A. SCOPE RRMC Laboratory Microbiology

Transcription

1 RUTLAND REGIONAL MEDICAL CENTER Page 1 of 13 DEPARTMENT: Laboratory Microbiology APPROVED DATE: 08/10/2017 TITLE: Microbiology collection, PREPARED BY: Sandy Niemczyk ENDORSED BY: Keith Leblanc Transport and APPROVED BY: Tony Masuck MD EFFECTIVE DATE: 3/30/2009 NEXT REVIEW DATE: biennial JOINT COMMISSION STANDARD: NA CMS FED# : NA A. SCOPE RRMC Laboratory Microbiology B. PURPOSE Almost nothing is more important to the effectiveness of a laboratory than a specimen that has been appropriately selected, collected, and transported. If these are not a priority, the laboratory can contribute little or nothing to patient care. s should be rejected if there is a risk to the safety of a patient; i.e. occasions where there is concern for the identity of the specimen, the wrong container type, incorrect transport conditions, etc. However, it is always important to double check if a specimen COULD be accepted. This may involve processing the specimen so as not to compromise specimen integrity while also evaluating the specimen for acceptability. C. POLICY RRMC lab staff will follow the steps outlined in the procedure section. D. DEFINITIONS N/A E. PROCEDURE General for Proper 1. Before collecting the specimen, consider the risk/benefit ratio of the collection procedure to the patient. Inadequate and/or inappropriately collected specimens for culture yield little useful clinical information and may actually be misleading. 2. Collect specimen before administering antimicrobial agents when possible. 3. Collect specimen with as little contamination from indigenous microflora as possible to ensure that the sample will be representative of the infected site. 4. Utilize appropriate collection devices. Use sterile equipment and aseptic technique to collect specimens to prevent introduction of microorganisms during invasive procedures. 5. Clearly label the specimen container with the patient s name, identification number and/or date of birth. Include the date and time of collection, and source of specimen. 6. Collect an adequate amount of specimen. Insufficient amounts of specimen may yield false-negative results. 7. Inform the clinical microbiology lab when rule-out requests are important. Consider geographic location and season when notifying the laboratory of rule-out requests. 8. Identify the specimen source and/or specific site correctly so that proper culture media will be selected during processing in the laboratory. 9. If a specimen is to be collected through intact skin, cleanse the skin first. For example, use 70% alcohol followed by 10% povidone-iodine or chloroprep scrub. 10. Collect specimens in sturdy, sterile, screw-cap, leakproof containers with lids that do not create an aerosol when opened. Safety Considerations for and Transport of s 1. Follow universal precaution guidelines. Treat all specimens as potentially hazardous.

2 RUTLAND REGIONAL MEDICAL CENTER Page 2 of Personnel must use appropriate barrier protection (such as gloves and laboratory coat or gown) when collecting or handling specimens. If splashing may occur, protective eyewear, face masks, and impervious aprons are also necessary. 3. Do not contaminate the external surface of the collection container and/or its accompanying paperwork. 4. Minimize direct handling of specimens in transit from the patient to the laboratory whenever possible. Use plastic sealable bags with a separate pouch for the laboratory requisition orders or transport carriers. 5. Never transport syringes with needles to the laboratory. Instead, transfer the contents to a sterile tube or cup, or remove the needle, recap the syringe and place the syringe in a sealable, leakproof plastic bag. General for Proper Transport 1. Transport all specimens to the laboratory promptly to ensure the survival and isolation of fastidious organisms and to prevent overgrowth by more hardy bacteria. This will provide a more accurate diagnosis of the infectious-disease process. 2. Alternatives to prompt delivery. Many specimens may be refrigerated at 2-8ºC. CSF, blood cultures, stool cultures, anaerobic cultures, and specimens submitted on selective media for Neisseria gonorrhoeae should not be refrigerated. Refer to details below: a. If blood is drawn into blood culture broth, hold it at room temperature. b. s that may harbor temperature-sensitive organisms such as Neisseria species should be left at room temperature. c. For anaerobic culture specimens, use anaerobic transport and maintain at room temperature. d. Stool s fresh specimens must be received in lab within one hour of collection or use transport kits with the following guidelines: (1) Enteric PCR specimen should be transferred into the orange top C&S vial within one hour of collection. (2) O&P specimen should be transferred into the black top vial within one hour of collection. (3) C. Difficile specimen should be refrigerated within one hour of collection. e. Hold CSF specimens at room temperature (unless they are to be cultured for viruses). f. All specimens for viral culture must be refrigerated. Use of Transport Systems 1. When using a swab for collection and transport of specimens, the test request should be considered prior to specimen collection. A specific type of swab may be necessary for the collection and transport of certain cultures. 2. Anaerobe transport systems are used to ensure the viability of anaerobic organisms in transit to the laboratory. The lab supplies two styles; one for fluids and a surgery pack for tissues. 3. Stool collection/transport systems are used to preserve stool specimens for ova and parasite exams. Stool specimens which will not reach the laboratory within one hour of passage must be preserved before organisms become distorted and/or disintegrate. Use Para-Pak transport system available from the lab. Acceptability 1. s which have been improperly collected or transported may not be processed. Processing and reporting results from such specimens may provide misleading information that can lead to misdiagnosis and inappropriate therapy. 2. Listed below are unacceptable specimens/situations: a. Unlabeled specimen or mislabeled b. Leaking container or obviously contaminated c. Barium enema stool for O&P exam d. Prolonged transport Page 2 of 13

