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Quan Z, Li M, Chen Y, Liang J, Takiff H, Gao Q. Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection. Eur J Clin Microbiol Infect Dis 2024; 43:297-304. [PMID: 38041721 DOI: 10.1007/s10096-023-04720-8] [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] [Received: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE To evaluate the performance of core genome multilocus sequence typing (cgMLST) for genotyping Mycobacterium tuberculosis (M.tuberculosis) Strains in regions where the lineage 2 strains predominate. METHODS We compared clustering by whole-genome SNP typing with cgMLST clustering in the analysis of WGS data of 6240 strains from five regions of China. Using both the receiver operating characteristic (ROC) curve and epidemiological investigation to determine the optimal threshold for defining genomic clustering by cgMLST. The performance of cgMLST was evaluated by quantifying the sensitivity, specificity and concordance of clustering between two methods. Logistic regression was used to gauge the impact of strain genetic diversity and lineage on cgMLST clustering. RESULTS The optimal threshold for cgMLST to define genomic clustering was determined to be ≤ 10 allelic differences between strains. The overall sensitivity and specificity of cgMLST averaged 99.6% and 96.3%, respectively; the concordance of clustering between two methods averaged 97.1%. Concordance was significantly correlated with strain genetic diversity and was 3.99 times (95% CI, 2.94-5.42) higher in regions with high genetic diversity (π > 1.55 × 10-4) compared to regions with low genetic diversity. The difference missed statistical significance, while concordance for lineage 2 strains (96.8%) was less than that for lineage 4 strains (98.3%). CONCLUSION : cgMLST showed a discriminatory power comparable to whole-genome SNP typing and could be used to genotype clinical M.tuberculosis strains in different regions of China. The discriminative power of cgMLST was significantly correlated with strain genetic diversity and was slightly lower with strains from regions with low genetic diversity.
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Affiliation(s)
- Zhuo Quan
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Meng Li
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Yiwang Chen
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Jialei Liang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Qian Gao
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China.
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2
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Nilgiriwala K, Rabodoarivelo MS, Hall MB, Patel G, Mandal A, Mishra S, Andrianomanana FR, Dingle K, Rodger G, George S, Crook DW, Hoosdally S, Mistry N, Rakotosamimanana N, Iqbal Z, Grandjean Lapierre S, Walker TM. Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction. J Clin Microbiol 2023; 61:e0157822. [PMID: 36815861 PMCID: PMC10035339 DOI: 10.1128/jcm.01578-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Universal access to drug susceptibility testing for newly diagnosed tuberculosis patients is recommended. Access to culture-based diagnostics remains limited, and targeted molecular assays are vulnerable to emerging resistance mutations. Improved protocols for direct-from-sputum Mycobacterium tuberculosis sequencing would accelerate access to comprehensive drug susceptibility testing and molecular typing. We assessed a thermo-protection buffer-based direct-from-sample M. tuberculosis whole-genome sequencing protocol. We prospectively analyzed 60 acid-fast bacilli smear-positive clinical sputum samples in India and Madagascar. A diversity of semiquantitative smear positivity-level samples were included. Sequencing was performed using Illumina and MinION (monoplex and multiplex) technologies. We measured the impact of bacterial inoculum and sequencing platforms on genomic read depth, drug susceptibility prediction performance, and typing accuracy. M. tuberculosis was identified by direct sputum sequencing in 45/51 samples using Illumina, 34/38 were identified using MinION-monoplex sequencing, and 20/24 were identified using MinION-multiplex sequencing. The fraction of M. tuberculosis reads from MinION sequencing was lower than from Illumina, but monoplexing grade 3+ samples on MinION produced higher read depth than Illumina (P < 0.05) and MinION multiplexing (P < 0.01). No significant differences in sensitivity and specificity of drug susceptibility predictions were seen across sequencing modalities or within each technology when stratified by smear grade. Illumina sequencing from sputum accurately identified 1/8 (rifampin) and 6/12 (isoniazid) resistant samples, compared to 2/3 (rifampin) and 3/6 (isoniazid) accurately identified with Nanopore monoplex. Lineage agreement levels between direct and culture-based sequencing were 85% (MinION-monoplex), 88% (Illumina), and 100% (MinION-multiplex). M. tuberculosis direct-from-sample whole-genome sequencing remains challenging. Improved and affordable sample treatment protocols are needed prior to clinical deployment.
