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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.

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.

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. UsingTransPhylo— 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 usesTransPhyloand 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.Author summaryFactors that affect infectious disease transmission are poorly understood, which impede efforts to prevent the spread of infectious diseases. Recently, software packages have been developed to infer transmission histories of infectious disease outbreaks using data from infectious disease genetics and epidemiology. These software packages have been used as part of methods to identify individual characteristics that affect infectious disease transmission. We used computer simulation to explore whether a statistical pipeline using the software packageTransPhylocan successfully identify individual risk factors for being an infection source in a realistic public health setting where only a small proportion of pathogens are sequenced. We simulated tuberculosis (TB) outbreaks with different odds of being an infection source for TB transmission between people living with and without HIV. We found that theTransPhylo-based pipeline consistently underestimated the odds ratio for the association between HIV and being an infection source for TB transmission. We then applied this method to data from a TB study from Botswana and found no evidence of an association between HIV and being an infection source for TB transmission. Identification of transmission risk factors may be difficult in settings with low sampling proportion for genetic data.

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

IntroductionCombining genomic and geospatial data can be useful for understanding Mycobacterium tuberculosis (Mtb) transmission in high tuberculosis burden settings.MethodsWe performed whole genome sequencing (WGS) on Mtb DNA extracted from sputum cultures from a population-based tuberculosis study conducted in 2012–2016 in Gaborone, Botswana. We used kernel density estimation, spatial K-functions, and created spatial distributions of phylogenetic trees. WGS-based clusters of isolates ≤5 single nucleotide polymorphisms were considered recent transmission, and large WGS-based clusters (≥10 members) were considered outbreaks.ResultsWe analyzed data from 1449 participants with culture-confirmed TB. Among these, 946 (65%) participants had both molecular and geospatial data. A total of 62 belonged to five large outbreaks (10–19 participants each). Geospatial clustering was detected in two of the five large outbreaks, suggesting heterogeneous spatial patterns within the community.ConclusionsIntegration of genomic and geospatial data identified distinct patterns of tuberculosis transmission in a high-tuberculosis burden setting. Targeted interventions in these smaller geographies may interrupt on-going transmission.

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.

HIV co-infection has been shown to be associated with lower tuberculosis (TB) bacterial load in studies conducted prior to widespread availability of antiretroviral therapy (ART). We investigated associations between HIV co-infection and TB bacterial load, accounting for differences in time to TB diagnosis, in a high prevalence setting with widespread ART use. In Gaborone, Botswana, 268 sputum samples from people with newly diagnosed TB were tested with Xpert MTB/RIF Ultra (Xpert). TB bacterial load and time to TB diagnosis were estimated using mean Xpert cycle threshold (CT) and symptom duration, respectively. Multiple linear regression models and causal mediation analysis were used to determine the associations between HIV and Xpert CT and assess the mediating effect of symptom duration. Mean CT values were higher in people living with HIV compared to people without HIV (22.7 vs 20.3, p < 0.001). Among those living with HIV, there was a negative relationship between CD4 count and mean CT value (Spearman’s rho -0.20, p = 0.06). After controlling for gender, age, and symptom duration, HIV status remained associated with CT value, with an average increase of 1.6 cycles (p = 0.009) among people with HIV and CD4 count > 200 cells/mm3and 2.1 cycles (p = 0.002) in those with a CD4 count ≤ 200 cells/mm3compared to individuals without HIV. Symptom duration was also found to be associated with CT value (p < 0.05). We found an indirect effect of HIV status on Xpert CT through the mediator, symptom duration (β = 0.33, p = 0.048), accounting for 13.5% of the relationship. Our findings suggest that time to TB diagnosis partially mediates the relationship between HIV status and CT value, but differences in pathophysiology between people with and without HIV likely play a dominant role in affecting TB bacterial burden.

Comorbidity of tuberculosis (TB) and depression may lead to delayed TB treatment initiation. A cross sectional study was conducted between January and December 2019 to examine the association between depression and delayed TB treatment initiation among newly diagnosed TB patients in Botswana. We used the Patient Health Questionnaire-9 and the ZUNG self-rating anxiety scale to assess depressive and anxiety symptoms, respectively. Delayed TB treatment was defined as experiencing common TB symptoms for more than 2 months before treatment initiation. We used Poisson regression models with robust variance to assess the association between covariates and delayed treatment initiation. Majority of the enrolled 180 study participants were males (n =116, 64.4%). Overall, 99 (55%) were co-infected with HIV; depression and anxiety symptoms were reported by 47.2% and 38.5% of the participants respectively. The prevalence of delayed TB treatment was 42.6% and 18.8% among participants who indicated symptoms of depression and among participants without depression respectively. After adjusting for age, HIV status, gender and anxiety symptoms, depression was still associated with delayed TB treatment (adjusted prevalence ratio [aPR] = 2.09; 95% CI = 1.23–3.57). Integrating management of depressive symptoms during TB treatment may help in improving overall TB treatment outcomes.

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.

