Integrating social contact and environmental data in evaluating tuberculosis transmission in a South African township

Prevalence and Predictors of Tuberculosis Infection in Children and Adolescents in Rural Uganda: A Cross-sectional Study

BACKGROUND

Much of the latent tuberculosis (TB) reservoir is established in childhood and adolescence. Yet, age-specific data on prevalence and predictors of infection in this population are sparse and needed to guide prevention and case finding.

METHODS

From December 2021 to June 2023, we measured TB infection in children 1-17 years in 25 villages in rural Southwestern Uganda. We defined TB infection as a positive QuantiFERON Gold Plus Test (QFT). We estimated overall and age-stratified population-level prevalence and adjusted risk ratios (aRR) of TB infection for individual, household, and community-based predictors, accounting for age, TB contact, and clustering by household.

RESULTS

Estimated TB infection prevalence was 9.6% [95% confidence interval (CI): 8.7-10.5%] among the 5789 participants, and prevalence varied slightly with age. Household-level risk factors included crowding (aRR: 1.25, 95% CI: 1.03-1.53), indoor cooking (aRR: 1.62, 95% CI: 1.14-2.30), living with ≥2 persons who drink alcohol (aRR: 1.47, 95% CI: 1.04-2.07). The predominant community-based risk factor was child mobility (aRR: 1.67, 95% CI: 1.24-2.26). In age-stratified analyses, household predictors were important in early childhood but not adolescence, where mobility was predominant (aRR: 1.66, 95% CI: 1.13-2.44).

CONCLUSION

We detected a high prevalence of TB infection in children and adolescents in rural Uganda. On a population level, TB risk factors change throughout the early life course, with child mobility a key risk factor in adolescence. Age-specific TB case finding and prevention strategies that address both household and extra-household risk factors are needed to address TB transmission.

Blurring cluster randomized trials and observational studies: Two-Stage TMLE for subsampling, missingness, and few independent units

Cluster randomized trials (CRTs) often enroll large numbers of participants; yet due to resource constraints, only a subset of participants may be selected for outcome assessment, and those sampled may not be representative of all cluster members. Missing data also present a challenge: if sampled individuals with measured outcomes are dissimilar from those with missing outcomes, unadjusted estimates of arm-specific endpoints and the intervention effect may be biased. Further, CRTs often enroll and randomize few clusters, limiting statistical power and raising concerns about finite sample performance. Motivated by SEARCH-TB, a CRT aimed at reducing incident tuberculosis infection, we demonstrate interlocking methods to handle these challenges. First, we extend Two-Stage targeted minimum loss-based estimation to account for three sources of missingness: (i) subsampling; (ii) measurement of baseline status among those sampled; and (iii) measurement of final status among those in the incidence cohort (persons known to be at risk at baseline). Second, we critically evaluate the assumptions under which subunits of the cluster can be considered the conditionally independent unit, improving precision and statistical power but also causing the CRT to behave like an observational study. Our application to SEARCH-TB highlights the real-world impact of different assumptions on measurement and dependence; estimates relying on unrealistic assumptions suggested the intervention increased the incidence of TB infection by 18% (risk ratio [RR]=1.18, 95% confidence interval [CI]: 0.85-1.63), while estimates accounting for the sampling scheme, missingness, and within community dependence found the intervention decreased the incident TB by 27% (RR=0.73, 95% CI: 0.57-0.92).

Tuberculin skin test surveys and the Annual Risk of Tuberculous Infection in school children in Northern KwaZulu-Natal

Tuberculin skin test surveys in primary school children can be used to quantify Mycobacterium tuberculosis transmission at community level. KwaZulu-Natal province, South Africa, is home to 11.5 million people and suffers a burden of tuberculosis disease that is among the highest in the world. The last tuberculin survey in the province was undertaken in 1979. We performed a tuberculin skin test survey nested within a demographic and health household surveillance programme in Northern KwaZulu-Natal. We enrolled children aged between six and eight years of age attending primary schools in this community. Mixture analysis was used to determine tuberculin skin test thresholds and the Annual Risk of Tuberculous Infection derived from age at testing and infection prevalence. The Community Infection Ratio, a measure of the relative importance of within-household and community transmission, was calculated from data on tuberculin positivity disaggregated by household tuberculosis contact. Between June and December 2013, we obtained tuberculin skin test results on 1240 children. Mixture analysis proved unstable, suggesting two potential thresholds for test positivity. Using a threshold of ≥10mm or treating all non zero reactions as positive yielded estimates of the Annual Risk of Tuberculous Infection of 1.7% (1.4-2.1%) or 2.4% (2.0-3.0%). Using the same thresholds and including children reported to be receiving TB treatment as cases, resulted in estimates of 2.0% (1.6-2.5%) or 2.7% (2.2-3.3%). The Community Infection Ratio was 0.58 (0.33-1.01). The force of infection in this community is lower than that observed in Western Cape province, South Africa, but higher than that observed in community settings in most other parts of the world. Children in this community are commonly infected with Mycobacterium tuberculosis outside the home. Interventions to interrupt transmission are urgently needed.

The impact of screening for tuberculosis exposure in the household in children with tuberculosis disease: A difficult riddle to solve

BACKGROUND

Tuberculosis (TB) infection is transmitted by sharing the same airway with people with active TB. Children are often not considered the source of TB bacilli, and index case investigation is carried out after diagnosis. Here, we describe the impact of the presence of a household index case on childhood TB disease.

METHODS

The data of patients aged between 1 month and 18 years who were diagnosed with TB were collected. We compared patients according to whether they had an index case in the household or not.

RESULTS

A total of 202 TB patients were enrolled, of whom 62 (30.7%) had a household index case. There was no significant difference in having a household index case between TB patients under the age of five (23.3%) and older children (33.8%) (p = .140). Pulmonary TB was present in 61.4% of the cases, and extrapulmonary TB was present in 38.6% of the cases. The rate of patients who had a household index case was significantly higher in pulmonary TB (46.8%) compared to extrapulmonary TB (5.1%) (p < .001). Pulmonary TB patients with a history of household contact were more likely to have diagnostic radiological findings (93.1%) compared to those without (75.8%) (p = .009). However, pulmonary TB patients without household contact history had a higher rate of diagnostic microbiological findings (59.1%) and constitutional symptoms (63.6%) (p = .019 and p = .013, respectively).

CONCLUSION

Household contact research is an important epidemiological tool. However, considering the contact rates in the household, new and more comprehensive public health programs are required to prevent the spread of childhood tuberculosis.

Monitoring the ventilation of living spaces to assess the risk of airborne transmission of infection using a novel Pocket CO2 Logger to track carbon dioxide concentrations in Tokyo

We employed carbon dioxide (CO2) concentration monitoring using mobile devices to identify location-specific risks for airborne infection transmission. We lent a newly developed, portable Pocket CO2 Logger to 10 participants, to be carried at all times, for an average of 8 days. The participants recorded their location at any given time as cinema, gym, hall, home, hospital, other indoors, other outgoings, pub, restaurant, university, store, transportation, or workplace. Generalized linear mixed model was used for statistical analysis, with the objective variable set to the logarithm of CO2 concentration. Analysis was performed by assigning participant identification as the random effect and location as the fixed effect. The data were collected per participant (seven males, four females), resulting in a total of 12,253 records. Statistical analysis identified three relatively poorly ventilated locations (median values > 1,000 ppm) that contributed significantly (p < 0.0001) to CO2 concentrations: homes (1,316 ppm), halls (1,173 ppm), and gyms (1005ppm). In contrast, two locations were identified to contribute significantly (p < 0.0001) to CO2 concentrations but had relatively low average values (<1,000 ppm): workplaces (705 ppm) and stores (620 ppm). The Pocket CO2 Logger can be used to visualize airborne infectious transmission risk by location to help guide recommendation regarding infectious disease policies, such as restrictions on human flow and ventilation measures and guidelines. In the future, large-scale surveys are expected to utilize the global positioning system, Wi-Fi, or Bluetooth of an individual's smartphone to improve ease and accuracy.

Airborne transmission risks of tuberculosis and COVID-19 in schools in South Africa, Switzerland, and Tanzania: Modeling of environmental data

The COVID-19 pandemic renewed interest in airborne transmission of respiratory infections, particularly in congregate indoor settings, such as schools. We modeled transmission risks of tuberculosis (caused by Mycobacterium tuberculosis, Mtb) and COVID-19 (caused by SARS-CoV-2) in South African, Swiss and Tanzanian secondary schools. We estimated the risks of infection with the Wells-Riley equation, expressed as the median with 2.5% and 97.5% quantiles (credible interval [CrI]), based on the ventilation rate and the duration of exposure to infectious doses (so-called quanta). We computed the air change rate (ventilation) using carbon dioxide (CO2) as a tracer gas and modeled the quanta generation rate based on reported estimates from the literature. The share of infectious students in the classroom is determined by country-specific estimates of pulmonary TB. For SARS-CoV-2, the number of infectious students was estimated based on excess mortality to mitigate the bias from country-specific reporting and testing. Average CO2 concentration (parts per million [ppm]) was 1,610 ppm in South Africa, 1,757 ppm in Switzerland, and 648 ppm in Tanzania. The annual risk of infection for Mtb was 22.1% (interquartile range [IQR] 2.7%-89.5%) in South Africa, 0.7% (IQR 0.1%-6.4%) in Switzerland, and 0.5% (IQR 0.0%-3.9%) in Tanzania. For SARS-CoV-2, the monthly risk of infection was 6.8% (IQR 0.8%-43.8%) in South Africa, 1.2% (IQR 0.1%-8.8%) in Switzerland, and 0.9% (IQR 0.1%-6.6%) in Tanzania. The differences in transmission risks primarily reflect a higher incidence of SARS-CoV-2 and particularly prevalence of TB in South Africa, but also higher air change rates due to better natural ventilation of the classrooms in Tanzania. Global comparisons of the modeled risk of infectious disease transmission in classrooms can provide high-level information for policy-making regarding appropriate infection control strategies.

