Proportion of tuberculosis transmission that takes place in households in a high-incidence area

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.

Systems analysis and improvement approach to optimize tuberculosis (SAIA-TB) screening, treatment, and prevention in South Africa: a stepped-wedge cluster randomized trial

BACKGROUND

The use of systems engineering tools, including the development and use of care cascades using routinely collected data, process mapping, and continuous quality improvement, is used for frontline healthcare workers to devise systems level change. South Africa experiences high rates of tuberculosis (TB) infection and disease as well as HIV co-infection. The Department of Health has made significant gains in HIV services over the last two decades, reaching their set "90-90-90" targets for HIV. However, TB services, although robust, have lagged in comparison for both disease and infection. The Systems Analysis and Improvement Approach (SAIA) is a five-step implementation science method, drawn from systems engineering, to identify, define, and implement workflow modifications using cascade analysis, process mapping, and repeated quality improvement cycles within healthcare facilities.

METHODS

This stepped-wedge cluster randomized trial will evaluate the effectiveness of SAIA on TB (SAIA-TB) cascade optimization for patients with TB and high-risk contacts across 16 clinics in four local municipalities in the Sarah Baartman district, Eastern Cape, South Africa. We hypothesize that SAIA-TB implementation will lead to a 20% increase in each of: TB screening, TB preventive treatment initiation, and TB disease treatment initiation during the 18-month intervention period. Focus group discussions and key informant interviews with clinic staff will also be conducted to determine drivers of implementation variability across clinics.

DISCUSSION

This study has the potential to improve TB screening, treatment initiation, and completion for both active disease and preventive measures among individuals with and without HIV in a high burden setting. SAIA-TB provides frontline health care workers with a systems-level view of their care delivery system with the aim of sustainable systems-level improvements.

TRIAL REGISTRATION

Clinicaltrials.gov, NCT06314386. Registered 18 March 2024, https://clinicaltrials.gov/study/NCT06314386 . NCT06314386.

Persistent Mycobacterium tuberculosis bioaerosol release in a tuberculosis-endemic setting

Pioneering studies linking symptomatic disease and cough-mediated release of Mycobacterium tuberculosis (Mtb) established the infectious origin of tuberculosis (TB), simultaneously informing the pervasive notion that pathology is a prerequisite for Mtb transmission. Our prior work has challenged this assumption: by sampling TB clinic attendees, we detected equivalent release of Mtb-containing bioaerosols by confirmed TB patients and individuals not receiving a TB diagnosis, and we demonstrated a time-dependent reduction in Mtb bioaerosol positivity during six-months' follow-up, irrespective of anti-TB chemotherapy. Now, by extending bioaerosol sampling to a randomly selected community cohort, we show that Mtb release is common in a TB-endemic setting: of 89 participants, 79.8% (71/89) produced Mtb bioaerosols independently of QuantiFERON-TB Gold status, a standard test for Mtb infection; moreover, during two-months' longitudinal sampling, only 2% (1/50) were serially Mtb bioaerosol negative. These results necessitate a reframing of the prevailing paradigm of Mtb transmission and infection, and may explain the current inability to elucidate Mtb transmission networks in TB-endemic regions.

High Tuberculosis Preventive Treatment Uptake and Completion Rates Using a Person-Centered Approach among Tuberculosis Household Contact in Yogyakarta

Coverage of tuberculosis preventive treatment (TPT) in Indonesia is inadequate, and persons who start TPT often do not complete treatment. In 2020, Zero TB Yogyakarta implemented person-centered contact investigation and shorter TPT regimen provision in collaboration with primary health care centers. Between 1 January 2020 and 31 August 2022, we assessed eligibility for TPT among household contacts of persons with bacteriologically confirmed TB (index cases) and offered them a 3-month TPT regimen (3RH or 3HP). A dedicated nurse monitored contacts on TPT for treatment adherence and side effects every week in the first month and every two weeks in the next months. Contacts were also able to contact a nurse by phone or ask for home visits at any point if they had any concerns. A total of 1016 contacts were eligible for TPT: 772 (78.8%) started short regimen TPT with 706 (91.5%) completing their TPT. Side effects were reported in 26 (39%) of the non-completion group. We conclude that high rates of TPT uptake and completion among contacts assessed as eligible for TPT can be achieved through person-centered care and the use of shorter regimens. Side-effect monitoring and management while on TPT is vital for improving TPT completion.

Determining the risk-factors for molecular clustering of drug-resistant tuberculosis in South Africa

BACKGROUND

Drug-resistant tuberculosis (DR-TB) epidemic is driven mainly by the effect of ongoing transmission. In high-burden settings such as South Africa (SA), considerable demographic and geographic heterogeneity in DR-TB transmission exists. Thus, a better understanding of risk-factors for clustering can help to prioritise resources to specifically targeted high-risk groups as well as areas that contribute disproportionately to transmission.

METHODS

The study analyzed potential risk-factors for recent transmission in SA, using data collected from a sentinel molecular surveillance of DR-TB, by comparing demographic, clinical and epidemiologic characteristics with clustering and cluster sizes. A genotypic cluster was defined as two or more patients having identical patterns by the two genotyping methods used. Clustering was used as a proxy for recent transmission. Descriptive statistics and multinomial logistic regression were used.

RESULT

The study identified 277 clusters, with cluster size ranging between 2 and 259 cases. The majority (81.6%) of the clusters were small (2-5 cases) with few large (11-25 cases) and very large (≥ 26 cases) clusters identified mainly in Western Cape (WC), Eastern Cape (EC) and Mpumalanga (MP). In a multivariable model, patients in clusters including 11-25 and ≥ 26 individuals were more likely to be infected by Beijing family, have XDR-TB, living in Nelson Mandela Metro in EC or Umgungunglovo in Kwa-Zulu Natal (KZN) provinces, and having history of imprisonment. Individuals belonging in a small genotypic cluster were more likely to infected with Rifampicin resistant TB (RR-TB) and more likely to reside in Frances Baard in Northern Cape (NC).

CONCLUSION

Sociodemographic, clinical and bacterial risk-factors influenced rate of Mycobacterium tuberculosis (M. tuberculosis) genotypic clustering. Hence, high-risk groups and hotspot areas for clustering in EC, WC, KZN and MP should be prioritized for targeted intervention to prevent ongoing DR-TB transmission.

