The escalating tuberculosis crisis in central and South American prisons

Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review

Tuberculosis remains a leading cause of infection-related mortality, and efforts to reduce its incidence have been hindered by an incomplete understanding of local Mycobacterium tuberculosis transmission dynamics. Advances in pathogen sequencing and spatial analysis have created new opportunities to map M tuberculosis transmission patterns more precisely. In this scoping review, we searched for studies combining pathogen genetics and location data to analyse the spatial patterns of M tuberculosis transmission and identified 142 studies published between 1994 and 2024. Secular changes in genetic methods were observed, with genome sequencing approaches largely replacing lower-resolution genotyping methods since 2020. The included studies addressed four primary research questions: how are tuberculosis cases and M tuberculosis transmission clusters geographically distributed; do spatially concentrated M tuberculosis clusters exist, and where are these areas located; when spatial concentration occurs, what host, pathogen, or environmental factors contribute to these patterns; and do identifiable relationships exist between the spatial proximity of tuberculosis cases and the genetic similarity of the M tuberculosis isolates infecting these individuals? Collectively, in this Review, we examined the available study data, evaluated the analytical requirements for addressing these questions, and discussed opportunities and challenges for future research. We found that the integration of spatial and genomic data can inform a detailed understanding of local M tuberculosis transmission patterns, but improved study designs and new analytical methods to address gaps in sampling completeness and to integrate additional movement data are needed to fully realise the potential of these tools.

Global perspectives on tuberculosis in prisons and incarceration centers - Risk factors, priority needs, challenges for control and the way forward

Tuberculosis (TB) remains a prominent cause of illness and mortality worldwide. Prisons are hotspots for TB transmission worldwide. We reviewed the literature on TB in prisons worldwide, including TB risk factors, delays in diagnosis including drug resistance, the treatment accorded, and operational and logistical issues of TB care in prison. The quantity and quality of data on TB in prisons varies worldwide. The TB incidence rate in prisons varies by World Health Organization region, with African countries having the highest rates of TB and TB/HIV co-infection. Its incidence rate among inmates is about 10 times higher than that of the general population. The growing prevalence of multidrug-resistant TB is particularly concerning, as it may affect high-risk settings and disproportionately affects vulnerable populations, such as prisoners and incarcerated individuals who go undiagnosed for extended periods of time. Factors that drive the high TB rates in prisons include limited access to health services such as TB care, overcrowding, poor ventilation, malnutrition, HIV, alcohol use disorders, illegal drug use, smoking, and other comorbidities, compounded by limited access to healthcare. Addressing TB in prisons requires a multifaceted approach, that includes improving living conditions, enhancing healthcare services, and developing innovative detection methods. The ongoing conflicts in Europe, the Middle East, Asia, and Africa further complicated TB prevention and control efforts in prisons, emphasizing the need for targeted interventions to address TB in these high-risk settings. Structured interventions tailored to the specific risk factors present in each environment should be investigated to effectively focus measures aimed at diminishing the overall burden of TB in prisons. Electronic record-keeping worldwide will allow for accurate data to be collected and shared.

National Active Case-Finding Program for Tuberculosis in Prisons, Peru, 2024

During January-September 2024, a national active case-finding program in Peru's prisons screened >38,000 persons for tuberculosis (TB) using chest radiography with automated interpretation and rapid molecular tests. The program found high percentages of TB, rifampin-resistant TB, and asymptomatic infections, demonstrating the urgent need for systematic screening among incarcerated populations.

Transmission of Mycobacterium tuberculosis in four prisons in Colombia

Our study aimed to describe the transmission dynamics and genotypic diversity of Mycobacterium tuberculosis in people deprived of liberty (PDL) in four Colombian prisons. Our cohort study included 64 PDL with bacteriologically confirmed pulmonary tuberculosis diagnosed in four Colombian prisons. The 132 isolates were genotyped using 24-mycobacterial interspersed repeated units-variable number tandem repeats (MIRUs-VNTR). A cluster was defined when ≥2 isolates from different PDL had the same genotype. Tuberculosis acquired in prison was considered when ≥2 persons were within the same cluster and had an epidemiological link. We mapped the place of residence before incarceration and within prisons. We assessed overcrowding and ventilation conditions in the prison that had clusters. We found that the most frequent genotypes were LAM (56.8%) and Haarlem (36.4%), and 45.3% of the PDL diagnosed with tuberculosis were clustered. Most PDL diagnosed in prison came from neighborhoods in Medellin with a high TB incidence. M. tuberculosis infection acquired in prison was detected in 19% of PDL, 9.4% had mixed infection, 3.1% reinfection, and 1.6% relapse. Clusters only appeared in one prison, in cell blocks with overcrowding >100%, and inadequate ventilation conditions. Prisons require the implementation of effective respiratory infection control measures to prevent M. tuberculosis transmission.

