Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania.

BACKGROUND: Mycobacterium tuberculosis presents several lineages each with distinct characteristics of evolutionary status, transmissibility, drug resistance, host interaction, latency, and vaccine efficacy. Whole genome sequencing (WGS) has emerged as a new diagnostic tool to reliably inform the occurrence of phylogenetic lineages of Mycobacterium tuberculosis and examine their relationship with patient demographic characteristics and multidrug-resistance development. METHODS: 191 Mycobacterium tuberculosis isolates obtained from a 2017/2018 Tanzanian drug resistance survey were sequenced on the Illumina Miseq platform at Supranational Tuberculosis Reference Laboratory in Uganda. Obtained fast-q files were imported into tools for resistance profiling and lineage inference (Kvarq v0.12.2, Mykrobe v0.8.1 and TBprofiler v3.0.5). Additionally for phylogenetic tree construction, RaxML-NG v1.0.3(25) was used to generate a maximum likelihood phylogeny with 800 bootstrap replicates. The resulting trees were plotted, annotated and visualized using ggtree v2.0.4 RESULTS: Most [172(90.0%)] of the isolates were from newly treated Pulmonary TB patients. Coinfection with HIV was observed in 33(17.3%) TB patients. Of the 191 isolates, 22(11.5%) were resistant to one or more commonly used first line anti-TB drugs (FLD), 9(4.7%) isolates were MDR-TB while 3(1.6%) were resistant to all the drugs. Of the 24 isolates with any resistance conferring mutations, 13(54.2%) and 10(41.6%) had mutations in genes associated with resistance to INH and RIF respectively. The findings also show four major lineages i.e. Lineage 3[81 (42.4%)], followed by Lineage 4 [74 (38.7%)], the Lineage 1 [23 (12.0%)] and Lineages 2 [13 (6.8%)] circulaing in Tanzania. CONCLUSION: The findings in this study show that Lineage 3 is the most prevalent lineage in Tanzania whereas drug resistant mutations were more frequent among isolates that belonged to Lineage 4.

The second national anti-tuberculosis drug resistance survey in Tanzania, 2017-2018.

OBJECTIVE: To determine the levels and patterns of resistance to first- and second-line anti-tuberculosis (TB) drugs among new and previously treated sputum smear positive pulmonary TB (PTB) patients. METHODS: We conducted a nationally representative cross-sectional facility-based survey in June 2017-July 2018 involving 45 clusters selected based on probability proportional to size. The survey aimed to determine the prevalence of anti-TB drug resistance and associated risk factors among smear positive PTB patients in Tanzania. Sputum samples were examined using smear microscopy, Xpert MTB/RIF, culture and drug susceptibility testing (DST). Logistic regression was used to account for missing data and sampling design effects on the estimates and their standard errors. RESULTS: We enrolled 1557 TB patients, including 1408 (90.4%) newly diagnosed and 149 (9.6%) previously treated patients. The prevalence of multidrug-resistant TB (MDR-TB) was 0.85% [95% confidence interval (CI): 0.4-1.3] among new cases and 4.6% (95% CI: 1.1-8.2) among previously treated cases. The prevalence of Mycobacterium tuberculosis strains resistant to any of the four first-line anti-TB drugs (isoniazid, rifampicin, streptomycin and ethambutol) was 1.7% among new TB patients and 6.5% among those previously treated. Drug resistance to all first-line drugs was similar (0.1%) in new and previously treated patients. None of the isolates displayed poly-resistance or extensively drug-resistant TB (XDR-TB). The only risk factor for MDR-TB was history of previous TB treatment (odds ratio = 5.7, 95% CI: 1.9-17.2). CONCLUSION: The burden of MDR-TB in the country was relatively low with no evidence of XDR-TB. Given the overall small number of MDR-TB cases in this survey, it will be beneficial focusing efforts on intensified case detection including universal DST.

Economic burden of tuberculosis in Tanzania: a national survey of costs faced by tuberculosis-affected households.

BACKGROUND: Although tuberculosis (TB) care is free in Tanzania, TB-associated costs may compromise access to services and treatment adherence resulting in poor outcomes and increased risk of transmission in the community. TB can impact economically patients and their households. We assessed the economic burden of TB on patients and their households in Tanzania and identified cost drivers to inform policies and programs for potential interventions to mitigate costs. METHODS: We conducted a nationally representative cross-sectional survey using a standard methodology recommended by World Health Organization. TB patients of all ages and with all types of TB from 30 clusters across Tanzania were interviewed during July - September 2019. We used the human capital approach to assess the indirect costs and a threshold of 20% of the household annual expenditure to determine the proportion of TB-affected households experiencing catastrophic cost. We descriptively analyzed the cost data and fitted multivariable logistic regression models to identify potential predictors of catastrophic costs. RESULTS: Of the 777 TB-affected households, 44.9% faced catastrophic costs due to TB. This proportion was higher (80.0%) among households of patients with multi-drug resistant TB (MDR-TB). Overall, cost was driven by income loss while accessing TB services (33.7%), nutritional supplements (32.6%), and medical costs (15.1%). Most income loss was associated with hospitalization and time for picking up TB drugs. Most TB patients (85.9%) reported worsening financial situations due to TB, and over fifty percent (53.0%) borrowed money or sold assets to finance TB treatment. In multivariable analysis, the factors associated with catastrophic costs included hospitalization (adjusted odds ratio [aOR] = 34.9; 95% confidence interval (CI):12.5-146.17), living in semi-urban (aOR = 1.6; 95% CI:1.0-2.5) or rural areas (aOR = 2.6; 95% CI:1.8-3.7), having MDR-TB (aOR = 3.4; 95% CI:1.2-10.9), and facility-based directly-observed treatment (DOT) (aOR = 7.2; 95% CI:2.4-26.6). CONCLUSION: We found that the cost of TB care is catastrophic for almost half of the TB-affected households in Tanzania; our findings support the results from other surveys recently conducted in sub-Saharan Africa. Collaborative efforts across health, employment and social welfare sectors are imperative to minimize household costs due to TB disease and improve access to care, patient adherence and outcomes.