3 RUTLAND REGIONAL MEDICAL CENTER Page 3 of 13 e. Non-sterile container. f. No date and time of collection and/or no source. g. Anaerobe cultures on unsuitable specimens (e.g. stool, mouth, vaginal) h. unsuitable for request (e.g. Anaerobe culture request with specimen in aerobic transport) i. Syringes with needle attached. j. Quantity not sufficient 3. As per lab procedure for specimen acceptability, staff will contact ordering physician/nurse to request repeat specimen, suggest alternate order or transport requirement, and/or to obtain additional information, if needed. Be sure all situations are documented on laboratory Green Sheets. 4. It is always important to double check if a specimen COULD be accepted. This may involve processing the specimen so as not to compromise specimen integrity while also evaluating the specimen for acceptability. F. RELATED POLICIES AND FORMS CAP Question: Supersedes Document Entitled: Document locations: MIC.13250, MIC Microbiology, Transport and Microbiology Procedure Manual, t:\lab\microbiology\procedure manual\specimen management\microbiology specimen collection, transport and storage.docx G. REFERENCES AND BIBLIOGRAPHY Microbiology Procedure References #2 and #8. H. APPENDIX Page 3 of 13

4 RUTLAND REGIONAL MEDICAL CENTER Page 4 of 13 Microbiology Abscess Remove surface exudate by wiping with sterile saline or 70% EtOH. Tissue or fluid is always superior to swab specimen. If swabs must be used, collect 2, 1 for culture and 1 for Gram stain. Open Aspirate if possible, or pass swab deep into lesion and firmly sample lesion s advancing edge. Swab transport system 2 h, RT 24 h, RT 1/day from same source A sample from the base of the lesion and a sample from the abscess wall are most productive. Closed Aspirate abscess wall material with needle and syringe. Aseptically transfer all material into anaerobic transport device or vial. Anaerobic transport system, 1 ml 2 h, RT 24 h, RT 1/day from same source Sampling of surface area can introduce colonizing bacterial not involved in infectious process. Bite wound See Abscess. Do not culture animal bite wounds 12 h old (agents are usually not recovered) unless they are on face or hand or unless signs of infection are present.

