Lab Guide Microbiology Section Lab Guide

Transcription

1 Lab Guide Microbiology Section Lab Guide

2 Abscesses and aspirates for bacterial culture Pus aspirate send in sterile leak proof in a sealed plastic bag with biohazard label. Pus aspirate is always superior to a swab specimen. Specify anatomic Site If pus aspirate cannot be sent; Swab in Amies transport medium can be used. Swab should be soaked in pus <2 hrs. at Room. STAT Microscopy: 30 min from Time Of Detection for samples from sterile site. Routine Microscopy: Culture: 48-72hrs Microscopy: Gram stain Culture: Aerobic and Anaerobic. Microscopy: No WBC's, No organisms seen Culture: No growth; presence of skin flora / normal flora Microscopy: Semi-quantitative report of WBC s, types of bacteria, fungi seen. All STAT Gram stains called to physician, if positive. Rejection Criteria Dry swab Culture: For significant isolates, susceptibility testing is. Aspirate received in syringe with needle attached. AWH Microbiology Laboratory Ext. # / 4190

3 Abscesses and aspirates for AFB culture Pus aspirate sent in sterile leak proof without fixative Pus aspirate is always superior to a swab specimen. Specify anatomic Site 2 hrs at Room Microscopy: For positive smear- one hour after detection time. Culture: 42 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Auramine O and Ziehl-Neelsen Culture: BACTEC MGIT Microscopy: No AFB seen. Culture: No growth / Culture contaminated / Unable to get pure culture / Fail to survive. Microscopy: Average number of AFB / 100 fields Culture: Growth of MTB complex with susceptibility to primary drugs SIRE or Growth of MOTT Laboratory Ext. # 6671 / 6675

4 Abscesses and aspirates for fungal culture Pus aspirate send in sterile leak proof without fixative Pus aspirate is always superior to a swab specimen. Specify anatomic Site <2 hrs at Room Microscopy: 24 hrs; when smear is positive one hour after detection time. Culture: up to 21 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Blankophor P Fluorescent. Culture: Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells, Yeast cells or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Laboratory Ext. #

5 Abscesses and aspirates for ova and parasite Minimum 0.5 ml of aspirate in sterile, leak proof container Specify anatomic Site 15 min at Room (Sun Fri) Microscopy: 24 hrs Microscopy: Wet mount, concentration, permanent stain No ova or parasites seen Ova or parasites seen Laboratory Ext. # / 1047/ 1647

6 Air Sampling culture (Environmental) Air sample using Samplair Lite Machine or by settle plates. Prior approval of specimen collection with Infection Control and Microbiology lab is a must. Rejection Criteria Air Sampling culture is from operation theaters and high risk areas (Hematology/ Oncology and bone marrow transplant unit). <2 hrs Room Sunday to Thursday - (only in the morning after arrangement with Infection Control and Microbiology lab) Culture: 48 hrs for bacterial culture. 5 days for fungal culture Culture: Aerobic Culture: No growth. Culture: Air sampling culture positive results (colony count, CFU) are reported to Infection Control Practitioners. Culture is as per Infection Control Policies. 1. Samples not sent in coordination with Infection Control Practitioners. 2. Duplicate specimens within 48hrs. 3. Improperly filled request form. 4. Unlabeled mislabeled or mismatched specimen. Laboratory Ext. # / )

7 Anal / rectal swab, scotch tape for ova and parasites Tape fixed on a glass slide and transported as soon as possible Rectal Swab in a transport medium 2 hrs at Room Sunday-Thursday / 7am 3pm Microscopy: 24 hrs Microscopy: Wet mount No ova or parasites seen E.vermicularis ova seen Laboratory Ext. # / 1047/ 1647

8 Aspergillus Galactomannan Antigen Test 5-7 ml of blood in sterile, plain (red top) or gel activator (yellow) tube BAL 10ml in sterile container < 2 hours at room temperature Every Wednesday 8 hrs Enzyme Immuno Assay (EIA) Negative Positive Laboratory Ext. # / )

9 Blood culture- aerobic and anaerobic / pediatric Adult- Obtain 20 ml of blood per culture. (One culture set consists of one bottle of aerobic culture medium and one bottle of anaerobic culture medium or two aerobic bottles) If less than 20 ml but more than 10 ml is obtained for the first set of bottles, divide the blood evenly into the aerobic and anaerobic bottle. If less than 10 ml is obtained for the second set of bottles, inject the entire volume into one bottle. Pediatric patients- Weight < 30 Kg; obtain as much blood as practical (1-4 ml minimum) and use pediatric culture system. For pediatric patients of weight > 30 Kg and or age of > 12 yrs., recommended volume are 10 ml and inoculate in to aerobic bottle. Specify venipuncture / anatomic site / Central line Note: Endocarditis- 2 to 3 sets in a 24 hrs. < 2 hrs. At Room. Do not refrigerate Microscopy:30 min from Time Of Detection.. Culture: Preliminary report: at 24 & at 48 hrs. Positive : hrs (after positive blood culture) Final Negative : 5 days Blood cultures incubated in automated blood culture system- BacT/ALERT. For positive culture: Microscopy: Gram stain Identification: MALDI-TOF and PCR (send to HGH Microbiology for rapid identification) & Routine VITEK (AW Microbiology) Culture: Aerobic and Anaerobic bacterial culture Negative after 5 days. Microscopy: All organisms reported All Gram Stains called to physician. Culture: All isolates are identified. Susceptibility results are reported when appropriate.

