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Waddell CJ, Saldana CS, Schoonveld MM, Meehan AA, Lin CK, Butler JC, Mosites E. Infectious Diseases Among People Experiencing Homelessness: A Systematic Review of the Literature in the United States and Canada, 2003-2022. Public Health Rep 2024; 139:532-548. [PMID: 38379269 PMCID: PMC11344984 DOI: 10.1177/00333549241228525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Homelessness increases the risk of acquiring an infectious disease. We conducted a systematic review of the literature to identify quantitative data related to infectious diseases and homelessness. We searched Google Scholar, PubMed, and SCOPUS for quantitative literature published from January 2003 through December 2022 in English from the United States and Canada. We excluded literature on vaccine-preventable diseases and HIV because these diseases were recently reviewed. Of the 250 articles that met inclusion criteria, more than half were on hepatitis C virus or Mycobacterium tuberculosis. Other articles were on COVID-19, respiratory syncytial virus, Staphylococcus aureus, group A Streptococcus, mpox (formerly monkeypox), 5 sexually transmitted infections, and gastrointestinal or vectorborne pathogens. Most studies showed higher prevalence, incidence, or measures of risk for infectious diseases among people experiencing homelessness as compared with people who are housed or the general population. Although having increased published data that quantify the infectious disease risks of homelessness is encouraging, many pathogens that are known to affect people globally who are not housed have not been evaluated in the United States or Canada. Future studies should focus on additional pathogens and factors leading to a disproportionately high incidence and prevalence of infectious diseases among people experiencing homelessness.
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Affiliation(s)
- Caroline J. Waddell
- Office of Readiness and Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Carlos S. Saldana
- Division of Infectious Disease, School of Medicine, Emory University, Atlanta, GA, USA
| | - Megan M. Schoonveld
- Office of Readiness and Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, US Department of Energy, Oak Ridge, TN, USA
| | - Ashley A. Meehan
- Office of Readiness and Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christina K. Lin
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Jay C. Butler
- Office of Readiness and Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Division of Infectious Disease, School of Medicine, Emory University, Atlanta, GA, USA
| | - Emily Mosites
- Office of Readiness and Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Sadovska D, Ozere I, Pole I, Ķimsis J, Vaivode A, Vīksna A, Norvaiša I, Bogdanova I, Ulanova V, Čapligina V, Bandere D, Ranka R. Unraveling tuberculosis patient cluster transmission chains: integrating WGS-based network with clinical and epidemiological insights. Front Public Health 2024; 12:1378426. [PMID: 38832230 PMCID: PMC11144917 DOI: 10.3389/fpubh.2024.1378426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
Background Tuberculosis remains a global health threat, and the World Health Organization reports a limited reduction in disease incidence rates, including both new and relapse cases. Therefore, studies targeting tuberculosis transmission chains and recurrent episodes are crucial for developing the most effective control measures. Herein, multiple tuberculosis clusters were retrospectively investigated by integrating patients' epidemiological and clinical information with median-joining networks recreated based on whole genome sequencing (WGS) data of Mycobacterium tuberculosis isolates. Methods Epidemiologically linked tuberculosis patient clusters were identified during the source case investigation for pediatric tuberculosis patients. Only M. tuberculosis isolate DNA samples with previously determined spoligotypes identical within clusters were subjected to WGS and further median-joining network recreation. Relevant clinical and epidemiological data were obtained from patient medical records. Results We investigated 18 clusters comprising 100 active tuberculosis patients 29 of whom were children at the time of diagnosis; nine patients experienced recurrent episodes. M. tuberculosis isolates of studied clusters belonged to Lineages 2 (sub-lineage 2.2.1) and 4 (sub-lineages 4.3.3, 4.1.2.1, 4.8, and 4.2.1), while sub-lineage 4.3.3 (LAM) was the most abundant. Isolates of six clusters were drug-resistant. Within clusters, the maximum genetic distance between closely related isolates was only 5-11 single nucleotide variants (SNVs). Recreated median-joining networks, integrated with patients' diagnoses, specimen collection dates, sputum smear microscopy, and epidemiological investigation results indicated transmission directions within clusters and long periods of latent infection. It also facilitated the identification of potential infection sources for pediatric patients and recurrent active tuberculosis episodes refuting the reactivation possibility despite the small genetic distance of ≤5 SNVs between isolates. However, unidentified active tuberculosis cases within the cluster, the variable mycobacterial mutation rate in dormant and active states, and low M. tuberculosis genetic variability inferred precise transmission chain delineation. In some cases, heterozygous SNVs with an allelic frequency of 10-73% proved valuable in identifying direct transmission events. Conclusion The complex approach of integrating tuberculosis cluster WGS-data-based median-joining networks with relevant epidemiological and clinical data proved valuable in delineating epidemiologically linked patient transmission chains and deciphering causes of recurrent tuberculosis episodes within clusters.