Signatures of transmission in within-host M. tuberculosis variation

Background

Because M. tuberculosis evolves slowly, transmission clusters often contain multiple individuals with identical consensus genomes, making it difficult to reconstruct transmission chains. Finding additional sources of shared M. tuberculosis variation could help overcome this problem. Previous studies have reported M. tuberculosis diversity within infected individuals; however, whether within-host variation improves transmission inferences remains unclear.

Methods

To evaluate the transmission information present in within-host M. tuberculosis variation, we re-analyzed publicly available sequence data from three household transmission studies, using household membership as a proxy for transmission linkage between donor-recipient pairs.

Findings

We found moderate levels of minority variation present in M. tuberculosis sequence data from cultured isolates that varied significantly across studies (mean: 6, 7, and 170 minority variants above a 1% minor allele frequency threshold, outside of PE/PPE genes). Isolates from household members shared more minority variants than did isolates from unlinked individuals in the three studies (mean 98 shared minority variants vs. 10; 0.8 vs. 0.2, and 0.7 vs. 0.2, respectively). Shared within-host variation was significantly associated with household membership (OR: 1.51 [1.30,1.71], for one standard deviation increase in shared minority variants). Models that included shared within-host variation improved the accuracy of predicting household membership in all three studies as compared to models without within-host variation (AUC: 0.95 versus 0.92, 0.99 versus 0.95, and 0.93 versus 0.91).

Interpretation

Within-host M. tuberculosis variation persists through culture and could enhance the resolution of transmission inferences. The substantial differences in minority variation recovered across studies highlights the need to optimize approaches to recover and incorporate within-host variation into automated phylogenetic and transmission inference.

Funding

NIAID: 5K01AI173385.

Finding and treating both tuberculosis disease and latent infection during population-wide active case finding for tuberculosis elimination

In recognition of the high rates of undetected tuberculosis in the community, the World Health Organization (WHO) encourages targeted active case finding (ACF) among "high-risk" populations. While this strategy has led to increased case detection in these populations, the epidemic impact of these interventions has not been demonstrated. Historical data suggest that population-wide (untargeted) ACF can interrupt transmission in high-incidence settings, but implementation remains lacking, despite recent advances in screening tools. The reservoir of latent infection-affecting up to a quarter of the global population -complicates elimination efforts by acting as a pool from which future tuberculosis cases may emerge, even after all active cases have been treated. A holistic case finding strategy that addresses both active disease and latent infection is likely to be the optimal approach for rapidly achieving sustainable progress toward TB elimination in a durable way, but safety and cost effectiveness have not been demonstrated. Sensitive, symptom-agnostic community screening, combined with effective tuberculosis treatment and prevention, should eliminate all infectious cases in the community, whilst identifying and treating people with latent infection will also eliminate tomorrow's tuberculosis cases. If real strides toward global tuberculosis elimination are to be made, bold strategies are required using the best available tools and a long horizon for cost-benefit assessment.

Safe CO2 threshold limits for indoor long-range airborne transmission control of COVID-19

CO₂-based infection risk monitoring is highly recommended during the current COVID-19 pandemic. However, the CO₂ monitoring thresholds proposed in the literature are mainly for spaces with fixed occupants. Determining CO₂ threshold is challenging in spaces with changing occupancy due to the co-existence of quanta and CO₂ remaining from previous occupants. Here, we propose a new calculation framework for deriving safe excess CO₂ thresholds (above outdoor level), C _t, for various spaces with fixed/changing occupancy and analyze the uncertainty involved. We categorized common indoor spaces into three scenarios based on their occupancy conditions, e.g., fixed or varying infection ratios (infectors/occupants). We proved that the rebreathed fraction-based model can be applied directly for deriving C _t in the case of a fixed infection ratio (Scenario 1 and Scenario 2). In the case of varying infection ratios (Scenario 3), C _t derivation must follow the general calculation framework due to the existence of initial quanta/excess CO₂. Otherwise, C _t can be significantly biased (e.g., 260 ppm) when the infection ratio varies greatly. C _t can vary significantly based on specific space factors such as occupant number, physical activity, and community prevalence, e.g., 7 ppm for gym and 890 ppm for lecture hall, indicating C _t must be determined on a case-by-case basis. An uncertainty of up to 6 orders of magnitude for C _t was found for all cases due to uncertainty in emissions of quanta and CO₂, thus emphasizing the role of accurate emissions data in determining C _t.

[Tuberculosis remains a public health issue in South Africa]

Tuberculosis is an airborne infectious disease that can damage the lungs and other body organs. Early detection of people infected with Koch's bacillus is important because tuberculosis is a contagious disease. It can be cured. It is still a very common disease in South Africa and is fatal for sixty thousand people per year. Tuberculosis remains a major health problem for which the public authorities must put in place more effective prevention and management policies, particularly by improving the training of nurses and doctors.

The Association Between Social Network Characteristics and Tuberculosis Infection Among Adults in 9 Rural Ugandan Communities

BACKGROUND

Social network analysis can elucidate tuberculosis transmission dynamics outside the home and may inform novel network-based case-finding strategies.

METHODS

We assessed the association between social network characteristics and prevalent tuberculosis infection among residents (aged ≥15 years) of 9 rural communities in Eastern Uganda. Social contacts named during a census were used to create community-specific nonhousehold social networks. We evaluated whether social network structure and characteristics of first-degree contacts (sex, human immunodeficiency virus [HIV] status, tuberculosis infection) were associated with revalent tuberculosis infection (positive tuberculin skin test [TST] result) after adjusting for individual-level risk factors (age, sex, HIV status, tuberculosis contact, wealth, occupation, and Bacillus Calmette-Guérin [BCG] vaccination) with targeted maximum likelihood estimation.

RESULTS

Among 3 335 residents sampled for TST, 32% had a positive TST results and 4% reported a tuberculosis contact. The social network contained 15 328 first-degree contacts. Persons with the most network centrality (top 10%) (adjusted risk ratio, 1.3 [95% confidence interval, 1.1-1.1]) and the most (top 10%) male contacts (1.5 [1.3-1.9]) had a higher risk of prevalent tuberculosis, than those in the remaining 90%. People with ≥1 contact with HIV (adjusted risk ratio, 1.3 [95% confidence interval, 1.1-1.6]) and ≥2 contacts with tuberculosis infection were more likely to have tuberculosis themselves (2.6 [ 95% confidence interval: 2.2-2.9]).

CONCLUSIONS

Social networks with higher centrality, more men, contacts with HIV, and tuberculosis infection were positively associated with tuberculosis infection. Tuberculosis transmission within measurable social networks may explain prevalent tuberculosis not associated with a household contact. Further study on network-informed tuberculosis case finding interventions is warranted.

Epidemiological correlates of overweight and obesity in the Northern Cape Province, South Africa

Background

In the past several decades, obesity has become a major public health issue worldwide, associated with increased rates of chronic disease and death. Like many developing nations, South Africa is experiencing rapid increases in BMI, and as a result, evidence-based preventive strategies are needed to reduce the increasing burden of overweight and obesity. This study aimed to determine the prevalence and predictors of overweight and obesity among a multi-ethnic cohort from the rural Northern Cape of South Africa.

Methods

These data were collected as part of a tuberculosis (TB) case-control study, with 395 healthy control participants included in the final analysis. Overweight and obesity were defined according to WHO classification. Multivariate linear models of BMI were generated using sex, age, education level, smoking, alcohol consumption, and diabetes as predictor variables. We also used multivariable logistic regression analysis to assess the relationship of these factors with overweight and obesity.

Results

The average BMI in our study cohort was 25.2. The prevalence of overweight was 18.0% and the prevalence of obesity was 25.0%. We find that female sex, being older, having more years of formal education, having diabetes, and being in a rural area are all positively associated with BMI in our dataset. Women (OR = 5.6, 95% CI [3.3-9.8]), rural individuals (OR = 3.3, 95% CI [1.9-6.0]), older individuals (OR = 1.02, 95% CI [1-1.04]), and those with more years of education (OR = 1.2, 95% CI [1.09-1.32]) were all more likely to be overweight or obese. Alternatively, being a smoker is negatively associated with BMI and decreases one's odds of being overweight or obese (OR = 0.28, 95% CI [0.16-0.46]).

Conclusions

We observed a high prevalence of overweight and obesity in this study. The odds of being overweight and obese were higher in women, those living in rural areas, and those with more education, and increases with age. Community-based interventions to control obesity in this region should pay special attention to these groups.

