JIPMER
Jawaharlal Institute of Postgraduate Medical Education & Research

Services

In-Patient Services


  • Exudate section

  • Urine & Stool section

  • Blood culture section

  • Anaerobic section

  • Mycobacteriology lab

  • Mycology lab

  • HIV lab

  • Molecular biology lab

  • Regional Influenza lab

  • Immunology lab

  • Parasitology lab

  • Virology lab

  • Superspeciality block

  • Hospital Infection Control


 
Section - Exudate
Appropriate specimen Inappropriate specimen Precautions while sending samples Turnaround time
  • Aspirates - CSF, Pleural aspirate, Joint aspirate, Pericardial aspirate, Peritoneal fluid
  • Pus
  • Swabs - Wound swabs, Ear swabs, Throat swabs
  • Respiratory specimen - Sputum, Tracheal aspirate, Bronchioalveolar lavage, Bronchial washings
  • Tissue bits - Diabetic foot, bed sores, Necrotizing fascitis
  • Peritoneal dialysis fluid
  • Genito-urinary samples - vaginal swabs, endometrial swabs, placental bits, cervical swab
  • Bone chips
  • Urethral swabs for gonorrhoea
  • Ocular specimen- conjunctival swab, corneal scraping, iris tissue, aqueous and vitreous aspirates
  • Swabs for surveillance cultures- nasal, axillary, perineal, web spaces
  • Tracheal swabs
  • Tracheal tips
  • Central line tips
  • Wound swabs in case of bedsore
  • Never refrigerate CSF samples collected in cases of suspected pyogenic meningitis
  • As far as possible collect specimens before starting antibiotic therapy
  • Wherever possible please collect pus/ tissue in place of swabs
  • Send tissue bits in sterile vials without saline
48 - 72 hours(in most cases)

 
Section - Blood culture
Sample Inappropriate specimens Precautions while sending samples Turnaround time
  • Blood in adult/ paediatric BACTEC bottles
  • Blood collected in adult/ paediatric conventional blood culture bottles
  • Bone marrow aspirate
Catheter tips
  • ConventionalBlood culture bottles should be inspected for turbidity prior to inoculation of sample, bottles found turbid prior to inoculation should not be used
  • Infective endocarditis-send minimum three (3)specimens from different sites(mention sites) 
  • Avoid sending pleural and ascitic fluid in BACTEC bottles
  • CRBSI- 2 specimens (central and peripheral) in BACTEC bottles, not in conventional blood culture and mention on the bottles and in the requisition forms
  • 48 hours (this is a preliminary report)
  • Final report shall be issued if only growth occurs after 48 hours and within a period of 7 days
  • Extended incubation upto 3 weeks for slow growing organisms like Brucella spp is possible after discussion with officer in charge

 
Section - Urine & Stool
Test Appropriate specimen Inappropriate specimen Precautions while sending samples Turnaround time
Urine culture
  • Mid stream clean catch  urine
  • Urine collected from catheter
  • Percutaneous nephrostomy sample
  • Suprapubic aspirate
  • Foley\'s Catheter Tip
  • Urine collected from Urobag
Ensure that sample is immediately transported to the laboratory without delay 48 hours
Stool culture(for Salmonella, Shigella, Vibrio cholerae, Yersinia enterocolitica, Campylobacter) • Stool for hangingdrop and culture (suspectedcholera)• Stool for cultureSensitivity• Rectal swabs (Send in Cary Blair Medium)
  • Faecal swabs
  • Stool not collected in sterile container
Ensure that sample is immediately transported to the laboratory without delay 48 – 72hrs

 
Section - Anaerobic culture
Appropriate specimen Inappropriate specimen Precautions while sending samples Turnaround time
  • Tissue bits
  • Biopsy specimen (Saline)
  • Aspirates
  • Pus
  • Suprapubic aspirate
  • Stool
  • Endotracheal apirate
  • All specimen should be sent to the laboratory in Robertson’s cooked meat (RCM) medium
  • RCM should be collected from the anaerobic culture section of Department of Microbiology
  • Swabs
  • Voided urine
  • Superficial material collected from skin surfaces
  • Sputum
Avoid sending material for culture in the needle and syringe.Transfer aspirated material to RCM. Negative report shall be issued after 6 days