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Affiliation(s)
- Darja Sadovska
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Ozere
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
- Department of Infectology, Riga Stradiņš University, Riga, Latvia
| | - Ilva Pole
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
| | - Jānis Ķimsis
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Annija Vaivode
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Anda Vīksna
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
- Department of Infectology, Riga Stradiņš University, Riga, Latvia
| | - Inga Norvaiša
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
| | - Ineta Bogdanova
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
| | - Viktorija Ulanova
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Valentīna Čapligina
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Dace Bandere
- Department of Pharmaceutical Chemistry, Riga Stradiņš University, Riga, Latvia
| | - Renāte Ranka
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
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Busatto C, Possuelo LG, Bierhals D, de Oliveira CL, de Souza MQ, Fanfa D, Barreto É, Schwarzbold P, Von Groll A, Portugal I, Perdigão J, Croda J, Andrews JR, da Silva PA, Ramis IB. Spread of Mycobacterium tuberculosis in Southern Brazilian persons deprived of liberty: a molecular epidemiology study. Eur J Clin Microbiol Infect Dis 2023; 42:297-304. [PMID: 36701032 DOI: 10.1007/s10096-023-04546-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
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.
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Affiliation(s)
- Caroline Busatto
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Lia Gonçalves Possuelo
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Dienefer Bierhals
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Carolina Larrosa de Oliveira
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Mariana Quaresma de Souza
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Dandara Fanfa
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Érika Barreto
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Pauline Schwarzbold
- 8ª Delegacia Penitenciária Regional, Superintendência Dos Serviços Penitenciários, Santa Cruz Do Sul, RS, Brazil
| | - Andrea Von Groll
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Isabel Portugal
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - João Perdigão
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Julio Croda
- Faculdade de Medicina, Universidade Federal Do Mato Grosso Do Sul, Campo Grande, Mato Grosso Do Sul, Brazil
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, Palo Alto, CA, US
| | - Pedro Almeida da Silva
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil.
- Rua General Osório S/N, Centro, Rio Grande Do Sul, Rio Grande, 96200190, Brazil.
| | - Ivy Bastos Ramis
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
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Miyahara R, Piboonsiri P, Chiyasirinroje B, Imsanguan W, Nedsuwan S, Yanai H, Tokunaga K, Palittapongarnpim P, Murray M, Mahasirimongkol S. Risk for Prison-to-Community Tuberculosis Transmission, Thailand, 2017-2020. Emerg Infect Dis 2023; 29:477-483. [PMID: 36823074 PMCID: PMC9973682 DOI: 10.3201/eid2903.221023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
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.
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Anselmo LMP, Gallo JF, Pinhata JMW, Peronni KC, da Silva WA, Ruy PDC, Conceição EC, Dippenaar A, Warren RM, Monroe AA, Oliveira RS, Bollela VR. New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing. Rev Soc Bras Med Trop 2023; 56:e0181. [PMID: 36820651 PMCID: PMC9957134 DOI: 10.1590/0037-8682-0181-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 10/10/2022] [Indexed: 02/22/2023] Open
Abstract
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.
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Affiliation(s)
- Lívia Maria Pala Anselmo
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, SP, Brasil.
| | - Juliana Failde Gallo
- Instituto Adolfo Lutz, Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, São Paulo, SP, Brasil.
| | | | | | - Wilson Araújo da Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, São Paulo, Brasil.
| | - Patricia de Cássia Ruy
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Centro de Medicina Genômica do Hospital das Clínicas, Ribeirão Preto, SP, Brasil.
| | - Emilyn Costa Conceição
- Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, 2000, Belgium.
| | - Robin Mark Warren
- Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Aline Aparecida Monroe
- Universidade de São Paulo, Escola de Enfermagem de Ribeirão Preto (EERP-USP), Ribeirão Preto, SP, Brasil.
| | - Rosangela Siqueira Oliveira
- Instituto Adolfo Lutz, Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, São Paulo, SP, Brasil.
| | - Valdes Roberto Bollela
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Clínica Médica, Ribeirão Preto, SP, Brasil.