BackgroundResearchers have increasingly recognized the adverse effects of smoking on tuberculosis (TB) outcomes. Smoking may be a maladaptive coping mechanism for depression and anxiety among TB patients; however, this association has not yet been investigated.Design/MethodsWe conducted a cross-sectional study among newly diagnosed TB patients between January and December 2019 in Gaborone, Botswana, and evaluated factors associated with cigarette smoking. Using the Patient Health Questionnaire-9 and the Zung Self-Rating Anxiety scale, we collected depression and anxiety scores, respectively; scores of ≥10 indicate depression and scores of ≥36 indicate anxiety. We performed Poisson regression analyses with robust variance to examine whether depression and anxiety were associated with smoking.ResultsOne hundred and eighty participants with TB were enrolled from primary health clinics. Among all enrollees, depression was reported in 46 (27.1%) participants, while anxiety was reported in 60 (44.4%) participants. Overall, 45 (25.0%) participants reported current smoking, and the median number of cigarettes per day was 10. Depressive symptoms were associated with a higher prevalence of smoking (aPR: 1.82; 95% CI = 1.11, 3.01) after adjusting for sex, HIV status, food insecurity, anxiety, and income. The association between anxiety symptoms and cigarette smoking did not reach statistical significance (aPR 1.26; 95% CI: 0.78-2.05).ConclusionsWe found the association between depressive symptoms and smoking among TB patients in Botswana to be significant and the association between anxiety symptoms and cigarette smoking insignificant. Future studies should further investigate these associations when addressing TB care.

Background Reduced ethambutol serum concentrations are commonly observed among TB patients co-infected with HIV and may lead to treatment failure. Objectives To perform a population pharmacokinetic study of ethambutol in HIV/TB patients, and to evaluate an intensified ethambutol weight-based dosing strategy to support pharmacokinetic target attainment. Methods We conducted a prospective study of ethambutol pharmacokinetics among HIV/TB patients administered first-line TB treatment in Botswana, with study visits before and after initiation of ART. Clinical and disease status markers, including HIV-associated systemic immune activation and gut dysfunction biomarkers, were evaluated as covariates of ethambutol pharmacokinetic parameters in non-linear mixed effects analysis. Monte Carlo simulations were performed to compare pharmacokinetic target attainment under standard and intensified weight-based ethambutol dosing strategies. Results We studied 40 HIV/TB patients prior to initiation of ART, of whom 24 returned for a second visit a median of 33 days following ART initiation. Ethambutol serum concentrations were best explained by a two-compartment model with first-order elimination, with a significant improvement in oral bioavailability following ART initiation. In Monte Carlo simulations, a supplementary ethambutol dose of 400 mg daily led to >2-fold improvements in pharmacokinetic target attainment probabilities in lung tissue, both before and after ART initiation. Conclusions Low serum ethambutol concentrations were commonly observed among HIV/TB patients in Botswana, and the oral bioavailability of ethambutol increased following ART initiation. Supplementary ethambutol dosing among HIV/TB patients may provide a strategy to optimize anti-TB treatment regimens in this high-risk population.

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.

Objectives: Pyrazinamide is a key drug in the first-line treatment regimen for tuberculosis, with a potent sterilizing effect. Although low pyrazinamide peak serum concentrations (Cmax) are associated with poor treatment outcomes, many resource-constrained settings do not have sufficient laboratory capacity to support therapeutic drug monitoring (TDM). The objective of this study was to determine whether a colorimetric test of urine can identify tuberculosis patients with adequate pyrazinamide exposures, as defined by serum Cmax above a target threshold. Methods: In the derivation study of healthy volunteers, three dose sizes of pyrazinamide were evaluated, and intensive pharmacokinetic blood sampling was performed over an 8-h period, with a timed urine void at 4 h post-dosing. Pyrazinamide in urine was isolated by spin column centrifugation with an exchange resin, followed by colorimetric analysis; the absorbance peak at 495 nm was measured. The urine assay was then evaluated in a study of 39 HIV/tuberculosis patients in Botswana enrolled in an intensive pharmacokinetic study. Receiver operating characteristics (ROC) curves were used to measure diagnostic accuracy. The guideline-recommended pyrazinamide serum Cmax target of 35 mg/l was evaluated in the primary analysis; this target was found to be predictive of favorable outcomes in a clinical study. Following this, a higher serum Cmax target of 58 mg/l was evaluated in the secondary analysis. Results: At the optimal cut-off identified in the derivation sample, the urine colorimetric assay was 97% sensitive and 50% specific to identify 35 of 39 HIV/tuberculosis patients with pharmacokinetic target attainment, with an area under the ROC curve of 0.81 (95% confidence interval 0.60–0.97). Diagnostic accuracy was lower at the 58 mg/l serum Cmax target, with an area under the ROC curve of 0.68 (95% confidence interval 0.48–0.84). Men were less likely than women to attain either serum pharmacokinetic target. Conclusions: The urine colorimetric assay was sensitive but not specific for the detection of adequate pyrazinamide pharmacokinetic exposures among HIV/tuberculosis patients in a high-burden setting. Keywords: Tuberculosis, Pyrazinamide, Pharmacokinetics, Human immunodeficiency virus, Point-of-care testing

During 2012–2015, 10 of 24 patients infected with matching genotypes of Mycobacterium tuberculosis received care at the same hospital in Gaborone, Botswana. Nosocomial transmission was initially suspected, but we discovered plausible sites of community transmission for 20 (95%) of 21 interviewed patients. Active case-finding at these sites could halt ongoing transmission.

