The document discusses diagnostic testing for infectious diseases. It describes the diagnostic cycle which includes pre-analytical, analytical, and post-analytical phases. It then provides detailed guidelines for collecting, transporting, and processing various specimen types including blood, respiratory, urine, wound/soft tissue, and stool samples. Key steps include using proper collection containers and transport methods, obtaining sufficient samples, and following rejection criteria to ensure sample quality and accurate results.

1. Laboratory Diagnosis of
Infectious diseases:
An overview of Diagnostic cycle.

2. Preanalytical
Phase
Analytical
phase
Post
analytical
phase
Diagnostic
cycle

3. THE DIAGNOSTIC CYCLE
PRE-ANALYTICAL PHASE
Visit
Examination
& Provisional
diagnosis
Collection
of sample
Identity
Requisition
Transport
Records

4. ANALYTICAL PHASE
Macroscopy Microscopy Culture
Biochemical
identification
Serology Molecular
Analysis

5. POST-ANALYTICAL PHASE
Reporting of
Identification &
Antibiotic sensitivity
Treatment

7. Specimen
Collection &
Transport
Collection
from actual
site with
minimum
contamination
Optimal
time of
collection
Sufficient
quantity of
specimen
Appropriate
collection
device,
container &
culture media
Proper
labelling of
containers
Obtain
samples
before
starting
antibiotics

8. BLOOD CULTURES
• One blood culture usually consists of
blood from a single venepuncture
inoculated into two separate bottles
(one aerobic, one anaerobic)
• Optimal blood-to-broth ratios are 1:5
to 1:10.
• Sodium polyanethol sulfonate (SPS)-
0.025 to 0.05%- is added as an
anticoagulant, an antiphagocytic agent
that inactivates complement, and a
neutralizing agent to inhibit effects if
many antimicrobial and antibacterial
factors in blood.

9. • Recommended total volume and numbers of blood cultures
Syringe needed Aerobic bottle Anaerobic bottle
Adult 20 ml 10 ml 10 ml
Pediatric 20 ml 2.5 -10 ml 2.5 -10 ml
Infant 3 ml 0.5 -1 ml 0.5-1 ml
Adult
(low volume) All None
• Timing of blood cultures
 Before or during fever spike
 Acute sepsis or another condition (osteomyelitis, meningitis,
pneumonia or pyelonephritis): two blood cultures of maximum
volume consecutively from different anatomical sites before
starting therapy

10.  Pyrexia of Unknown Origin, Subacute Bacterial Endocarditis or
other continuous bacteraemia or fungemia: maximum of three
blood cultures with maximum volume
 Patients on antimicrobial therapy : Sample is drawn when
antimicrobial agents are at their lowest concentration.
• Skin antisepsis and collection of blood from venepuncture
 A different venepuncture site for each blood culture is selected.
 If blood for culture is required to be drawn through a port in an
indwelling catheter, the second culture must be from a peripheral
site.
 Vigrous cleaning is done with 70% isopropyl or ethyl alcohol.
Allowed to dry.
 Swab or wipe concentric circles of 1 to 2% tincture of iodine,
moving outward from centre of the site.
 Allow the iodine to dry and avoid touching the site.

11.  First the aerobic bottle is inoculated and then the anaerobic bottle.
• Collection of blood from intravascular catheters
 Comparison of cultures that are drawn through an indwelling
intravenous catheter and through a peripheral site may be useful
for diagnosis of catheter related sepsis.
 Bottles are labelled with patient name, site, date and time of draw.
 Using two separate alcohol preps, catheter hub connection is
scrubbed for 15 sec with 70% alcohol. Air dry.
 Wear gloves, disconnect tubing or cap of catheter and attach
syringe to collect discard blood ( 3ml for adults and 0.2ml for
pediatric patients), which is not used for culture.
 Using a new syringe, blood for culture is collected through the hub.
Quickly reconnect tubing.

