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Coleman M, Martinez L, Theron G, Wood R, Marais B. Mycobacterium tuberculosis Transmission in High-Incidence Settings-New Paradigms and Insights. Pathogens 2022; 11:1228. [PMID: 36364978 PMCID: PMC9695830 DOI: 10.3390/pathogens11111228] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 12/01/2023] Open
Abstract
Tuberculosis has affected humankind for thousands of years, but a deeper understanding of its cause and transmission only arose after Robert Koch discovered Mycobacterium tuberculosis in 1882. Valuable insight has been gained since, but the accumulation of knowledge has been frustratingly slow and incomplete for a pathogen that remains the number one infectious disease killer on the planet. Contrast that to the rapid progress that has been made in our understanding SARS-CoV-2 (the cause of COVID-19) aerobiology and transmission. In this Review, we discuss important historical and contemporary insights into M. tuberculosis transmission. Historical insights describing the principles of aerosol transmission, as well as relevant pathogen, host and environment factors are described. Furthermore, novel insights into asymptomatic and subclinical tuberculosis, and the potential role this may play in population-level transmission is discussed. Progress towards understanding the full spectrum of M. tuberculosis transmission in high-burden settings has been hampered by sub-optimal diagnostic tools, limited basic science exploration and inadequate study designs. We propose that, as a tuberculosis field, we must learn from and capitalize on the novel insights and methods that have been developed to investigate SARS-CoV-2 transmission to limit ongoing tuberculosis transmission, which sustains the global pandemic.
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Affiliation(s)
- Mikaela Coleman
- WHO Collaborating Centre for Tuberculosis and the Sydney Institute for Infectious Diseases, The University of Sydney, Sydney 2006, Australia
- Tuberculosis Research Program, Centenary Institute, The University of Sydney, Sydney 2050, Australia
| | - Leonardo Martinez
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Grant Theron
- DSI-NRF 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 7602, South Africa
| | - Robin Wood
- Desmond Tutu Health Foundation and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7700, South Africa
| | - Ben Marais
- WHO Collaborating Centre for Tuberculosis and the Sydney Institute for Infectious Diseases, The University of Sydney, Sydney 2006, Australia
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2
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Country-wide genotyping of Mycobacterium tuberculosis complex in Singapore, 2011–2017. Tuberculosis (Edinb) 2022; 134:102204. [DOI: 10.1016/j.tube.2022.102204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022]
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3
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Acosta F, Martínez-Lirola M, Sola-Campoy PJ, Sicilia J, Guerra-Galán T, Maus SR, Muñoz P, Pérez-Lago L, García de Viedma D. Insights into the Complexity of a Dormant Mycobacterium tuberculosis Cluster Once Transmission Is Resumed. Microbiol Spectr 2022; 10:e0138121. [PMID: 35044196 PMCID: PMC8768656 DOI: 10.1128/spectrum.01381-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/13/2021] [Indexed: 12/03/2022] Open
Abstract
Genotyping tools help identify the complexity in Mycobacterium tuberculosis transmission clusters. We carried out a thorough analysis of the epidemiological and bacteriological complexity of a cluster in Almería, Spain. The cluster, initially associated with Moroccan migrants and with no secondary cases identified in 4 years, then reappeared in Spanish-born individuals. In one case, two Mycobacterium tuberculosis clonal variants were identified. We reanalyzed the cluster, supported by the characterization of multiple cultured isolates and respiratory specimens, whole-genome sequencing, and epidemiological case interviews. Our findings showed that the cluster, which was initially thought to have restarted activity with just a single case harboring a small degree of within-host diversity, was in fact currently growing due to coincidental reactivation of past exposures, with clonal diversity transmitted throughout the cluster. In one case, within-host diversity was amplified, probably due to prolonged diagnostic delay. IMPORTANCE The precise study of the dynamics of tuberculosis transmission in socio-epidemiologically complex scenarios may require more thorough analysis than the standard molecular epidemiology strategies. Our study illustrates the epidemiological and bacteriological complexity present in a transmission cluster in a challenging epidemiological setting with a high proportion of migrant cases. The combination of whole-genome sequencing, refined and refocused epidemiological interviews, and in-depth analysis of the bacterial composition of sputa and cultured isolates was crucial in order to correctly reinterpret the true nature of this cluster. Our global approach allowed us to reinterpret correctly the unnoticed epidemiological and bacteriological complexity involved in the Mycobacterium tuberculosis transmission event under study, which had been overlooked by the usual molecular epidemiology approaches.
