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Zhang H, Liu M, Fan W, Sun S, Fan X. The impact of Mycobacterium tuberculosis complex in the environment on one health approach. Front Public Health 2022; 10:994745. [PMID: 36159313 PMCID: PMC9489838 DOI: 10.3389/fpubh.2022.994745] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/18/2022] [Indexed: 01/26/2023] Open
Abstract
Tuberculosis caused by the Mycobacterium tuberculosis complex (MTBC) has become one of the leading causes of death in humans and animals. Current research suggests that the transmission of MTBC in the environment indirectly transmit to humans and animals with subsequent impact on their wellbeing. Therefore, it is of great significance to take One Health approach for understanding the role of MTBC in not only the interfaces of humans and animals, but also environment, including soil, water, pasture, air, and dust, etc., in response to the MTBC infection. In this review, we present the evidence of MTBC transmission from environment, as well as detection and control strategies in this interface, seeking to provide academic leads for the global goal of End Tuberculosis Strategy under multidisciplinary and multisectoral collaborations.
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Comín J, Madacki J, Rabanaque I, Zúñiga-Antón M, Ibarz D, Cebollada A, Viñuelas J, Torres L, Sahagún J, Klopp C, Gonzalo-Asensio J, Brosch R, Iglesias MJ, Samper S. The MtZ Strain: Molecular Characteristics and Outbreak Investigation of the Most Successful Mycobacterium tuberculosis Strain in Aragon Using Whole-Genome Sequencing. Front Cell Infect Microbiol 2022; 12:887134. [PMID: 35685752 PMCID: PMC9173592 DOI: 10.3389/fcimb.2022.887134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Since 2004, a tuberculosis surveillance protocol has been carried out in Aragon, thereby managing to detect all tuberculosis outbreaks that take place in the community. The largest outbreak was caused by a strain named Mycobacterium tuberculosis Zaragoza (MtZ), causing 242 cases as of 2020. The main objective of this work was to analyze this outbreak and the molecular characteristics of this successful strain that could be related to its greater transmission. To do this, we first applied whole-genome sequencing to 57 of the isolates. This revealed two principal transmission clusters and six subclusters arising from them. The MtZ strain belongs to L4.8 and had eight specific single nucleotide polymorphisms (SNPs) in genes considered to be virulence factors [ptpA, mc3D, mc3F, VapB41, pks15 (two SNPs), virS, and VapC50]. Second, a transcriptomic study was carried out to better understand the multiple IS6110 copies present in its genome. This allowed us to observe three effects of IS6110: the disruption of the gene in which the IS6110 is inserted (desA3), the overexpression of a gene (ppe38), and the absence of transcription of genes (cut1:Rv1765c) due to the recombination of two IS6110 copies. Finally, because of the disruption of ppe38 and ppe71 genes by an IS6110, a study of PE_PGRS secretion was carried out, showing that MtZ secretes these factors in higher amounts than the reference strain, thereby differing from the hypervirulent phenotype described for the Beijing strains. In conclusion, MtZ consists of several SNPs in genes related to virulence, pathogenesis, and survival, as well as other genomic polymorphisms, which may be implicated in its success among our population.
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Affiliation(s)
- Jessica Comín
- Grupo de Genética de Micobacterias, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | - Jan Madacki
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, Université de Paris, CNRS UMR 3525, Paris, France
| | - Isabel Rabanaque
- Departamento de Geografía y Ordenación del Territorio, Universidad de Zaragoza, Zaragoza, Spain.,Instituto Universitario de Investigación en Ciencias Ambientales de Aragón, Zaragoza, Spain.,Fundación Instituto de Investigación Sanitaria (IIS) Aragón, Zaragoza, Spain
| | - María Zúñiga-Antón
- Departamento de Geografía y Ordenación del Territorio, Universidad de Zaragoza, Zaragoza, Spain.,Instituto Universitario de Investigación en Ciencias Ambientales de Aragón, Zaragoza, Spain.,Fundación Instituto de Investigación Sanitaria (IIS) Aragón, Zaragoza, Spain
| | - Daniel Ibarz
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Alberto Cebollada
- Unidad de Biocomputación, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | - Jesús Viñuelas
- Hospital Universitario Miguel Servet, Zaragoza, Spain.,Grupo de Estudio de Infecciones por Micobacterias (GEIM), Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, Madrid, Spain
| | | | - Juan Sahagún
- Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | | | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, Université de Paris, CNRS UMR 3525, Paris, France
| | - María-José Iglesias
- Fundación Instituto de Investigación Sanitaria (IIS) Aragón, Zaragoza, Spain.,Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias, Madrid, Spain
| | - Sofía Samper
- Grupo de Genética de Micobacterias, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain.,Fundación Instituto de Investigación Sanitaria (IIS) Aragón, Zaragoza, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias, Madrid, Spain
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Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review. Pathogens 2022; 11:pathogens11020252. [PMID: 35215195 PMCID: PMC8875843 DOI: 10.3390/pathogens11020252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.
