Epidemiology of co-infections in tuberculosis patients in Tanzania : HIV, helminth infection and respiratory pathogens

Background: Tuberculosis (TB) caused by Mycobacterium tuberculosis complex is a global public health concern, causing significant morbidity and mortality. The resource limited settings are the worst hit, especially where there is also high burden of co-infections which increase the risk of developing TB and negatively affect TB treatment outcomes. HIV, helminth and respiratory pathogens are prevalent in Tanzania, a country that is in among the top 30 high burden countries as categorized by World Health Organization (WHO). There is epidemiological evidence of increased risk of developing TB with HIV, and little evidence on the association of TB and helminth infection and respiratory pathogens. It is therefore important to understand the epidemiology of TB and co-infections, so that we can design interventions that will address the burden of TB and relevant co-infections. The objectives: The main objective of this PhD thesis was to determine the burden and the association of HIV, helminth and respiratory pathogens (viruses and bacteria) co-infections and TB at Temeke district, Dar es Salaam, Tanzania. The specific objectives were: i) to determine the treatment outcome of TB and HIV co-infected patients routinely diagnosed at Temeke district treated under home- and facility-based direct observed therapy (DOT), ii) to determine the prevalence of helminth infection and respiratory pathogens among smear positive TB cases and household contact controls without TB, iii) to investigate the risk factors for helminth infection and respiratory pathogens among smear-positive TB cases and household contact controls without TB, and iv) to determine the clinical effects of helminth infection and respiratory pathogens on clinical phenotypes and clinical outcomes among smear-positive TB patients. Methods: This PhD is nested within a large TB cohort in Dar es Salaam region (TB-DAR): a prospective collection of clinical data and biological specimens to study the epidemiology of tuberculosis, including molecular epidemiology and the evaluation of new diagnostics and biomarkers). There are two distinctive methodological parts as described below: Objective 1: We obtained anonymized electronic data from the TB district register of all adult TB patients (aged ≥15 years) who were notified between 2010 and 2013 in a single geographical area of two TB sub-districts (Wailes I and Wailes II) in the Temeke district, Dar es Salaam, Tanzania. Objective 2-4: We consecutively enrolled ≥18 years TB patients and household contact controls between November 2013 until October 2015 to reach the required sample size. Any individual living in the same household as the index TB patients enrolled in the study is referred to as a household contact control. Controls at recruitment were free of symptoms and signs suggestive of TB, healthy on physical examination, and had a negative Xpert MTB/RIF result (Cepheid; California, USA). We collected sputum, nasopharyngeal swabs, stool and urine samples from TB patients and household controls at recruitment. Löwenstein-Jensen mycobacterial culture was used to confirm TB. Kato-katz and Bearman methods for detection of soil transmitted helminths infections from stool. Urine filtration and Circulating Cathodic Antigen (CCA) assay for detection of Schistosomiasis. Nasopharyngeal swabs samples were analyzed using Allplex™ Respiratory full panel assay and PCR Anyplex™II RV16 for detection of respiratory bacterial and viral pathogens respectively. Principle findings: In a study to determine the treatment outcome of TB and HIV co-infected patients routinely diagnosed at Temeke district treated