Performance of five dynamic models in predicting tuberculosis incidence in three prisons in Thailand

This study examined the ability of the following five dynamic models for predicting pulmonary tuberculosis (PTB) incidence in a prison setting: the Wells-Riley equation, two Rudnick & Milton-proposed models based on air changes per hour and liters per second per person, the Issarow et al. model, and the applied susceptible-exposed-infected-recovered (SEIR) tuberculosis (TB) transmission model. This 1-year prospective cohort study employed 985 cells from three Thai prisons (one prison with 652 cells as the in-sample, and two prisons with 333 cells as the out-of-sample). The baseline risk of TB transmission for each cell was assessed using the five dynamic models, and the future PTB incidence was calculated as the number of new PTB cases per cell and the number of new PTB cases per 1,000 person-years (incidence rate). The performance of the dynamic models was assessed by a four-step standard assessment procedure (including model specification tests, in-sample model fitting, internal validation, and external validation) based on the Negative Binomial Regression model. A 1% increase in baseline TB transmission probability was associated with a 3%-7% increase in future PTB incidence rate, depending on the dynamic model. The Wells-Riley model exhibited the best performance in terms of both internal and external validity. Poor goodness-of-fit was observed in all dynamic models (chi-squared goodness-of-fit tests of 70.75-305.1, 8 degrees of freedom, p < .001). In conclusion, the Wells-Riley model was the most appropriate dynamic model, especially for large-scale investigations, due to its fewer parameter requirements. Further research is needed to confirm our findings and gather more data to improve these dynamic models.

Mass incarceration as a driver of the tuberculosis epidemic in Latin America and projected effects of policy alternatives: a mathematical modelling study

BACKGROUND

Tuberculosis incidence is increasing in Latin America, where the incarcerated population has nearly quadrupled since 1990. We aimed to quantify the impact of historical and future incarceration policies on the tuberculosis epidemic, accounting for effects in and beyond prisons.

METHODS

In this modelling study, we calibrated dynamic compartmental transmission models to historical and contemporary data from Argentina, Brazil, Colombia, El Salvador, Mexico, and Peru, which comprise approximately 80% of the region's incarcerated population and tuberculosis burden. The model was fit independently for each country to incarceration and tuberculosis data from 1990 to 2023 (specific dates were country dependent). The model does not include HIV, drug resistance, gender or sex, or age structure. Using historical counterfactual scenarios, we estimated the transmission population attributable fraction (tPAF) for incarceration and the excess population-level burden attributable to increasing incarceration prevalence since 1990. We additionally projected the effect of alternative incarceration policies on future population tuberculosis incidence.

FINDINGS

Population tuberculosis incidence in 2019 was 29·4% (95% uncertainty interval [UI] 23·9-36·8) higher than expected without the rise in incarceration since 1990, corresponding to 34 393 (28 295-42 579) excess incident cases across countries. The incarceration tPAF in 2019 was 27·2% (20·9-35·8), exceeding estimates for other risk factors like HIV, alcohol use disorder, and undernutrition. Compared with a scenario where incarceration rates remain stable at current levels, a gradual 50% reduction in prison admissions and duration of incarceration by 2034 would reduce population tuberculosis incidence by over 10% in all countries except Mexico.

INTERPRETATION

The historical rise in incarceration in Latin America has resulted in a large excess tuberculosis burden that has been under-recognised to date. International health agencies, ministries of justice, and national tuberculosis programmes should collaborate to address this health crisis with comprehensive strategies, including decarceration.

FUNDING

National Institutes of Health.

Mass incarceration as a driver of the tuberculosis epidemic in Latin America and projected impacts of policy alternatives: A mathematical modeling study

Background

Tuberculosis incidence is increasing in Latin America, where the incarcerated population has nearly quadrupled since 1990. The full impact of incarceration on the tuberculosis epidemic, accounting for effects beyond prisons, has never been quantified.

Methods

We calibrated dynamic compartmental transmission models to historical and contemporary data from Argentina, Brazil, Colombia, El Salvador, Mexico, and Peru, which comprise approximately 80% of the region's incarcerated population and tuberculosis burden. Using historical counterfactual scenarios, we estimated the transmission population attributable fraction (tPAF) for incarceration and the excess population-level burden attributable to increasing incarceration prevalence since 1990. We additionally projected the impact of alternative incarceration policies on future population tuberculosis incidence.

Findings

Population tuberculosis incidence in 2019 was 29.4% (95% UI, 23.9-36.8) higher than expected without the rise in incarceration since 1990, corresponding to 34,393 (95% UI, 28,295-42,579) excess incident cases across countries. The incarceration tPAF in 2019 was 27.2% (95% UI, 20.9-35.8), exceeding estimates for other risk factors like HIV, alcohol use disorder, and undernutrition. Compared to a scenario where incarceration rates remain stable at current levels, a gradual 50% reduction in prison admissions and duration of incarceration by 2034 would reduce population tuberculosis incidence by over 10% in all countries except Mexico.

Interpretation

The historical rise in incarceration in Latin America has resulted in a large excess tuberculosis burden that has been under-recognized to-date. International health agencies, ministries of justice, and national tuberculosis programs should collaborate to address this health crisis with comprehensive strategies, including decarceration.

Funding

National Institutes of Health.