12. • Specimen Transport
 Blood cultures should not be refrigerated. They are generally held
at room temperature until processed, for a maximum of 4 h.
• Rejection Criteria
 Blood cultures that are received unlabelled.
 If the tube or bottle is cracked or broken.
 Labelled blood cultures are not rejected even if medium is expired,
volume or number of bottles is insufficient, or bottles are received
>12 h after collection.

13. Lower Respiratory Tract Cultures
• Expectorated
sputum
• Induced sputum
 Used for Pneumocystis carinii and Mycobacterium tuberculosis
 Patient’s mouth is rinsed thoroughly with sterile water or saline.
 Using and ultrasonic nebulizer, patient is made to inhale approx. 20 to
30ml of 30% NaCl.

14. • Tracheostomy and endotracheal aspirates
 The specimen is aspirated into a sterile sputum
trap or leak proof cup.
 Tracheostomy aspirate should not be cultured
unless clinical pneumonia is present (fever and
infiltrates). Tracheostomy is followed by
colonization within 24h of insertion, and results
may not correlate with disease.
• Bronchoscopy specimens
 Include BAL samples, bronchial washings,
transbronchial biopsy specimens.
 Culture BAL samples quantitatively or
semiquantitatively for bacterial pathogens
Mucus
extractor for
ET aspirates

15. • Specimen Transport
 Specimens are collected in leakproof cups and
labelled with source of material.
 Specimens are labelled with demographic
information, date and time of collection, and site
of collection.
 Provisional diagnosis should be mentioned for
proper evaluation of the cultures.
 Appropriate tests should be requested. Anaerobic
cultures should be limited to specimens that are
not contaminated with upper respiratory
microbiota (eg. Biopsy samples) and only when
aspiration pneumonia or similar disease is being
considered.
 Specimens should be stored at 2 to 80C until
cultures can be submitted or processed.
Sputum
sample
container

16. • Rejection Criteria
 Repeat cultures at intervals of less than every 48 h.
 24 h sputum collection
 Contaminated sputum and endotracheal specimens per Gram stain
rejection criteria
 Saliva
 Nasal washes and aspirates or swabs of nares
 Throat specimens
 Specimens for anaerobic culture, except transtracheal aspirates,
biopsy samples, pleural fluid or other uncontaminated specimens.
 For specimens delayed in transit time more than 2 h without
refrigeration.

17. URINE CULTURES
• Clean voided midstream urine collection
 Females- labia are held apart, vulva is washed from front to back
 Circumcised males- no preparation.
 Uncircumcised males- foreskin is retracted, glans penis is washed
 Patient is asked to collect voided urine directly into a disposable
leak proof container, instructing the patient to not halt and restart
the urine stream for a “midstream” collection but preferably move
the container into the path of already voiding urine.
• Catheter urine
 Using a needle and syringe, urine is collected through the catheter
port, after cleaning with alcohol.
 Urine obtained from a catheter bag should not be send.
• Timing of specimen collection
 Early morning specimens should be obtained whenever possible.
 Fluids should not be forced in order to have the patient void urine.

18. • Specimen Transport
 Urine should be transported to the lab after collection or,
if urine cannot be delivered within 2 h after collection, can
be refrigerated for up to 24 h.
• Rejection Criteria
 No evidence of refrigeration and the specimen is >2 h old.
 Collection time and method of collection have not been
provided.
 24- h urine collections
 Foley catheter tips
 Urine from the bag of a catheterized patient
 Specimens that arrive in leaky containers
 Except for suprapubic bladder aspirates, reject specimen
requests for anaerobic culture.
Urine
sample
container

19. Wound and Soft tissue cultures
• Specimen should be collected prior to initiation of therapy and only from
wounds that are clinically infected or deteriorating or that fail to heal
over a long period.
• Skin or mucosal surfaces should be cleansed.
 Closed wounds and aspirates- disinfected with 2% chlorhexidine or 70%
alcohol followed by iodine solution (1 to 2% tincture of iodine or a 10%
solution of povidine-iodine)
 Open wounds should be debrided, and thoroughly rinsed with sterile
saline prior to collection.
• Viable infected tissue should be sampled, rather than superficial debris.
• Swab collection should be avoided if aspirates or biopsy samples can be
obtained.