10 All positive results are called to the physician. Rejection Criteria Patient labels covering the barcode labels of the culture bottles Labels attached to blood culture bottles and or the blood bottles visually stained with patient s blood Note: Place the patient label on each bottle & label each Culture bottle with the site of specimen collection. When applying patient identification labels, do not cover the bar code label on the blood culture bottles. AWH Microbiology /4190

11 Body fluids for bacterial culture Aspirate fluid in a sterile leak proof container. Specify anatomic site Minimum 1.0 ml < 2 hrs at room temperature If transport is delayed more than 2 hrs, please refrigerate (2-8 o C), do not freeze. STAT Microscopy: 30 min from Time Of Detection for samples from sterile site. Routine Microscopy: hours Culture: 48-72hrs Microscopy: Gram stain Culture: Aerobic & Anaerobic Microscopy: No Organism Seen, No WBC seen Culture: No Growth Microscopy: Semi-quantitative report of WBCs, types of bacteria, fungus seen. Culture: All isolates are identified, susceptibility testing is. All positive results are called to the physician. AWH Microbiology /4190

12 Body Fluids for AFB culture Aspirate fluid in a sterile leak proof container. Specify anatomic site Minimum ml 2 hrs at Room Microscopy: For positive smear- one hour after detection time. Culture: 42 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Auramine O and Ziehl-Neelsen Culture: BACTEC MGIT Microscopy: No AFB seen. Culture: No growth / Culture contaminated / Unable to get pure culture / Fail to survive. Microscopy: Report Average no. of AFB / 100 fields Culture: Growth of MTB complex with susceptibility to primary drugs SIRE or Growth of MOTT Laboratory Ext. # 6671 / 6675

13 Body fluids for fungal culture Aspirate fluid in a sterile leak proof container. Specify anatomic site Minimum 1.0 ml <2 hrs at room temperature Microscopy: same day. Culture: 48 hours-10 days Microscopy: Blankophor P Fluorescent Culture: 2 set in Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Laboratory Ext. #

14 Bone marrow for bacterial culture in pediatric blood culture bottles (1-2 ml) for aerobic. An additional specimen may be collected in sterile tube with heparin (>1 ml) for fungal and parasitic workup. < 2 hrs. At Room. Do not refrigerate Microscopy: 30 min from Time Of Detection. Culture: Preliminary report: 48 hrs. Positive : hrs (after positive blood culture) Final Negative : 5 days Blood cultures incubated in automated blood culture system- BacT/ALERT. For positive culture: Microscopy: Gram stain Culture: Aerobic and anaerobic bacterial culture Negative after 5 days. Microscopy: All Organisms reported All Gram Stains called to physician. Culture: All isolates are identified. Susceptibility results are reported when appropriate. All positive results are called to the physician Rejection Criteria Patient labels covering the barcode labels of the culture bottles Labels attached to blood culture bottles and or the blood bottles visually stained with patient s blood Note: Place the patient label on each bottle & label each Culture bottle with the site of specimen collection. When applying patient identification labels, do not cover the bar code label on the blood culture bottles. AWH Microbiology /4190

15 Bone marrow for AFB culture In sterile leak proof container with sodium polyanethol sulfonate (SPS) 2 hrs at Room Microscopy: For positive smear- one hour after detection time. Culture: 42 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Auramine O and Ziehl-Neelsen Culture: BACTEC MGIT Microscopy: No AFB seen. Culture: No growth / Culture contaminated / Unable to get pure culture / Fail to survive. Microscopy: Report Average no. of AFB / 100 fields Culture: Growth of MTB complex with susceptibility to primary drugs SIRE or Growth of MOTT Rejection Criteria Bone marrow specimen sent in unsterile tube Laboratory Ext. # 6671 / 6675

16 Bone marrow for fungal culture ml tube with SPS or Heparin. <2 hrs at room temperature Microscopy: 24 hrs; when smear is positive one hour after detection time. Culture: Up to 21 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Blankophor P Fluorescent. Culture: Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells, Yeast cells or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Rejection Criteria Bone marrow specimen sent in unsterile tube Laboratory Ext. #

17 Bone marrow for parasitic investigation ml tube with SPS or Heparin <2 hrs at Room Microscopy: 24 hrs Microscopy: Giemsa stain Negative for ova / parasite Positive for ova / parasite Laboratory Ext. # / 1047/ 1647

18 Bronchoscopy specimens for bacterial culture Broncho-alveolar lavage / bronchial wash / bronchial brush in a sterile screw capped container ml 2 hrs at room temperature > 2 hrs, store at C Microscopy :24-48 hours Culture : 48-72hrs Microscopy: Gram stain Culture: Aerobic, Microscopy: No WBCs; No organism seen. Culture: No growth / Normal upper respiratory flora Microscopy: Semi quantitative report of WBC s, type of bacteria, fungus seen Culture: Significant isolates reported along with Susceptibility result when appropriate. AWH Microbiology /4190

19 Catheter tip for culture Arterial Tip, Balloon Tip, Broviac, Hickman, PICC, Central venous, Double-lumen, Hemodialysis, Subclavian, Swan Ganz, Triple Lumen, Umbilical catheter, CSF Shunt Tip 5 cm distal end of the catheter tip in sterile container 2 hrs at room temperature > 2 hrs, store at C Culture : 48-72hrs Culture: Aerobic, Rejection Criteria Culture: No growth Culture: Significant isolates reported along with Susceptibility result when appropriate. Catheter tip samples sent as a routine (on removal) without collecting blood culture. AWH Microbiology /4190

