• Throat or nasopharyngeal swabs
• Gingival or other intraoral surface swabs
• Expectorated sputum, endotracheal aspirate, bronchial washings
• Voided or catheterized urine
• Vaginal or cervical swabs
• Gastric and small bowel contents

• Rectal swabs and feces (except for specific etiologic agents)
• Surface swabs from ulcers and wounds
  • Collect material from below the surface
• Material adjacent to a mucous membrane that has not been adequately decontaminated

Tests:

Anaerobic Culture (ANACUL)

Note: Anaerobic cultures require a separate test order.

Transport Device:

Anaerobic Transport Medium

eSwab

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

For superficial ulcers:

1. Collect material from below the surface after surface debridement or by the use a needle and syringe.
2. Cleanse rubber stopper of anaerobic transport vial with alcohol.
   • Allow to dry 1 minute before inoculating.
3. Push the needle through septum.
4. Aseptically inject all abscess material on top of agar.

Additional notes:

Tissue or aspirates are always superior to swab specimens; swabs are sub-optimal.

If a swab must be used for an open abscess, eSwab is preferred.

When using an eSwab:

• Pass the swab deep into the base of the lesion to firmly sample the fresh border.

Tests:

Tissue Culture & Gram Stain (TISCUL)

Transport Device:

Sterile Container

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Only submit bone that appears infected.

Avoid contamination from skin or sinus tracts.

Tests:

Body Fluid Culture & Gram Stain (BFCUL)

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Instructions:

1. Prepare puncture site as for surgical incision.
2. Inoculate blood culture bottle or Isolator (lysis-centrifugation) tube.

Additional notes:

Routine bacterial culture of bone marrow is rarely useful.

Tests:

Catheter Tip Culture (CTCUL)

Transport Device:

Sterile Container

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Instructions:

1. Cleanse the skin around the catheter site with alcohol.
2. Aseptically remove the catheter.
3. Clip 5 cm of distal tip directly into a sterile container.

Foley catheter tips, chest tube tips, and abdominal drainage tips are not acceptable for culture.

Additional Information:
The clinical relevance of catheter tip cultures is controversial: a positive culture may indicate contamination during removal. Therefore, blood cultures are the essential test for diagnosing catheter-related bacteremia.

Tests:

Wound Culture & Gram Stain (WCUL)

Anaerobic Culture (ANACUL)

Transport Device:

Sterile Container

Sterile Aliquot Tube

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Instructions:

1. Cleanse site by wiping with sterile saline or 70% alcohol.
2. Aspirate the area of maximum inflammation (commonly the center) with a needle and syringe. Irrigation with a small amount of sterile saline may be necessary.
3. Transfer specimen to a sterile container.
4. If an anaerobic infection is suspected, transfer specimen to an anaerobic transport device, and add an Anaerobic Culture (ANACUL) to the order.

Tests:

CSF Culture & Gram Stain (CSFCUL)

Transport Device:

Sterile Container

Sterile Aliquot Tube

Optimal Transport:

< 2 hours at ambient (room) temperature.

Do not refrigerate.

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Instructions:

1. Aseptically collect CSF from a lumbar puncture into sterile tubes.
2. Send the second tube to the Microbiology Laboratory.
3. Include specimen description on requisition.

Additional Information:
If an anaerobic infection is suspected, order an additional Anaerobic Culture (ANACUL).

Shunt specimens include a broth culture incubated for 14 days to optimize recovery of Cutibacterium acnes (formerly Propionibacterium).

CSF Gram stains are performed STAT (within 1 hour of receipt) in the laboratory.

Tests:

Wound Culture & Gram Stain (WCUL)

Anaerobic Culture (ANACUL)

Transport Device:

Anaerobic Transport Medium

Sterile Container

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Instructions:

1. Cleanse the area with sterile saline.
2. Perform tissue biopsy or aspirate inflammatory material from the base of the ulcer.

Additional Information:
Swab specimens are sub-optimal.

Tests:

Wound Culture & Gram Stain (WCUL)

Anaerobic Culture (ANACUL)

Transport Device:

Anaerobic Transport Medium

Sterile Container

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Instructions:

1. Cleanse and debride the wound before obtaining specimens.
2. Obtain a deep tissue specimen by scraping with a sterile scalpel or dermal curette (curettage), or biopsy from the base of a debrided ulcer.
3. Aspirate purulent secretions.