 
Mycology Section      
Appropriate specimen Inappropriate specimen Precautions while sending samples Turnaround time
  • CSF for latex agglutination (Cryptococcal antigen)
24 hrs
  • Aspirates - CSF, Pleural aspirate, Joint aspirate, pericardial aspirate, peritoneal fluid, aqueous humour, vitreous aspirate
  • Respiratory specimen -
  • Sputum, Tracheal aspirate,
  • Bronchioalveolar lavage,
  • Bronchial washings
  • Urine
  • Skin scrapings
  • Hair Clippings
  • Nail clippings
  • Pus
  • Tissue biopsy
Swabs 4 weeks

 
Section - Parasitology        
Test Appropriate specimen Inappropriate specimen Precautions while sending samples Turnaround time
Stool wet mount for ova and cyst Stool specimen 2 hrs
Stool examination by concentration for ova and cysts Stool specimen 4 hrs
Modified acid fast staining for Coccidian parasites Stool specimen 2 hrs
Stool / aspirates for Amoebic culture Liver abscess Stool 3 days
Wet mount of CSF/Corneal scrapings for Acanthamoeba Corneal scrapings CSF 2 hrs
Indirect Haemagglutination test for amoebiasis Serum 3 days
Indirect Haemagglutination test for Filariasis Serum 3 days
Indirect Haemagglutination test Hydatid disease Serum 3 days
Immunochromatographic test(ICT) for malarial parasite Anticoagulated blood 2 hrs
Peripheral blood smear for malaria parasite Anticoagulated blood 2 hours
Co-agglutination for Cysticercosis antigen in serum and urine Serum 2 hrs
Co-agglutination test for Hydatid antigen in serum Seruum 2 hrs
Western blot for Cysticercosis antibodies in serum Serum 2 days
Western Blot for Hydatid antibodies in serum Serum 2 days

 
Section - Virology section
Test Appropriate specimen Inappropriate specimen Special precautions Turnaround time
ELISA for detection of HBsAg Serum specimen 24 hrs
ICT for detection of HBsAg Serum specimen To be done after discussion with microbiologist 2 hrs
ELISA for detection of HBeAg Serum specimen 7 days (test done every Thursday)
ELISA for detection of anti HBe antibodies Serum specimen 7 days (test done every Thursday)
ELISA for detection of IgM Anti HBc antibodies Serum specimen 7 days (test done every Wednesday)
ELISA for detection of Anti HCV antibodies Serum specimen 48 hrs (test done every Tuesday, Thursday & Saturday)
ELISA for detection of IgM Anti HAV antibodies Serum specimen 7 days (test done every Monday)
ELISA for detection of IgM Anti HEV antibodies Serum specimen 7 days (test done every Tuesday)
ICT for detection of Dengue NS1 antigen Serum specimen Done after discussion with Microbiologist 2 hours
ELISA for detection of Dengue NS1 antigen Serum specimen 48 hours (test done every Monday, Wednesday & Friday)
ELISA for detection of Dengue IgM antibodies Serum specimen 48 hours (test done every Monday, Wednesday & Friday)
ELISA for detection of IgM Anti Chikungunya antibodies Serum sample 7 days (test done every Friday)
Smears for CMV inclusion bodies Urine 24 hours
Indirect Immunofluorescence Test for Respiratory viruses(RSV, Influenza, Parainfluenza ,Human Metapneumovirus, Adenovirus Throat swab Nasopharyngeal aspirate Sample to be sent in Viral Transport medium 24 hours
Indirect Fluorescent Antibody (IFA) Test for Herpes Simplex Virus Skin scrapings Sample to be sent in Viral Transport medium 24 hours
Viral culture for Herpes Simplex virus Skin scrapings Sample to be sent in Viral Transport medium Negative report shall be given after 7 days

 
Section - HIV        
Test Appropriate specimen Inappropriate specimen Special precautions Turn around time
HIV 1 & 2  test (Anti HIV 1 & 2 antibodies by rapid test) Serum Test is performed only after complete written consent and HIV pretest counselling 24 hrs
CD4 counts EDTA blood Serum Sample collection will be done on the day of test by Staff of Department of Microbiology 24 hrs (Test is done on every Monday and Friday)
Viral load determination for HIV1 EDTA blood Serum 7 days (test done every Thursday)