20. • Containers:
 Anaerobe transport vial for small tissues.
 Sterile cup for large tissues with nonbacteriostatic
saline on a gauze pad to keep moist.
 Syringes
 Broth culture medium in small sterile snap –top
microcentrifuge tubes for FNA
 Swabs (ideally, submit two, one for Gram stain and
one for culture)
• Specimen collection
 Cold abscesses- infected material is aspirated with
needle and syringe.
 Open wounds- superficial area is cleansed with
sterile saline. Overlying debris is removed with
scalpel and swabs or sponges. Biopsy or curette
sample is collected from base or advancing margin
of lesion.
Anaerobic
specimen
collector
Swabs

21.  Pus- deepest portion of the lesion or exudate is
aspirated with a syringe and needle.
 Tissue and biopsy samples- 3- to 4-mm biopsy
samples are collected, avoiding necrotic areas.
• Label specimen and requisition
 Demographic information of the patient.
 Type of specimen (deep tissue, superficial tissue,
decubitus, catheter site, boil, abscess, cellulitis,
aspirate, pus, drainage, surgical incision site, etc.)
should be described. Anatomic location (arm,
leg, etc.) should be mentioned
 Collection time and date should be recorded
 Diagnosis, including cause and clinical signs of
infection should be mentioned.
 Antimicrobial therapy prior to specimen
collection should be mentioned
Aspiration of
pus using
needle &
syringe

22. • Specimen transport
 Aspirates and tissues should be delivered to the lab within 30 min
 Tissues should be kept moist to preserve organism viability
 Specimen should not be refrigerated or incubated
• Rejection Criteria
 Specimens in container with formalin
 If numerous squamous epithelial cells are present on Gram stain
 Swabs that have been delayed in transit more than 1 h if they are not in
some transport system.
 For multiple requests (AFB, fungal, bacterial and viral) but little
specimen.

23. Faecal Culture for Aerobic Pathogens
• Patient should pass stool into a clean, dry pan.
• Transfer at least 5 ml of diarrhoeal stool, 1 g of material or a walnut
sized portion of stool.
• Container:
 Clean, leak proof container with a tight fitting lid or
 Buffered glycerol saline
 Modified Cary-Blair medium
 Stool enrichment broths
 Anaerobic transport tube for C. difficile culture
• Rectal swabs
 Pass the tip of a sterile swab approx. 1 in. beyond the anal sphincter
 Carefully rotate the swab to sample the anal crypts, and withdraw
the swab
• Timing
 Submit specimen during acute stage of infection (usually 5 to 7
days)

24. Anaerobic Culture
• The best specimen is obtained by using a needle and syringe.
• Tissue samples and biopsy samples are also very good specimens.
• The least desirable specimen is collected by swab
• Specimen Transport
 Tissue samples, biopsy samples, or curettings should be placed into
an anaerobic transport device or a sterile tube or petri dish. All this
is placed into a sealable plastic bag that generates an anaerobic
atmosphere.
 If specimens must be collected by swab, swabs should be
transported in a tube containing anaerobic transport medium.
 Transport containers – Syringe or needle for aspiration, Tube or vial,
Swab/plastic jacket system, Bio-bag or plastic pouch.

25. Fungal Culture
• Respiratory specimens- Sputum, tracheal secretions and BAL fluid.
• CSF
• Blood
• Tissue, Bone Marrow and Body Fluids
• Skin, Hair and Nail-
 Skin scraping.
 Nail clippings should be taken from discoloured, dystrophic or
brittle parts of nails.
 The hairs are removed by plucking them with forceps
• Urine
• Vaginal secretions
• Stool
• Eye-
 corneal scrapings are taken from base and margins of ulcer
aseptically using Kimura’s spatula under 4% xylocaine
 Aspiration of hypopyon in keratomycosis.