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Affiliation(s)
- Fermin Acosta
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | - Pedro J. Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Jon Sicilia
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Teresa Guerra-Galán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Sandra R. Maus
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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4
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Suppli CH, Norman A, Folkvardsen DB, Gissel TN, Weinreich UM, Koch A, Wejse C, Lillebaek T. First outbreak of multi-drug resistant tuberculosis (MDR-TB) in Denmark involving six Danish-born cases. Int J Infect Dis 2022; 117:258-263. [PMID: 35158061 DOI: 10.1016/j.ijid.2022.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Denmark is a tuberculosis (TB) and multi-drug resistant (MDR) TB low-incidence country at 5 and 0.05 cases per 100.000 population, respectively. Until 2018, transmission of MDR-TB was nonexistent except for few pairwise related family-cases. In this study we describe the first MDR-TB outbreak in Denmark. METHODS Based on genotyping of all Mycobacterium tuberculosis (Mtb) culture-positive cases in Denmark spanning three decades, six molecular- and epidemiologically linked Danish-born cases were identified as the first cluster of MDR-TB in Denmark. The primary case was diagnosed posthumously in 2010 followed by five epidemiologically linked cases from 2018 through 2019. RESULTS AND CONCLUSION Through a combination of routine Mtb genotyping and clinical epidemiological surveillance data, we identified the first Danish MDR-TB outbreak spanning 10 years and were able to disclose the specific transmission pathways in detail guiding the outbreak investigations. The occurrence of an MDR-TB outbreak in a resource rich TB low incidence setting like Denmark, highlights the importance of a collaborative control system combining classical contact tracing; timely identification of drug resistant TB through rapid diagnostics; and a close collaboration between clinicians, classical- and molecular epidemiologists for the benefit of TB control.
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Affiliation(s)
- Camilla Hiul Suppli
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Tina Nørregaard Gissel
- Department of Internal Medicine, Region Hospital Viborg, Heibergs Alle 4F, DK-8800 Viborg, Denmark
| | - Ulla Møller Weinreich
- Department of Respiratory Diseases, Aalborg University Hospital, Aalborg, Mølleparkvej 4, DK-9000 Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Søndre Skovvej 15, DK-9000 Aalborg, Denmark
| | - Anders Koch
- Global Health Section, Department of Public Health, University of Copenhagen Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark; Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark; Department of Infectious Diseases, Rigshospitalet University Hospital, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Christian Wejse
- GloHAU, Center for Global Health, Dept of Public Health, Aarhus University, Bartholins Allé 2, DK-8000 Aarhus C, Denmark; Dept of Infectious Diseases, Institute for Clinical Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Artillerivej 5, DK-2300 Copenhagen, Denmark; Global Health Section, Department of Public Health, University of Copenhagen Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark.
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5
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Asadi L, Croxen M, Heffernan C, Dhillon M, Paulsen C, Egedahl ML, Tyrrell G, Doroshenko A, Long R. How much do smear-negative patients really contribute to tuberculosis transmissions? Re-examining an old question with new tools. EClinicalMedicine 2022; 43:101250. [PMID: 35036885 PMCID: PMC8743225 DOI: 10.1016/j.eclinm.2021.101250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sputum smear microscopy is a common surrogate for tuberculosis infectiousness. Previous estimates that smear-negative patients contribute 13-20% of transmissions and are, on average, 20 to 25% as infectious as smear-positive cases are understood to be high. Herein, we use an ideal real-world setting, a comprehensive dataset, and new high-resolution techniques to more accurately estimate the true transmission risk of smear-negative cases. METHODS We treated all adult culture-positive pulmonary TB patients diagnosed in the province of Alberta, Canada from 2003 to 2016 as potential transmitters. The primary data sources were the Alberta TB Registry and the Provincial Laboratory for Public Health. We measured, as primary outcomes, the proportion of transmissions attributable to smear-negative sources and the relative transmission rate. First, we replicated previous studies by using molecular (DNA) fingerprint clustering. Then, using a prospectively collected registry of TB contacts, we defined transmission events as active TB amongst identified contacts who either had a 100% DNA fingerprint match to the source case or a clinical diagnosis. We supplemented our analysis with genome sequencing on temporally and geographically linked DNA fingerprint clusters of cases not identified as contacts. FINDINGS There were 1176 cases, 563 smear-negative and 613 smear-positive, and 23,131 contacts. Replicating previous studies, the proportion of transmissions attributable to smear-negative source cases was 16% (95% CI, 12-19%) and the relative transmission rate was 0.19 (95% CI, 0.14-0.26). With our combined approach, the proportion of transmission was 8% (95% CI, 3-14%) and the relative transmission rate became 0.10 (95% CI, 0.05-0.19). INTERPRETATION When we examined the same outcomes as in previous studies but refined transmission ascertainment with the addition of conventional epidemiology and genomics, we found that smear-negative cases were ∼50% less infectious than previously thought. FUNDING Alberta Innovates Health Solutions.