Tuberculosis Infection in Children and Adolescents

The burden of tuberculosis (TB) in children and adolescents remains very significant. Several million children and adolescents are infected with TB each year worldwide following exposure to an infectious TB case and the risk of progression from TB infection to tuberculosis disease is higher in this group compared to adults. This review describes the risk factors for TB infection in children and adolescents. Following TB exposure, the risk of TB infection is determined by a combination of index case characteristics, contact features, and environmental determinants. We also present the recently recommended approaches to diagnose and treat TB infection as well as novel tests for infection. The tests for TB infection have limitations and diagnosis still relies on an indirect immunological assessment of cellular immune response to Mycobacterium tuberculosis antigens using immunodiagnostic testing. It is recommended that TB exposed children and adolescents and those living with HIV receive TB preventive treatment (TPT) to reduce the risk of progression to TB disease. Several TPT regimens of similar effectiveness and safety are now available and recommended by the World Health Organisation.

Transmissibility of tuberculosis among students and non-students: an occupational-specific mathematical modelling

BACKGROUND

Recently, despite the steady decline in the tuberculosis (TB) epidemic globally, school TB outbreaks have been frequently reported in China. This study aimed to quantify the transmissibility of Mycobacterium tuberculosis (MTB) among students and non-students using a mathematical model to determine characteristics of TB transmission.

METHODS

We constructed a dataset of reported TB cases from four regions (Jilin Province, Xiamen City, Chuxiong Prefecture, and Wuhan City) in China from 2005 to 2019. We classified the population and the reported cases under student and non-student groups, and developed two mathematical models [nonseasonal model (Model A) and seasonal model (Model B)] based on the natural history and transmission features of TB. The effective reproduction number (R_eff) of TB between groups were calculated using the collected data.

RESULTS

During the study period, data on 456,423 TB cases were collected from four regions: students accounted for 6.1% of cases. The goodness-of-fit analysis showed that Model A had a better fitting effect (P < 0.001). The average R_eff of TB estimated from Model A was 1.68 [interquartile range (IQR): 1.20-1.96] in Chuxiong Prefecture, 1.67 (IQR: 1.40-1.93) in Xiamen City, 1.75 (IQR: 1.37-2.02) in Jilin Province, and 1.79 (IQR: 1.56-2.02) in Wuhan City. The average R_eff of TB in the non-student population was 23.30 times (1.65/0.07) higher than that in the student population.

CONCLUSIONS

The transmissibility of MTB remains high in the non-student population of the areas studied, which is still dominant in the spread of TB. TB transmissibility from the non-student-to-student-population had a strong influence on students. Specific interventions, such as TB screening, should be applied rigorously to control and to prevent TB transmission among students.

Mycobacterium tuberculosis Transmission in High-Incidence Settings-New Paradigms and Insights

Tuberculosis has affected humankind for thousands of years, but a deeper understanding of its cause and transmission only arose after Robert Koch discovered Mycobacterium tuberculosis in 1882. Valuable insight has been gained since, but the accumulation of knowledge has been frustratingly slow and incomplete for a pathogen that remains the number one infectious disease killer on the planet. Contrast that to the rapid progress that has been made in our understanding SARS-CoV-2 (the cause of COVID-19) aerobiology and transmission. In this Review, we discuss important historical and contemporary insights into M. tuberculosis transmission. Historical insights describing the principles of aerosol transmission, as well as relevant pathogen, host and environment factors are described. Furthermore, novel insights into asymptomatic and subclinical tuberculosis, and the potential role this may play in population-level transmission is discussed. Progress towards understanding the full spectrum of M. tuberculosis transmission in high-burden settings has been hampered by sub-optimal diagnostic tools, limited basic science exploration and inadequate study designs. We propose that, as a tuberculosis field, we must learn from and capitalize on the novel insights and methods that have been developed to investigate SARS-CoV-2 transmission to limit ongoing tuberculosis transmission, which sustains the global pandemic.

Detection of M. tuberculosis in the environment as a tool for identifying high-risk locations for tuberculosis transmission

Tuberculosis (TB) remains a leading cause of infectious mortality globally, yet most cases cannot be epidemiologically linked even with extensive contact investigations and whole genome sequencing. Consequently, there remain major gaps in our understanding of where and when M. tuberculosis (Mtb) exposures occur. We aimed to investigate whether Mtb can be detected in environments where TB patients were recently present, which could serve as a tool for characterizing exposure risk. We collected 389 environment surface (ES) swabs from two high TB burden prisons in Brazil, sampling 41 (n = 340) cells occupied by individuals with active TB and 7 (n = 49) cells from individuals without TB. In a subset of pooled swabs (n = 6) and a swab from a cigarette lighter from the cell with active TB patients, we enriched Mtb DNA using RNA-bait hybrid capture assays and performed whole genome sequencing. In prison cells, Mtb DNA was detected in 55/340 (16 %) of ES swabs from cells occupied by active TB patients and none (0/49) from cells in which no active TB patients were present. Mtb was detected in 13/16 (81 %) prison cells occupied by the individuals with high/medium sputum Xpert Mtb load and 8/25 (32 %) with low/very low sputum Mtb load (p = 0.003). Seven hybrid capture samples had a median genomic coverage of 140×. rpoB mutations conferring high-level rifampin resistance were detected in 3/7 ES swabs. Mtb was frequently detectable in environments recently occupied by individuals with active TB. This approach could be applied in congregate environments to identify and characterize high-risk settings for Mtb exposure.

Improving Estimates of Social Contact Patterns for Airborne Transmission of Respiratory Pathogens

Data on social contact patterns are widely used to parameterize age-mixing matrices in mathematical models of infectious diseases. Most studies focus on close contacts only (i.e., persons spoken with face-to-face). This focus may be appropriate for studies of droplet and short-range aerosol transmission but neglects casual or shared air contacts, who may be at risk from airborne transmission. Using data from 2 provinces in South Africa, we estimated age mixing patterns relevant for droplet transmission, nonsaturating airborne transmission, and Mycobacterium tuberculosis transmission, an airborne infection where saturation of household contacts occurs. Estimated contact patterns by age did not vary greatly between the infection types, indicating that widespread use of close contact data may not be resulting in major inaccuracies. However, contact in persons >50 years of age was lower when we considered casual contacts, and therefore the contribution of older age groups to airborne transmission may be overestimated.

Importance of ventilation and occupancy to Mycobacterium tuberculosis transmission rates in congregate settings

BACKGROUND

Ventilation rates are a key determinant of the transmission rate of Mycobacterium tuberculosis and other airborne infections. Targeting infection prevention and control (IPC) interventions at locations where ventilation rates are low and occupancy high could be a highly effective intervention strategy. Despite this, few data are available on ventilation rates and occupancy in congregate locations in high tuberculosis burden settings.

METHODS

We collected carbon dioxide concentration and occupancy data in congregate locations and public transport on 88 occasions, in Cape Town, South Africa. For each location, we estimated ventilation rates and the relative rate of infection, accounting for ventilation rates and occupancy.

RESULTS

We show that the estimated potential transmission rate in congregate settings and public transport varies greatly between different settings. Overall, in the community we studied, estimated infection risk was higher in minibus taxis and trains than in salons, bars, and shops. Despite good levels of ventilation, infection risk could be high in the clinic due to high occupancy levels.

CONCLUSION

Public transport in particular may be promising targets for infection prevention and control interventions in this setting, both to reduce Mtb transmission, but also to reduce the transmission of other airborne pathogens such as measles and SARS-CoV-2.

Population-based sequencing of Mycobacterium tuberculosis reveals how current population dynamics are shaped by past epidemics

Transmission is a driver of tuberculosis (TB) epidemics in high-burden regions, with assumed negligible impact in low-burden areas. However, we still lack a full characterization of transmission dynamics in settings with similar and different burdens. Genomic epidemiology can greatly help to quantify transmission, but the lack of whole genome sequencing population-based studies has hampered its application. Here, we generate a population-based dataset from Valencia region and compare it with available datasets from different TB-burden settings to reveal transmission dynamics heterogeneity and its public health implications. We sequenced the whole genome of 785 Mycobacterium tuberculosis strains and linked genomes to patient epidemiological data. We use a pairwise distance clustering approach and phylodynamic methods to characterize transmission events over the last 150 years, in different TB-burden regions. Our results underscore significant differences in transmission between low-burden TB settings, i.e., clustering in Valencia region is higher (47.4%) than in Oxfordshire (27%), and similar to a high-burden area as Malawi (49.8%). By modeling times of the transmission links, we observed that settings with high transmission rate are associated with decades of uninterrupted transmission, irrespective of burden. Together, our results reveal that burden and transmission are not necessarily linked due to the role of past epidemics in the ongoing TB incidence, and highlight the need for in-depth characterization of transmission dynamics and specifically tailored TB control strategies.

