Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana.

Combining genomic and geospatial data can be useful for understanding Mycobacterium tuberculosis transmission in high-burden tuberculosis (TB) settings. We performed whole-genome sequencing on M. tuberculosis DNA extracted from sputum cultures from a population-based TB study conducted in Gaborone, Botswana, during 2012-2016. We determined spatial distribution of cases on the basis of shared genotypes among isolates. We considered clusters of isolates with ≤5 single-nucleotide polymorphisms identified by whole-genome sequencing to indicate recent transmission and clusters of ≥10 persons to be outbreaks. We obtained both molecular and geospatial data for 946/1,449 (65%) participants with culture-confirmed TB; 62 persons belonged to 5 outbreaks of 10-19 persons each. We detected geospatial clustering in just 2 of those 5 outbreaks, suggesting heterogeneous spatial patterns. Our findings indicate that targeted interventions applied in smaller geographic areas of high-burden TB identified using integrated genomic and geospatial data might help interrupt TB transmission during outbreaks.

Depression, Anxiety, and Cigarette Smoking Among Patients with Tuberculosis.

Smoking adversely affects tuberculosis (TB) outcomes and may be associated with depression and anxiety among people diagnosed with TB in Botswana. We conducted a cross-sectional study among patients newly diagnosed with TB in Gaborone, Botswana, evaluating factors associated with self-reported cigarette smoking. We performed Poisson regression analyses with robust variance to examine whether depressive and anxiety symptoms were associated with smoking. Among 180 participants with TB enrolled from primary health clinics, depressive symptoms were reported in 47 (26.1%) participants and anxiety symptoms were reported in 85 (47.2%) participants. Overall, 45 (25.0%) participants reported current smoking. Depressive symptoms were associated with a higher prevalence of smoking (adjusted prevalence ratio [aPR]: 2.04; 95% confidence interval [CI]: 1.29-3.25) in the adjusted analysis. The association between anxiety symptoms and smoking did not reach statistical significance (aPR: 1.26; 95% CI: 0.77-2.05). Future studies should further investigate these associations when addressing TB care.

Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission.

Identifying host factors that influence infectious disease transmission is an important step toward developing interventions to reduce disease incidence. Recent advances in methods for reconstructing infectious disease transmission events using pathogen genomic and epidemiological data open the door for investigation of host factors that affect onward transmission. While most transmission reconstruction methods are designed to work with densely sampled outbreaks, these methods are making their way into surveillance studies, where the fraction of sampled cases with sequenced pathogens could be relatively low. Surveillance studies that use transmission event reconstruction then use the reconstructed events as response variables (i.e., infection source status of each sampled case) and use host characteristics as predictors (e.g., presence of HIV infection) in regression models. We use simulations to study estimation of the effect of a host factor on probability of being an infection source via this multi-step inferential procedure. Using TransPhylo-a widely-used method for Bayesian estimation of infectious disease transmission events-and logistic regression, we find that low sensitivity of identifying infection sources leads to dilution of the signal, biasing logistic regression coefficients toward zero. We show that increasing the proportion of sampled cases improves sensitivity and some, but not all properties of the logistic regression inference. Application of these approaches to real world data from a population-based TB study in Botswana fails to detect an association between HIV infection and probability of being a TB infection source. We conclude that application of a pipeline, where one first uses TransPhylo and sparsely sampled surveillance data to infer transmission events and then estimates effects of host characteristics on probabilities of these events, should be accompanied by a realistic simulation study to better understand biases stemming from imprecise transmission event inference.

Tuberculosis attributed to transmission within healthcare facilities, Botswana-The Kopanyo Study.

