Specimen Collection

Maximum care must be taken to collect only those specimens that may yield pathogens, rather than colonizing flora or contaminants. Specific rules for the collection

of material vary, depending upon the source of the specimen, but several general principles apply.



• Make every effort to obtain specimens prior to the initiation of antimicrobial therapy.

• Collect the specimen at optimal times (for example, early morning sputum for AFB culture).

• Wear gloves, gowns, masks, and/or goggles, when appropriate, when collecting specimens from sterile sites. Use strict aseptic technique.

• When obtaining specimens from normally sterile sites such as pleural or joint spaces, cerebrospinal fluid, or the peritoneum, take care to minimize contamination by

the normal colonizing flora of the skin or mucous membranes.

• Collect an adequate volume of specimen; send tissue or fluid whenever possible rather than submitting a specimen collected on a swab.

• Swabs are not optimal for fungal culture, anaerobe cultures, decubitus ulcers, mycobacterial cultures MTB/ RIF assay (gene Xpert), perirectal abscesses, and oral

abscesses.

• Label all specimen containers with identifying information about the patient (name and hospital MR number ) *and the specimen source, date, time of collection

and other required information should be clearly filled/mentioned on".

• Notify the laboratory in advance if special tests are requested or if unusual pathogens, including potential agents of bioterrorism, are suspected.

• Place warning labels on specimens from patients suspected of having highly contagious diseases and notify the laboratory supervisor.

• If there is any question about the optimal sample to collect, contact the microbiology laboratory before obtaining specimens.

• Specimens should be sent to microbiology in sterile, leak-proof containers.

• Fluids obtained in syringes (eg, paracentesis, joint aspirate, needle drainage of abscess), specimen can be sent in the original syringe with needle removed and

replaced with a cap.

• Send the specimen to the laboratory as soon as possible after collection.

• If a delay is unavoidable, most specimens (with the exception of blood, cerebrospinal fluid, joint fluid, Respiratory tract specimens, tissue, abscess fluid, and cultures

for Neisseria gonorrhoeae) should be refrigerated until transported.

• Desiccation of the sample must be avoided.

Collect purulent material aseptically:



• From an undrained abscess: use a sterile needle and syringe after appropriate surface decontamination.

• For large abscesses: open with a sterile scalpel and collect the expressed material with a sterile syringe.

• Transport 5 to 10 ml of aspirated material in sterile container. (Pus obtained from the abscess in syringe can be sent in the original syringe with needle removed and

replaced with a cap).

• Determine the type of culture bottles to utilize, as indicated per physician's order(aerobic / anaerobic).

• Make every effort to send blood culture before starting antibiotics. • Prepare the skin and draw blood aseptically • Do not Refrigerate the Blood Culture.

Adults:

• Atleast 20 mL should be collected, with inoculation of 10 mL into an aerobic bottle and 10 mL into an anaerobic bottle. If ≤10 mL of blood is obtained, all of the specimen should be inoculated into the aerobic culture bottle.

Children:

• A blood culture set usually consists of one aerobic bottle and one anaerobic bottle. At least two, preferably three, blood culture sets should be obtained. Single blood

culture should be avoided.

• A total of two blood culture sets is usually adequate when continuous bacteremia is

suspected and the pretest probability of bacteremia is high (as in patients with suspected IE who have not received prior antimicrobial therapy).

• A total of three blood culture sets is appropriate for circumstances in which bacteremia due to a pathogen not likely to be a contaminant is anticipated (as in intra-

abdominal sepsis or pneumonia) and when the pretest probability of bacteremia is low to moderate. The first two blood cultures, obtained with separate

venipunctures, may be obtained in sequence, with collection of the third blood culture four to six hours later.

• A total of four blood culture sets are rarely needed; collection may be considered when the pretest probability of bacteremia is high and the anticipated pathogen is

likely to be a common contaminant, such coagulase-negative Staphylococci. Clinical examples include prosthetic valve endocarditis or endovascular infections due

to infected devices, such as pacemakers or grafts. As many as four blood culture sets may also be necessary to diagnose endocarditis in patients who have received

antimicrobial therapy in the preceding two weeks.

• In children, it may not be possible to obtain sufficient blood to inoculate more than a single blood culture bottle; in such cases, all of the blood should be inoculated

into an aerobic bottle.

• Collect the fluid strictly using aseptic technique with a sterile needle and syringe and place in sterile container or direct inoculation to blood culture vials.

• Volume of fluid should be at least 1 to 10 mL, but send as much fluid as possible.

• Do not send Sterile Body Fluids on swabs.

Only for diagnosis and management of central venous catheter-related bloodstream infections.


• Cleanse skin around insertion site with alcohol.

• Send catheter tip (5 cm) in sterile container.

• Catheter tip must be accompanied with 2 peripheral blood cultures.