26. Collection of Faecal samples for Parasitology
• All faecal specimens should be collected prior to the administration
of antibiotics or antidiarrhoeal agents.
• Use of mineral oil, bismuth, and barium prior to faecal collection
should be avoided
• Faecal specimen is collected in a clean, wide mouthed container
and transfer it to a container with a tight-fitted lid.
• Specimen transport
 Specimen is transported to the lab as soon as possible, or kept
refrigerated until transport is possible.
• Rejection criteria
 Dried specimens
(diarrhoeic, semiformed, or formed).
Stool sample
container

27. ANALYTICAL PHASE
Blood Culture
• Macroscopic signs of growth caused by organisms
commonly encountered in blood culture
 Haemolysis- Streptococci, Staphylococci,
Listeria spp, Clostridia, Bacillus
 Turbidity- Aerobic GNB, Staphylococci, Bacteroides.
 Gas formation- Aerobic GNB, anaerobes
 Pellicle formation- Pseudomonas spp., Bacillus spp., yeast cells
 Clotting- Staphylococcus aureus
 Visible colonies (“puffballs”)- staphylococcus, streptococci
• Microscopy- A thin smear is Gram stained from the broth or agar
immediately when suggestive of growth 24h for optimal pt. care.
• Subcultured to agar media and biochemical tests based on Gram
stain results.
Bac T
Alert

28. Lower Respiratory Tract Cultures
• Inoculation
 Most purulent or most blood–tinged
portion of the specimen is selected
 In case of bronchoscopy, quantitative
cultures are performed on BAL samples
 Gram stain is prepared
 Using a sterile swab, stick or pipette,
inoculate specimen on blood agar, chocolate agar, and MacConckey
agar
• Incubation
 Plates are incubated at 35 to 370C in 5% CO2 for a minimum of 48 h.

29. • Direct Tests
 Gram stain: note cells and bacteria
• Culture examination
 Plates are observed at 24 h
 Plates are incubated for an additional 24 to 48 h, which is useful to
detect moulds and slow growing, fastidious gram negative rods
 Gram stain result is used as a guide to interpreting the culture.
 Presence of inflammatory cells and bacteria is used in deciding
on the extent of processing the culture
 If the culture does not match the smear results, the smear is
reviewed a second time.

30.  Organisms present in significant amounts are identified, defined as
colony types that are not considered part of normal respiratory
microbiota and are present in following amounts:
Large numbers in the second or greater quadrant of the plate
>104 in a BAL sample
Any amount of selected pathogens in a patient with cystic
fibrosis
 Small amount of selected pathogens in the culture that are
consistent with an etiological agent seen in the Gram stain
associated with inflammatory cells
 Colonies in the first quadrant of the plate, only if there is little
or no other microbiota on the plate and the smear suggests
inflammation
 Subcultured on blood agar &/or chocolate agar to obtain isolated
colonies for accurate identifications from mixed cultures
• Biochemical tests and AST

31. Urine Cultures
• Microscopic and other methods
 Gram stain is useful in rapidly determining the type and count of
bacteria and cells in urine and should be performed on request.
 Detection of pyuria- Detect by either Gram stain or urinalysis, from
examination of freshly collected uncentrifuged urine. Pyuria with a
WBC count of >10/µl (or >5 per high-power field in conventional
urinalysis) has a specificity of 90% for predicting CA-UTI with >105
CFU/ml but a sensitivity of only 37%.
• Culture methods
 Only streak the blood plate for colony count. Other plates should be
streaked in quadrants for isolation of colonies, rather than for
colony count, to minimize delays in obtaining isolated colonies and
false-negative culture results due to antimicrobial inhibition.
 Inoculation methods: Calibrated-loop method, Pipette inoculation
method

