About Us

The National Microbiology Reference laboratory (NMRL) is a public health facility established with the mandate to offer reference testing and to oversee quality assurance programs in microbiology.  The laboratory is accredited on ISO 15189:2012 for medical laboratories and ISO 17043:2010 for proficiency test panel production.

Key Functions

  • Laboratory based surveillance of diseases
  • Public health research
  • Training
  • Food safety
  • Monitoring and evaluation
  • Support supervision
  • Quality assurance including production of Proficiency test panel
  • Disease outbreak investigations
  • Specialized diagnostic testing
  • Formulation of Policy guidelines
  • Inter laboratory networking


  • NMRL comprises of three sections: Clinical section In the Clinical section the laboratory analyzes clinical samples which includes cultures for stool, urine, blood, pus swabs among others. Most of these samples are for  outbreaks investigation. The laboratory also participates in antimicrobial resistant (AMR) surveillance. The clinical laboratory is ISO 15189:2012 accredited Public health section The public health section analyses bacteria in water to ascertain the presence of faucal coliforms. The faucal coliforms are predictors of the occurrence of pathogens such as Vcholerae, Shigella, and Salmonella spp. Food samples are also analyzed for bacterial food poisoning. Some of the food analyzed includes; vegetable salads, milk/milk products, fresh juices, and beer. Environmental sample and efficacy testing disinfectant, detergents, antiseptic soaps and hand sanitizers are also analyzed. The public health laboratory based on ISO 17025Quality assurance The Quality assurance section assures national quality of the test kits for bacterial pathogens. The NMRL also produces bacteriology proficiency test (PT) panels (such as stool culture). The laboratory provides the panels to 25 county referral laboratories and private hospital laboratories.  The QA/ PT laboratory is based on ISO 17043:2010.

Media gallery

Test Menus/ Samples

sampleTime after collection to reach the laboratorySize/qtyCost (Ksh)/testTurn Around Time/Days
Water cultureWithin 24 hrs on ice pack250—500ml3,0007
Food cultureWithin 24 hrs on ice pack25—75 grams2,0007
Stool cultureMinimum of  2 hrs if not possible transport in Cary Blair transport media5 grams5004
Rectal swabTransport in cary Blair within  2 hrs, at room temperatureCean, sterile swab5004
CSF cultureWithin 1 hour   if not transport in Trans-isolate media within 24 hours (Do not refrigerate)2-5 ml5004
Blood cultureWithin 1 hour  (Do not refrigerate)5-10 ml for adults, 2-5ml from children and 0.5-2ml for infants5007
Urine cultureWithin 1 hour  if not refrigerate for not more than 24 hrs≥ 1.0 ml (≥ 15ml if microscopy is to be done5004
Swabs (genital, eye, etc)Within 1 hour, placed in appropriate transport mediaDo not refrigerateClean, sterile swab5004
Efficacy test for disinfectants etcWithin 24 hours. Put in a sterile leak-proof container at room temperature.10-50 ml5004
Sputum culture (non TB)Within 1 hour  in a Sterile leak-proof container if not refrigerate for not more than 24 hrs5-10 ml5004
Bacterial IsolatesPlaced in appropriate transport media within  24 hours, refrigerated if there is a delayclean, sterile swab5004
Molecular AnalysisWithin 24 hrs on ice pack2mlDepending on request3
Bacteriology proficiency tests panels (offered 3 times/year)Free10

*For public health requests, the charges are free and may be reviewed from time to time.

Testing services trends (Year 2016 and 2017)

The samples analysed in the year 2016 and 2017 included water for bacterial outbreak investigation and for surveillance purposes, food for  bacterial analysis of outbreak investigation and for surveillance purposes,, efficacy involves checking for the suitability of the detergents, hand sanitizers to attain disinfection ability, environmental swabs to check the hygiene status of services such as hospital theatre services and food processing factories and stool samples for diagnosis of bacterial pathogens that cause disease such as typhoid fever. The figure shows the testing trends of the tests done. There was a decline in the total same samples done for water in 2017 compared to 2016, while there was an increase in stool samples in 2017 compared to 2016.

Testing services trends (Year 2016, 2017, 2018)

The country has experienced cholera outbreak for the last four year. The figure shows the trends of the cholera workload for the last three years. In the year 2016, the samples were higher (1319) compared to 2017 and 2018. These shows a decline of cholera outbreak.


  • The NMRL was accredited on ISO 15189 for medical laboratories on May 2016 and has put in place strategies to sustain the standards. As a result of the accreditation, the laboratory has been called upon by other county laboratories for mentorship on both quality and technical systems
  • The laboratory was able to attain accreditation on Proficiency Testing (PT) for ISO 17043:2010
  • The laboratory has expanded PT tests menu from 4 to 5 tests
  • The laboratory has expanded coverage of external quality assurance (EQA) participating laboratories from 21 to 25
  • The laboratory was able to adequately respond to cholera outbreaks by assisting the county laboratories with testing and provision of tests kits.

Role of NMRL in the devolved system

  • Provision of bacterial proficiency panels (EQA)
  • Mentor the counties in the quality systems ISO 15189:2012
  • Assist the county laboratories in responding to disease outbreaks
  • Training and mentorship of peripheral laboratories in microbiology techniques
  • Routine public health surveillance in food and water suitability for consumption in conjunction with the county public health officers.
  • The laboratory is currently the hub for anti-microbial resistance (AMR) where it is involved in quality control for antimicrobial susceptibility testing

Future plans

The NMRL hopes to increase the number of participating laboratories on external quality assurance from 25 to 30; Increase the workload to up to 3,000 samples per yea

Pursue accreditation for ISO 17025 for food and water bacterial analysis in the next year.