Assessment of tuberculosis transmission probability in three Thai prisons based on five dynamic models

This study aimed to assess and compare the probability of tuberculosis (TB) transmission based on five dynamic models: the Wells-Riley equation, two Rudnick & Milton-proposed models based on air changes per hour (ACH) and liters per second per person (L/s/p), the model proposed by Issarow et al, and the Applied Susceptible-Exposed-Infected-Recovered (SEIR) TB transmission model. This study also aimed to determine the impact of model parameters on such probabilities in three Thai prisons. A cross-sectional study was conducted using data from 985 prison cells. The TB transmission probability for each cell was calculated using parameters relevant to the specific model formula, and the magnitude of the model agreement was examined by Spearman's rank correlation and Bland-Altman plot. Subsequently, a multiple linear regression analysis was conducted to investigate the influence of each model parameter on the estimated probability. Results revealed that the median (Quartiles 1 and 3) of TB transmission probability among these cells was 0.052 (0.017, 0.180). Compared with the pioneered Wells-Riley's model, the remaining models projected discrepant TB transmission probability from less to more commensurate to the degree of model modification from the pioneered model as follows: Rudnick & Milton (ACH), Issarow et al., and Rudnick & Milton (L/s/p), and the applied SEIR models. The ventilation rate and number of infectious TB patients in each cell or zone had the greatest impact on the estimated TB transmission probability in most models. Additionally, the number of inmates in each cell, the area per person in square meters, and the inmate turnover rate were identified as high-impact parameters in the applied SEIR model. All stakeholders must urgently address these influential parameters to reduce TB transmission in prisons. Moreover, further studies are required to determine their relative validity in accurately predicting TB incidence in prison settings.

Specific Mycobacterium tuberculosis Strain Circulating in Prison Revealed by Cost-Effective Amplicon Sequencing

This scientific study focuses on tuberculosis (TB) within prison settings, where persons deprived of liberty (PDL) face significantly higher rates of the disease compared to the general population. The research employs the low-cost amplicon sequencing of Mycobacterium tuberculosis strains, aiming first to identify specific lineages and also to detect mutations associated with drug resistance. The method involves multiplex amplification, DNA extraction, and sequencing, providing valuable insights into TB dynamics and resistance-mutation profiles within the prison system at an affordable cost. The study identifies a characteristic lineage (X) circulating among PDLs in the penitentiary system in Uruguay, absent in the general population, and notes its prevalence at prison entry. No high-confidence mutations associated with drug resistance were found. The findings underscore the importance of molecular epidemiology in TB control, emphasizing the potential for intra-prison transmissions and the need for broader studies to understand strain dynamics.

Excess tuberculosis risk during and following incarceration in Paraguay: a retrospective cohort study

Background

The increased risk of tuberculosis (TB) among people deprived of liberty (PDL) is due to individual and institution-level factors. We followed a cohort of PDL from 5 prisons in Paraguay to describe the risk of TB during incarceration and after they were released.

Methods

We linked a 2013 national census of prisons with TB records from the TB Program from 2010 to 2021 to identify TB notifications among incarcerated and formerly incarcerated individuals. We used multivariable Cox regression models to quantify the risk of TB during and following incarceration and to identify risk factors associated with TB.

Findings

Among 2996 individuals incarcerated, 451 (15.1%) were diagnosed with TB. Of these, 262 (58.1%) cases occurred during incarceration and 189 (41.9%) occurred in the community after release. In prison, the hazard ratio of developing TB was 1.97 (95% CI: 1.52-2.61) after six months of incarceration and increased to 2.78 (95% CI: 1.82-4.24) after 36 months compared with the first six months. The overall TB notification rate was 2940 per 100,000 person-years. This rate increased with the duration of incarceration from 1335 per 100,000 person-years in the first year to 8455 per 100,000 person-years after 8 years. Among former prisoners, the rate of TB decreased from 1717 in the first year after release to 593 per 100 000 person-years after 8 years of follow up.

Interpretation

Our study shows the alarming risk of TB associated with prison environments in Paraguay, and how this risk persists for years following incarceration. Effective TB control measures to protect the health of people during and following incarceration are urgently needed.

Funding

Paraguay National Commission of Science and Technology grant CONACYT PIN 15-705 (GS, GES, SA).

Pre-extensively drug-resistant and extensively drug-resistant tuberculosis in Latin America and the Caribbean: A systematic review and meta-analysis

BACKGROUND

The growing threat from pre-extensively drug-resistant tuberculosis (pre-XDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) poses a major public health concern in Latin America and the Caribbean (LAC). Therefore, this study aimed to summarize the available evidence on the prevalence of pre-XDR-TB and XDR-TB among patients with multidrug-resistant tuberculosis in LAC.

METHODS

A systematic review was conducted in the following databases on June 3, 2023: PubMed, Scopus, Ovid Medline, Web of Science, Scielo and LILACS. We estimated pooled proportions using a random effects model (Dersimonian and Laird). The 95% confidence intervals (95% CI) were calculated using the binomial exact method (Clopper-Pearson Method). Subgroup (by time period and country) and sensitivity analyses were performed.

RESULTS

Twenty-nine studies were eligible for qualitative synthesis and 27 for meta-analysis (n = 15,565). The pooled prevalence of XDR-TB in the study participants was 5% (95% CI: 3%-6%), while that of pre-XDR-TB was 10% (95% CI 7%-14%). Cuba (6%, 95% CI 0%-17%) and Peru (6%, 95% CI 5%-7%) had the highest pooled prevalence of XDR-TB. Regarding pre-XDR-TB, Brazil (16%, 95% CI 11%-22%) and Peru (13%, 95% CI: 9%-16%) showed the highest prevalence.