Strong Effect of Demographic Changes on Tuberculosis Susceptibility in South Africa

South Africa is among the world's top eight TB burden countries, and despite a focus on HIV-TB co-infection, most of the population living with TB are not HIV co-infected. The disease is endemic across the country with 80-90% exposure by adulthood. We investigated epidemiological risk factors for tuberculosis (TB) in the Northern Cape Province, South Africa: an understudied TB endemic region with extreme TB incidence (645/100,000) and the lowest provincial population density. We leveraged the population's high TB incidence and community transmission to design a case-control study with population-based controls, reflecting similar mechanisms of exposure between the groups. We recruited 1,126 participants with suspected TB from 12 community health clinics, and generated a cohort of 878 individuals (cases =374, controls =504) after implementing our enrollment criteria. All participants were GeneXpert Ultra tested for active TB by a local clinic. We assessed important risk factors for active TB using logistic regression and random forest modeling. Additionally, a subset of individuals were genotyped to determine genome-wide ancestry components. Male gender had the strongest effect on TB risk (OR: 2.87 [95% CI: 2.1-3.8]); smoking and alcohol consumption did not significantly increase TB risk. We identified two interactions: age by socioeconomic status (SES) and birthplace by residence locality on TB risk (OR = 3.05, p = 0.016) - where rural birthplace but town residence was the highest risk category. Finally, participants had a majority Khoe-San ancestry, typically greater than 50%. Epidemiological risk factors for this cohort differ from other global populations. The significant interaction effects reflect rapid changes in SES and mobility over recent generations and strongly impact TB risk in the Northern Cape of South Africa. Our models show that such risk factors combined explain 16% of the variance (r2) in case/control status.

Global-, Regional-, and National-Level Impacts of the COVID-19 Pandemic on Tuberculosis Diagnoses, 2020-2021

Evaluating cross-country variability on the impact of the COVID-19 pandemic on tuberculosis (TB) may provide urgent inputs to control programs as countries recover from the pandemic. We compared expected TB notifications, modeled using trends in annual TB notifications from 2013-2019, with observed TB notifications to compute the observed to expected (OE) ratios for 170 countries. We applied the least absolute shrinkage and selection operator (LASSO) method to identify the covariates, out of 27 pandemic- and tuberculosis-relevant variables, that had the strongest explanatory power for log OE ratios. The COVID-19 pandemic was associated with a 1.55 million (95% CI: 1.26-1.85, 21.0% [17.5-24.6%]) decrease in TB diagnoses in 2020 and a 1.28 million (0.90-1.76, 16.6% [12.1-21.2%]) decrease in 2021 at a global level. India, Indonesia, the Philippines, and China contributed the most to the global declines for both years, while sub-Saharan Africa achieved pre-pandemic levels by 2021 (OE ratio = 1.02 [0.99-1.05]). Age-stratified analyses revealed that the ≥ 65-year-old age group experienced greater relative declines in TB diagnoses compared with the under 65-year-old age group in 2020 (RR = 0.88 [0.81-0.96]) and 2021 (RR = 0.88 [0.79-0.98]) globally. Covariates found to be associated with all-age OE ratios in 2020 were age-standardized smoking prevalence in 2019 (β = 0.973 [0.957-990]), school closures (β = 0.988 [0.977-0.998]), stay-at-home orders (β = 0.993 [0.985-1.00]), SARS-CoV-2 infection rate (β = 0.991 [0.987-0.996]), and proportion of population ≥65 years (β = 0.971 [0.944-0.999]). Further research is needed to clarify the extent to which the observed declines in TB diagnoses were attributable to disruptions in health services, decreases in TB transmission, and COVID-19 mortality among TB patients.

Population-Based Severe Acute Respiratory Syndrome Coronavirus 2 Whole-Genome Sequencing and Contact Tracing During the Coronavirus Disease 2019 Pandemic in Switzerland

BACKGROUND

Testing and contact tracing (CT) can interrupt transmission chains of SARS-CoV-2. Whole-genome sequencing (WGS) can potentially strengthen these investigations and provide insights on transmission.

METHODS

We included all laboratory-confirmed COVID-19 cases diagnosed between 4 June and 26 July 2021, in a Swiss canton. We defined CT clusters based on epidemiological links reported in the CT data and genomic clusters as sequences with no single-nucleotide polymorphism (SNP) differences between any 2 pairs of sequences being compared. We assessed the agreement between CT clusters and genomic clusters.

RESULTS

Of 359 COVID-19 cases, 213 were sequenced. Overall, agreement between CT and genomic clusters was low (Cohen's κ = 0.13). Of 24 CT clusters with ≥2 sequenced samples, 9 (37.5%) were also linked based on genomic sequencing but in 4 of these, WGS found additional cases in other CT clusters. Household was most often reported source of infection (n = 101 [28.1%]) and home addresses coincided well with CT clusters: In 44 of 54 CT clusters containing ≥2 cases (81.5%), all cases in the cluster had the same reported home address. However, only a quarter of household transmission was confirmed by WGS (6 of 26 genomic clusters [23.1%]). A sensitivity analysis using ≤1-SNP differences to define genomic clusters resulted in similar results.

CONCLUSIONS

WGS data supplemented epidemiological CT data, supported the detection of potential additional clusters missed by CT, and identified misclassified transmissions and sources of infection. Household transmission was overestimated by CT.

Impact on Tuberculosis Notification During COVID-19 Pandemic in India: A Narrative Review

Various programs are being weakened due to the COVID-19 pandemic, and the tuberculosis (TB) program is no exception. TB case detection and notification is one of the worst affected areas. The study aims to assess India's TB reporting status during this pandemic and find possible solutions. Data analysis has been obtained from the India TB notification open-source database. Relevant literature research has been done to determine the measures based on various efforts made by different Indian states. There was a review of all TB notifications in 2019, 2020, and 2021 and a deficiency in notifications. Between 2019 and 2021, the country's TB notification ratio experienced a significant adaptation. In 2020, all states reported a decline in private and public TB case reports. In the nation, only a few private TB notifications were lost. In April 2020, there were the fewest notifications, which began to decline in February 2020. When states began implementing cutting-edge programs like the Integrated TB COVID Case Search and Active Case Finding (ACF), the notification trend improved in May 2020. The notifications of TB cases decreased significantly due to the present COVID-19 pandemic, which has consequences for the disease's stealthy spread throughout homes and communities. However, the situation may be better with an integrated strategy for managing TB-COVID cases.

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.

Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020

BACKGROUND

Whole genome sequencing (WGS) is increasingly used by tuberculosis (TB) programs to monitor Mycobacterium tuberculosis (Mtb) transmission. We aimed to characterise the molecular epidemiology of TB and Mtb transmission in the low-incidence setting of Victoria, Australia, and assess the utility of WGS.

METHODS

WGS was performed on all first Mtb isolates from TB cases from 2017 to 2020. Potential clusters (≤12 single nucleotide polymorphisms [SNPs]) were investigated for epidemiological links. Transmission events in highly-related (≤5 SNPs) clusters were classified as likely or possible, based on the presence or absence of an epidemiological link, respectively. Case characteristics and transmission settings (as defined by case relationship) were summarised. Poisson regression was used to examine associations with secondary case number.