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Affiliation(s)
| | | | - Michael B Hall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Grishma Patel
- Foundation for Medical Research, Mumbai, Maharashtra, India
| | - Ayan Mandal
- Foundation for Medical Research, Mumbai, Maharashtra, India
| | - Shefali Mishra
- Foundation for Medical Research, Mumbai, Maharashtra, India
| | | | - Kate Dingle
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Gillian Rodger
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Sophie George
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Sarah Hoosdally
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Nerges Mistry
- Foundation for Medical Research, Mumbai, Maharashtra, India
| | | | - Zamin Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Simon Grandjean Lapierre
- Mycobacteriology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Immunopathology Axis, Centre de Recherche du Centre Hospitalier, Université de Montréal, Montréal, Québec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montréal, Québec, Canada
| | - Timothy M Walker
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- Oxford University, Clinical Research Unit, Ho Chi Minh City, Vietnam
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3
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Oostvogels S, Ley SD, Heupink TH, Dippenaar A, Streicher EM, De Vos E, Meehan CJ, Dheda K, Warren R, Van Rie A. Transmission, distribution and drug resistance-conferring mutations of extensively drug-resistant tuberculosis in the Western Cape Province, South Africa. Microb Genom 2022; 8. [PMID: 35471145 PMCID: PMC9453078 DOI: 10.1099/mgen.0.000815] [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] [Indexed: 11/25/2022] Open
Abstract
Extensively drug-resistant tuberculosis (XDR-TB), defined as resistance to at least isoniazid (INH), rifampicin (RIF), a fluoroquinolone (FQ) and a second-line injectable drug (SLID), is difficult to treat and poses a major threat to TB control. The transmission dynamics and distribution of XDR Mycobacterium tuberculosis (Mtb) strains have not been thoroughly investigated. Using whole genome sequencing data on 461 XDR-Mtb strains, we aimed to investigate the geographical distribution of XDR-Mtb strains in the Western Cape Province of South Africa over a 10 year period (2006–2017) and assess the association between Mtb sub-lineage, age, gender, geographical patient location and membership or size of XDR-TB clusters. First, we identified transmission clusters by excluding drug resistance-conferring mutations and using the 5 SNP cutoff, followed by merging clusters based on their most recent common ancestor. We then consecutively included variants conferring resistance to INH, RIF, ethambutol (EMB), pyrazinamide (PZA), SLIDs and FQs in the cluster definition. Cluster sizes were classified as small (2–4 isolates), medium (5–20 isolates), large (21–100 isolates) or very large (>100 isolates) to reflect the success of individual strains. We found that most XDR-TB strains were clustered and that including variants conferring resistance to INH, RIF, EMB, PZA and SLIDs in the cluster definition did not significantly reduce the proportion of clustered isolates (85.5–82.2 %) but increased the number of patients belonging to small clusters (4.3–12.4 %, P=0.56). Inclusion of FQ resistance-conferring variants had the greatest effect, with 11 clustered isolates reclassified as unique while the number of clusters increased from 17 to 37. Lineage 2 strains (lineage 2.2.1 typical Beijing or lineage 2.2.2 atypical Beijing) showed the large clusters which were spread across all health districts of the Western Cape Province. We identified a significant association between residence in the Cape Town metropole and cluster membership (P=0.016) but no association between gender, age and cluster membership or cluster size (P=0.39). Our data suggest that the XDR-TB epidemic in South Africa probably has its origin in the endemic spread of MDR Mtb and pre-XDR Mtb strains followed by acquisition of FQ resistance, with more limited transmission of XDR Mtb strains. This only became apparent with the inclusion of drug resistance-conferring variants in the definition of a cluster. In addition to the prevention of amplification of resistance, rapid diagnosis of MDR, pre-XDR and XDR-TB and timely initiation of appropriate treatment is needed to reduce transmission of difficult-to-treat TB.
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Affiliation(s)
- Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- *Correspondence: Selien Oostvogels,
| | - Serej D. Ley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
- Present address: Sefunda AG, Muttenz, Switzerland
| | - Tim H. Heupink
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Elizabeth M. Streicher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Elise De Vos
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute, South Africa
- South African MRC Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Rob Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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4
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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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Dohál M, Dvořáková V, Šperková M, Porvazník I, Cabibbe AM, Trovato A, Spitaleri A, Rasmussen EM, Pršo K, Škereňová M, Cirillo DM, Solovič I, Mokrý J. Anti-tuberculosis drug resistance in Slovakia, 2018-2019: The first whole-genome epidemiological study. J Clin Tuberc Other Mycobact Dis 2022; 26:100292. [PMID: 35005254 PMCID: PMC8717600 DOI: 10.1016/j.jctube.2021.100292] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Euro-American lineage 4.7 was the most represented among the XDR-TB/MDR-TB resistant strains. Seven of 12 isolates (58%) belonged to the same recent transmission chain. Strains originally from Eastern European countries were diagnosed in patients without any epidemiological links with these countries. Incidence of resistant XDR-TB/MDR-TB in Slovakia, while low, still should be taken to monitor.
Objective The resistance of Mycobacterium (M.) tuberculosis to antituberculosis drugs poses a major threat to global public health. Whole genome sequencing (WGS) is an increasingly preferred method in the diagnostics and monitoring of the transmission dynamics of resistant forms of tuberculosis (TB). The aim of the study was to, for the first time, use the sequencing-based analysis to study the transmission and resistance patterns of a systematic and recent collection of extensively drug resistant (XDR) and multidrug resistant tuberculosis (MDR-TB) isolates and to expand our knowledge about drug resistant (DR) TB epidemiological dynamics in Slovakia. Design A total of 495 patients with pulmonary TB, who were referred to National Reference Laboratory for Mycobacteriology (Vyšné Hágy, Slovakia) in the years 2018–2019, were studied. Out of the total of 495 patients, 4 XDR-TB (0.8%) and 8 (1.6%) MDR-TB isolates were identified by conventional drug susceptibility testing on Löwenstein-Jensen solid medium and subjected to whole genome sequencing. Sequencing data were evaluated for molecular-epidemiological analysis and identification of resistance patterns. Results Phylogenetic and cluster analysis showed extensive recent transmission events and the predominance of Euro-American lineage 4.7 in Slovakia. However, phylogenetic analysis revealed the circulation of several lineages that originally occurred in Eastern European countries. Resistance patterns for first- and second-line antituberculosis drugs characterized by whole genome sequencing were in high concordance with the results of phenotypic drug susceptibility testing. Conclusion Forty percent of at least MDR-TB isolates were not genetically linked, indicating that appropriate measures should be taken to monitor and prevent the spread of drug-resistant tuberculosis within the country as well as in other regions.