under home- and facility-based DOT: data of 4,835 adult TB patients were analyzed, with a median age of 35 years, 2,943 (60.9%) were men and TB/HIV co-infection prevalence of 39.9%. A total of 3,593 (74.3%) patients were treated under home-based DOT. Patients on home-based DOT were more likely to die compared to patients on facility-based DOT (RR 2.04, 95% Confidence Interval [95% CI]: 1.52-2.73), and more likely to complete TB treatment (RR 1.14, 95% CI: 1.06-1.23), but less likely to have a successful treatment outcome (RR 0.94, 95% CI: 0.92-0.97). Home-based DOT was preferred by women (adjusted Odds Ratio [aOR] 1.55, 95% CI: 1.34-1.80, p<0.001), older people (aOR 1.01 for each year increase, 95% CI: 1.00-1.02, p=0.001) and patients with extra-pulmonary TB (aOR 1.45, 95% CI: 1.16-1.81, p=0.001), but less frequently by patients on a retreatment regimen (aOR 0.12, 95% CI: 0.08-0.19, p<0.001). In a study to assess the association of TB and helminth infection: a total of 597 TB patients and 375 household contact controls were included. The median age was 33 years and 60.2% (585/972) were men. The prevalence of any helminth infection among TB patients was 31.8% (190/597) and 25.9% (97/375) among controls. Strongyloides stercoralis was the predominant helminth species (16.6%, 161), followed by hookworm (9.0%, 87) and Schistosoma mansoni (5.7%, 55). An infection with any helminth was not associated with TB (aOR 1.26, 95% CI: 0.88-1.80, p=0.22), but S. mansoni infection was (aOR 2.15, 95% CI: 1.03-4.45, p=0.040). Moreover, S. mansoni infection was associated with lower sputum bacterial load (aOR 2.63, 95% CI: 1.38-5.26, p=0.004) and tended to have fewer lung cavitations (aOR 0.41, 95% CI: 0.12-1.16, p=0.088). When assessing the interaction between TB and respiratory pathogens: we analyzed 794 study participants, of which 489 (61.6%) were TB patients and 305 (38.4%) were household contact controls. The median age of the study participants was 33 years; 61% (484/794) were men, and 21% (168/ 794) were HIV-positive. TB patients had a higher prevalence of HIV (28.6%; 140/489) than controls (9.2%; 28/305). Overall prevalence of respiratory viral pathogens was 20.4% (160/794; 95%CI 17.7-23.3%) and of bacterial pathogens 38.2% (303/794; 95%CI 34.9-41.6%). TB patients and controls did not differ in the prevalence of respiratory viruses (Odds Ratio [OR] 1.00, 95%CI 0.71-1.44), but respiratory bacteria were less frequently detected in TB patients (OR 0.70, 95%CI 0.53-0.94). TB patients with both respiratory viruses and respiratory bacteria were likely to have more severe disease (adjusted OR [aOR] 1.6, 95%CI 1.1-2.4; p=0.011). TB patients with respiratory viruses tended to have more frequent lung cavitations (aOR 1.6, 95%CI 0.93-2.7; p=0.089). Conclusion: TB patients under home-based DOT had more risk factors for death such as older age, HIV infection and sputum smear-negative TB, and had higher TB mortality compared to patients under facility-based DOT. Assessment of TB mortality risk factors and offering additional clinical care could be beneficial in reducing TB mortality. Further operational research is warranted to monitor implementation of DOT and discern other risk factors for deaths. S. mansoni infection was an independent risk factor for active TB and altered the clinical presentation in TB patients. S. mansoni infection may play a role in TB pathogenesis in humans. Bidirectional screening of TB and helminth including treatment for both diseases should be considered in a clinical management of patients. Respiratory viruses are common for both TB patients and household controls. TB patients may present with more severe TB disease, particularly when they are co- infected with both bacteria and viruses

