toxoplasma gondi
CRS-Rubella
Varicella zoster
Cytomegalovirus
HIV
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 Protozoa
Entamoeba histolytica Balantidium coli Giardia lamblia Cryptosporidium parvum Trichomonas vaginalis
Disease Amoebiasis Balatidiasis Giardiasis/ Lambliasis Cryptosporidiosis Trichomoniasis
Site of infection Large intestine Ileum – large intestine Small intestine (duodenum, jejunum, Small intestine Genito-urinray tract (vagina, urethra,
bile duct, gall bladder) prostate gland)
Transmission Feco – oral Feco – oral Feco – oral Feco – oral Sexual
Trophozoite Morphology Granular endoplasm 2 nuclei Pear shaped No trophozoites or cysts Oval or pear shaped
Clear ectoplasm Macro nucleus – kidney shaped Bilaterally symmetrical Life cycle occurs through Undulating membrane
Elongated Micro nucleus – rounded small Posterior end tapered infective oocysts, sporozites, Single nucleolus
Single eccentric nucleus Anterior end rounded merozites and macro & micro Axosystole long
Nucleolus – acentric central karyosome Bi nucleated gamonts 4 flagella at the anterior end
Peripheral chromatin Central axosystole
Endoplasm includes RBC & food Sucking disc on ventral surface to
vacuoles attach on mucosa
Features Motile - pseudopodia Motile – cilia Motile – flagella Motile – flagella
Feeding form
Inside the host
Reproduction Binary fission Transverse binary fission Longitudinal binary fission Longitudinal binary fission
Cyst Morphology Round/ oval Thick wall Oval No cysts
Smaller Smaller Smaller
1-4 nuclei 2-4 nuclei
Sausage shaped chromatid bodies Thin outer wall
Features Infective Infective Passed in faeces
Non motile Passed in faeces
Passed in faeces
Outside the host
Dominant resistant form
Clinical features Hepatic amoebiasis Forms nests and small abscesses Adhere to epithelium Watery diarrhoea Erythema
Amoebic abscess Intense inflammation of the Absorb nutrients Purulent discharge
mucosa and submucosa of ileum Act as a barrier for gut absorption Itchiness
Diarrhoea
Steatorrhea
Reduced pancreatic lipase activity
Blood mucous diarrhoea Found Found Not found Not found
Diagnosis Trophozoites – diarrhoea Trophozoites in loose stools Trophozoites in loose stools Light microscopy on stool smears Light microscopy – mobile parasite on wet
Cysts – chronic infection, carriers Cycts in formed stools Cycts in formed stools (special stains, concentration mount
Light microscopy – wet smear on Light microscopy – wet mount Light microscopy – wet smear on techniques) Fixed parasite on stained slide
saline or iodine (motile parasite) or stained smear saline or iodine Serology – IFAT (indirect Culture
Culture (fixed parasite) fluroscent antibody test) IgA
Serology PCR Acid KOH test
PCR Fluorscent antibody test
Worldwide distribution Yes No No Yes Yes
Human is the only reservoir Only pathogenic ciliate Most common gut protozoan Common cause of watery One of the most resistant trophozoite
Largest intestinal protozoa pathogen diarrhoea in HIV/ AIDS, travellers
Least common protozoan and children
pathogen Found in animals
Found in animals

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 Ascaris lumbricoides (Round Necator americanus (Hook Strongyloides stercoralis Trichinella spiralis Trichuris trichiura (whip worm) Enterobius vermiclaris
worm) worm) (Facultative parasite) (STH) (Pin worm)

Habitat Jejunum of man Jejunum of man Duodenum & Jejunum (Under Pig/ Rat/ Man Small intestine Large intestine, caecum & Caecum, appendix &
(not attached) (STH) (STH) mucosa) / Dogs /Monkeys appendix of man (mainly) adjascent portion of
ascending colon of man
(mainly)
Indication Ascariasis Necatoriasis Strongyloidiasis Trichinosis Trichuriasis Enterobiasis
Male 15-25 cm/ curved posterior end 0.7cm Head bent sharply 0.7 mm (In soil) 1-2mm/ curved posterior end 30-45mm / coiled posterior end 2-5mm/ curved posterior
opposite to the body end
curvature
Female 20-40cm 1cm 2mm 2-4mm/ bluntly rounded 35-50mm / bluntly rounded 8-13mm
posterior end posterior end
Egg Round/oval, unsegmented Oval bluntly rounded ends. In soil from free living, Viviparous → No egg, produce Lemon shape/paddy seed shape Plano – convex
ovum Segmented ovum, colourless. Adult worms in soil OR in larva. Outer coat is bile stained →brown Thick double wall →
Mamillated outer albuminoid Shell → thin transparent mucosa due to parthenogenesis at ends → mucoid plugs colourless
layer. hyaline egg hatches out in produce rhabditiform larva Larva deposit in mucosa→ Develop in water and soil (need Ovoviviparous →
Hyaline shell in middle soil. which convert to filariform circulation→encyst in striated moist) form rhabditiform larva rhabditiform larva inside
(thick transparent glycogen) (moulting twice) muscle No soil phase
If unfertilized → barrel shape + No soil phase
granules
Epidemics URBAN in children Rural In tropics Raw meat consuming countries Tropics with poor sanitary Widest distribution
(5-9 yrs) In adults > children Not common in SL Common in children co-exist with Family infection, common
ascariasis in children
Infective Egg with Rhabditiform larva (L2) Filariform larva (L3) Filariform larva which is Encysted larvae form pork Embryonated eggs which are New laid eggs become
stage produced by rhabditiform larva produced by rhabditiform larva infected after 4-6 hrs
from eggs
Diagnostic Fertilized eggs in faeces Eggs in faeces Rhabditiform larvae in fresh Encysted larvae in muscle biopsy Eggs in faeces Adults worms in faeces
stage faeces & In duodenal fluid Serology Egg in perianal swabs
Complications Majority → Asymptomatic Due to larva penetration Majority → Asymptomatic Majority → Asymptomatic Majority → Asymptomatic Pruritus of perianal &
Allergy for larva  Ground itch Perineal region→ due to
Abdominal pain
Ascaris pneumonitis  Maculo-papules Moderatly mid epigastric pain Due to intestinal invasion migration of gravid female
Loeffler’s syndrome  Erythema Nausea  Vomiting worm
Dysentery Malnutrition
Malnutrition Vomitting  Diarrhoea Cause restlessness,
 Low appetite Due to migratory larvae  Abdominal pain irritability,
Nausea Weight loss
 Competition for  Pneumonitis Heavily weight loss  Nausea Sleep disturbances
micronutrients Dysentery Anaemia
 Inhibit trypsin → inhibit Malabsorption Vomiting Appendicitis → due to
Due to blood sucking adult Due to muscle invasion
protein digestion worm. Fat diarrhoea  Periorbital oedema blockage from adult
(Iron
 Change in intestinal
Reduce food
 Severe anemia  Fever worms
Larva currens in auto infections intake Rectal deficiency)
epithelium  Skin rashes
 Low growth & cognitive Hyperinfection Xn → High  Elevated muscle enzymes prolapse Granuloma formation →
function parasite confined to GIT  Eosinophilia – due to Due to migration of gravid
 Vit A deficiency straining in frequent stool passage female worm
Disseminated strongyloides in Due to encystment More prone to Amoebiasis (E.
immunosuppressed people hystolitica)
Ascaris migrations  Weakness
Bacterial & viral infection
 Cachexia
Surgical emergencies
(volvulus,obstruction) Malnutrition
Trichuris dysentery Syndrome
(TDS)
Wasting (Low weight for height)
Stunting (Low height for age)