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Affiliation(s)
- Matúš Dohál
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Slovakia
| | - Věra Dvořáková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Miluše Šperková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia, Faculty of Health, Catholic University, Ružomberok, Slovakia.,Faculty of Health, Catholic University, Ružomberok, Slovakia
| | | | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Kristián Pršo
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Slovakia
| | - Mária Škereňová
- Biomedical Center Martin, Department of Molecular Medicine, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Slovakia, Department of Clinical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Slovakia
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia, Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Slovakia
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6
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Dohál M, Porvazník I, Solovič I, Mokrý J. Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections. Microorganisms 2021; 9:microorganisms9112237. [PMID: 34835363 PMCID: PMC8621650 DOI: 10.3390/microorganisms9112237] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Infections caused by non-tuberculous mycobacteria (NTM) have been a public health problem in recent decades and contribute significantly to the clinical and economic burden globally. The diagnosis of infections is difficult and time-consuming and, in addition, the conventional diagnostics tests do not have sufficient discrimination power in species identification due to cross-reactions and not fully specific probes. However, technological advances have been made and the whole genome sequencing (WGS) method has been shown to be an essential part of routine diagnostics in clinical mycobacteriology laboratories. The use of this technology has contributed to the characterization of new species of mycobacteria, as well as the identification of gene mutations encoding resistance and virulence factors. Sequencing data also allowed to track global outbreaks of nosocomial NTM infections caused by M. abscessus complex and M. chimaera. To highlight the utility of WGS, we summarize recent scientific studies on WGS as a tool suitable for the management of NTM-induced infections in clinical practice.
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Affiliation(s)
- Matúš Dohál
- Biomedical Center Martin, Department of Pharmacology, Jessenius Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia;
- Correspondence: ; Tel.: +42-19-0252-4199
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, 059 81 Vyšné Hágy, Slovakia; (I.P.); (I.S.)
- Faculty of Health, Catholic University, 034 01 Ružomberok, Slovakia
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, 059 81 Vyšné Hágy, Slovakia; (I.P.); (I.S.)
- Faculty of Health, Catholic University, 034 01 Ružomberok, Slovakia
| | - Juraj Mokrý
- Biomedical Center Martin, Department of Pharmacology, Jessenius Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia;
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Asare P, Asante-Poku A, Osei-Wusu S, Otchere ID, Yeboah-Manu D. The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa. Front Public Health 2021; 9:706651. [PMID: 34368069 PMCID: PMC8342769 DOI: 10.3389/fpubh.2021.706651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.
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Affiliation(s)
- Prince Asare
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Adwoa Asante-Poku
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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8
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Gan SH, KhinMar KW, Ang LW, Lim LKY, Sng LH, Wang YT, Chee CBE. Recurrent Tuberculosis Disease in Singapore. Open Forum Infect Dis 2021; 8:ofab340. [PMID: 34307732 PMCID: PMC8297698 DOI: 10.1093/ofid/ofab340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/23/2021] [Indexed: 11/12/2022] Open
Abstract
Background Previously treated (ie, recurrent) tuberculosis (TB) cases account for approximately 7%-8% of incident TB globally and in Singapore. Molecular fingerprinting has enabled the differentiation of these patients into relapsed or reinfection cases. Methods Patient demographics, disease characteristics, and treatment information were obtained from the national TB notification registry and TB Control Unit. We performed a retrospective, case-control study to evaluate factors associated with recurrent TB disease in Singapore citizens and permanent residents with culture-positive TB from 2006 to 2013 and who developed a second episode of culture-positive TB up to 2016 using multivariable logistic regression analyses. Results Ninety-one cases with culture-positive first and recurrent TB disease episodes were identified. Recurrent TB was associated with age ≥60 years (adjusted odds ratio [aOR], 1.98 [95% confidence interval {CI}, 1.09-3.61), male sex (aOR, 2.29 [95% CI, 1.22-4.51]), having concomitant pulmonary and extrapulmonary TB (aOR, 3.10 [95% CI, 1.59-6.10]) and extrapulmonary TB alone (aOR, 3.82 [95% CI, 1.12-13.31]), and was less likely in non-Malays (aOR, 0.52 [95% CI, .27-.99]). DNA fingerprinting results for both episodes in 49 cases differentiated these into 28 relapsed and 21 reinfection cases. Relapse was associated with having concomitant pulmonary and extrapulmonary TB (aOR, 9.24 [95% CI, 2.50-42.42]) and positive sputum acid-fast bacilli smear (aOR, 3.95 [95% CI, 1.36-13.10]). Conclusions Relapse and reinfection contributed to 57% and 43%, respectively, of recurrent TB in Singapore. Our study highlights the underappreciated association of concomitant pulmonary and extrapulmonary TB as a significant risk factor for disease relapse.
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Affiliation(s)
- Suay Hong Gan
- Tuberculosis Control Unit, Tan Tock Seng Hospital, Singapore
| | | | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore
| | - Leo K Y Lim
- National Centre for Infectious Diseases, Singapore
| | - Li Hwei Sng
- Department of Pathology, Singapore General Hospital, Singapore
| | - Yee Tang Wang
- Tuberculosis Control Unit, Tan Tock Seng Hospital, Singapore
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9
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Asare P, Otchere ID, Bedeley E, Brites D, Loiseau C, Baddoo NA, Asante-Poku A, Osei-Wusu S, Prah DA, Borrell S, Reinhard M, Forson A, Koram KA, Gagneux S, Yeboah-Manu D. Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana. Front Med (Lausanne) 2020; 7:161. [PMID: 32509791 PMCID: PMC7248928 DOI: 10.3389/fmed.2020.00161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/09/2020] [Indexed: 01/08/2023] Open
Abstract
Whole genome sequencing (WGS) is progressively being used to investigate the transmission dynamics of Mycobacterium tuberculosis complex (MTBC). We used WGS analysis to resolve traditional genotype clusters and explored the spatial distribution of confirmed recent transmission clusters. Bacterial genomes from a total of 452 MTBC isolates belonging to large traditional clusters from a population-based study spanning July 2012 and December 2015 were obtained through short read next-generation sequencing using the illumina HiSeq2500 platform. We performed clustering and spatial analysis using specified R packages and ArcGIS. Of the 452 traditional genotype clustered genomes, 314 (69.5%) were confirmed clusters with a median cluster size of 7.5 genomes and an interquartile range of 4–12. Recent tuberculosis (TB) transmission was estimated as 24.7%. We confirmed the wide spread of a Cameroon sub-lineage clone with a cluster size of 78 genomes predominantly from the Ablekuma sub-district of Accra metropolis. More importantly, we identified a recent transmission cluster associated with isoniazid resistance belonging to the Ghana sub-lineage of lineage 4. WGS was useful in detecting unsuspected outbreaks; hence, we recommend its use not only as a research tool but as a surveillance tool to aid in providing the necessary guided steps to track, monitor, and control TB.