Multidrug-resistant tuberculosis (TB) is an alarming threat, and targeted deep sequencing (DS) may be an effective method for rapid identification of drug-resistant profiles, including detection of heteroresistance. We evaluated the sensitivity and specificity of targeted DS versus phenotypic drug susceptibility testing (pDST) among patients starting first-line anti-TB therapy in Botswana. Overall, we found high concordance between DS and pDST. Lower sensitivity of DS, which targets established high-confidence resistance variants, was observed for detecting isoniazid resistance among HIV-infected patients.

Mycobacterium tuberculosis complex (MTBC) is divided into several major phylogenetic lineages, with differential distribution globally. Using population-based data collected over a three year period, we performed 24-locus Mycobacterial Interspersed Repeat Unit – Variable Number Tandem Repeat (MIRU-VNTR) genotyping on all culture isolates from two districts of the country that differ in tuberculosis (TB) incidence (Gaborone, the capital, and Ghanzi in the Western Kalahari). The study objective was to characterize the molecular epidemiology of TB in these districts. Overall phylogenetic diversity mirrored that reported from neighboring Republic of South Africa, but differences in the two districts were marked. All four major lineages of M. tuberculosis were found in Gaborone, but only three of the four major lineages were found in Ghanzi. Strain diversity was lower in Ghanzi, with a large proportion (38%) of all isolates having an identical MIRU-VNTR result, compared to 6% of all isolates in Gaborone with the same MIRU-VNTR result. This study demonstrates localized differences in strain diversity by two districts in Botswana, and contributes to a growing characterization of MTBC diversity globally.

BackgroundDolutegravir (DTG) has recently been recommended as a preferred first-line regimen for the treatment of new and treatment-experienced HIV-infected patients. However, potential drug interactions between DTG and rifampicin remain a clinical and public health concern.MethodsWe analyzed HIV and Tuberculosis (TB) treatment outcomes of HIV-infected patients concomitantly receiving rifampicin- and DTG-based regimens under programmatic conditions in Botswana. The outcomes of interest were successful TB treatment and viral load suppression. We used multivariable logistic models to determine predictors for each outcome of interest.ResultsA total of 1225 patients were included in the analysis to evaluate predictors of successful TB outcome. Among patients on DTG and non-DTG regimens, 90.9% and 88.3% achieved favorable TB treatment outcomes, respectively. Of those who received DTG-based regimen; 44% received once-daily dosing and 53% twice-daily dosing. We found that DTG was associated with favorable TB treatment outcome (adjusted odds ratio = 1.56; 95% confidence interval = 1.06 to 2.31), after adjusting for age, gender, and CD4 cell counts. High rates of viral load suppression were found across all antiretroviral therapy (ART) regimen categories (>92% for all). We did not find an independent association between DTG and viral suppression after adjustment of other covariates.ConclusionsThe use of DTG-based ART regimens in patients coinfected with TB and HIV lead to favorable TB and HIV treatment outcomes, comparable to those achieved with alternative ART regimens. Our results provide reassurance to TB and HIV programs about the overall programmatic concomitant use of these first-line treatment regimens for the management of HIV and TB coinfected patients.

Cancer patients are at higher risk of tuberculosis (TB) infection, especially in hospital settings with high TB/HIV burden. The study was implemented among adult patients admitted to the largest tertiary-level referral hospital in Botswana. We estimated the TB prevalence at admission and the rate of newly diagnosed TB after hospitalization in the medical and oncology wards, separately. Presumptive TB cases were identified at admission through symptom screening and underwent the diagnostic evaluation through GeneXpert. Patients with no evidence of TB were followed-up until TB diagnosis or the end of the study. In the medical and oncology wards, four of 867 admitted patients and two of 240 had laboratory-confirmed TB at admission (prevalence = 461.4 and 833.3 per 100,000, respectively.) The post-admission TB rate from the medical wards was 28.3 cases per 1,000 person-year during 424.5 follow-up years (post-admission TB rate among HIV-positive versus. -negative = 54.1 and 9.8 per 1,000 person-year, respectively [Rate Ratio = 5.5]). No post-admission TB case was detected from the oncology ward. High rates of undetected TB at admission at both medical and oncology wards, and high rate of newly diagnosed TB after admission at medical wards suggest that TB screening and diagnostic evaluation should target all patients admitted to a hospital in high-burden settings.

Aminoglycosides such as amikacin continue to be part of the backbone of treatment of multidrug-resistant tuberculosis (MDR-TB). We measured amikacin concentrations in 28 MDR-TB patients in Botswana receiving amikacin therapy together with oral levofloxacin, ethionamide, cycloserine, and pyrazinamide and calculated areas under the concentration-time curves from 0 to 24 h (AUC 0–24 ). The patients were followed monthly for sputum culture conversion based on liquid cultures. The median duration of amikacin therapy was 184 (range, 28 to 866) days, at a median dose of 17.30 (range 11.11 to 19.23) mg/kg. Only 11 (39%) patients had sputum culture conversion during treatment; the rest failed. We utilized classification and regression tree analyses (CART) to examine all potential predictors of failure, including clinical and demographic features, comorbidities, and amikacin peak concentrations ( C max ), AUC 0–24 , and trough concentrations. The primary node for failure had two competing variables, C max of 0–24 of 41 kg was a secondary node with a score of 35% relative to the primary node. The area under the receiver operating characteristic curve for the CART model was an R 2 = 0.90 on posttest. In patients weighing >41 kg, sputum conversion was 3/3 (100%) in those with an amikacin C max of ≥67 mg/liter versus 3/15 (20%) in those with a C max of C max and AUC 0–24 below the threshold, 7/7 (100%) failed, compared to 7/15 (47%) of those who had these parameters above threshold (RR = 2.14; 95% CI, 1.25 to 43.68). These amikacin dose-schedule patterns and exposures are virtually the same as those identified in the hollow-fiber system model.