OBJECTIVE: Healthcare facilities are a well-known high-risk environment for transmission of M. tuberculosis, the etiologic agent of tuberculosis (TB) disease. However, the link between M. tuberculosis transmission in healthcare facilities and its role in the general TB epidemic is unknown. We estimated the proportion of overall TB transmission in the general population attributable to healthcare facilities. METHODS: We combined data from a prospective, population-based molecular epidemiologic study with a universal electronic medical record (EMR) covering all healthcare facilities in Botswana to identify biologically plausible transmission events occurring at the healthcare facility. Patients with M. tuberculosis isolates of the same genotype visiting the same facility concurrently were considered an overlapping event. We then used TB diagnosis and treatment data to categorize overlapping events into biologically plausible definitions. We calculated the proportion of overall TB cases in the cohort that could be attributable to healthcare facilities. RESULTS: In total, 1,881 participants had TB genotypic and EMR data suitable for analysis, resulting in 46,853 clinical encounters at 338 healthcare facilities. We identified 326 unique overlapping events involving 370 individual patients; 91 (5%) had biologic plausibility for transmission occurring at a healthcare facility. A sensitivity analysis estimated that 3%-8% of transmission may be attributable to healthcare facilities. CONCLUSIONS: Although effective interventions are critical in reducing individual risk for healthcare workers and patients at healthcare facilities, our findings suggest that development of targeted interventions aimed at community transmission may have a larger impact in reducing TB.

Characterizing tuberculosis transmission dynamics in high-burden urban and rural settings.

Mycobacterium tuberculosis transmission dynamics in high-burden settings are poorly understood. Growing evidence suggests transmission may be characterized by extensive individual heterogeneity in secondary cases (i.e., superspreading), yet the degree and influence of such heterogeneity is largely unknown and unmeasured in high burden-settings. We conducted a prospective, population-based molecular epidemiology study of TB transmission in both an urban and rural setting of Botswana, one of the highest TB burden countries in the world. We used these empirical data to fit two mathematical models (urban and rural) that jointly quantified both the effective reproductive number, [Formula: see text], and the propensity for superspreading in each population. We found both urban and rural populations were characterized by a high degree of individual heterogeneity, however such heterogeneity disproportionately impacted the rural population: 99% of secondary transmission was attributed to only 19% of infectious cases in the rural population compared to 60% in the urban population and the median number of incident cases until the first outbreak of 30 cases was only 32 for the rural model compared to 791 in the urban model. These findings suggest individual heterogeneity plays a critical role shaping local TB epidemiology within subpopulations.

The association of household food insecurity and HIV infection with common mental disorders among newly diagnosed tuberculosis patients in Botswana.

OBJECTIVE: To determine the association between food insecurity and HIV infection with depression and anxiety among new tuberculosis (TB) patients. DESIGN: Our cross-sectional study assessed depression, anxiety and food insecurity with Patient Health Questionnaire (PHQ-9), Zung Anxiety Self-Assessment Scale (ZUNG) and Household Food Insecurity Access Scale, respectively. Poisson regression models with robust variance were used to examine correlates of depression (PHQ-9 ≥ 10) and anxiety (ZUNG ≥ 36). SETTING: Gaborone, Botswana. PARTICIPANTS: Patients who were newly diagnosed with TB. RESULTS: Between January and December 2019, we enrolled 180 TB patients from primary health clinics in Botswana. Overall, 99 (55·0 %) were HIV positive, 47 (26·1 %), 85 (47·2 %) and 69 (38·5 %) indicated depression, anxiety and moderate to severe food insecurity, respectively. After adjusting for potential confounders, food insecurity was associated with a higher prevalence of depression (adjusted prevalence ratio (aPR) = 2·30; 95 % CI 1·40, 3·78) and anxiety (aPR = 1·41; 95 % CI 1·05, 1·91). Prevalence of depression and anxiety was similar between HIV-infected and HIV-uninfected participants. Estimates remained comparable when restricted to HIV-infected participants. CONCLUSIONS: Mental disorders may be affected by food insecurity among new TB patients, regardless of HIV status.

Vulvar cancer in Botswana in women with and without HIV infection: patterns of treatment and survival outcomes.