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Affiliation(s)
- Prince Asare
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.,West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Edmund Bedeley
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Diana Ahu Prah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Sonia Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Audrey Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Korle-Bu, Accra, Ghana
| | - Kwadwo Ansah Koram
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.,West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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10
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Guthrie JL, Kong C, Roth D, Jorgensen D, Rodrigues M, Hoang L, Tang P, Cook V, Johnston J, Gardy JL. Molecular Epidemiology of Tuberculosis in British Columbia, Canada: A 10-Year Retrospective Study. Clin Infect Dis 2019; 66:849-856. [PMID: 29069284 PMCID: PMC5850024 DOI: 10.1093/cid/cix906] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/17/2017] [Indexed: 11/14/2022] Open
Abstract
Background Understanding regional molecular epidemiology allows for the development of more efficient tuberculosis prevention strategies in low-incidence settings. Methods We analyzed 24-locus mycobacterial interspersed repetitive-unit–variable-number tandem repeat (MIRU-VNTR) genotyping for 2290 Mycobacterium tuberculosis clinical isolates collected in the province of British Columbia (BC), Canada, in 2005–2014. Laboratory data for each isolate were linked to case-level clinical and demographic data. These data were used to describe the molecular epidemiology of tuberculosis across the province. Results We detected >1500 distinct genotypes across the 4 major M. tuberculosis lineages, reflecting BC’s diverse population. Disease site and clustering rates varied across lineages, and MIRU-VNTR was used to group the 2290 isolates into 189 clusters (2–70 isolates per cluster), with an overall clustering rate of 42.4% and an estimated local transmission rate of 34.1%. Risk factors for clustering varied between Canadian-born and foreign-born individuals; the former had increased odds (odds ratio, 7.8; 95% confidence interval [CI], 6.2–9.6) of belonging to a genotypic cluster, although nearly one-quarter of clusters included both Canadian- and foreign-born persons. Large clusters (≥10 cases) occurred more frequently within the M. tuberculosis Euro-American lineage, and individual-level risk factors associated with belonging to a large cluster included being Canadian born (adjusted odds ratio, 3.3; 95% CI, 2.3–4.8), residing in a rural area (2.3; 1.2–4.5), and illicit drug use (2.0; 1.2–3.4). Conclusions Although tuberculosis in BC largely arises through reactivation of latent tuberculosis in foreign-born persons, locally transmitted infections occur in discrete populations with distinct disease and risk factor profiles, representing groups for targeted interventions.
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Affiliation(s)
| | - Clare Kong
- British Columbia Centre for Disease Control Public Health Laboratory
| | - David Roth
- British Columbia Centre for Disease Control
| | | | - Mabel Rodrigues
- British Columbia Centre for Disease Control Public Health Laboratory
| | - Linda Hoang
- British Columbia Centre for Disease Control Public Health Laboratory.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Victoria Cook
- British Columbia Centre for Disease Control.,Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - James Johnston
- British Columbia Centre for Disease Control.,Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia.,British Columbia Centre for Disease Control
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11
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Mai TQ, Martinez E, Menon R, Van Anh NT, Hien NT, Marais BJ, Sintchenko V. Mycobacterium tuberculosis Drug Resistance and Transmission among Human Immunodeficiency Virus-Infected Patients in Ho Chi Minh City, Vietnam. Am J Trop Med Hyg 2019; 99:1397-1406. [PMID: 30382014 DOI: 10.4269/ajtmh.18-0185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Vietnam has a high burden of tuberculosis (TB) and multidrug-resistant (MDR) TB, but drug resistance patterns and TB transmission dynamics among TB/human immunodeficiency virus (HIV) coinfected patients are not well described. We characterized 200 Mycobacterium tuberculosis isolates from TB/HIV coinfected patients diagnosed at the main TB referral hospital in Ho Chi Minh City, Vietnam. Phenotypic drug susceptibility testing (DST) for first-line drugs, spoligotyping, and 24-locus mycobacterial interspersed repetitive unit (MIRU-24) analysis was performed on all isolates. The 24-locus mycobacterial interspersed repetitive unit clusters and MDR isolates were subjected to whole genome sequencing (WGS). Most of the TB/HIV coinfected patients were young (162/174; 93.1% aged < 45 years) males (173; 86.5% male). Beijing (98; 49.0%) and Indo-Oceanic (70; 35.0%) lineage strains were most common. Phenotypic drug resistance was detected in 84 (42.0%) isolates, of which 17 (8.5%) were MDR; three additional MDR strains were identified on WGS. Strain clustering was reduced from 84.0% with spoligotyping to 20.0% with MIRU-24 typing and to 13.5% with WGS. Whole genome sequencing identified five additional clusters, or members of clusters, not recognized by MIRU-24. In total, 13 small (two to three member) WGS clusters were identified, with less clustering among drug susceptible (2/27; 7.4%) than among drug-resistant strains (25/27; 92.6%). On phylogenetic analysis, strains from TB/HIV coinfected patients were interspersed among strains from the general community; no major clusters indicating transmission among people living with HIV were detected. Tuberculosis/HIV coinfection in Vietnam was associated with high rates of drug resistance and limited genomic evidence of ongoing M. tuberculosis transmission among HIV-infected patients.
