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.


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


Microscopy and Conventional culture method


Microscopy and Conventional culture method


Microscopy and Conventional culture method


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


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 antigen detection (ICT)


RA Factor

Latex agglutination

Anti Streptolysin O antibody (ASO)

Latex agglutination


Phone : 0484 – 2858010
E-mail: medmicrobiology@aims.amrita.edu