20 Cerebrospinal fluid (CSF) for Bacterial culture Collect CSF into Sterile leak-proof tubes. Submit the sterile tube with CSF to Microbiology as soon as possible 1 ml <2 hrs at room temperature. Do not refrigerate from 7am 11PM, After 11PM Samples will be sent to HMC Microbiology STAT Microscopy: 1 hr from time received in AW CP until reporting CSF bacterial latex Agglutination Test: Positive Latex results relayed within 30 min. Culture: Preliminary within 24 hrs. Final: hrs Microscopy: Gram stain and India Ink Bacterial Antigen Latex: CSF bacterial latex Agglutination Test when WBC count is abnormal. Culture: Aerobic Microscopy: No organism seen CSF bacterial latex Agglutination Test: Negative Culture: No Growth Microscopy: Types of bacteria, fungus seen. All Gram Stains informed to physician. CSF bacterial latex Agglutination Test: Positive results informed to physician. Culture: All isolates are completely identified. Susceptibility results are reported when appropriate. All positive results are informed to the physician. Rejection Criteria Duplicate specimen collected within 48hrs in patients with shunts, EVD, Omaya etc. and not from Lumbar puncture AWH Microbiology /90 HMC Microbiology lab (Tel # /2038) after 11 pm

21 Cerebrospinal fluid (CSF) for AFB culture Collect CSF into Sterile leak-proof sterile tubes. Submit the sterile tube with CSF to Microbiology as soon as possible 2 to 3 ml, optimal is upto10 ml 2 hrs at room temperature Microscopy: For positive smear- one hour after detection time. Culture: 42 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Auramine O and Ziehl-Neelsen Culture: BACTEC MGIT Microscopy: No AFB seen. Culture: No growth / Culture contaminated / Unable to get pure culture / Fail to survive. Microscopy: Report Average no. of AFB / 100 fields Culture: Growth of MTB complex with susceptibility to primary drugs SIRE or Growth of MOTT Rejection Criteria sent in unsterile tube Laboratory Ext. # 6671 / 6675

22 Cerebrospinal fluid (CSF) for fungal culture CSF into sterile leak-proof container Submit the sterile tube with CSF to Microbiology as soon as possible 2-3 ml <2 hrs at room temperature Microscopy Stat: 1 hour Cryptococcal antigen Detection: 1 hour Culture: 48 hours- 10 days Microscopy: Blankophor P Fluorescent and India ink if requested. Cryptococcal latex antigen Culture: 2 set in Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Cryptococcal latex antigen- Negative Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Cryptococcal latex antigen- Positive Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Laboratory Ext. #

23 Cerebrospinal fluid (CSF) for parasites CSF into sterile leak-proof container 0 1 ml <2 hrs at Room Microscopy: 24 hrs for Giemsa Microscopy: Giemsa Culture when available Negative for Acanthamoeba / Naegleria / Balamuthia Species Detection of Acanthamoeba / Naegleria / Balamuthia Species Laboratory Ext. # / 1047/ 1647

24 Cervical / Urethral swabs for bacterial culture Swab in Amies transport medium It is preferable to send two swabs, one for culture and one for microscopy. Room temperature. Swabs for suspected case of gonorrhea, should be transported within 2 hrs. Microscopy : hrs Culture: hrs. Microscopy: Wet mount. Gram stain. Culture: Aerobic. Wet mount: Trichomonas vaginalis not seen Gram Stain: No diplococci seen Culture: No Growth / Normal perineal flora isolated / Growth of coliforms Microscopy: Wet mount: Trichomonas vaginalis seen Gram stain: Gram Negative Diplococci (intracellular / Extracellular) seen. Culture: Significant isolates reported along with susceptibility result when appropriate. AWH Microbiology /90

25 Chlamydia trachomatis direct antigen detection For adults- urethral, cervical, rectal swabs, For Pediatrics- ocular and nasopharyngeal swabs, collected on sterile swab < 2 hrs. at room temperature Sunday to Thursday in the morning s accepted on all days Same Day, except weekend DFA: Qualitative direct immunofluorescence test DFA Chlamydia: Negative DFA Chlamydia: Positive Significant results are called to the physician Laboratory Ext. # / 1047

26 Corneal abscess swab / ulcer scrapings for bacterial culture in sterile container or directly inoculated Blood agar plate, Chocolate agar plate. < 2 hrs. At Room STAT Microscopy: 1 hr. Microscopy: hrs Culture: 48-72hrs Microscopy: Gram stain, Giemsa stain (if specimen received on slides send to HMC Microbiology) Culture: Aerobic Microscopy: No organism seen, No WBC seen Culture: No Growth Microscopy: Semi-quantitative report of WBCs, types of bacteria, fungus seen. Culture: All significant organisms, susceptibility testing. Significant results are informed to the physician AWH Microbiology /90

27 Corneal abscess swab / ulcer scrapings for fungal culture in sterile container or directly inoculated Sabroud s agar (SDA). <2 hrs at room temperature Microscopy: 24 hrs Culture: up to 21 days Microscopy: Blankophor P Fluorescent stain (if specimen received and not inoculated plates) Culture: 2 set in Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Rejection Criteria Laboratory Ext. #

28 Corneal abscess swab / ulcer scrapings / Contact lens and fluid for parasitic examination Corneal abscess swab / ulcer scrapings / contact lens and fluid, submitted to the laboratory as soon as possible after collection. 30 min at room temperature Sunday-Thursday- 7am 3pm Microscopy: 24 hrs for Giemsa Microscopy: Giemsa Stain Culture when available Negative for Acanthamoeba cysts and trophozoites Detection of Acanthamoeba cysts and trophozoites Laboratory Ext. # / 1047

29 Diphtheria culture Throat swab, nasopharyngeal, laryngeal and wound swabs in Amies transport medium If cutaneous diphtheria is suspected, collect skin, throat, and nasopharynx specimens. <2 hrs at room temperature STAT Microscopy: 1 hr. Culture: hours Microscopy: Gram stain, Albert s Stain Culture: Aerobic Microscopy: Gram positive bacilli with metachromatic granules not seen. Culture: Corynebacterium diphtheriae not isolated. Microscopy: Gram positive bacilli with metachromatic granules seen. Culture: Growth of Corynebacterium diphtheria along with antimicrobial susceptibility result. Note- All positive results are called to the physician within 1 hour from the time of detection. Laboratory Ext. # / 1047