FINDINGS

Of 1844 TB cases, 1276 (69.2%) had sequenced isolates, with 182 (14.2%) in 54 highly-related clusters, 2-40 cases in size. Following investigation, 140 cases (11.0% of sequenced) were classified as resulting from likely/possible local-transmission, including 82 (6.4%) for which transmission was likely. Common identified transmission settings were social/religious (26.4%), household (22.9%) and family living in different households (7.1%), but many were uncertain (41.4%). While household transmission featured in many clusters (n = 24), clusters were generally smaller (median = 3 cases) than the fewer that included transmission in social/religious settings (n = 12, median = 7.5 cases). Sputum-smear-positivity was associated with higher secondary case numbers.

INTERPRETATION

WGS results suggest Mtb transmission commonly occurs outside the household in our low-incidence setting. Further work is required to optimise the use of WGS in public health management of TB.

FUNDING

The Victorian Tuberculosis Program receives block funding for activities including case management and contact tracing from the Victorian Department of Health. No specific funding for this report was received by manuscript authors or the Victorian Tuberculosis Program, and the funders had no role in the study design, data collection, data analysis, interpretation or report writing.

Preventive Treatment for Household Contacts of Drug-Susceptible Tuberculosis Patients

People who live in the household of someone with infectious pulmonary tuberculosis are at a high risk of tuberculosis infection and subsequent progression to tuberculosis disease. These individuals are prioritized for contact investigation and tuberculosis preventive treatment (TPT). The treatment of TB infection is critical to prevent the progression of infection to disease and is prioritized in household contacts. Despite the availability of TPT, uptake in household contacts is poor. Multiple barriers prevent the optimal implementation of these policies. This manuscript lays out potential next steps for closing the policy-to-implementation gap in household contacts of all ages.

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.

Model-based Analysis of Tuberculosis Genotype Clusters in the United States Reveals High Degree of Heterogeneity in Transmission and State-level Differences Across California, Florida, New York, and Texas

BACKGROUND

Reductions in tuberculosis (TB) transmission have been instrumental in lowering TB incidence in the United States. Sustaining and augmenting these reductions are key public health priorities.

METHODS

We fit mechanistic transmission models to distributions of genotype clusters of TB cases reported to the Centers for Disease Control and Prevention during 2012-2016 in the United States and separately in California, Florida, New York, and Texas. We estimated the mean number of secondary cases generated per infectious case (R0) and individual-level heterogeneity in R0 at state and national levels and assessed how different definitions of clustering affected these estimates.

RESULTS

In clusters of genotypically linked TB cases that occurred within a state over a 5-year period (reference scenario), the estimated R0 was 0.29 (95% confidence interval [CI], .28-.31) in the United States. Transmission was highly heterogeneous; 0.24% of simulated cases with individual R0 >10 generated 19% of all recent secondary transmissions. R0 estimate was 0.16 (95% CI, .15-.17) when a cluster was defined as cases occurring within the same county over a 3-year period. Transmission varied across states: estimated R0s were 0.34 (95% CI, .3-.4) in California, 0.28 (95% CI, .24-.36) in Florida, 0.19 (95% CI, .15-.27) in New York, and 0.38 (95% CI, .33-.46) in Texas.

CONCLUSIONS

TB transmission in the United States is characterized by pronounced heterogeneity at the individual and state levels. Improving detection of transmission clusters through incorporation of whole-genome sequencing and identifying the drivers of this heterogeneity will be essential to reducing TB transmission.

Prevalence of proximate risk factors of active tuberculosis in latent tuberculosis infection: A cross-sectional study from South India

The prevalence of proximate risk factors for active tuberculosis (TB) in areas of high prevalence of latent tuberculosis infection (LTBI) is not clearly understood. We aimed at assessing the prevalence of non-communicable multi-morbidity focusing on diabetes mellitus (DM), malnutrition, and hypertension (HTN) as common risk factors of LTBI progressing to active TB. In a cross-sectional study, 2,351 adults (45% male and 55% female) from villages in the Kancheepuram district of South India were enrolled between 2013 and 2020. DM was defined as HbA1c >6.4%, undernutrition was defined as low body mass index (LBMI) <18.5 kg/m², obesity was classified as BMI ≥25 kg/m², HTN was reported as systolic pressure >130 mmHg, and LTBI was defined as positive (≥ 0.35 international units/ml) by QuantiFERON Gold In-Tube assay. A total of 1,226 individuals (52%) were positive for LTBI out of 2351 tested individuals. The prevalence of DM and pre-diabetes mellitus (PDM) was 21 and 35%, respectively, HTN was 15% in latent tuberculosis (LTB)-infected individuals. The association of DM [odds ratio (OR)]; adjusted odds ratio (aOR) (OR = 1.26, 95% CI: 1.13-1.65; aOR = 1.19, 95% CI: 1.10-1.58), PDM (OR = 1.11, 95% CI: 1.0-1.35), and HTN (OR = 1.28, 95% CI: 1.11-1.62; aOR = 1.18, 95% CI: 1.0-1.56) poses as risk factors of LTBI progression to active TB. The prevalence of LBMI 9% (OR = 1.07, 95% CI: 0.78-1.48) and obesity 42% (OR = 0.85, 95% CI: 0.70-1.03) did not show any statistically significant association with LTB-infected individuals. The present evidence of a high burden of multi-morbidity suggests that proximate risk factors of active TB in LTBI can be managed by nutrition and lifestyle modification.

Predominance of the Mycobacterium tuberculosis Beijing strain amongst children from a high tuberculosis burden township in South Africa

The objective was to determine the molecular epidemiology and drug susceptibility patterns of Mycobacterium tuberculosis (MTB) of children and their household contacts (HHC) in Umlazi, a high TB-burden township in South Africa. Sixty eight MTBRifPLUS positive TB-infected children (TIC) (≤14 years) and 111 HHC were enrolled. Drug susceptibility testing (DST) was performed on sputum samples using the proportion method and GenoType® MTBDR. Genotyping of MTB was conducted using IS6110-restriction fragment length polymorphism (RFLP) and spoligotyping. Rifampicin (RIF) susceptibility was observed in 67/68 TIC. GenoType® MTBDRplus and phenotypic DST identified drug resistant strains in five of 16 culture-confirmed TIC. The Beijing strain was identified in six and the F15/LAM4/KZN strain in one of the 13 TIC respectively. Four patients with unknown RFLP strains belonged to spoligoclades S, T1, T3 variant and X2. The S-lineage and an unknown strain were identified in two HHC. MDR-TB and pre-XDR-TB were identified in one HHC each. Household transmission could not be determined as none of the culture-confirmed TIC resided with the six culture-confirmed contacts. The predominance of the hypervirulent Beijing strain and presence of drug-resistant strains must be considered in the implementation of effective TB control strategies and development of efficacious vaccines.

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.

Are we underestimating the annual risk of infection with Mycobacterium tuberculosis in high-burden settings?