Aerosolization of Mycobacterium tuberculosis by Tidal Breathing

Rationale: Interrupting tuberculosis (TB) transmission requires an improved understanding of how and when the causative organism, Mycobacterium tuberculosis (Mtb), is aerosolized. Although cough is commonly assumed to be the dominant source of Mtb aerosols, recent evidence of cough-independent Mtb release implies the contribution of alternative mechanisms. Objectives: To compare the aerosolization of Mtb bacilli and total particulate matter from patients with TB during three separate respiratory maneuvers: tidal breathing (TiBr), FVC, and cough. Methods: Bioaerosol sampling and Mtb enumeration by live-cell, fluorescence microscopy were combined with real-time measurement of CO₂ concentration and total particle counts from 38 patients with GeneXpert-positive TB before treatment initiation. Measurements and Main Results: For all maneuvers, the proportions of particles detected across five size categories were similar, with most particles falling between 0.5-5 μm. Although total particle counts were 4.8-fold greater in cough samples than either TiBr or FVC, all three maneuvers returned similar rates of positivity for Mtb. No correlation was observed between total particle production and Mtb count. Instead, for total Mtb counts, the variability between individuals was greater than the variability between sampling maneuvers. Finally, when modelled using 24-hour breath and cough frequencies, our data indicate that TiBr might contribute more than 90% of the daily aerosolized Mtb among symptomatic patients with TB. Conclusions: Assuming the number of viable Mtb organisms released offers a reliable proxy of patient infectiousness, our observations imply that TiBr and interindividual variability in Mtb release might be significant contributors to TB transmission among active cases.

Estimating the contribution of transmission in primary healthcare clinics to community-wide TB disease incidence, and the impact of infection prevention and control interventions, in KwaZulu-Natal, South Africa

BACKGROUND

There is a high risk of Mycobacterium tuberculosis (Mtb) transmission in healthcare facilities in high burden settings. WHO guidelines on tuberculosis (TB) infection prevention and control (IPC) recommend a range of measures to reduce transmission in healthcare settings. These were evaluated primarily based on evidence for their effects on transmission to healthcare workers in hospitals. To estimate the overall impact of IPC interventions, it is necessary to also consider their impact on community-wide TB incidence and mortality.

METHODS

We developed an individual-based model of Mtb transmission in households, primary healthcare (PHC) clinics, and all other congregate settings. The model was parameterised using data from a high HIV prevalence community in South Africa, including data on social contact by setting, by sex, age, and HIV/antiretroviral therapy status; and data on TB prevalence in clinic attendees and the general population. We estimated the proportion of disease in adults that resulted from transmission in PHC clinics, and the impact of a range of IPC interventions in clinics on community-wide TB.

RESULTS

We estimate that 7.6% (plausible range 3.9%-13.9%) of non-multidrug resistant and multidrug resistant TB in adults resulted directly from transmission in PHC clinics in the community in 2019. The proportion is higher in HIV-positive people, at 9.3% (4.8%-16.8%), compared with 5.3% (2.7%-10.1%) in HIV-negative people. We estimate that IPC interventions could reduce incident TB cases in the community in 2021-2030 by 3.4%-8.0%, and deaths by 3.0%-7.2%.

CONCLUSIONS

A non-trivial proportion of TB results from transmission in clinics in the study community, particularly in HIV-positive people. Implementing IPC interventions could lead to moderate reductions in disease burden. We recommend that IPC measures in clinics should be implemented for their benefits to staff and patients, but also for their likely effects on TB incidence and mortality in the surrounding community.

COVID-19 hot-spot strategy: a special innovation in pandemic response, Oyo State Nigeria

BACKGROUND

COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a pandemic. Oyo state, Nigeria with a population of 9,233,010, recorded the first case of COVID-19 on the 12th of March 2020 and it is among the highest contributing States to the nation's burden of the disease with 3267 confirmed cases, including 40 deaths as of date, with an overall test positivity rate of 18.1%, far higher compared to the National average within a limited period from recorded index case. A 'Hotspot strategy' was designed by the Presidential Task Force on COVID-19 and Oyo State was selected to implement the strategy through upscaling case detection, isolation and treatment, quarantine of contacts and strengthening public health and social measures.

METHODS

We used a descriptive cross-sectional survey of 3 identified hotspot Local Government Areas (LGAs) in Oyo State using mobile phones under Surveillance, Outbreak Response Management and Analysis System (SORMAS) platform to collect data from October to December 2020. Interventions comprised of enhanced active case search, contact line listing, contact investigation, and contact follow-up as well as to facilitate data collection and entry, community sensitization and management of alert/rumors. Baseline information and that after the 3-month period was then analyzed with the descriptive statistics presented.

RESULTS

The implementation of the hotspot strategy was shown to have had a major impact in Irepo LGA, where more than a 100% increase in samples tested, confirmed cases, contacts listed and contacts followed were recorded, while there were no significance changes noticed in Ibadan North and Lagelu LGAs. However, test positivity rates among contacts were found to be quite high in Ibadan North LGA (48%), compared to the other two, even though Lagelu LGA (5.7%) tested more contacts than Ibadan North.

CONCLUSION

The observed increase in number of samples tested, cases confirmed, contact listed and investigated as well as test positivity rate in the 3 LGAs after the intervention implies that the hotspot strategy can be said to have contributed positively to the sensitivity of COVID-19 surveillance in Oyo State, Nigeria. This implies that strengthening this 'hotspot strategy' may be a key area of focus to improve COVID-19 surveillance sensitivity and response and in turn may help in breaking the transmission and bringing the pandemic to a halt.

Estimating Tuberculosis Transmission Risks in a Primary Care Clinic in South Africa: Modeling of Environmental and Clinical Data

BACKGROUND

Congregate settings, such as healthcare clinics, may play an essential role in Mycobacterium tuberculosis (Mtb) transmission. Using patient and environmental data, we studied transmission at a primary care clinic in South Africa.

METHODS

We collected patient movements, cough frequency, and clinical data, and measured indoor carbon dioxide (CO2) levels, relative humidity, and Mtb genomes in the air. We used negative binomial regression model to investigate associations.

RESULTS

We analyzed 978 unique patients who contributed 14 795 data points. The median patient age was 33 (interquartile range [IQR], 26-41) years, and 757 (77.4%) were female. Overall, median CO2 levels were 564 (IQR 495-646) parts per million and were highest in the morning. Median number of coughs per day was 466 (IQR, 368-503), and overall median Mtb DNA copies/μL/day was 4.2 (IQR, 1.2-9.5). We found an increased presence of Mtb DNA in the air of 32% (95% credible interval, 7%-63%) per 100 additional young adults (aged 15-29 years) and 1% (0-2%) more Mtb DNA per 10% increase of relative humidity. Estimated cumulative transmission risks for patients attending the clinic monthly for at least 1 hour range between 9% and 29%.

CONCLUSIONS

We identified young adults and relative humidity as potentially important factors for transmission risks in healthcare clinics. Our approach should be used to detect transmission and evaluate infection control interventions.

Direct estimates of absolute ventilation and estimated Mycobacterium tuberculosis transmission risk in clinics in South Africa

Healthcare facilities are important sites for the transmission of pathogens spread via bioaerosols, such as Mycobacterium tuberculosis. Natural ventilation can play an important role in reducing this transmission. We aimed to measure rates of natural ventilation in clinics in KwaZulu-Natal and Western Cape provinces, South Africa, then use these measurements to estimate Mycobacterium tuberculosis transmission risk. We measured ventilation in clinic spaces using a tracer-gas release method. In spaces where this was not possible, we estimated ventilation using data on indoor and outdoor carbon dioxide levels. Ventilation was measured i) under usual conditions and ii) with all windows and doors fully open. Under various assumptions about infectiousness and duration of exposure, measured absolute ventilation rates were related to risk of Mycobacterium tuberculosis transmission using the Wells-Riley Equation. In 2019, we obtained ventilation measurements in 33 clinical spaces in 10 clinics: 13 consultation rooms, 16 waiting areas and 4 other clinical spaces. Under usual conditions, the absolute ventilation rate was much higher in waiting rooms (median 1769 m3/hr, range 338-4815 m3/hr) than in consultation rooms (median 197 m3/hr, range 0-1451 m3/hr). When compared with usual conditions, fully opening existing doors and windows resulted in a median two-fold increase in ventilation. Using standard assumptions about infectiousness, we estimated that a health worker would have a 24.8% annual risk of becoming infected with Mycobacterium tuberculosis, and that a patient would have an 0.1% risk of becoming infected per visit. Opening existing doors and windows and rearranging patient pathways to preferentially use better ventilated clinic spaces result in important reductions in Mycobacterium tuberculosis transmission risk. However, unless combined with other tuberculosis infection prevention and control interventions, these changes are insufficient to reduce risk to health workers, and other highly exposed individuals, to acceptable levels.

Sociological variety and the transmission efficiency of Mycobacterium tuberculosis: a secondary analysis of qualitative and quantitative data from 15 communities in Zambia

OBJECTIVES

Selected Zambian communities formed part of a cluster randomised trial: the Zambia and South Africa TB and AIDS Reduction study (ZAMSTAR). There was wide variability in the prevalence of Mycobacterium tuberculosis infection and tuberculosis (TB) disease across these communities. We sought to clarify whether specific communities could have been more/less vulnerable to M. tuberculosis transmission as a result of sociological variety relevant to transmission efficiency.

DESIGN

We conducted a mixed methods secondary analysis using existing data sets. First, we analysed qualitative data to categorise and synthesise patterns of socio-spatial engagement across communities. Second, we compared emergent sociological variables with a measure of transmission efficiency: the ratio of the annual risk of infection to TB prevalence.

SETTING

ZAMSTAR communities in urban and peri-urban Zambia, spanning five provinces.