CONCLUSIONS

The pooled prevalence of pre-XDR-TB and XDR-TB in LAC was 10% and 5%, respectively. Governments should strengthen drug-resistance surveillance and TB programs.

Prison as a driver of recent transmissions of multidrug-resistant tuberculosis in Callao, Peru: a cross-sectional study

Background

We sought to identify resistance patterns and key drivers of recent multidrug-resistant tuberculosis (MDR-TB) transmission in a TB-prevalent area in Peru.

Methods

Cross-sectional study including MDR Mycobacterium tuberculosis complex (Mtbc) strains identified in Callao-Peru between April 2017 and February 2019. Mtbc DNA was extracted for whole genome sequencing which was used for phylogenetic inference, clustering, and resistance mutation analyses. Clusters indicative of recent transmission were defined based on a strain-to-strain distance of ≤5 (D5) single nucleotide polymorphisms (SNPs). Epidemiologic factors linked to MDR-TB clustering were analyzed using Poisson regression.

Findings

171 unique MDR-Mtbc strains were included; 22 (13%) had additional fluoroquinolone resistance and were classified as pre-XDR. Six strains (3.5%) harboured bedaquiline (BDQ) resistance mutations and were classified as MDR + BDQ. 158 (92%) Mtbc strains belonged to lineage 4 and 13 (8%) to lineage 2. Using a cluster threshold of ≤5 SNPs, 98 (57%) strains were grouped in one of the 17 D5 clusters indicative of recent transmission, ranging in size from 2 to the largest cluster formed by 53 4.3.3 strains (group_1). Lineage 4.3.3 strains showed the overall highest cluster rate (43%). In multivariate analyses, current or previous imprisonment was independently associated with being part of any MDR-TB transmission clusters (adjusted prevalence ratio [aPR], 1.45; 95% CI, 1.09-1.92).

Interpretation

Pre-XDR-TB emerged in more than 10% of the MDR-TB strains investigated. Transmission of 4.3.3 Mtbc strains especially of the dominant group_1 clone is a major driver of the MDR-TB epidemic in Callao. Current or previous imprisonment was linked to recent MDR-TB transmissions, indicating an important role of prisons in driving the MDR-TB epidemic.

Funding

This work was supported in part by the ERANet-LAC Network of the European Union, Latin America and the Caribbean Countries on Joint Innovation and Research Activities, and FONDECYT. Additional support was received from Leibniz Science Campus Evolutionary Medicine of the Lung, the Deutsche Forschungsgemeinschaft (German Research Foundation, under Germany's Excellence Strategy-EXC 2167 Precision Medicine in Inflammation), and the Research Training Group 2501 TransEvo.

Tuberculosis in prison: What about after release? The example of French Guiana

INTRODUCTION

Tuberculosis is a major cause of mortality worldwide. Prisoners in Guiana have multiple risk factors. The primary objective of this study was to describe tuberculosis occurring in prison and after release in French Guiana between 2008 and 2020. Secondary objectives were to identify tuberculosis risk factors and determine annual incidences.

METHODS

A retrospective cohort study of tuberculosis cases was carried out at the Guiana prison between 2008 and 2020. Data were collected from prison registers and cross-referenced with the list of tuberculosis notifications in French Guiana.

RESULTS

A total of 36 cases of tuberculosis were studied. Incidence was high, at 263/100,000 per year, higher than elsewhere in France and comparable to that in Brazil. Despite visibly effective screening on entry, with little evidence of intra-prison circulation of tuberculosis, 39% of patients were diagnosed within two years of leaving prison (76% were symptomatic). This could be explained by the high prevalence of latent forms (LTI).

DISCUSSION

Continued screening on entry, in combination with annual radiological and clinical screening, and reinforced follow-up on release seem indicated to improve patient management and the search for possible LTI.

Prioritizing persons deprived of liberty in global guidelines for tuberculosis preventive treatment

In this Policy Forum piece, Aditya Narayan and colleagues discuss the challenges and opportunities for tuberculosis preventive treatment in carceral settings.

The impact of the COVID-19 pandemic on TB diagnosis in the Brazilian prison population, 2020-2021

BACKGROUND: TB is an infectious disease with a worldwide impact. TB is closely associated with social and housing conditions, exerting a significant impact on the prison population, which is particularly susceptible to the disease. Evidence suggests that the COVID-19 pandemic has exacerbated social vulnerability. This study therefore aimed to analyse the impact of the pandemic on the diagnosis of new cases of TB in the Brazilian prison population in the years 2020 and 2021.METHODS: This is an ecological study involving cases of TB recorded in the prison population of Brazil from 2015 to 2021. Data were collected from the Brazil's Information System for Notifiable Diseases.RESULTS: The incidence of TB in the prison population in Brazil fell from 1,005.9/100,000 population between 2015 and 2019 to 852.3/100,000 population between 2020 and 2021. In 2021, there was a deficit of 539 cases (-7.6%) compared to what was expected for the year. In 2020, there was a 10% reduction in TB diagnoses in January and February, reaching 3.8% in March. A negative percentage was observed in most of the subsequent months. In 2021, the year began with a 21.6% decline in January, returning to positive values only in August and September.CONCLUSION: The first years of the COVID-19 pandemic resulted in underdiagnosis of TB in the Brazilian prison population.