5 RUTLAND REGIONAL MEDICAL CENTER Page 5 of 13 Blood culture Disinfection of culture bottle: apply 70% isopropyl alcohol to rubber stoppers and wait 1 min. Disinfection of venipuncture site: 1. After location of the vein, scrub the venipuncture site with ChloraPrep (swabstick) for 30 seconds. 2. Allow site to air dry before venipuncture. 3. Do not re-palpate vein at this point. 4. Collect blood. BacT/Alert aerobic & anaerobic blood culture bottle 2-bottle set used for adult blood collection 1-bottle used for pediatric collection Volumes: Children under 12: 1-4 ml of blood per venipuncture in pediatric bottle 2 h, RT 24 h, RT or per instructions 3 sets in 24 h Acute sepsis: 2-3 sets from separate sites, all within 10 min Endocarditis, acute: 3 sets from 3 sites over 1-2 h Endocarditis, subacute: 3 sets from 3 sites taken 15 min apart; if negative at 24 h, obtain 3 more sets. Fever of unknown origin: 2-3 sets from separate sites 1 h apart; if negative at 24 h, obtain 2-3 more sets. Adults: 20 ml of blood per venipuncture divided into aerobic and anaerobic bottles. Bone Marrow Prepare puncture site as for surgical incision Inoculate Blood Culture Bottle 24 h, RT if in culture bottle 24 h, RT 1/day Small volumes of Bone Marrow may be inoculated directly onto culture media or into broth Burn Clean and debride the wound prior to specimen collection. Sterile screw-cap tube or cup 2 hour, RT 24 h, RT None Process for aerobic culture only. Surface cultures of burns may be misleading.

6 RUTLAND REGIONAL MEDICAL CENTER Page 6 of 13 Catheter I.V. 1. Cleanse skin around catheter site with alcohol. 2. Aseptically remove and clip 5-cm distal tip of catheter directly into sterile tube. 3. Transport directly to Microbiology laboratory to prevent drying. Sterile screw-cap tube or cup 1 hour, RT 24 h, 4ºC None Acceptable i.v.catheters for semiquantitative culture (Maki method): central, CVP, Hickman, Broviac, peripheral, arterial, umbilical, hyperalimentation, Swan-Ganz. Foley Do not culture, since growth represents distal urethral flora. Reject: Not acceptable for culture. Cellulitis 1. Cleanse site by wiping with sterile saline or 70% alcohol. 2. Aspirate area of maximum inflammation (commonly center rather than leading edge) with fine needle and syringe. 3. Draw small amount of sterile saline into syringe and aspirate into sterile screw-cap tube. CSF 1. Disinfect site with 2% iodine tincture.. 2. Insert a needle with astylet at L3-L4, L4-L5, or L5-S1 interspace. 3. On reaching the subarachnoid space, remove the stylet and collect 1-2 ml of fluid in each of three leakproof tubes. Sterile tube 1 hour, RT 24 h, RT None Yield of potential pathogens is only 25-35%. Sterile screw-cap tube. Minimum amount required: Bacteria, 1 ml; Fungi, 2 ml; AFB, 2 ml; Virus, 1 ml Bacteria: never refrigerate; 15 min, RT Virus: transport on ice; 15 min, 4 C 24 h, RT 72 h, 4 C None Obtain blood cultures also. If only 1 tube of CSF is collected, it should be submitted to microbiology first; otherwise submit tube #2. Aspirate of brain abscess or a biopsy may be necessary to detect anaerobic bacteria or parasites.