The annual risk of infection with Mycobacterium tuberculosis determines a population's exposure level and thus the fraction of incident tuberculosis resulting from recent infection (often considered as having occurred within the past 2 years). Contemporary annual risk of infection estimates centre around 1% in most high-burden countries. We present three arguments why these estimates-primarily derived from cross-sectional tuberculin surveys in young school children (aged 5-12 years)-might underrepresent the true annual risk of infection. First, young children are expected to have lower risk of infection than older adolescents and adults (ie, those aged 15 years and older). Second, exposure might not lead to a positive test result in some individuals. Third, cross-sectional surveys might overlook transient immune responses. Accounting for these biases, the true annual risk of infection among adults in high-burden settings is probably closer to 5-10%. Consequently, most tuberculosis in those settings should reflect infection within the past 2 years rather than remote infection occurring many years ago. Under this reframing, major reductions in tuberculosis incidence could be achievable by focusing on the minority of people who have been recently infected.

The impact of the COVID-19 pandemic and associated suppression measures on the burden of tuberculosis in India

Background

Tuberculosis (TB) is a major cause of death globally. India carries the highest share of the global TB burden. The COVID-19 pandemic has severely impacted diagnosis of TB in India, yet there is limited data on how TB case reporting has changed since the pandemic began and which factors determine differences in case notification.

Methods

We utilized publicly available data on TB case reporting through the Indian Central TB Division from January 2017 through April of 2021 (prior to the first COVID-19 related lockdown). Using a Poisson model, we estimated seasonal and yearly patterns in TB case notification in India from January 2017 through February 2020 and extended this estimate as the counterfactual expected TB cases notified from March 2020 through April 2021. We characterized the differences in case notification observed and those expected in the absence of the pandemic by State and Territory. We then performed a linear regression to examine the relationship between the logit ratio of reported TB to counterfactual cases and mask use, mobility, daily hospitalizations/100,000 population, and public/total TB case reporting.

Results

We found 1,320,203 expected cases of TB (95% uncertainty interval (UI) 1,309,612 to 1,330,693) were not reported during the period from March 2020 through April 2021. This represents a 63.3% difference (95% UI 62.8 to 63.8) in reporting. We found that mobility data and average hospital admissions per month per population were correlated with differences in TB case notification, compared to the counterfactual in the absence of the pandemic (p > 0.001).

Conclusion

There was a large difference between reported TB cases in India and those expected in the absence of the pandemic. This information can help inform the Indian TB program as they consider interventions to accelerate case finding and notification once the pandemic related TB service disruptions improve. Mobility data and hospital admissions are surrogate measures that correlate with a greater difference in reported/expected TB cases and may correlate with a disruption in TB diagnostic services. However, further research is needed to clarify this association and identify other key contributors to gaps in TB case notifications in India.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07078-y.

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.

Conditional cash transfers to incentivize tuberculosis screening: Description of a novel strategy for contact investigation in rural South Africa

BACKGROUND

Providing incentives to screen close contacts for tuberculosis (TB) is an alternative to traditional household-based contact investigation. We aimed to characterize patients and contexts for which this incentive-based strategy might be preferred.

METHODS

This is a secondary analysis of a cluster randomized trial of TB contact investigation in Limpopo District, South Africa, conducted between 2016-2020. Twenty-eight clinics were randomly allocated to household-based versus incentive-based contact investigation. In the incentive-based arm, index participants and contacts received transport reimbursement and incentives for TB screening and microbiological diagnosis of contacts. We estimated the absolute difference in mean number of contacts per index participant with household-based versus incentive-based contact investigation, overall and within sub-groups of index participants.

RESULTS

A total of 3776 contacts (1903 in the incentive-based and 1873 in the household-based arm) were referred by 2501 index participants. A higher proportion of contacts in the incentive-based than household-based arm were adults (72% vs 59%) and reported chronic TB symptoms (25% vs 16%) or ever smoking (23% vs 11%). Index participants who walked or bicycled to clinic referred 1.03 more contacts per index (95%CI:0.48-1.57) through incentive-based than household-based investigation. Index participants living with >5 household members referred 0.48 more contacts per index (95%CI:0.03-0.94) through household-based than incentive-based investigation.

CONCLUSIONS

Relative to household-based contact investigation, incentive-based investigation identifies contacts who appear to be at higher risk for active TB. Incentive-based investigation may be more appropriate for index participants who can easily access the clinic, whereas household-based investigation should be prioritized for patients with large households.

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.

Assessing a transmission network of Mycobacterium tuberculosis in an African city using single nucleotide polymorphism threshold analysis

Tuberculosis (TB) is the leading cause of death in humans by a single infectious agent worldwide with approximately two billion humans latently infected with the bacterium Mycobacterium tuberculosis. Currently, the accepted method for controlling the disease is Tuberculosis Directly Observed Treatment Shortcourse (TB-DOTS). This program is not preventative and individuals may transmit disease before diagnosis, thus better understanding of disease transmission is essential. Using whole-genome sequencing and single nucleotide polymorphism analysis, we analyzed genomes of 145 M. tuberculosis clinical isolates from active TB cases from the Rubaga Division of Kampala, Uganda. We established that these isolates grouped into M. tuberculosis complex (MTBC) lineages 1, 2, 3, and 4, with the most isolates grouping into lineage 4. Possible transmission pairs containing ≤12 SNPs were identified in lineages 1, 3, and 4 with the prevailing transmission in lineages 3 and 4. Furthermore, investigating DNA codon changes as a result of specific SNPs in prominent virulence genes including plcA and plcB could indicate potentially important modifications in protein function. Incorporating this analysis with corresponding epidemiological data may provide a blueprint for the integration of public health interventions to decrease TB transmission in a region.

The effectiveness of contact investigation among contacts of tuberculosis patients: a systematic review and meta-analysis

BACKGROUND

We aimed to evaluate the effectiveness of contact investigation in comparison to passive case-detection alone and estimated the yield of co-prevalent and incident tuberculosis (TB), and latent tuberculosis infection (LTBI) among contacts of patients with TB.

METHODS

A systematic search was undertaken of studies published between January 1, 2011 and October 1, 2019 in the English language. The proportion of contacts diagnosed with co-prevalent TB, incident TB and/or LTBI was estimated. Evaluation of the effectiveness of contact investigation included randomised trials, while the yield of contact investigation (co-prevalent and incident TB and LTBI) was assessed in non-randomised studies.