32. • Incubation
 In ambient air overnight at 35 to 370C
 If convenient, blood agar and CNA is incubated in 5% CO2 to enhance
growth of gram- positive organisms.
• Examination of culture media
 Cultures that have been incubated overnight are examined but a final
reading is made at 18 h.
 For positive cultures, culture media is examined for quantity and
morphological type of organisms present
 Normal urogenital flora is not identified to the genus or species level
 Identification is done always to the species level if oxidase positive and
indole positive, since such organisms are pathogens regardless of the
count (eg. Aeromonas and Vibrio spp.)

33. Wound and Soft tissue culture
• Inoculation
 Anaerobic culture is performed first, preferably in an anaerobic
chamber. Incubated immediately.
 Smear is always prepared after the culture has been inoculated.
• Gram stain
 Relative numbers of WBCs, epithelial cells, and bacterial and fungal
morphotypes are recorded
• Culture workup
 Plates and broths are read daily

34.  Generally up to three microorganisms are identified if any of the
following is true:
 PMNs are present on direct smear
 Specimen was collected from a normally sterile site
The specimen was of good quality (eg. No or few epithelial
cells present)
The organism was seen on direct smear
 Any number of microorganisms that only grow on chocolate agar,
and not on blood agar ( N. gonorrhoea, Haemophilus, and
Francisella) are identified
• Microorganism is identified and AST is performed

35. Faecal Culture for Aerobic Pathogens
• Wet preparations are performed for faecal leukocytes from fresh
stools.
• Culture Methods
 Inoculation of media- Swab is rolled over one small area of blood
agar and Mac Conckey media and streaked in quadrants for isolated
colonies. Use larger amounts of specimen for HEK, XLD and SS
agars.
• Biochemical tests performed
• Salmonella and Shigella somatic (O) antigens are tested for
agglutination when the screening biochemical tests fit.

36. Anaerobic Culture
• Macroscopic Examination
 Presence of blood, purulence, necrotic tissue, foul odour, and
sulphur granules.
• Specimen preparation
 Purulent specimens are vortexed grossly in the anaerobic transport
vial to ensure even distribution of microorganisms.
 Bone or tissue are grounded with approximately 1ml of liquid
medium to make a thick paste.
 Swabs are wringed out in 0.5ml of liquid medium and then treated
as a liquid specimen
 Large volume of nonpurulent material is centrifuged. Sediment is
used to inoculate the media and to prepare the Gram stain
• Inoculation of media
 Media for anaerobic culture:

37. Brucella agar with 5% sheep blood supplemented with vitamin K
and hemin for isolation of most organisms
Phenylethyl alcohol (PEA)- sheep blood agar for the inhibition of
enteric and other facultatively anaerobic gram-negative bacilli
that may overgrow the anaerobes. PEA also reduces the
spreading or swarming characteristic of some anaerobes.
Kanamycin-Vancomycin-laked blood agar for selection of
pigmented Prevotella and other Bacteroides spp.
Bacteroides bile esculin agar
Chopped meat broth or THIO (supplemented with Vit K &
hemin)
Prereduced anaerobically sterilized (PRAS) media

38. • Inoculation procedure
 Prepared specimen is transferred onto the appropriate aerobic and
anaerobic media, liquid medium and a slide for Gram stain.
• Incubation
• Microscopic Examination
 Gram staining: Reveals the types
and relative numbers of microorganisms
and host cells present and serves as a
QC measure for the adequacy of
anaerobic techniques.
Anaerobic
Chamber

39. Fungal Culture
• Inoculation of media
 The number of media inoculated may be dependent on the
specimen type and amount.
 Both non-selective (SDA and BHI) and selective media should be
included, and specialized media may be required for specimens in
which difficult-to-grow etiological agents are suspected.
• Incubation
 Fungal cultures are incubated at 300C for
a minimum of 4weeks.
 Plates should be examined daily for first
7 days and at least twice per week thereafter.