7 RUTLAND REGIONAL MEDICAL CENTER Page 7 of 13 Decubitus ulcer See comment. A swab specimen is NOT the specimen of choice. 1. Cleanse surface with sterile saline. 2. If a sample biopsy is not available, vigorously swab the base of the lesion. 3. Place the swab in appropriate transport system. Anaerobic system (for tissue) or swab transport 2 h, RT 24 h, RT 1/day from same source Decubitus swab provides little clinical information; discourage the use of swabs for this specimen. Tissue biopsy sample or needle aspirate is specimen of choice. Ear Inner Outer Tympanocentesis is reserved for complicated, recurrent, or chronic persistent otitis media. 1. For intact ear drum, clean ear canal with soap solution, and collect fluid via syringe aspiration technique. 2. For ruptured ear drum, collect fluid on flexible-shaft swab via auditory speculum. 1. Remove any debris or crust from ear canal. 2. Obtain sample by firmly rotating culture swab in outer canal. Sterile tube, swab transport medium, or anaerobic system. 2 h, RT 24 h, RT 1/day from same source Swab transport. 2 h, RT 24 h, 4 C 1/day from same source Throat or nasopharyngeal cultures are not predictive of agents responsible for otitis media and should not be submitted for that purpose. For otitis externa, vigorous swabbing is required. Eye Conjunctiva 1. Sample both eyes with separate swabs (premoistened with sterile saline) by rolling swab over each conjunctiva. 2. Inoculate medium at time of collection. 3. Smear swabs onto 2 slides for staining. Direct culture inoculation: BAP and CHOC or swab transport medium. Note: Call lab to obtain culture media. Plates: 1 hour, RT Swabs: 2 h, RT 24 h, RT None Sample both conjunctiva to determine indigenous microflora. Uninfected eye serves as a control. Corneal scrapings 1. Obtain conjunctival swab specimens see above 2. Instill 2 drops of local anesthetic. 3. Using sterile spatula, scrape ulcers or lesions, and inoculate scraping directly onto media. 4. Apply remaining material to 2 clean glass slides for staining. Direct culture inoculation: BAP, CHOC, and SAB DEX. Note: Call lab to obtain culture media. Plates: 1 hour, RT Swabs: 2 h, RT 24 h, RT None Take swabs for culture prior to anesthetic application; corneal scrapings can be obtained after.

8 RUTLAND REGIONAL MEDICAL CENTER Page 8 of 13 Feces Enteric Pathogen PCR Pass directly into clean, dry container. Transport to microbiology laboratory within 1 h of collection, or transfer to enteric transport system (available from laboratory). Leakproof, widemouth container or enteric transport system, 2 g. Unpreserved, 1 h, RT Enteric transport system: 48 h, RT 1/day Do not routinely perform for patients whose length of stay is > 3 days and admitting diagnosis is not gastroenteritis. Diaper is unacceptable. Clostridium difficile Ova and Parasite Pass liquid or soft stool directly into clean, dry container. Soft stool is defined as stool assuming shape of its container. Pass directly into clean, dry container. Transport to Microbiology laboratory within 1 hour of collection, or transfer to preservative (Totalfix container is available from laboratory). Leakproof, widemouth container, 5 ml Clean, dry, leakproof wide-mouth container or Total- Fix transport system. 1 h, RT 1-24 h, 4ºC > 24 h, -20ºC Unpreserved, 1 hr, RT. Preserved, 1 hr - 1 wk. RT Preserved, 1 hr - 1 wk. RT 7 days if negative, 10 days if positive 1/day Patients should be over 6 months of age and should be passing 5 stools with liquid or soft consistency per 24 h. s should not be contaminated with water or urine. s which contain bismuth, barium, magnesia, mineral oil, or gallbladder dye are not acceptable. Lactoferrin (fecal leukocytes) Rectal swab Pass directly into clean, dry container. Transport to microbiology laboratory within 1 h of collection, or transfer to ova and parasite transport system (available from laboratory). 1. Carefully insert swab ~1 in. (2.54 cm) beyond anal sphincter. 2. Gently rotate swab to sample anal crypts. 3. Feces should be visible on the swab for detection of diarrheal pathogens. Sterile, leakproof, wide-mouth container Unpreserved: 1 h, RT 24 h, 4ºC 1/day Swab transport. 2 h, RT 24 h, RT 1/day For detection of VRE, GC, Shigella and Campylobacter, HSV, and anal carriage of Group B Strep or for patients unable to pass specimen. Fistulas See Abscess.

