Department of Bacteriology​

The Clinical Bacteriology laboratory in the Department of Bacteriology, Medical Research Institute (MRI), was known as the ‘Main lab’ – the pioneer unit of the ‘De Soyza Bacteriological Institute’ at the inception in 1900. The laboratory served as the main laboratory for ‘General Hospital, Colombo’, now the National Hospital of Sri Lanka. 

Sir Aldo Castellani, an Italian pathologist and a microbiologist was the first director of the De Soyza Bacteriological Institute who introduced various laboratory tests in bacteriology for the first time in Sri Lanka. Some of the pioneering bacteriological tests introduced by him included diagnosis of enteric fever and tuberculosis. In 1905, Sir Aldo Castellani discovered the causative organism in Yaws. 

Over the years, Bacteriology has grown in to a gigantic discipline that branched into many important subdivisional laboratories; Clinical microbiology (main lab), Leptospira, Food and Water microbiology, Anaerobic bacteriology, Enteric pathogens, Quality Control and Molecular Biology in bacteriology

The consultants served in this Department are as follows:

Sir Aldo Castellani, Dr. E. Schmid, Dr. Nitiyanandan, Dr. T. Velaudapillai, Dr. Palasuntheram,             Dr. R.S.B. Wickramasinghe,  Dr. Maya Atapattu, Dr. Philomina Chandrasiri, Dr. Praneetha Somaratne,  Dr. K. Karunaratne and Dr. Kavan Cooray.


Journal of the  Medical Research Institute – Inaugural volume October, 1985

Personal communication – Mr. L. Suraweera, (Former) Sup. MLT/MRI

Written by Dr. Lilani Karunanayake (02.05.2023)

The present Consultant Microbiologists serving in the Department of Bacteriology
Dr. Lilani Karunanayake MD2010Clinical Microbiology & Molecular Biology, Leptospirosis, Quality Control & Media Preparation
Dr. Sujatha Pathirage MD2012Food & Water Microbiology, Enteric & Anaerobic bacteriology
The present Consultant Microbiologists serving in the Department of Bacteriology

In the Department of Bacteriology there are five laboratories divided into two divisions.

Lab One – Clinical Bacteriology Laboratory

  • Clinical Microbiology & Molecular Biology
  • National Reference Laboratory for Leptospirosis
  • Quality Control & media preparation laboratory

Lab Two

  • Enteric Bacteriology Laboratory
  • Food and Water Microbiology
Lab One – Clinical Bacteriology Laboratory

Clinical Bacteriology Laboratory (CBL), is accredited to ISO 15189 standard, certified by the Sri Lanka Accreditation Board (SLAB), which is a full member of the International Laboratory Accreditation Cooperation (ILAC).

The accredited Clinical Bacteriology Laboratory (CBL) includes,  

  • Clinical Microbiology and Molecular Biology Laboratory; designated National Reference Laboratory for antimicrobial resistance (AMR) surveillance
  • National Reference Laboratory for Leptospirosis
  • Quality Control & media preparation laboratory

It is Sri Lanka’s only government-owned, first clinical microbiology laboratory with international accreditation. There are 36 accredited microbiological investigations in bacteriology, serology and molecular biology.

The above laboratories are under the leadership of Dr. Lilani Karunanayake, Consultant Clinical Microbiologist working with a team of devoted staff providing the best quality services possible in healthcare. Available list of Microbiology Examinations in Clinical Bacteriology.


To achieve excellence in microbiology diagnostics and reference services in the South-East Asian region.


The Clinical Bacteriology Laboratory is committed to provide an efficient, reliable and innovative service in microbiology based on quality management system to achieve total customer satisfaction.  

Further, it contributes towards improvements in the diagnosis and surveillance of infectious diseases in the country by professional and technological advancements through teaching, training, quality assurance and medical research.

Service hours

Normal working hours open to public: Monday to Friday: 8am to 4pm and Saturday: 8am to 12pm

Working hours for consultants and medical officers: Monday to Friday: 8.30am to 4.15pm

Technical staff: Monday to Friday: 8.00am to 4.00 pm and Saturday: 8.00am to 12.00pm

All samples are received by a Resident MLT (RMLT) in out of hours.