F1F2 Repeat Campaign 2014AL 

Teania solium (Pork tapeworm)
 Globular scolex
 4 suckers
 Rostellum Taeniasis- due to adult worms
 2 rows of hooks
Cysticercosis- due to invasion of larval stage
 >15 lateral uterine branches in gravid
segments Cerebral – convulsions focal lesions
 Spherical egg
Ocular – blurred vision, retinal detachment
Taenia saginata (Beef Tapeworm)
 Quadrangular scolex
 4 suckers
 No rostellum or hooks
 >15 lateral branches in gravid segments
 Spherical egg

Dipylidium caninum (Dog Tapeworm) Echinococcus granulosus (Dog Tapeworm)

 Found in dogs  Smallest found in SL
 Humans are infected by ingesting fleas containing larval stage  Cause hydatis disease / Cystic echinococcosis → cause
pressure symptoms
Hymenolepis diminuta (Rat tapeworm)  Slow growing
 Definitive host → Rats small intestine
 Intermediate host → Rat flea
 Human are accidentally infected by food via infected fleas
 Diagnose by eggs and faeces Hymenolepis nana (Dwarf tapeworm)
 Found in SL  In India- Not found in SL
 No intermediate host
Diphyllobothrium latum (Fish Tapeworm)  Definitive hosts are humans and rats
 Not found in SL
 Adults worms are in humans Bertiella studeri (Monkey Tapeworm)
 Infected by eating raw fish with larva  Definitive host → Monkey
 Inhibit ileum & compete for Vit B12  Intermediate host → Mites
 May cause pernicious anaemia  Found in SL (In southern province)

F1F2 Repeat Campaign 2014AL 

 PARASITOLOGY
PRACTICAL HANDBOOK

Foundation Module 2
Infectious and Parasitic Diseases Module
DEPARTMENT OF PARASITOLOGY
FACULTY OF MEDICINE, COLOMBO

1
FOUNDATION MODULE 2/ INFECTIOUS AND PARASITIC DISEASES
MODULE

This manual has been designed to help you with your practical classes in Parasitology during the
Foundation Module 2 and Infectious and Parasitic Diseases Module.

Brief descriptions of the medically important parasitic stages and gross specimens have been
provided. However, it is by no means complete and should be supplemented by further reading
of recommended text books in Parasitology.

Before starting any practical work:

Read the instructions
Listen to the demonstrator
Label all slides to be used
And if you have any doubts ask questions.

Prepared by:

Professor Deepika Fernando

Dr. Sharmini Gunawardena
Dr. Sanath Senanayake

Technical Assistance
Ms. Himali Gunatilaka
Ms. Dilhani Samarakoon

4th October 2012

2
 Contents Page Number

PRACTICALS:

Use of the Microscope 3

Malaria 6

Filariasis, Lishmaniasis, Toxoplasmosis and Trypanosomiasis 14

Intestinal and Urogenital Protozoa 16

Intestinal Nematodes, Cestodes and Trematodes 23

Medicali important Arthropodes 30

Snakes 36

3
PRACTICAL: USE OF THE MICROSCOPE

Introduction
The microscope is one of the most important instruments in a biology laboratory. There are many
small objects such as the malaria parasites which cannot be seen by the unaided human eye. The
microscope magnifies the images of such objects thus making them visible.

Microscopes used in clinical practice use a beam of light to view specimens and thus they are
called light microscopes. As these use two lens systems they are termed compound light
microscopes. A compound light microscope with a single eye-piece is called monocular; one
with two eye-pieces, binocular.

(2) (1)

(4)
(3)
(5)

(6)

(6 a)
Condenser (7)
(10)
(8)

(11)
(9)

(12)

Parts of the microscope

Practical Exercise : Identify the parts of the microscope given below:

1. Eye-piece (the ocular lens)

• It is the uppermost series of lenses through which an object is viewed.
• The lens magnifies the image formed by the objective. The magnifying power of the eye-
piece is in the range 5x-20x.
• A movable pointer may be attached to the inside of the eye-piece.
• In binocular microscopes, the two eye-pieces can be moved closer or farther apart to
adjust for the distance between the eyes by pulling–pushing motion or by turning a
knurled ring.

2. Microscope tube
• Holds the nosepiece at one end and the eye piece at the other end.
• It can be of the monocular or the binocular type.
• Conducts light rays.

3. Arm
• Supports the upper parts and provides a carrying handle.

4
 4. Nose-piece
• The nose-piece is attached beneath the arm of the microscope tube.
• It carries the objectives and rotates with them.
• The objectives are arranged in sequential order of their magnifying power from lower to
higher. This helps to prevent the immersion oil from getting on to the intermediate
objectives.