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Affiliation(s)
- Trinh Quynh Mai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.,Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Centre for Infectious Disease and Microbiology-Public Health, ICPMR, Westmead Hospital, Sydney, Australia
| | - Elena Martinez
- Centre for Infectious Disease and Microbiology-Public Health, ICPMR, Westmead Hospital, Sydney, Australia.,Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Ranjeeta Menon
- Centre for Infectious Disease and Microbiology-Public Health, ICPMR, Westmead Hospital, Sydney, Australia.,Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | | | | | - Ben J Marais
- Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Vitali Sintchenko
- Centre for Infectious Disease and Microbiology-Public Health, ICPMR, Westmead Hospital, Sydney, Australia.,Sydney Medical School and Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
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12
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Lande L, Alexander DC, Wallace RJ, Kwait R, Iakhiaeva E, Williams M, Cameron ADS, Olshefsky S, Devon R, Vasireddy R, Peterson DD, Falkinham JO. Mycobacterium avium in Community and Household Water, Suburban Philadelphia, Pennsylvania, USA, 2010-2012. Emerg Infect Dis 2019; 25:473-481. [PMID: 30789130 PMCID: PMC6390762 DOI: 10.3201/eid2503.180336] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Attention to environmental sources of Mycobacterium avium complex (MAC) infection is a vital component of disease prevention and control. We investigated MAC colonization of household plumbing in suburban Philadelphia, Pennsylvania, USA. We used variable-number tandem-repeat genotyping and whole-genome sequencing with core genome single-nucleotide variant analysis to compare M. avium from household plumbing biofilms with M. avium isolates from patient respiratory specimens. M. avium was recovered from 30 (81.1%) of 37 households, including 19 (90.5%) of 21 M. avium patient households. For 11 (52.4%) of 21 patients with M. avium disease, isolates recovered from their respiratory and household samples were of the same genotype. Within the same community, 18 (85.7%) of 21 M. avium respiratory isolates genotypically matched household plumbing isolates. Six predominant genotypes were recovered across multiple households and respiratory specimens. M. avium colonizing municipal water and household plumbing may be a substantial source of MAC pulmonary infection.
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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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Bah SY, Morang'a CM, Kengne-Ouafo JA, Amenga-Etego L, Awandare GA. Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa. Front Genet 2018; 9:575. [PMID: 30538723 PMCID: PMC6277583 DOI: 10.3389/fgene.2018.00575] [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: 06/18/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023] Open
Abstract
Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.
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Affiliation(s)
- Saikou Y Bah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Vaccine and Immunity Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Collins Misita Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Jonas A Kengne-Ouafo
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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16
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Guthrie JL, Delli Pizzi A, Roth D, Kong C, Jorgensen D, Rodrigues M, Tang P, Cook VJ, Johnston J, Gardy JL. Genotyping and Whole-Genome Sequencing to Identify Tuberculosis Transmission to Pediatric Patients in British Columbia, Canada, 2005-2014. J Infect Dis 2018; 218:1155-1163. [PMID: 29757395 PMCID: PMC6107743 DOI: 10.1093/infdis/jiy278] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/08/2018] [Indexed: 12/21/2022] Open
Abstract
Background Tuberculosis (TB) in children is often an indicator of recent transmission. Genotyping and whole-genome sequencing (WGS) can enhance pediatric TB investigations by confirming or refuting transmission events. Methods Mycobacterium tuberculosis isolates from all pediatric patients <18 years with culture-confirmed TB in British Columbia (BC) from 2005 to 2014 (n = 49) were genotyped by Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeat (MIRU-VNTR) and compared with adult isolates. Genotypically clustered cases underwent WGS. Clinical, demographic, and contact data were reviewed for each case. Results Twenty-three children were Canadian-born, 7 to Canadian-born parents (CBP) and 16 to foreign-born parents (FBP). Of the 26 foreign-born children, all were born in Asia (81%) or Africa (19%). Using molecular and epidemiological data, we determined that 15 children had acquired their infection within BC, and household transmission explained all 7 Canadian-born (FBP) children that acquired TB locally. In contrast, 6 of 7 Canadian-born (CBP) children were exposed via a non-household community source. Eight Canadian-born (FBP) children acquired their infections through travel to their parents' place of birth. All but 1 of the foreign-born children acquired their infection outside of BC. Conclusions Genotyping and genomic data reveal that drivers of pediatric transmission vary according to a child's age, birthplace, and their parents' place of birth.
