Category Archives: Public Health

Occupational health and safety concerns that affect employee’s perfomance in East African Portland Cement

Mutindi M. J., Gatebe E.G., Gitu L.M.

Coping with Emerging Infectious Diseases: Experience from the East Africa Public Health Laboratory Networking–Operational Research Project in Kenya

Githui W.A[1], Wanzala P[2]., Kiptoo M[3]

 Center for Respiratory Disease Research (CRDR), Kenya Medical Research Institute

  1. Center for Respiratory Disease Research (CRDR), Kenya Medical Research Institute
  2. Center for Public Health Research (CPHR), Kenya Medical Research Institute
  3. KEMRI Graduate School of Health Sciences (KGSHS), Kenya Medical Research Institute

 Email of corresponding


In the global picture according to the National Institute of Allergy and Infectious Diseases, emerging infectious diseases are commonly defined as outbreaks of previously unknown diseases or known diseases that are rapidly increasing in incidence or geographic range in the last 2 decades. Emerging diseases include Ebola, HIV infections, SARS, Lyme disease, Escherichia coli (E. coli) O157:H7, Hantavirus, dengue fever, and West Nile virus to name a few.  Emerging infectious diseases are categorized based on the nature and characteristics of infectious agents that cause the emerging infections into   4 categories.  These  are (a) known pathogens occur in new niches(i.e chikungunya virus) (b) Known pathogens of new biologic phenotypes(Drug-resistant strains) (c) Novel infectious pathogens (Ebola virus) (d) Known disease of unknown etiology due to ‘unrecognized’ pathogens (Helicobacter pylor). Combinations of 6 factors provide these categories which include (i) changes in human demographics and behavior; (ii) advances in technology and changes in industry practices; (iii) economic development and changes in land use patterns; (iv) dramatic increases in volume and speed of international travel and commerce; (v) microbial mutation and adaptation; and (vi) inadequate public health capacity.  The environmental public health and laboratory biosafety implications of these pathogens are of major concern [1, 2, 3].

Reemerging diseases are those that reappear after they have been on a significant decline. Reemergence may happen because of a breakdown in public health measures for diseases that were once under control. They can also happen when new strains of known pathogens appear. Human behavior affects re-emergence. For example, overuse of antibiotics has led to drug-resistant pathogens and allowed a return of diseases that once were treatable and controllable. Reemerging diseases include malaria where drug-resistant Plasmodium strains are widespread, as are insecticide-resistant strains of the mosquitoes that carry the parasites. Others include strains of Multi-Drug Resistant tuberculosis (MDR-TB), cholera, pertussis, influenza, pneumococcal disease, and gonorrhea. Lack of fast tracking these strains may hamper effective public health interventions [4, 5, 6].

The World Bank is supporting the East Africa Public Health Laboratory Networking Project (EAPHLNP), a regional project involving five East African countries, namely Burundi, Kenya, Rwanda, Uganda and Tanzania. In the year 2010, the Ministry of Public Health and Sanitation identified Kenya Medical Research Institute (KEMRI) to take the leading role in the coordination of Operational Research (OR) activities in this project within Kenya and other East African member states. KEMRI established a secretariat as a coordination body both in Kenya and regionally. The rolling-out of actual OR activities in Kenya started in February 2013.  Three thematic areas relating to the global threat of the emerging infectious diseases were addressed in this study. These include: evaluation of the Impact of New Tuberculosis Diagnostics on Patient Health Outcomes in Kenya; surveillance of common circulating enteric pathogens and their antimicrobial susceptibility patterns in Kenya and evaluation of the efficacy of fixed artemisinin combinations therapy (ACT) [(artemether-lumefantrine) CoArtem® and (Dihydroartemisinin-piperaquine) Duo-cotexin®], in patients in Kenya.


OR project broad strategic objectives:

 (i) To provide oversight and guidance in carrying out the operational research activities under the regional project;

(ii) To facilitate local and regional capacity to carry out operational research and evaluation in medical diagnostics, and involve not only the public health laboratories, but also stakeholders such as research institutions, academic institutions and civil society groups.