OBJECTIVES: Vulvar cancer is a rare gynecological malignancy. However, the incidence of human papillomavirus (HPV)-associated vulvar disease is increasing, particularly in low- and middle-income countries. HIV infection is associated with an increased risk of HPV-associated vulvar cancer. We evaluated treatment patterns and survival outcomes in a cohort of vulvar cancer patients in Botswana. The primary objective of this study was to determine overall survival and the impact of treatment modality, stage, and HIV status on overall survival. METHODS: Women with vulvar cancer who presented to oncology care in Botswana from January 2015 through August 2019 were prospectively enrolled in this observational cohort study. Demographics, clinical characteristics, treatment, and survival data were collected. Factors associated with survival including age, HIV status, stage, and treatment were evaluated. RESULTS: Our cohort included 120 women with vulvar cancer. Median age was 42 (IQR 38-47) years. The majority of patients were living with HIV (89%, n=107) that was well-controlled on antiretroviral treatment. Among women with HIV, 54.2% (n=58) were early stage (FIGO stage I/II). In those without HIV, 46.2% (n=6) were early stage (stage I/II). Of the 95 (79%) patients who received treatment, 20.8% (n=25) received surgery, 67.5% (n=81) received radiation therapy, and 24.2% (n=29) received chemotherapy, either alone or in combination. Median follow-up time of all patients was 24.7 (IQR 14.2-39.1) months and 2- year overall survival for all patients was 74%. Multivariate analysis demonstrated improved survival for those who received surgery (HR 0.26; 95% CI 0.08 to 0.86) and poor survival was associated with advanced stage (HR 2.56; 95% CI 1.30 to 5.02). Survival was not associated with HIV status. CONCLUSIONS: The majority of women with vulvar cancer in Botswana are young and living with HIV infection. Just under half of patients present with advanced stage, which was associated with worse survival. Improved survival was seen for those who received surgery.

Five-year overall survival following chemoradiation therapy for locally advanced cervical carcinoma in women living with and without HIV infection in Botswana.

PURPOSE: To compare updated prospective 5-year survival outcomes of cervical cancer patients living with and without human immunodeficiency virus (HIV) infection who initiated curative chemoradiation therapy (CRT) in a resource-limited setting. METHODS & MATERIALS: Women in Botswana with locally advanced cervical cancer were enrolled in a prospective, observational, cohort study from July 2013 through January 2015. Survival outcomes were analyzed after 5 years of follow-up. RESULTS: This cohort included 143 women initiating curative CRT. Sixty-seven percent (n = 96) of cohort were women living with HIV (WLWH), all of whom were receiving antiretroviral therapy (ART) at the time of treatment initiation and boasted a median CD4 count of 481 cells/µL (IQR, 351-579 µL). The 5-year overall survival (OS) rates were 56.8% (95% CI, 40.0-70.5%) for patients without HIV infection and 55.1% (95% CI, 44.2-64.7%) for WLWH (p = 0.732). Factors associated with superior 5-year OS on multivariate analyses included baseline hemoglobin > 10 g/dL (hazard ratio (HR) 0.90, 95% CI, 0.83-0.98, p = 0.015), lower stage at diagnosis (stage I and II vs. III and IV) (HR 1.39, 95% CI 1.09-1.76, p = 0.007), and higher EQD2 (HR 0.98, 95% CI 0.97-0.99, p = 0.001). CONCLUSIONS: Five-year OS was not impacted by HIV status in this population of WLWH with well-managed infection who initiated curative treatment for cervical cancer in Botswana. Regardless of HIV status, hemoglobin levels and stage at diagnosis were associated with survival. These findings suggest that treatment for cervical cancer in WLWH with well-controlled infection need not be altered solely due to HIV status.

Chemoradiation versus radiation alone in stage IIIB cervical cancer patients with or without human immunodeficiency virus.