PARTICIPANTS

Fifteen communities, each served by a health facility offering TB treatment to a population of at least 25 000. TB notification rates were at least 400 per 100 000 per annum and HIV seroprevalence was estimated to be high.

RESULTS

Crowding, movement, livelihoods and participation in recreational activity differed across communities. Based on 12 socio-spatial indicators, communities were qualitatively classified as more/less spatially crowded and as more/less socially 'open' to contact with others, with implications for the presumptive risk of M. tuberculosis transmission. For example, watching video shows in poorly ventilated structures posed a presumptive risk in more socially open communities, while outdoor farming and/or fishing were particularly widespread in communities with lower transmission measures.

CONCLUSIONS

A dual dynamic of 'social permeability' and crowding appeared relevant to disparities in M. tuberculosis transmission efficiency. To reduce transmission, certain socio-spatial aspects could be adjusted (eg, increasing ventilation on transport), while more structural aspects are less malleable (eg, reliance on public transport). We recommend integrating community level typologies with genome sequencing techniques to further explore the significance of 'social permeability'.

TRIAL REGISTRATION NUMBER

ISRCTN36729271.

Monitoring the presence and persistence of SARS-CoV-2 in water-food-environmental compartments: State of the knowledge and research needs

The recent spread of severe acute respiratory syndrome coronavirus (SAR-CoV-2) and the accompanied coronavirus disease 2019 (COVID-19) has continued ceaselessly despite the implementations of popular measures, which include social distancing and outdoor face masking as recommended by the World Health Organization. Due to the unstable nature of the virus, leading to the emergence of new variants that are claimed to be more and rapidly transmissible, there is a need for further consideration of the alternative potential pathways of the virus transmissions to provide the needed and effective control measures. This review aims to address this important issue by examining the transmission pathways of SARS-CoV-2 via indirect contacts such as fomites and aerosols, extending to water, food, and other environmental compartments. This is essentially required to shed more light regarding the speculation of the virus spread through these media as the available information regarding this is fragmented in the literature. The existing state of the information on the presence and persistence of SARS-CoV-2 in water-food-environmental compartments is essential for cause-and-effect relationships of human interactions and environmental samples to safeguard the possible transmission and associated risks through these media. Furthermore, the integration of effective remedial measures previously used to tackle the viral outbreaks and pandemics, and the development of new sustainable measures targeting at monitoring and curbing the spread of SARS-CoV-2 were emphasized. This study concluded that alternative transmission pathways via human interactions with environmental samples should not be ignored due to the evolving of more infectious and transmissible SARS-CoV-2 variants.

Tuberculosis in Adolescents and Young Adults: Emerging Data on TB Transmission and Prevention among Vulnerable Young People

Adolescents and young adults (AYA, ages 10-24 years) comprise a uniquely important but understudied population in global efforts to end tuberculosis (TB), the leading infectious cause of death by a single agent worldwide prior to the COVID-19 pandemic. While TB prevention and care strategies often overlook AYA by grouping them with either children or adults, AYA have particular physiologic, developmental, and social characteristics that require dedicated approaches. This review describes current evidence on the prevention and control of TB among AYA, including approaches to TB screening, dynamics of TB transmission among AYA, and management challenges within the context of unique developmental needs. Challenges are considered for vulnerable groups of AYA such as migrants and refugees; AYA experiencing homelessness, incarceration, or substance use; and AYA living with HIV. We outline areas for needed research and implementation strategies to address TB among AYA globally.

The impact of COVID-19 on TB: a review of the data

Early in the COVID-19 pandemic, models predicted hundreds of thousands of additional TB deaths as a result of health service disruption. To date, empirical evidence on the effects of COVID-19 on TB outcomes has been limited. Here we summarise the evidence available at a country level, identifying broad mechanisms by which COVID-19 may modify TB burden and mitigation efforts. From the data, it is clear that there have been substantial disruptions to TB health services and an increase in vulnerability to TB. Evidence for changes in Mycobacterium tuberculosis transmission is limited, and it remains unclear how the resources required and available for the TB response have changed. To advocate for additional funding to mitigate the impact of COVID-19 on the global TB burden, and to efficiently allocate resources for the TB response, requires a significant improvement in the TB data available.

COVID-19 outbreak and Urban dynamics: regional variations in India

India was the second highest COVID-19 affected country in the world with 2.1 million cases by 11th August. This study focused on the spatial transmission of the pandemic among the 640 districts in India over time, and aimed to understand the urban-centric nature of the infection. The connectivity context was emphasized that possibly had inflicted the outbreak. Using the modes of transmission data for the available cases, the diffusion of this disease was explained. Metropolitans contributed three-fourths of total cases from the beginning. The transport networks attributed significantly in transmitting the virus from the urban containment zones. Later, there was a gradual shift of infections from urban to rural areas; however, the numbers kept increasing in the former. The massive reverse migration after lockdown spiked the infected cases further. Districts with airports reported more with influx of international passengers. A profound east-west division in April with higher infections in the southern and western districts existed. By mid-May eastern India saw a steep rise in active cases. Moran's I analysis showed a low autocorrelation initially which increased over time. Hotspot clustering was observed in western Maharashtra, eastern Tamil Nadu, Gujarat and around Kolkata by the second week of August. The diffusion was due to travel, exposure to infected individuals and among the frontline workers. Spatial regression models confirmed that urbanization was positively correlated with higher incidences of infections. Transit mediums, especially rail and aviation were positively associated. These models validated the crucial role of spatial proximity in diffusion of the pandemic.

The effect of occupant distribution on energy consumption and COVID-19 infection in buildings: A case study of university building

The occupant density in buildings is one of the major and overlooked parameters affecting the energy consumption and virus transmission risk in buildings. HVAC systems energy consumption is highly dependent on the number of occupants. Studies on the transmission of COVID-19 virus have indicated a direct relationship between occupant density and COVID-19 infection risk. This study aims to seek the optimum occupant distribution patterns that account for the lowest number of infected people and minimum energy consumption. A university building located in Tehran has been chosen as a case study, due to its flexibility in performing various occupant distribution patterns. This multi-objective optimization problem, with the objective functions of energy consumption and COVID-19 infected people, is solved by NSGA-II algorithm. Energy consumption is evaluated by EnergyPlus, then it is supplied to the algorithm through a co-simulation communication between EnergyPlus and MATLAB. Results of this optimization algorithm for 5 consequent winter and summer days, represent optimum occupant distribution patterns, associated with minimum energy consumption and COVID-19 infected people for winter and summer. Building air exchange rate, class duration, and working hours of the university, as the COVID-19 controlling approaches were studied, and promising results have been obtained. It was concluded that an optimal population distribution can reduce the number of infected people by up to 56% and energy consumption by 32%. Furthermore, it was concluded that virtual learning is an excellent approach in universities to control the number of infections and energy consumption.

Tuberculosis infection and disease in South African adolescents with perinatally acquired HIV on antiretroviral therapy: a cohort study

INTRODUCTION

There are limited data on Tuberculosis (TB) in adolescents with perinatally acquired HIV (APHIV). We examined the incidence and determinants of TB infection and disease in the Cape Town Adolescent Antiretroviral Cohort (CTAAC).

METHODS

Youth between nine and fourteen years on antiretroviral therapy (ART) for more than six months in public sector care, and age-matched HIV-negative adolescents, were enrolled between July 2013 through March 2015 and followed six-monthly. Data were censored on 31 October 2018. Symptom screening, chest radiograph, viral load, CD4 count, QuantiFERON (QFT) and sputum for Xpert MTB/RIF, microscopy, culture and sensitivity were performed annually. TB infection was defined by a QFT of >0.35 IU/mL. TB diagnosis was defined as confirmed (culture or Xpert MTB/RIF positive) or unconfirmed (clinical diagnosis and started on TB treatment). Analyses examined the incidence and determinants of TB infection and disease.

RESULTS

Overall 496 HIV+ and 103 HIV-negative participants (median age at enrolment 12 years (interquartile range, IQR 10.6 to 13.3) were followed for a median of 3.1 years (IQR 3.0 to 3.4); 50% (298/599) were male. APHIV initiated ART at median age 4.4 years (IQR 2.1 to 7.6). At enrolment, 376/496 (76%) had HIV viral load <40 copies/mL, median CD4 count was 713 cells/mm3 and 179/559 (32%) were QFT+, with no difference by HIV status (APHIV 154/468, 33%; HIV negative 25/91, 27%; p = 0.31). The cumulative QFT+ prevalence was similar (APHIV 225/492, 46%; 95%CI 41% to 50%; HIV negative 44/98, 45%; 95% CI 35% to 55%; p = 0.88). APHIV had a higher incidence of all TB disease than HIV-negative adolescents (2.2/100PY, 95% CI 1.6 to 3.1 vs. 0.3/100PY, 95% CI 0.04 to 2.2; IRR 7.36, 95% CI 1.01 to 53.55). The rate of bacteriologically confirmed TB in APHIV was 1.3/100 PY compared to 0.3/100PY for HIV-negative adolescents, suggesting a fourfold increased risk of developing TB disease in APHIV despite access to ART. In addition, a positive QFT at enrolment was not predictive of TB in this population.

CONCLUSIONS

High incidence rates of TB disease occur in APHIV despite similar QFT conversion rates to HIV-negative adolescents. Strategies to prevent TB in this vulnerable group must be strengthened.