9 RUTLAND REGIONAL MEDICAL CENTER Page 9 of 13 Fluids: abdominal, amniotic, ascites, bile, joint, paracentesis, pericardial, peritoneal, pleural, synovial, thoracentesis 1. Disinfect overlying skin with 2% iodine tincture or chlorhexidine. 2. Obtain specimen via percutaneous needle aspiration or surgery. 3. Transport to laboratory immediately. 4. Always submit as much fluid as possible; never submit swab dipped in fluid. Sterile screw-cap tube or anaerobic transport system Bacteria, 1 ml; Fungi, 10 ml; Mycobacteria, 10 ml 15 min, RT 24 h, RT Pericardial fluid and fluids for fungal cultures: 24 h, 4 C None Hold pericardial fluid at 4 C for up to 24 h if processing is delayed. Gangrenous tissue See Abscess. Do not sample superficial tissue; tissue biopsy samples or aspirates are preferred. Genital: female Amniotic 1. Aspirate via amniocentesis, Cesarean section, or intrauterine catheter. 2. Transfer fluid to anaerobic transport system. Anaerobic transport system, 1 ml. 15 min, RT 24 h, RT None Swabbing of vaginal membrane is not acceptable because of vaginal contamination. Bartholin 1. Disinfect skin with an iodine preparation. 2. Aspirate fluid from ducts. Anaerobic transport system, 1 ml. 2 h, RT 24 h, RT 1/day Cervix 1. Visualize cervix with speculum without lubricant. 2. Remove mucus and/or secretions from cervix with swab, and discard swab. 3. Firmly yet gently, sample endocervical canal with a newly obtained sterile swab. Cul-de-sac Submit aspirate or fluid. Anaerobic transport system, 1 ml. Swab transport. 2 h, RT 24 h, RT 1/day Viral and chlamydial tests require separate collection and transport kits and are sent to reference lab. 2 h, RT 24 h, RT 1/day Endometrium 1. Collect transcervical aspirate via telescoping catheter. 2. Transfer entire amount to anaerobic transport system. Anaerobic transport system, 1 ml. 2 h, RT 24 h, RT 1/day Products of Conception 1. Submit portion of tissue in sterile container. 2. If obtained by Cesarean section, immediately transfer to anaerobic transport system. Sterile tube or anaerobic transport system. 2 h, RT 24 h, RT 1/day Do not process lochia.

10 RUTLAND REGIONAL MEDICAL CENTER Page 10 of 13 Urethra Vagina Genital: female or male Lesion Genital: Male Collect 1 hr. after patient has urinated. 1. Remove exudate from urethral orifice. 2. Collect discharge material on swab by massaging urethra against pubic symphysis through vagina. 1. Wipe away an excessive amount of secretion or discharge. 2. Obtain secretions from mucosal membrane of vaginal vault with a sterile swab. 1. Clean lesion with sterile saline, and remove the surface of the lesion with sterile scalpel blade. 2. Allow transudate to accumulate. 3. While pressing base of lesion, firmly sample exudate with a sterile swab. Swab transport 2 h, RT 24 h, RT 1/day If no discharge can be obtained, wash external urethra with betadine soap, and rinse with water. Then insert urethrogenital swab 2-4 cm into urethra, and rotate swab for 2 s. Swab transport 2 h, RT 24 h, RT 1/day For intrauterine devices, place entire device into sterile container, and submit at room temperature. Swab transport 2 h, RT 24 h, RT 1/day Prostate 1. Clean glans with soap and water. 2. Massage prostate through rectum. 3. Collect fluid on sterile swab or in sterile tube. Swab transport or sterile tube 2 h, RT 24 h, RT 1/day More relevant results may be obtained by also using urine specimens obtained immediately before and after massage. Urethra Insert urethrogenital swab 2-4 cm into urethral lumen, rotate swab, and leave it in place for at least 2 s. Swab transport 2 h, RT 24 h, RT 1/day Pilonidal cyst See Abscess.