30 Duodenal Aspirate for ova and parasites collected in screw capped container. 2 hrs at Room Sunday-Thursday- 7am 3pm Microscopy: 24 hrs Microscopy: Wet mount, Concentration, Trichrome stain No ova or parasites seen Ova or parasites seen Laboratory Ext. # / 1047

31 Ear swabs- middle ear / external ear for bacterial culture Swab in Amies transport medium. < 2 hrs at room temperature Microscopy: hours Culture : hours Microscopy: Gram stain Culture: Aerobic & Anaerobic No growth / Normal skin flora isolated. Normal skin flora including coliforms. Microscopy: Semi quantitative report of WBC s, types of bacteria, fungus seen. Culture: All significant isolates identified, susceptibility testing. AWH Microbiology /90

32 Ear swabs- middle ear / external ear for fungal culture in sterile container / swab in Amies transport medium. <2 hrs at room temperature Microscopy: 24 hrs Culture: up to 10 days Microscopy: Blankophor P Fluorescent stain (if specimen received and not inoculated plates) Culture: 2 set in Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Laboratory Ext. #

33 Endometrial tissue / swab for culture Collect specimens aseptically in sterile container / endometrial swab in Amies medium Tissue specimens are superior to swabs. <2 hrs at room temperature Routine Microscopy: hrs Culture: 48 hours-10 days Microscopy: Gram Stain Culture: Aerobic and Anaerobic Microscopy: No organisms seen. Culture: No growth Microscopy: Semi-quantitative report of WBCs, types of bacteria, fungus seen. Culture: All significant organisms, susceptibility testing. Significant pathogens will be phoned to physicians. AWH Microbiology /90

34 Endotracheal secretions for bacterial culture Collect into sterile leak proof wide mouth container. Minimum of 2 ml. < 2 hours at room temperature s may be refrigerated for up to 2 hr. Microscopy: hrs Culture: 48-72hrs Microscopy: Gram stain Culture: Aerobic Microscopy: Normal respiratory flora Culture: No growth / Normal respiratory flora Microscopy: Semi-quantitative report of WBCs, predominant type of bacteria, and fungus seen. Note: Culture only if the quality of the specimen is good (WBC > Epithelial Cells) otherwise the specimen is considered to be contaminated with oropharyngeal flora and will not be cultured. Culture : Significant isolates reported along with Susceptibility result when appropriate. Rejection Criteria Endotracheal tubes (tip) Endotracheal or tracheal secretion swab, except sputum swab from CF patients and PCD patients AWH Microbiology /90

35 Endotracheal secretions for fungal culture in sterile container <2 hrs at room temperature Microscopy: 24 hrs Culture: up to 10 days Microscopy: Blankophor P Fluorescent stain (if specimen received and not inoculated plates) Culture: 2 set in Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Laboratory Ext. #

36 Environmental specimens for culture Rejection Criteria Environmental swabs in Amies medium, fluids in sterile container. Prior approval of specimen collection with Infection Unit is must <2 hrs at room temperature Sunday to Thursday - (only in the morning after arrangement with Medical Microbiologist) Culture: hrs for Bacterial culture. 5 Days for Fungal culture. Culture: Aerobic conditions. Culture: No growth. Culture: Environmental sampling culture positive results are reported to Infection Control Practitioners. Culture is under guidelines of Infection Control Policies and coordination with Infection Control Practitioners. Samples not sent in coordination with Infection Control Practitioners. AWH Microbiology /90

37 Eye - Conjunctiva, Eyelid (blepharitis) swab for bacterial culture Swab in Amies transport medium or directly inoculated on Blood agar plate and Chocolate agar < 2 hrs at room temperature STAT Microscopy: 1 hr. (for neonates) Microscopy: hrs Culture: 48-72hrs Microscopy: Gram stain Culture: Aerobic Microscopy: No Organism Seen, No WBC seen Culture: No Growth or Normal skin flora Microscopy: Semi-quantitative report of WBCs, types of bacteria, fungus seen. Culture: All significant organisms, susceptibility testing. Significant Results are called to the physician AWH Microbiology /90

38 Gastric wash or lavage for AFB culture Rejection Criteria Collect in early morning before patients eat and while they are still in bed. Perform lavage with 25 to 50 ml of chilled, sterile distilled water. Recover sample and place in a leakproof sterile container such as a 50-mL conical tube. 25 to 50 ml 1 hrs at Room Microscopy: For positive smear- one hour after detection time. Culture: 42 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Auramine O and Ziehl-Neelsen Culture: BACTEC MGIT Microscopy: No AFB seen. Culture: No growth / Culture contaminated / Unable to get pure culture / Fail to survive. Microscopy: Report Average no. of AFB / 100 fields Culture: Growth of MTB complex with susceptibility to primary drugs SIRE or Growth of MOTT Gastric lavage sent on swab Laboratory Ext. # 6671 / 6675

39 Hair for fungal culture Collect at least affected hairs taken in a sterile Petri dish, or Sterile glossy paper with the base of the shaft intact and placed in clean container. <2 hrs at room temperature Microscopy: 24 hrs Culture: up to 21 days Microscopy: Blankophor P Fluorescent stain. Culture: 2 set in Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Fungal elements seen. Culture: Significant fungus isolates reported when appropriate. Laboratory Ext. #