Inflammatory Determinants of Differential Tuberculosis Risk in Pre-Adolescent Children and Young Adults

The risk of progression from Mycobacterium tuberculosis (M.tb) infection to active tuberculosis (TB) disease varies markedly with age. TB disease is significantly less likely in pre-adolescent children above 4 years of age than in very young children or post-pubescent adolescents and young adults. We hypothesized that pro-inflammatory responses to M.tb in pre-adolescent children are either less pronounced or more regulated, than in young adults. Inflammatory and antimicrobial mediators, measured by microfluidic RT-qPCR and protein bead arrays, or by analyzing published microarray data from TB patients and controls, were compared in pre-adolescent children and adults. Multivariate analysis revealed that M.tb-uninfected 8-year-old children had lower levels of myeloid-associated pro-inflammatory mediators than uninfected 18-year-old young adults. Relative to uninfected children, those with M.tb-infection had higher levels of similar myeloid inflammatory responses. These inflammatory mediators were also expressed after in vitro stimulation of whole blood from uninfected children with live M.tb. Our findings suggest that myeloid inflammation is intrinsically lower in pre-pubescent children than in young adults. The lower or more regulated pro-inflammatory responses may play a role in the lower risk of TB disease in this age group.

Phenotype Definition for "Resisters" to Mycobacterium tuberculosis Infection in the Literature-A Review and Recommendations

Tuberculosis (TB) remains a worldwide problem. Despite the high disease rate, not all who are infected with Mycobacterium Tuberculosis (Mtb) develop disease. Interferon-γ (IFN-γ) specific T cell immune assays such as Quantiferon and Elispot, as well as a skin hypersensitivity test, known as a tuberculin skin test, are widely used to infer infection. These assays measure immune conversion in response to Mtb. Some individuals measure persistently negative to immune conversion, despite high and prolonged exposure to Mtb. Increasing interest into this phenotype has led to multiple publications describing various aspects of these responses. However, there is a lack of a unified "resister" definition. A universal definition will improve cross study data comparisons and assist with future study design and planning. We review the current literature describing this phenotype and make recommendations for future studies.

Transcriptomic Profiles of Confirmed Pediatric Tuberculosis Patients and Household Contacts Identifies Active Tuberculosis, Infection, and Treatment Response Among Indian Children

BACKGROUND

Gene expression profiling is emerging as a tool for tuberculosis diagnosis and treatment response monitoring, but limited data specific to Indian children and incident tuberculosis infection (TBI) exist.

METHODS

Sixteen pediatric Indian tuberculosis cases were age- and sex-matched to 32 tuberculosis-exposed controls (13 developed incident TBI without subsequent active tuberculosis). Longitudinal samples were collected for ribonucleic acid sequencing. Differential expression analysis generated gene lists that identify tuberculosis diagnosis and tuberculosis treatment response. Data were compared with published gene lists. Population-specific risk score thresholds were calculated.

RESULTS

Seventy-one genes identified tuberculosis diagnosis and 25 treatment response. Within-group expression was partially explained by age, sex, and incident TBI. Transient changes in gene expression were identified after both infection and treatment. Application of 27 published gene lists to our data found variable performance for tuberculosis diagnosis (sensitivity 0.38-1.00, specificity 0.48-0.93) and treatment response (sensitivity 0.70-0.80, specificity 0.40-0.80). Our gene lists found similarly variable performance when applied to published datasets for diagnosis (sensitivity 0.56-0.85, specificity 0.50-0.85) and treatment response (sensitivity 0.49- 0.86, specificity 0.50-0.84).

CONCLUSIONS

Gene expression profiles among Indian children with confirmed tuberculosis were distinct from adult-derived gene lists, highlighting the importance of including distinct populations in differential gene expression models.

Rescuing ESAT-6 Specific CD4 T Cells From Terminal Differentiation Is Critical for Long-Term Control of Murine Mtb Infection

In most cases, Mycobacterium tuberculosis (Mtb) causes life-long chronic infections, which poses unique challenges for the immune system. Most of the current tuberculosis (TB) subunit vaccines incorporate immunodominant antigens and at this point, it is poorly understood how the CD4 T cell subsets recognizing these antigens are affected during long-term infection. Very little is known about the requirements for sustainable vaccine protection against TB. To explore this, we screened 62 human-recognized Mtb antigens during chronic murine Mtb infection and identified the four most immunodominant antigens in this setting (MPT70, Rv3020c, and Rv3019c and ESAT-6). Combined into a subunit vaccine, this fusion protein induced robust protection both in a standard short-term model and in a long-term infection model where immunity from BCG waned. Importantly, replacement of ESAT-6 with another ESAT-6-family antigen, Rv1198, led to similar short-term protection but a complete loss of bacterial control during chronic infection. This observation was further underscored, as the ESAT-6 containing vaccine mediated sustainable protection in a model of post-exposure vaccination, where the ESAT-6-replacement vaccine did not. An individual comparison of the CD4 T cell responses during Mtb infection revealed that ESAT-6-specific T cells were more terminally differentiated than the other immunodominant antigens and immunization with the ESAT-6 containing vaccine led to substantially greater reduction in the overall T cell differentiation status. Our data therefore associates long-term bacterial control with the ability of a vaccine to rescue infection-driven CD4T cell differentiation and future TB antigen discovery programs should focus on identifying antigens with the highest accompanying T cell differentiation, like ESAT-6. This also highlights the importance of long-term readouts in both preclinical and clinical studies with TB vaccines.

Understanding building-occupant-microbiome interactions toward healthy built environments: A review

Built environments, occupants, and microbiomes constitute a system of ecosystems with extensive interactions that impact one another. Understanding the interactions between these systems is essential to develop strategies for effective management of the built environment and its inhabitants to enhance public health and well-being. Numerous studies have been conducted to characterize the microbiomes of the built environment. This review summarizes current progress in understanding the interactions between attributes of built environments and occupant behaviors that shape the structure and dynamics of indoor microbial communities. In addition, this review also discusses the challenges and future research needs in the field of microbiomes of the built environment that necessitate research beyond the basic characterization of microbiomes in order to gain an understanding of the causal mechanisms between the built environment, occupants, and microbiomes, which will provide a knowledge base for the development of transformative intervention strategies toward healthy built environments. The pressing need to control the transmission of SARS-CoV-2 in indoor environments highlights the urgency and significance of understanding the complex interactions between the built environment, occupants, and microbiomes, which is the focus of this review.

Excess Risk of Tuberculous Infection among Extra-Household Contacts of Tuberculosis Cases in an African City

RATIONALE

Although households of tuberculosis cases represent a setting for intense transmission of M. tuberculosis, household exposure accounts for less than 20% of transmission within a community.

OBJECTIVES

To estimate excess risk of M. tuberculosis infection among household and extra-household contacts of index cases.

METHODS

We performed a cross-sectional study in Kampala, Uganda, to delineate social networks of tuberculosis cases and matched controls without tuberculosis. We estimated the age-stratified prevalence difference of tuberculous infection between case and control networks, partitioned as household and extra-household contacts.

RESULTS

We enrolled 123 index cases, 124 index controls, and 2415 first-degree network contacts. The prevalence of infection was highest among household contacts of cases (61.5%), lowest among household contacts of controls (25.2%), and intermediary among extra-household tuberculosis contacts (44.9%) and extra-household control contacts (41.2%). The age-adjusted prevalence difference between extra-household contacts of cases and their controls was 5.4%. The prevalence of infection was similar among the majority of extra-household case contacts and corresponding controls (47%).

CONCLUSIONS

Most first-degree social network members of tuberculosis cases do not have adequate contact with the index case to experience additional risk for infection but appear instead to acquire infection through unrecognized exposures with infectious cases in the community.

Novel approach to estimate tuberculosis transmission in primary care clinics in sub-Saharan Africa: protocol of a prospective study

INTRODUCTION

Tuberculosis (TB) transmission is difficult to measure, and its drivers are not well understood. The effectiveness of infection control measures at healthcare clinics and the most appropriate intervention strategies to interrupt transmission are unclear. We propose a novel approach using clinical, environmental and position-tracking data to study the risk of TB transmission at primary care clinics in TB and HIV high burden settings in sub-Saharan Africa.

METHODS AND ANALYSIS

We describe a novel and rapid study design to assess risk factors for airborne TB transmission at primary care clinics in high-burden settings. The study protocol combines a range of different measurements. We will collect anonymous data on the number of patients, waiting times and patient movements using video sensors. Also, we will collect acoustic sound recordings to determine the frequency and intensity of coughing. Environmental data will include indoor carbon dioxide levels (CO₂ in parts per million) and relative humidity. We will also extract routinely collected clinical data from the clinic records. The number of Mycobacterium tuberculosis particles in the air will be ascertained from dried filter units using highly sensitive digital droplet PCR. We will calculate rebreathed air volume based on people density and CO₂ levels and develop a mathematical model to estimate the risk of TB transmission. The mathematical model can then be used to estimate the effect of possible interventions such as separating patient flows or improving ventilation in reducing transmission. The feasibility of our approach was recently demonstrated in a pilot study in a primary care clinic in Cape Town, South Africa.

ETHICS AND DISSEMINATION

The study was approved by the University of Cape Town (HREC/REF no. 228/2019), the City of Cape Town (ID-8139) and the Ethics Committee of the Canton Bern (2019-02131), Switzerland. The results will be disseminated in international peer-reviewed journals.