40. Faecal sample examination for Parasites
• Macroscopic Examination
 Consistency
 Surface of faecal specimen for the presence of blood and mucus.
 Areas of blood or mucus are sampled for examination of trophic
amoeba
• Microscopic examination
 Saline and iodine wet mounts are prepared
 Examined under 10x. Use 40x objective
for more detailed study.
• Floatation and concentration methods are used
for the recovery of all protozoa, eggs, and larvae
present. Iodine and
Saline
mounts

41. Molecular Techniques
Potentially infected individual
Sampling: Tissue, blood, urine, respiratory secretion
Microbe detection procedures
Direct target nucleic acid detection Target nucleic acid amplification
and detection
In-situ nucleic Nucleic acid In vivo amplification
acid detection purification In vitro amplification
DNA, RNA 1. PCR
Target detection by 2. LCR, NASBA, SDA
1. Dot or slot blot hybridisation Amplified target DNA
2. Restriction fragment length 1. Gel electrophoresis
polymorphism (RFLP) analysis 2. Dot or slot blot hybridisation
3. Pulsed-field electrophoresis 3. Southern procedure
4. Solid phase capture &

42. Antibiotic susceptibility testing
• Only isolates producing an infection should be tested.
• In most situations a disk diffusion is adequate to guide clinical
therapy
• Choice of antimicrobial agents and the susceptibility pattern is
guided by recommendations of CLSI
• Only antimicrobial agents appropriate for the infection should be
included in a report.
• Antimicrobial agents that do not penetrate into a site should not
be reported for organisms isolated from that site
• Commercial systems include Vitek which uses
a computer assisted analysis of growth in
plastic cards to calculate MIC.
Kirby-Bauer
disk diffusion
method

43. Post-analytical Phase
Blood culture
• Reporting results
 For “No growth cultures”, length of incubation is indicated: “No
growth after x days of incubation” for both preliminary and final
reports.
 Positive cultures:
Gram stain results of all positive cultures are reported
immediately
Number of positive cultures compared with total number of
specimens collected for specific patient.
Date and time of collection and receipt.
Date and time of positive result is reported and whether it was
from a catheter draw or a peripheral draw.

44. For single positive cultures with microorganisms generally considered
skin contaminants, only minimal identification is performed and AST is
not done. Reported as “one set of two positive. Isolation does not
necessarily mean infection. No susceptibility tests performed. Contact
laboratory for further information.”
• Interpretation
 The report of a positive culture generally means that the patient is
bacteremic. However, skin microbiota may infect the culture,
causing a false-positive result or pseudobacteremia.
 Mixed cultures can be present and account for a significant number
of bacteremias.
 Performance and reporting of AST are critical for timely patient care
and increase the chance of appropriate therapy and cure.

45. Lower Respiratory Tract Cultures
• Reporting results
 Gram stained smear is reported. Rare (<1 in 20 fields) numbers of
bacteria seen in the smear are not reported.
 Reported as: “No growth of pathogens or normal upper respiratory
tract microorganisms” if there is no growth on any plates
 Positive reporting
Preliminary and final results are reported as “Isolates consistent
with microorganisms encountered in the upper respiratory
tract” if no pathogens isolated
All pathogens are reported and AST is performed.

46. • Interpretation
 A positive culture with S. pneumoniae or H. influenzae generally
indicates infection with that organism, although carriage may lead
to false positive results.
 A positive culture with a predominant gram-negative rod or
S. aureus generally indicates infection with that organism if smear
suggests an infectious process involving the corresponding
morphology.
 A negative culture cannot rule out infection.