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Affiliation(s)
- Leyla Asadi
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Matthew Croxen
- The Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Courtney Heffernan
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Mannat Dhillon
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Catherine Paulsen
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Mary Lou Egedahl
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Greg Tyrrell
- The Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Alexander Doroshenko
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
| | - Richard Long
- The Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Room 8334A, 3rd Floor, Aberhart Centre, 11402 University Avenue NW, Edmonton, Edmonton, AB T6G 2J3, Canada
- Corresponding author.
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6
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Silva DS, Cook VJ, Johnston JC, Gardy J. Ethical challenges in the treatment of non-refugee migrants with tuberculosis in Canada. J Public Health (Oxf) 2021; 43:e701-e705. [PMID: 33316055 PMCID: PMC8677445 DOI: 10.1093/pubmed/fdaa222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/18/2020] [Accepted: 11/07/2020] [Indexed: 11/14/2022] Open
Abstract
While attention to the ethical issues that migrants face in accessing tuberculosis care has increased in the last few years, most of the attention has focused on challenges that refugees face when emigrating. Less attention has been given to ethical challenges that arise in the context of providing tuberculosis treatment and care to non-refugee migrants in high-income countries (HIC), particularly those that do not face immediate danger or violence. In this paper, we analyze some of the ethical challenges associated with treating migrants with tuberculosis in the Canadian context. In particular, we will discuss (i) inter- and intra-jurisdictional issues that challenge quotidian public health governance structures, and (ii) the ethical imperative for the Canadian government and its provinces to clearly differentiate access to healthcare from a person's immigration status to help overcome power imbalances that may exist between public health workers and their clients. The arguments presented herein could potentially apply to other HIC with some form of universal health coverage.
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Affiliation(s)
- Diego S Silva
- Sydney Health Ethics, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2050, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Camperdown, NSW 2050, Australia
| | - Victoria J Cook
- TB Services, Clinical Prevention Services, BCCDC, Vancouver, BC V5Z 4R4, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - James C Johnston
- TB Services, Clinical Prevention Services, BCCDC, Vancouver, BC V5Z 4R4, Canada
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer Gardy
- Surveillance, Data, and Epidemiology, Bill and Melinda Gates Foundation, Seattle, WA 98109, USA
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7
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Romanowski K, Sobkowiak B, Guthrie JL, Cook VJ, Gardy JL, Johnston JC. Using Whole-genome Sequencing to Determine the Timing of Secondary Tuberculosis in British Columbia, Canada. Clin Infect Dis 2021; 73:535-537. [PMID: 32812027 PMCID: PMC8326569 DOI: 10.1093/cid/ciaa1224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 11/17/2022] Open
Abstract
Combined with epidemiological data, whole-genome sequencing (WGS) can help better resolve individual tuberculosis (TB) transmission events to a degree not possible with traditional genotyping. We combine WGS data with patient-level data to calculate the timing of secondary TB among contacts of people diagnosed with active TB in British Columbia, Canada.
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Affiliation(s)
- Kamila Romanowski
- British Columbia Centre for Disease Control, Vancouver, Canada.,University of British Columbia, Vancouver, Canada
| | - Benjamin Sobkowiak
- British Columbia Centre for Disease Control, Vancouver, Canada.,University of British Columbia, Vancouver, Canada
| | | | - Victoria J Cook
- British Columbia Centre for Disease Control, Vancouver, Canada.,University of British Columbia, Vancouver, Canada
| | | | - James C Johnston
- British Columbia Centre for Disease Control, Vancouver, Canada.,University of British Columbia, Vancouver, Canada
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8
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Martínez-Lirola M, Jajou R, Mathys V, Martin A, Cabibbe AM, Valera A, Sola-Campoy PJ, Abascal E, Rodríguez-Maus S, Garrido-Cárdenas JA, Bonillo M, Chiner-Oms Á, López B, Vallejo-Godoy S, Comas I, Muñoz P, Cirillo DM, van Soolingen D, Pérez-Lago L, García de Viedma D. Integrative transnational analysis to dissect tuberculosis transmission events along the migratory route from Africa to Europe. J Travel Med 2021; 28:6211020. [PMID: 33822988 DOI: 10.1093/jtm/taab054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/26/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Growing international migration has increased the complexity of tuberculosis transmission patterns. Italy's decision to close its borders in 2018 made of Spain the new European porte entrée for migration from the Horn of Africa (HA). In one of the first rescues of migrants from this region at the end of 2018, tuberculosis was diagnosed in eight subjects, mainly unaccompanied minors. METHODS Mycobacterium tuberculosis isolates from these recently arrived migrants were analysed by Mycobacterial Interspersed Repetitive-Unit/Variable-Number of Tandem Repeat (MIRU-VNTR) and subsequent whole genome sequencing (WGS) analysis. Data were compared with those from collections from other European countries receiving migrants from the HA and a strain-specific PCR was applied for a fast searching of common strains. Infections in a cellular model were performed to assess strain virulence. RESULTS MIRU-VNTR analysis allowed identifying an epidemiological cluster involving three of the eight cases from Somalia (0 single-nucleotide polymorphisms between isolates, HA cluster). Following detailed interviews revealed that two of these cases had shared the same migratory route in most of the trip and had spent a long time at a detention camp in Libya. To confirm potential en route transmission for the three cases, we searched the same strain in collections from other European countries receiving migrants from the HA. MIRU-VNTR, WGS and a strain-specific PCR for the HA strain were applied. The same strain was identified in 12 cases from Eritrea diagnosed soon after their arrival in 2018 to the Netherlands, Belgium and Italy. Intracellular replication rate of the strain did not reveal abnormal virulence. CONCLUSIONS Our study suggests a potential en route transmission of a pan-susceptible strain, which caused at least 15 tuberculosis cases in Somalian and Eritrean migrants diagnosed in four different European countries.