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Affiliation(s)
- Jennifer L Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Andy Delli Pizzi
- Public Health and Preventive Medicine Residency Program, Cumming School of Medicine, University of Calgary, Alberta
| | - David Roth
- British Columbia Centre for Disease Control, Vancouver, 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
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - 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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17
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Wyllie DH, Davidson JA, Grace Smith E, Rathod P, Crook DW, Peto TEA, Robinson E, Walker T, Campbell C. A Quantitative Evaluation of MIRU-VNTR Typing Against Whole-Genome Sequencing for Identifying Mycobacterium tuberculosis Transmission: A Prospective Observational Cohort Study. EBioMedicine 2018; 34:122-130. [PMID: 30077721 PMCID: PMC6116353 DOI: 10.1016/j.ebiom.2018.07.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 12/24/2022] Open
Abstract
Background Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing is widely used in high-income countries to determine Mycobacterium tuberculosis relatedness. Whole-genome sequencing (WGS) is known to deliver greater specificity, but no quantitative prospective comparison has yet been undertaken. Methods We studied isolates from the English Midlands, sampled consecutively between 1 January 2012 and 31 December 2015. In addition to routinely performed MIRU-VNTR typing, DNA was extracted from liquid cultures and sequenced using Illumina technology. Demographic and epidemiological data for the relevant patients were extracted from the Enhanced Tuberculosis Surveillance system run by Public Health England. Closely related samples, defined using a threshold of five single nucleotide variants (SNVs), were compared to samples with identical MIRU-VNTR profiles, to samples from individuals with shared epidemiological risk factors, and to those with both characteristics. Findings 1999 patients were identified for whom at least one M. tuberculosis isolate had been MIRU-VNTR typed and sequenced. Comparing epidemiological risk factors with close genetic relatedness, only co-residence had a positive predictive value of over 5%. Excluding co-resident individuals, 18.6% of patients with identical MIRU-VNTR profiles were within 5 SNVs. Where patients also shared social risk factors and ethnic group, this rose to 48%. Only 8% of MIRU-VNTR linked pairs in lineage 1 were within 5 SNV, compared to 31% in lineage 4. Interpretation In the setting studied, this molecular epidemiological study shows MIRU-VNTR typing and epidemiological risk factors are poorly predictive of close genomic relatedness, assessed by SNV. MIRU-VNTR performance varies markedly by lineage. Funding Public Health England, Health Innovation Challenge Fund, NIHR Health Protection Research Unit Oxford, NIHR Oxford Biomedical Research Centre. M. tuberculosis relatedness was measured by MIRU-VNTR typing and single nucleotide variants (SNV). In consecutive isolates in England, only 20% of samples with identical MIRU-VNTR profiles were within 5 SNVs. MIRU-VNTR is more predictive of close relatedness in lineage 4 (Euro-American) lineages than in other lineages.
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Affiliation(s)
- David H Wyllie
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; Public Health England Academic Collaborating Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK.
| | - Jennifer A Davidson
- Tuberculosis Section, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - E Grace Smith
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham BS9 5SS
| | - Priti Rathod
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham BS9 5SS
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; The National Institute for Health Research, Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK
| | - Esther Robinson
- Public Health England National Regional Mycobacteriology Laboratory North and Midlands, Heartlands Hospital, Birmingham BS9 5SS
| | - Tim Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Colin Campbell
- Tuberculosis Section, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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18
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Guthrie JL, Alexander DC, Marchand-Austin A, Lam K, Whelan M, Lee B, Furness C, Rea E, Stuart R, Lechner J, Varia M, McLean J, Jamieson FB. Technology and tuberculosis control: the OUT-TB Web experience. J Am Med Inform Assoc 2018; 24:e136-e142. [PMID: 27589943 DOI: 10.1093/jamia/ocw130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/02/2016] [Indexed: 11/12/2022] Open
Abstract
Objective Develop a tool to disseminate integrated laboratory, clinical, and demographic case data necessary for improved contact tracing and outbreak detection of tuberculosis (TB). Methods In 2007, the Public Health Ontario Laboratories implemented a universal genotyping program to monitor the spread of TB strains within Ontario. Ontario Universal Typing of TB (OUT-TB) Web utilizes geographic information system (GIS) technology with a relational database platform, allowing TB control staff to visualize genotyping matches and microbiological data within the context of relevant epidemiological and demographic data. Results OUT-TB Web is currently available to the 8 health units responsible for >85% of Ontario's TB cases and is a valuable tool for TB case investigation. Users identified key features to implement for application enhancements, including an e-mail alert function, customizable heat maps for visualizing TB and drug-resistant cases, socioeconomic map layers, a dashboard providing TB surveillance metrics, and a feature for animating the geographic spread of strains over time. Conclusion OUT-TB Web has proven to be an award-winning application and a useful tool. Developed and enhanced using regular user feedback, future versions will include additional data sources, enhanced map and line-list filter capabilities, and development of a mobile app.
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Affiliation(s)
| | - David C Alexander
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | | | - Karen Lam
- Public Health Ontario, Toronto, Ontario, Canada
| | | | - Brenda Lee
- Public Health Ontario, Toronto, Ontario, Canada
| | - Colin Furness
- Faculty of Information, University of Toronto, Toronto, Ontario, Canada.,Institute for Health Policy, Management, and Evaluation, University of Toronto
| | - Elizabeth Rea
- Toronto Public Health, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto
| | | | | | - Monali Varia
- Peel Public Health, Mississauga, Ontario, Canada
| | | | - Frances B Jamieson
- Public Health Ontario, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto
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19
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Tagini F, Greub G. Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review. Eur J Clin Microbiol Infect Dis 2017; 36:2007-2020. [PMID: 28639162 PMCID: PMC5653721 DOI: 10.1007/s10096-017-3024-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022]
Abstract
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
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Affiliation(s)
- F Tagini
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland
| | - G Greub
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland.
