• Kochi: (0) 484 2852100, 6682100, Faridabad: 0129-2851234


The Department of Microbiology aims to continuously strive for the highest possible standard in diagnostic services, teaching, and research activities. The department is committed in its endeavor to work with all health care professionals to assure that all the services provided by us are clinically relevant, that test results are delivered in a timely fashion so that it aids clinical decision making.

Diagnostic Services

The department runs a 24 hour, dedicated clinical microbiology laboratory which provides high quality diagnostic services to the clinical departments. The laboratory has no holidays. The laboratory is NABL accredited (ISO 15189:2007) since 2008.

A. Bacteriology

The bacteriology section uses a combination of standard identification techniques and automated technology to identify bacteria and their antibiotic susceptibility pattern. Samples processed include the following.

Blood Automated BacT/Alert 3D & BACTEC
Cerebrospinal Fluid (CSF) Microscopy and Automated BacT/Alert 3D ; Conventional culture
Sterile Body fluids

  • Joint fluid
  • Pericardial fluid
  • Pleural fluid
  • Peritoneal fluid
Microscopy and Automated BacT/Alert 3D ; Conventional culture
Bone marrow Automated BacT/Alert 3D
Respiratory Samples

  • Bronchoalveolar lavage(BAL)
  • Bronchial wash
  • Endotracheal aspirate
  • Expectorated sputum
  • Induced sputum
  • Nasopharyngeal aspirates (pediatric only)
  • Throat swab
  • Nasal swab (MRSA screening)
  • Paranasal sinus aspirate
Microscopy and Conventional culture method
Urine Microscopy and Conventional culture method
Stool Microscopy and Conventional culture method
Tissue Microscopy and Conventional culture method
Wounds Microscopy and Conventional culture method
Ocular Samples

  • Aqueous humor
  • Corneal scraping
  • Conjunctival swab
  • Vitreous humor
Microscopy and Conventional culture method
Genitourinary Samples

  • Cervical swab
  • Prostatic fluid
  • Semen
  • Urethral swab
  • High vaginal swab
Microscopy and Conventional culture method
Pus Microscopy and Conventional culture method
Miscellaneous Fluids

  • Bile
  • Gastric Aspirate
  • Peritoneal dialysate
Microscopy and Conventional culture method

  • Catheter tips
  • Drain tips
  • Biopsy
Microscopy and Conventional culture method
Water for bacteriological evaluation Conventional culture method
Surveillance cultures for Hospital Infection Control Conventional culture method
Anaerobic culture Conventional culture method
Ear Swab Microscopy and Conventional culture method

Identification  and Susceptibility of the organisms isolated in culture is performed using VITEK2 compact for isolates from blood and sterile body fluids and gram negative non fermenter bacilli. The other bacteria are identified  by  recommended conventional techniques. Antimicrobial susceptibility is performed using the current CLSI (M 100-S23) guidelines in VITEK2 and Kirby Bauer’s disc diffusion method. Serotyping is performed for Salmonella,Shigella, Vibrio, Beta hemolytic streptococci etc.

B. Mycology

The Mycology laboratory is involved in identification and speciation of yeast, filamentous and dimorphic fungi. It also performs antifungal susceptibility testing for yeasts and yeast like fungi. The following facilities are available with the department currently:

  • Direct Microscopic examination.
    • KOH
    • Calcoflour white
    • India Ink
  • Fungal culture.
  • Fungal identification (yeasts, dimorphic,filamentous).
  • Cryptococcal antigen detection test.
  • Antifungal susceptibility testing for yeasts.
C. Parasitology

The parasitology section supports the diagnostic wing with the following investigations.

  • Malaria antigen detection (Immunochromatographic test)
  • Stool Microscopy for cysts/trophozoites/helminthic eggs/larvae and adult worms
  • Stool concentration methods
  • Modified Acid fast staining for coccidian parasites
  • Microscopy
    • Of hydatid fluid
    • Pus from amoebic liver abscess
    • CSF for free living amoebae (Naegleria & Acanthamoeba)
  • Identification of adult worms

The mycobacteriology laboratory has an RNTCP designated microscopy centre (DMC) attached to it . The laboratory offers the following tests:

  • Ziehl Neelsen staining for Acid fast bacilli from sputum and extrapulmonary specimens
  • Microscopy of slit skin smears for lepra bacilli
  • Auramine phenol staining for Mycobacterium spp
  • Solid culture for pulmonary and extrapulmonary tuberculosis
  • Automated culture for tuberculosis (BacT/Alert 3D)
  • Culture and identification of Atypical mycobacteria
  • Rapid identification of MTB complex using MPT64 antigen
E. Serology

The serology section of the department deals with pre operative screening of patients using VITROS (Enhanced chemiluminisence assay). The other tests offered by this section are:

Bacterial Serology

Syphilis serology Screening with RPR

Confirmation with TPHA

VDRL(Flocculation) for CSF

Leptospira serology Anti-leptospiral antibody IgM (ELISA)
Enteric fever serology Widal Test
Brucella serology Anti-brucella antibody IgM (ELISA)


Viral Serology

Hepatitis B serology
  • Anti HBs antibody ECLIA
  • HB-Core IgM antibody ELISA
  • HB-Core Total antibody ELISA
  • Anti HBe antibody ELISA
Hepatitis C serology
  • Anti HCV antibody ELISA
  • Anti HCV antibody ECLIA
Hepatitis A serology Anti HAV IgM antibody ELISA
Hepatitis E serology Anti HEV IgM antibody ELISA
HIV serology
  • HIV p24 antigen/antibody assay ELISA
  • HIV 1/2 Antibody ECLIA
HSV1/2 serology Anti HSV1/2 Ig M antibody ELISA
CMV serology
  • Anti CMV IgM ELISA
  • Anti CMV IgG ELISA
Rubella serology Anti Rubella IgM ELISA
  • Anti EBV IgM ELISA
  • Anti Dengue IgM ELISA
  • Mycoplasma IgM ELISA


Parasite serology

Toxoplasma serology Anti Toxoplasma IgM ELISA
Malaria Malaria antigen detection (ICT)



RA Factor Latex agglutination
Anti Streptolysin O antibody (ASO) Latex agglutination

Doctors /Faculties

Contact Us

Emergency Contact

   Phone: 0484 – 2858010

   Email: medmicrobiology@aims.amrita.edu

Ambulance Services

   Phone: 0484 - 2856041

   Fax: 0484 - 2856035

   Email: ambulanceservices@aims.amrita.edu

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