Global, regional, and national estimates of tuberculosis incidence and case detection among incarcerated individuals from 2000 to 2019: a systematic analysis

BACKGROUND

People who are incarcerated are at high risk of developing tuberculosis. We aimed to estimate the annual global, regional, and national incidence of tuberculosis among incarcerated populations from 2000 to 2019.

METHODS

We collected and aggregated data for tuberculosis incidence and prevalence estimates among incarcerated individuals in published and unpublished literature, annual tuberculosis notifications among incarcerated individuals at the country level, and the annual number of incarcerated individuals at the country level. We developed a joint hierarchical Bayesian meta-regression framework to simultaneously model tuberculosis incidence, notifications, and prevalence from 2000 to 2019. Using this model, we estimated trends in absolute tuberculosis incidence and notifications, the incidence and notification rates, and the case detection ratio by year, country, region, and globally.

FINDINGS

In 2019, we estimated a total of 125 105 (95% credible interval [CrI] 93 736-165 318) incident tuberculosis cases among incarcerated individuals globally. The estimated incidence rate per 100 000 person-years overall was 1148 (95% CrI 860-1517) but varied greatly by WHO region, from 793 (95% CrI 430-1342) in the Eastern Mediterranean region to 2242 (1515-3216) in the African region. Global incidence per 100 000 person-years between 2000 and 2012 among incarcerated individuals decreased from 1884 (95% CrI 1394-2616) to 1205 (910-1615); however, from 2013 onwards, tuberculosis incidence per 100 000 person-years was stable, from 1183 (95% CrI 876-1596) in 2013 to 1148 (860-1517) in 2019. In 2019, the global case detection ratio was estimated to be 53% (95% CrI 42-64), the lowest over the study period.

INTERPRETATION

Our estimates suggest a high tuberculosis incidence rate among incarcerated individuals globally with large gaps in tuberculosis case detection. Tuberculosis in incarcerated populations must be addressed with interventions specifically tailored to improve diagnoses and prevent transmission as a part of the broader global tuberculosis control effort.

FUNDING

National Institutes of Health.

Tuberculosis in Prisons: Importance of Considering the Clustering in the Analysis of Cross-Sectional Studies

The level of clustering and the adjustment by cluster-robust standard errors have yet to be widely considered and reported in cross-sectional studies of tuberculosis (TB) in prisons. In two cross-sectional studies of people deprived of liberty (PDL) in Medellin, we evaluated the impact of adjustment versus failure to adjust by clustering on prevalence ratio (PR) and 95% confidence interval (CI). We used log-binomial regression, Poisson regression, generalized estimating equations (GEE), and mixed-effects regression models. We used cluster-robust standard errors and bias-corrected standard errors. The odds ratio (OR) was 20% higher than the PR when the TB prevalence was >10% in at least one of the exposure factors. When there are three levels of clusters (city, prison, and courtyard), the cluster that had the strongest effect was the courtyard, and the 95% CI estimated with GEE and mixed-effect models were narrower than those estimated with Poisson and binomial models. Exposure factors lost their significance when we used bias-corrected standard errors due to the smaller number of clusters. Tuberculosis transmission dynamics in prisons dictate a strong cluster effect that needs to be considered and adjusted for. The omission of cluster structure and bias-corrected by the small number of clusters can lead to wrong inferences.

Scaling up evidence-based approaches to tuberculosis screening in prisons

People deprived of liberty have among the highest rates of tuberculosis globally. The incidence of tuberculosis is ten times greater than the incidence of tuberculosis in the general population. In 2021, WHO updated its guidance to strongly recommend systematic screening for tuberculosis in prisons and penitentiary systems. Which case-finding strategies should be adopted, and how to effectively implement these strategies in these settings, will be crucial questions facing ministries of health and justice. In this Viewpoint, we review the evidence base for tuberculosis screening and diagnostic strategies in prisons, highlighting promising approaches and knowledge gaps. Drawing upon past experiences of implementing active case-finding and care programmes in settings with a high tuberculosis burden, we discuss challenges and opportunities for improving the tuberculosis diagnosis and treatment cascade in these settings. We argue that improved transparency in reporting of tuberculosis notifications and outcomes in prisons and renewed focus and resourcing from WHO and other stakeholders will be crucial for building the commitment and investments needed from countries to address the continued crisis of tuberculosis in prisons.

New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing

BACKGROUND

The rate of tuberculosis (TB) infection among the prison population (PP) in Brazil is 28 times higher than that in the general population, and prison environment favors the spread of TB.

OBJECTIVE

To describe TB transmission dynamics and drug resistance profiles in PP using whole-genome sequencing (WGS).

METHODS

This was a retrospective study of Mycobacterium tuberculosis cultivated from people incarcerated in 55 prisons between 2016 and 2019; only one isolate per prisoner was included. Information about movement from one prison to another was tracked. Clinical information was collected, and WGS was performed on isolates obtained at the time of TB diagnosis.

RESULTS

Among 134 prisoners included in the study, we detected 16 clusters with a total of 58 (43%) cases of M. tuberculosis. Clusters ranged from two to seven isolates with five or fewer single nucleotide polymorphism (SNP) differences, suggesting a recent transmission. Six (4.4%) isolates were resistant to at least one anti-TB drug. Two of these clustered together and showed resistance to rifampicin, isoniazid, and fluoroquinolones, with 100% concordance between WGS and phenotypic drug-susceptibility testing. Prisoners with clustered isolates had a high amount of movement between prisons (two to eight moves) during the study period.