Implementing tuberculosis patient cost surveys in resource-constrained settings: lessons from Tanzania.

Tuberculosis (TB) disproportionally affects persons and families who are economically and socially disadvantaged. Therefore, a patient cost survey was conducted in Tanzania to evaluate the costs incurred by patients and their households before and after the diagnosis of TB. It was the first survey in Tanzania to ascertain baseline information and experience for subsequent surveys. This paper aims to share the experience encountered during the survey to ensure a standardized approach and elimination of potential barriers for the implementation of future surveys. A total of 777 TB patients from 30 clusters selected based on probability proportional to the size were interviewed during the study period. As the sample size was calculated based on notification data from the previous year, some health facilities experienced an inadequate number of TB patients during the study to meet the allocated cluster size for the survey. Most facilities had poor recording and recordkeeping in TB registers where deaths were not registered, and some patients had not been assigned district identification numbers. Fixed days for TB drug refills in health facilities affected the routine implementation of the survey as the interviews were conducted when patients visited the facility to pick up the drugs. Tablets used to collect data failed to capture the geographic location in some areas. The households of TB patients lost to follow-up and those who had died during TB treatment were not included in the survey. When planning and preparing for patient costs surveys, it is important to consider unforeseen factors which may affect planned activities and findings. During the survey in Tanzania, the identified challenges included survey logistics, communications, patient enrollment, and data management issues. To improve the quality of the findings of future surveys, it may be reasonable to revise survey procedures to include households of TB patients who were lost to follow-up and those who died during TB treatment; the households of such patients may have incurred higher direct and indirect costs than households whose patient was cured as a result of receiving TB treatment.

Who Has Mycobacterial Disease? A Cross Sectional Study in Agropastoral Communities in Tanzania.

OBJECTIVE: To determine and describe clinical symptoms, demographic characteristics and environmental exposures as determinants of pulmonary mycobacterial diseases among patients examined for tuberculosis in agropastoral communities in Northern Tanzania. METHODS: This was a cross sectional study. Sputum samples were collected from patients attending three hospitals in Tanzania, and were investigated for pulmonary tuberculosis by microscopy between November 2010 and June 2012. The patients were interviewed about background information, and potential exposure to mycobacteria. RESULTS: We examined 1,711 presumptive tuberculosis cases where 936 (54.2%) were males and 775 (45.3%) females. Of all the study participants, 277 (16%) were found to have sputum samples positive for mycobacteria; 228 (13%) were smear positive, 123 (7%) were culture positive and 74 (4%) were positive by both smear microscopy and culture. Of the 123 mycobacterial culture positive, 15 (12.2%) had non-tuberculous mycobacteria. Males were more likely than females to be positive for mycobacteria. Factors associated with mycobacterial disease were loss of appetite, age groups below 41 years, and being a male. Among HIV negative patients, loss of appetite, age below 20 years and being a male were associated with being mycobacterial positive. Among HIV positive patients, males and those patients with a persistently coughing family member were more likely to harbor mycobacteria. CONCLUSION: The findings in this study show that both M. tuberculosis and non-tuberculous mycobacterial strains were prevalent in the study community. Some risk factors were identified. Although the reported predictors may improve screening for mycobacterial diseases, their use requires some precaution.

Experienced and Perceived Risks of Mycobacterial Diseases: A Cross Sectional Study among Agropastoral Communities in Northern Tanzania.

OBJECTIVE: The current study was conducted to assess experienced risk factors and perceptions of mycobacterial diseases in communities in northern Tanzania. METHODS: We conducted a cross-sectional study in Arusha and Manyara regions in Northern Tanzania. We enrolled tuberculosis (TB) patients attending Mount Meru Hospital, Enduleni Hospital and Haydom Lutheran Hospitals in Arusha municipality, Ngorongoro and Mbulu districts, respectively. Patient addresses were recorded during their first visit to the hospitals. Patients with confirmed diagnosis of TB by sputum smear microscopy and/or culture at central laboratory were followed up and interviewed using pre-tested questionnaires, and selected relatives and neighbors were also interviewed. The study was conducted between June 2011 and May 2013. RESULTS: The study involved 164 respondents: 41(25%) were TB patients, 68(41.5%) were their relatives and 55(33.5%) their neighbors. Sixty four (39%) knew a risk factor for mycobacterial disease. Overall, 64(39%) perceived to be at risk of mycobacterial diseases. Exposure to potential risks of mycobacterial diseases were: keeping livestock, not boiling drinking water, large family, smoking and sharing dwelling with TB patients. Rural dwellers were more often livestock keepers (p<0.01), more often shared dwelling with livestock (p<0.01) than urban dwellers. More primary school leavers reported sharing dwelling with TB patients than participants with secondary and higher education (p = 0.01). CONCLUSION: Livestock keeping, sharing dwelling with livestock, sharing household with a TB patient were perceived risk factors for mycobacterial diseases and the participants were exposed to some of these risk factors. Improving knowledge about the risk factors may protect them from these serious diseases.