Bioinformatics mentorship in a resource limited setting.

BACKGROUND: The two recent simultaneous developments of high-throughput sequencing and increased computational power have brought bioinformatics to the forefront as an important tool for effective and efficient biomedical research. Consequently, there have been multiple approaches to developing bioinformatics skills. In resource rich environments, it has been possible to develop and implement formal fully accredited graduate degree training programs in bioinformatics. In resource limited settings with a paucity of expert bioinformaticians, infrastructure and financial resources, the task has been approached by delivering short courses on bioinformatics-lasting only a few days to a couple of weeks. Alternatively, courses are offered online, usually over a period of a few months. These approaches are limited by both the lack of sustained in-person trainer-trainee interactions, which is a key part of quality mentorships and short durations which constrain the amount of learning that can be achieved. METHODS: Here, we pioneered and tested a bioinformatics training/mentorship model that effectively uses the available expertise and computational infrastructure to deliver an in-person hands-on skills training experience. This is done through a few physical lecture hours each week, guided personal coursework over the rest of the week, group discussions and continuous close mentorship and assessment of trainees over a period of 1 year. RESULTS: This model has now completed its third iteration at Makerere University and has successfully mentored trainees, who have progressed to a variety of viable career paths. CONCLUSIONS: One-year (intermediate) skills based in-person bioinformatics training and mentorships are viable, effective and particularly appropriate for resource limited settings.

Excess Risk of Tuberculosis Infection Among Extra-household Contacts of Tuberculosis Cases in an African City.

BACKGROUND: Although households of tuberculosis (TB) cases represent a setting for intense transmission of Mycobacterium tuberculosis, household exposure accounts for <20% of transmission within a community. The aim of this study was to estimate excess risk of M. tuberculosis infection among household and extra-household contacts of index cases. METHODS: We performed a cross-sectional study in Kampala, Uganda, to delineate social networks of TB cases and matched controls without TB. We estimated the age-stratified prevalence difference of TB infection between case and control networks, partitioned as household and extra-household contacts. RESULTS: We enrolled 123 index cases, 124 index controls, and 2415 first-degree network contacts. The prevalence of infection was highest among household contacts of cases (61.5%), lowest among household contacts of controls (25.2%), and intermediary among extra-household TB contacts (44.9%) and extra-household control contacts (41.2%). The age-adjusted prevalence difference between extra-household contacts of cases and their controls was 5.4%. The prevalence of infection was similar among the majority of extra-household case contacts and corresponding controls (47%). CONCLUSIONS: Most first-degree social network members of TB cases do not have adequate contact with the index case to experience additional risk for infection, but appear instead to acquire infection through unrecognized exposures with infectious cases in the community.

Community drivers of tuberculosis diagnostic delay in Kampala, Uganda: a retrospective cohort study.

BACKGROUND: Recent approaches to TB control have focused on identifying and treating active cases to halt further transmission. Patients with TB symptoms often delay to seek care, get appropriate diagnosis, and initiate effective treatment. These delays are partly influenced by whom the patients contact within their community network. We aimed to evaluate the community drivers of diagnostic delay in an urban setting in Uganda. METHODS: In this study we analyze data from a retrospective cohort of 194 TB patients in Kampala, Uganda. We characterized the patterns of contacts made by patients seeking care for TB symptoms. The main outcome of interest was total community contact delay, defined as the time patients spent seeking care before visiting a provider capable of diagnosing TB. RESULTS: Visits to health providers without access to appropriate diagnostic services accounted for 56% of contacts made by cohort members, and were significantly associated with community contact delay, as were symptoms common to other prevalent illnesses, such as bone and joint pain. CONCLUSIONS: Education programs aimed at primary care providers, as well as other community members, may benefit case identification, by informing them of rarer symptoms of TB, potential for co-infections of TB and other prevalent diseases, and the availability of diagnostic services.

Association between tuberculosis in men and social network structure in Kampala, Uganda.

