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

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.

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.

Human T-lymphotropic virus 1/2 infection among prisoners of a major penitentiary complex of Goiás State, Central-West Brazil

Introduction

Studies on human T-lymphotropic virus 1/2 (HTLV-1/2) infection are scarce in incarcerated population. Therefore, this study estimated the prevalence of HTLV-1/2 infection among prisoners of the major penitentiary complex of Goiás State, Central-West Brazil, comparing it with available data from other Brazilian regions.

Methods

A cross-sectional study was conducted with 910 prisoners of the major penitentiary complex in the State of Goiás, Central-West Brazil. All participants were interviewed, and their serum samples were tested for anti-HTLV-1/2 using an enzyme-linked immunosorbent assay (ELISA; Murex HTLV-I + II, DiaSorin, Dartford, UK). Seropositive samples were submitted for confirmation by a line immunoassay (INNO-LIA HTLV I/II, Fujirebio, Europe N.V., Belgium).

Results

The majority of participants were males (83.1%), between 25 and 39 years old (56.1%; mean age: 31.98 years), self-reported brown ethnicity (56.2%) and reported 9 years or less of formal education (41.4%). Most reported using non-injectable illicit drugs and various sexual behaviors that present risk for sexually transmitted infections (STIs). The prevalence of anti-HTLV-1/2 was 0.33% (95% CI: 0.07-0.96), HTLV-1 (0.22%) and HTLV-2 (0.11%). The two HTLV-1 seropositive prisoners reported high-risk sexual behaviors, and the HTLV-2 seropositive individual was breastfed during childhood (> 6 months) by her mother and three other women.

Conclusion

These data revealed a relatively low seroprevalence of HTLV-1/2 in prisoners in Central-West Brazil, and evidence of HTLV-1 and HTLV-2 circulation in the major penitentiary complex of Goiás State. Given the prevalence of high-risk sexual behaviors, there is a crucial need to intensify education and health programs in prisons to effectively control and prevent HTLV-1/2 and other STIs.

Community-based active-case finding for tuberculosis: navigating a complex minefield

Community-based active case finding (ACF) for tuberculosis (TB) involves an offer of screening to populations at risk of TB, oftentimes with additional health promotion, community engagement and health service strengthening. Recently updated World Health Organization TB screening guidelines conditionally recommend expanded offer of ACF for communities where the prevalence of undiagnosed pulmonary TB is greater than 0.5% among adults, or with other structural risk factors for TB. Subclinical TB is thought to be a major contributor to TB transmission, and ACF, particularly with chest X-ray screening, could lead to earlier diagnosis. However, the evidence base for the population-level impact of ACF is mixed, with effectiveness likely highly dependent on the screening approach used, the intensity with which ACF is delivered, and the success of community- and health-system participation. With recent changes in TB epidemiology due to the effective scale-up of treatment for HIV in Africa, the impacts of the COVID-19 pandemic, and the importance of subclinical TB, researchers and public health practitioners planning to implement ACF programmes must carefully and repeatedly consider the potential population and individual benefits and harms from these programmes. Here we synthesise evidence and experience from implementing ACF programmes to provide practical guidance, focusing on the selection of populations, screening algorithms, selecting outcomes, and monitoring and evaluation. With careful planning and substantial investment, community-based ACF for TB can be an impactful approach to accelerating progress towards elimination of TB in high-burden countries. However, ACF cannot and should not be a substitute for equitable access to responsive, affordable, accessible primary care services for all.

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.

Signatures of transmission in within-host M. tuberculosis variation

Background

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

Methods

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

Findings

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

Interpretation

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

Funding

NIAID: 5K01AI173385.

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.

Spread of Mycobacterium tuberculosis in Southern Brazilian persons deprived of liberty: a molecular epidemiology study

To evaluate the genetic diversity and clustering rates of M. tuberculosis strains to better understand transmission among persons deprived of liberty (PDL) in Rio Grande do Sul (RS), southern Brazil. This is a cross-sectional study, including strains of M. tuberculosis isolated from PDL, stored at the Central Laboratory of RS, in the period from 2013 to 2018. The molecular characterization was performed using the MIRU-VNTR 15 loci method. A total of 598 M. tuberculosis strains were genotyped, and 37.5% were grouped into 53 clusters. Cluster sizes ranged from 2 to 34 strains. The largest cluster of the study had strains from 34 PDL, and 58.8% of the PDL of this cluster were in P01. Among the clusters formed, in 60.3%, there was at least one strain from P01. The most common strains in RS were LAM (53.2%) and Haarlem (31.1%). The LAM strain was the most likely to form clusters, and Haarlem was associated with anti-TB drug resistance. This was translational research, and the results can collaborate with the TB control programs, leading to improved strategies that allow the reduction of the TB burden in prisons.