5. Objectives (objective lenses)

a. Low-power objective: holds the low power lens used to view the object (10x).
b. High-power objective: holds the high power lens used to view the object in even greater
detail (40x).
c. Oil immersion objective: holds the oil immersion lens and is used in conjunction with
immersion oil to view objects with the highest magnification (100x).
• The image of the specimen first passes through the objective.
• The magnifying power is marked on the lens and is usually colour-coded for easy
identification.

6. Mechanical stage
• A movable stage that aids in the accurate and steady positioning of the slide.
• The mechanical stage allows the slide to be moved to the left, right, forward or backward
by rotating the knobs.
• It is fitted with fine vernier graduations as on a ruler. This helps in relocating a specific
field of examination.

7. Condenser
• Focuses the light onto the specimen and illuminates it.
• It controls the amount of light and contrast.

8. Diaphragm
• Controls the amount of illumination used to view the object.

9. Light source/ Illumination

• A mirror or a built-in light source is used for illumination in the microscope.
• It directs a beam of light up through the object.

10. Coarse-adjustment knob

• Knob used to bring the object into approximate focus.
• Used only with the low-power objectives.

11. Fine-adjustment knob

• Knob used to bring the object into final focus.
• The fine focusing knob changes the distance between the specimen slide and objective
very slowly and is used to view objects with high power objectives.

12. Base
• The flat surface of the microscope that rests on the table.

The magnification

The objective forms an enlarged image of the object. The eye-piece enlarges this image still
more. The total enlargement or magnification is the product of the magnifying powers of the
objective and the eye-piece.

For example, if the magnifying power of the eye-piece is 10x and that of the objective is 100x,
the total magnification is 10x100 = 1000.

5
Practical exercise: Use of the light microscope

1. Ensure that the light intensity control is set to low, turn on the light and increase the
brightness to give a bright light output.
2. Raise the sub-stage condenser fully and adjust the iris of the diaphragm for minimum
light. (In most new models the condenser is fixed and the need to adjust it does not arise).
3. Rotate the nosepiece to get the low power objective (x10) into position i.e. above the
condenser.
4. Take the stage down using the coarse adjustment control and place the specimen slide on
the stage using the retaining mechanisms to hold it in place.
5. While looking carefully from a side, take the stage up close to the objective lens (do not
knock the lens on the slide; this cannot normally occur when a low power objective is
chosen).
6. Set the eye-pieces to the correct width for your eyes so that you can look down through
both comfortably.
7. Focusing: look into the eyepieces (with both eyes open) slowly lower the stage to bring
the specimen into focus. Use the coarse adjustment control first and then the fine one.
Slight movements of the specimen while focusing by using the mechanical stage controls,
may aid you to find the object.
8. Proceed and examine the specimen under higher magnification. Depending on the
specimen and the magnification used, you will need to:
• Adjust the condenser if necessary
If adjustable it should be at a low position when low power objectives are used. When
changing to higher magnifications, slowly raise it up to get a sharp and crisp image (this
must be done only after a specimen has been focused on the stage).
• Set the Iris Diaphragm
When the iris-diaphragm is fully opened, the image is flooded with light and definition is
lost due to “white-out”. As the diaphragm is closed, controlling the amount of light
passing through the condenser, the image becomes clearer and sharper as the contrast
improves.
9. Using the oil immersion lens:
Once you have focused the specimen under low power, centre it in your field of view,
place a drop of oil (on the illuminated spot of the slide) and bring the oil immersion lens
into position. Once you have changed to the oil immersion lens, use only the fine focus
knob (fine focus adjustment) to focus.
When light passes through glass into air it bends from the original direction. Thereby, in
the microscope, the light rays bend as it is passing through the glass slide on the
microscope stage into the layer of air between it and the objective lens. This limits the
amount of light entering the objective and also affects its resolving power resulting in the
production of a poor image. The bending effect of light is avoided by the use of
immersion oil which has the same optical properties as glass. The commercially available
immersion oil for microscopes has the same refractive index as glass. Thus replacing the
layer of air between the lens and the slide with immersion oil gives a well defined image
of the specimen.
10. Once you have finished examining:
Move the stage down and remove the slide. Change to a low power objective, reduce the
light intensity to minimum and switch off the lamp.

6
PRACTICAL : MALARIA

PRECAUTIONS IN HANDLING A BLOOD SAMPLE

The principal blood borne diseases are:

• Hepatitis
• Acquired Immunodeficiency Syndrome (AIDS)
• Malaria

The collection and handling of blood samples present a potential risk of infection. This risk can
be reduced by taking the following precautions:

• Wear protective gloves when handling blood or taking blood samples.

• Avoid getting blood, including that from unstained slides, on your fingers or hands.
• Cover any cuts or abrasions on your hands with adhesive dressings.
• Take care not to prick yourself or others with any sharp instrument that has been in
contact with blood.
• Never use disposable lancets more than once.
• Always wash your hands with soap and water after completing any task that involves the
handling of blood.
• If blood does get on to your skin, wipe it off quickly with cotton wool dampened with
alcohol and wash the affected area with soap and water as soon as possible.
• Any materials contaminated with blood, such as lancets, cotton swabs and discarded
slides, should be boiled for 20 minutes, or placed in a solution of bleach or sodium
hypochlorite (available chlorine level 10 000 parts per million), then disposed of safely
by burial or incineration.

TYPE OF SAMPLE REQUIRED FOR MALARIA DIAGNOSIS

The blood for malaria parasite detection can be taken by finger prick method or by venepuncture.
If venous blood is collected by venepuncture the blood is transferred to EDTA (Ethylene
Diamine Tetra Acetate) tubes.

Collection of blood by finger–

prick method

Collection of blood by
venepuncture

7
METHOD OF CAPILLARY BLOOD COLLECTION FOR MICROSCOPY

Whenever possible the specimen should be collected before treatment. Malaria is excluded with
3 negative smears taken 12 hours apart. Further films are needed if clinical suspicion is high.

Labeling the slide

Label the slide with a wax pencil by writing at one end

of the slide. The label should contain the patient’
name/reference number and date

Disinfecting the finger & Stimulation of blood circulation

Clean and disinfect the finger with a cotton wool

soaked in 70% isopropyl alcohol.