40 High vaginal swabs for culture High vaginal swab in Amies transport medium It is preferable to send two swabs- one for culture and one for microscopy. <2 hrs at room temperature Microscopy: hrs. Culture: hrs. Microscopy: Wet mount. Gram stain. Culture: Aerobic Wet mount- Trichomonas vaginalis not seen Gram Stain - Normal vaginal flora Culture- Normal Vaginal flora Microscopy: Wet mount: Trichomonas vaginalis seen Gram stain: Yeast with or without hyphal filaments Evidence of vaginosis: Gram Stain smear suggestive of bacterial vaginosis Culture: Significant isolates reported when appropriate. Rejection Criteria Low vaginal swab AWH Microbiology /90

41 Insect / adult worm or proglotid for identification Passed / voided specimen in isotonic saline in clean sterile container. Do not use ethanol or formalin to preserve the specimen Insect in sterile container. 2 hrs at Room 24 hrs Macroscopic / Microscopic Evaluation - Rejection Criteria Identification of appropriate species Veterinary specimens Laboratory Ext. # / 1047

42 Intra-uterine contraceptive device (IUCD) culture IUCD in a sterile leak proof container. <2 hrs at room temperature Microscopy: hrs Culture : Preliminary report :48-72 hrs Final report: 07 days Microscopy: Gram stain Culture: Anaerobic conditions. Microscopy- No organisms resembling Actinomyces seen on Gram stain Culture- No growth / Normal vaginal flora Microscopy: Report the presence of branching Gram positive bacilli resembling Actinomyces. Culture: Actinomyces species reported along with susceptibility result when appropriate. Rejection Criteria sent in formalin AWH Microbiology /90

43 Nail scrapings for fungal culture taken in a sterile Petri dish, or Sterile glossy paper <2 hrs at room temperature Microscopy: 24 hrs Culture: up to 21 days Microscopy: Blankophor P Fluorescent stain. Culture: 2 set in Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Laboratory Ext. #

44 Nasal swabs for MRSA Screening/ Other samples for MRSA Routine Culture Cepheid Collection Device, Copan double plastic swab (red cap) Nasal Swabs for MRSA screening / Culture will be accepted from patient as per corporate infection MRSA policy (CL <2 hrs at room temperature PCR: Same day Culture: 72 hrs PCR: GeneXpert MRSA assay Culture: Aerobic GeneXpert MRSA assay- MRSA DNA Not detected Culture: No MRSA isolated GeneXpert MRSA assay - MRSA DNA DETECTED Culture: MRSA positive results are reported to Infection Control Practitioners. Rejection Criteria Routine screening of patients for MRSA is not done. Please refer to Infection control policy CL 7252 for selection of patients. Use of different swab than Cepheid Collection Device, Copan double plastic swab (red cap) AWH Microbiology /90

45 Nasal swabs for MRSA/MSSA Specific PCR Cepheid Collection Device, Copan double plastic swab (red cap) Nasal Swabs for MRSA/MSSA screening will be accepted from patient as per corporate infection MRSA policy (CL 7252). <2 hrs at room temperature 2-4 Hrs GeneXpert MRSA/MSSA assay GeneXpert MRSA assay- Negative for MRSA DNA GeneXpert MRSA assay- Negative for MSSA DNA GeneXpert MRSA assay - Positive for MRSA DNA Results are reported to Infection Control Practitioners. GeneXpert MRSA assay - Positive for MSSA DNA Results are reported to Infection Control Practitioners Rejection Criteria Routine screening of patients for MRSA is not done. Please refer to Infection control policy CL 7252 for selection of patients. Use of different swab than Cepheid Collection Device, Copan double plastic swab (red cap) laboratory (Tel # )

46 Nasopharyngeal aspirate for B. pertussis Nasopharyngeal aspirate (secretion) Per nasal swab, and nasopharyngeal swab in charcoalbased transport medium (Regan-Lowe) <2 hrs at Room Microscopy: hours Culture: Preliminary report : 48 hrs Final report : 12 days Microscopy: Gram stain Culture: Aerobic Microscopy: No gram negative coccobacilli seen. Culture: Negative for Bordetella species Microscopy- Gram negative coccobacilli seen. Culture- Culture positive for Bordetella species Rejection Criteria Cough plates should not be used as they are not sensitive. Rayon or cotton swabs should be avoided. AWH Microbiology /90

47 Placental tissue for culture Collect specimens aseptically in sterile container <2 hrs at room temperature Microscopy Stat: 1-2 hours Routine Microscopy: hrs Culture: 48 hours-10 days Microscopy: Gram Stain Culture: Aerobic and Anaerobic Microscopy: No organisms seen. Culture: No growth Microscopy: Semi-quantitative report of WBCs, types of bacteria, fungus seen. Culture: All significant organisms, susceptibility testing. Significant pathogens will be phoned to physicians. Rejection Criteria Placental swabs AWH Microbiology /90

48 Rectal swabs for Vancomycin resistant Enterococci (VRE) Rectal swab in Amies transport medium. Prior approval of specimen collection with Infection control is must <2 hrs at room temperature Sunday to Thursday - (only in the morning after arrangement with Medical Microbiologist) Culture: hrs. Culture: Aerobic Culture: No VRE isolated Culture: VRE positive results are reported to Infection Control Practitioners. Culture is under guidelines of Infection Control Policies and in coordination with Infection Control Practitioners. laboratory (Tel # )