 Rationale for choice of the research designs is in line with the project goals as outlined in the broad strategic objectives. Three research proposals on TB, malaria and enteric were developed and adopted regionally through a carefully guided process by Operational Research (OR) Secretariat at KEMRI.  The TB and Enterics studies necessitated five satellite and five non-satellite sites per country, while for the malaria study, choice of sites depends on endemicity of the disease in each country. The TB study is a prospective quasi-experimental utilizing both qualitative and quantitative methods. This study is being conducted in two phases: namely a validation phase and a quasi-experimental phase. The validation phase is a cross-sectional design involving determination of the diagnostic test values (sensitivity, specificity, positive and negative predictive test values) of combinations of  new TB diagnostics including Gene Xpert alone; Optimized Sputum Smear Microscopy (OSSM) commonly known as Lead Emitted Diode-Fluorescent Microscopy (LED-FM) and Gene Xpert; Gene Xpert ,OSSM, and Mycobacteria Growth Incubation Test(MGIT) vs Ziehl-Neelsen stain (ZN) as bench mark) as well as repeating all the tests that are performed  at the study sites using the same samples  at the KEMRI TB research laboratory and comparing results to determine reproducibility. In the  Quasi-experimental phase:  which is ongoing, satellite sites form the intervention arm  where new diagnostic tools including GeneXpert and LED-FM were introduced  in a STEP-WISE process (still awaiting for introduction of MGIT), while the  non-satellite sites continue with routine TB health care services using  microscopy ZN and/or LED-FM (where available) for diagnosis. The enterics study is cross-sectional to determine prevalence of emerging bacterial enterics pathogens. The study   involves identification of emerging resistance of enteric bacterial pathogens as well as molecular phase for characterization of virulence genes associated with E.coli strains.   The malaria study is a two-arm randomized clinical trial. It is a prospective evaluation of clinical and parasitological as well as molecular responses to directly observed treatment for uncomplicated P. falciparum malaria.

Project Achievements

 The project has been successfully implemented for the three studies and is ongoing at national and regional level.  In this issue, a supplement has been established to document some of the preliminary results from Kenya.

Nine topics are included: Performance of GeneXpert in Kenya is being documented for the first time. Findings indicate that GeneXpert has potential for use in the diagnosis of TB particularly in HIV positive persons presumed to have Tuberculosis [7]. An article on performance of clinical indicators in comparison with  laboratory results indicate possibility of using clinical signs and symptoms in routine diagnosis for TB where laboratory diagnosis is not available [8]. It is now evident that sputum specimen quality assessment should be considered as an integral part of routine laboratory diagnosis of TB especially in HIV negative individuals as indicated in an article by Orina et al  [9]. High proportion of non-adherence to follow up among HIV positive persons presumed to have TB has been shown to be a cause for concern to the national TB program [10]. In addition, there is a diminishing trend of antimicrobial agent to treat cases of enteric bacterial diseases due to resistance to all options of antibiotic available in Kenya. In addition, emergences of E.coli pathotype such as Entroheamorhagic E. Coli (EHEC) that are associated with severe diarrhea and could be fetal causative agents of Hemolytic uremic syndrome as well as hemorrhagic colitis are documented [11]. The malaria study on the efficacy of CoArtem® and Duo-cotexin® has only been conducted in one site and the results will be disseminated later.

Other components that complement OR activities which have been included in the supplement are: capacity building in OR which involved development of research methodology and scientific writing curriculum and teaching manuals which have facilitated training of clinical and laboratory personnel from the project study sites in Kenya and the region. Emphasis  is made on the need to strengthen capacity building in operational research, especially at the established project centres of excellence in order to adequately address public health related issues [12]. To fast track OR data capture, application of barcode technology can facilitate patients’ data linkages and verification in a multisite study leading to increased efficiency and effectiveness in maintaining patient records[13]. Finally, the importance of conducting M&E consistently and timely is emphasized in order to provide opportunities of early identification and correction of any protocol deviations [14].