CONCLUSIONS

WGS demonstrated the recent transmission of TB within prisons in Brazil. The high movement among prisoners seems to be related to the transmission of the same M. tuberculosis strain within the prison system. Screening for TB before and after the movement of prisoners using rapid molecular tests could play a role in reducing transmission.

Phylogeography and transmission of Mycobacterium tuberculosis spanning prisons and surrounding communities in Paraguay

Recent rises in incident tuberculosis (TB) cases in Paraguay and the increasing concentration of TB within prisons highlight the urgency of targeting strategies to interrupt transmission and prevent new infections. However, whether specific cities or carceral institutions play a disproportionate role in transmission remains unknown. We conducted prospective genomic surveillance, sequencing 471 Mycobacterium tuberculosis complex genomes, from inside and outside prisons in Paraguay's two largest urban areas, Asunción and Ciudad del Este, from 2016 to 2021. We found genomic evidence of frequent recent transmission within prisons and transmission linkages spanning prisons and surrounding populations. We identified a signal of frequent M. tuberculosis spread between urban areas and marked recent population size expansion of the three largest genomic transmission clusters. Together, our findings highlight the urgency of strengthening TB control programs to reduce transmission risk within prisons in Paraguay, where incidence was 70 times that outside prisons in 2021.

Evaluation of chest X-ray with automated interpretation algorithms for mass tuberculosis screening in prisons: a cross-sectional study

Background

The World Health Organization (WHO) recommends systematic tuberculosis (TB) screening in prisons. Evidence is lacking for accurate and scalable screening approaches in this setting. We aimed to assess the accuracy of artificial intelligence-based chest x-ray interpretation algorithms for TB screening in prisons.

Methods

We performed prospective TB screening in three male prisons in Brazil from October 2017 to December 2019. We administered a standardized questionnaire, performed a chest x-ray in a mobile unit, and collected sputum for confirmatory testing using Xpert MTB/RIF and culture. We evaluated x-ray images using three algorithms (CAD4TB version 6, Lunit version 3.1.0.0 and qXR version 3) and compared their accuracy. We utilized multivariable logistic regression to assess the effect of demographic and clinical characteristics on algorithm accuracy. Finally, we investigated the relationship between abnormality scores and Xpert semi-quantitative results.

Findings

Among 2075 incarcerated individuals, 259 (12.5%) had confirmed TB. All three algorithms performed similarly overall with area under the receiver operating characteristic curve (AUC) of 0.88-0.91. At 90% sensitivity, only LunitTB and qXR met the WHO Target Product Profile requirements for a triage test, with specificity of 84% and 74%, respectively. All algorithms had variable performance by age, prior TB, smoking, and presence of TB symptoms. LunitTB was the most robust to this heterogeneity but nonetheless failed to meet the TPP for individuals with previous TB. Abnormality scores of all three algorithms were significantly correlated with sputum bacillary load.

Interpretation

Automated x-ray interpretation algorithms can be an effective triage tool for TB screening in prisons. However, their specificity is insufficient in individuals with previous TB.

Funding

This study was supported by the US National Institutes of Health (grant numbers R01 AI130058 and R01 AI149620) and the State Secretary of Health of Mato Grosso do Sul.

Epidemiology and control strategies for tuberculosis in countries with the largest prison populations

Tuberculosis (TB) is a serious infectious disease, and its control is considered a challenge, especially among vulnerable populations such as prisoners. The occurrence of TB in prisons is an alarming public health problem in many countries. This integrative review aims to describe the epidemiology of TB and control strategies for this disease in countries with the largest prison populations. Studies have shown that it is essential to know the prevalence of TB in prisons of each country. This is because it can serve as an indication of the need for action in prisons to reduce TB rates, including improving the structure of prison environments, rapidly and accurately diagnosing new cases, identifying drug-resistant strains, and implementing effective and directly observed treatment for TB.

Observatorios sociales nacionales y regional de tuberculosis en ocho países de Latinoamérica y el Caribe

Poner fin a la tuberculosis (TB) requiere de un enfoque y participación multisectorial, incluyendo a la sociedad civil organizada. Entonces con el apoyo de un proyecto regional financiado por el Fondo Mundial (OBSERVA TB), desde el año 2019 se conformaron observatorios sociales de tuberculosis en 8 países de Latinoamérica y el Caribe (LAC) (Bolivia, Colombia, El Salvador, Guatemala, Haití, México, Perú y República Dominicana) y un Observatorio Social Regional de TB, como expresión de la implementación del enfoque ENGAGE-TB impulsado por la Organización Mundial de la Salud. Este artículo presenta el modelo de implementación, los avances y los desafíos de los observatorios sociales de tuberculosis. A diciembre de 2021, se incluyeron 135 organizaciones de la sociedad civil de LAC en los 8 observatorios implementados, espacios que sirven como plataformas para la vigilancia social, la incidencia política y el monitoreo social de las respuestas nacionales contra la TB, además de contribuir a los indicadores del ENGAGE-TB relacionados a la detección de casos TB y a los apoyos durante el tratamiento. Por ello, recomendamos la consolidación y expansión de los observatorios existentes, así como la participación de otros países de la región LAC.