49 Respiratory specimens for AFB culture Sputum (for 2 consecutive days), Endo-tracheal secretions, BAL / BW in a sterile, wide mouth disposable container (preferably 50 ml falcon tube). Note- For follow up of patients on therapy, collect at weekly intervals only for AFB staining, beginning at 2 weeks after initiation of therapy until 2 consecutive smear negative results are obtained. If first smear negative result is obtained the second smear should be repeated on following day. Second Culture is done for two consecutive samples after 2 months of therapy. Third Culture of another two consecutive samples is done at end of therapy. Collect 5-10 ml (min 3ml) early-morning specimen 2 hrs at room temperature Microscopy: For positive smear- one hour after detection time. Culture: 42 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Auramine O and Ziehl-Neelsen Culture: BACTEC MGIT Microscopy: No AFB seen. Culture: No growth / Culture contaminated / Unable to get pure culture / Fail to survive. Microscopy: Report Average no. of AFB / 100 fields Culture: Growth of MTB complex with susceptibility to primary drugs SIRE or Growth of MOTT Rejection Criteria Salivary sputum except for patient on therapy in the TB unit and induced sputum Third consecutive sputum and other pulmonary samples from same patient Pooled sputum specimens Swabs are not recommended for the culture of Mycobacterium, since they provide limited material. Laboratory Ext. # 6671 / 6675

50 Respiratory specimens for AFB PCR Sputum Endo-tracheal secretions, BAL / BW in a sterile, wide mouth disposable container (preferably 50 ml falcon tube). Note- Test should be ordered along with culture and smear for new patients suspected of TB Collect 5-10 ml (min 3ml) early-morning specimen 2 hrs at room temperature Next day, Positive PCR- one hour after detection time. GeneXpert TB PCR AFB PCR: Positive/Negative MTB DNA: Detected /Not Detected Rifampicin(RIF) Resistant: Detected/Not Detected Positive, MTB DNA Detected Rif resistance Detected Positive, MTB DNA Detected Rif resistance Not Detected Negative, MTB DNA Not Detected Please Note: As documented by WHO, RIF resistance is rarely encountered by itself, and usually indicates resistance to a number of other anti-tb drugs. It is most commonly seen in multi-drug resistant strains and has a reported frequency of greater than 95 % in such isolates A negative TB PCR result alone is not enough to rule out TB diagnosis. This test should be run in conjunction with TB Culture GeneXpert Real Time PCR is not approved by FDA for extra pulmonary samples. Rejection Criteria Salivary sputum except for patient on therapy in the TB unit and induced sputum Third consecutive sputum and other pulmonary samples from same patient Pooled sputum specimens Swabs are not recommended for the culture of Mycobacterium, since they provide limited material. Test is already on other pulmonary specimen

51 Laboratory Ext. # 6671 / 6675

52 Respiratory tract specimens for P. jirovecii Sputum / Endotracheal secretions / Bronchoscopy specimen in sterile screw capped container. 5 ml 2 hrs at room temperature Sunday to Thursday only in the morning s accepted on all days. Microscopy: 8-24hrs Microscopy: DFA- Direct Fluorescent antigen assay GMS- Gomori methinamine silver stain Microscopy: DFA- Negative for P. jirovecii GMS Stain- Negative for P. jirovecii Microscopy: DFA- Cysts of P.jirovecii seen GMS Stain- Cysts of P.jirovecii seen laboratory (Tel # )

53 Respiratory specimens for fungal culture Sputum / Sputum induced/ Endotracheal secretions / Bronchoscopy specimen in sterile screw capped container. > 1 ml. <2 hrs at room temperature Microscopy: 24 hrs Culture: 48 hours-10 days Microscopy: Blankophor P Fluorescent stain. Culture: 2 set in Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Culture: Significant fungus isolates reported along with Susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Laboratory Ext. #

54 Respiratory s for Ova & parasite Sputum / Sputum, induced / Endotracheal secretions / Bronchoscopy specimen in sterile screw capped container for the diagnosis of Paragonimus westermani eggs, Strongyloides stercoralis, Acaris lumbricoides and hookworm larvae. > 1 ml 15 min at Room Sunday-Thursday- 7am 3pm Microscopy: 1 hr. Microscopy: Wet Mount Culture: Axenic culture for Strongyloides / hookworm larvae Microscopy: No ova / parasite seen Culture: negative for Strongyloides / hookworm larvae Microscopy: ova / parasite seen Culture: Strongyloides larvae / hookworm detected Laboratory Ext. # / 1047

55 Semen, prostatic secretion for bacterial culture Collect the specimen in a Sterile leak proof container. Note: More relevant results may be obtained by giving a urine specimen collected immediately before and after massage along with the Prostatic secretion to indicate urethral and bladder organisms. < 2 hours at room temperature Microscopy hrs Culture: hrs. Microscopy: Gram stain. Culture: Aerobic conditions. No organisms seen, normal genital flora Microscopy : Semi-quantitative report of WBCs, types of bacteria, fungi seen Culture: Significant isolates reported along with susceptibility result when appropriate. AWH Microbiology /90

56 Sigmoidoscopy material for ova & parasite Sigmoidoscopy specimen in a screw capped container 30 min at Room Sunday-Thursday / 7am 3pm Microscopy: 24 hrs Microscopy: Wet mount, Concentration, Permanent stain No ova or parasites seen ova or parasites seen Laboratory Ext. # / 1047

57 Skin scraping for fungal culture taken in a sterile petri dish, or sterile glossy paper. <2 hrs at room temperature Microscopy: 24 hrs Culture: up to 21 days Microscopy: Blankophor P Fluorescent stain. Culture: 2 set in Aerobic condition: 37 C and 25 C. Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Laboratory Ext. #

58 Sputum for bacterial culture Collect into sterile leak proof wide mouth container. > 2 ml < 2 hours at room temperature s may be refrigerated for up to 8 hrs Microscopy: hrs Culture: 48-72hrs Microscopy: Gram stain Culture: Aerobic Microscopy: Normal respiratory flora Culture: No growth / Normal respiratory flora Microscopy: Semi-quantitative report of WBCs, predominant type of bacteria, and fungus seen. Note: Culture only if the quality of the specimen is good (WBC> Epithelial Cells) otherwise the specimen is considered to be contaminated with oropharyngeal flora and will not be cultured. Culture : Significant isolates reported along with susceptibility result when appropriate. AWH Microbiology /90