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6
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Farjo M, Brooke CB. Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2. mSphere 2023; 8:e0054422. [PMID: 36695609 PMCID: PMC9942562 DOI: 10.1128/msphere.00544-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Tracking the spread of infection amongst individuals within and between communities has been a major challenge during viral outbreaks. With the unprecedented scale of viral sequence data collection during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the possibility of using phylogenetics to reconstruct past transmission events has been explored as a more rigorous alternative to traditional contact tracing; however, the reliability of sequence-based inference of transmission networks has yet to be directly evaluated. E. E. Bendall, G. Paz-Bailey, G. A. Santiago, C. A. Porucznik, et al. (mSphere 7:e00400-22, 2022, https://doi.org/10.1128/mSphere.00400-22) evaluate the potential of this technique by applying best practices sequence comparison methods to three geographically distinct cohorts that include known transmission pairs and demonstrate that linked pairs are often indistinguishable from unrelated samples. This study clearly establishes how low viral diversity limits the utility of genomic methods of epidemiological inference for SARS-CoV-2.
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Affiliation(s)
- Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Stewart RJ, Raz KM, Burns SP, Kammerer JS, Haddad MB, Silk BJ, Wortham JM. Tuberculosis Outbreaks in State Prisons, United States, 2011-2019. Am J Public Health 2022; 112:1170-1179. [PMID: 35830666 PMCID: PMC9342802 DOI: 10.2105/ajph.2022.306864] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2022] [Indexed: 11/04/2022]
Abstract
Objectives. To understand the frequency, magnitude, geography, and characteristics of tuberculosis outbreaks in US state prisons. Methods. Using data from the National Tuberculosis Surveillance System, we identified all cases of tuberculosis during 2011 to 2019 that were reported as occurring among individuals incarcerated in a state prison at the time of diagnosis. We used whole-genome sequencing to define 3 or more cases within 2 single nucleotide polymorphisms within 3 years as clustered; we classified clusters with 6 or more cases during a 3-year period as tuberculosis outbreaks. Results. During 2011 to 2019, 566 tuberculosis cases occurred in 41 state prison systems (a median of 3 cases per state). A total of 19 tuberculosis genotype clusters comprising 134 cases were identified in 6 state prison systems; these clusters included a subset of 5 outbreaks in 2 states. Two Alabama outbreaks during 2011 to 2017 totaled 20 cases; 3 Texas outbreaks during 2014 to 2019 totaled 51 cases. Conclusions. Only Alabama and Texas reported outbreaks during the 9-year period; only Texas state prisons had ongoing transmission in 2019. Effective interventions are needed to stop tuberculosis outbreaks in Texas state prisons. (Am J Public Health. 2022;112(8):1170-1179. https://doi.org/10.2105/AJPH.2022.306864).
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Affiliation(s)
- Rebekah J Stewart
- The authors are with the Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Kala M Raz
- The authors are with the Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Scott P Burns
- The authors are with the Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - J Steve Kammerer
- The authors are with the Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Maryam B Haddad
- The authors are with the Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Benjamin J Silk
- The authors are with the Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Jonathan M Wortham
- The authors are with the Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
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8
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Walter KS, Dos Santos PCP, Gonçalves TO, da Silva BO, da Silva Santos A, de Cássia Leite A, da Silva AM, Figueira Moreira FM, de Oliveira RD, Lemos EF, Cunha E, Liu YE, Ko AI, Colijn C, Cohen T, Mathema B, Croda J, Andrews JR. The role of prisons in disseminating tuberculosis in Brazil: A genomic epidemiology study. LANCET REGIONAL HEALTH. AMERICAS 2022; 9. [PMID: 35647574 PMCID: PMC9140320 DOI: 10.1016/j.lana.2022.100186] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
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.