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Affiliation(s)
| | - Rana Jajou
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Vanessa Mathys
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Anandi Martin
- Université catholique de Louvain (UCLouvain) & Syngulon, 4102, Seraing, Belgium
| | - Andrea Maurizio Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ana Valera
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Pedro J Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Estefanía Abascal
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Sandra Rodríguez-Maus
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | - Magdalena Bonillo
- Unidad de Prevención, Promoción y Vigilancia de la Salud del Área Sanitaria Norte de Almería. Consejería de Salud. Junta de Andalucia, Almería, Spain
| | - Álvaro Chiner-Oms
- Centro Superior de Investigación en Salud Pública (FISABIO)-Universitat de València, Valencia, Spain
| | - Begoña López
- UPPV Distrito Sanitario Granada metropolitano, Granada, Spain
| | | | - Iñaki Comas
- Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain.,CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dick van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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9
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Kumar DS, Ronald LA, Romanowski K, Rose C, Shulha HP, Cook VJ, Johnston JC. Risk of active tuberculosis in migrants diagnosed with cancer: a retrospective cohort study in British Columbia, Canada. BMJ Open 2021; 11:e037827. [PMID: 33653739 PMCID: PMC7929860 DOI: 10.1136/bmjopen-2020-037827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES To describe the association between types of cancer and active tuberculosis (TB) risk in migrants. Additionally, in order to better inform latent TB infection (LTBI) screening protocols, we assessed proportion of active TB cases potentially preventable through LTBI screening and treatment in migrants with cancer. DESIGN Population-based, retrospective cohort study. SETTING British Columbia (BC), Canada. PARTICIPANTS 1 000 764 individuals who immigrated to Canada from 1985 to 2012 and established residency in BC at any point up to 2015. PRIMARY AND SECONDARY OUTCOME MEASURES Using linked health administrative databases and disease registries, data on demographics, comorbidities, cancer type, TB exposure and active TB diagnosis were extracted. Primary outcomes included: time to first active TB diagnoses, and risks of active TB following cancer diagnoses which were estimated using Cox extended hazard regression models. Potentially preventable TB was defined as active TB diagnosed >6 months postcancer diagnoses. RESULTS Active TB risk was increased in migrants with cancer ((HR (95% CI)) 2.5 (2.0 to 3.1)), after adjustment for age, sex, TB incidence in country of origin, immigration classification, contact status and comorbidities. Highest risk was observed with lung cancer (HR 11.2 (7.4 to 16.9)) and sarcoma (HR 8.1 (3.3 to 19.5)), followed by leukaemia (HR 5.6 (3.1 to 10.2)), lymphoma (HR 4.9 (2.7 to 8.7)) and gastrointestinal cancers (HR 2.7 (1.7 to 4.4)). The majority (65.9%) of active TB cases were diagnosed >6 months postcancer diagnosis. CONCLUSION Specific cancers increase active TB risk to varying degrees in the migrant population of BC, with approximately two-thirds of active TB cases identified as potentially preventable.
