Specimen

management
• Specimens should be obtained to preclude or minimize
the possibility of introducing contaminating
microorganisms that are not involved in the infectious
process.
Timing of Collection
• During the acute phase of illness (viral)
• Before antimicrobial therapy has started
Specimen Volume
• Must be adequate for the performance of the
microbiological studies requested
• Swab –
– Polyester tipped swab on a plastic shaft
– Avoid the ff:
• Calcium alginate (inactivates HSV)
• Cotton (toxic to N. gonorrheae)
• Wooden shafts (toxic to C. trachomatis)
Specimen Transportation
• Should be place in an appropriate container
– Biohazard bag
• ASAP
– Within 2 hours of collection
• Must be labeled (name, identification number of the
person from whom the specimen was collected, the source
of the specimen, and the date and time it was collected.)
• CSF and specimen for N. gonorrheae must not be
refrigerated
Specimen Preservation
• Preservatives
– PVA
– Buffered formalin (O&P)
– Boric acid
• Holding media – maintains the viability w/o supporting the
growth
*addition of charcoal – to absorb fatty acids
– Stuart’s
for N. gonorrhoeae and B. pertussis
– Amie’s
• Anticoagulants
SPS (0.025%w/v)
Storage Temperature
• Urine, stool, viral specimens, sputa, swabs, and foreign
devices such as catheters should be stored at 4° C.
• Serum for serologic studies may be frozen for up to 1
week at –20° C
• Tissues or specimens for long-term storage should be
frozen at –70° C
 Unacceptable specimens

• Any specimen received in formalin

• 24-hour sputum collections
• Specimens in containers from which the sample has leaked
• Specimens that have been inoculated onto agar plates that have
dried out or are out-dated
 Unacceptable specimens

• Specimens contaminated with barium, chemical dyes, or

oily chemicals
• Foley catheter tips
• Duplicate specimens (except blood cultures) received in a
24-hour period
• Blood catheter tips submitted for patients without
concomitant positive blood culture
 Unacceptable specimens
The following specimens should be rejected for anaerobic culture:
• Gastric washings
• Urine other than suprapubic aspirate
• Stool (except for recovery of Clostridium difficile for epidemiologic
studies or for diagnosis of bacteria associated with food poisoning)
 Unacceptable specimens
The following specimens should be rejected for anaerobic culture:
• Oropharyngeal specimens, except deep tissue samples obtained
during a surgical procedure
• Sputum
• Swabs of ileostomy or colostomy sites
• Superficial skin specimens
Blood
• bacteria responsible for bacteremia, sepsis, infections of
native and prosthetic valves, suppurative
thrombophlebitis, mycotic aneurysms, and infections of
vascular grafts
• before beginning antimicrobial therapy when any one or a
combination of the following are present: fever (38° C or
greater), hypothermia (36° C or lower), leukocytosis
(especially with a left shift), granulocytopenia, or
hypotension.
Blood
• Bacteremia—the presence of bacteria in the bloodstream
—may or may not be a sign of disease.
• Septicemia is a disease.
a serious disease characterized by chills, fever,
prostration, and the presence of bacteria or their toxins in
the bloodstream.
Blood
• minimize contamination of blood specimens by skin flora
• skin first is cleaned with alcohol (70% isopropyl or ethyl
alcohol) and then with a 1–2% iodine solution, an
iodophor, or chlorhexidine.
• Adults (20-30mL), pedia (1-5mL)
Blood
0.02–0.05% sodium polyanethol sulfonate
• inhibits coagulation, phagocytosis, and complement
activation, and inactivates aminoglycosides.
Heparin
• Viral cultures
• it may inhibit growth of gram-positive bacteria and yeast
CSF
• to diagnose meningitis and, less frequently, viral encephalitis
CSF
• Obtained by lumbar puncture
• Submitted in 3-4 tubes
– Chemistry/sero
– Microbiology
– Hematology
– Special tests
• Centrifuge at min of 1500g for 15mins
Other Body Fluids
• Pericardial, thoracic, or peritoneal cavity, or from joint
spaces
• 1-5mL , 10–15 mL is optimal for recovery of mycobacteria
and fungi
• fluid is centrifuged at 1500–2500 g for 20–30 minutes
Tissues
• histopathology of the lesion serves not only to differentiate between
infection and malignancy but also to distinguish between a
suppurative and a granulomatous process.
• placed into a sterile, wide-mouthed, screw-capped container
• finely minced with sterile scissors or scalpels, added to a small
volume of broth, and then rendered homogeneous either in a tissue
grinder, mortar and pestle, or stomacher to provide a 20%
suspension.
• stored under refrigeration for at least 2 weeks before being
discarded.
Respiratory Tract
• Washings or swab specimens are collected for detection of
Bordetella pertussis
• A swab is the preferred specimen for C. trachomatis, C.
pneumoniae, and Corynebacterium diphtheriae.
• Throat swab specimens are most commonly collected to
diagnose group A streptococcal pharyngitis.
Respiratory Tract
• Sputum
– determine the etiologic agents of pneumonia
– collected early in the morning before eating.
– rinses his or her mouth with water and then
expectorates a specimen, preferably 5–10 mL, resulting
from a deep cough
– REJECT if : > 10 EC /lpf
– ACCEPTABLE: <25 EC and >25 PMN/lpf
Urinary Tract
• clean-catch, midstream urine specimen
• Suprapubic urine (anaerobic culture)
• ≥10^5CFU of bacteria per millilitre of urine was considered highly
indicative of infection
• 0.001-mL loop - all urine specimens
• 0.01-mL loop - women with suspected acute urethral syndrome and
suprapubic aspirates
• all urine specimens must be processed within 30 minutes of
collection, or refrigerated at 4°C
Urinary Tract
Genital cultures
• For venereal diseases
• Endocervical specimens are
collected to determine the
etiologic agents of cervicitis and
to identify asymptomatic persons
infected with an organism that
causes sexually transmitted
disease.
Throat Swab
• collected to determine whether a patient has strep throat
Proper Technique for Obtaining a Throat Swab Specimen
• Using a tongue depressor to hold the patient’s tongue down, observe the back of the throat and
tonsillar area for localized areas of inflammation (redness) and exudate.
• Remove a Dacron or calcium alginate swab from its packet.
• Under direct observation, carefully but firmly rub the swab over any areas of inflammation or
exudate or over the tonsils and posterior pharynx.

• Do not touch the cheeks, teeth, or gums with the swab as you withdraw it from the
mouth.
• Insert the swab back into its packet and crush the transport medium vial in the transport container.
• Transport the swab to the laboratory as soon as possible. If transport will be delayed beyond 1 hour,
refrigerate the swab.
References
• Bailey’s and Scotts Diagnostic Microbiology
– Chapter 5 Specimen Management

• Henry’s Clinical Diagnosis and Mgt. by Lab Mtds.

– Chapter 63 Specimen collection and Handling for Diagnosis of Disease

• Burton’s Microbiology for Health Sciences

– Chapter 13 Diagnosing Infectious Disease