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Affiliation(s)
- Katharine S Walter
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States
| | | | | | - Bruna Oliveira da Silva
- Health Sciences Research Laboratory, Federal University of Grande Dourados, Dourados, Brazil
| | - Andrea da Silva Santos
- Health Sciences Research Laboratory, Federal University of Grande Dourados, Dourados, Brazil
| | | | - Alessandra Moura da Silva
- School of Medicine, Federal University of Mato Grosso do Sul, School of Medicine, Campo Grande, Brazil
| | | | | | - Everton Ferreira Lemos
- School of Medicine, Federal University of Mato Grosso do Sul, School of Medicine, Campo Grande, Brazil
| | - Eunice Cunha
- Laboratory of Bacteriology, Central Laboratory of Mato Grosso do Sul, Campo Grande, Brazil
| | - Yiran E Liu
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States.,Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, United States
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States.,Instituto Gonçalo¸ Moniz, Fundação Oswaldo Cruz, Salvador, BA, Brazil
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, United States
| | - Julio Croda
- School of Medicine, Federal University of Mato Grosso do Sul, School of Medicine, Campo Grande, Brazil.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States.,Mato Grosso do Sul Office, Oswaldo Cruz Foundation, Campo Grande, Brazil
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States
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Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review. Pathogens 2022; 11:pathogens11020252. [PMID: 35215195 PMCID: PMC8875843 DOI: 10.3390/pathogens11020252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.
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10
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Gil RM, Freeman TL, Mathew T, Kullar R, Fekete T, Ovalle A, Nguyen D, Kottkamp A, Poon J, Marcelin JR, Swartz TH. Lesbian, Gay, Bisexual, Transgender, and Queer (LGBTQ+) Communities and the Coronavirus Disease 2019 Pandemic: A Call to Break the Cycle of Structural Barriers. J Infect Dis 2021; 224:1810-1820. [PMID: 34323998 PMCID: PMC9103180 DOI: 10.1093/infdis/jiab392] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has disproportionately impacted lesbian, gay, bisexual, transgender, and queer (LGBTQ+) communities. Many disparities mirror those of the human immunodeficiency virus (HIV)/AIDS epidemic. These health inequities have repeated throughout history due to the structural oppression of LGBTQ+ people. We aim to demonstrate that the familiar patterns of LGBTQ+ health disparities reflect a perpetuating, deeply rooted cycle of injustice imposed on LGBTQ+ people. Here, we contextualize COVID-19 inequities through the history of the HIV/AIDS crisis, describe manifestations of LGBTQ+ structural oppression exacerbated by the pandemic, and provide recommendations for medical professionals and institutions seeking to reduce health inequities.
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Affiliation(s)
- Raul Macias Gil
- Department of Infectious Diseases, Kaiser Permanente Northern
California, Napa/Solano, California, USA
| | - Tracey L Freeman
- Medical Scientist Training Program, University of Pittsburgh-Carnegie Mellon
University, Pittsburgh,
Pennsylvania, USA
| | - Trini Mathew
- Division of Infectious Diseases and International Medicine, Beaumont
Hospital, Royal Oak, Michigan, USA
| | - Ravina Kullar
- Expert Stewardship, Inc, Newport Beach,
California, USA
| | - Thomas Fekete
- Department of Medicine, Temple University Lewis Katz School of
Medicine, Philadelphia, Pennsylvania, USA
| | - Anais Ovalle
- Division of Infectious Diseases, Dartmouth Hitchcock Medical
Center, Dartmouth, New Hampshire, USA
| | - Don Nguyen
- Medical Scientist Training Program, University of Pittsburgh-Carnegie Mellon
University, Pittsburgh,
Pennsylvania, USA
| | - Angélica Kottkamp
- Division of Infectious Diseases, New York University Grossman School of
Medicine, New York, New York, USA
| | - Jin Poon
- Department of Family Medicine, Kaiser Permanente Northern
California, Vallejo, California, USA
| | - Jasmine R Marcelin
- Division of Infectious Diseases, University of Nebraska Medical
Center, Omaha, Nebraska, USA
| | - Talia H Swartz
- Division of Infectious Diseases, Department of Medicine, Icahn School of
Medicine at Mount Sinai, New York, New York, USA
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11
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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. THE LANCET. MICROBE 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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12
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Didelot X, Kendall M, Xu Y, White PJ, McCarthy N. Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo. Curr Protoc 2021; 1:e60. [PMID: 33617114 PMCID: PMC7995038 DOI: 10.1002/cpz1.60] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not directly informative about transmission events between individuals. TransPhylo is a software tool implemented as an R package designed to bridge the gap between pathogen phylogenies and transmission trees. TransPhylo is based on a combined model of transmission between hosts and pathogen evolution within each host. It can simulate both phylogenies and transmission trees jointly under this combined model. TransPhylo can also reconstruct a transmission tree based on a dated phylogeny, by exploring the space of transmission trees compatible with the phylogeny. A transmission tree can be represented as a coloring of a phylogeny where each color represents a different host of the pathogen, and TransPhylo provides convenient ways to plot these colorings and explore the results. This article presents the basic protocols that can be used to make the most of TransPhylo. © 2021 The Authors. Basic Protocol 1: First steps with TransPhylo Basic Protocol 2: Simulation of outbreak data Basic Protocol 3: Inference of transmission Basic Protocol 4: Exploring the results of inference.