BACKGROUND: Heteroresistant Mycobacterium tuberculosis infections (defined as concomitant infection with drug-resistant and drug-susceptible strains) may explain the higher risk of poor tuberculosis treatment outcomes observed among patients with mixed-strain M. tuberculosis infections. We investigated the clinical effect of mixed-strain infections while controlling for pretreatment heteroresistance in a population-based sample of patients with tuberculosis starting first-line tuberculosis therapy in Botswana. METHODS: We performed 24-locus mycobacterial interspersed repetitive unit–variable number tandem-repeat analysis and targeted deep sequencing on baseline primary cultured isolates to detect mixed infections and heteroresistance, respectively. Drug-sensitive, micro-heteroresistant, macro-heteroresistant, and fixed-resistant infections were defined as infections in which the frequency of resistance was

Item does not contain fulltext BACKGROUND: Treatment outcomes for multidrug-resistant tuberculosis remain poor. We aimed to estimate the association of treatment success and death with the use of individual drugs, and the optimal number and duration of treatment with those drugs in patients with multidrug-resistant tuberculosis. METHODS: In this individual patient data meta-analysis, we searched MEDLINE, Embase, and the Cochrane Library to identify potentially eligible observational and experimental studies published between Jan 1, 2009, and April 30, 2016. We also searched reference lists from all systematic reviews of treatment of multidrug-resistant tuberculosis published since 2009. To be eligible, studies had to report original results, with end of treatment outcomes (treatment completion [success], failure, or relapse) in cohorts of at least 25 adults (aged >18 years). We used anonymised individual patient data from eligible studies, provided by study investigators, regarding clinical characteristics, treatment, and outcomes. Using propensity score-matched generalised mixed effects logistic, or linear regression, we calculated adjusted odds ratios and adjusted risk differences for success or death during treatment, for specific drugs currently used to treat multidrug-resistant tuberculosis, as well as the number of drugs used and treatment duration. FINDINGS: Of 12 030 patients from 25 countries in 50 studies, 7346 (61%) had treatment success, 1017 (8%) had failure or relapse, and 1729 (14%) died. Compared with failure or relapse, treatment success was positively associated with the use of linezolid (adjusted risk difference 0.15, 95% CI 0.11 to 0.18), levofloxacin (0.15, 0.13 to 0.18), carbapenems (0.14, 0.06 to 0.21), moxifloxacin (0.11, 0.08 to 0.14), bedaquiline (0.10, 0.05 to 0.14), and clofazimine (0.06, 0.01 to 0.10). There was a significant association between reduced mortality and use of linezolid (-0.20, -0.23 to -0.16), levofloxacin (-0.06, -0.09 to -0.04), moxifloxacin (-0.07, -0.10 to -0.04), or bedaquiline (-0.14, -0.19 to -0.10). Compared with regimens without any injectable drug, amikacin provided modest benefits, but kanamycin and capreomycin were associated with worse outcomes. The remaining drugs were associated with slight or no improvements in outcomes. Treatment outcomes were significantly worse for most drugs if they were used despite in-vitro resistance. The optimal number of effective drugs seemed to be five in the initial phase, and four in the continuation phase. In these adjusted analyses, heterogeneity, based on a simulated I(2) method, was high for approximately half the estimates for specific drugs, although relatively low for number of drugs and durations analyses. INTERPRETATION: Although inferences are limited by the observational nature of these data, treatment outcomes were significantly better with use of linezolid, later generation fluoroquinolones, bedaquiline, clofazimine, and carbapenems for treatment of multidrug-resistant tuberculosis. These findings emphasise the need for trials to ascertain the optimal combination and duration of these drugs for treatment of this condition. FUNDING: American Thoracic Society, Canadian Institutes of Health Research, US Centers for Disease Control and Prevention, European Respiratory Society, Infectious Diseases Society of America.