OBJECTIVE: Cervical cancer remains the most common cancer among women in sub-Saharan Africa and is also a leading cause of cancer related deaths among these women. The benefit of chemoradiation in comparison with radiation alone for patients with stage IIIB disease has not been evaluated prospectively in women living with human immunodeficiency virus (HIV). We assessed the survival of chemoradiation versus radiation alone among stage IIIB cervical cancer patients based on HIV status. METHODS: Between February 2013 and June 2018, patients with International Federation of Gynecology and Obstetrics (FIGO) 2009 stage IIIB cervical cancer with or without HIV and treated with chemoradiation or radiation alone, were prospectively enrolled in an observational cohort study. Overall survival was evaluated using the Kaplan-Meier method. Cox proportional hazards modeling was used to analyze associations with survival. RESULTS: Among 187 patients, 63% (n=118) of women had co-infection with HIV, and 48% (n=69) received chemoradiation. Regardless of HIV status, patients who received chemoradiation had improved 2 year overall survival compared with those receiving radiation alone (59% vs 41%, p<0.01), even among women living with HIV (60% vs 38%, p=0.02). On multivariable Cox regression analysis, including all patients regardless of HIV status, 2 year overall survival was associated with receipt of chemoradiation (hazard ratio (HR) 0.63, p=0.04) and total radiation dose ≥80 Gy (HR 0.57, p=0.02). Among patients who received an adequate radiation dose of ≥80 Gy, adjusted overall survival rates were similar between chemoradiation versus radiation alone groups (HR 1.07; p=0.90). However, patients who received an inadequate radiation dose of <80 Gy, adjusted survival was significantly higher in chemoradiation versus radiation alone group (HR 0.45, p=0.01). CONCLUSIONS: Addition of chemotherapy to standard radiation improved overall survival, regardless of HIV status, and is even more essential in women who cannot receive full doses of radiation.

Population-Based Geospatial and Molecular Epidemiologic Study of Tuberculosis Transmission Dynamics, Botswana, 2012-2016.

Tuberculosis (TB) elimination requires interrupting transmission of Mycobacterium tuberculosis. We used a multidisciplinary approach to describe TB transmission in 2 sociodemographically distinct districts in Botswana (Kopanyo Study). During August 2012-March 2016, all patients who had TB were enrolled, their sputum samples were cultured, and M. tuberculosis isolates were genotyped by using 24-locus mycobacterial interspersed repetitive units-variable number of tandem repeats. Of 5,515 TB patients, 4,331 (79%) were enrolled. Annualized TB incidence varied by geography (range 66-1,140 TB patients/100,000 persons). A total of 1,796 patient isolates had valid genotyping results and residential geocoordinates; 780 (41%) patients were involved in a localized TB transmission event. Residence in areas with a high burden of TB, age <24 years, being a current smoker, and unemployment were factors associated with localized transmission events. Patients with known HIV-positive status had lower odds of being involved in localized transmission.

Management of Head and Neck Cancers With or Without Comorbid HIV Infection in Botswana.

OBJECTIVES/HYPOTHESIS: Head and neck cancer (HNC) is the fifth most common malignancy in sub-Saharan Africa, a region with hyperendemic human immunodeficiency virus (HIV)-infection. HIV patients have higher rates of HNC, yet the effect of HIV-infection on oncologic outcomes and treatment toxicity is poorly characterized. STUDY DESIGN: Prospective observational cohort study. METHODS: HNC patients attending a government-funded oncology clinic in Botswana were prospectively enrolled in an observational cohort registry from 2015 to 2019. Clinical characteristics were analyzed via Cox proportional hazards and logistic regression followed by secondary analysis by HIV-status. Overall survival (OS) was evaluated via Kaplan-Meier. RESULTS: The study enrolled 149 patients with a median follow-up of 23 months. Patients presented with advanced disease (60% with T4-primaries), received limited treatment (19% chemotherapy, 8% surgery, 29% definitive radiation [RT]), and had delayed care (median time from diagnosis to RT of 2.5 months). Median OS was 36.2 months. Anemia was associated with worse survival (HR 2.74, P = .001). Grade ≥ 3 toxicity rate with RT was 30% and associated with mucosal subsite (OR 4.04, P = .03) and BMI < 20 kg/m2 (OR 6.04, P = .012). Forty percent of patients (n = 59) were HIV-infected; most (85%) were on antiretroviral therapy, had suppressed viral loads (90% with ≤400 copies/mL), and had immunocompetent CD4 counts (median 400 cells/mm3 ). HIV-status was not associated with decreased receipt or delays of definitive RT, worse survival, or increased toxicity. CONCLUSIONS: Despite access to government-funded care, HNC patients in Botswana present late and have delays in care, which likely contributes to suboptimal survival outcomes. While a disproportionate number has comorbid HIV infection, HIV-status does not adversely affect outcomes. LEVEL OF EVIDENCE: 2c Laryngoscope, 131:E1558-E1566, 2021.

Differences in Outcomes of Chemoradiation in Women With Invasive Cervical Cancer by Human Immunodeficiency Virus Status: A Systematic Review.