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20
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Wan X, Koster K, Qian L, Desmond E, Brostrom R, Hou S, Douglas JT. Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis. PLoS One 2017; 12:e0175330. [PMID: 28394899 PMCID: PMC5386241 DOI: 10.1371/journal.pone.0175330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/25/2017] [Indexed: 02/05/2023] Open
Abstract
With its airborne transmission and prolonged latency period, Mycobacterium tuberculosis spreads worldwide as one of the most successful bacterial pathogens and continues to kill millions of people every year. M. tuberculosis lineage 1 is inferred to originate ancestrally based on the presence of the 52-bp TbD1 sequence and analysis of single nucleotide polymorphisms. Previously, we briefly reported the complete genome sequencing of M. tuberculosis strains 96121 and 96075, which belong to the ancient Manila family and modern Beijing family respectively. Here we present the comprehensive genomic analyses of the Manila family in lineage 1 compared to complete genomes in lineages 2-4. Principal component analysis of the presence and absence of CRISPR spacers suggests that Manila isolate 96121 is distinctly distant from lineages 2-4. We further identify a truncated whiB5 gene and a putative operon consisting of genes encoding a putative serine/threonine kinase PknH and a putative ABC transporter, which are only found in the genomes of Manila family isolates. Six single nucleotide polymorphisms are uniquely conserved in 38 Manila strains. Moreover, when compared to M. tuberculosis H37Rv, 59 proteins are under positive selection in Manila family isolate 96121 but not in Beijing family isolate 96075. The unique features further serve as biomarkers for Manila strains and may shed light on the limited transmission of this ancestral lineage outside of its Filipino host population.
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Affiliation(s)
- Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Kent Koster
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Lishi Qian
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Edward Desmond
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Richard Brostrom
- TB Control Program, Hawaii State Department of Health, Honolulu, Hawaii, United States of America
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, United States of America
| | - James T. Douglas
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, United States of America
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21
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Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Ann N Y Acad Sci 2016; 1388:59-77. [PMID: 28009051 DOI: 10.1111/nyas.13273] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
Abstract
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission.
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Affiliation(s)
- Jennifer L Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.,Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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22
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Stucki D, Brites D, Jeljeli L, Coscolla M, Liu Q, Trauner A, Fenner L, Rutaihwa L, Borrell S, Luo T, Gao Q, Kato-Maeda M, Ballif M, Egger M, Macedo R, Mardassi H, Moreno M, Tudo Vilanova G, Fyfe J, Globan M, Thomas J, Jamieson F, Guthrie JL, Asante-Poku A, Yeboah-Manu D, Wampande E, Ssengooba W, Joloba M, Henry Boom W, Basu I, Bower J, Saraiva M, Vaconcellos SEG, Suffys P, Koch A, Wilkinson R, Gail-Bekker L, Malla B, Ley SD, Beck HP, de Jong BC, Toit K, Sanchez-Padilla E, Bonnet M, Gil-Brusola A, Frank M, Penlap Beng VN, Eisenach K, Alani I, Wangui Ndung'u P, Revathi G, Gehre F, Akter S, Ntoumi F, Stewart-Isherwood L, Ntinginya NE, Rachow A, Hoelscher M, Cirillo DM, Skenders G, Hoffner S, Bakonyte D, Stakenas P, Diel R, Crudu V, Moldovan O, Al-Hajoj S, Otero L, Barletta F, Jane Carter E, Diero L, Supply P, Comas I, Niemann S, Gagneux S. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat Genet 2016; 48:1535-1543. [PMID: 27798628 PMCID: PMC5238942 DOI: 10.1038/ng.3704] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/27/2016] [Indexed: 12/30/2022]
Abstract
Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.
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Affiliation(s)
- David Stucki
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Leïla Jeljeli
- Forschungszentrum Borstel, Germany.,Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Mireia Coscolla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Qingyun Liu
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Lukas Fenner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Liliana Rutaihwa
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Tao Luo
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qian Gao
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | | | - Marie Ballif
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Matthias Egger
- Institute for Social and Preventive Medicine, University of Bern, Switzerland
| | - Rita Macedo
- Laboratòrio de Saùde Publica, Lisbon, Portugal
| | - Helmi Mardassi
- Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | | | | | - Janet Fyfe
- Victorian Infectious Diseases Reference Laboratory, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory, Victoria, Australia
| | | | | | | | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Eddie Wampande
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Willy Ssengooba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda.,Department of Global Health, University of Amsterdam, Amsterdam, the Netherlands
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - W Henry Boom
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, USA
| | - Indira Basu
- LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - James Bower
- LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Margarida Saraiva
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | | | | | - Anastasia Koch
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa
| | - Robert Wilkinson
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa.,Department of Medicine, Imperial College London, UK.,The Francis Crick Institute Mill Hill Laboratory, London, UK
| | - Linda Gail-Bekker
- Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town, South Africa
| | - Bijaya Malla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | - Serej D Ley
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland.,Papua New Guinea Institute of Medical Research, Goroka, PNG
| | - Hans-Peter Beck
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
| | | | - Kadri Toit
- Tartu University Hospital United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | | | - Ana Gil-Brusola
- Department of Microbiology, University Hospital La Fe, Valencia, Spain
| | - Matthias Frank
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Veronique N Penlap Beng
- Institute Laboratory for Tuberculosis Research (LTR), Biotechnology Center (BTC), University of Yaoundé I, Yaoundé, Cameroon
| | - Kathleen Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Issam Alani
- Department of Medical Laboratory Technology, Faculty of Medical Technology, Baghdad, Iraq
| | - Perpetual Wangui Ndung'u
- Institute of Tropical Medicine and Infectious Diseases (ITROMID), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Gunturu Revathi
- Department of Pathology, Aga Khan University Hospital (AKUH), Nairobi, Kenya
| | - Florian Gehre
- Insitute of Tropical Medicine, Antwerp, Belgium.,Medical Research Council, Fajara, the Gambia
| | | | - Francine Ntoumi
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany.,Fondation Congolaise pour la Recherche Médicale, Université Marien Gouabi, Brazzaville, Congo
| | - Lynsey Stewart-Isherwood
- Right to Care and the Clinical HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Nyanda E Ntinginya
