Anthony KebiraWillie GithuiAberi, Ruth Moraa2024-02-012024-02-012023https://ir-library.ku.ac.ke/handle/123456789/27404A Thesis Submitted in Partial Fulfilment of the Requirements for the Award of Degree of Master of Science (Medical Microbiology) in the School of Pure and Applied Sciences of Kenyatta University, September 2023.Globally, awareness of nontuberculous mycobacteria (NTM) as an agent causing pulmonary diseases is currently on the rise. Similarity in clinical manifestation with pulmonary tuberculosis (PTB) caused by Mycobacterium tuberculosis complex (MTBc) and lack of routine surveillance have led to limited information on the burden of NTM especially in sub-Saharan Africa. These challenges have led to pulmonary infections due to NTM being misdiagnosed and hence poor patient management. In Kenya, like most sub-Saharan African countries, there is scarce information on the burden of NTM due to limited laboratory diagnosis of tuberculosis (TB) using non-distinguishing sputum smear microscopy. Inorder to significantly add value on currently scarce information on the burden of pulmonary infections caused by NTM in Kenya, this study sort to determine the magnitude, drug susceptibility patterns and geographical distribution of NTM isolated from presumptive PTB patients in selected sites in Kenya. This study was part of a main East Africa Public Health Laboratory Networking (EAPHLN) study where a stratified sampling approach was used to collect sputum specimens from consenting participants. The participants were presumptive PTB patients who presented themselves at different government health facilities in Kenya. These included Wajir, Machakos, Kitale, Busia, Malindi, Lamu, Narok, Kisii and Nyahururu. In the main study, a total of 3,782 sputum specimens were collected and triple packed before shipping to Kenya Medical Research Institute TB laboratory for analysis. The sputum specimens were analyzed using GeneXpert MTB/Rif, direct sputum smear for Ziehl-Neelsen (ZN) and fluorescent microscopy. Culture was done on solid Lowenstein-Jensen and liquid Mycobacteria Growth Indicator Tube (MGIT) media. All ZN positive isolates were appropriately archived regardless of culture media used. For this study, random sampling was used to select 124 isolates that were MGIT-ZN positive but negative by TBcID-Capillia assay (Becton Dickinson, Sparks, USA). The isolates were subcultured in MGIT media (MGITTM; BD Sparks, USA) to ascertain viability after which GenoType Mycobacterium assays (HAIN Lifescience, Nehren, Germany) were used to identify NTM to species level. Drug susceptibility to the first line anti-tuberculous drugs (rifampicin, ethambutol and isoniazid) was determined using resistance ratio method. Geographical distribution of NTM was determined by correlating identified NTM with information from the facility where the specimens were collected from. Out of 124 isolates analyzed, 24 (19.3%) were identified as NTM, 20 (16.1%) as MTBc, 56 (45.2%) as other bacteria with high guanine and cytosine content, 21 (16.9%) were negative for mycobacteria while 3 (2.4%) mycobacteria could not be identified to species level. Of the 24 NTM, 15 were isolated from males and 9 from females. Out of the 24 NTM, Mycobacterium intracellulare 10/24 (41.7%) and Mycobacterium fortuitum 4/24 (16.7%) were predominant. Mycobacterium mucogenicum and Mycobacterium gordonae were the least identified at 2/24 (8.3%), each. All 24 characterized NTM were resistant to the first line anti-TB drugs. The 24 NTM were identified in 5 of the 8 facilities, with Wajir having the highest (CI95% 2046-54.27, p=0.002) compared to other facilities. The magnitude of NTM isolated from people presumed to have PTB was high in this study. There are also high levels of resistance of NTM to routinely prescribed first line anti-TB drugs. Therefore, there is need to identify mycobacteria to species level for appropriate patient management.enMagnitudeGeographical DistributionNontuberculous Mycobacteria SpeciesPulmonaryTuberculosis PatientsKenyaPresumptiveThesis