Risk for Prison-to-Community Tuberculosis Transmission, Thailand, 2017-2020

To determine contributions of previously incarcerated persons to tuberculosis (TB) transmission in the community, we performed a healthcare facility-based cohort study of TB patients in Thailand during 2017-2020. We used whole-genome sequencing of Mycobacterium tuberculosis isolates from patients to identify genotypic clusters and assess the association between previous incarceration and TB transmission in the community. We identified 4 large genotype clusters (>10 TB patients/cluster); 28% (14/50) of the patients in those clusters were formerly incarcerated. Formerly incarcerated TB patients were more likely than nonincarcerated patients to be included in large clusters. TB patients within the large genotype clusters were geographically dispersed throughout Chiang Rai Province. Community TB transmission in the community was associated with the presence of formerly incarcerated individuals in Thailand. To reduce the risk for prison-to-community transmission, we recommend TB screening at the time of entry and exit from prisons and follow-up screening in the community.

Dynamics of Respiratory Infectious Diseases in Incarcerated and Free-Living Populations: A Simulation Modeling Study

BACKGROUND

Historically, correctional facilities have had large outbreaks of respiratory infectious diseases like COVID-19. Hence, importation and exportation of such diseases from correctional facilities raises substantial concern.

METHODS

We developed a stochastic simulation model of transmission of respiratory infectious diseases within and between correctional facilities and the community. We investigated the infection dynamics, key governing factors, and relative importance of different infection routes (e.g., incarcerations and releases versus correctional staff). We also developed machine-learning meta-models of the simulation model, which allowed us to examine how our findings depended on different disease, correctional facility, and community characteristics.

RESULTS

We find a magnification-reflection dynamic: a small outbreak in the community can cause a larger outbreak in the correction facility, which can then cause a second, larger outbreak in the community. This dynamic is strongest when community size is relatively small as compared with the size of the correctional population, the initial community R-effective is near 1, and initial prevalence of immunity in the correctional population is low. The timing of the correctional magnification and community reflection peaks in infection prevalence are primarily governed by the initial R-effective for each setting. Because the release rates from prisons are low, our model suggests correctional staff may be a more important infection entry route into prisons than incarcerations and releases; in jails, where incarceration and release rates are much higher, our model suggests the opposite.

CONCLUSIONS

We find that across many combinations of respiratory pathogens, correctional settings, and communities, there can be substantial magnification-reflection dynamics, which are governed by several key factors. Our goal was to derive theoretical insights relevant to many contexts; our findings should be interpreted accordingly.

HIGHLIGHTS

We find a magnification-reflection dynamic: a small outbreak in a community can cause a larger outbreak in a correctional facility, which can then cause a second, larger outbreak in the community.For public health decision makers considering contexts most susceptible to this dynamic, we find that the dynamic is strongest when the community size is relatively small, initial community R-effective is near 1, and the initial prevalence of immunity in the correctional population is low; the timing of the correctional magnification and community reflection peaks in infection prevalence are primarily governed by the initial R-effective for each setting.We find that correctional staff may be a more important infection entry route into prisons than incarcerations and releases; however, for jails, the relative importance of the entry routes may be reversed.For modelers, we combine simulation modeling, machine-learning meta-modeling, and interpretable machine learning to examine how our findings depend on different disease, correctional facility, and community characteristics; we find they are generally robust.

Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis

Detecting factors associated with transmission is important to understand disease epidemics, and to design effective public health measures. Clustering and terminal branch lengths (TBL) analyses are commonly applied to genomic data sets of Mycobacterium tuberculosis (MTB) to identify sub-populations with increased transmission. Here, I used a simulation-based approach to investigate what epidemiological processes influence the results of clustering and TBL analyses, and whether differences in transmission can be detected with these methods. I simulated MTB epidemics with different dynamics (latency, infectious period, transmission rate, basic reproductive number R0, sampling proportion, sampling period, and molecular clock), and found that all considered factors, except for the length of the infectious period, affect the results of clustering and TBL distributions. I show that standard interpretations of this type of analyses ignore two main caveats: (1) clustering results and TBL depend on many factors that have nothing to do with transmission, (2) clustering results and TBL do not tell anything about whether the epidemic is stable, growing, or shrinking, unless all the additional parameters that influence these metrics are known, or assumed identical between sub-populations. An important consequence is that the optimal SNP threshold for clustering depends on the epidemiological conditions, and that sub-populations with different epidemiological characteristics should not be analyzed with the same threshold. Finally, these results suggest that different clustering rates and TBL distributions, that are found consistently between different MTB lineages, are probably due to intrinsic bacterial factors, and do not indicate necessarily differences in transmission or evolutionary success.