Diagnostic Delay and Associated Factors among Patients with Pulmonary Tuberculosis in Dar es Salaam, Tanzania.

Tanzania is among the 30 countries with the highest tuberculosis (TB) burdens. Because TB has a long infectious period, early diagnosis is not only important for reducing transmission, but also for improving treatment outcomes. We assessed diagnostic delay and associated factors among infectious TB patients. We interviewed new smear-positive adult pulmonary TB patients enrolled in an ongoing TB cohort study in Dar es Salaam, Tanzania, between November 2013 and June 2015. TB patients were interviewed to collect information on socio-demographics, socio-economic status, health-seeking behaviour, and residential geocodes. We categorized diagnostic delay into ≤ 3 or > 3 weeks. We used logistic regression models to identify risk factors for diagnostic delay, presented as crude (OR) and adjusted Odds Ratios (aOR). We also assessed association between geographical distance (incremental increase of 500 meters between household and the nearest pharmacy) with binary outcomes. We analysed 513 patients with a median age of 34 years (interquartile range 27-41); 353 (69%) were men. Overall, 444 (87%) reported seeking care from health care providers prior to TB diagnosis, of whom 211 (48%) sought care > 2 times. Only six (1%) visited traditional healers before TB diagnosis. Diagnostic delay was positively associated with absence of chest pain (aOR = 7.97, 95% confidence intervals [CI]: 3.15-20.19; P < 0.001), and presence of hemoptysis (aOR = 25.37, 95% CI: 11.15-57.74; P < 0.001) and negatively associated with use of medication prior to TB diagnosis (aOR = 0.31, 95% CI: 0.14-0.71; P = 0.01). Age, sex, HIV status, education level, household income, and visiting health care facilities (HCFs) were not associated with diagnostic delay. Patients living far from pharmacies were less likely to visit a HCF (incremental increase of distance versus visit to any facility: OR = 0.51, 95% CI: 0.28-0.96; P = 0.037). TB diagnostic delay was common in Dar es Salaam, and was more likely among patients without prior use of medication and presenting with hemoptysis. Geographical distance to HCFs may have an impact on health-seeking behaviour. Increasing community awareness of TB signs and symptoms could further reduce diagnostic delays and interrupt TB transmission

Preservation of sputum samples with cetylpyridinium chloride (CPC) for tuberculosis cultures and Xpert MTB/RIF in a low-income country

Culture contamination with environmental bacteria is a major challenge in tuberculosis (TB) laboratories in hot and humid climate zones. We studied the effect of cetylpyridinium chloride (CPC) preservation on culture results and performance of Xpert MTB/RIF.; Consecutive sputum samples from microscopy smear-positive TB patients were collected. Two-hundred samples were equally split in two aliquots, one aliquot was treated with CPC and stored at ambient temperature for 7 days. The second aliquot was immediately processed. Samples were decontaminated for 20, 15 or 10 min, and subsequently cultured on Löwenstein-Jensen medium. Furthermore, 50 samples were stored for 7, 14 and 21 days, and 100 CPC-pretreated samples tested by Xpert MTB/RIF.; CPC pretreated samples showed a higher culture yield compared to non-treated sputum samples across all decontamination times: 94% vs. 73% at 10 min (p = 0.01), 94% vs. 64% at 15 min (p = 0.004), and 90% vs. 52% at 20 min (p &lt; 0.001). The quantitative culture grading was consistently higher in CPC treated compared to non-CPC treated samples. The proportion of contaminated cultures was lower in CPC pretreated samples across all decontamination times (range 2-6%) compared to non-CPC treated samples (15-16%). For storage times of CPC treated samples of 7, 14, and 21 days, 84, 86, and 84% of the respective cultures were positive. Of 91 CPC treated samples with a positive culture, 90 were also Xpert MTB/RIF positive.; CPC increases culture yield, decreases the proportion of contamination, and does not alter the performance of Xpert MTB/RIF

Prevalence and clinical relevance of helminth co-infections among tuberculosis patients in urban Tanzania

Helminth infections can negatively affect the immunologic host control, which may increase the risk of progression from latent Mycobacterium tuberculosis infection to tuberculosis (TB) disease and alter the clinical presentation of TB. We assessed the prevalence and determined the clinical relevance of helminth co-infection among TB patients and household contact controls in urban Tanzania.; Between November 2013 and October 2015, we enrolled adult (≥18 years) sputum smear-positive TB patients and household contact controls without TB during an ongoing TB cohort study in Dar es Salaam, Tanzania. We used Baermann, FLOTAC, Kato-Katz, point-of-care circulating cathodic antigen, and urine filtration to diagnose helminth infections. Multivariable logistic regression models with and without random effects for households were used to assess for associations between helminth infection and TB.; A total of 597 TB patients and 375 household contact controls were included. The median age was 33 years and 60.2% (585/972) were men. The prevalence of any helminth infection among TB patients was 31.8% (190/597) and 25.9% (97/375) among controls. Strongyloides stercoralis was the predominant helminth species (16.6%, 161), followed by hookworm (9.0%, 87) and Schistosoma mansoni (5.7%, 55). An infection with any helminth was not associated with TB (adjusted odds ratio (aOR) 1.26, 95% confidence interval (CI): 0.88-1.80, p = 0.22), but S. mansoni infection was (aOR 2.15, 95% CI: 1.03-4.45, p = 0.040). Moreover, S. mansoni infection was associated with lower sputum bacterial load (aOR 2.63, 95% CI: 1.38-5.26, p = 0.004) and tended to have fewer lung cavitations (aOR 0.41, 95% CI: 0.12-1.16, p = 0.088).; S. mansoni infection was an independent risk factor for active TB and altered the clinical presentation in TB patients. These findings suggest a role for schistosomiasis in modulating the pathogenesis of human TB. Treatment of helminths should be considered in clinical management of TB and TB control programs