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Affiliation(s)
- Divjot S Kumar
- Division of Respiratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa A Ronald
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Kamila Romanowski
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Caren Rose
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Hennady P Shulha
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Victoria J Cook
- Division of Respiratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - James C Johnston
- Division of Respiratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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10
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The value of the continuous genotyping of multi-drug resistant tuberculosis over 20 years in Spain. Sci Rep 2020; 10:20433. [PMID: 33235225 PMCID: PMC7686341 DOI: 10.1038/s41598-020-77249-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/02/2020] [Indexed: 11/16/2022] Open
Abstract
Molecular epidemiology of circulating clinical isolates is crucial to improve prevention strategies. The Spanish Working Group on multidrug resistant tuberculosis (MDR-TB) is a network that monitors the MDR-TB isolates in Spain since 1998. The aim of this study was to present the study of the MDR-TB and extensively drug-resistant tuberculosis (XDR-TB) patterns in Spain using the different recommended genotyping methods over time by a national coordinated system. Based on the proposed genotyping methods in the European Union until 2018, the preservation of one method, MIRU-VNTR, applied to selected clustered strains permitted to maintain our study open for 20 years. The distribution of demographic, clinical and epidemiological characteristics of clustered and non-clustered cases of MDR/XDR tuberculosis with proportion differences as assessed by Pearson’s chi-squared or Fisher’s exact test was compared. The differences in the quantitative variables using the Student's-t test and the Mann–Whitney U test were evaluated. The results obtained showed a total of 48.4% of the cases grouped in 77 clusters. Younger age groups, having a known TB case contact (10.2% vs 4.7%) and XDR-TB (16.5% vs 1.8%) were significantly associated with clustering. The largest cluster corresponded to a Mycobacterium bovis strain mainly spread during the nineties. A total of 68.4% of the clusters detected were distributed among the different Spanish regions and six clusters involving 104 cases were grouped in 17 and 18 years. Comparison of the genotypes obtained with those European genotypes included in The European Surveillance System (TESSy) showed that 87 cases had become part of 20 European clusters. The continuity of MDR strain genotyping in time has offered a widespread picture of the situation that allows better management of this public health problem. It also shows the advantage of maintaining one genotyping method over time, which allowed the comparison between ancient, present and future samples.
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11
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Guthrie JL, Strudwick L, Roberts B, Allen M, McFadzen J, Roth D, Jorgensen D, Rodrigues M, Tang P, Hanley B, Johnston J, Cook VJ, Gardy J. Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting. Epidemiol Infect 2020; 148:e15. [PMID: 32014080 PMCID: PMC7019559 DOI: 10.1017/s0950268820000072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/04/2019] [Accepted: 01/09/2020] [Indexed: 11/29/2022] Open
Abstract
Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005-2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.
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Affiliation(s)
- J. L. Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - L. Strudwick
- Yukon Communicable Disease Control, Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - B. Roberts
- Yukon Communicable Disease Control, Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - M. Allen
- Yukon Communicable Disease Control, Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - J. McFadzen
- Yukon Communicable Disease Control, Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - D. Roth
- British Columbia Centre for Disease Control, Vancouver, Canada
| | - D. Jorgensen
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - M. Rodrigues
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - P. Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - B. Hanley
- Department of Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - J. Johnston
- British Columbia Centre for Disease Control, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - V. J. Cook
- British Columbia Centre for Disease Control, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - J.L. Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control, Vancouver, Canada
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12
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Correa-Macedo W, Cambri G, Schurr E. The Interplay of Human and Mycobacterium Tuberculosis Genomic Variability. Front Genet 2019; 10:865. [PMID: 31620169 PMCID: PMC6759583 DOI: 10.3389/fgene.2019.00865] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis (TB), caused by the human pathogens Mycobacterium tuberculosis (Mtb) and Mycobacterium africanum, has plagued humanity for millennia and remains the deadliest infectious disease in the modern world. Mycobacterium tuberculosis and M. africanum can be subdivided phylogenetically into seven lineages exhibiting a low but significant degree of genomic diversity and preferential geographic distributions. Human genetic variability impacts all stages of TB pathogenesis ranging from susceptibility to infection with Mtb, progression of infection to disease, and the development of distinct clinical subtypes. The genetic study of severe childhood TB identified strong inborn single-gene errors revealing crucial pathways of vulnerability to TB. However, the identification of major TB-susceptibility genes on the population level has remained elusive. In particular, the replication of findings from candidate and genome-wide association studies across distinct human populations has proven difficult, thus hampering the characterization of reliable host molecular markers of susceptibility. Among the possible confounding factors of genetic association studies is Mtb genomic variability, which generally was not taken into account by human genetic studies. In support of this possibility, Mtb lineage was found to be a contributing factor to clinical presentation of TB and epidemiological spread of Mtb in exposed populations. The confluence of pathogen and human host genetic variability to TB pathogenesis led to the consideration of a possible coadaptation of Mtb strains and their human hosts, which should reveal itself in significant interaction effects between Mtb strain and TB-susceptibility/resistance alleles. Here, we present some of the most consistent findings of genetic susceptibility factors in human TB and review studies that point to genome-to-genome interaction between humans and Mtb lineages. The limited results available so far suggest that analyses considering joint human–Mtb genomic variability may provide improved power for the discovery of pathogenic drivers of the ongoing TB epidemic.