Tuberculosis in prison inmates in Southern Brazil: investigating the epidemiological and operational indicators

BACKGROUND

Tuberculosis is a worldwide public health problem and is more prevalent in specific populations, such as prisoners. The aim of this study was to analyze the epidemiological and operational indicators of tuberculosis in prisoners in a southern region of Brazil.

METHODS

This was a descriptive, observational study, utilizing secondary data from the Notifiable Diseases Information System on tuberculosis cases diagnosed in prisoners in the state of Rio Grande do Sul, southern Brazil, from 2014 to 2018. Prisoner data used to calculate incidence were extracted from reports by the National Penitentiary Department.

RESULTS

From 2014 to 2018, 3,557 tuberculosis cases were reported in Rio Grande do Sul prisoners. The incidence rate of tuberculosis in prisoners was 1,235/100,000 individuals in 2014 and 1,430/100,000 individuals in 2018. The proportion of new TB cases tested for HIV was high, 83.4% in this period; among those tested, 12.9% were HIV coinfected. The proportion of new cases of pulmonary tuberculosis confirmed by laboratory criteria was 52.6% in this period. In total, 18.4% of new pulmonary tuberculosis cases were initiated on directly observed treatment in this period, and 36.4% of contacts of new cases of pulmonary tuberculosis with laboratory confirmation were examined. Among retreatment pulmonary tuberculosis cases, 82.4% were laboratory-confirmed.

CONCLUSIONS

Tuberculosis incidence is increasing on a per-capita and absolute basis in Rio Grande do Sul. Laboratory confirmation, HIV testing, directly observed treatment, and contact investigation rates were all low, indicating the need to improve medical and public health measures for tuberculosis control in prisons.

Excess tuberculosis cases and deaths following an economic recession in Brazil: an analysis of nationally representative disease registry data

BACKGROUND

In 2019, tuberculosis incidence and mortality in Brazil were 46 and 3·3 per 100 000 population, respectively, and the country has reported rising tuberculosis case rates since 2016, following an economic crisis beginning in mid-2014. We aimed to estimate the number of excess tuberculosis cases and deaths during the recession period, and assessed potential causes.

METHODS

In this multi-level regression modelling study, we extracted tuberculosis case notifications from Brazil's National Notifiable Disease Information System (known as SINAN), and tuberculosis deaths from the Mortality Information System (known as SIM), for all ages. We fitted mixed-effects regression models estimating trends in these outcomes-stratified by sex, age group, and state-during the pre-recession period (Jan 1, 2010-Dec 31, 2014). We calculated excess cases and deaths between Jan 1, 2015, and Dec 31, 2019 (the recession period) as the difference between reported values and a counterfactual of continued pre-recession trends. We examined the relationship between excess cases and possible explanatory factors using ordinary least squares regression. We tested the robustness of our findings to alternative model specifications related to the pre-recession period and criteria for defining tuberculosis deaths.

FINDINGS

We estimated 22 900 excess tuberculosis cases (95% uncertainty interval 18 100-27 500) during 2015-19. By 2019, reported cases were 12% (10-13) higher than predicted by historical trends. 54% (44-66) of excess cases occurred among 20-29-year-old men. In this group, reported cases in 2019 were 30% (25-36) higher than predicted. Excess cases were positively associated with an increasing fraction of cases among incarcerated individuals (p=0·001) and higher unemployment (p=0·04) at the state level. Estimated excess deaths for 2015-19 were not statistically significant from 0 (-600 [-2100 to 1000]). These results were robust to alternative definitions of the pre-recession period and criteria for defining tuberculosis deaths.

INTERPRETATION

Tuberculosis cases in Brazil rose substantially in 2015-19 during the recession, largely affecting young men. This increase seems to be linked to increasing tuberculosis transmission among incarcerated populations. Rising tuberculosis case rates threaten tuberculosis control in Brazil, and highlight the threat posed by prison-based tuberculosis transmission.

FUNDING

US National Institutes of Health.

TRANSLATION

For the Portuguese translation of the abstract see Supplementary Materials section.

The role of prisons in disseminating tuberculosis in Brazil: A genomic epidemiology study

Background

Globally, prisons are high-incidence settings for tuberculosis. Yet the role of prisons as reservoirs of M. tuberculosis, propagating epidemics through spillover to surrounding communities, has been difficult to measure directly.

Methods

To quantify the role of prisons in driving wider community M. tuberculosis transmission, we conducted prospective genomic surveillance in Central West Brazil from 2014 to 2019. We whole genome sequenced 1152 M. tuberculosis isolates collected during active and passive surveillance inside and outside prisons and linked genomes to detailed incarceration histories. We applied multiple phylogenetic and genomic clustering approaches and inferred timed transmission trees.

Findings

M. tuberculosis sequences from incarcerated and non-incarcerated people were closely related in a maximum likelihood phylogeny. The majority (70.8%; 46/65) of genomic clusters including people with no incarceration history also included individuals with a recent history of incarceration. Among cases in individuals with no incarceration history, 50.6% (162/320) were in clusters that included individuals with recent incarceration history, suggesting that transmission chains often span prisons and communities. We identified a minimum of 18 highly probable spillover events, M. tuberculosis transmission from people with a recent incarceration history to people with no prior history of incarceration, occurring in the state’s four largest cities and across sampling years. We additionally found that frequent transfers of people between the state’s prisons creates a highly connected prison network that likely disseminates M. tuberculosis across the state.