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

Background

The risk of infection from respiratory pathogens increases according to the contact rate between the infectious case and susceptible contact, but the definition of adequate contact for transmission is not standard. In this study we aimed to identify factors that can explain the level of contact between tuberculosis cases and their social networks in an African urban environment.

Methods

This was a cross-sectional study conducted in Kampala, Uganda from 2013 to 2017. We carried out an exploratory factor analysis (EFA) in social network data from tuberculosis cases and their contacts. We evaluated the factorability of the data to EFA using the Kaiser-Meyer-Olkin Measure of Sampling Adequacy (KMO). We used principal axis factoring with oblique rotation to extract and rotate the factors, then we calculated factor scores for each using the weighted sum scores method. We assessed construct validity of the factors by associating the factors with other variables related to social mixing.

Results

Tuberculosis cases (N = 120) listed their encounters with 1154 members of their social networks. Two factors were identified, the first named “Setting” captured 61% of the variance whereas the second, named ‘Relationship’ captured 21%. Median scores for the setting and relationship factors were 10.2 (IQR 7.0, 13.6) and 7.7 (IQR 6.4, 10.1) respectively. Setting and Relationship scores varied according to the age, gender, and nature of the relationship among tuberculosis cases and their contacts. Family members had a higher median setting score (13.8, IQR 11.6, 15.7) than non-family members (7.2, IQR 6.2, 9.4). The median relationship score in family members (9.9, IQR 7.6, 11.5) was also higher than in non-family members (6.9, IQR 5.6, 8.1). For both factors, household contacts had higher scores than extra-household contacts (p < .0001). Contacts of male cases had a lower setting score as opposed to contacts of female cases. In contrast, contacts of male and female cases had similar relationship scores.

Conclusions

In this large cross-sectional study from an urban African setting, we identified two factors that can assess adequate contact between tuberculosis cases and their social network members. These findings also confirm the complexity and heterogeneity of social mixing.

2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission

With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in coronavirus disease 2019 (COVID-19), corporate entities, federal, state, county, and city governments, universities, school districts, places of worship, prisons, health care facilities, assisted living organizations, daycares, homeowners, and other building owners and occupants have an opportunity to reduce the potential for transmission through built environment (BE)-mediated pathways. Over the last decade, substantial research into the presence, abundance, diversity, function, and transmission of microbes in the BE has taken place and revealed common pathogen exchange pathways and mechanisms. In this paper, we synthesize this microbiology of the BE research and the known information about SARS-CoV-2 to provide actionable and achievable guidance to BE decision makers, building operators, and all indoor occupants attempting to minimize infectious disease transmission through environmentally mediated pathways. We believe this information is useful to corporate and public administrators and individuals responsible for building operations and environmental services in their decision-making process about the degree and duration of social-distancing measures during viral epidemics and pandemics.

Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment

In the constructed habitat in which we spend up to 90% of our time, architectural design influences occupants' behavioral patterns, interactions with objects, surfaces, rituals, the outside environment, and each other. Within this built environment, human behavior and building design contribute to the accrual and dispersal of microorganisms; it is a collection of fomites that transfer microorganisms; reservoirs that collect biomass; structures that induce human or air movement patterns; and space types that encourage proximity or isolation between humans whose personal microbial clouds disperse cells into buildings. There have been recent calls to incorporate building microbiology into occupant health and exposure research and standards, yet the built environment is largely viewed as a repository for microorganisms which are to be eliminated, instead of a habitat which is inexorably linked to the microbial influences of building inhabitants. Health sectors have re-evaluated the role of microorganisms in health, incorporating microorganisms into prevention and treatment protocols, yet no paradigm shift has occurred with respect to microbiology of the built environment, despite calls to do so. Technological and logistical constraints often preclude our ability to link health outcomes to indoor microbiology, yet sufficient study exists to inform the theory and implementation of the next era of research and intervention in the built environment. This review presents built environment characteristics in relation to human health and disease, explores some of the current experimental strategies and interventions which explore health in the built environment, and discusses an emerging model for fostering indoor microbiology rather than fearing it.

The age-specific burden and household and school-based predictors of child and adolescent tuberculosis infection in rural Uganda

BACKGROUND

The age-specific epidemiology of child and adolescent tuberculosis (TB) is poorly understood, especially in rural areas of East Africa. We sought to characterize the age-specific prevalence and predictors of TB infection among children and adolescents living in rural Uganda, and to explore the contribution of household TB exposure on TB infection.

METHODS

From 2015-2016 we placed and read 3,121 tuberculin skin tests (TST) in children (5-11 years old) and adolescents (12-19 years old) participating in a nested household survey in 9 rural Eastern Ugandan communities. TB infection was defined as a positive TST (induration ≥10mm or ≥5mm if living with HIV). Age-specific prevalence was estimated using inverse probability weighting to adjust for incomplete measurement. Generalized estimating equations were used to assess the association between TB infection and multi-level predictors.

RESULTS

The adjusted prevalence of TB infection was 8.5% (95%CI: 6.9-10.4) in children and 16.7% (95% CI:14.0-19.7) in adolescents. Nine percent of children and adolescents with a prevalent TB infection had a household TB contact. Among children, having a household TB contact was strongly associated with TB infection (aOR 5.5, 95% CI: 1.7-16.9), but the strength of this association declined among adolescents and did not meet significance (aOR 2.3, 95% CI: 0.8-7.0). The population attributable faction of TB infection due to a household TB contact was 8% for children and 4% among adolescents. Mobile children and adolescents who travel outside of their community for school had a 1.7 (95% CI 1.0-2.9) fold higher odds of TB infection than those who attended school in the community.

CONCLUSION

Children and adolescents in this area of rural eastern Uganda suffer a significant burden of TB. The majority of TB infections are not explained by a known household TB contact. Our findings underscore the need for community-based TB prevention interventions, especially among mobile youth.

Spatial distribution of tuberculosis in a rural region of Western Province, Papua New Guinea

Introduction

There is a high burden of tuberculosis (TB) in the Western Province, Papua New Guinea. This study aims to describe the spatial distribution of TB in the Balimo District Hospital (BDH) catchment area to identify TB patient clusters and factors associated with high rates of TB.

Methods

Information about TB patients was obtained from the BDH TB patient register for the period 26 April 2013 to 25 February 2017. The locations of TB patients were mapped, and the spatial scan statistic was used to identify high- and low-rate TB clusters in the BDH catchment area.

Results

A total of 1568 patients were mapped with most being from the Balimo Urban (n = 252), Gogodala Rural (n = 1010) and Bamu Rural (n = 295) local level government (LLG) areas. In the Gogodala region (Balimo Urban and Gogodala Rural LLGs), high-rate clusters occurred closer to the town of Balimo, while low-rate clusters were located in more remote regions. In addition, closer proximity to Balimo was a predictor of high-rate clustering.

Discussion

There is heterogeneity in the distribution of TB in the Balimo region. Active case-finding activities indicated potential underdiagnosis of TB and the possibility of associated missed diagnoses of TB. The large BDH catchment area emphasizes the importance of the hospital in managing TB in this rural region.

Intensified household contact tracing, prevention and treatment support versus enhanced standard of care for contacts of tuberculosis cases in South Africa: study protocol for a household cluster-randomised trial

BACKGROUND

Household contact tracing of index TB cases has been advocated as a key part of TB control for many years, but has not been widely implemented in many low-resource setting because of the current dearth of high quality evidence for effectiveness. Innovative strategies for earlier, more effective treatment are particularly important in contexts with hyper-endemic levels of HIV, where levels of TB infection remain extremely high.

METHODS

We present the design of a household cluster-randomised controlled trial of interventions aimed at improving TB-free survival and reducing childhood prevalence of Mycobacterium tuberculosis infection among household contacts of index TB cases diagnosed in two provinces of South Africa. Households of index TB cases will be randomly allocated in a 1:1 ratio to receive either an intensified home screening and linkage for TB and HIV intervention, or enhanced standard of care. The primary outcome will compare between groups the TB-free survival of household contacts over 15 months. All participants, or their next-of-kin, will provide written informed consent to participate.

DISCUSSION

Evidence from randomised trials is required to identify cost-effective approaches to TB case-finding that can be applied at scale in sub-Saharan Africa.

TRIAL REGISTRATION

ISRCTN16006202 (01/02/2017: retrospectively registered) and NHREC4399 (11/04/2016: prospectively registered). Protocol version: 4.0 (date: 18th January 2018).

Age-specific prevalence of TB infection among household contacts of pulmonary TB: Is it time for TB preventive therapy?

BACKGROUND

Household contacts (HHCs) of TB patients are at high risk of developing evidence of latent TB infection (LTBI) and active disease from the index patient. We estimated the age-specific prevalence of LTBI and the force of infection (FI), as a measure of recent transmission, among HHCs of active TB patients.

METHODS

A cross-sectional analysis of HHCs of pulmonary TB patients enrolled in a prospective study, 'CTRIUMPh', was conducted at two sites in India. LTBI was defined as either a positive tuberculin skin test (induration ≥5 mm) or QuantiFERON-Gold in tube test (value ≥0.35 IU/ml) and was stratified by age. FI, which is a measure of recent transmission of infection and calculated using changes in age-specific prevalence rates at specific ages, was calculated. Factors associated with LTBI were determined by logistic regression models.