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4
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Perez-Sepulveda BM, Heavens D, Pulford CV, Predeus AV, Low R, Webster H, Dykes GF, Schudoma C, Rowe W, Lipscombe J, Watkins C, Kumwenda B, Shearer N, Costigan K, Baker KS, Feasey NA, Hinton JCD, Hall N. An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes. Genome Biol 2021; 22:349. [PMID: 34930397 PMCID: PMC8690886 DOI: 10.1186/s13059-021-02536-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium. Following the optimization of a logistics pipeline that involved shipping isolates as thermolysates in ambient conditions, the project assembled a diverse collection of 10,419 isolates from low- and middle-income countries. The genomes were sequenced using the LITE pipeline for library construction, with a total reagent cost of less than USD$10 per genome. Our method can be applied to other large bacterial collections to underpin global collaborations.
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Affiliation(s)
| | | | - Caisey V. Pulford
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alexander V. Predeus
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Ross Low
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Hermione Webster
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Gregory F. Dykes
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - Will Rowe
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
- University of Birmingham, Birmingham, UK
| | | | - Chris Watkins
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Neil Shearer
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Karl Costigan
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kate S. Baker
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Nicholas A. Feasey
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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5
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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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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. THE LANCET. MICROBE 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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Comín J, Cebollada A, Ibarz D, Viñuelas J, Vitoria MA, Iglesias MJ, Samper S. A whole-genome sequencing study of an X-family tuberculosis outbreak focus on transmission chain along 25 years. Tuberculosis (Edinb) 2020; 126:102022. [PMID: 33341027 DOI: 10.1016/j.tube.2020.102022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 01/31/2023]
Abstract
Lineage 4/X-family of Mycobacterium tuberculosis is not very notorious, except for the CDC1551 strain. One strain of this family, named Ara50, caused one of the largest tuberculosis outbreaks of the Aragon region, Spain, during the 1990s and remained until 2018. These X-strains are characterised by high transmissibility and by carrying a low copy number of IS6110 in their genomes. Epidemiological data of the 61 patients consisted of inmates, HIV seropositives, intravenous drug users and the homeless. The application of whole-genome sequencing (WGS) to 36 out of 61 isolates, selected by IS6110-RFLP, allowed to confirm 32 as recent transmissions. We found 10 SNPs in genes considered as virulence factors, five of them specific of this strain. WGS identified three sub-clusters (CLSs). The largest one, sub-CLS 1, included 10 cases. Seven of them shared a SNP in the mce3C gene, considered a virulence factor gene. Sub-CLS 2 involved familiar cases, and no link was known for sub-CLS 3. Finally, the strain showed efficacy in latency as a confirmed epidemiological link was established between two cases, with 6 years of distance in their diagnosis. This outbreak study combined epidemiological and molecular analyses in order to elucidate tuberculosis transmission.
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Affiliation(s)
- Jessica Comín
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, C/de San Juan Bosco, 13, 50009, Zaragoza, Spain.
| | - Alberto Cebollada
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, C/de San Juan Bosco, 13, 50009, Zaragoza, Spain.
| | - Daniel Ibarz
- Universidad de Zaragoza, C/Domingo Miral S/N, 50009, Zaragoza, Spain.
| | - Jesús Viñuelas
- Hospital Universitario Miguel Servet, Paseo Isabel la Católica, 1-3, 50009, Zaragoza, Spain; Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, C/Agustín de Bentacourt, No 13, 28003, Madrid, Spain; Fundación IIS Aragón, C/de San Juan Bosco, 13, 50009, Zaragoza, Spain.