11 RUTLAND REGIONAL MEDICAL CENTER Page 11 of 13 Respiratory Tract, lower Bronchoalveolar lavage, bronchial brush, trach asp 1. Place aspirate or washing in a sputum trap. 2. Place brush in sterile container with saline. Sterile container, >1 ml. 2 h, RT 24 h, 4 C 1/day ml of fluid needed for quantitative analysis. Sputum, expectorated 1. Collect specimen under direct supervision of nurse or physician. 2. Have patient rinse or gargle with water. 3. Instruct patient to cough deeply to produce lower respiratory specimen (not postnasal fluid). Collect into sterile container. Sterile container, > 1 ml. 2 h, RT 24 h, 4 C 1/day Quality of specimen determined by low number of squamous epithelial cells. Sputum, induced Respiratory tract, upper Oral Nasal 1. Have patient rinse mouth with water after brushing gums and tongue. 2. With aid of nebulizer, have patient inhale 25 ml of 3-10% sterile saline. 3. Collect induced sputum into sterile container. 1. Remove oral secretions or debris from surface of lesion with swab, and discard swab. 2. Using second swab, vigorously sample lesion, avoiding any areas of normal tissue. 1. Use swab premoistened with sterile saline. Insert 2 cm into nares. 2. Rotate swab against nasal mucosa. Sterile container 2 h, RT 24 h, RT 1/day Histoplasma capsulatum and Blastomyces dermatitidis survive for only short periods once specimen is obtained. Fungal recovery is primarily for Cryptococcus spp. and some filamentous fungi; other yeasts rarely cause lower repiratory tract invection. Swab transport 2 h, RT 24 h, RT 1/day Discourage sampling of superficial tissue for bacterial evaluation. Tissue biopsy samples or needle aspirates are specimens of choice. Swab transport 2 h, RT 24 h, RT 1/day Anterior nares cultures are used for detecting staphylococcal carriage

12 RUTLAND REGIONAL MEDICAL CENTER Page 12 of 13 Nasopharynx Throat 1. Gently insert calcium alginate swab into posterior nasopharynx via nose. 2. Rotate swab slowly for 5 s to absorb secretions. 3. Remove swab and place in transport medium. 1. Depress tongue with tongue depressor. 2. Sample posterior pharynx, tonsils, and inflamed areas with a sterile swab. Swab transport 2 h, RT 24 h, RT 1/day Sinus specimens are collected surgically by needle aspirate, never a swab. Nasopharyngeal and throat specimen do not represent sinus specimen. Swab transport 2 h, RT 24 h, RT 1/day Throat cultures are contraindicated for patient with inflamed epiglottis. Tissue 1. Submit in sterile container. 2. For small samples, add several drops of sterile saline to keep moist. 3. Do not allow tissue to dry out. 4. Place in anaerobic transport system. Sterile, moist screw cap container or anaerobic transport system. Sterile saline may be added if needed. 1hour, RT 24 h, RT None Always submit as much tissue as possible. Never submit swab that has simply been rubbed over surface. Urine Female, midstream 1. Thoroughly clean urethral area with soap and water. 2. Rinse area with wet gauze pads. 3. While holding labia apart, begin voiding. 4. After several milliliters have passed, collect midstream portion without stopping flow of urine. Sterile wide-mouth container, 1 ml or urine culture transport kit. 1 h, RT 24 h, 4ºC 1/day For suspected bacterial cystitis (or upper UTI). Refer to special procedures for urine chlamydia and gonorrhea. Male, midstream 1. Clean the glans with soap and water. 2. Rinse area with wet gauze pads. 3. While holding foreskin retracted, begin voiding. 4. After several milliliters have passed, collect midstream portion without stopping flow of urine. Sterile wide-mouth container, 1 ml or urine culture transport kit. 1 h, RT 24 h, 4ºC 1/day For suspected bacterial cystitis (or upper UTI). Refer to special procedures for urine chlamydia and gonorrhea.

13 RUTLAND REGIONAL MEDICAL CENTER Page 13 of 13 Straight Catheter 1. Thoroughly clean urethral area with soap and water. 2. Rinse area with wet gauze pads. 3. Aseptically insert catheter into bladder. 4. Allow ~15 ml to pass; then collect urine to be submitted in sterile container. Sterile leakproof container 1 h, RT 24 h, 4ºC 1/day Not recommended for routine urine culture because of potential contamination problems. Procedure may introduce urethral flora into bladder. Indwelling Catheter 1. Disinfect catheter collection port with 70% alcohol. 2. Use needle and syringe to aseptically collect 5-10 ml of urine. 3. Transfer sample to sterile tube or container. Sterile leakproof container 1 h, RT 24 h, 4ºC 1/day Foley catheter tips are not acceptable for culture and should not be submitted or accepted. Wound See Abscess. a Swab transport and anaerobic transport systems available from laboratory b Transport all specimens in leak-proof plastic bags with a separate compartment for the requisition