  1. Sample collection guide clinical microbiology 2023
  2. Specimen Collection for IB-VPD (Invasive Bacterial Vaccine-Preventable Diseases) surveillance 2023
  3. Specimen Collection guide for molecular tests 2023
  4. Meningococcal sepsis and meningitis specimen Collection guide 2023
Clinical Microbiology and Moleculer Biology

Eight new reference Leptospira serovars from human and animals have been added from Sri Lanka to the world literature (gem, alice, weerasinghe, ratnapura, ceylonica, jeyaweera, lanka and animal spp.)  In 1971, Dr. Nityananda identified many different serotypes and their reservoir hosts in Sri Lanka. The findings suggested the existence of a diversity of serotypes maintained by different maintenance hosts such as rodents, domestic farm animals and dogs [K. Nithyananda,‘Leptospirosis in Ceylon]. In 1962, a serological survey of occupational groups showed rice field workers, sewer workers, workers in coconut plantations and desiccated coconut mills, sugar cane workers, abattoir workers, fish market workers and river bathers were as at risk of leptospirosis.

Heads of National Reference Laboratory for Leptospirosis
1953 – Dr. K. Nityananda, Consultant Bacteriologist
1970’s – Dr. M. Atapattu, Consultant Microbiologist
2000 – Dr. Philomina Chandrasiri, Consultant Clinical Microbiologist
2003 – Dr. Praneetha Somarathne, Consultant Clinical Microbiologist
2011 to date – Dr. Lilani Karunanayake, Consultant Clinical Microbiologist

Quality Control and Media preparation laboratory (room no: 353, 361)

Quality assurance (QA) is an essential component of a clinical bacteriology laboratory. Laboratories practicing the principles of quality assurance generate reliable, relevant and cost-effective results, delivered timely and in the best interest of the patient.

National External Quality Assessment Scheme in Clinical Microbiology

25 Years


Quality Control laboratory is the Proficiency Testing Provider (PTP) of the accredited ‘National External Quality Assessment Scheme in Microbiology’ conducted for the state and private sector microbiology laboratories in Sri Lanka. This program was granted accreditation to ISO 17043 standards as the PTP in 2021 by the Sri Lanka Accreditation Board (SLAB).

NEQAS in clinical microbiology was commenced in 1997 by Dr. R.S.B. Wickremasinghe and Dr. M. Atapattu, Consultant Bacteriologists worked in the Department of Bacteriology.  

Objectives of the NEQAS program

  • to improve the quality of medical laboratories in Sri Lanka conducting bacteriological investigations
  • to standardize the performance of bacteriological techniques and antibiotic susceptibility testing
  • to encourage use of standard reagents / methodology in bacterial identification and antimicrobial susceptibility testing (AST) to support quality control of  in microbiology
  • to monitor laboratory performance of clinical diagnostic microbiology
  • to evaluate internal quality control measures
  • to facilitate information exchange and continuing education among NEQAS  laboratory Network
  • stimulate performance improvement to ensure credibility of the laboratory
  • to support the accreditation program of microbiology laboratories

Scope of Tests in clinical microbiology

  • Gram stain interpretation
  • Bacterial culture identification
  • Antimicrobial Susceptibility Testing (AST) and result interpretation


Clinical microbiology laboratories in hospitals, universities or institutions in public or private sector, are eligible to request for enrollment in the program.

The participation is voluntary unless made mandatory by the Ministry of Health, Sri Lanka.

Laboratories are encouraged to enroll before the 30th of January each year. PT surveys for new member laboratories will be commenced only at the beginning of each year.

Enrollment is free for public sector hospitals and a nominal annual payment is charged from the private sector laboratories.

Contact details

Proficiency Testing Coordinator & Technical Advisor :

Dr. Lilani Karunanayake, Consultant Clinical Microbiologist

Technical Coordinator:

Mrs. A. Vayishnavi, senior Medical Laboratory Technologist

Postal Address:       

Quality Control Laboratory, Department of Bacteriology

Medical Research Institute, Dr. Danister de Silva Mawatha,

Colombo 08, Sri Lanka

Telephone: 009411 269 3532 – 35 EXT: PTP laboratory – 353           

Proficiency Testing Coordinator / Consultant – 332

Fax: 0094112691495 (Director office)

E mail:

Team members

Proficiency Testing Coordinator & Technical Advisor – Dr. Lilani   Karunanayake, Consultant Clinical Microbiologist, Head, QC laboratory

Assistant Coordinator – Dr. P.H.P.D. Somaratne, Medical Officer

Technical Coordinator – Mrs. A. Vayishnavi, senior Medical Laboratory Technologist / Quality Control Laboratory