BACKGROUND: Globally, tuberculosis disease (TB) is more common among males than females. Recent research proposes that differences in social mixing by sex could alter infection patterns in TB. We examine evidence for two mechanisms by which social-mixing could increase men's contact rates with TB cases. First, men could be positioned in social networks such that they contact more people or social groups. Second, preferential mixing by sex could prime men to have more exposure to TB cases. METHODS: We compared the networks of male and female TB cases and healthy matched controls living in Kampala, Uganda. Specifically, we estimated their positions in social networks (network distance to TB cases, degree, betweenness, and closeness) and assortativity patterns (mixing with adult men, women, and children inside and outside the household). RESULTS: The observed network consisted of 11,840 individuals. There were few differences in estimates of node position by sex. We found distinct mixing patterns by sex and TB disease status including that TB cases have proportionally more adult male contacts and fewer contacts with children. CONCLUSIONS: This analysis used a network approach to study how social mixing patterns are associated with TB disease. Understanding these mechanisms may have implications for designing targeted intervention strategies in high-burden populations.

Defining adequate contact for transmission of Mycobacterium tuberculosis in an African urban environment.

BACKGROUND: The risk of infection from respiratory pathogens increases according to the contact rate between the infectious case and susceptible contact, but the definition of adequate contact for transmission is not standard. In this study we aimed to identify factors that can explain the level of contact between tuberculosis cases and their social networks in an African urban environment. METHODS: This was a cross-sectional study conducted in Kampala, Uganda from 2013 to 2017. We carried out an exploratory factor analysis (EFA) in social network data from tuberculosis cases and their contacts. We evaluated the factorability of the data to EFA using the Kaiser-Meyer-Olkin Measure of Sampling Adequacy (KMO). We used principal axis factoring with oblique rotation to extract and rotate the factors, then we calculated factor scores for each using the weighted sum scores method. We assessed construct validity of the factors by associating the factors with other variables related to social mixing. RESULTS: Tuberculosis cases (N = 120) listed their encounters with 1154 members of their social networks. Two factors were identified, the first named "Setting" captured 61% of the variance whereas the second, named 'Relationship' captured 21%. Median scores for the setting and relationship factors were 10.2 (IQR 7.0, 13.6) and 7.7 (IQR 6.4, 10.1) respectively. Setting and Relationship scores varied according to the age, gender, and nature of the relationship among tuberculosis cases and their contacts. Family members had a higher median setting score (13.8, IQR 11.6, 15.7) than non-family members (7.2, IQR 6.2, 9.4). The median relationship score in family members (9.9, IQR 7.6, 11.5) was also higher than in non-family members (6.9, IQR 5.6, 8.1). For both factors, household contacts had higher scores than extra-household contacts (p < .0001). Contacts of male cases had a lower setting score as opposed to contacts of female cases. In contrast, contacts of male and female cases had similar relationship scores. CONCLUSIONS: In this large cross-sectional study from an urban African setting, we identified two factors that can assess adequate contact between tuberculosis cases and their social network members. These findings also confirm the complexity and heterogeneity of social mixing.

Four Degrees of Separation: Social Contacts and Health Providers Influence the Steps to Final Diagnosis of Active Tuberculosis Patients in Urban Uganda.

BACKGROUND: Delay in tuberculosis (TB) diagnosis adversely affects patients' outcomes and prolongs transmission in the community. The influence of social contacts on steps taken by active pulmonary TB patients to seek a diagnosis has not been well examined. METHODS: A retrospective study design was use to enroll TB patients on treatment for 3 months or less and aged ≥18 years from 3 public clinics in Kampala, Uganda, from March to July 2014. Social network analysis was used to collect information about social contacts and health providers visited by patients to measure the number of steps and time between onset of symptoms and final diagnosis of TB. RESULTS: Of 294 TB patients, 58 % were male and median age was 30 (IQR: 24-38) years. The median number of steps was 4 (IQR: 3, 7) corresponding to 70 (IQR: 28,140) days to diagnosis. New patients had more steps and time to diagnosis compared retreatment patients (5 vs. 3, P < 0.0001; 84 vs. 46 days P < 0.0001). Fifty-eight percent of patients first contacted persons in their social network. The first step to initiate seeking care accounted for 41 % of the patients' time to diagnosis while visits to non-TB providers and TB providers (without a TB diagnosis) accounted for 34 % and 11 % respectively. New TB patients vs. retreatment (HR: 0.66, 95 % CI; 1.11, 1.99), those who first contacted a non-TB health provider vs. contacting social network (HR: 0.72 95 % CI; 0.55, 0.95) and HIV seronegative vs. seropositive patients (HR: 0.70, 95 % CI; 0.53, 0.92) had a significantly lower likelihood of a timely final diagnosis. CONCLUSIONS: There were four degrees of separation between the onset of symptoms in a TB patient and a final diagnosis. Both social and provider networks of patients influenced the diagnostic pathways. Most delays occurred in the first step which represents decisions to seek help, and through interactions with non-TB health providers. TB control programs should strengthen education and active screening in the community and in health care settings to ensure timely diagnosis of TB.