The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study.

Each day, approximately 27,000 people become ill with tuberculosis (TB), and 4,000 die from this disease. Pulmonary TB is the main clinical form of TB, and affects the lungs with a considerably heterogeneous manifestation among patients. Immunomodulation by an interplay of host-, environment-, and pathogen-associated factors partially explains such heterogeneity. Microbial communities residing in the host's airways have immunomodulatory effects, but it is unclear if the inter-individual variability of these microbial communities is associated with the heterogeneity of pulmonary TB. Here, we investigated this possibility by characterizing the microbial composition in the sputum of 334 TB patients from Tanzania, and by assessing its association with three aspects of disease manifestations: sputum mycobacterial load, severe clinical findings, and chest x-ray (CXR) findings. Compositional data analysis of taxonomic profiles based on 16S-rRNA gene amplicon sequencing and on whole metagenome shotgun sequencing, and graph-based inference of microbial associations revealed that the airway microbiome of TB patients was shaped by inverse relationships between Streptococcus and two anaerobes: Selenomonas and Fusobacterium. Specifically, the strength of these microbial associations was negatively correlated with Faith's phylogenetic diversity (PD) and with the accumulation of transient genera. Furthermore, low body mass index (BMI) determined the association between abnormal CXRs and community diversity and composition. These associations were mediated by increased abundance of Selenomonas and Fusobacterium, relative to the abundance of Streptococcus, in underweight patients with lung parenchymal infiltrates and in comparison to those with normal chest x-rays. And last, the detection of herpesviruses and anelloviruses in sputum microbial assemblage was linked to co-infection with HIV. Given the anaerobic metabolism of Selenomonas and Fusobacterium, and the hypoxic environment of lung infiltrates, our results suggest that in underweight TB patients, lung tissue remodeling toward anaerobic conditions favors the growth of Selenomonas and Fusobacterium at the expense of Streptococcus. These new insights into the interplay among particular members of the airway microbiome, BMI, and lung parenchymal lesions in TB patients, add a new dimension to the long-known association between low BMI and pulmonary TB. Our results also drive attention to the airways virome in the context of HIV-TB coinfection

Boosting effect of IL-7 in interferon gamma release assays to diagnose Mycobacterium tuberculosis infection

A quarter of the world's population is estimated to be infected with Myobacterium tuberculosis (Mtb). Infection is detected by immune response to M. tuberculosis antigens using either tuberculin skin test (TST) and interferon gamma release (IGRA's), tests which have low sensitivity in immunocompromised. IL-7 is an important cytokine for T-cell function with potential to augment cytokine release in in-vitro assays. This study aimed to determine whether the addition of IL-7 in interferon-gamma release assays (IGRAs) improves its diagnostic performance of Mtb infection.; 44 cases with confirmed TB and 45 household contacts without TB were recruited and 1ml of blood was stimulated in two separate IGRA's tube set: one set of standard Quantiferon TB gold tubes mitogen, TB antigen and TB Nil; one set of customized Quantiferon TB gold tubes with added IL-7. Following IFN-γ and IP-10 release was determined using ELISA.; We found that the addition of IL-7 led to significantly higher release of IFN-γ in individuals with active TB from 4.2IU/ml (IQR 1.4-6.9IU/ml) to 5.1IU/ml (IQR 1.5-8.1IU/ml, p = 0.0057), and we found an indication of a lower release of both IFN-γ and IP-10 in participants with negative tests.; In TB cases addition of IL-7 in IGRA tubes augments IFN-γ but not IP-10 release, and seems to lower the response in controls. Whether IL-7 boosted IGRA holds potential over standard IGRA needs to be confirmed in larger studies in high and low TB incidence countries