Additional Information:
Swab specimens are sub-optimal.

Do not culture a diabetic foot wound unless it appears infected (Clin Infect Dis 2012; 54).

Tests:

Ear Culture & Gram Stain (EARCSM)

Transport Device:

eSwab

Sterile Container

Sterile Aliquot Tube

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Inner Ear
For intact eardrum:

1. Clean ear canal with soap solution.
2. Collect fluid via syringe aspiration.
3. Submit in sterile container.

For ruptured eardrum:

1. Collect fluid on flexible shaft swab via an auditory speculum.

Tympanocentesis should be reserved for complicated, recurrent, or chronic persistent otitis media.

Outer Ear

1. Use moistened swab to remove any debris or crust from ear canal.
2. Obtain sample by firmly rotating swab in outer canal.

For otitis externa, vigorous swabbing is required “ surface swabbing may miss streptococcal cellulitis.

Tests:

Eye Culture (EYEC)

Eye Culture & Gram Stain (EYECSM)

Transport Device:

eSwab

Blood Agar Plate (BAP)

Chocolate Agar Plate (CHOC)

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Conjunctiva:

1. Sample each eye with separate swabs (pre-moistened with sterile saline) by rolling over the conjunctiva.
   • When only one eye is infected, sampling both can help distinguish indigenous microflora from true pathogens.
2. Media (BAP, CHOC) may be inoculated at the time of collection.
3. Prepare smears by rolling swab over 1 to 2 cm area of the slide.

Corneal Scrapings (collected by an ophthalmologist):

1. Using a sterile spatula, scrape the ulcers and lesions.
2. Inoculate scrapings directly onto media.
3. Prepare smears by rubbing material onto a 1 to 2 cm area of a slide.

Vitreous Fluid:

1. Prepare eye for needle aspiration of fluid.
2. Transfer fluid to sterile container or directly inoculate media.

Tests:

H. pylori Culture (HPYCUL)

Transport Device:

Optimal Transport:

Immediate transport on ice or cold pack

Stability:

< 48 hours, refrigerated

Collection Guidelines:

Due to the fastidious nature of H. pylori, a culture is only indicated when patients have failed therapy, and susceptibility testing is required.

One or two gastric biopsy specimens from the antrum and corpus are recommended for culture.

Call the microbiology lab (216.444.5870) to obtain transport media: Brucella broth with glycerol.

Tissue may be placed in a sterile container with a small amount of sterile saline if transport time is < 4 hours. Fecal specimens are unacceptable.

Tests:

Bacterial Vaginosis Gram Stain (BVSTN)

Transport Device:

Optimal Transport:

‰¤ 12 hours at ambient (room) temperature

Stability:

‰¤ 1 week at ambient (room) temperature

Collection Guidelines:

Determination of a score for the relative amounts of microbial morphologies observed in a Gram stain of vaginal fluid is the definitive method for diagnosing bacterial vaginosis.

Normal Score (0-3): A predominance of medium to large gram positive bacilli suggestive of lactobacilli is consistent with normal vaginal flora.

Intermediate Score (4-6): An intermediate score suggests a transition from normal vaginal flora.

Predominant Score (7-10): A predominance of gram-negative or gram variable rods suggestive of Gardnerella vaginalis, Mobiluncus, and Bacteroides species is consistent with bacterial vaginosis.

Tests:

Mycoplasma Culture (MYPLAS)

Transport Device:

Universal Transport Media (UTM) 3 mL
Regular-Tip Flocked Swab

Optimal Transport:

< 2 hours, refrigerated

Stability:

Ambient (room) temperature: < 8 hours

Refrigerated fluid NOT in UTM: < 24 hours

Refrigerated in UTM:  < 48 hours

Frozen in UTM: 1 month

Collection Guidelines:

Instructions:

1. Place swab or 1 mL of specimen in Universal Transport Media (UTM).
2. Transport media must be inoculated at point of collection.

Adherence to proper specimen collection, transport guidelines, and temperature are critical to isolation of the organisms.

Dry swabs, swabs in bacterial transport media, or swabs in M4RT media will be rejected.