59 Stool for routine culture Clean leak proof wide mouth container gm. < 1 hr. at room temperature. If transportation is delayed, store at (4-8 0 C) and submit within 24 hrs Culture: 48-72hrs Culture: Aerobic and microaerophilic Campy antigen test Culture: No Salmonella-Shigella, Campylobacter spp, Enteropathogenic E. coli and Enterohaemorrhagic E. coli isolated Campy antigen test- Negative Culture: Following significant isolates will be identified at species level and susceptibility will be - Salmonella spp. group isolated Shigella spp. isolated Enteropathogenic E. coli isolated. Poly group Enterohaemorrhagic E. coli isolated Campylobacter spp. Isolated Rejection Criteria More than two specimens/patient without prior consultation with Microbiology s from inpatients after the third hospital day, without prior consultation with Microbiology AWH Microbiology /90

60 Stool for AFB culture Stool specimen in clean leak proof wide mouth container. Note- Utility of culturing stool for acid-fast bacilli remains controversial and should be discouraged; however, stool samples from immunocompromised patients may be submitted, mainly to detect MOTT gm. 2 hrs at Room Microscopy: For positive smear- one hour after detection time. Culture: 42 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Auramine O and Ziehl-Neelsen Culture: BACTEC MGIT Microscopy: No AFB seen. Culture: No growth / Culture contaminated / Unable to get pure culture / Fail to survive Microscopy: Report Average no. of AFB / 100 fields Culture: Growth of MTB complex with susceptibility to primary drugs SIRE or Growth of MOTT Laboratory Ext. # 6671 / 6675

61 Stool for Ova and Parasite collected in screw capped container. If possible, three specimens passed at intervals of 2-3 days should be examined over a period of 1 week gm. 2 hrs at Room Sunday-Thursday- 7am 3pm 24 hrs Microscopy: Wet mount, concentration, permanent stain No ova or parasites seen ova or parasites seen Laboratory Ext. # / 1047

62 Stool for Adenovirus and Rotavirus Clean leak proof wide mouth container gm. <1 hr. at room temperature 8-24 hrs Chromatographic immunoassay technique Adenovirus: Negativa Rotavirus: Negative Adenovirus: Positive Rotavirus: Positive AWH Microbiology /90

63 Stool for Clostridium difficile toxin Stool in sterile leak proof wide mouth container > 5ml 1 hr. at room temperature or < 24h at 4 O C s accepted on all days hrs 1. C. diff Quick Check Complete- Immunochromatography 2. GeneXpert C. difficile BT Assay- PCR Clostridium difficile Toxin A&B: Negative Clostridium difficile Toxin A&B: Positive Rejection Criteria Formed/Hard stools Positive results are called to the physician and informed to Infection Control Practitioners Infant < 1 year Patients with previous negative results within a week Patients with positive tests should not have repeated testing for cure before 28 days s that have been preservative AWH Microbiology /90

64 Stool for Shiga Toxin / Verotoxin (Enterohaemorrhagic E. coli) assay Stool in sterile leak proof wide mouth container Bloody or liquid stools collected within 6 days of onset from patients with abdominal cramps have the highest yield. 1 hr. at room temperature or < 24h at 4 O C s accepted on all days. Test on Tuesday in the morning only 8-24 hrs Enzyme Immunoassay Shiga Toxin (I/II) - Negative Shiga Toxin (I/II) Positive laboratory (Tel # / 1047)

65 Stool for Helicobacter pylori antigens Stool in sterile leak proof wide mouth container Test also can be used for treatment effectiveness, relapse or eradication. 1 hr. at room temperature or < 72h at 2-8 O C s accepted on all days Test on Sunday, Tuesday & Thursday in the morning only 8-24 hrs EIA: Enzyme Immunoassay Helicobacter pylori Antigen Negative Helicobacter pylori Antigen Positive laboratory (Tel # / 1047) & Alkhor Microbiology (Tel# )

66 Stool for occult blood Stool specimen in sterile screw cap container. Avoid iron supplements, red meat, vitamin C, barium meal for 3days, if the recommended dietary preparation is not followed, it can cause analytical false positives. <2 hrs at Room 8-24 hrs Guaiac test (Hema screen kit) Negative Positive AWH Microbiology /90

67 Throat swab for routine culture Throat swab in Amies transport medium <2 hrs at room temperature Culture: hrs. Culture: Aerobic / Anaerobic conditions Culture: No growth or growth of normal upper respiratory flora. Streptococcus Group A, C, G, and Arcanobacterium haemolyticum isolated. NOTE: Gonococcal pharyngitis, Vincent's angina and screening for Meningococcal carriers will be done upon request. AWH Microbiology /90

68 Tissue / biopsy for bacterial culture Collect specimens aseptically in sterile container. Any tissue requiring cultures should be sent fresh and not in formalin. Send a piece of necrotic tissue (and not the whole tissue removed during surgery). <2 hrs at room temperature Microscopy Stat: 1-2 hours Routine Microscopy: hrs Culture: 48 hours-10 days Microscopy: Gram Stain Culture: Aerobic and Anaerobic Microscopy: No organisms seen. Culture: No growth Microscopy: Semi-quantitative report of WBCs, types of bacteria, fungus seen. Culture: All significant organisms, susceptibility testing. Significant pathogens will be phoned to physicians. Rejection Criteria sent in formalin Large piece of tissue removed during surgery AWH Microbiology /90

