Microbiology

SR NOTESTTEST COMPONENTSMETHODSPECIMEN/TRANSPORTTATCLINICAL APPLICATIONS
1AFBAFBConventional microscopic examination after ZN stainAll specimens except blood
Miscellaneous specimens ( Urine, Pus, Sputum, Body Fluids like pleural, peritoneal, pericardial, gastric, bronchial, semen etc.) in a sterile, screw capped container OR Tissue in sterile normal saline OR Swabs in sterile normal saline OR Bone marrow in 1 Green Top (Sodium Heparin) tube, OR smeared onto 4 clean glass slides fixed IMMEDIATELY in 95% ethanol for 30 minutes and air dried. For gastric lavage , patient should be fasting for previous 12 hours. Transport the gastric lavage specimens within 4 hrs of collection. Specify type of specimen on container and test request form. Ship refrigerated.
Report Same DayDetection of Mycobacterium spp (AFB) by Microscopy
2AFB CULTUREAFB stain from concentration material. Differentiation of Mycobacterium between MTB and NTM/MOTTLiquid rapid culture on MGIT. Followed by Differentiation between MTB and NTM/MOTT by TBMPT64Ag Card test.All specimens except blood
Blood/Bone Marrow: Collect 8 mL (5 mL min.) Blood/Bone marrow in Myco F / Lytic bottle available from ADL. Mix by gentle inversion 8–10 times. Ship at 18–22°C.
CSF: Collect 2 mL (1 mL min.) CSF in a Red Top (No Additive) tube or sterile screw capped container. Do not use SST gel barrier tubes. Ship refrigerated. Pus/Body fluids (Pleural/Pericardial/Ascitic/ Synovial/Ocular) Aspirates /Semen/ BAL Bronchial washings: Submit as much as possible (1 mL min.) in sterile screw capped container. Ship refrigerated.
Endometrial curettings/Tissue: Submit in sterile normal saline in a sterile screw capped container. Ship refrigerated.
Swabs: Submit swabs in 1 mL sterile normal saline in sterile screw capped container. Ship refrigerated.
Sputum/Urine: Submit 2 Spot (random) morning samples, 5-10 mL (1 mL min.) sputum/10 mL (5 mL min.) urine in sterile screw capped container. Do not pool the samples. Ship refrigerated. Gastric Lavage: Submit 5-10 mL (2 mL min.) gastric lavage in a sterile screw capped container. Ship refrigerated . Overnight fasting is mandatory.
Priliminary reports at 10 and 20 days and final repot at 42 days or earlier if positive. If smear positive for AFB and culture negative till 42 days then final report at 56 days.Detection of Mycobacterium spp. (MTB or NTM/MOTT) from any clinical specimen
3AFBIFAFB BY FLUORSCENT STAINFluorescent stain and Fluorescent microscopyMiscellaneous specimens ( Urine, Pus, Sputum, Body Fluids like pleural, peritoneal, pericardial, gastric, bronchial, semen etc.) in a sterile, screw capped container OR Tissue in sterile normal saline OR Swabs in sterile normal saline OR Bone marrow in 1 Green Top (Sodium Heparin) tube, OR smeared onto 4 clean glass slides fixed iIMMEDIATELY in 95% ethanol for 30 minutes and air dried. For gastric lavage , patient should be fasting for previous 12 hours. Transport the gastric lavage specimens within 4 hrs of collection. Specify type of specimen on container and test request form. Ship refrigerated.Report Same DayDetection of AFB.
Immunoflourescense increases detection chances by Microscopy (Increased sensitivity of detection as compared to light microscopy)
4ANAEROBIC CULTUREGram stain, ZN stain, KOH, Anaerobic growth if any. Identification of anaerobic organism on MALDI TOFConventional anaerobic culture and automatic identification on MALDI TOF after growthAll sample except blood (Blood anaerobic culture is done by BACTEC method under entry Batctec anaerobic)
Collection and transportation under strict anerobic condition. Dry swab not allowed. Anaerobic transport medium is required.
5 daysIsolation of Anaerobic organism
5AUTOI (Identification on Vitek)-Automated identification on Vitek 2 compact systemPure growth of bacteria or yeast on plate or slant
Submit pure isolate on appropriate media. Ship refrigerated. DO NOT FREEZE. Specify collection site and provide brief clinical history.
48 hrsIdentification of Bacteria/Yeast by automated system
6BACTEC AEROBIC-Rapid Automated Aerobic Culture on BACTEC FX 200, Identification and SensitivityBLOOD/8-10ML/CULTURE BOTTLE. or FLUID/PUS/TISSUE in CULTURE BOTTLE/STERILE CONTAINER
Collect 8-10 mL blood aseptically in special Plus Aerobic bottle available from SMPL. Mix by gentle swirling. Ship at room temperature.