- National Institute of Medical Research, Mbeya Medical Research Centre (NIMR-MMRC), Mbeya, Tanzania
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), partner site Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany; German Centre for Infection Research (DZIF), partner site Munich, Germany
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Girts Skenders
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Riga, Latvia
| | - Sven Hoffner
- WHO Supranational TB Reference Laboratory, Department of Microbiology, The Public Health Agency of Sweden, Solna, Sweden
| | - Daiva Bakonyte
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Petras Stakenas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Valeriu Crudu
- National Tuberculosis Reference Laboratory, Phthysiopneumology Institute, Chisinau, Republic of Moldova
| | - Olga Moldovan
- 'Marius Nasta' Pneumophtisiology Institute, Bucharest, Romania
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Larissa Otero
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Francesca Barletta
- Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit-Tuberculosis, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - E Jane Carter
- Alpert School of Medicine at Brown University, Providence, Rhode Island, USA.,Moi University School of Medicine, Eldoret, Kenya
| | - Lameck Diero
- Moi University School of Medicine, Eldoret, Kenya
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000 Lille, France
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), 46010, Valencia, Spain.,CIBER Epidemiology and Public Health, Madrid, Spain
| | - Stefan Niemann
- Forschungszentrum Borstel, Germany.,German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Switzerland
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23
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Lee RS, Behr MA. The implications of whole-genome sequencing in the control of tuberculosis. Ther Adv Infect Dis 2015; 3:47-62. [PMID: 27034776 DOI: 10.1177/2049936115624630] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The availability of whole-genome sequencing (WGS) as a tool for the diagnosis and clinical management of tuberculosis (TB) offers considerable promise in the fight against this stubborn epidemic. However, like other new technologies, the best application of WGS remains to be determined, for both conceptual and technical reasons. In this review, we consider the potential value of WGS in the clinical laboratory for the detection of Mycobacterium tuberculosis and the prediction of antibiotic resistance. We also discuss issues pertaining to data generation, interpretation and dissemination, given that WGS has to date been generally performed in research labs where results are not necessarily packaged in a clinician-friendly format. Although WGS is far more accessible now than it was in the past, the transition from a research tool to study TB into a clinical test to manage this disease may require further fine-tuning. Improvements will likely come through iterative efforts that involve both the laboratories ready to move TB into the genomic era and the front-line clinical/public health staff who will be interpreting the results to inform management decisions.
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Affiliation(s)
- Robyn S Lee
- McGill University, Department of Epidemiology, Biostatistics and Occupational Health, The Research Institute of the McGill University Health Centre and McGill International TB Centre, Montreal, QC, Canada
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24
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Abstract
The phenotypic methods of smear microscopy, culture and indirect drug susceptibility testing (DST) remain the 'gold standard' diagnostics for tuberculosis (TB) in 2015. However, this review demonstrates that genotypic methods are in the ascendancy. Current-generation nucleic acid amplification tests (NAATs) are important supplementary tests for the rapid direct detection of (multidrug-resistant) TB in specific clinical settings. Genotypic detection is already the preferred method of detecting rifampicin and pyrazinamide resistance. Next-generation NAATs able to detect about 10 colony forming units/mL of sputum could replace culture as the initial test for detecting TB. Whole genome sequencing could also plausibly replace phenotypic DST but much work is required in method standardisation, database development and elucidation of all resistance gene determinants. The challenge then will be to rollout these increasingly complex and expensive diagnostics in the low-income countries where TB is prevalent.
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25
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Takiff HE, Feo O. Clinical value of whole-genome sequencing of Mycobacterium tuberculosis. THE LANCET. INFECTIOUS DISEASES 2015; 15:1077-1090. [PMID: 26277037 DOI: 10.1016/s1473-3099(15)00071-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/27/2015] [Accepted: 05/20/2015] [Indexed: 01/25/2023]
Abstract
Whole-genome sequencing (WGS) is now common as a result of new technologies that can rapidly sequence a complete bacterial genome for US$500 or less. Many studies have addressed questions about tuberculosis with WGS, and knowing the sequence of the entire genome, rather than only a few fragments, has greatly increased the precision of molecular epidemiology and contact tracing. Additionally, topics such as the mutation rate, drug resistance, the target of new drugs, and the phylogeny and evolution of the Mycobacterium tuberculosis complex bacteria have been elucidated by WGS. Nonetheless, WGS has not explained differences in transmissibility between strains, or why some strains are more virulent than others or more prone to development of multidrug resistance. With advances in technology, WGS of clinical specimens could become routine in high-income countries; however, its relevance will probably depend on easy to use software to efficiently process the sequences produced and accessible genomic databases that can be mined in future studies.
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Affiliation(s)
- Howard E Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas, Venezuela; Unité de Génétique Mycobactérienne, Insitut Pasteur, Paris, France.
| | - Oscar Feo
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas, Venezuela
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26
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A microbiological revolution meets an ancient disease: improving the management of tuberculosis with genomics. Clin Microbiol Rev 2015; 28:523-39. [PMID: 25810419 DOI: 10.1128/cmr.00124-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis (TB) is an ancient disease with an enormous global impact. Despite declining global incidence, the diagnosis, phenotyping, and epidemiological investigation of TB require significant clinical microbiology laboratory resources. Current methods for the detection and characterization of Mycobacterium tuberculosis consist of a series of laboratory tests varying in speed and performance, each of which yields incremental information about the disease. Since the sequencing of the first M. tuberculosis genome in 1998, genomic tools have aided in the diagnosis, treatment, and control of TB. Here we summarize genomics-based methods that are positioned to be introduced in the modern clinical TB laboratory, and we highlight how recent advances in genomics will improve the detection of antibiotic resistance-conferring mutations and the understanding of M. tuberculosis transmission dynamics and epidemiology. We imagine the future TB clinic as one that relies heavily on genomic interrogation of the M. tuberculosis isolate, allowing for more rapid diagnosis of TB and real-time monitoring of outbreak emergence.
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