M. tuberculosis Infection Attributable to Exposure in Social Networks of Tuberculosis Cases in an Urban African Community.

Background: The persistence of tuberculosis today and its global disparity send a powerful message that effective tuberculosis control must respond to its regional epidemiology. Active case finding through contact investigation is a standard protocol used for tuberculosis control, but its effectiveness has not been established, especially in endemic areas. Methods: To quantify the potential effectiveness of contact investigation in Kampala, Uganda, we used a cross-sectional design to evaluate the social networks of 123 tuberculosis index cases and 124 controls without tuberculosis. Results: Tuberculous infection was present in 515 of 989 tuberculosis case contacts (52.1%) and 396 of 1026 control contacts (38.6%; adjusted prevalence ratio, 1.4; 95% CI, 1.3-1.6). The proportion of infected participants with known exposure within the social network of the tuberculosis case was 35%. The population-attributable fraction was 11.1% for any known exposure, with 7.3% attributable to household exposure and 3.4% attributable to extrahousehold exposure. Conclusions: This low population-attributable fraction indicates that contact tracing in the social networks of index cases will have only a modest effect in reducing tuberculous infection in a community. New approaches to community-level active case finding are needed.

Patient satisfaction among persons living with HIV/AIDS and receiving antiretroviral therapy in urban Uganda: A factor analysis.

INTRODUCTION: Patient satisfaction is an important predictor of health outcomes among patients in HIV/AIDS treatment and care, yet it is rarely measured in routine clinic settings in most of Africa. The aims of our study were to evaluate the internal validity and reliability of the Consumer Assessment of Healthcare Providers and Systems instrument for measuring satisfaction, assess the general level of patient satisfaction, and identify the factors associated with the level of satisfaction among patients receiving antiretroviral therapy in Uganda. MATERIALS AND METHODS: We conducted a cross-sectional study of 475 HIV/AIDS-infected patients from July to August 2015 in Kampala, Uganda. Eligible participants were 18 years or older, consented to the study and receiving antiretroviral therapy and outpatient care at the selected public health clinic. This study used a modified version of the validated Consumer Assessment of Healthcare Providers and Systems (CAHPS) instrument to assess the level of satisfaction among HIV/AIDS patients receiving outpatient care. We collected data on socio-demographics, clinical variables and 18-items adapted from the CAHPS instrument rating satisfaction with aspects of health services. We conducted an exploratory factor analysis to assess the internal validity of the 18 items and multiple linear regression analysis of factors associated with patient satisfaction with care. RESULTS: Majority of the respondents were females (76.8%), and the mean age was 37 years (SD = 10). The modified CAHPS instrument had high internal consistency (Cronbach's α = 0.94) for measuring satisfaction with HIV/AIDS care. Female sex (p = 0.016), perceived providers' technical and interpersonal skills (p = 0.022), emotional health (p = 0.032), and quality of reception services (p<0.001) were significantly associated with satisfaction in this urban HIV/AIDS public clinic. CONCLUSION: The reliability of the CAHPS instrument was high for measuring satisfaction. Providers' technical and interpersonal skills, and the quality of reception services are key to achieving patient satisfaction. Health system interventions to address the gaps identified will enhance the quality of patient-centered HIV/AIDS care in the Ugandan setting.

Acceptability, Usefulness, and Ease of Use of an Enhanced Video Directly Observed Treatment System for Supporting Patients With Tuberculosis in Kampala, Uganda: Explanatory Qualitative Study.