PURPOSE: Cervical cancer is one of the leading causes of cancer death among women worldwide, and women living with human immunodeficiency virus (HIV) carry the highest burden of disease. Chemoradiation (CRT) is the current standard treatment for locally advanced cervical cancer, without specific treatment modifications based on HIV status. This systematic review evaluates existing literature reporting differences in outcomes between HIV+ and HIV- women with invasive cervical cancer treated with CRT. METHODS AND MATERIALS: Searches were conducted through Pubmed, Ovid MEDLINE, Embase, Scopus, Web of Science, and Cochrane Library. Two researchers independently conducted article selection; articles were selected by title, then abstract, and then by full text content. Data were extracted using a structured form. RESULTS: Thirteen articles were included in the analysis, all of which were either retrospective or prospective cohort studies published between 2012 and 2018, and most of which were conducted in Sub-Saharan Africa. Treatment outcomes included treatment response, survival, toxicities, and quality of life. The majority of studies (8 of 13) reported no differences in treatment outcomes by HIV status. Out of 8 studies that assessed survival, 6 reported no significant difference based on HIV status. All 4 studies assessing treatment response found no significant differences based on HIV status. Among 6 studies primarily assessing treatment toxicity, 3 showed no differences based on HIV status. Factors affecting treatment outcomes, such as treatment selection bias, pretreatment hemoglobin levels, and antiretroviral therapy administration, were not systematically accounted for. CONCLUSIONS: The majority of studies analyzed showed no differences in treatment outcomes, including overall toxicity, treatment response, or mortality, on the basis of HIV infection status. These results suggest CRT should continue to be the treatment of choice for locally invasive cervical cancer regardless of HIV status. Further study is required to more precisely account for other variables that influence treatment outcome.

Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer.

INTRODUCTION: We characterized the cervical 16S rDNA microbiome of patients in Botswana with high-grade cervical dysplasia and locally advanced cervical cancer. METHODS: This prospective study included 31 patients: 21 with dysplasia and 10 with cancer. The Shannon diversity index was used to evaluate alpha (intra-sample) diversity, while the UniFrac (weighted and unweighted) and Bray-Curtis distances were employed to evaluate beta (inter-sample) diversity. The relative abundance of microbial taxa was compared among samples using linear discriminant analysis effect size. RESULTS: Alpha diversity was significantly higher in patients with cervical cancer than in patients with cervical dysplasia (P<0.05). Beta diversity also differed significantly (weighted UniFrac Bray-Curtis, P<0.01). Neither alpha diversity (P=0.8) nor beta diversity (P=0.19) varied by HIV status. The results of linear discriminant analysis effect size demonstrated that multiple taxa differed significantly between patients with cervical dysplasia vs cancer. Lachnospira bacteria (in the Clostridia class) were particularly enriched among cervical dysplasia patients, while Proteobacteria (members of the Firmicutes phyla and the Comamonadaceae family) were enriched in patients with cervical cancer. DISCUSSION: The results of our study suggest that differences exist in the diversity and composition of the cervical microbiota between patients with cervical dysplasia and patients with cervical cancer in Botswana. Additional studies are warranted to validate these findings and elucidate their clinical significance among women living in sub-Saharan Africa, as well as other regions of the world.

Association Between CD4 Count and Chemoradiation Therapy Outcomes Among Cervical Cancer Patients With HIV.

