Walter Katharine S, Dos Santos Paulo César Pereira, Gonçalves Thais Oliveira, da Silva Bruna Oliveira, da Silva Santos Andrea, de Cássia Leite Alessandra, da Silva Alessandra Moura, Figueira Moreira Flora Martinez, de Oliveira Roberto Dias, Lemos Everton Ferreira, Cunha Eunice, Liu Yiran E, Ko Albert I, Colijn Caroline, Cohen Ted, Mathema Barun, Croda Julio, Andrews Jason R
Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States.
Health Sciences Research Laboratory, Federal University of Grande Dourados, Dourados, Brazil.
Lancet Reg Health Am. 2022 May;9. doi: 10.1016/j.lana.2022.100186. Epub 2022 Feb 1.
Globally, prisons are high-incidence settings for tuberculosis. Yet the role of prisons as reservoirs of , propagating epidemics through spillover to surrounding communities, has been difficult to measure directly.
To quantify the role of prisons in driving wider community transmission, we conducted prospective genomic surveillance in Central West Brazil from 2014 to 2019. We whole genome sequenced 1152 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.
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, 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 across the state.
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 across highly connected prison networks, both amplifying and propagating risk in surrounding communities.
Brazil's National Council for Scientific and Technological Development and US National Institutes of Health.
在全球范围内，监狱是结核病的高发病场所。然而，监狱作为传染源，通过传播到周边社区引发疫情，其作用一直难以直接衡量。
为了量化监狱在推动更广泛社区传播中的作用，我们于2014年至2019年在巴西中西部进行了前瞻性基因组监测。我们对在监狱内外主动和被动监测期间收集的1152株分离株进行了全基因组测序，并将基因组与详细的监禁历史相关联。我们应用了多种系统发育和基因组聚类方法，并推断了定时传播树。
在最大似然系统发育中，被监禁者和非被监禁者的序列密切相关。大多数（70.8%；46/65）基因组聚类包括无监禁史的人，也包括近期有监禁史的人。在无监禁史的个体病例中，50.6%（162/320）处于包括近期有监禁史个体的聚类中，这表明传播链通常跨越监狱和社区。我们确定了至少18起极有可能的溢出事件，即从近期有监禁史的人传播到无监禁史的人，这些事件发生在该州四个最大城市以及不同采样年份。我们还发现，该州监狱之间人员的频繁转移形成了一个高度连通的监狱网络，这可能会在全州传播（疾病）。
我们通过整合基因组和空间信息，开发了一个用于衡量从高发病环境向周边社区溢出的框架。我们的研究结果表明，在这种情况下，监狱不仅是疾病储存库，还通过高度连通的监狱网络进行传播，放大并传播周边社区的（疾病）风险。
巴西国家科学技术发展委员会和美国国立卫生研究院。
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