Puncturing the finger

Puncture the ball of the finger with a sterile lancet

Collection of blood for the thin smear

Apply gentle pressure on the finger and collect a
single small drop of blood, about this size •, on the
middle of the slide. This is for preparation of the thin
smear.

8
Collection of blood for the thick smear

Apply further pressure to express more blood

and collect two or three larger drops, about this
size •, on the slide about 1cm inner to label.

Thin smear preparation

Wipe the remaining blood away from the finger with a
piece of cotton wool.

Preparation of the thin smear: use a second clean slide as

a “spreader”. Touch the small drop (in the middle of the
slide) with the spreader and allow the blood to run along
its edge. Firmly push the spreader along the slide,
keeping the spreader at an angle of 45°. Make sure that
the spreader is in even contact with the surface of the
slide all the time the blood is being spread.

Thick smear preparation

Preparation of a thick smear: Using the corner of the

spreader, quickly join the drops of blood and spread
them to make an even, thick smear. The circular thick
smear should be about 1 cm (1/3 inch) in diameter.
Allow the thick smear to dry.

The smears for staining and examination looks as given below:

9
IMPORTANCE OF PREPARING THICK AND THIN SMEARS

• About 20 times more blood can be examined in a thick smear than in a thin smear in the
same period of time. A thick blood smear is therefore more suitable for the rapid
detection of malaria parasites. The detection of malaria parasites may not be successful
by examining only a thin smear if the parasitaemia is low. Therefore, examining a thick
smear is of utmost importance. In a stained thick smear, as the red cells are lysed, the
intact stained parasites are readily made out against a clear background. Thick smears are
also used for the estimation of parasite density.

• Thin smears are required to confirm the species and stage of the malaria parasite present.
As the thin film is fixed the red cells are intact and so are the parasites within them and as
such their morphology can be studied. Thin films are also suitable to calculate
parasitaemia as individual cells can be easily counted.

PRACTICAL EXERCISE: USE THE MICROSCOPE AND EXAMINE THE STAINED

BLOOD SMEAR PROVIDED

1. Switch on the light source.

2. Adjust the eyepieces by sliding them horizontally until they fit both eyes comfortably and
the two fields merge.
3. Place the dry stained slide on the stage. Make sure that the slide is not upside down.
Secure the slide to the slide holder of the mechanical stage.
4. Rotate the nose-piece to bring the 10x objective into position and raise the stage to its
maximum.
5. Move the slide with the adjustment knobs to bring the tail end of the blood smear into the
field of view.
6. Focus the “tail end” of the blood smear under the 10x objective using the coarse focusing
knob and lowering the stage. Obtain sufficient illumination by closing or opening the iris
diaphragm. For low power objectives light has to be reduced and for higher power
objectives it has to be increased.

Examine the tail end of the thin

blood smear where the red cells do
not overlap with each other.

‘Tail end’ of the thin smear

7. Shift the 10x objective away and add a drop of immersion oil on to the illuminated spot
of the smear and bring the 100x objective into position.
8. Open the iris diaphragm fully. Focus the cells using only the fine adjustment (fine
focusing) knob. (Do not use the coarse adjustment knob to focus. This is to prevent any
possible damage to the lens).
9. Identify the species and stage of any parasite on the smear.
10. After examination, lower the stage and swing the lowest power objective into position
before removing the slide (Never attempt to remove the slide when 40x or 100x
objectives are in position as this may scratch and damage the lenses).
11. Wipe off any oil from the lenses and the microscope stage using lens tissue that has been
provided.
12. Switch off the microscope.

10
DEMONSTRATIONS

STAGES OF Plasmodium vivax

a) Ring stage – Blood smear x 1000

- Red cell enlarged

- Red cell surface may show very fine pink dots- stippling or
Schuffner’s dots
- With the standard stains (Giemsa’s or Leishmann’s) the
cytoplasm stains blue and the nucleus red
- Parasite shows a coarse (thick) cytoplasm with a single nucleus
(Lasts about 10-12 hours in the blood)

b) Amoeboid stage – Blood smear x 1000

- Red cell enlarged

- Stippling marked
- Amoeboid trophozoite with irregular cytoplasm with scattered
yellow brown malarial pigment and a single nucleus
(Lasts about 24 hours)

c) Mature schizont – Blood smear x 1000

- Red cell enlarged

- Stippling marked
- Pink nuclei 14-24
- Malarial pigment clumped in center

d) Female gametocyte – Blood smear x 1000

- Enlarged red cell

- Schuffner’s dots
- Parasite occupies almost entire cell
- Compact nucleus usually eccentric
- Evenly scattered malarial pigment

e) Male gametocyte – Blood smear x 1000

- First three points as above

- Diffuse nucleus usually central
- Evenly scattered malarial pigment

11
STAGES OF Plasmodium falciparum

a) Ring stage – Blood smear x 1000

- Red cell not enlarged

- Clefts may be seen in the red cell: Maurer’s clefts
- Small delicate thin hair like ring of cytoplasm stains blue with standard stains (Giemsa’s
or leishmann’s) single nucleus stains red in color
- Multiple parasites may be seen inside a single red cell – Polyparasitism
- May have two nuclei in a ring - Double nuclear phenomenon
- "Accole" forms may be found closely applied to the edge of the red cell
(Ring stage lasts about 24 hours in the blood)
The late trophozoites and schizonts of P. falciparum are not usually seen in peripheral blood.

b) Female gametocyte - Blood smear x 1000

- Crescent shaped, longer and more pointed than the male gametocyte
- Compact pink nucleus in center
- Surrounded by a halo of jet black malarial pigment

c) Male gametocyte - Blood smear x 1000

- Sausage shaped
- Rounded ends
- Diffused nucleus
- Scattered pigment

12
THE FOLLOWING ARE THE STAGES OF THE PARASITE THAT MAY BE SEEN
WHEN EXAMINING UNDER OIL IMMERSION (X100) OBJECTIVE.

Stages of Plasmodium vivax

13
Stages of Plasmodium falciparum

14
PRACTICAL : FILARIASIS, LEISHMANIASIS, TOXOPLASMOSIS &
TRYPANOSOMIASIS
FILARIASIS

Wuchereria bancrofti – microfilaria x 1000

- Smooth graceful curves

- Cephalic space square
- Body nuclei regularly arranged, discrete,
countable, similar in size and shape
- Tail devoid of nuclei
- Sheath visible

Dirofilaria repens adult – filarial worm of dog which can cause a zoonotic infection
in humans.