| | - María Asunción Vitoria
- Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, C/Agustín de Bentacourt, No 13, 28003, Madrid, Spain; Hospital Clínico Universitario Lozano Blesa, Avda. San Juan Bosco, 15, 50009, Zaragoza, Spain.
| | - María José Iglesias
- Universidad de Zaragoza, C/Domingo Miral S/N, 50009, Zaragoza, Spain; Fundación IIS Aragón, C/de San Juan Bosco, 13, 50009, Zaragoza, Spain; CIBER de Enfermedades Respiratorias, Av. Monforte de Lemos, 3-5. Pabellón 11, Planta 0, 28029, Madrid, Spain.
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, C/de San Juan Bosco, 13, 50009, Zaragoza, Spain; Fundación IIS Aragón, C/de San Juan Bosco, 13, 50009, Zaragoza, Spain; CIBER de Enfermedades Respiratorias, Av. Monforte de Lemos, 3-5. Pabellón 11, Planta 0, 28029, Madrid, Spain.
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Refrégier G, Sola C, Guyeux C. Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis. BMC Genomics 2020; 21:841. [PMID: 33256602 PMCID: PMC7708916 DOI: 10.1186/s12864-020-07178-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 10/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (H37Rv and BCG), it gave a biased idea of CRISPR diversity and ignored diversity in the neighbouring cas-genes. RESULTS We set up tailored pipelines to explore the diversity of CRISPR-cas locus in Short Reads. We analyzed data from a representative set of 198 clinical isolates as evidenced by well-characterized SNPs. We found a relatively low diversity in terms of spacers: we recovered only the 68 spacers that had been described in 2000. We found no partial or global inversions in the sequences, letting always the Direct Variant Repeats (DVR) in the same order. In contrast, we found an unexpected diversity in the form of: SNPs in spacers and in Direct Repeats, duplications of various length, and insertions at various locations of the IS6110 insertion sequence, as well as blocks of DVR deletions. The diversity was in part specific to lineages. When reconstructing evolutionary steps of the locus, we found no evidence for SNP reversal. DVR deletions were linked to recombination between IS6110 insertions or between Direct Repeats. CONCLUSION This work definitively shows that CRISPR locus of M. tuberculosis did not evolve by classical CRISPR adaptation (incorporation of new spacers) since the last most recent common ancestor of virulent lineages. The evolutionary mechanisms that we discovered could be involved in bacterial adaptation but in a way that remains to be identified.
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Affiliation(s)
- Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, cedex, 91198, Gif-sur-Yvette, France.
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, cedex, 91198, Gif-sur-Yvette, France.
| | - Christophe Guyeux
- FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
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Maung HMW, Palittapongarnpim P, Aung HL, Surachat K, Nyunt WW, Chongsuvivatwong V. Geno-Spatial Distribution of Mycobacterium Tuberculosis and Drug Resistance Profiles in Myanmar-Thai Border Area. Trop Med Infect Dis 2020; 5:E153. [PMID: 33007895 PMCID: PMC7709706 DOI: 10.3390/tropicalmed5040153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022] Open
Abstract
Worldwide, studies investigating the relationship between the lineage of Mycobacterium tuberculosis (MTB) across geographic areas has empowered the "End TB" program and understand transmission across national boundaries. Genomic diversity of MTB varies with geographical locations and ethnicity. Genomic diversity can also affect the emergence of drug resistance. In Myanmar, we still have limited genetic information about geographical, ethnicity, and drug resistance linkage to MTB genetic information. This study aimed to describe the geno-spatial distribution of MTB and drug resistance profiles in Myanmar-Thailand border areas. A cross-sectional study was conducted with a total of 109 sequenced isolates. The lineages of MTB and the potential associated socio-demographic, geographic and clinical factors were analyzed using Fisher's exact tests. p value of statistically significance was set at < 0.05. We found that 67% of the isolates were lineage 1 (L1)/East-African-Indian (EAI) (n = 73), followed by lineage 2 (L2)/Beijing (n = 26), lineage 4 (L4)/European American (n = 6) and lineage 3 (L3)/Delhi/Central Asian (n = 4). "Gender", "type of TB patient", "sputum smear grading" and "streptomycin resistance" were significantly different with the lineages of MTB. Sublineages of L1, which had never been reported elsewhere in Myanmar, were detected in this study area. Moreover, both ethnicity and lineage of MTB significantly differed in distribution by patient location. Diversity of the lineage of MTB and detection of new sublineages suggested that this small area had been resided by a heterogeneous population group who actively transmitted the disease. This information on distribution of lineage of MTB can be linked in the future with those on the other side of the border to evaluate cross-border transmission.