RESULTS

Data were extracted from 244 studies, of which 187 studies measured the proportion of contacts diagnosed with TB disease and 135 studies measured LTBI prevalence. Individual randomised trials demonstrated that contact investigation increased TB case notification (RR 2.5 [95% CI: 2.0-3.2]), TB case detection (OR 1.34 [95% CI: 0.43-4.24]) and decreased mortality (RR 0.6 [95% CI: 0.4-0.8]) and population TB prevalence (risk ratio 0.82 [95% CI: 0.64-1.04]).The overall pooled prevalence of TB was 3.6% (95% CI: 3.3-4.0%; I²=98.9%, 181 studies). The pooled prevalence of microbiologically-confirmed TB was 3.2% (95% CI: 2.6-3.7%; I²=99.5%, 106 studies). The pooled incidence of TB was highest in the first year after exposure to index patients (2.0%, 95% CI: 1.1-3.3%; I²=96.2%, 14 studies) and substantially lower five years after exposure to index patient (0.5%, 95% CI: 0.3-0.9%; 1 study). The pooled prevalence of LTBI among contacts was 42.4% (95% CI: 38.5-46.4%; I²=99.8%, 135 studies).

CONCLUSIONS AND RELEVANCE

This systematic review and meta-analysis found that contact investigation was effective in high-burden settings. The higher pooled prevalence estimates of microbiologically-confirmed TB compared to previous reviews suggests newer rapid molecular diagnostics contribute to increased case detection.

Addressing gaps in adolescent tuberculosis programming and policy in Nigeria from a public health perspective

OBJECTIVES

Tuberculosis (TB) is a leading infectious cause of death globally. Of the estimated 10 million people who developed active TB in 2019, 1.8 million (18%) were adolescents and young adults aged 15-24 years. Adolescents have poorer rates of TB screening, treatment initiation and completion compared to adults. Unfortunately, there is relatively less programme, research and policy focus on TB for adolescents aged 10-19 years. This article reviews the scope of health services and the relevant policy landscape for TB case notification and care/treatment, TB/HIV management, and latent TB infection for adolescents in Nigeria. Additionally, it discusses considerations for TB vaccines in this population.

CONTENT

All Nigeria Federal Ministry of Health policy documents relevant to adolescent health services and TB, and published between 2000 and 2020 underwent narrative review. Findings were reported according to the service areas outlined in the Objectives.

SUMMARY AND OUTLOOK

Nine policy documents were identified and reviewed. While multiple policies acknowledge the needs of adolescents in public health and specifically in TB programming, these needs are often not addressed in policy, nor in program integration and implementation. The lack of age-specific epidemiologic and clinical outcomes data for adolescents contributes to these policy gaps. Poor outcomes are driven by factors such as HIV co-infection, lack of youth-friendly health services, and stigma and discrimination. Policy guidelines and innovations should include adaptations tailored to adolescent needs. However, these adaptations cannot be developed without robust epidemiological data on adolescents at risk of, and living with TB. Gaps in TB care integration into primary reproductive, maternal-child health and nutrition services should be addressed across multiple policies, and mechanisms for supervision, and monitoring and evaluation of integration be developed to guide comprehensive implementation. Youth-friendly TB services are recommended to improve access to quality care delivered in a patient-centered approach.

Duration of Exposure Among Close Contacts of Patients With Infectious Tuberculosis and Risk of Latent Tuberculosis Infection

BACKGROUND

Predictors of latent tuberculosis infection (LTBI) among close contacts of persons with infectious tuberculosis (TB) are incompletely understood, particularly the number of exposure hours.

METHODS

We prospectively enrolled adult patients with culture-confirmed pulmonary TB and their close contacts at 9 health departments in the United States and Canada. Patients with TB were interviewed and close contacts were interviewed and screened for TB and LTBI during contact investigations.

RESULTS

LTBI was diagnosed in 1390 (46%) of 3040 contacts, including 624 (31%) of 2027 US/Canadian-born and 766 (76%) of 1013 non-US/Canadian-born contacts. In multivariable analysis, age ≥5 years, male sex, non-US/Canadian birth, smear-positive index patient, and shared bedroom with an index patient (P < .001 for each), as well as exposure to >1 index patient (P < .05), were associated with LTBI diagnosis. LTBI prevalence increased with increasing exposure duration, with an incremental prevalence increase of 8.2% per 250 exposure hours (P < .0001). For contacts with <250 exposure hours, no difference in prevalence was observed per 50 exposure hours (P = .63).

CONCLUSIONS

Hours of exposure to a patient with infectious TB is an important LTBI predictor, with a possible risk threshold of 250 hours. More exposures, closer exposure proximity, and more extensive index patient disease were additional LTBI predictors.

Assortative social mixing and sex disparities in tuberculosis burden

Globally, men have higher tuberculosis (TB) burden but the mechanisms underlying this sex disparity are not fully understood. Recent surveys of social mixing patterns have established moderate preferential within-sex mixing in many settings. This assortative mixing could amplify differences from other causes. We explored the impact of assortative mixing and factors differentially affecting disease progression and detection using a sex-stratified deterministic TB transmission model. We explored the influence of assortativity at disease-free and endemic equilibria, finding stronger effects during invasion and on increasing male:female prevalence (M:F) ratios than overall prevalence. Variance-based sensitivity analysis of endemic equilibria identified differential progression as the most important driver of M:F ratio uncertainty. We fitted our model to prevalence and notification data in exemplar settings within a fully Bayesian framework. For our high M:F setting, random mixing reduced equilibrium M:F ratios by 12% (95% CrI 0-30%). Equalizing male case detection there led to a 20% (95% CrI 11-31%) reduction in M:F ratio over 10 years-insufficient to eliminate sex disparities. However, this potentially achievable improvement was associated with a meaningful 8% (95% CrI 4-14%) reduction in total TB prevalence over this time frame.

Transmission Modeling with Regression Adjustment for Analyzing Household-based Studies of Infectious Disease: Application to Tuberculosis

BACKGROUND

Household contacts of people infected with a transmissible disease may be at risk due to this proximate exposure, or from other unobserved sources. Understanding variation in infection risk is essential for targeting interventions.

METHODS

We develop an analytical approach to estimate household and exogenous forces of infection, while accounting for individual-level characteristics that affect susceptibility to disease and transmissibility. We apply this approach to a cohort study conducted in Lima, Peru, of 18,544 subjects in 4,500 households with at least one active tuberculosis (TB) case and compare the results to those obtained by Poisson and logistic regression.

RESULTS

HIV-coinfected (susceptibility hazard ratio [SHR] = 3.80, 1.56-9.29), child (SHR = 1.72, 1.32-2.23), and teenage (SHR = 2.00, 1.49-2.68) household contacts of TB cases experience a higher hazard of TB than do adult contacts. Isoniazid preventive therapy (SHR = 0.30, 0.21-0.42) and Bacillus Calmette-Guérin (BCG) vaccination (SHR = 0.66, 0.51-0.86) reduce the risk of disease among household contacts. TB cases without microbiological confirmation exert a smaller hazard of TB among their close contacts compared with smear- or culture-positive cases (excess hazard ratio = 0.88, 0.82-0.93 for HIV- cases and 0.82, 0.57-0.94 for HIV+ cases). The extra household force of infection results in 0.01 (95% confidence interval [CI] = 0.004, 0.028) TB cases per susceptible household contact per year and the rate of transmission between a microbiologically confirmed TB case and susceptible household contact at 0.08 (95% CI = 0.045, 0.129) TB cases per pair per year.