TOXOPLASMOSIS

Toxoplasma gondii

a) Pseudocysts with tachyzoites x 100

- Nuclei of macrophages stain purple

- Free cresentic shaped tachyzoites with
one end rounded and other end
pointed

b) True cyst in brain tissue x 100

- Thick walled cyst

- Elongated bradyzoites with a single
terminal nucleus enclosed within

15
TRYPANOSOMIASIS

Trypanosoma species – Trypomastigote form in blood smear x 1000

Trypanosoma gambiense and T.rhodesiense cause African trypanosomiasis or sleeping
sickness, while T.cruzi is the causative agent of Chagas disease.

- Found extra-cellularly
- Spindle shaped
- Blunt posterior end and narrow anterior end
- Nucleus oval large centrally placed
- Flagellum arises from the posterior end

LEISHMANIASIS

Leishmania species - The causative agent of Visceral leishmaniasis and Cutaneous

leishmaniasis belong to the genus Leishmania. The Leishmania parasite exists in two
morphological forms an amastigote and a promastigote. The amastigote is the only form of
parasite found in man while the promastigote is found in the sand fly gut and when
Leishmania are cultured.

Amastigote form x 1000

- Round to oval body
- Nucleus and rod shaped kinetoplast together gives it a
“dot and dash” appearance
- Found within the phagocytic vacuoles of the macrophages

16
PRACTICAL : INTESTINAL AND UROGENITAL PROTOZOA
COLLECTION OF FAECAL SAMPLES
Collection of appropriate faecal samples must take into account the various parasitic
forms that can occur within the human gastrointestinal tract, particular attention being paid to the
most convenient stage that will confirm the presence of parasites and identify species.
The irregular release of helminth ova and protozoan cysts (especially in chronic
infections) makes it necessary to examine three samples routinely from each patient, on alternate
days. On occasion up to six samples may be necessary in a clinically suspect case. Confirmation
of successful treatment can be made by further examination of a single sample after completion
of treatment.
METHOD OF COLLECTION
• Collect approximately 10g of fresh faeces uncontaminated by urine or water, using a
wooden spatula, into a clean, leakproof, wide-mouthed container with a screw cap
e.g. yogurt cup.
• The container should be free from antiseptics and disinfectants.
• Label the samples clearly with the patient’s name, reference number, date and time of
collection. All samples should be accompanied by a request form, from the physician
giving the relevant clinical details and recent travel history.
• Samples and forms from patients with confirmed or suspected diagnosis of certain
infectious diseases such as AIDS or hepatitis should be clearly labeled with a ‘risk of
infection’ “Biohazard” vinyl tape.
• Most viable parasites are susceptible to desiccation or temperature variation. If the
time lapse between collection and observation is considerable, depending on the
parasite, it may be necessary to add some form of preservative to the faeces to retain
the morphology as near to the original as possible. Formed samples can be kept in a
refrigerator at + 4° C for a short while, but not in an incubator. Whole worms or
segments passed should be placed in a separate container.

DELIVERY AND TRANSPORTATION

• Formed faecal samples without evidence of blood or mucus should be examined
during the day of passage. It is possible to store these samples for up to 4 hours at +
4° C.
• Soft, unformed or liquid faecal samples and those containing blood or mucus may
contain vegetative, trophozoite forms of protozoa. These samples should be delivered
to the laboratory with the minimum of delay, preferably within 30 minutes to 1 hour
of collection. (Amoebic trophozoites may still be active in unformed faeces up to
several hours after passage but the time depends on the external temperature and is
unpredictable).

MACROSCOPIC EXAMINATION OF STOOLS

a) Consistency
Faecal consistency varies with diet but certain clinical conditions associated with parasite
presence may be suggested by particular consistencies. The presence of protozoal trophozoites in
the stools will depend on the consistency and the frequency of passage of faeces. Trophozoites
are more likely to be found in (ii) or (iii) and cysts in (i).

Stools should be recorded as:

(i) Formed : Normal shape and consistency. Formed stools from which the water content
has been reabsorbed will contain few trophozoites and principally the cyst
stage of protozoa.
(ii) Semi-formed or unformed : Soft faeces with no regular shape.
(iii) Liquid : Note colour and any flakes of mucus or blood present.

17
b) Composition
The stool may contain blood and mucus as evidence of ulceration or colitis due to invasive
amoebae, bacillary dysentery or inflammatory bowel conditions. It may also indicate occult
blood from gastric ulcers or conditions such as giardiasis. It may also have pus, froth,
undigested food, vegetable fibres, fat etc.

Faeces may contain adult helminthes such as Ascaris lumbricoides, Enterobius vermicularis or
segments of Taenia sp. Gravid Taenia segments are frequently motile for several days and may
migrate to the top of the container.

c) Colour
Pale yellowish stool are passed in steatorrhoeac conditions such as giardiasis or tropical sprue.
Dark or black stools occur when iron or bismuth is taken or when there is intestinal
haemorrhage.

d) Smell

e) Amount

MICROSCOPIC EXAMINATION OF STOOLS

DIRECT MICROSCOPY OF STOOLS

Direct microscopy is used to observe cellular exudate and motile protozoan trophozoites, as they
are killed or distorted during concentration techniques. The presence of other parasitic stages,
undigested food, bacteria, yeasts, crystals or fat globules are also noted. All fresh stools (less
than 4 hours old) which are semiformed, unformed, liquid or show the presence of blood and / or
mucus should be examined by direct microscopy. Routine direct microscopy on formed stools is
unnecessary unless there is external blood or mucus. Any blood or mucus present should be
examined separately as it is more likely to contain trophozoites. Trophozoites die rapidly, so
unformed stools should be looked at as soon as possible after voiding, preferably within 30
minutes of being passed.