Medical Laboratory Technologist – Ms. K.D.D. Karavita

Health Laboratory Aide – Mr. D.N. Wijesinghe

Support staff – Mrs. G. Dilhara, Mrs. D. Ushetti

Quality Manager – Mrs. K.D.N. Gunawardena

Internal Auditor – Mrs. S. de Silva

Workshop 2023 Theme: ‘Laboratory quality towards better patient care’

Workshop 2023 Theme: ‘Laboratory quality towards better patient care’

National Training Workshop on Clinical Microbiology for NEQAS participants – for Microbiologists and Medical Laboratory Technologists

The 2-day program for 100 participants held on 16 & 17th February 2023 to mark the 25th Anniversary of the ‘National External Quality Assessment Scheme in (NEQAS) clinical microbiology’. The second edition of the ‘Handbook on National External Quality Assessment Scheme in Clinical Bacteriology’ was launched.

Further, Dr. Sudath Dharmaratne DDGLS/MOH awarded certificates to appreciate the laboratory staff for their dedication in achieving accreditation to the Clinical Bacteriology Laboratory and the NEQAs program. The event was sponsored by the WHO, Sri Lanka.

CBL is the first and only government-owned microbiology laboratory to achieve accreditation status so far.

Laboratory visit to District General Hospital, Nuwara Eliya – with Dr. M. Abeywardene, Consultant Clinical Microbiologist and her team - Visited five microbiology laboratories in the Uva Province for on-site assessment

One-Day National Training workshop for NEQAS laboratory network was held @ MRI auditorium with lectures and bench training.

In November 2016, a one-day program was held on ‘Quality Assurance in Bacteriology for Medical Laboratory Technologists (MLT’s)’ of microbiology laboratories in both state- and private- sector institutions participating in NEQAS in Bacteriology, MRI. Workshop included lectures and demonstration of lab-based detection methods for antibiotic- resistant bacteria.

Enteric Bacteriology Laboratory

Enteric Bacteriology Laboratory is the National Reference Laboratory for Enteric Bacteria. We provide our services to state and private sector. 


  1. Isolation and identification of enteric bacteria from clinical specimens
  2. Identification of enteric bacteria from isolates
  3. antibiotic susceptibility testing
  4. Salmonella and Shigella serotyping on isolates
  5. Screening of food handlers
  6. Outbreak  investigation

Microbiological identification and/or serotyping:

  1. Salmonella
  2. Shigella
  3. Campylobacter
  4. Vibrio cholerae
  5. Vibrio parahaemolyticus
  6. Standard Agglutination Test for Salmonella
  7. Brucella antibody test
  8. ASOT
  9. Helicobactor pylori IgM in serum
  10. Standard Agglutination Test for Salmonella
  11. Brucella antibody test
  12. ASOT
  13. zHelicobactor pylori IgM in serum

 Quality Control:

Participation in the WHO Global Foodborne Infections Network External Quality Assurance System (EQAS) 


Serological assays:

  1. Standard Agglutination Test for Salmonella
  2. Standard Agglutination Test for Brucella abortus and B.melitensis
  3. Anti-Streptolysin O Titre (ASOT)
  4. Helicobactor pylori IgM/ IgG in serum
  5. Monospot test for Infectious Mononucleosis
  6. Weil-Felix test for rickettssial diseases

An Accredited Laboratory by 


 by the letter dated 08.07.2019( TL-CF-087-01)

Food and Water Laboratory of the MRI offers comprehensive, highest quality microbiological testing of food and water. We are the leading laboratory for Food & Water microbiological analysis in the state sector. Also, provide our services to the private sector.


To contribute towards the achievement of the mission of the institution by fulfilling the research and service functions of food and water microbiology.

Our Services:
  • Testing of food for microbiological quality
  • Testing of food in outbreak investigations
  • Testing of water for drinking water quality
  • Testing of water quality for recreational activity
  • Testing for Legionella spp. in water used in air conditioning and cooling towers
Microbiology testing: (includes detection and quantification) 
  • Aerobic  Plate Count (APC)
  • Presumptive Coliform count (PCC)
  • E. coli                                                            
  • Yeast and molds                                                          
  • Listeria monocytogenes
  • Salmonella Spp.
  • Clostridium perfringens
  • Staphylococcus(coagulase positive)                             
  • Bacillus cereus               
  • Vibrio cholerae
  • Vibrio parahaemolyticus
  • Legionella spp

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