CONCLUSIONS

Accounting for exposure to infected household contacts permits estimation of risk factors for disease susceptibility and transmissibility and comparison of within-household and exogenous forces of infection.

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.

Antimicrobial resistance and COVID-19: Intersections and implications

Before the coronavirus 2019 (COVID-19) pandemic began, antimicrobial resistance (AMR) was among the top priorities for global public health. Already a complex challenge, AMR now needs to be addressed in a changing healthcare landscape. Here, we analyse how changes due to COVID-19 in terms of antimicrobial usage, infection prevention, and health systems affect the emergence, transmission, and burden of AMR. Increased hand hygiene, decreased international travel, and decreased elective hospital procedures may reduce AMR pathogen selection and spread in the short term. However, the opposite effects may be seen if antibiotics are more widely used as standard healthcare pathways break down. Over 6 months into the COVID-19 pandemic, the dynamics of AMR remain uncertain. We call for the AMR community to keep a global perspective while designing finely tuned surveillance and research to continue to improve our preparedness and response to these intersecting public health challenges.

Protective impacts of household-based tuberculosis contact tracing are robust across endemic incidence levels and community contact patterns

There is an emerging consensus that achieving global tuberculosis control targets will require more proactive case finding approaches than are currently used in high-incidence settings. Household contact tracing (HHCT), for which households of newly diagnosed cases are actively screened for additional infected individuals is a potentially efficient approach to finding new cases of tuberculosis, however randomized trials assessing the population-level effects of such interventions in settings with sustained community transmission have shown mixed results. One potential explanation for this is that household transmission is responsible for a variable proportion of population-level tuberculosis burden between settings. For example, transmission is more likely to occur in households in settings with a lower tuberculosis burden and where individuals mix preferentially in local areas, compared with settings with higher disease burden and more dispersed mixing. To better understand the relationship between endemic incidence levels, social mixing, and the impact of HHCT, we developed a spatially explicit model of coupled household and community transmission. We found that the impact of HHCT was robust across settings of varied incidence and community contact patterns. In contrast, we found that the effects of community contact tracing interventions were sensitive to community contact patterns. Our results suggest that the protective benefits of HHCT are robust and the benefits of this intervention are likely to be maintained across epidemiological settings.

First approach to the population structure of Mycobacterium tuberculosis complex in the indigenous population in Puerto Nariño-Amazonas, Colombia

Introduction

Tuberculosis affects vulnerable groups to a greater degree, indigenous population among them.

Objective

To determine molecular epidemiology of clinical isolates of Mycobacterium tuberculosis circulating in an indigenous population through Spoligotyping and 24-loci MIRU-VNTR.

Methodology

A descriptive cross-sectional study was conducted in 23 indigenous communities of Puerto Nariño-Amazonas, Colombia. Recovered clinical isolates were genotyped. For genotyping analyzes global SITVIT2 database and the MIRU-VNTRplus web portal were used.

Results

74 clinical isolates were recovered. Genotyping of clinical isolates by spoligotyping determined 5 different genotypes, all of them belonged to Euro-American lineage. By MIRU-VNTR typing, a total of 14 different genotypes were recorded. Furthermore, polyclonal infection was found in two patients from the same community. The combination of the two methodologies determined the presence of 19 genotypes, 8 formed clusters with 63 clinical isolates in total. Based on epidemiological information, it was possible to establish a potential chain of active transmission in 10/63 (15.9%) patients.

Conclusions

High genomic homogeneity was determined in the indigenous population suggesting possible chains of active transmission. The results obtained showed that specific genotypes circulating among the indigenous population of Colombia are significantly different from those found in the general population.

Risk factors for TB among household contacts of patients with smear-positive TB in eight provinces of Vietnam: a nested case-control study

BACKGROUND

Tuberculosis (TB) continues to account for significant morbidity and mortality annually. Household contacts (HHCs) of persons with TB are a key population for targeting prevention and control interventions. We aimed to identify risk factors associated with developing TB among HHCs.

METHODS

We conducted a nested case-control study among HHCs in eight provinces in Vietnam who were enrolled in a randomized control trial of active case finding for TB. Cases were any HHCs diagnosed and registered with TB within the Vietnam National TB programme during two years of follow-up. Controls were selected by simple random sampling from the remaining HHCs. Risk factor data were collected at enrolment and during follow-up. A logistic regression model was developed to determine predictors of TB among HHCs.

RESULTS

We selected 1,254 HHCs for the analysis; 214 cases and 1,040 controls. Underlying characteristics varied between both groups; cases were older, more likely to be male, higher proportion of reported previous TB and diabetes. Risk factors associated with a TB diagnosis included being male (aOR 1.4; 95% CI: 1.03-2.0), residing in an urban setting (aOR 1.8; 1.3-2.5), prior TB (aOR 4.6; 95% CI: 2.5-8.7), history of diabetes (aOR 3.1; 95% CI: 1.7-5.8), current smoking (aOR 3.1; 95% CI: 2.2-4.4) and prolonged history of coughing in the source case at enrolment (OR 1.6; 95% CI: 1.1-2.3).

CONCLUSIONS

Household contacts remain and important key population for TB prevention and control. TB programmes should ensure effective contact investigations are implemented for household contacts, particularly those with additional risk factors for developing tuberculosis.

Quantitative aerobiologic analysis of an influenza human challenge-transmission trial

Despite evidence that airborne transmission contributes to influenza epidemics, limited knowledge of the infectiousness of human influenza cases hinders pandemic preparedness. We used airborne viral source strength and indoor CO₂ monitoring from the largest human influenza challenge-transmission trial (EMIT: Evaluating Modes of Influenza Transmission, ClinicalTrials.gov number NCT01710111) to compute an airborne infectious dose generation rate q = 0.11 (95% CI 0.088, 0.12)/h and calculate the quantity of airborne virus per infectious dose σ = 1.4E + 5 RNA copies/quantum (95% CI 9.9E + 4, 1.8E + 5). We then compared these calculated values to available data on influenza airborne infectious dose from several previous studies, and applied the values to dormitory room environments to predict probability of transmission between roommates. Transmission risk from typical, moderately to severely symptomatic influenza cases is dramatically decreased by exposure reduction via increasing indoor air ventilation. The minority of cases who shed the most virus (ie, supershedders) may pose great risk even in well-ventilated spaces. Our modeling method and estimated infectiousness provide a ground work for (a) epidemiologic studies of transmission in non-experimental settings and (b) evaluation of the extent to which airborne exposure control strategies could limit transmission risk.

Interpretation of serial interferon-gamma test results to measure new tuberculosis infection among household contacts in Zambia and South Africa

BACKGROUND

A more stringent QuantiFERON-TB Gold In-Tube (QFT) conversion (from negative to positive) definition has been proposed to allow more definite detection of recent tuberculosis (TB) infection. We explored alternative conversion definitions to assist the interpretation of serial QFT results and estimate incidence of TB infection in a large cohort study.