Author(s): Shin, SS; Modongo, C; Zetola, NM; Wang, Q; Phologolo, T; Kestler, M; Ho-Foster, A | Abstract: ObjectiveTo compare daily exposure to tuberculosis (TB) patients between HIV-infected and non-HIV-infected health care workers (HCWs), and examine the uptake of antiretroviral therapy (ART) and isoniazid preventive therapy (IPT) among HIV-infected HCWs in Botswana.DesignWe conducted a cross-sectional study among HCWs in 30 hospitals and clinics. We determined self-reported exposure frequency to TB patients and HIV status through in-person interviews. HCWs with unknown or negative HIV status were offered rapid HIV testing. Multivariable Poisson regression modeling with robust variance was used to estimate the association between HIV status and daily exposure to TB patients.ResultsOf 1877 participants enrolled, 1388 (73.9%) with complete data were included in this study. Among 277 (20.0%) HIV-infected participants, 14.3% were newly diagnosed, 57.8% were on ART, and 34.3% reported previously receiving IPT. Daily exposure to TB patients was reported by respectively 48.4% and 52.9% of HIV-infected and non-infected participants. After adjusting for sex, age, occupation, and department, the rates of daily TB exposure remained similar between HIV-infected and non-HIV-infected participants (prevalence ratio 0.96, 95%CI 0.85-1.08).ConclusionsWe found similar rates of exposure to TB patients between HIV-infected and non-HIV-infected HCWs. Improved efforts are needed to reduce nosocomial exposure to TB among HIV-infected HCWs.

Public health decision-making is a complex process that demands careful rational and ethical reasoning based on sound scientific evidence. When evaluating the potential benefits and outcomes of public health programs, policymakers often find themselves in challenging situations due to competing needs, limited resources, and lack of access to quality data, among others. In recent years, mathematical modelling has gained increasing popularity in public health practice for its ability to assist with projecting outcomes of intervention strategies and policies.

Aminoglycosides, such as amikacin, are used to treat multidrug-resistant tuberculosis. However, ototoxicity is a common problem and is monitored using peak and trough amikacin concentrations based on World Health Organization recommendations. Our objective was to identify clinical factors predictive of ototoxicity using an agnostic machine learning method. We used classification and regression tree (CART) analyses to identify clinical factors, including amikacin concentration thresholds that predicted audiometry-confirmed ototoxicity among 28 multidrug-resistant pulmonary tuberculosis patients in Botswana. Amikacin concentrations were measured for all patients. The quantitative relationship between predictive factors and the probability of ototoxicity were then identified using probit analyses. The primary predictors of ototoxicity on CART analyses were cumulative days of therapy, followed by cumulative area under the concentration-time curve (AUC), which improved on the primary predictor by 87%. The area under the receiver operating curve was 0.97 on the test set. Peak and trough were not predictors in any tree. When algorithms were forced to pick peak and trough as primary predictors, the area under the receiver operating curve fell to 0.46. Probit analysis revealed that the probability of ototoxicity increased sharply starting after 6 months of therapy to near maximum at 9 months. A 10% probability of ototoxicity occurred with a threshold cumulative AUC of 87,232 days · mg · h/liter, while that of 20% occurred at 120,000 days · mg · h/liter. Thus, cumulative amikacin AUC and duration of therapy, and not peak and trough concentrations, should be used as the primary decision-making parameters to minimize the likelihood of ototoxicity in multidrug-resistant tuberculosis.

Cervical cancer is the leading cause of cancer-related mortality in the developing world, where HIV and Mycobacterium tuberculosis (TB) infection are also endemic. HIV infection is independently associated with increased morbidity and mortality among women with cervical cancer. TB is believed to increase the risk of malignancies and could cause chronic inflammation in the gynecologic tract. However, the relationship between cervical cancer and TB in settings hyperendemic for HIV is unknown. We found that 18 (10%) of a cohort of 180 women with cervical cancer in Botswana had a history of TB disease. Age and HIV infection were also associated with a history of TB disease. Our data show that prior TB disease is highly prevalent among patients with cervical cancer infected with HIV. The coexistence of cervical cancer, HIV infection, and prior TB infection might be higher than expected in the general population. Prospective studies are needed to better determine the impact of the collision of these three world health epidemics.

Pyrazinamide is the main driver of sterilizing effect in the standard regimen in adults and older children, and this effect is concentration-dependent. Tuberculosis patients co-infected with human immunodeficiency virus (HIV) have an increased risk for poor tuberculosis treatment outcomes and adverse drug events. We sought to determine whether measures of systemic immune activation were related to pyrazinamide pharmacokinetics among HIV/tuberculosis patients. We conducted a prospective cohort study of pyrazinamide pharmacokinetics in HIV/tuberculosis patients in Gaborone, Botswana. Patients underwent intensive pharmacokinetic sampling before and after the initiation of antiretroviral therapy, which can increase immune activation in HIV/tuberculosis. Compartmental pharmacokinetic modeling was performed to determine whether variability in systemic immune activation was related to variability in pyrazinamide pharmacokinetic parameters. Forty HIV/tuberculosis patients completed the first pharmacokinetic sampling visit, and 24 patients returned for a second visit following antiretroviral therapy initiation. The pyrazinamide plasma concentration-versus-time data were best explained by a one-compartment model with first-order elimination, and a combined additive and proportional residual error model. Pyrazinamide clearance was higher in men than women. Expression of CD38 and HLA- DR on CD8+T cells, a measure of HIV-associated immune activation, was inversely related to pyrazinamide clearance, with increasing immune activation associated with decreasing pyrazinamide clearance. Future studies should verify this finding in larger numbers of tuberculosis patients with and without HIV co-infection.