Additional Information:
Specimens from nongenital sites will be sent to a reference laboratory (order UMPLAS).

To detect Mycoplasma pneumoniae from respiratory sites, a molecular test is required.

Tests:

Neisseria gonorrhoeae Culture (MISCGC)

Transport Device:

Optimal Transport:

Immediate transport at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Neisseria gonorrhoeae Culture Collection Instructions:

1. Collect specimen for cultures with a sterile swab.
2. Inoculate directly to a Jembec plate.
3. Place white tablet into the hole of Jembec plate to provide a CO₂-enriched atmosphere.
4. Close top of the plate tightly, then place into a plastic bag.
5. Keep the plate and specimen at ambient (room) temperature, and deliver to lab as soon as possible.

If a Jembec plate is unavailable, an aerobic culturette swab may be used if transported to laboratory immediately.

Endocervical Collection Instructions:

1. Remove cervical mucus with swab, then discard.
2. Insert a second swab into endocervical canal and rotate against walls.
3. Allow time for organisms to absorb onto the swab surface.

Urethral Collection Instructions:

1. Collect urethral specimens at least 1 hour after the patient has urinated.
2. Insert small swab 2-4 cm into urethral lumen, and rotate.
3. Leave the swab in place for 2 seconds to facilitate absorption.

Additional Information:

Because of the labile nature of the organism, a negative culture does not rule out N. gonorrhoeae infection. Overgrowth by normal microbiota may make it impossible to rule out N. gonorrhoeae.

Specimens are screened for N. gonorrhoeae only.

False negative results may occur with delayed transport.

Tests:

Urine Culture (URCUL)

Transport Device:

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Instructions:
Place urine specimens before and after massage in preservative tubes (see Urine Culture tab).

Label specimens as follows:

1. VB1 (voided bladder 1): 1^st 10cc of urine – represents urethra
2. VB2: midstream urine – represents bladder
3. EPS (expressed prostatic fluid): Prostate secretions after massage – represents prostate
4. VB3: also represents prostate

If one specimen grows far more bacteria than others, the infection is localized to the urethra, bladder, or prostate.

Tests:

Bronchoscopy Culture & Gram Stain (BALCSM)

Transport Device:

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours, refrigerated

Collection Guidelines:

Instructions:

1. Collect fluid in a sputum trap.
2. Transfer fluid to leak-proof container.
3. Place collection brush in a sterile container with 1 ml sterile saline.

Additional Information:

If transportation is delayed, refrigerate the collected specimens.

Separate test orders are required to rule out the presence of mycobacteria, fungi, viruses, and atypical bacterial pathogens in respiratory specimens.

Blood cultures are recommended for patients being evaluated for pneumonia.

Tests:

Cystic Fibrosis Culture (CFRCUL)

Transport Device:

Throat swab/culturette

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours, refrigerated

Collection Guidelines:

Instructions:

1. Prior to sputum collection, instruct the patient to rinse mouth with water.
2. Collect specimen, then send to laboratory.

Additional Information:

If transportation is delayed, refrigerate the collected specimens.

Separate test orders are required to rule out the presence of mycobacteria, fungi, viruses, and atypical bacterial pathogens.

Tests:

Legionella culture (LEGCUL)

Transport Device:

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 48 hours, refrigerated

Collection Guidelines:

If transportation is delayed, refrigerate the collected specimens.Specimens from non-respiratory sites should not be submitted for Legionella culture unless there is a high index of clinical suspicion to support the request.

Urine antigen assays for L. pneumophila serogroup 1 will be in positive in ~90 – 95% of patients with severe disease due to the Pontiac monoclonal subtype of serogroup 1, but positive in only 50% of these patients with mild disease. The urine antigen assay is unreliable for the diagnosis of severe Legionnaire’s Disease caused by L. pneumophila other than serogroup 1 or a different Legionella species (detects less than 5 – 40% of cases).

Tests:

MRSA Culture Screen (MRSASC)

MRSA/S. aureus Culture (SANSAL)

Transport Device:

Dual Swab with Amies Transport Medium

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 48 hours at ambient (room) temperature

Collection Guidelines:

Instructions:

1. Insert a sterile swab into the nose until resistance is met at the level of the turbinates (approximately 1-2 cm into one nostril).
2. Rotate the swab against the nasal mucosa for 3 seconds. Apply slight pressure with a finger on the outside of the nose to ensure good contact between swab and inside of nose.
3. Using the same swab, repeat the process for the other nostril.