Chronic airflow obstruction in Tanzania - a cross-sectional study

Chronic obstructive pulmonary disease is a global problem and available data from sub-Saharan Africa is very limited.; A cross-sectional facility-based pilot study among patients and visitors to an urban and a rural primary healthcare facility was conducted in coastal Tanzania. The primary outcome was the prevalence of chronic airflow obstruction.; The final analysis included 598 participants with valid post-bronchodilator spirometry. Applying ATS/ERS spirometric criteria, chronic airflow obstruction was found in n = 24 (4%, CI95 2.7-5.9) participants and in n = 30 (5%, CI95 3.5-7.1) applying GOLD spirometric criteria. To analyse risk factors for chronic airflow obstruction including those not meeting ATS/ERS or GOLD criteria, FEF25-75 and FEV1% predicted was analysed in participants without evidence of pulmonary restriction among those exposed or not exposed to risk factors (n = 552). FEV1% predicted, but in particular FEF25-75 decreased with increasing symptom severity of shortness of breath as well as limitations in daily activities of participants. Cooking in general and cooking with biomass fuels vs. gas or electricity was associated with significantly lower FEF25-75, but not with lower FEV1% predicted. Participants having refrained from taking a job because of shortness of breath exhibited lower FEF25-75 (p &lt; 0.01). A history of prior active TB was the most relevant risk factor associated with a decrease in FEF25-75 as well as FEV1% predicted.; This study demonstrated a relevant prevalence of chronic airflow obstruction in primary healthcare attendants and healthy visitors of a Tanzanian hospital. Using the baseline data provided, larger and population-based studies are needed to validate these findings. TB may have more impact on development of chronic airway obstruction than smoking in Africa. Due to the influence of age on the GOLD definition of chronic airflow obstruction, studies should report results using both ATS/ERS and GOLD definitions and include age-stratified analysis. Analysis of FEV1 and in particular FEF25-75 may yield additional information on risk factors and earlier stages of chronic airflow obstruction

Home-Based and Facility-Based Directly Observed Therapy of Tuberculosis Treatment under Programmatic Conditions in Urban Tanzania.

INTRODUCTION Decentralization of Directly Observed Treatment (DOT) for tuberculosis (TB) to the community (home-based DOT) has improved the coverage of TB treatment and reduced the burden to the health care facilities (facility-based DOT). We aimed to compare TB treatment outcomes in home-based and facility-based DOT under programmatic conditions in an urban setting with a high TB burden. METHODOLOGY A retrospective analysis of a cohort of adult TB patients (≥15 years) routinely notified between 2010 and 2013 in two representative TB sub-districts in the Temeke district, Dar es Salaam, Tanzania. We assessed differences in treatment outcomes by calculating Risk Ratios (RRs). We used logistic regression to assess the association between DOT and treatment outcomes. RESULTS Data of 4,835 adult TB patients were analyzed, with a median age of 35 years, 2,943 (60.9%) were men and TB/HIV co-infection prevalence of 39.9%. A total of 3,593 (74.3%) patients were treated under home-based DOT. Patients on home-based DOT were more likely to die compared to patients on facility-based DOT (RR 2.04, 95% Confidence Interval [95% CI]: 1.52-2.73), and more likely to complete TB treatment (RR 1.14, 95% CI: 1.06-1.23), but less likely to have a successful treatment outcome (RR 0.94, 95% CI: 0.92-0.97). Home-based DOT was preferred by women (adjusted Odds Ratio [aOR] 1.55, 95% CI: 1.34-1.80, p<0.001), older people (aOR 1.01 for each year increase, 95% CI: 1.00-1.02, p = 0.001) and patients with extra-pulmonary TB (aOR 1.45, 95% CI: 1.16-1.81, p = 0.001), but less frequently by patients on a retreatment regimen (aOR 0.12, 95% CI: 0.08-0.19, p<0.001). CONCLUSIONS/SIGNIFICANCE TB patients under home-based DOT had more frequently risk factors of death such as older age, HIV infection and sputum smear-negative TB, and had higher mortality compared to patients under facility-based DOT. Further operational research is needed to monitor the implementation of DOT under programmatic conditions