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Affiliation(s)
- Wilian Correa-Macedo
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada.,The McGill International TB Centre, McGill University, Montreal, QC, Canada.,Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Geison Cambri
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada.,Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada.,The McGill International TB Centre, McGill University, Montreal, QC, Canada.,Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada.,Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
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13
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Guthrie JL, Ronald LA, Cook VJ, Johnston J, Gardy JL. The problem with defining foreign birth as a risk factor in tuberculosis epidemiology studies. PLoS One 2019; 14:e0216271. [PMID: 31039191 PMCID: PMC6490926 DOI: 10.1371/journal.pone.0216271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/17/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To examine how stratifying persons born outside Canada according to tuberculosis (TB) incidence in their birth country and other demographic factors refines our understanding of TB epidemiology and local TB transmission. BACKGROUND Population-level TB surveillance programs and research studies in low incidence settings often report all persons born outside the country in which the study is conducted as "foreign-born"-a single label for a highly diverse population with variable TB risks. This may mask important TB epidemiologic trends and not accurately reflect local transmission patterns. METHODS We used population-level data from two large cohorts in British Columbia (BC), Canada: an immigration cohort (n = 337,492 permanent residents to BC) and a genotyping cohort (n = 2290 culture-confirmed active TB cases). We stratified active TB case counts, incidence rates, and genotypic clustering (an indicator of TB transmission) in BC by birth country TB incidence, age at immigration, and years since arrival. RESULTS Persons from high-incidence countries had a 12-fold higher TB incidence than those emigrating from low-incidence settings. Estimates of local transmission, as captured by genotyping, versus reactivation of latent TB infection acquired outside Canada varied when data were stratified by birthplace TB incidence, as did patient-level characteristics of individuals in each group, such as age and years between immigration and diagnosis. CONCLUSION Categorizing persons beyond simply "foreign-born", particularly in the context of TB epidemiologic and molecular data, is needed for a more accurate understanding of TB rates and patterns of transmission.
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Affiliation(s)
- Jennifer L. Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Lisa A. Ronald
- British Columbia Centre for Disease Control, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Victoria J. Cook
- British Columbia Centre for Disease Control, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - James Johnston
- British Columbia Centre for Disease Control, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Jennifer L. Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control, Vancouver, Canada
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14
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Guthrie JL, Marchand-Austin A, Cronin K, Lam K, Pyskir D, Kong C, Jorgensen D, Rodrigues M, Roth D, Tang P, Cook VJ, Johnston J, Jamieson FB, Gardy JL. Universal genotyping reveals province-level differences in the molecular epidemiology of tuberculosis. PLoS One 2019; 14:e0214870. [PMID: 30943250 PMCID: PMC6447219 DOI: 10.1371/journal.pone.0214870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/21/2019] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES Compare the molecular epidemiology of tuberculosis (TB) between two large Canadian provinces-Ontario and British Columbia (BC)-to identify genotypic clusters within and across both provinces, allowing for an improved understanding of genotype data and providing context to more accurately identify clusters representing local transmission. DESIGN We compared 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping for 3,314 Ontario and 1,602 BC clinical Mycobacterium tuberculosis isolates collected from 2008 through 2014. Laboratory data for each isolate was linked to case-level records to obtain clinical and demographic data. RESULTS The demographic characteristics of persons with TB varied between provinces, most notably in the proportion of persons born outside Canada, which was reflected in the large number of unique genotypes (n = 3,461). The proportion of clustered isolates was significantly higher in BC. Substantial clustering amongst non-Lineage 4 TB strains was observed within and across the provinces. Only two large clusters (≥10 cases/cluster) representing within province transmission had interprovincial genotype matches. CONCLUSION We recommend expanding analysis of shared genotypes to include neighbouring jurisdictions, and implementing whole genome sequencing to improve identification of TB transmission, recognize outbreaks, and monitor changing trends in TB epidemiology.
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Affiliation(s)
- Jennifer L. Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- Public Health Ontario, Toronto, Canada
| | | | - Kirby Cronin
- Public Health Ontario, Toronto, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Karen Lam
- Public Health Ontario, Toronto, Canada
| | | | - Clare Kong
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - Danielle Jorgensen
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - Mabel Rodrigues
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - David Roth
- British Columbia Centre for Disease Control, Vancouver, Canada
| | - Patrick Tang
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Victoria J. Cook
- British Columbia Centre for Disease Control, Vancouver, Canada
- Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - James Johnston
- British Columbia Centre for Disease Control, Vancouver, Canada
- Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - Frances B. Jamieson
- Public Health Ontario, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Jennifer L. Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control, Vancouver, Canada
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15
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Guthrie JL, Strudwick L, Roberts B, Allen M, McFadzen J, Roth D, Jorgensen D, Rodrigues M, Tang P, Hanley B, Johnston J, Cook VJ, Gardy JL. Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region. Epidemiol Infect 2019; 147:e188. [PMID: 31364521 PMCID: PMC6518594 DOI: 10.1017/s0950268819000670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/22/2019] [Accepted: 03/17/2019] [Indexed: 11/17/2022] Open
Abstract
Few studies have used genomic epidemiology to understand tuberculosis (TB) transmission in rural and remote settings - regions often unique in history, geography and demographics. To improve our understanding of TB transmission dynamics in Yukon Territory (YT), a circumpolar Canadian territory, we conducted a retrospective analysis in which we combined epidemiological data collected through routine contact investigations with clinical and laboratory results. Mycobacterium tuberculosis isolates from all culture-confirmed TB cases in YT (2005-2014) were genotyped using 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) and compared to each other and to those from the neighbouring province of British Columbia (BC). Whole genome sequencing (WGS) of genotypically clustered isolates revealed three sustained transmission networks within YT, two of which also involved BC isolates. While each network had distinct characteristics, all had at least one individual acting as the probable source of three or more culture-positive cases. Overall, WGS revealed that TB transmission dynamics in YT are distinct from patterns of spread in other, more remote Northern Canadian regions, and that the combination of WGS and epidemiological data can provide actionable information to local public health teams.