Summary Objectives We determined the performance of a sensor array (an electronic nose) made of 8 metalloporphyrins coated quartz microbalances sensors for the diagnosis and prognosis of pulmonary tuberculosis (TB) using exhaled breath samples. Methods TB cases and healthy controls were prospectively enrolled. Signals from volatile organic compounds (VOCs) in breath samples were measured at days 0, 2, 7, 14, and 30 of TB therapy and correlated with clinical and microbiological measurements. Results Fifty one pulmonary TB cases and 20 healthy HIV-uninfected controls were enrolled in the study. 31 (61%) of the 51 pulmonary TB cases were coinfected with HIV. At day 0 (before TB treatment initiation) the sensitivity of our device was estimated at 94.1% (95% confidence interval [CI], 83.8–98.8%) and specificity was 90.0% (95% CI, 68.3–98.8%) for distinguishing TB cases from controls. Time-dependent changes in the breath signals were identified as time on TB treatment progressed. Time-dependent signal changes were more pronounced among HIV-uninfected patients. Conclusion The identification of VOCs' signals in breath samples using a sensor array achieved high sensitivity and specificity for the diagnosis of TB and allowed following signal changes during TB treatment.

(See the editorial commentary by Khan and Behr on pages 1682–4.) Previous studies have demonstrated that 10%–20% of individuals living in settings with a high burden of tuberculosis have infection with >1 Mycobacterium tuberculosis strain [1]. In some cases, patients can have heterogeneous results of drug-susceptibility tests (DSTs) during a single case of tuberculosis. Several mechanisms, including culture contamination, concurrent infection by >1 M. tuberculosis strain (ie, mixed infections), and heteroresistance within a single clonal M. tuberculosis population, could underlie the finding of heterogeneous drug susceptibility results in patients with tuberculosis [1–7]. Studies have demonstrated that patients with drug-susceptible tuberculosis can have poor treatment outcomes if they are also infected with a drug-resistant strain that is not detected and treated [1–4, 8]. Previous studies have suggested that patients with multidrug-resistant (MDR) tuberculosis (ie, tuberculosis due to strains with bacteriologically confirmed resistance to isoniazid and rifampicin) can be infected with multiple M. tuberculosis strains that may be drug susceptible [5–7]. However, the clinical impact of heterogeneous DST results among patients receiving treatment for MDR tuberculosis is unknown. According to international tuberculosis treatment guidelines, the composition of appropriate treatment regimens should focus on treating the most resistant isolate, based on the DST results for all isolates collected from a patient during a single tuberculosis episode [9–12]. Thus, isoniazid and rifampicin are not recommended for treating MDR tuberculosis. However, isoniazid and rifampicin are 2 of the most effective drugs used to treat drug-susceptible tuberculosis [13, 14], and it is possible that their use in treatment regimens may improve the clinical outcomes of patients with MDR tuberculosis with concurrent infection by pansusceptible isolates. To begin to address this question, we hypothesized that the patients with concurrent infection with drug-susceptible and MDR M. tuberculosis isolates would have worse clinical outcomes than patients with MDR tuberculosis without concurrent infection with drug-susceptible M. tuberculosis.

Objectives Alcohol use has been linked to risky sexual behaviour and it has been identified as an important modifiable factor to prevent HIV infection. However, the evidence of a link between alcohol use and risky sexual behaviour is mixed. In this paper, we examine the role of alcohol use in sexual risk taking among women in Botswana. Methods Participants were recruited by stratified proportional random sampling and were administered a survey interview that collected information on HIV/AIDS knowledge, risky sexual behaviour and alcohol use. Logistic regression and bivariate probit analyses were used to examine the association between alcohol use and high-risk sexual behaviour. Results 239 women were interviewed. 168 (70%) had high levels of HIV/AIDS knowledge. We found no significant protective effect of good HIV/AIDS knowledge over high-risk sex behaviour (adjusted OR 0.74, 95% CI 0.38 to 1.42). However, alcohol use before sex was associated with high-risk sex behaviour (adjusted OR 3.04, 95% CI 1.11 to 6.45). However, bivariate probit analysis that simultaneously estimates risky sexual behaviour and alcohol use revealed an insignificant association between alcohol use and risky sex, highlighting the potential presence of other unobserved individual factors that are associated with alcohol use and risky sex. Conclusions Knowledge about HIV may not be sufficient to decrease risky sexual behaviour. Alcohol consumption was associated with an increased probability of high-risk sexual intercourse. However, the relationship between alcohol use and risky sex may also be a marker of a third omitted variable (such as overall risk-taking propensity). Further research is needed to identify factors associated with alcohol use and high-risk sex.

Background Rifampicin is the key drug responsible for sterilizing activities in the first-line TB treatment regimen. Damage to the gut during acute and chronic HIV infection may inhibit drug absorptive capacity. We sought to test the hypothesis that markers of intestinal damage, bacterial translocation and systemic immune activation would relate to rifampicin bioavailability among HIV/TB patients. Patients and methods We conducted a prospective cohort study of rifampicin pharmacokinetics in HIV/TB patients in Gaborone, Botswana. We performed two intensively sampled pharmacokinetic visits, before and after ART initiation. Non-linear mixed-effects modelling was performed to determine whether variability in markers of gut damage, microbial translocation or systemic immune activation contributed to variability in rifampicin bioavailability before and after the initiation of ART. Results We enrolled 40 HIV/TB patients in the first pharmacokinetic visit and 24 patients returned for the second pharmacokinetic visit after initiating ART. Low rifampicin exposure, as defined by the maximum serum concentration, was observed in 40% of patients prior to initiating ART and 46% of patients after initiating ART. In the non-linear mixed-effects model, we did not observe significant covariate effects of markers of gut damage, microbial translocation or immune activation on rifampicin bioavailability before and after ART initiation. Discussion Markers of intestinal damage, microbial translocation and systemic immune activation did not explain variability in rifampicin bioavailability. The a priori identification of HIV/TB patients at risk for low rifampicin concentrations remains a challenge, supporting a role for therapeutic drug monitoring during HIV/TB therapy.