Interpretation

We developed a framework for measuring spillover from high-incidence environments to surrounding communities by integrating genomic and spatial information. Our findings indicate that, in this setting, prisons serve not only as disease reservoirs, but also disseminate M. tuberculosis across highly connected prison networks, both amplifying and propagating M. tuberculosis risk in surrounding communities.

Funding

Brazil’s National Council for Scientific and Technological Development and US National Institutes of Health.

Follow-up of a cohort of patients with noncystic fibrosis bronchiectasis for 1 year

OBJECTIVE

The objective of this study was to evaluate the quality of life of patients with noncystic fibrosis bronchiectasis during a 1-year follow-up by using the EuroQol - 5 Dimensions - 3 Levels (EQ-5D-3L) questionnaire.

METHODS

A cohort study was conducted with 100 patients with noncystic fibrosis bronchiectasis and followed up with face-to-face visits or by telephone contact every 3 months for 1 year. All patients were recruited from a single referral center for bronchiectasis. At the time of recruiting and at the end of 1 year, the EQ-5D-3L questionnaire was applied to evaluate the patients' quality of life. Variables, such as exacerbation, emergency care, comorbidities, hemoptysis, colonization, and hospitalization, were assessed.

RESULTS

Of the 100 patients, 99 completed the study and 72% were women. There were no marked limitations in the mobility and self-care domains during the follow-up. At the end of the follow-up, 32 patients were extremely anxious or depressed. The quality of life assessed by using EQ-5D-3L had an initial mean score of 0.545 and of 0.589 after 1 year, which was statistically significant (p=0.011).

CONCLUSION

Patients with noncystic fibrosis bronchiectasis have a poor quality of life, and the EQ-5D-3L questionnaire may be a tool for monitoring patients with bronchiectasis.

Codon usage divergence of important functional genes in Mycobacterium tuberculosis

Sequence characteristics are usually used to explain the adaptive ability to hosts, metabolism, genetic diversity, drug resistance, and infectivity of Mycobacterium tuberculosis. Exploring the codon usage pattern of coding sequences in Mycobacterium tuberculosis is of great significance. In the present study, two hundred random complete genomes of Mycobacterium tuberculosis were downloaded from the National Center for Biotechnology Information database. The important codon usage pattern, such as the codon bias index, the effective number of codons, the relative synonymous codon usage as well as the base component, of twenty one specific functional genes were counted or calculated. The differences of the relative synonymous codon usage values among those functional genes, and the summation of the standard deviations of codon usage parameters were used to evaluate the divergence degree of the concerned genes. The results show that among the concerned genes, 1) all genes are high GC sequences, the codon usage frequency corresponding to each amino acid of these functional genes had a significant bias; 2) the genes of those with high effective number of codons, such as the coding sequences of Myco-bacterial membrane protein large family, usually have higher divergences; and 3) genes with lower divergences, such as the ag85A and the sigH, are usually highly conserved and are often used as drug target genes. The findings of the present work would improve new understandings on the evolution of Mycobacterium tuberculosis and on the measures to prevent and control tuberculosis from the gene engineering.

Pooling Sputum Samples for Efficient Mass Tuberculosis Screening in Prisons

BACKGROUND

Although systematic tuberculosis screening in high-risk groups is recommended by WHO, implementation in prisons has been limited due to resource constraints. Whether Xpert Ultra sputum pooling could be a sensitive and efficient approach to mass screening in prisons is unknown.

METHODS

1,280 sputum samples were collected from inmates in Brazil during mass screening and tested using Xpert G4. We selected samples for mixing in pools of 4, 8, 12, and 16, which were then tested using Ultra. In each pool, a single positive sample of differing Xpert mycobacterial loads was used. Additionally, 10 pools of 16 negative samples each were analyzed as controls. We then simulated tuberculosis screening at prevalences of 0.5-5% and calculated the cost per tuberculosis case detected at different sputum pooling sizes.

RESULTS

The sensitivity and specificity of sputum pooling were high (sensitivity: 94%; 95% CI: 88-98; specificity: 100%, 95% CI: 84-100). Sensitivity was greater in pools in which the positive sample had a high mycobacterial load compared to those that were very low (100% vs 88%). In settings with a higher tuberculosis prevalence, pools of 4 and 8 were more efficient than larger pool sizes. Larger pools decreased the costs by 87% at low prevalences whereas smaller pools fitted greater at higher prevalences (57%).

CONCLUSIONS

Sputum pooling using Ultra was a sensitive strategy for tuberculosis screening. This approach was more efficient than individual testing across a broad range of simulated tuberculosis prevalence settings and could enable active case finding to be scaled while containing costs.

A turn-on probe for detecting antituberculotic drug-induced liver injury in mice via NIR-II fluorescence/optoacoustic imaging

A turn-on optoacoustic and NIR-II fluorescent probe for imaging antituberculotic drug-induced liver injury has been developed. Probe TC-H2O2 responds to hepatic H2O2, thus releasing chromophore TC-NN, which displays prominent NIR-II fluorescence and optoacoustic signals for diagnosing liver injury.