Preparation of saline and iodine wet mounts for direct microscopy of stools

Materials and reagents

1. Wooden applicator sticks or matches

2. Microscope slides (75x25 mm)

3. Cover slips

4. Pens or markers for indelible labeling

5. Dropping bottles containing:

isotonic saline solution (0.85%; 8.5 g/l)∗
Lugol’s iodine (1% solution)

Procedure

1. With a wax pencil or marker, write the patient’s name or identification number and the date
at the left-hand end of the slide.

2. Place a drop of saline in the center of the left half of the slide and place a drop of iodine
solution in the center of the right half of the slide (Note: iodine wet mount preparations are
most useful for protozoa, less so for helminths).

18
3. With an applicator stick or match, pick up a small portion of faeces (approximately 2 mg
which is about the size of a match head) and add it to the drop of saline: add a similar portion
to the drop of iodine. Mix the faeces in each drop until a suspension is formed.

4. Cover each drop with a cover slip by holding the cover slip at an angle, touching the edge of
the drop, and gently lowering the cover slip onto the slide so that air bubbles are not
produced (Note: ideal preparations containing 2 mg of faeces are uniform – not so thick that
faecal debris can obscure organisms, nor so thin that blank spaces are present)

5. Examine the preparations with the 10x objective or, if needed for identification, the high
power objective of the microscope (40x), in a systematic manner (either up and down or
laterally) so that the entire cover slip area is observed. When organisms or suspicious objects
are seen, switch to higher magnification for more detailed morphology of the object in
question.

DISPOSAL

1. Discard slides, coverslips and ekel applicators into 1% aqueous lysol in a wide mouthed
container. Slides and coverslips are cleaned and reused as given in the following step while
the applicators are thrown away. Since coverslips are fragile these are collected and cleaned
separately.
2. Keep overnight.
3. Wash in running tap-water for 1 hour.
4. Boil in soap water (65g of soap in a gallon of water) and let cool to room temperature.
5. Wash in running tap-water for 1 hour.
6. Wipe dry with clean cloth and use.

19
DEMONSTRATIONS

1: ENTAMOEBA HISTOLYTICA X 1000

a) Trophozoite in iron haematoxylin stain x 1000

- Outer ectoplasm wide and clear, inner endoplasm is finely granular and “ground glass”
like in appearance.
- Pseudopodia visible
- Ingested red blood cells present
- Nucleus with uniform peripheral chromatin and centrally located karyosome

b) Trophozoite in a tissue section x 1000

- Trophozoites with ingested RBC
- Nuclei of intestinal epithelial cells

c) Cyst in Trichrome stain x 1000

- Sausage shaped chromatoidal bodies stain red
- Cytoplasm stains bluish green to purple.
- Nuclei < 4
- Glycogen vacuoles

d) Cyst in Iron Haematoxylin stain x 1000

20
2. ENTAMOEBA COLI X 1000

a) Trophozoite in iron haematoxylin stain x 1000

- Ectoplasm is granular and less well differentiated from endoplasm
- Endoplasm is more granular and more vacuolated
- May contain bacteria, yeast (rarely red blood cells)
- Pseudopodia have more sluggish movements
- Nucleus has heavier peripheral chromatin and a larger eccentric karyosome

b) Cyst in lodine x 400

- Generally larger than E.histolytica
- Chromatoidal bodies if present are splinter like with pointed ends
- Glycogen vacuole in immature cyst may be more heavily stained brown
- Contains 1-8 nuclei

c) Cyst in Saline x 400

d) Cyst in Iron Haematoxylin stain x 1000

21
3. BLASTOCYSTIS HOMINIS - Iron Haemotoxylin x 1000

- Central vacuole
- Nuclei darkly stained
- Cytoplasm visible
- Outer cell membrane

4. BALANTIDIUM COLI

a) Trophozoite x 1000 b) Cyst x 1000

- Cilia visible - Round in shape
- Kidney shaped macronucleus - Large macronucleus
- Rounded micronucleus - Smaller micronucleus
- Cilia may be faintly visible

5. TRICHOMONAS VAGINALIS

Trophozoite x 1000
- Oval in shape
- 3-5 anterior flagellae
- Undulating membrane extends more than half of the body length
- An axostyle
- Nucleus in anterior part of body

No cyst stage

22
6. GIARDIA INTESTINALIS

a) Trophozoite x 1000
- Pear shaped
- Bilaterally symmetrical
- Ventral surface has a sucking disc
- 4 pairs of flagella present
- Nuclei visible

b) Cyst in wet mount x 1000

- Cyst wall present
- 2-4 nuclei
- Contains the remains of axonemes and parabasal bodies

7. Cryptosporidium oocyst - Ziehl-Neelsen stain x 1000

- Small, round in shape about 4µ in diameter.

- A mature oocyst contains 4 sporozoites.

23
PRACTICAL - INTESTINAL NEMATODES

CLASSIFICATION

Helminths

Nematodes Cestodes Trematodes

Taenia solium Fasciola hepatica

T.saginata Clonorchis sinensis
Echinococcus granulosus Fasiolopsis buski
Hymenolepis diminuta Paragonimus westermani
Hymenolepis nana Schistosoma sp.

Small Intestinal Large Intestinal

Nematodes Nematodes
Ascaris lumbricoides Enterobius vermicularis
Necator americanus Trichuris trichiura
Strongyloides stercoralis
Trichinella spiralis

NEMATODES

1. ASCARIS LUMBRICOIDES (ROUND WORM)

a) Adult male and female worm (gross)

- Posterior end curved in males 10-30 cm in length
- Females are 20-40 cm in length

b) Fertilized egg x 400

- Round or oval in shape
- Outer albuminoid layer is coarsely mammillated
- Thick transparent glycogen middle layer (hyaline shell)
- Unsegmented ovum

24
c) Unfertilized egg x 400
- Longer and narrower than the fertilized egg (barrel shaped)
- Thinner mammillated outer coat
- Thinner shell
- Amorphous mass of disorganized granules inside
- No clear demarcation of layers

Unfertilized egg

Fertilized egg

2. NECATOR AMERICANUS (HOOKWORM)

a) Adult male or female (universal low power)