Author(s): Shin, Sanghyuk S; Modongo, Chawangwa; Boyd, Rosanna; Caiphus, Cynthia; Kuate, Lesego; Kgwaadira, Botshelo; Zetola, Nicola M | Abstract: BackgroundFew studies have examined multidrug-resistant (MDR) tuberculosis (TB) treatment outcomes among HIV-infected persons after widespread expansion of antiretroviral therapy (ART). We describe MDR-TB treatment outcomes among HIV-infected and HIV-uninfected patients in Botswana after ART expansion.MethodsWe retrospectively reviewed data from patients who started MDR-TB therapy in Botswana during 2006-2013. Multivariable regression models were used to compare treatment outcomes between HIV-infected and HIV-uninfected patients.ResultsWe included 588 MDR-TB patients in the analysis, of whom, 47 (8.0%) and 9 (1.5%) were diagnosed with pre-extensively drug-resistant (XDR)-TB and XDR-TB, respectively. Of the 408 (69.4%) HIV-infected patients, 352 (86.0%) were on ART or started ART during treatment, and median baseline CD4 T-cell count was 234 cells/mm. Treatment success rates were 79.4% and 73.0% among HIV-uninfected and HIV-infected patients, respectively (P = 0.121). HIV-infected patients with CD4 T-cell count l100 cells/mm were more likely to die during treatment compared with HIV-uninfected patients (adjusted risk ratio = 1.890; 95% CI: 1.098 to 3.254).ConclusionsHigh rates of treatment success were achieved with programmatic management of MDR-TB and HIV in Botswana after widespread expansion of ART. However, a 2-fold increase in mortality was observed among HIV-infected persons with baseline CD4 l100 cells/mm compared with HIV-uninfected persons.

Aims Immune activation, which is characteristic of both tuberculosis (TB) and human immunodeficiency virus (HIV) infection, is associated with impaired drug metabolism. We tested the hypothesis that elevated levels of systemic immune activation among adults with HIV/TB initiating ART would be associated with impaired clearance of isoniazid. Methods We conducted a prospective observational study of isoniazid pharmacokinetics and systemic immune activation prior to and one month after antiretroviral therapy (ART) initiation. Non-linear mixed effects analysis was performed to measure the covariate effect of immune activation on isoniazid clearance in a model that also included N-acetyltransferase-2 (NAT-2) genotype and inter-occasional variability on clearance (thereby analyzing the pharmacokinetic data before and after ART initiation in a single model). Results We enrolled 40 patients in the pharmacokinetic visit prior to ART, and 24 patients returned for the second visit a median of 33 days after initiating antiretroviral therapy. The isoniazid concentration data were best described by a 2-compartment model with first-order elimination. After accounting for NAT-2 genotype, increasing levels of CD38 and HLA-DR expression on CD8+ T cells (CD38+DR+CD8+) were associated with decreasing isoniazid clearance. Conclusion HIV/TB patients with high levels of immune activation demonstrated impaired isoniazid clearance. Future efforts should determine the role of this relationship in clinical hepatotoxicity events.

Introduction Mycobacterium tuberculosis (Mtb) is transmitted from person to person via airborne droplet nuclei. At the community level, Mtb transmission depends on the exposure venue, infectiousness of the tuberculosis (TB) index case and the susceptibility of the index case's social network. People living with HIV infection are at high risk of TB, yet the factors associated with TB transmission within communities with high rates of TB and HIV are largely undocumented. The primary aim of the Kopanyo study is to better understand the demographic, clinical, social and geospatial factors associated with TB and multidrug-resistant TB transmission in 2 communities in Botswana, a country where 60% of all patients with TB are also infected with HIV. This manuscript describes the methods used in the Kopanyo study. Methods and analysis The study will be conducted in greater Gaborone, which has high rates of HIV and a mobile population; and in Ghanzi, a rural community with lower prevalence of HIV infection and home to the native San population. Kopanyo aims to enrol all persons diagnosed with TB during a 4-year study period. From each participant, sputum will be cultured, and for all Mtb isolates, molecular genotyping (24-locus mycobacterial interspersed repetitive units-variable number of tandem repeats) will be performed. Patients with matching genotype results will be considered members of a genotype cluster, a proxy for recent transmission. Demographic, behavioural, clinical and social information will be collected by interview. Participant residence, work place, healthcare facilities visited and social gathering venues will be geocoded. We will assess relationships between these factors and cluster involvement to better plan interventions for reducing TB transmission. Ethics Ethical approval from the Independent Review Boards at the University of Pennsylvania, US Centers for Disease Control and Prevention, Botswana Ministry of Health and University of Botswana has been obtained.