BACKGROUND: In Botswana, nearly two-thirds of cervical cancer patients are HIV-positive. This study examined the relationship between CD4 count and chemoradiation therapy outcomes among cervical cancer patients with HIV. SETTING: A prospective cohort study of 231 HIV-positive women with locally invasive cervical cancer was conducted in Gaborone, Botswana from January 2015 to February 2018. METHODS: Primary outcome was survival, defined as time from scheduled end of chemoradiation therapy to death or last contact with patient. Nadir CD4 count was defined as lowest CD4 available before cancer diagnosis. Delta CD4 count was defined as improvement from nadir CD4 to CD4 at cancer diagnosis. Hazard ratio (HR) analyses were adjusted for presenting variables (age, baseline hemoglobin, cancer stage, and performance status) and treatment variables (chemotherapy cycles and radiation dose). RESULTS: Two hundred thirty-one patients were included in nadir CD4 analysis; 139 were included in delta CD4 analysis. Higher delta CD4 was significantly associated with reduced mortality after adjusting for presenting and treatment variables (CD4 100-249: HR 0.45, 95% CI: 0.21 to 0.95; CD4 ≥250: HR 0.45, 95% CI: 0.20 to 1.02). Higher nadir CD4 showed a trend toward reduced mortality after adjusting for presenting and treatment variables (HR 0.94, 95% CI: 0.84 to 1.06). CONCLUSIONS: Higher delta CD4 (greater improvement from nadir CD4 to CD4 at cervical cancer diagnosis) is significantly associated with lower mortality. Although not statistically significant, data suggest that higher nadir CD4 may reduce mortality. These results reinforce the importance of early HIV diagnosis and antiretroviral therapy initiation, as their effects influence cervical cancer outcomes years later.

The theory of planned behavior as a behavior change model for tobacco control strategies among adolescents in Botswana.

BACKGROUND: Behavioral intentions (motivational factors), attitudes, subjective norm (social pressures), and perceived behavioral control promote or discourage smoking behavior among adolescents. OBJECTIVE: To assess students' behavioral intentions, attitudes, subjective norms and perceived behavioral control on smoking using the Theory of Planned Behavior. The prevalence of smoking among the adolescents is also calculated. METHODS: In this cross-sectional study, structured self-administered questionnaires were used to collect data from adolescents in primary and secondary schools. Data on demographics, behavioral intentions, attitudes, subjective norms, and perceived behavioral control towards smoking were collected. Pearson product moment correlations and logistic regression models were used to determine factors associated with current smoking. RESULTS: A total sample of 2554 (mean age = 15; Range = 12-18 years) students participated in the study. Twenty-nine percent (n = 728) of the students had tried smoking at least once. Smoking was predicted by attitudes, subjective norms, perceived behavioral control and intention.There was a strong association between having a parent or guardian, caregiver or close friend who smoked (p < 0.001) and being a smoker. The majority of students (57%) conveyed that adults talked to them about the harmful effects of cigarette smoking and 50% had discussed smoking concerns with their friends. Students who had positive attitudes towards smoking like "smoking makes you confident" were more likely to be current smokers (OR: 1.63, 95% CI: 1.03-2.59). The feeling or conviction that they could refuse a cigarette if offered was an impediment from smoking (OR: 0.18, 95% CI: 0.13-0.26). CONCLUSIONS: Attitudes, subjective norms, and perceived behavioral control contributed significantly to the students' smoking. Right attitudes must be cultivated and behavioral control must be strengthened for early effective interventions to curtail smoking among adolescents.

Possible Transmission Mechanisms of Mixed Mycobacterium tuberculosis Infection in High HIV Prevalence Country, Botswana.

Tuberculosis caused by concurrent infection with multiple Mycobacterium tuberculosis strains (i.e., mixed infection) challenges clinical and epidemiologic paradigms. We explored possible transmission mechanisms of mixed infection in a population-based, molecular epidemiology study in Botswana during 2012-2016. We defined mixed infection as multiple repeats of alleles at >2 loci within a discrete mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) result. We compared mixed infection MIRU-VNTR results with all study MIRU-VNTR results by considering all permutations at each multiple allele locus; matched MIRU-VNTR results were considered evidence of recently acquired strains and nonmatched to any other results were considered evidence of remotely acquired strains. Among 2,051 patients, 34 (1.7%) had mixed infection, of which 23 (68%) had recently and remotely acquired strains. This finding might support the mixed infection mechanism of recent transmission and simultaneous remote reactivation. Further exploration is needed to determine proportions of transmission mechanisms in settings where mixed infections are prevalent.

A Neighbor-Based Approach to Identify Tuberculosis Exposure, the Kopanyo Study.

Contact investigation is one public health measure used to prevent tuberculosis by identifying and treating persons exposed to Mycobacterium tuberculosis. Contact investigations are a major tenet of global tuberculosis elimination efforts, but for many reasons remain ineffective. We describe a novel neighbor-based approach to reframe contact investigations.