Aerobic culture which includes enrichment, which increases detection chances as compared to platting method in case of fluid/pus/tissue. Also includes aerobic culture of blood
7BACTEC ANAEROBIC-Rapid Automated Anaerobic Culture on BACTEC FX 200 and IdentificationBLOOD/8-10ML/CULTURE BOTTLE. or FLUID/PUS/TISSUE in CULTURE BOTTLE/STERILE CONTAINER
Collect 8-10 mL blood aseptically in special Plus Anerobic bottle. Mix by gentle swirling. Ship at room temperature.
Anaerobic culture which includes enrichment, which increases detection chances as compared to platting method in case of fluid/pus/tissue. Also includes anerobic culture of blood
8BACTEC MYCO-Rapid Automated fungal Culture/NTM culture on BACTEC FX 200BLOOD/1-5ML/CULTURE BOTTLE. or FLUID/PUS/TISSUE in CULTURE BOTTLE/STERILE CONTAINER
Collect 8-10 mL whole blood / body fluids aseptically in a Myco / F-Lytic bottle available from ADL. Mix by gentle swirling. Ship at room temperature.
Rapid culture system for detection of yeast/fungus/MOTT/NTM from blood and other body fluid.
9Calcoflour StaininigCALCOFLUOR STAININIGFluorescent microscopyAll specimens except Blood6 hrsHighly sensitive method for detection of Yeast or Fungus by Florescent staining.
10FUNGUS CULTUREGram stain, AFB stain, KOH, Identification of fungus grown, Colony countConventional Fungus Culture and Rapid Culture for Yeast.CSF: 2 mL (1 mL min.) in a Red Top (No Additive) tube or sterile screw capped vial. Do not use SST gel barrier tubes. Ship refrigerated. Bone Marrow: 2 mL (0. 5 mL min.) Bone marrow in 1 Green Top (Sodium Heparin) tube. Ship refrigerated. Pus/Body fluids (Pleural/ Pericardial/ Ascitic/ Synovial/ Ocular/ Bronchial washings/BAL). Aspirates /Semen/ Stool: Submit as much as possible (1 mL/1g min.) in sterile screw capped container. Ship refrigerated. Endometrial curettings/Tissue: Submit in sterile normal saline in a sterile screw capped container. Ship refrigerated. Swabs: Submit swabs in 1 mL sterile normal saline in sterile screw capped container. Ship refrigerated. Sputum/Urine: Submit 2 Spot (random) morning samples, 5–10 mL (1 mL min.) sputum/10 mL (5 mL min.) urine in sterile screw capped container. Ship refrigerated. Skin: Submit 2–3 mm scrapings from periphery of active skin lesion in sterile container or between 2 sterile glass slides. Wrap slides in black paper. Ship refrigerated. Hair: Submit plucked 10–12 infected, lustreless hair including root in a sterile container. Ship refrigerated. Nail: Submit clippings and powdery material from friable and discolored region of affected nail. Ship refrigerated.10 daysDetection of fungal infection by culture method.
11FUNGUS MICAntifungal susceptibility with MIC value and interpretation of Posaconazole, Amphotericin-B, Fluconazole, Itraconazole, Ketoconazole, Flucytosine, Voriconazole, CaspofunginBroth microdilutionPure growth of Yeast from any sample72 hrsSusceptibility of Antifungal drugs against any Yeast or Aspergillus spp, by MIC method
12Genexpert-TbMTB detection, Rifampicin susceptibilityRT-PCR by GeneXpertAny specimen except blood/2ml/Sterile container
In case of Bone marrow, sample is to be collected in sterile container containing distilled water in double volume of bone marrow sample
6 hrs. Next day after cut off timeHighly sensitive and specific method for rapid detection of MTB infection and Rif susceptibility, directly from clinical specimen.
13Gram - StainGRAM STAIN EXAMINATION :Light Microscopy after gram stainAny specimen except blood/1ml/Sterile container4 hrsDetection of any microorganism and pus cells by microscopic examination. Gram stain from Vaginal swab for diagnosis of Bacterial vaginosis (Nugent score)
14IDENTIFICATION BY MALDI TOF (Mass Spectrometry)Identification of organism by MALDI TOFMass spectrometryUpto 48 hrs of culture growth or any bacteria or yeast. Growth on Blood agar or LJ medium or MGIT in case of NTM or MTB. Hyphal growth on plate or slant.2 hrsUltra rapid identification of any Bacteria, Yeast, Hyphal fungus, Mycobacteium spp from growth
15KOH PREPARATIONLight MicroscopySubmit Skin, Nail scrapings, Hair ( including root), Cerebrospinal fluid, in a sterile screw capped container OR 2 mL whole blood / bone marrow in 1 Green Top (Sodium Heparin) tube. Ship at 18–22°C. Submit Body fluid, Sputum, Bronchial washings / Tissue in a sterile screw capped container OR Oral/Genital/wound swabs in 0. 5 mL sterile normal saline. Ship refrigerated. 4 hrsDetection of Fungal infection in clinical specimen by Microscopy. Also for Detection of Candidial Vaginosis.