69 Tissue / biopsy for AFB culture Aseptically collected tissues in sterile containers without fixatives or preservatives. Specify anatomic site >1g 2 hrs at Room If delay is anticipated, specimen should be protected from drying by adding sterile saline and maintaining a temperature of 2 8 C. Microscopy: For positive smear- one hour after detection time. Culture: 42 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Auramine O and Ziehl-Neelsen Culture: BACTEC MGIT Microscopy: No AFB seen. Culture: No growth / Culture contaminated / Unable to get pure culture / Fail to survive Microscopy: Report Average no. of AFB / 100 fields Culture: Growth of MTB complex with susceptibility to primary drugs SIRE or Growth of MOTT Rejection Criteria Tissue specimen sent in fixatives Laboratory Ext. # 6671 / 6675

70 Tissue / biopsy for fungal culture Collect specimens aseptically in sterile container <2 hrs at room temperature Microscopy: Same day. Culture: 48 hours-10 days Microscopy: Blankophor P Fluorescent Culture: 2 sets in Aerobic condition: 37 C and 25 C Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Rejection Criteria Tissue specimen sent in fixatives Laboratory Ext. #

71 Tissue / biopsy for ova and parasite examination Tissue / biopsy in sterile leak proof container Specify anatomic Site 15 min at Room Microscopy: 24 hrs Microscopy: Impression smear, H/E, Trichrome stain No ova or parasites seen Ova or parasites seen Laboratory Ext. # / 1047

72 Tongue / oral cavity swab for fungal culture Collect specimens aseptically in sterile container <2 hrs at room temperature Microscopy: Same day. Culture: Not routinely, only on special request Microscopy: Blankophor P Fluorescent Culture: Aerobic condition: 37 C and 25 C Microscopy: No Fungal elements seen. Culture: No fungus isolated Microscopy: Yeast like-cells seen, Yeast cells seen or fungal elements seen. Culture: Significant fungus isolates reported along with susceptibility results (for Candida only) when appropriate. Significant fungal pathogens will be phoned to physicians Laboratory Ext. #

73 Urine Microscopy/reflex culture Rejection Criteria Mid-stream urine specimen in sterile container. Specify method of collection (Midstream, catheter, nephrostomy urine, cystoscopy urine, suprapubic bladder aspirate, etc.). > 5ml If collected in Boric acid container- 20 ml minimum At room temperature. (Any delay, refrigeration C is essential.) For > 2hrs delay, Boric acid container at room temperature (up to 24 hrs). Microscopy: hours Culture: hrs Microscopy- IRIS Automated Urine Microscopy Analyzer Culture. Semi-quantitative aerobic Microscopy. <10 WBCs / µl < 10 RBCs / µl Cast & Crystals- absent Yeast- Absent Estimate the range of WBCs and RBCs.(per µl) Record casts, crystals & yeast if present and state the type of casts & crystals. Culture: No growth. Microscopy. Quantitative analysis of WBCs and RBCs Casts and crystals if present and state type Culture: Significant isolates reported along with Susceptibility result when appropriate. Foley catheter tips 24hr urine specimens and urine from the bag of catheterized patients are unacceptable. Delayed specimen more than 24hrs in Boric acid container or more than 2hrs in plain container without refrigeration. AWH Microbiology /90

74 Urine for AFB culture First morning specimen in sterile container (midstream is never advised). Collect urine specimen on 2 consecutive days ml (prefer up to 40 ml) 2 hrs at Room Microscopy: For positive smear- one hour after detection time. Culture: 42 days; when culture becomes positive the preliminary report is released within 24 hours of detection time. Microscopy: Auramine O and Ziehl-Neelsen Culture: BACTEC MGIT Microscopy: No AFB seen. Culture: No growth / Culture contaminated / Unable to get pure culture / Fail to survive Microscopy: Report Average no. of AFB / 100 fields Rejection Criteria 24 h pooled specimen Culture: Growth of MTB complex with susceptibility to primary drugs SIRE or growth of MOTT Urine from bag. Urine received in Boric acid container. Laboratory Ext. # 6671 / 6675

75 Urine for ova and parasites Collect urine in sterile container without Boric acid. For Schist stoma hematobium, collect urine specimen between- noon to 3 pm. 2 hrs at Room Microscopy: 24 hrs Microscopy: Wet mount No ova / parasite seen Ova / parasite seen Rejection Criteria Request for more than three specimens for single episode Received Boric acid container Laboratory Ext. # / 1047

76 Urine for Legionella Antigen Urine in Sterile wide-mouth container < 2 hrs at room temperature or at 4-8 O C for > 2hrs. (Sun Thu) 8-24 hrs Immunochromatographic card test Legionella Antigen Detection: Negative Legionella Antigen Detection: Positive Significant Results are called to the physician laboratory (Tel # )

77 Vulval swab for culture Vulval swab in Amies transport medium It is preferable to send two swabs- one for culture and one for microscopy. <2 hrs at room temperature Microscopy: hrs. Culture: hrs. Microscopy: Gram stain. Culture: Aerobic Gram Stain - Normal vaginal flora Culture- Normal Vaginal flora Microscopy: Gram stain: Yeast with or without hyphal filaments Evidence of vaginitis- WBC s and organisms seen Culture: Significant isolates reported when appropriate. AWH Microbiology /90

78 Wound specimen for bacterial culture Wound swab in Amies transport medium. Tissue or pus aspirate in Sterile leak proof container, are always superior to a swab specimen; Specify anatomic site <2 hrs at room temperature. Microscopy: hours Culture: 48-72hrs Microscopy: Gram stain Culture: Aerobic / Anaerobic Microscopy: No pus cells, No organisms seen Culture: No growth; presence of skin flora, or fecal flora. Microscopy: Semi-quantitative report of WBCS, types of bacteria, fungi seen. Culture: Significant isolates, susceptibly testing. Significant results are informed to physician Superficial wound swabs are not cultured for anaerobes. Rejection Criteria Aspirate received in syringe. with needle attached AWH Microbiology /90