- Head curvature opposite to body curvature
- Small cylindrical worm
- Tapering anteriorly
- Approximately 1cm long

b) Hookworm egg x 400

- Broadly oval with bluntly rounded ends
- Colourless
- Thin walled
- Segmented ovum

25
3. TRICHURIS TRICHIURA (WHIP WORM)

a) Adult male and female worms (gross specimen)

- Posterior end bluntly rounded in the female and curved in the male

b) Whipworm egg x 400

- Like a paddy seed
- Outer coat is bile stained and appears brown in colour
- At either end there are transparent polar prominences (mucoid plug)

4. ENTEROBIUS VERMICULARIS (PINWORM)

a) Adult male and female (gross specimen)

- Spindle shaped

b) Pinworm egg x 400

- Plano-convex
- Thick double wall colourless
- Rhabditiform larva present inside

26
CESTODES

Adult worm: genital pore

situated laterally, no uterine
pore
TAENIA Taenid egg: Spherical, very
SOLIUM
thin, hyaline outer membrane,
embroyphore with six
hooklets insite

Scolex: globular, 4 cup

shaped suckers, projection
like a beak (rostellum), 2
rows of hooks at the base of
the rostellum.

Cysticercus cellulosae: thin

walled cyst, invaginated
scolex with suckers and
chitinized hooks

Gravid proglottid: central

uterus, <12 lateral branches

Mature segments: square

shaped, lateral pore.

27
 Adult worm: genital
pore situated laterally,
no uterine pore
TAENIA Taenid egg: Spherical,
SAGINATA
very thin, hyaline outer
membrane,
embroyphore with six
hooklets inside

Scolex: quadrate, 4
suckers, no rostellum,
no hooks

Cysticercus bovis: cyst

like structure,
protoscolices visible.
thin walled cyst,
invaginated scolex with
suckers and chitinized
hooks

Gravid proglottid:
contains uterus with
eggs, >12 lateral
branches, lateral
genital pore

Mature segments:
square shaped, lateral
pore, Similar to
T.solium mature
proglottids.

28
HYMENOLEPIS Egg: spherical,
DIMINUTA onchosphere with 6
Rat Tape Worm hooklets

Scolex: club shaped,

retractable, rostellum, 4
small suckers, no hooks

Cysticercoid larvae:
tailed larvae

Mature proglottid:
Rhomboid shaped 3
round testes, bi-lobed
ovary and lateral genital
pore

Gravid segment:
contains uterus with
eggs, 4mm in length,
broad

HYMENOLEPIS NANA Egg: oval shaped, hyaline

Dwarf Tape Worm outer shell, inner
membrane, polar
filaments, hexacanth
embryo

Scolex: globular,
retractable rostellum with
single row of small hooks,
4 suckers
Mature Proglottid: broad,
bilobed ovary, 3 round
testicles in each segment,
lateral genital pore

Gravid proglottid: long,

0.6 mm in length, filled
with eggs

29
 ECHINOCOCCUS Adult worm: scolex
GRANULOSUS has a rostellum armed
Dog Tape Worm with hooks arranged
in two rows, 1-2
immature segments, a
single gravid segment
half the body length
containing a branched
uterus
Hydatid cyst in
section: with 3
coverings (pericyst,
ectocyst, endocyst), a
brood capsule and
protoscolices

Protoscolices: cyst
with invaginated
scolex, scolex with
double crown of
hooklets and four
suckers

TREMATODES

FASCIOLA HEPATICA
Leaf like caecae heavily
branched
Testis in tandem position
Ovary to the right of the midline
Coiled uterus

FASCIOLOPSIS BUSKI
Intestinal caeca not branched
with two characteristic lateral
indentations
Testis in tandem position, ovary
at the centre to the right of the
midline

CLONORCHIS SINENSIS
Narrow anterior end, round
posterior end
Unbranched caeca
Testis in tandem position, ovary
anterior to the testis in midline

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PRACTICAL – ARTHROPODS

CLASSIFICATION

Phylum Arthropods

Class Insecta Arachnida

Order Anoplura Diptera Siphonaptera Hemiptera Acarina

(lice) (flies) (fleas) (bugs) (ticks and mites)

1. LICE

a) Pediculus humanus capitis (head louse)

b) Pediculus humanus corporis (body louse)

Adult x 100
- Flattened dorsoventrally
- Tip of abdomen bifurcated – “w” shaped in females
- Tip of abdomen not bifurcated in the male
- Abdomen has 7 segments

Egg (Nit) x 100

- Operculated
- Cemented to fibers of clothing (or hairs)
- Whitish in colour

Medical importance
1) Are vectors of
- Louse borne epidemic typhus due to Rickettsia prowazeki
- Trench fever due to Bartonella quintana
- Louse borne relapsing fever due to Borrelia recurrentis
2) Causes pruritus

c) Phthirus pubis (crab louse)

Adult x 100
- Smaller than the body louse
- Less differentiation between the thorax and abdomen
- 3 pairs of legs
- 1st pair of legs more slender with smaller claws
- In the female the tip of the abdomen is bifurcated – “w” shaped

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2. FLIES

a) Musca domestica (house fly)

Adult
- 6-9 mm in length
- Four broad dark longitudinal stripes on thorax on dorsal aspect
- Wings- 4th vein bends sharply to join the costa near the 3rd vein.
Egg
- Creamy white
- 1mm in length
- Banana shaped
- Two rib like thickenings along its dorsal surface
Larva x 40
- 12 segments
- Tapers gradually towards the anterior end
- First segment has a pair of mouth hooks
Medical importance
- House fly adult acts as a mechanical vector and transmits disease
- House fly larvae have occasionally caused urogenital and traumatic myiasis

b) Glossina (tsetse fly)

Wing- There is a closed cell “hatchet cell” between the 4th and 5th veins
Medical importance
- Transmits African Trypanosomiasis (sleeping sickness)

c) Phlebotomus (sand fly)

- Hairy
- Three very long pairs of legs
- Head bent acutely down
- Large black eyes
- wings kept erect “V”- shaped when at rest
- 2nd vein divided
- Found in Sri Lanka
Medical importance: Transmits
- Leishmaniasis
- Sand fly fever (viral)
- Oroya fever (Bartonella species)