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Affiliation(s)
- J. L. Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - L. Strudwick
- Yukon Communicable Disease Control, Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - B. Roberts
- Yukon Communicable Disease Control, Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - M. Allen
- Yukon Communicable Disease Control, Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - J. McFadzen
- Yukon Communicable Disease Control, Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - D. Roth
- British Columbia Centre for Disease Control, Vancouver, Canada
| | - D. Jorgensen
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - M. Rodrigues
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, Canada
| | - P. Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - B. Hanley
- Department of Health and Social Services, Government of Yukon, Whitehorse, Canada
| | - J. Johnston
- British Columbia Centre for Disease Control, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - V. J. Cook
- British Columbia Centre for Disease Control, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - J. L. Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
- British Columbia Centre for Disease Control, Vancouver, Canada
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16
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Meehan CJ, Moris P, Kohl TA, Pečerska J, Akter S, Merker M, Utpatel C, Beckert P, Gehre F, Lempens P, Stadler T, Kaswa MK, Kühnert D, Niemann S, de Jong BC. The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology. EBioMedicine 2018; 37:410-416. [PMID: 30341041 PMCID: PMC6284411 DOI: 10.1016/j.ebiom.2018.10.013] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/17/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. Multiple methods with specific performance characteristics exist for detecting recent transmission chains, usually by clustering strains based on genotype similarities. With such a large variety of methods available, informed selection of an appropriate approach for determining transmissions within a given setting/time period is difficult. METHODS This study combines whole genome sequence (WGS) data derived from 324 isolates collected 2005-2010 in Kinshasa, Democratic Republic of Congo (DRC), a high endemic setting, with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated. FINDINGS Our results suggest that clusters based on Spoligotyping could encompass transmission events that occurred almost 200 years prior to sampling while 24-loci-MIRU-VNTR often represented three decades of transmission. Instead, WGS based genotyping applying low SNP or cgMLST allele thresholds allows for determination of recent transmission events, e.g. in timespans of up to 10 years for a 5 SNP/allele cut-off. INTERPRETATION With the rapid uptake of WGS methods in surveillance and outbreak tracking, the findings obtained in this study can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period. For high resolution cluster analyses, WGS-SNP and cgMLST based analyses have similar clustering/timing characteristics even for data obtained from a high incidence setting.
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Affiliation(s)
- Conor J Meehan
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium.
| | - Pieter Moris
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; Adrem Data Lab (Adrem), Department of Mathematics and Computer Science, University of Antwerp, Antwerp 2020, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp 2020, Belgium
| | - Thomas A Kohl
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Jūlija Pečerska
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Suriya Akter
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Matthias Merker
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Christian Utpatel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Patrick Beckert
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Florian Gehre
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Serekunda, Gambia; Department Infectious Diseases Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg 20359, Germany
| | - Pauline Lempens
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Tanja Stadler
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Michel K Kaswa
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; National Tuberculosis Program, Kinshasa, DR Congo
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, 07745 JENA, Germany
| | - Stefan Niemann
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Bouke C de Jong
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
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17
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Martin MA, Lee RS, Cowley LA, Gardy JL, Hanage WP. Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission. Microb Genom 2018; 4. [PMID: 30303479 PMCID: PMC6249434 DOI: 10.1099/mgen.0.000217] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole genome sequencing in conjunction with traditional epidemiology has been used to reconstruct transmission networks of Mycobacterium tuberculosis during outbreaks. Given its low mutation rate, genetic diversity within M. tuberculosis outbreaks can be extremely limited - making it difficult to determine precisely who transmitted to whom. In addition to consensus SNPs (cSNPs), examining heterogeneous alleles (hSNPs) has been proposed to improve resolution. However, few studies have examined the potential biases in detecting these hSNPs. Here, we analysed genome sequence data from 25 specimens from British Columbia, Canada. Specimens were sequenced to a depth of 112-296×. We observed biases in read depth, base quality, strand distribution and read placement where possible hSNPs were initially identified, so we applied conservative filters to reduce false positives. Overall, there was phylogenetic concordance between the observed 2542 cSNP and 63 hSNP loci. Furthermore, we identified hSNPs shared exclusively by epidemiologically linked patients, supporting their use in transmission inferences. We conclude that hSNPs may add resolution to transmission networks, particularly where the overall genetic diversity is low.