47. Urine Culture
• Reporting results
 Gram stain results for bacteria & cells per Gram stain are reported.
 Negative results
If no growth is observed on all media, report “ No growth after
48hrs “
 Positive results
If only urogenital or skin microbiota is observed, report as such.
Mixed cultures are reported with the count in CFU per millilitre,
followed by “Multiple bacterial morphotypes present; possible
contamination; suggest appropriate recollection, with timely
delivery to the laboratory, if clinically indicated”

48. • Interpretation
 A mixed culture in an uncomplicated outpatient population likely
indicates contamination.
 Low levels (<104/ml) of organisms commonly found on the skin and
external and internal genitalia are considered to be contaminants,
but in selected circumstances, a count of Enterobacteriacae of 102
CFU/ml or more, especially for Salmonella, can be considered
significant.
 Performance of AST directly from the urine specimen is not
recommended.

49. Wound and soft tissue infections
• Reporting results
 Report gram stain results as soon as possible, generally within 1 h
for specimens from critical sites.
 Report all negative cultures as “ no growth in-------days”
 Report individually those organisms that are always considered
pathogenic with enumeration, using preliminary identification
initially and the genus and species as the final identification.
 Due to their known virulence factors, indicate the presence of the
following species: Beta-haemolytic Streptococci, S. aureus, P.
aeruginosa, Clostridium perfringens, Pigmented anaerobes,
Bacteroides spp., Mixed anaerobes.
 Report AST on gram-negative rods, enterococci, or S. aureus
 When multiple morphologies are present, report with minimal
identification
 Additionally, if mixed microbiota are cultured with no predominant
microorganism, report as GI, oronasal, skin, or genital microbiota.

50. • Interpretation
 Performance of AST is not indicated in cases of mixed microbiota
indicative of infection of the abdominal cavity with bowel contents.
Treatment should include broad-spectrum coverage for normal
intestinal microbiota.
 Use of the Gram stain can improve the accuracy of evaluating the
importance of each potential pathogen. Organism present in the
Gram stain of an appropriately collected specimen correlate with
≥105 organisms per g of tissue.
 Microbial load in an acute wound can predict delayed healing or
infection.
 Many wound infections are polymicrobic, and the isolation of an
organism in culture may or may not correlate with infection of the
wound.

51. Faecal culture for aerobic pathogens
• Reporting results
 If gram negative enteric microbiota are not present in the cultures,
add a comment “no normal enteric gram-negative rods isolated”.
 Positive cultures: report presumptive presence of any enteric
pathogens with or without quantitation. Report the pathogen with
the preliminary designation as “probable” until the identification is
confirmed by both biochemical testing and serology.
 Report AST on Shigella, Aeromonas, Plesiomonas, Edwardsiella,
Vibrio, Yersinia and selected cases of Salmonella.
 Generally report only ampicillin, cotrimoxazole, and a quinolone.
• Interpretation
 The isolation of a stool pathogen may not identify the cause of the
disease. Eg. Salmonella is present in the carrier state, without
disease.

52. Fungal culture
• Reporting and interpretation of yeast:
Nitrate assimilation test for yeast speciation
Sporulation
Carbohydrate fermentation tests
• Reporting and interpretation of mould:
Reporting the growth of a mould as soon as such growth is
evident but before identification structures are formed is
important where immunocompromised patients are concerned
but is not normally necessary in cases of subcutaneous infection
of immunocompetent patients.

53. Parasitic infestations
• To ensure the recovery of parasitic organisms that are passed
intermittently and in fluctuating numbers, the examination of a
minimum of three specimens collected over a 7- to 10- day period
is recommended.
• Report the presence of adult helminths .Morphology and size are
usually adequate for identification of pinworm and Ascaris adults
and tapeworm proglottids.
• Report the presence of blood on or in the faecal sample

54. References
• Clinical Microbiology Procedure Handbook by Henry D. Isenberg, 2nd
edition
• Koneman’s Colour Atlas & Textbook of Diagnostic Microbiology, 6th
edition
• Mackie Mc Cartney Practical Medical Microbiology, 14th edition