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

Ks, Walter; Pcp, dos Santos; To, Goncalves; Bo, da Silva; AdS, Santos; AdC, Leite; Jp, da Silva; Fmf, Moreira; Oliveira, de; Ef, Lemos; Cunha, Eunice Atsuko Totumi; Liu, Ye; Ko, Albert I.; Colijn, Caroline; Cohen, Ted; Mathema, Barun; Croda, Júlio; Andrews, Jason R

doi:10.1101/2021.06.22.21259360

Cited by 3 publications

(1 citation statement)

References 53 publications

(71 reference statements)

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“…This disparity was a result of increased communicable and non-communicable disease mortality post-release and corresponds to studies reporting high incidence of infectious diseases [49,50] and chronic medical conditions [51] among formerly incarcerated individuals. Recent work in Mato Grosso do Sul found bacterial genomic evidence of new tuberculosis diagnoses among formerly incarcerated individuals that could be traced to transmission within carceral facilities [52], indicating that elevated communicable disease mortality post-release may at least be partially attributable to incarceration. However, more data are needed to determine the respective contribution of incarceration versus pre-existing vulnerabilities to disease mortality post-release.…”

Section: Mortality Post-releasementioning

confidence: 99%

All-cause and cause-specific mortality during and following incarceration in Brazil: a retrospective cohort study

Liu

Lemos

Gonçalves

et al. 2021

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Background Mortality during and after incarceration is poorly understood in low- and middle-income countries. The need to address this knowledge gap is especially urgent in South America, which has the fastest growing prison population in the world. In Brazil, data on mortality during and after incarceration are lacking. Methods and Findings We linked incarceration and mortality databases for the Brazilian state of Mato Grosso do Sul to obtain a cohort of 114,751 individuals with recent incarceration. Between January 1, 2009 and December 31, 2018, we identified 3127 deaths of individuals with recent incarceration (705 in detention; 2422 following release). We analyzed age- standardized, all-cause and cause-specific mortality rates among individuals detained in different facility types and following release, compared to non-incarcerated residents. Deaths in custody were 2.2 times the number reported by the national prison administration (n = 317). Incarcerated men and boys experienced elevated mortality, compared with the non-incarcerated population, due to increased risk of death from violence, suicide, and communicable diseases, with the highest standardized incidence rate ratio (IRR) in semi-open prisons (2.4; 95% CI, 2.0-2.8), police stations (3.1; 95% CI, 2.5-3.9), and youth detention (8.1; 95% CI, 5.9-10.8). Incarcerated women had increased mortality from suicide (IRR = 6.0, 95% CI 1.2-17.7) and communicable diseases (IRR = 2.5, 95% CI 1.1-5.0). We additionally modeled mortality rates over time during and after incarceration from all causes, violence, or suicide. Following release from prison, mortality was markedly elevated for men (IRR=3.0; 95% CI, 2.8- 3.1) and women (IRR=2.4; 95% CI, 2.1-2.9). The risk of violent death and suicide was highest immediately post-release and declined over time; however, all-cause mortality remained elevated eight years post-release. The limitations of this study include inability to establish causality, uncertain reliability of data during incarceration, and underestimation of mortality rates due to imperfect database linkage. Conclusions Incarcerated individuals in Brazil experienced increased mortality from violence, suicide, and communicable diseases. Mortality was heightened following release for all leading causes of death, with particularly high risk of early violent death and elevated all-cause mortality up to eight years post-release. These disparities may have been under-recognized in Brazil due to underreporting and insufficient data.

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Section: Mortality Post-releasementioning

confidence: 99%

All-cause and cause-specific mortality during and following incarceration in Brazil: a retrospective cohort study

Liu

Lemos

Gonçalves

et al. 2021

Preprint

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Use of rapid molecular tuberculosis diagnostics across Brazil’s incarcerated population

Fajer

Costa

Pelissari

et al. 2021

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BackgroundIncarcerated individuals in Brazil are at high-risk of tuberculosis (TB), but their access to World Health Organization recommended diagnostics is poorly understood.MethodsWe conducted a retrospective cross-sectional study of newly diagnosed TB cases in Brazil’s notifiable disease registry, which includes information on diagnostic tests performed, from January 2015 through December 2018. We quantified reported use of TB diagnostics across incarcerated and non-incarcerated populations and tested for municipality-level factors associated with diagnostic usage among the incarcerated population with generalized linear regression.ResultsBetween 2015 and 2018, 258,014 individuals were newly diagnosed with TB, including 27,400 (10.6%) incarcerated individuals. Among these, 27.5% had an Xpert MTB/RIF test reported; 71.5% had sputum smear; 34.1% had culture; 70.9% had chest radiography. Xpert MTB/RIF use was greater among incarcerated than non-incarcerated individuals (36.2% vs 26.5%, p<0.001). However, we found spatial heterogeneity in state-level use of both Xpert MTB/RIF (range: 4.7-72.4% cases diagnosed) and chest radiography (range: 11.7-88.4%) in prisons. We identified seven municipalities with large incarcerated populations (>5000) with rates of Xpert MTB/RIF usage below the national average in incarcerated individuals.ConclusionPrioritizing expansion of rapid molecular diagnostics in prisons, particularly in regions with limited current usage of molecular diagnostics, will be an essential component of TB control.

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

Menardo

2022

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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 difference 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, and molecular clock), and found that all these factors, except the length of the infectious period and R0, 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. 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.

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

Cited by 3 publications

References 53 publications

All-cause and cause-specific mortality during and following incarceration in Brazil: a retrospective cohort study

All-cause and cause-specific mortality during and following incarceration in Brazil: a retrospective cohort study

Use of rapid molecular tuberculosis diagnostics across Brazil’s incarcerated population

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

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