16LPA (Line Probe Assay) MTB-MDRLPAMTBMDRPCR followed by Membrane hybridizationAny AFB smear positive sample4 daysDetection of MTB infection by PCR + Hybridization method along with detection of Isonizide and Rifampicin drug susceptibility status directly from specimen.
17LPA(Line Probe Assay Plus) MTB- XDRLPAMTBXDRPCR followed by Membrane hybridizationAny AFB smear positive sample4 daysDetection of MTB infection by PCR + Hybridization method along with detection of Quinolones and Aminoglycosides drug susceptibility status directly from specimen.
18LPA NT-MASLPANTMASPCR followed by Membrane hybridizationPure gorwth of NTM in MGIT tube/LJ slant/Media plate4 daysFor Speciation of NTM/MOTT (Additional species)
19LPA NT-MCMLPANTMCMPCR followed by Membrane hybridizationPure gorwth of NTM in MGIT tube/LJ slant/Media plate4 daysFor Speciation of NTM/MOTT (Common Mycobacteria)
20MODIFIED ZN STAIN-Light MicroscopyStool sample in case of testing for Cryptospora/Isospora/Microspora. Sputum, Pus, Tissue, BAL for Nocardia. Slit skin smears for Lepra bacilli.4 hrsFor detection of Nocardia spp in clinical specimen.
21NTM / MOTT DRUGSusceptibily results with MIC values of Linezolid, Trimethoprim / Sulphamethaxole, Ciprofloxacin, Imipenem, Moxifloxacin, Cefepime, Cefoxitin, Augmentin, Amikacin, Ceftriaxone, Doxycycline, Minocycline, Tigecycline, Tobramycin, ClarithromycinBroth microdilutionPure gorwth of NTM in MGIT tube/LJ slant/Media plate5 daysSusceptibility of NTM/MOTT with MIC values
22PRIMARY STAINGram stain, AFB stain, KOH, AFB by IF, Calcofluor whiteMicroscopic examination after various stainsAny specimen except blood4 hrsAll primary stains for detection of any infectious agent from clinical specimen.
23PYOGENIC CULTURE AND SENSITIVITY FOR BACTERIAGram stain, ZN stain, Oragnism isolated, Colony countAerobic culture and susceptibility repoting of bacteria by Kirby bauer methodAny specimen except blood48-72 hrsCulture of bacteria from specimen along with its identification, colony count and susceptibility by Kirby bauer method.
24SENSITIVITY ON VITEK (MIC)Antibiotic susceptibilities with MIC values as per tesing organismsMIC reporting by turbidometric monitoring of bacterial or yeast growthPure growth of bacteria or yeast24 hrsSusceptibility of bacteria with MIC values
25Cryptococcal AntigenQualitative and Quantitative detection of Cryptococcal antigenImmunochromatographic dipstick assayCSF/1ml/Sterile container
Serum/1ml/Plain bulb
4 hrsFor Detection of Cryptococcal antigen from CSF or Serum.
26India Ink PreparationINDIA INK PREPARATIONLight MicroscopyCSF/1ml/Leak proof container3 hrs
27MIC BY E-TESTMIC BY E-TESTEpsilometer MIC detectionPure growth of Bacteria/Yeast on media plate or slant24 hrs
28SPECIAL CULTURESelective/ Enriched culture of required organismSpecimen in sterile container10 days
29TB DRUG SENSITIVITYSusceptibility of drugsMGIT (Liquid medium) and LJ SlantPure growth of MTB15 days
30BIOFIRE MENINGITIS panelEscherichia Coli
Haemophilus Influenzae
Listeria Monocytogenes
Neisseria Meningitidis
Streptococcus Agalactiae
Streptococcus Pneumoniae
Cytomegalovirus (CMV)
Enterovirus
Herpes Simplex Virus I (HSV I)
Herpes Simplex Virus 2 (HSV 2)
Human Herpes Virus 6 (HHV-6)
Human Parechovirus
Varicella Zoster Virus (VZV)
Cryptococcus Neoformans/Gattii
Auotmated Nested multiplex PCRCSF/1-3ML/LEAK PROOF CONTAINER transported with ICE PACKS3 hrs
31Streptococcus pneumoniae Ag detection-Immunochromatographic assayUrine and CSF. Both samples - RT - within 24 hrs/ 2-8° C x 14 days.4 hrs
32Streptococcus A detection from Throat swabImmunochromatographic assayThroat swab in transport medium at RT4 hrs
33Listeria monocytogenes Ag detection form stoolImmunochromatographic assayStool in leak proof container. 2-8°C for 2 days4 hrs