Samples from other anatomic sites may be submitted.

Additional Information:

If transportation is delayed, refrigerate the collected specimens.

This test should not be used to diagnose and treat infections.

Tests:

Sinus Culture & Gram Stain (SINUSC)

Anaerobic Culture (ANACUL)

Transport Device:

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours, refrigerated

Collection Guidelines:

Instructions:

1. Aspirate with needle and syringe.
2. Cleanse rubber stopper of anaerobic transport vial with alcohol.
3. Push needle through septum and inject specimen on top of agar.

If transportation is delayed, refrigerate the collected specimens.

Tests:

Respiratory Culture & Gram Stain (RCULST)

Transport Device:

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours, refrigerated

Collection Guidelines:

Instructions:

1. Prior to sputum collection, instruct the patient to rinse mouth with water.
2. Collect specimen, then send to laboratory.

Additional Information:

If transportation is delayed, refrigerate the collected specimens.

Separate test orders are required to rule out the presence of mycobacteria, fungi, viruses, and atypical bacterial pathogens in respiratory specimens.

Blood cultures are recommended for patients being evaluated for pneumonia.

Tests:

Throat Culture – Routine Group A Strep (THRCUL)

Transport Device:

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 48 hours at ambient (room) temperature

Collection Guidelines:

Instructions:

1. Use culturette swab to sample inflamed areas and exudate from the posterior pharynx.
2. Place swab in transport medium.

Additional Information:

If transportation is delayed, refrigerate the collected specimens.

Guidelines for the diagnosis of Group A streptococcal pharyngitis are available from IDSA (Clin Infect Dis 2012; 55:e86-102).

Tests:

Body Fluid Culture & Gram Stain (BFCUL)

Anaerobic Culture (ANACUL)

Transport Device:

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Instructions:

1. Disinfect overlying skin with iodine or chlorhexidine preparation.
2. Obtain specimen with needle and syringe.
3. Push needle through septum of transport container.
4. Inject fluid into sterile container (or Port-A-Cul vial if an anaerobic culture is also ordered).

Do not submit a swab specimen for this test under any circumstance.

Fluid may be inoculated into a blood culture bottle (up to 10 ml) if a separate 1 ml aliquot is also provided for the preparation of a Gram stain and inoculation of solid media.

Additional Information:
Broth cultures do not reflect bacterial burden, and a true pathogen may be obscured by overgrowth of more rapidly growing bacteria.

Anaerobic Cultures (ANACUL) require a separate order.

Abscess and drainage from tubes should be submitted with an order for a Wound Culture (WCUL) rather than body fluid culture.

Media and incubation conditions are employed for the recovery of aerobic bacteria from normally sterile body fluids (synovial, peritoneal, pericardial, pleural, and amniotic).

Tests:

Aeromonas/Plesiomonas Culture (AERPLE)

Campylobacter Culture (CAMPY)

Stool Culture (STCUL)

Vibrio Culture (VIBCUL)

Yersinia Culture (YERCUL)

Transport Device:

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

Unpreserved: < 2 hours at ambient (room) temperature

Preserved: < 72 hours, refrigerated in Cary-Blair/Stool Culture Transport container

Collection Guidelines:

Instructions:

• Transfer stool into Cary-Blair/Stool Culture Transport container immediately after collection and prior to transport.
  • This will help to optimize recovery of fastidious pathogens, such as Shigella.

Alternatively, stool may be transported in a sterile container if it will be received by the laboratory within 2 hours of collection.

Additional Information:

If transportation is delayed, refrigerate non-preserved stool/feces specimens.

Requests for stool culture on patients who have been in the hospital > 3 days will be rejected (there is a low likelihood of the enteric pathogens screened for in this test causing diarrhea in this population).

Tests:

Tissue Culture & Gram Stain (TISCUL)

Anaerobic Culture (ANACUL)

Transport Device:

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Add drops of sterile saline to keep small pieces of tissue moist.

If an anaerobic infection is suspected, transfer the specimen to an anaerobic transport device and add an Anaerobic Culture (ANACUL) to the order.