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Affiliation(s)
- Htet Myat Win Maung
- National TB Programme, Department of Public Health, Ministry of Health and Sports, Naypyitaw 15011, Myanmar;
- Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Htin Lin Aung
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
| | - Komwit Surachat
- Information and Communication Technology Programme, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand;
| | - Wint Wint Nyunt
- National TB Reference Laboratory, National TB Programme, Department of Public Health, Yangon 11011, Myanmar;
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An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data. INFECTION GENETICS AND EVOLUTION 2020; 79:104152. [DOI: 10.1016/j.meegid.2019.104152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/15/2019] [Accepted: 12/20/2019] [Indexed: 11/19/2022]
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11
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Folkvardsen DB, Norman A, Rasmussen EM, Lillebaek T, Jelsbak L, Andersen ÅB. Recurrent tuberculosis in patients infected with the predominant Mycobacterium tuberculosis outbreak strain in Denmark. New insights gained through whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2020; 80:104169. [PMID: 31918042 DOI: 10.1016/j.meegid.2020.104169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/20/2019] [Accepted: 01/01/2020] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Recurrent tuberculosis (TB) is defined by more than one TB episode per patient and is caused by reinfection with a new M. tuberculosis (Mtb) strain or relapse with the previous strain. In Denmark, a major TB outbreak caused by one specific Mtb genotype "DKC2" is ongoing. Of the 892 patients infected with DKC2 between 1992 and 2014, 32 had recurrent TB with 67 TB episodes in total. METHODS The 32 cases were evaluated in terms of number of single-nucleotide polymorphism (SNP) differences and time between episodes derived from whole-genome sequencing data. RESULTS For four TB cases, the subsequent episodes could be confirmed as relapse and for one case as reinfection. Eight cases with SNP differences <6, theoretically indicating relapse, could be classified as likely reinfections based on phylogenetic analysis in combination with geographical data. Subsequent TB episodes for the remaining 19 cases could not be classified as relapse or reinfection even though they all had a SNP difference of <6 SNPs. CONCLUSIONS In newer studies, investigating recurrent TB with the use of WGS, the number of SNPs has been used to distinguish between relapse and reinfection. The algorithm proposed for this is not valid in the Danish TB outbreak setting as our findings challenge the interpretation of few SNP differences as representing relapse. However, when including phylogenetic analysis and geographical data in the analysis, classification of 13 of the 32 cases were possible.
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Affiliation(s)
- Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Denmark.
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | | | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Åse Bengård Andersen
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Denmark; Research Unit for Infectious Diseases, Department of Clinical Research, University of Southern Denmark, Denmark
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van der Werf MJ, Ködmön C. Whole-Genome Sequencing as Tool for Investigating International Tuberculosis Outbreaks: A Systematic Review. Front Public Health 2019; 7:87. [PMID: 31058125 PMCID: PMC6478655 DOI: 10.3389/fpubh.2019.00087] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022] Open
Abstract
Background: Whole-genome sequencing (WGS) can support the investigation of tuberculosis (TB) outbreaks. The technique has been applied to estimate the timing and directionality of transmission and to exclude cases from an investigation. This review assesses how WGS was applied in international outbreak investigations and discusses the advantages and challenges of the application of WGS. Methods: Databases were searched for reports on international TB outbreak investigations. Information was extracted on: Why was WGS applied?; How was WGS applied?; Organizational issues; WGS methodology; What was learned/what were the implications of the WGS investigation?; and challenges and lessons learned. Results: Three studies reporting on international outbreak investigations were identified. Retrospective WGS sequencing was performed in all studies and prospective typing in two to study TB transmission. In one study, WGS data were produced centrally (i.e., in one laboratory) and analysis was done centrally. In two studies, WGS data production was done in a decentralized manner, and analysis was centralized in one laboratory. Three groups of professionals were involved in the international outbreak investigation: public health authorities, laboratory experts, and clinicians. The reported WGS methodology applied differed between the studies in some aspects, e.g., sequencing platform; quality measures, percentage of the reference genome covered, and the mean genomic coverage; analysis, use of a reference genome or de novo assembly; and software used for alignment and analysis. In all three studies, in-house scripts were used for variance calling, and the single nucleotide polymorphism (SNP) approach was used for analysis. All outbreak investigation reports stated that WGS refuted suspected transmission events and provided supporting evidence for epidemiological data. Several challenges were reported of which most were not related to WGS. The only challenge related to WGS was the timeframe of getting WGS data if WGS is not routinely performed. Conclusions: WGS was considered a useful addition in international TB outbreak investigations. Further standardization of the WGS methodology and good structures for international collaboration and coordination are needed to take full advantage of this new technology. Whether the use of WGS results in earlier detection of cases and thus limits transmission still needs to be determined.