Immunosuppression resulting from HIV infection increases the risk of progression to active tuberculosis (TB) both in individuals newly exposed to Mycobacterium tuberculosis (MTB) and in those with latent infections. We hypothesized that HIV-positive individuals who do not develop TB, despite living in areas where it is hyperendemic, provide a model of natural resistance. We performed a genome-wide association study of TB resistance by using 581 HIV-positive Ugandans and Tanzanians enrolled in prospective cohort studies of TB; 267 of these individuals developed active TB, and 314 did not. A common variant, rs4921437 at 5q33.3, was significantly associated with TB (odds ratio = 0.37, p = 2.11 × 10(-8)). This variant lies within a genomic region that includes IL12B and is embedded in an H3K27Ac histone mark. The locus also displays consistent patterns of linkage disequilibrium across African populations and has signals of strong selection in populations from equatorial Africa. Along with prior studies demonstrating that therapy with IL-12 (the cytokine encoded in part by IL12B, associated with longer survival following MTB infection in mice deficient in CD4 T cells), our results suggest that this pathway might be an excellent target for the development of new modalities for treating TB, especially for HIV-positive individuals. Our results also indicate that studying extreme disease resistance in the face of extensive exposure can increase the power to detect associations in complex infectious disease.

Multidrug-Resistant tuberculosis (MDR-TB) rates had been historically low in Botswana. However, national surveys have revealed a progressive rise in the prevalence of MDR-TB, which, as of 2002, accounted for over 10% of the TB cases requiring retreatment.1 While data suggest that patients with TB have excellent response to treatment in Africa, the data with regard to MDR-TB in Africa are less encouraging. Studies from South Africa have shown that patients with MDR-TB in general have extremely poor outcomes.2 Understanding the factors leading to the development of MDR-TB is therefore critical. Although the clearest risk factors for the development of MDR-TB are a history of previous antituberculosis treatment and human immunodeficiency virus (HIV) infection, other, potentially modifiable factors have not received enough attention.3,4 Alcohol abuse is widespread in sub-Saharan Africa, the epicenter of the TB, MDR-TB and HIV pandemics, and has been associated with medical non-adherence, poor health status and overall worse clinical outcomes.5–8 It has been reported that patients diagnosed with TB have higher alcohol intake than persons without TB.9–12 Moreover, HIV-infected patients have higher alcohol consumption than non-HIV-infected patients, and patients co-infected with TB and HIV have higher alcohol consumption than either TB or HIV-infected patients.6,8,13 Although these mechanisms strongly support the role of alcohol use as an important modifiable risk factor for the development of TB, data regarding its relative role in the development of MDR-TB are lacking.3 The objective of this study was to describe the patterns of alcohol use among MDR-TB patients and to determine whether alcohol use is associated with the development of MDR-TB in Botswana.

Nosocomial transmission of pulmonary tuberculosis (PTB) is a problem in resource-limited settings. However, the degree of TB exposure and the intermediate- and long-term morbidity and mortality of hospital-associated TB is unclear. In this study we determined: 1) the nature, patterns and intensity of TB exposure occurring in the context of current TB cohorting practices in medical centre with a high prevalence of TB and HIV; 2) the one-year TB incidence after discharge; and 3) one-year TB-related mortality after hospital discharge. Factors leading to nosocomial TB exposure were collected daily over a 3-month period. Patients were followed for 1-year after discharge. TB incidence and mortality were calculated and logistic regression was used to determine the factors associated with TB incidence and mortality during follow up. 1,094 patients were admitted to the medical wards between May 01 and July 31, 2010. HIV was confirmed in 690/1,094 (63.1%) of them. A total of 215/1,094 (19.7%) patients were diagnosed with PTB and 178/1,094 (16.3%) patients died during the course of their hospitalization; 12/178 (6.7%) patients died from TB-related complications. Eventually, 916 (83.7%) patients were discharged and followed for one year after it. Of these, 51 (5.6%) were diagnosed with PTB during the year of follow up (annual TB rate of 3,712 cases per 100,000 person per year). Overall, 57/916 (6.2%) patients died during the follow up period, of whom 26/57 (45.6%) died from confirmed TB. One-year TB incidence rate and TB-associated mortality were associated with the number of days that the patient remained hospitalized, the number of days spent in the cohorting bay (regardless of whether the patient was eventually diagnosed with TB or not), and the number and proximity to TB index cases. There was no difference in the performance of each of these 3 measurements of nosocomial TB exposure for the prediction of one-year TB incidence. Substantial TB exposure, particularly among HIV-infected patients, occurs in nosocomial settings despite implementation of cohorting measures. Nosocomial TB exposure is strongly associated with one-year TB incidence and TB-related mortality. Further studies are needed to identify strategies to reduce such exposure among susceptible patients.

We examined factors associated with mixed-strain Mycobacterium tuberculosis infections among patients at high risk for drug-resistant tuberculosis in Botswana. Thirty-seven (10.0%) of 370 patients with tuberculosis had mixed M. tuberculosis infections, based on 24-locus mycobacterial interspersed repetitive unit-variable number of tandem repeats genotyping. In log-binomial regression analysis, age