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Affiliation(s)
- Michael A Martin
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Robyn S Lee
- 2Department of Epidemiology, Harvard University, Boston, MA 02115, USA
| | - Lauren A Cowley
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jennifer L Gardy
- 3School of Population and Public Health, University of British Columbia, Vancouver, Canada.,4British Columbia Centre for Disease Control, Vancouver, Canada
| | - William P Hanage
- 1Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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18
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Azimi T, Nasiri MJ, Zamani S, Hashemi A, Goudarzi H, Fooladi AAI, Feizabadi MM, Fallah F. High genetic diversity among Mycobacterium tuberculosis strains in Tehran, Iran. J Clin Tuberc Other Mycobact Dis 2018; 11:1-6. [PMID: 31720383 PMCID: PMC6830142 DOI: 10.1016/j.jctube.2018.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 01/21/2018] [Accepted: 01/29/2018] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Tuberculosis (TB) still remains an important public health problem in Iran. The genotyping of Mycobacterium tuberculosis isolates is expected to lead to a better understanding of M. tuberculosis transmission in Tehran, the most populated city of Iran. MATERIALS AND METHODS A total of 2300 clinical specimens were obtained from TB suspected patients who were referred to a TB center in Tehran from Jan 2014 to Dec 2016. Identification was performed using both conventional and molecular methods. The presence of resistance to rifampicin was examined by the GeneXpert MTB/RIF. The standard 15-locus mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing method was applied to genotype of clinical isolates. RESULTS Of 2300 specimens, 80 isolates were identified as M. tuberculosis by using biochemical and molecular tests. Of 80 M. tuberculosis isolates, 76 (95%) had unique genotypic profiles and 4 (5%) shared a profile with one or more other strains. Based on single loci variation (SLV) 4 clonal complexes were observed. NEW-1 was found to be the most predominant lineage (22.5%) followed by West African (1.25%), Central Asian (CAS)/Delhi (1.25%), Bovis (1.25%), H37Rv (1.25%) and multiple matches (1.25%). Loci MIRU10, MIRU26, MTUB21 and QUB26 were found as highly discriminative. No mutation was detected in the hotspot region of rifampicin by using GeneXpert MTB/RIF. CONCLUSIONS Our study findings show that there was considerable genotypic diversity among M. tuberculosis isolates in Tehran. The 15-locus MIRU-VNTR showed high HGDI and could be used as a first-line genotyping method for epidemiological studies.
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Affiliation(s)
- Taher Azimi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samin Zamani
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ali Hashemi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Systems Biology and Poisonings institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Medical Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Fallah
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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19
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Universal Genotyping for Tuberculosis Prevention Programs: a 5-Year Comparison with On-Request Genotyping. J Clin Microbiol 2018. [PMID: 29540458 PMCID: PMC5925716 DOI: 10.1128/jcm.01778-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Prospective universal genotyping of tuberculosis (TB) isolates is used by many laboratories to detect clusters of cases and inform contact investigations. Prior to universal genotyping, most TB prevention programs genotyped isolates on request only, relying on requests from public health professionals whose knowledge of a patient's clinical, demographic, and epidemiological characteristics suggested potential transmission. To justify the switch from on-request to universal genotyping—particularly in the public health domain, with its limited resources and competing priorities—it is important to demonstrate the additional benefit provided by a universal genotyping program. We compared the clustering patterns revealed by retrospective 24-locus mycobacterial interspersed repetitive unit–variable-number tandem repeat genotyping of all culture-positive isolates over a 5-year period to the patterns previously established by our genotyping-on-request program in the low-incidence setting of British Columbia, Canada. We found that 23.8% of isolates were requested during the study period, and while requested isolates had increased odds of belonging to a genotype cluster (adjusted odds ratio, 2.3; 95% confidence interval, 1.5 to 3.3), only 54.6% clustered with the requested comparator strain. Universal genotyping revealed 94 clusters ranging in size from 2 to 53 isolates (mean = 5) and involving 432 individuals. On-request genotyping missed 54 (57.4%) of these clusters and 130 (30.1%) clustered individuals. Our results underscore that TB patient networks are complex, with unrecognized linkages between patients, and a prospective province-wide universal genotyping program provides an informative, bias-free tool to explore transmission to a degree not possible with on-request genotyping.
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