 
Section – Immunology      
Test Appropriate specimen Inappropriate specimen Precautions while sending samples
Widal Test for Enteric Fever Serum 24 hours
Standard agglutination test for Brucellosis Serum 24 hours
Paul Bunnel Test forInfectious mononucleosis Serum 24 hours
Weil-Felix test for Rickettsiosis Serum 24 hours
Cold agglutination Test for Primary atypical pneumonia Serum 24 hours
VDRL Test for Syphilis Serum Test put up once a week (Thursday)
TPHA Test for Syphilis Serum Test put up once a week (Thursday)
Test for detection of Rheumatoid factor Serum 24 hours
Test for detection of Antistreptolysin O Serum 24 hours
Test for C-Reactive protein Serum 24 hours
IFA Test for detection of Antinuclear antibodies(ANA) Serum Test put up once a week (Friday)
ELISA for detection of ds DNA Serum Test put up once a week (Monday)
Leptospira – IgM antibody detection Serum Once a week (Based on the number of samples)

 
Section - Mycobacteriology lab
Appropriate specimen Inappropriate specimen Precautions while sending samples Turnaround time
  • Sputum – Only two sputum samples (early morning & spot ) should be collected
  • Bronchial washings
  • Bronchioalveolar lavage
  • Aspirates
  • Urine
  • Gastric aspirate:10-12 ml of gastric aspirate fluid should be collected in sterile container containing Sodium bicarbonate. (Containers for gastric aspirate can be collected from Mycobacteriology laboratory)
  • Bone marrow
  • Pus
  • Stool
  • Sample for renal tuberculosis: 40-100 ml of early morning urine sample for three (3) consecutive days. Sterile containers for the same may be obtained from Mycobacteriology laboratory
  • Saliva
  • Specimens not labelled or incorrectly labelled
  • Specimens collected in unsterile containers
  • Specimens sent in syringes
  • Clotted samples
  • Bone marrow and other specimens containing blood should be sent either in Sodium polyanethol sulfonate or heparin (EDTA should  not be used as it is inhibitory to Mycobacteria)
  • 10 - 12 ml of Gastric aspirate should be added to the sterile container containing 100 mg of Sodium bicarbonate within 30 min.
Negative report shall be issued after 8 week

 
Section - Molecular biology        
Test Appropriate specimen Inappropriate specimen Precautions while sending samples Turnaround time
PCR for Mycobacterium tuberculosis
  • CSF
  • All aspirates
  • Biopsy specimen
SputumUrineBloodBrochoalveolar lavageWound swabs Ensure that sample is immediately transferred to the laboratory 72 - 96 hours
Multiplex PCR for Entamoeba histolytica/ dispar/ moshkovskii • StoolLiver abscess pus - Ensure that sample is immediately transferred to the laboratory 72 - 96 hours
PCR for Herpes simplex virus CSF - Ensure that sample is immediately transferred to the laboratory 72 - 96 hours
Real time PCR for Entamoeba histolytica
  • Liver abscess pus
- Ensure that sample is immediately transferred to the laboratory 48 hours

 
Section - Superspeciality block      
Test Appropriate specimen Precautions while sending samples Turnaround time
ELISA for detection of IgM Anti Toxoplasma antibodies Serum TORCH panel testing can be done with single sample 7 days (test done every Wednesday)
ELISA for detection of IgM Anti Rubella antibodies Serum TORCH panel testing can be done with single sample 7 days (test done every Wednesday)
ELISA for detection of IgM Anti Cytomegalo Virus antibodies Serum TORCH panel testing can be done with single sample 7 days (test done every Wednesday)
ELISA for IgM Anti Herpes Simplex Virus antibodies Serum TORCH panel testing can be done with single sample 7 days (test done every Wednesday)

 
Section - Regional Influenza laboratory
Test Appropriate I specimen nappropriate specimen Special precautions
Real time PCR for Influenza virus Throat swabs, Nasal swabs Sample should be sent in viral transport medium 24 - 48 hours

 
Hospital Infection Control
Test Turnaround time
Sterility check of blood bags 10 days
Sterility check of intravenous fluids/ disinfectants 1 week
Sterility check of bone bank samples 1 week
Active surveillance cultures for specified reasons 1 week

Out-Patient Services

All the services listed for the in-patients are also available for the out-patients

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