RESULTS

Of 1020 HHCs of 441 adult pulmonary TB cases, there were 566 (55%) females and 289 (28%) children aged ≤15 y. While screening for the study 3% of HHC were diagnosed with active TB. LTBI prevalence among HHCs of pulmonary TB was 47% at <6 y, 53% between 6-14 y and 78% between 15-45 y. FI increased significantly with age, from 0.4 to 1.15 in the HHCs cohort (p=0.05).

CONCLUSION

This study observed an increased prevalence of LTBI and FI among older children and young adults recently exposed to infectious TB in the household. In addition to awareness of coughing etiquette and general hygiene, expanding access to TB preventive therapy to all HHCs, including older children, may be beneficial to achieve TB elimination by 2035.

Tuberculin skin test conversion and primary progressive tuberculosis disease in the first 5 years of life: a birth cohort study from Cape Town, South Africa

Background

Tuberculosis is a leading cause of global childhood mortality. However, the epidemiology and burden of tuberculosis in infancy is not well understood. We aimed to investigate tuberculin skin test conversion and tuberculosis in the Drakenstein Child Health study, a South African birth cohort in a community in which tuberculosis incidence is hyperendemic.

Methods

In this prospective birth cohort study, we enrolled pregnant women older than 18 years who were between 20 and 28 weeks' gestation and who were attending antenatal care in a peri-urban, impoverished South African setting. We followed up their children for tuberculosis from birth until April 1, 2017, or age 5 years. All children received BCG vaccination at birth. Tuberculin skin tests were administered to children at 6, 12, 24, 36, 48, and 60 months of age, and at the time of a lower respiratory tract infection. An induration reaction of 10 mm or more was considered to be a tuberculin skin test conversion. To prevent boosting, we censored children with a reactive, negative tuberculin skin test.

Findings

Among 915 mother-child pairs (201 [22%] HIV-positive mothers and two [<1%] HIV-positive children), 147 (16%) children had tuberculin skin test conversion, with increasing cumulative hazard with age (0·08 at 6 months, 0·17 at 12 months, 0·22 at 24 months, and 0·37 at age 36 months). For every 100 child-years, the incidence was 11·8 (95% CI 10·0-13·8) for tuberculin skin test conversion, 2·9 (2·4-3·7) for all diagnosed tuberculosis, and 0·7 (0·4-1·0) for microbiologically confirmed tuberculosis. Isoniazid preventive therapy was effective in averting disease progression (adjusted hazard ratio 0·22, 95% CI 0·08-0·63; p<0·0001). Children with a lower respiratory tract infection were significantly more likely to also have tuberculosis than were those without one (2·27, 1·42-3·62; p<0·0001).

Interpretation

Greater focus should be placed on the first years of life as a period of high burden of transmission and clinical expression of tuberculosis infection and disease. Multifaceted interventions, such as isoniazid preventive therapy and tuberculosis screening of infants with LRTIs, beginning early in life, are needed in high-burden settings.

Funding

Bill & Melinda Gates Foundation, Medical Research Council South Africa, and National Research Foundation South Africa.

The relative fitness of drug-resistant Mycobacterium tuberculosis: a modelling study of household transmission in Peru

The relative fitness of drug-resistant versus susceptible bacteria in an environment dictates resistance prevalence. Estimates for the relative fitness of resistant Mycobacterium tuberculosis (Mtb) strains are highly heterogeneous and mostly derived from in vitro experiments. Measuring fitness in the field allows us to determine how the environment influences the spread of resistance. We designed a household structured, stochastic mathematical model to estimate the fitness costs associated with multidrug resistance (MDR) carriage in Mtb in Lima, Peru during 2010–2013. By fitting the model to data from a large prospective cohort study of TB disease in household contacts, we estimated the fitness, relative to susceptible strains with a fitness of 1, of MDR-Mtb to be 0.32 (95% credible interval: 0.15–0.62) or 0.38 (0.24–0.61), if only transmission or progression to disease, respectively, was affected. The relative fitness of MDR-Mtb increased to 0.56 (0.42–0.72) when the fitness cost influenced both transmission and progression to disease equally. We found the average relative fitness of MDR-Mtb circulating within households in Lima, Peru during 2010–2013 to be significantly lower than concurrent susceptible Mtb. If these fitness levels do not change, then existing TB control programmes are likely to keep MDR-TB prevalence at current levels in Lima, Peru.

Contact tracing strategies in household and congregate environments to identify cases of tuberculosis in low- and moderate-incidence populations

BACKGROUND

Tuberculosis is an infectious bacterial disease that is spread via respiratory droplets from infected individuals to susceptible contacts. To eliminate this disease from low- and medium-incidence settings, people who are most likely to be infected (contacts) must be identified. Recently, study authors have examined alternate approaches to contact tracing methods that demonstrate improved detection and prioritization of contacts. The comparative benefit of these methods has not been established.

OBJECTIVES

To assess the effectiveness of novel methods of contact tracing versus current standard of care to identify latent and active cases in low- to moderate-incidence settings.

SEARCH METHODS

We searched CENTRAL, MEDLINE, Embase, LILACS, Web of Science, and CINAHL up to 15 July 2019. We also searched for clinical trials and examined reference lists and conference proceedings.

SELECTION CRITERIA

Randomized controlled trials (RCTs) and cluster-RCTs of contact tracing strategies that included alternate approaches (other than standard practice).

DATA COLLECTION AND ANALYSIS

Two review authors independently assessed identified articles for eligibility and quality using prespecified criteria.

MAIN RESULTS

No trials met the inclusion criteria of this review. Several study authors described an alternate method for examining contacts and performing social network analysis but did not compare this with the current contact tracing approach.

AUTHORS' CONCLUSIONS

This Cochrane Review highlights the lack of research in support of the current contact tracing method and the need for RCTs to compare new methods such as social network analysis to improve contact tracing processes.

Prevalence and Determinants of QuantiFERON-Diagnosed Tuberculosis Infection in 9810 Mongolian Schoolchildren

BACKGROUND

There is controversy regarding the potential influence of vitamin D deficiency, exposure to environmental tobacco smoke, BCG vaccination, season, and body habitus on susceptibility to Mycobacterium tuberculosis (MTB) infection.

METHODS

We conducted a cross-sectional analysis to identify determinants of a positive QuantiFERON-TB Gold (QFT) assay result in children aged 6-13 years attending 18 schools in Ulaanbaatar, Mongolia. Data relating to potential risk factors for MTB infection were collected by questionnaire, physical examination, and determination of serum 25-hydroxyvitamin D (25[OH]D) concentrations. Risk ratios (RRs) were calculated with adjustment for potential confounders, and population attributable fractions (PAFs) were calculated for modifiable risk factors identified.

RESULTS

Nine hundred forty-six of 9810 (9.6%) participants had a positive QFT result. QFT positivity was independently associated with household exposure to pulmonary tuberculosis (adjusted RR [aRR], 4.75 [95% confidence interval {CI}, 4.13-5.46, P < .001]; PAF, 13.1% [95% CI, 11.1%-15.0%]), vitamin D deficiency (aRR, 1.23 [95% CI, 1.08-1.40], P = .002; PAF, 5.7% [95% CI, 1.9%-9.3%]), exposure to environmental tobacco smoke (1 indoor smoker, aRR, 1.19 [95% CI, 1.04-1.35]; ≥2 indoor smokers, aRR, 1.30 [95% CI, 1.02-1.64]; P for trend = .006; PAF, 7.2% [95% CI, 2.2%-12.0%]), and increasing age (aRR per additional year, 1.14 [95% CI, 1.10-1.19], P < .001). No statistically significant independent association was seen for presence of a BCG scar, season of sampling, or body mass index.

CONCLUSIONS

Vitamin D deficiency and exposure to environmental tobacco smoke are potentially modifiable risk factors for MTB infection.

Spatial clustering of drug-resistant tuberculosis in Hlabisa subdistrict, KwaZulu-Natal, 2011-2015

SETTING:

Incidence rates of tuberculosis (TB) in South Africa are among the highest in the world, and drug resistance is a major concern. Understanding geographic variations in disease may guide targeted interventions.

OBJECTIVE:

To characterise the spatial distribution of drug-resistant TB (DR-TB) in a rural area of KwaZulu-Natal, South Africa, and to test for clustering.

DESIGN:

This was a cross-sectional analysis of DR-TB patients managed at a rural district hospital from 2011 to 2015. We mapped all patients in hospital data to local areas, and then linked to a population-based demographic surveillance system to map the patients to individual homesteads. We used kernel density estimation to visualise the distribution of disease and tested for clustering using spatial scan statistics.

RESULTS:

There were 489 patients with DR-TB in the subdistrict; 111 lived in the smaller demographic surveillance area. Spatial clustering analysis identified a high-risk cluster (relative risk of DR-TB inside vs. outside cluster 3.0, P <0.001) in the south-east, a region characterised by high population density and a high prevalence of human immunodeficiency virus infection.

CONCLUSION:

We have demonstrated evidence of a geographic high-risk cluster of DR-TB. This suggests that targeting interventions to spatial areas of highest risk, where transmission may be ongoing, could be effective.