Lessons learnt and way forward

There were lessons learnt by the OR secretariat both at national and regional level. Overall, multi-disciplinary multi-site OR studies can be implemented successfully in partnership with non-research institutions through appropriate planning, initiation, implementation, mentorship programmes and team work. In addition, constant communication, periodic supervision coupled with efficient data management and M&E programmes will ensure success of the studies. We look forward to the completion of the entire project, both in Kenya and regionally, when findings for all the studies in all participating countries will be compared to inform policy both at national and regional level.


  1. Ron B, George A. An Unnatural History of Emerging Infections.  General Anthropology. 2014; 21:1–4.
  2. Chua KB,  Gubler DJ.. Perspectives of public health laboratories in emerging infectious diseases.  Emerging Microbes and Infections (2013) 2, e37; doi:10.1038/emi.2013.34; published online 26 June 2013
  4.  Satcher D. Emerging infections: getting ahead of the curve. Emerg Infect Dis. 1995;1:1–6
  5. Morse S. Factors in the emergence of infectious diseases. Emerg Infect Dis. 1995; 1:7–15.
  6. Eckardt I. Challenging complexity: conceptual issues in an approach to new disease. Ann N Y Acad Sci. 1994; 740:408–17.
  7. Githui W.A, Mwangi M., Orina F., Kiptoo M., Ogaro T., Wanzala P., Sang W.K., Omar S.,Kariuki J.N.. Performance of Ziehl-Neelsen Microscopy, Light Emitting Diode –FM and Xpert MTB/RIF in the Diagnosis of Tuberculosis in People with Presumptive TB from results in the diagnosis of pulmonary tuberculosis in patients from EAPHLNP project study sites in Kenya. Afr J Health Sci. 2014; 27(4)supp: 433-448.
  8. Wanzala P., Githui W.A, Mwangi M., Kiptoo M., Sang W.K., Orina F., Kariuki J.N., Ogaro T., Inter and intra examiner reliability of clinical signs and symptoms in comparison  with  laboratory results. Afr J Health Sci. 2014; 27(4)supp: 450-468.
  9. Orina F., Mwangi M., Githui W.A, Ogaro T, Kiptoo M., Sang W.K., Kariuki J.N., Wanzala P.Effect of sputum quality on Xpert® MTB/RIF results in the detection of Mycobacterium tuberculosis from persons presumed to have Tuberculosis  in EAPHLN project Operational Research study sites in Kenya. Afr J Health Sci. 2014; 27(4)supp: 469-481.
  10.  Ogaro T., Mwangi M., Githui W.,Kiptoo M., Kariuki J.,   Wanzala P. Orina F. Follow-up of HIV positive sputum smear negative presumptive Tuberculosis patients in a study to evaluate the impact of new Tuberculosis diagnostics on patient health outcomes in Kenya. Afr J Health Sci. 2014; 27(4) supp: 482-492.
  11. Sang W, Githui W.A, Kiptoo M. Kariuki J.N., Wanzala P., Mwangi M., Omar S., Emerging Antimicrobial Resistance patterns of Enteric Pathogens isolated from children under 5 years of age in five EAPHLNP study sites in Kenya. Afr J Health Sci. 2014; 27(4) supp: 493-508.
  12. Kiptoo M, Githui W, Wanzala P, Kariuki J, Mwangi M, Omar S, Kimani F, Ogaro T, Orina F, Sang W. Impact of research methodology and scientific writing training in transforming clinical and laboratory personnel to research scientists at the EAPHLNP study sites in Kenya. Afr J Health Sci. 2014; 27(4) supp: 509-515.
  13. Orina F, Kariuki J.N, Githui W.A, Kiptoo M., Sang W.K., Mwangi M., Wanzala P. Application of barcode technology to enhance electronic quality-assured data collection and analysis in operational research EAPHLN project study sites in Kenya. Afr J Health Sci. 2014; 27(4) supp: 516-525.
  14.  Kariuki J.N., Mwangi M., Githui W.A, Kiptoo M., Orina F., Sang W.K., Omar S., Wanzala P.  The role of monitoring and evaluation in assessing progress of operational research in the EAPHLNP study sites in Kenya. Afr J Health Sci. 2014; 27(4) supp: 526-543.


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