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3. BUGS

a) Cimex lectularius (bed bug)

- Pyramidal shaped flattened head
- Head has prominent compound eyes
- Oval dorsoventrally flattened body
- Tip of abdomen bifurcated in female – “w” shaped
- Tip of abdomen not bifurcated in males – “v” shaped
- Each of the 3 thoracic segments bear a pair of legs that terminate as claws

b) Reduviid bug
- Long narrow head
- Prominent compound eyes
- Long antenna
- 3 segmented proboscis
- Dark brown in colour
Medical importance
- Transmits Chagas disease (American trypanosomiasis)

4. FLEAS

Medical importance
Acts as a vector of disease
- Bubonic plague - caused by the bacillus Yersinia pestis
- Endemic typhus - caused by Rickettsia typhi
- Cestode infections - H.diminuta, Dipylidium caninum

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5. TICKS

Hard ticks & Soft ticks

Medical importance
1) Acts as a vector for diseases
a) Rickettsial diseases
- Rocky mountain spotted fever by R.rickettsiae
- Tick borne typhus
- Q fever- Coxiella burnetti
b) Viral diseases
- Colorado tick fever
- Kyasanur forest disease
c) Bacterial and spirochaete disease
- Tick borne relapsing fever
- Lyme disease - Borrelia burgdorferi
- Tularemia - Francisella tularensis
d) Protozoal disease- Babesiosis

6. MITES

a) Sarcoptes scabiei
Adult x 100
- Whitish, disc shaped and dorso-ventrally flattened
- 4 pairs of short stumpy legs

Medical importance
e) Lesions appear as itchy papules at sites of each mite and later develop into pustules
due to secondary infections.
f) Secondary infection of lesions by B.haemolytic Streptococci can result in
glomerulonephritis.

b) Trombiculid mite
Larva x 100
- Reddish orange
- 3 pairs of legs
- On dorsal surface a rectangular plate / scutum bearing feathered septae together
with 2 flagelliform sensillae
Medical importance
- Vector for Rickettsia tsutsugamushi which causes scrub typhus

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MOSQUITOES

1. Anopheles culicifacies (transmits malaria)

Adult x 40
- Anterior border of wing has 4 sharply defined pale areas and a 5th at the wing tip

2. Culex spp.
Adult x 40
Culex quinquefasciatus (transmits bancroftian filariasis)
Culex gelidus (transmits Japanese Encephalitis)

- Absence of any positive markings characteristic of Culex species

3. Mansonia species (vector of Brugia malayi in South and South East Asia,
transmits Dirofilaria repens to humans)
Adult x 40

- Wings covered with flat, broad, light and dark scales giving the wings a
speckled (salt and pepper) appearance

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4. Aedes species (transmits yellow fever, dengue fever, dengue haemorrhagic
fever, Dirofilaria repens)
Adult
- Black in colour
- Silvery scales on body
- Legs show a banded appearance

Aedes aegypti- thorax shows a silvery

lyre shaped marking on the dorsal
surface.

Aedes albopictus – shows a “l”

shaped mark on thorax.

Culicine species adult mosquitoes

lie horizontal to the surface

Anopheles adult mosquito lies at a

45 degree angle

36
PRACTICAL : SNAKES
1. ELAPIDS

Ceylon cobra Special Features

Naja naja naja

Largest elapid up to 6 feet

Light and dark brown or blackish in colour with a

white speckled appearance along the length of the
body.

The vertebrals are not enlarged.

Sub-caudals are divided (biserial).

Only hooded snake found in Sri Lanka (hood found

between head and body).

Characteristic spectacle shaped marking on dorsal

surface just below head.

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Ceylon krait Special Features
Bungarus ceylonicus
Brownish black or black with broad white bands on
the dorsum which are continued on the belly (on the
ventral aspect)

Oval head

Vertebrals enlarged

Subcaudals undivided

Common krait (Bun garus caeruleus) Special Features

Black glossy snake oily appearance
Vertebrals enlarged
Sub-caudals undivided
Thin white bands in pairs on the dorsum only. No
bands on the belly. Belly is whitish.

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 2. VIPERS

Russell’s viper (Vipera russelli) Special features

3 longitudinal rows of characteristic oval/round
markings along the length of the body. One row
runs along the median dorsal line and other two on
either side. Each spot is dark brown with an inner
black and outer white margin.

Saw scaled viper (Echis carinatus)

Characteristic dagger shape or “Bird’s foot”
marking on the head
Serrated costal scales on both sides of the body
Dorsally the colour is brown with dark blotches
and a wavy line on the side of the body.

Hump nosed viper (Hypnale spp)

Large head scales which is an exception from the
other vipers.
The snout ends in a hump like prominence.
Typical brown mottled appearance with a series of
brown oval spots on either side of the spine.

Green pit viper (Trimeresurus

trigonocephalus) A black stripe runs from the eye to the angle of
jaw on each side.

*Pit vipers
The hump nosed viper and Green pit viper are referred to as the pit vipers due to the presence of
the Loreal pit on the head between the nostrils and the eye on either side. These are sensitive
thermal receptors which help to locate warm blooded prey.

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 3. COLUBRIDES

Cat snake Special features

Boiga spp
Conspicuous neck which makes the head
look triangular.
Brown mottled appearance with a series of
brown oval spots on either side of spine,
similar to the body markings of the Hump
nosed viper.
A long thin tail.

No hump on the head

The Ceylon Wolf snake (Cercaspis carinatus)

Looks morphologically similar to the Sri
Lankan Krait.

Subcaudals undivided

Vertebrals are not enlarged.

Rat snake (Ptyas mucosa)

Large snake.
Grows up to 6 feet.
Belly is whitish yellow
Subcaudals biserial

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 4. OTHER IMPORTANT SNAKES

Python (Python molurus)

Quadrangular patches on body
Non venomous
Can kill the victim by constriction.

Earth snake
Earth worm like.
Non venomous

Sea snake (Hydrophis ornatus ornatus)

Its head is small with a slender neck.
The body is flattened from side to
side
Have a paddle like (laterally
compressed) tail with a rounded end

Fresh water snakes (Cerberus rhynchops rhynchops)

Body and tail are cylindrical

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