METHODS

We used QFT serial results from TB household contacts aged ≥15 years, collected at baseline and during two follow-up visits (2006-2011) as part of a cohort study in 24 communities in Zambia and South Africa (SA). Conversion rates using the manufacturers' definition (interferon-gamma (IFN-g) < 0.35 to ≥0.35, 'def1') were compared with stricter definitions (IFN-g < 0.2 to ≥0.7 IU/ml, 'def2'; IFN-g < 0.2 to ≥1.05 IU/ml, 'def3'; IFN-g < 0.2 to ≥1.4 IU/ml, 'def4'). Poisson regression was used for analysis.

RESULTS

One thousand three hundred sixty-five individuals in Zambia and 822 in SA had QFT results available. Among HIV-negative individuals, the QFT conversion rate was 27.4 per 100 person-years (CI:22.9-32.6) using def1, 19.0 using def2 (CI:15.2-23.7), 14.7 using def3 (CI:11.5-18.8), and 12.0 using def4 (CI:9.2-15.7). Relative differences across def1-def4 were similar in Zambia and SA. Using def1, conversion was less likely if HIV positive not on antiretroviral treatment compared to HIV negative (aRR = 0.7, 95%CI = 0.4-0.9), in analysis including both countries. The same direction of associations were found using def 2-4.

CONCLUSION

High conversion rates were found even with the strictest definition, indicating high incidence of TB infection among household contacts of TB patients in these communities. The trade-off between sensitivity and specificity using different thresholds of QFT conversion remains unknown due to the absence of a reference standard. However, we identified boundaries within which an appropriate definition might fall, and our strictest definition plausibly has high specificity.

Blood RNA signatures predict recent tuberculosis exposure in mice, macaques and humans

Tuberculosis (TB) is the leading cause of death due to a single infectious disease. Knowing when a person was infected with Mycobacterium tuberculosis (M.tb) is critical as recent infection is the strongest clinical risk factor for progression to TB disease in immunocompetent individuals. However, time since M.tb infection is challenging to determine in routine clinical practice. To define a biomarker for recent TB exposure, we determined whether gene expression patterns in blood RNA correlated with time since M.tb infection or exposure. First, we found RNA signatures that accurately discriminated early and late time periods after experimental infection in mice and cynomolgus macaques. Next, we found a 6-gene blood RNA signature that identified recently exposed individuals in two independent human cohorts, including adult household contacts of TB cases and adolescents who recently acquired M.tb infection. Our work supports the need for future longitudinal studies of recent TB contacts to determine whether biomarkers of recent infection can provide prognostic information of TB disease risk in individuals and help map recent transmission in communities.

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.

Bioaerosol sampling of patients with suspected pulmonary tuberculosis: a study protocol

BACKGROUND

Tuberculosis (TB) is transmitted in bioaerosols containing Mycobacterium tuberculosis (Mtb). Despite being central to ongoing TB transmission, no routine diagnostic assay exists to measure Mtb in bioaerosols. Furthermore, published studies of Mtb in bioaerosol samples have been limited to individuals with sputum-positive pulmonary TB. Notably, TB diagnosis is based on clinical symptoms and sputum laboratory findings. This is despite the fact that approximately half of all patients commencing TB treatment are sputum-negative, resulting in a high proportion of presumptive treatments. Here, we propose to use a sensitive air sampling protocol to investigate the prevalence of Mtb-containing bioaerosols in both sputum-positive and sputum-negative TB suspects, at the same time evaluating the potential to identify unrecognized transmitters of TB.

METHODS

Our parallel-group design will identify viable Mtb in bioaerosols produced by individuals attending a TB clinic in South Africa. Sampling will be performed on eligible individuals presenting with symptoms indicative of TB and repeated at 14 days if initially positive. Participants will be prospectively classified into three distinct groups based on National TB Control Program (NTBCP) criteria: Group A, TB notification with sputum-based laboratory confirmation; Group B, TB notification with empiric diagnosis; and Group C, individuals not notified. Group C individuals with detectable Mtb bioaerosol will be monitored until resolution of clinical and laboratory status. Collection of bioaerosol specimens will be via two consecutive sampling modalities: (1) direct sampling following a specific respiratory manoeuvre; and (2) indirect sampling during passive respiratory activity. Bioaerosol specimens will be analyzed for viable Mtb using DMN-trehalose staining and live-cell fluorescence microscopy. Mtb genomes and mycobacterial and host lipids will be detected using droplet digital PCR and mass spectrometry analyses, respectively. The primary objective is to determine the prevalence of Mtb bioaerosols in all TB clinic attendees and in each of the groups. Secondary objectives are to investigate differences in prevalence of Mtb bioaerosol by HIV status and current isoniazid preventive therapy (IPT) use; we will also determine the impact of anti-TB chemotherapy on Mtb-containing bioaerosol production.

DISCUSSION

Respiratory bioaerosol has a potential role in non-invasive TB diagnosis, infectivity measurement and treatment monitoring.

TRIAL REGISTRATION

ClinicalTrials.gov: NCT04241809 . Date of Registration: 27/1/2020.

A Framework for Network-Based Epidemiological Modeling of Tuberculosis Dynamics Using Synthetic Datasets

We present a framework for discrete network-based modeling of TB epidemiology in US counties using publicly available synthetic datasets. We explore the dynamics of this modeling framework by simulating the hypothetical spread of disease over 2 years resulting from a single active infection in Washtenaw County, MI. We find that for sufficiently large transmission rates that active transmission outweighs reactivation, disease prevalence is sensitive to the contact weight assigned to transmissions between casual contacts (that is, contacts that do not share a household, workplace, school, or group quarter). Workplace and casual contacts contribute most to active disease transmission, while household, school, and group quarter contacts contribute relatively little. Stochastic features of the model result in significant uncertainty in the predicted number of infections over time, leading to challenges in model calibration and interpretation of model-based predictions. Finally, predicted infections were more localized by household location than would be expected if they were randomly distributed. This modeling framework can be refined in later work to study specific county and multi-county TB epidemics in the USA.

A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015

Tuberculosis (TB) remains a public health threat in low TB incidence countries, through a combination of reactivated disease and onward transmission. Using surveillance data from the United Kingdom (UK) and the Netherlands (NL), we demonstrate a simple and predictable relationship between the probability of observing a cluster and its size (the number of cases with a single genotype). We demonstrate that the full range of observed cluster sizes can be described using a modified branching process model with the individual reproduction number following a Poisson lognormal distribution. We estimate that, on average, between 2010 and 2015, a TB case generated 0.41 (95% CrI 0.30,0.60) secondary cases in the UK, and 0.24 (0.14,0.48) secondary cases in the NL. A majority of cases did not generate any secondary cases. Recent transmission accounted for 39% (26%,60%) of UK cases and 23%(13%,37%) of NL cases. We predict that reducing UK transmission rates to those observed in the NL would result in 538(266,818) fewer cases annually in the UK. In conclusion, while TB in low incidence countries is strongly associated with reactivated infections, we demonstrate that recent transmission remains sufficient to warrant policies aimed at limiting local TB spread.