• Swabs and leading-edge aspirates with or without injection of saline fail to yield etiologic agents in the majority of cases.

• If an unusual organism is suspected, a leading-edge (advancing margin) punch biopsy is recommended.

• Place the biopsy in a sterile container with a small volume of non-bacteriostatic saline and transport to the lab as soon as possible.

• Aseptic technique should be strictly followed — The overlying skin should be cleaned with alcohol and a disinfectant such as povidone-iodine or chlorhexidine (0.5

percent in alcohol 70 percent); the antiseptic should be allowed to dry before the procedure is begun.

• After the skin is cleaned and allowed to dry, a sterile drape with an opening over the lumbar spine should be placed on the patient.

• PPE should be donned.Face masks should be used by individuals who place a catheter or inject material into the spinal canal (CDC).

• Insert the needle.. Collect 10 to 15ml volume of CSF. (more volume has to be drawn if additional tests like mycobacterial or fungal culture are required).

• Collect the fluid into three sterile leak-proof tubes. The tubes are to be numbered sequentially in the order in which they are collected.(

tube 1 for chemical studies, tube 2 for culture, tube 3 for cell counts).

• Cap the tubes tightly.

• Transport immediately to lab at ambient temperature.

• DO NOT refrigerate CSF.

• External ear cultures are processed as superficial wounds.

• Middle ear fluid will be processed as a sterile body fluid. If the diagnosis is otitis media, the specimen of choice is middle ear fluid collected by tympanocentesis. Use

swab to collect material from ruptured ear drum.

• Please indicate specific ear source.

• Grasp the swab cap with fingers.

• Be careful to avoid contacting the swab or stick with your fingers.

• Insert premoistened swab into nares. Sweep around the interior surface of the anterior nares.

• Perform on both nares with one swab.

• Place into transport media. Transport at ambient temperature.

• Nares swabs are only acceptable for MSSA/MRSA surveillance, not routine culture.


Note: This is an inappropriate specimen for anything other than the assessment of Staphylococcal colonization.

• Assure patient cooperation to get an adequate specimen.

• Instruct the patient as follows:

a. Rinse mouth with tap water to remove food particles and debris.

b. Have patient breathe deeply and cough several times to achieve a deep specimen.

c. Patient should expectorate into dry, sterile container.

d. Patients suspected of having tuberculosis should expectorate sputum in the early morning, into a sterile container with lid sealed tightly. Leaking specimens may

be cancelled.

e. Transport immediately at ambient temperature.

f. Expectorated sputum is acceptable for bacterial, and fungal cultures and AFB testing (GeneXpert).

g. Microbiologist will determine the number of squamous epithelial cells present for specimen adequacy and reject samples for bacterial culture that are not

indicative of deeply expectorated specimens.

h. In patients with clinical and chest x-ray findings compatible with tuberculosis, collect 3 first morning sputum specimens (on 3 separate days) for AFB testing.

For routine culture:


• Send 2-5 gms approx. in sterile wide-mouth container or enteric transport medium (Cary-Blair) if transport will exceed 1 hour.

• Do not send specimens for routine culture on patients who develop diarrhea after three days of hospitalization and whose admitting diagnosis was not diarrhea.

For ova and parasite examination:


• Send sample in sterile wide-mouth container.

• Fresh specimens should be examined immediately; do not send specimens on inpatients who develop diarrhea after three days of hospitalization.

• Tissue collection is an invasive procedure and requires surgery by a trained physician.

• Collect tissue aseptically. Include material from both the center and the edge of the lesion.

• Transport in sterile container. Keep moist; add sterile (non-bacteriostatic saline) if necessary.


• Do not submit tissue in formalin

Give the patient a sterile, dry, wide-necked, leak proof container and request a 10–20 ml specimen of mid stream, clean catch urine specimen as follows:

Female patients

Wash the hands. Cleanse the area around the urethral opening with clean water, dry the area with a sterile gauze pad, and collect the urine with the labia held apart.

Male patients

Wash the hands before collecting a specimen.Cleanse the area . Rim of container should not be touched.

Indwelling catheter urine

• The catheter tubing should be clamped off above the port to allow the collection of freshly voided urine. The catheter port or wall of the tubing should then be

cleaned vigorously with 70% ethanol, and urine aspirated via a needle and syringe; the integrity of the closed system must be maintained.

• Transfer the urine to a sterile specimen container.

• Do not collect urine from the drainage bag.

• Urine catheter tip cultures are not acceptable.

• Actual tissue, aspirates, and fluids are always specimens of choice, especially from surgery.

• For superficial wounds/ulcer/lesion : Wipe area with normal saline to remove as much of the superficial flora as possible.

• Swab stick with Stuart's or Amie's transport medium should be preferably used.

• Swab along leading edge of the wound.

• In case of delay to lab, keep the sample at room temperature.