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Affiliation(s)
- Xavier Didelot
- School of Life Sciences and Department of StatisticsUniversity of WarwickUnited Kingdom
| | - Michelle Kendall
- School of Life Sciences and Department of StatisticsUniversity of WarwickUnited Kingdom
| | - Yuanwei Xu
- Center for Computational Biology, Institute of Cancer and Genomic SciencesUniversity of BirminghamUnited Kingdom
| | - Peter J. White
- Department of Infectious Disease Epidemiology, School of Public HealthImperial College LondonUnited Kingdom
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public HealthImperial College LondonUnited Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling and Health Economics, School of Public HealthImperial College LondonUnited Kingdom
- Modelling and Economics Unit, National Infection ServicePublic Health EnglandLondonUnited Kingdom
| | - Noel McCarthy
- Warwick Medical SchoolUniversity of WarwickUnited Kingdom
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13
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Miyahara R, Smittipat N, Juthayothin T, Yanai H, Disratthakit A, Imsanguan W, Intralawan D, Nedsuwan S, Chaiyasirinroje B, Bupachat S, Tokunaga K, Mahasirimongkol S, Palittapongarnpim P. Risk factors associated with large clusters of tuberculosis patients determined by whole-genome sequencing in a high-tuberculosis-burden country. Tuberculosis (Edinb) 2020; 125:101991. [DOI: 10.1016/j.tube.2020.101991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 07/26/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022]
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14
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van der Werf MJ, Ködmön C. Whole-Genome Sequencing as Tool for Investigating International Tuberculosis Outbreaks: A Systematic Review. Front Public Health 2019; 7:87. [PMID: 31058125 PMCID: PMC6478655 DOI: 10.3389/fpubh.2019.00087] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022] Open
Abstract
Background: Whole-genome sequencing (WGS) can support the investigation of tuberculosis (TB) outbreaks. The technique has been applied to estimate the timing and directionality of transmission and to exclude cases from an investigation. This review assesses how WGS was applied in international outbreak investigations and discusses the advantages and challenges of the application of WGS. Methods: Databases were searched for reports on international TB outbreak investigations. Information was extracted on: Why was WGS applied?; How was WGS applied?; Organizational issues; WGS methodology; What was learned/what were the implications of the WGS investigation?; and challenges and lessons learned. Results: Three studies reporting on international outbreak investigations were identified. Retrospective WGS sequencing was performed in all studies and prospective typing in two to study TB transmission. In one study, WGS data were produced centrally (i.e., in one laboratory) and analysis was done centrally. In two studies, WGS data production was done in a decentralized manner, and analysis was centralized in one laboratory. Three groups of professionals were involved in the international outbreak investigation: public health authorities, laboratory experts, and clinicians. The reported WGS methodology applied differed between the studies in some aspects, e.g., sequencing platform; quality measures, percentage of the reference genome covered, and the mean genomic coverage; analysis, use of a reference genome or de novo assembly; and software used for alignment and analysis. In all three studies, in-house scripts were used for variance calling, and the single nucleotide polymorphism (SNP) approach was used for analysis. All outbreak investigation reports stated that WGS refuted suspected transmission events and provided supporting evidence for epidemiological data. Several challenges were reported of which most were not related to WGS. The only challenge related to WGS was the timeframe of getting WGS data if WGS is not routinely performed. Conclusions: WGS was considered a useful addition in international TB outbreak investigations. Further standardization of the WGS methodology and good structures for international collaboration and coordination are needed to take full advantage of this new technology. Whether the use of WGS results in earlier detection of cases and thus limits transmission still needs to be determined.
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Affiliation(s)
| | - Csaba Ködmön
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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