Extensively drug-resistant tuberculosis 'hotspots' and sociodemographic associations in Durban, South Africa

<sec> <title>BACKGROUND</title> In KwaZulu-Natal, South Africa, the incidence of extensively drug-resistant tuberculosis (XDR-TB) is driven by the transmission of resistant strains. As data suggest that cases may be spatially clustered, we sought to identify 'hotspots' and describe these communities. </sec> <sec> <title>METHODS</title> We enrolled XDR-TB patients diagnosed from 2011 to 2014 in eThekwini. Global positioning system (GPS) coordinates for participant homes were collected and hotspots were identified based on population-adjusted XDR-TB incidence. The sociodemographic features of hotspots were characterised using census data. For a subset of participants, we mapped non-home XDR-TB congregate locations and compared these with results including only homes. </sec> <sec> <title>RESULTS</title> Among 132 participants, 75 (57%) were female and 87 (66%) lived in urban or suburban locations. Fifteen of 197 census tracts were identified as XDR-TB hotspots with ≥95% confidence. Four spatial mapping methods identified one large hotspot in northeastern eThekwini. Hotspot communities had higher proportions of low educational attainment (12% vs. 9%) and unemployment (29.3% vs. 20.4%), and lower proportion of homes with flush toilets (36.4% vs. 68.9%). The case density shifted towards downtown Durban when congregate locations (e.g., workplaces) for 43 (33%) participants were mapped. </sec> <sec> <title>CONCLUSIONS</title> In eThekwini, XDR-TB case homes were clustered into hotspots with more poverty indicators than non-hotspots. Prevention efforts targeting hotspot communities and congregate settings may be effective in reducing community transmission. </sec>.

Partitioning the risk of tuberculosis transmission in household contact studies

Household contact studies of tuberculosis (TB) are a common way to study disease transmission dynamics. However these studies lack a mechanism for accounting for community transmission, which is known to be significant, particularly in high burden settings. We illustrate a statistical approach for estimating both the correlates with transmission of TB in a household setting and the probability of community transmission using a modified Bayesian mixed-effects model. This is applied to two household contact studies in Vitória, Brazil from 2008-2013 and Kampala, Uganda from 1995-2004 that enrolled households with an individual that was recently diagnosed with pulmonary TB. We estimate the probability of community transmission to be higher in Uganda (ranging from 0.21 to 0.69, depending on HHC age and HIV status of the index case) than in Brazil (ranging from 0.13 for young children to 0.50 in adults). These estimates are consistent with a higher overall burden of disease in Uganda compared to Brazil. Our method also estimates an increasing risk of community-acquired TB with age of the household contact, consistent with existing literature. This approach is a useful way to integrate the role of the community in understanding TB disease transmission dynamics in household contact studies.

Community-wide Screening for Tuberculosis in a High-Prevalence Setting

BACKGROUND

The World Health Organization has set ambitious targets for the global elimination of tuberculosis. However, these targets will not be achieved at the current rate of progress.

METHODS

We performed a cluster-randomized, controlled trial in Ca Mau Province, Vietnam, to evaluate the effectiveness of active community-wide screening, as compared with standard passive case detection alone, for reducing the prevalence of tuberculosis. Persons 15 years of age or older who resided in 60 intervention clusters (subcommunes) were screened for pulmonary tuberculosis, regardless of symptoms, annually for 3 years, beginning in 2014, by means of rapid nucleic acid amplification testing of spontaneously expectorated sputum samples. Active screening was not performed in the 60 control clusters in the first 3 years. The primary outcome, measured in the fourth year, was the prevalence of microbiologically confirmed pulmonary tuberculosis among persons 15 years of age or older. The secondary outcome was the prevalence of tuberculosis infection, as assessed by an interferon gamma release assay in the fourth year, among children born in 2012.

RESULTS

In the fourth-year prevalence survey, we tested 42,150 participants in the intervention group and 41,680 participants in the control group. A total of 53 participants in the intervention group (126 per 100,000 population) and 94 participants in the control group (226 per 100,000) had pulmonary tuberculosis, as confirmed by a positive nucleic acid amplification test for Mycobacterium tuberculosis (prevalence ratio, 0.56; 95% confidence interval [CI], 0.40 to 0.78; P<0.001). The prevalence of tuberculosis infection in children born in 2012 was 3.3% in the intervention group and 2.6% in the control group (prevalence ratio, 1.29; 95% CI, 0.70 to 2.36; P = 0.42).

CONCLUSIONS

Three years of community-wide screening in persons 15 years of age or older who resided in Ca Mau Province, Vietnam, resulted in a lower prevalence of pulmonary tuberculosis in the fourth year than standard passive case detection alone. (Funded by the Australian National Health and Medical Research Council; ACT3 Australian New Zealand Clinical Trials Registry number, ACTRN12614000372684.).

Immunological mechanisms of human resistance to persistent Mycobacterium tuberculosis infection

Mycobacterium tuberculosis is a leading cause of mortality worldwide and establishes a long-lived latent infection in a substantial proportion of the human population. Multiple lines of evidence suggest that some individuals are resistant to latent M. tuberculosis infection despite long-term and intense exposure, and we term these individuals 'resisters'. In this Review, we discuss the epidemiological and genetic data that support the existence of resisters and propose criteria to optimally define and characterize the resister phenotype. We review recent insights into the immune mechanisms of M. tuberculosis clearance, including responses mediated by macrophages, T cells and B cells. Understanding the cellular mechanisms that underlie resistance to M. tuberculosis infection may reveal immune correlates of protection that could be utilized for improved diagnostics, vaccine development and novel host-directed therapeutic strategies.

Effect of mixed infection on TB dynamics

Poor living conditions, overcrowding and strain diversity are some of the factors that influence mixed infection in Tuberculosis (TB) at the population level. We formulate a mathematical model for mixed infection in TB using nonlinear ordinary differential equations where such factors were represented as probabilities of acquiring mixed infection. A qualitative analysis of the model shows that it exhibits multiple endemic equilibria and backward bifurcation for certain parameter values. The reactivation rate and transmission rate of individuals with mixed infection were of importance as well as the probabilities for latent individuals to acquire mixed infection. We calculate the prevalence of mixed infection from the model and the effect of mixed infection on TB incidence, TB prevalence and Mycobacterium tuberculosis (MTB) infection rate. Numerical simulations show that mixed infection may explain high TB incidences in areas which have a high strain diversity, poor living conditions and are overcrowded even without HIV.