BACKGROUND: In tuberculosis (TB) control, nonadherence to treatment persists as a barrier. The traditional method of ensuring adherence, that is, directly observed therapy, faces significant challenges that hinder its widespread adoption. Digital adherence technologies such as video directly observed therapy (VDOT) are emerging as promising solutions. However, as these novel technologies gain momentum, a critical gap is the lack of comprehensive studies evaluating their efficacy and the unique experiences of patients in Africa. OBJECTIVE: The aim of this study was to assess patients' experiences that affected acceptability, usefulness, and ease of use with an enhanced VDOT system during monitoring of TB treatment. METHODS: We conducted individual open-ended interviews in a cross-sectional exit qualitative study in Kampala, Uganda. Thirty participants aged 18-65 years who had completed the VDOT randomized trial were purposively selected to represent variability in sex, adherence level, and HIV status. We used a hybrid process of deductive and inductive coding to identify content related to the experience of study participation with VDOT. Codes were organized into themes and subthemes, which were used to develop overarching categories guided by constructs adapted from the modified Technology Acceptance Model for Resource-Limited Settings. We explored participants' experiences regarding the ease of use and usefulness of VDOT, thereby identifying the facilitators and barriers to its acceptability. Perceived usefulness refers to the benefits users expect from the technology, while perceived ease of use refers to how easily users navigate its various features. We adapted by shifting from assessing perceived to experienced constructs. RESULTS: The participants' mean age was 35.3 (SD 12) years. Of the 30 participants, 15 (50%) were females, 13 (43%) had low education levels, and 22 (73%) owned cellphones, of which 10 (45%) had smartphones. Nine (28%) were TB/HIV-coinfected, receiving antiretroviral therapy. Emergent subthemes for facilitators of experienced usefulness and ease of VDOT use were SMS text message reminders, technology training support to patients by health care providers, timely patient-provider communication, family social support, and financial incentives. TB/HIV-coinfected patients reported the added benefit of adherence support for their antiretroviral medication. The external barriers to VDOT's usefulness and ease of use were unstable electricity, technological malfunctions in the app, and lack of cellular network coverage in rural areas. Concerns about stigma, disease disclosure, and fear of breach in privacy and confidentiality affected the ease of VDOT use. CONCLUSIONS: Overall, participants had positive experiences with the enhanced VDOT. They found the enhanced VDOT system user-friendly, beneficial, and acceptable, particularly due to the supportive features such as SMS text message reminders, incentives, technology training by health care providers, and family support. However, it is crucial to address the barriers related to technological infrastructure as well as the privacy, confidentiality, and stigma concerns related to VDOT.

Ethical, Legal, and Sociocultural Issues in the Use of Mobile Technologies and Call Detail Records Data for Public Health in the East African Region: Scoping Review.

BACKGROUND: The exponential scale and pace of real-time data generated from mobile phones present opportunities for new insights and challenges across multiple sectors, including health care delivery and public health research. However, little attention has been given to the new ethical, social, and legal concerns related to using these mobile technologies and the data they generate in Africa. OBJECTIVE: The objective of this scoping review was to explore the ethical and related concerns that arise from the use of data from call detail records and mobile technology interventions for public health in the context of East Africa. METHODS: We searched the PubMed database for published studies describing ethical challenges while using mobile technologies and related data in public health research between 2000 and 2020. A predefined search strategy was used as inclusion criteria with search terms such as "East Africa," "mHealth," "mobile phone data," "public health," "ethics," or "privacy." We screened studies using prespecified eligibility criteria through a two-stage process by two independent reviewers. Studies were included if they were (1) related to mobile technology use and health, (2) published in English from 2000 to 2020, (3) available in full text, and (4) conducted in the East African region. We excluded articles that (1) were conference proceedings, (2) studies presenting an abstract only, (3) systematic and literature reviews, (4) research protocols, and (5) reports of mobile technology in animal subjects. We followed the five stages of a published framework for scoping reviews recommended by Arksey and O'Malley. Data extracted included title, publication year, target population, geographic region, setting, and relevance to mobile health (mHealth) and ethics. Additionally, we used the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) Extension for Scoping Reviews checklist to guide the presentation of this scoping review. The rationale for focusing on the five countries in East Africa was their geographic proximity, which lends itself to similarities in technology infrastructure development. RESULTS: Of the 94 studies identified from PubMed, 33 met the review inclusion criteria for the final scoping review. The 33 articles retained in the final scoping review represent studies conducted in three out of five East African countries: 14 (42%) from Uganda, 13 (39%) from Kenya, and 5 (16%) from Tanzania. Three main categories of concerns related to the use of mHealth technologies and mobile phone data can be conceptualized as (1) ethical issues (adequate informed consent, privacy and confidentiality, data security and protection), (2) sociocultural issues, and (3) regulatory/legal issues. CONCLUSIONS: This scoping review identified major cross-cutting ethical, regulatory, and sociocultural concerns related to using data from mobile technologies in the East African region. A comprehensive framework that accounts for the critical concerns raised would be valuable for guiding the safe use of mobile technology data for public health research purposes.