Extensions to Bayesian generalized linear mixed effects models for household tuberculosis transmission

Evaluation of TB elimination strategies in Canadian Inuit populations: Nunavut as a case study

Tuberculosis (TB) continues to disproportionately affect Inuit populations in Canada with some communities having over 300 times higher rate of active TB than Canadian-born, non-Indigenous people. Inuit Tuberculosis Elimination Framework has set the goal of reducing active TB incidence by at least 50% by 2025, aiming to eliminate it by 2030. Whether these goals are achievable with available resources and treatment regimens currently in practice has not been evaluated. We developed an agent-based model of TB transmission to evaluate timelines and milestones attainable in Nunavut, Canada by including case findings, contact-tracing and testing, treatment of latent TB infection (LTBI), and the government investment on housing infrastructure to reduce the average household size. The model was calibrated to ten years of TB incidence data, and simulated for 20 years to project program outcomes. We found that, under a range of plausible scenarios with tracing and testing of 25%–100% of frequent contacts of detected active cases, the goal of 50% reduction in annual incidence by 2025 is not achievable. If active TB cases are identified rapidly within one week of becoming symptomatic, then the annual incidence would reduce below 100 per 100,000 population, with 50% reduction being met between 2025 and 2030. Eliminating TB from Inuit populations would require high rates of contact-tracing and would extend beyond 2030. The findings indicate that time-to-identification of active TB is a critical factor determining program effectiveness, suggesting that investment in resources for rapid case detection is fundamental to controlling TB.

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TB elimination in Inuit populations would likely extend beyond timelines outlined in action plans.

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Rapid case findings combined with testing of frequent contacts are fundamental to TB control.

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Reducing average household size has minimal effect on rates of TB incidence.

A proposed framework to guide evidence synthesis practice for meta-analysis with zero-events studies

OBJECTIVE

In evidence synthesis practice, researchers often face the problem of how to deal with zero-events. Inappropriately dealing with zero-events studies may lead to research waste and mislead healthcare practice. We propose a framework to guide researchers to better deal with zero-events in meta-analysis.

STUDY DESIGN AND SETTING

We used two dimensions, one with respect to the total events count across all studies in the comparative arms in a meta-analysis, and a second with respect to whether included studies have single or both arms with zero-events, to establish the framework for the classification of meta-analysis with zero-events studies. A dataset from Cochrane systematic reviews was used to evaluate the classification.

RESULTS

The proposed framework classifies meta-analysis with zero-events studies into six subtypes. The classification matched well to the large real-world dataset. The applicability of existing methods for zero-events were then presented under each meta-analysis subtype based on this framework, with a 5-step principle to help researchers in evidence synthesis practice.

CONCLUSIONS

The proposed framework should be considered by researchers when making decisions on the selection of the synthesis methods in a meta-analysis. It also provides a reasonable basis for the development of methodological guidelines to deal with zero-events in meta-analysis.

Mycobacterium tuberculosis progresses through two phases of latent infection in humans

Little is known about the physiology of latent Mycobacterium tuberculosis infection. We studied the mutational rates of 24 index tuberculosis (TB) cases and their latently infected household contacts who developed active TB up to 5.25 years later, as an indication of bacterial physiological state and possible generation times during latent TB infection in humans. Here we report that the rate of new mutations in the M. tuberculosis genome decline dramatically after two years of latent infection (two-sided p < 0.001, assuming an 18 h generation time equal to log phase M. tuberculosis, with latency period modeled as a continuous variable). Alternatively, assuming a fixed mutation rate, the generation time increases over the latency duration. Mutations indicative of oxidative stress do not increase with increasing latency duration suggesting a lack of host or bacterial derived mutational stress. These results suggest that M. tuberculosis enters a quiescent state during latency, decreasing the risk for mutational drug resistance and increasing generation time, but potentially increasing bacterial tolerance to drugs that target actively growing bacteria.

Particle sizes of infectious aerosols: implications for infection control

The global pandemic of COVID-19 has been associated with infections and deaths among health-care workers. This Viewpoint of infectious aerosols is intended to inform appropriate infection control measures to protect health-care workers. Studies of cough aerosols and of exhaled breath from patients with various respiratory infections have shown striking similarities in aerosol size distributions, with a predominance of pathogens in small particles (<5 μm). These are immediately respirable, suggesting the need for personal respiratory protection (respirators) for individuals in close proximity to patients with potentially virulent pathogens. There is no evidence that some pathogens are carried only in large droplets. Surgical masks might offer some respiratory protection from inhalation of infectious aerosols, but not as much as respirators. However, surgical masks worn by patients reduce exposures to infectious aerosols to health-care workers and other individuals. The variability of infectious aerosol production, with some so-called super-emitters producing much higher amounts of infectious aerosol than most, might help to explain the epidemiology of super-spreading. Airborne infection control measures are indicated for potentially lethal respiratory pathogens such as severe acute respiratory syndrome coronavirus 2.

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.

Assessment of tuberculosis contact investigation in Shanghai, China: An 8-year cohort study

BACKGROUND

Tuberculosis (TB) contact investigation has been observed as a useful programmatic tool in active case finding. We collected data of contact cases to evaluate the effectiveness of TB contact investigation programme in Shanghai, China.

METHODS

Since 2009, we screened and followed up the close contacts of bacteria-positive TB cases in Songjiang, Shanghai and calculated the incidence of TB in close contacts and confirmed the transmission by genotyping and sequencing.

RESULTS

A total of 4584 close contacts of 1765 contagious TB index cases were followed up for an average of 4 years. About 62 contacts (333/100 000, 95% CI: 256-428) developed TB excluding 6 co-prevalent cases. The contact cases consisted 1.50% (39/2592) of all the bacteria-positive cases in population. Transmission links were confirmed in 60% (9/15) familial contacts and 22% (2/9) in non-familial contacts. Source cases come from more than close contacts and both index and contact cases created other secondary cases in community.

CONCLUSIONS

Familial contacts are more likely to acquire TB from the index, indicating the priority of family members in TB contact investigation in China. However, most non-familial contacts were infected from sources in the community and contact cases attributed little to case finding in the TB-prevalent setting. Thus, active case finding should be strengthened in general population.