Ultrasound in managing extrapulmonary tuberculosis: a randomized controlled two-center study

Patients with clinically suspected tuberculosis are often treated empirically, as diagnosis - especially of extrapulmonary tuberculosis - remains challenging. This leads to an overtreatment of tuberculosis and to underdiagnosis of possible differential diagnoses.; This open-label, parallel-group, superiority randomized controlled trial is done in a rural and an urban center in Tanzania. HIV-positive and -negative adults (≥18 years) with clinically suspected extrapulmonary tuberculosis are randomized in a 1:1 ratio to an intervention- or control group, stratified by center and HIV status. The intervention consists of a management algorithm including extended focused assessment of sonography for HIV and tuberculosis (eFASH) in combination with chest X-ray and microbiological tests. Treatment with anti-tuberculosis drugs is started, if eFASH is positive, chest X-ray suggests tuberculosis, or a microbiological result is positive for tuberculosis. Patients in the control group are managed according national guidelines. Treatment is started if microbiology is positive or empirically according to the treating physician. The primary outcome is the proportion of correctly managed patients at 6 months (i.e patients who were treated with anti-tuberculosis treatment and had definite or probable tuberculosis, and patients who were not treated with anti-tuberculosis treatment and did not have tuberculosis). Secondary outcomes are the proportion of symptom-free patients at two and 6 months, and time to death. The sample size is 650 patients.; This study will determine, whether ultrasound in combination with other tests can increase the proportion of correctly managed patients with clinically suspected extrapulmonary tuberculosis, thus reducing overtreatment with anti-tuberculosis drugs.; PACTR, Registration number: PACTR201712002829221, registered December 1st 2017

Pathways and associated costs of care in patients with confirmed and presumptive tuberculosis in Tanzania : a cross-sectional study

To assess pathways and associated costs of seeking care from the onset of symptoms to diagnosis in patients with confirmed and presumptive tuberculosis (TB).; Cross-sectional study.; District hospital in Dar es Salaam, Tanzania.; Bacteriologically confirmed TB and presumptive TB patients.; We calculated distance in metres and visualised pathways to healthcare up to five visits for the current episode of sickness. Costs were described by medians and IQRs, with comparisons by gender and poverty status.; Of 100 confirmed and 100 presumptive TB patients, 44% of confirmed patients sought care first at pharmacies after the onset of symptoms, and 42% of presumptive patients did so at hospitals. The median visits made by confirmed patients was 2 (range 1-5) and 2 (range 1-3) by presumptive patients. Patients spent a median of 31% of their monthly household income on health expenditures for all visits. The median total direct costs were higher in confirmed compared with presumptive patients (USD 27.4 [IQR 18.7-48.4] vs USD 19.8 [IQR 13.8-34.0], p=0.02), as were the indirect costs (USD 66.9 [IQR 35.5-150.0] vs USD 46.8 [IQR 20.1-115.3], p&lt;0.001). The indirect costs were higher in men compared with women (USD 64.6 [IQR 31.8-159.1] vs USD 55.6 [IQR 25.1-141.1], p&lt;0.001). The median total distance from patients' household to healthcare facilities for patients with confirmed and presumptive TB was 2338 m (IQR 1373-4122) and 2009 m (IQR 986-2976) respectively.; Patients with confirmed TB have complex pathways and higher costs of care compared with patients with presumptive TB, but the costs of the latter are also substantial. Improving access to healthcare and ensuring integration of different healthcare providers including private, public health practitioners and patients themselves could help in reducing the complex pathways during healthcare seeking and optimal healthcare utilisation