Tests:

Urine Culture (URCUL)

Transport Device:

Culture & Sensitivity Urine Transport Kit

Optimal Transport:

Preserved: < 24 hours at either ambient (room) temperature or refrigerated

Unpreserved: < 2 hours at ambient (room) temperature

Stability:

Preserved: < 48 hours at either ambient (room) temperature or refrigerated

Unpreserved: < 2 hours at ambient (room) temperature; < 24 hours, refrigerated

Collection Guidelines:

If transportation is delayed, refrigerate non-preserved urine specimens.

Transferring Urine Into a C&S Urine Transport Kit:

1. Submerge the tip of transfer straw into urine specimen.
2. Push the C&S preservative grey top tube into the transfer straw.
3. Hold in position until flow stops; it must be filled to the minimum fill line on the tube (3 ml).
4. Remove the tube, and leave the transfer straw in urine specimen container.
5. Shake tube vigorously to mix sample.

If both a C&S tube (gray top) and urinalysis (red/yellow) are being collected, transfer the urine to C&S tube (gray top) first.

Voided Midstream Clean Catch Method:
Patients should be instructed to wash hands prior to collection and offered exam gloves.

Female Patients:

1. Instruct the patient to sit on the toilet with their legs apart, and the labia spread apart with one hand.
2. Patient should void in the toilet; then, while continuing to void, the patient should hold specimen container in midstream to collect sample.

Male Patients:

1. Instruct the patient to retract foreskin if uncircumcised.
2. Patient should void in the toilet; then, while continuing to void, the patient should hold specimen container in midstream to collect sample.

Indwelling (foley) Catheter or Suprapubic Tube (SPT):

1. Perform hand hygiene; apply clean gloves.
2. Clamp drainage tubing a minimum of 12 inches below the sampling port; allow 30 minutes for urine to fill the tubing to slightly above the sampling port.
3. Clean the entry port with alcohol by scrubbing for 20 seconds. Wait for the port to dry.
4. Perform urine collection from sampling port using a BD Vacutainer Luer-Lok Access Device: position the device over center of sampling port, then push it on and rotate clock-wise until it fits securely.
5. Push a C&S Preservative Tube over the holder portion of Access Device.
6. Once the tube is completely filled, remove the tube from the holder.
7. Invert the tube 8-10 times.

Do not collect urine from collection bag.

Straight Catheter:

1. Thoroughly cleanse the urethral opening with betadine or chlorasept.
2. Pass catheter using sterile technique into the bladder.
3. After discarding initial 15 to 30 ml of urine, transfer urine to a C&S Preservative Tube (preferred for this method) or a sterile container.

Cystoscopy:

1. Specimens obtained while cystoscope is in the bladder should be labled as CB for catheterized bladder.
2. Specimens of irrigated fluid passing from bladder though ureteral catheters should be labeled as WB (washed bladder urine).
3. Specimens collected with ureteral catheters passed to midureter or renal pelvis should be labeled as “LK-1“, “RK-1“, “LK-2“, and “RK-2” (LK for left kidney, RK for right kidney).

Stoma (cystostomy, ileal conduit, nephrostomy, ureterostomy):

1. Remove the external device; discard any urine within it.
2. Gently cleanse the stoma.
3. Using a sterile technique, insert a catheter into the cleansed stoma.
4. Collect the urine by aspirating back on the syringe.
5. After discarding initial 15 to 30 ml of urine, transfer urine to a C&S Preservative Tube (preferred for this method) or a sterile container.

Tests:

Wound Culture & Gram Stain (WCUL)

Anaerobic Culture (ANACUL)

Transport Device:

Anaerobic Transport Medium

eSwab

Optimal Transport:

< 2 hours at ambient (room) temperature

Stability:

< 24 hours at ambient (room) temperature

Collection Guidelines:

Instructions

1. Remove surface exudate by wiping with sterile saline or 70% alcohol.
2. Aspirate abscess material with a needle and syringe.
3. Cleanse rubber stopper of anaerobic transport vial with alcohol.
   • Allow to dry 1 minute before inoculating.
4. Push needle through septum.
5. Aseptically inject all abscess material on top of agar.
6. If anaerobic culture is not required, submit aspirate in sterile container.