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Affiliation(s)
| | - Csaba Ködmön
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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13
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Nikolayevskyy V, Niemann S, Anthony R, van Soolingen D, Tagliani E, Ködmön C, van der Werf MJ, Cirillo DM. Role and value of whole genome sequencing in studying tuberculosis transmission. Clin Microbiol Infect 2019; 25:1377-1382. [PMID: 30980928 DOI: 10.1016/j.cmi.2019.03.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. OBJECTIVES To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission. SOURCES A total of 69 peer-reviewed publications identified in Pubmed database. CONTENT Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles. IMPLICATIONS WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached.
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Affiliation(s)
- V Nikolayevskyy
- Public Health England, London, UK; Imperial College, London, UK.
| | - S Niemann
- Molecular and Experimental Mycobacteriology, National Reference Centre for Mycobacteria, Research Centre, Borstel, Germany; German Centre for Infection Research, Borstel site, Germany
| | - R Anthony
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D van Soolingen
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - E Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - C Ködmön
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - M J van der Werf
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - D M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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14
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Koster KJ, Largen A, Foster JT, Drees KP, Qian L, Desmond E, Wan X, Hou S, Douglas JT. Genomic sequencing is required for identification of tuberculosis transmission in Hawaii. BMC Infect Dis 2018; 18:608. [PMID: 30509214 PMCID: PMC6276198 DOI: 10.1186/s12879-018-3502-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background Tuberculosis (TB) caused an estimated 1.4 million deaths and 10.4 million new cases globally in 2015. TB rates in the United States continue to steadily decline, yet rates in the State of Hawaii are perennially among the highest in the nation due to a continuous influx of immigrants from the Western Pacific and Asia. TB in Hawaii is composed of a unique distribution of genetic lineages, with the Beijing and Manila families of Mycobacterium tuberculosis (Mtb) comprising over two-thirds of TB cases. Standard fingerprinting methods (spoligotyping plus 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats [MIRU-VNTR] fingerprinting) perform poorly when used to identify actual transmission clusters composed of isolates from these two families. Those typing methods typically group isolates from these families into large clusters of non-linked isolates with identical fingerprints. Next-generation whole-genome sequencing (WGS) provides a new tool for molecular epidemiology that can resolve clusters of isolates with identical spoligotyping and MIRU-VNTR fingerprints. Methods We performed WGS and SNP analysis and evaluated epidemiological data to investigate 19 apparent TB transmission clusters in Hawaii from 2003 to 2017 in order to assess WGS’ ability to resolve putative Mtb clusters from the Beijing and Manila families. This project additionally investigated MIRU-VNTR allele prevalence to determine why standard Mtb fingerprinting fails to usefully distinguish actual transmission clusters from these two Mtb families. Results WGS excluded transmission events in seven of these putative clusters, confirmed transmission in eight, and identified both transmission-linked and non-linked isolates in four. For epidemiologically identified clusters, while the sensitivity of MIRU-VNTR fingerprinting for identifying actual transmission clusters was found to be 100%, its specificity was only 28.6% relative to WGS. We identified that the Beijing and Manila families’ significantly lower Shannon evenness of MIRU-VNTR allele distributions than lineage 4 was the cause of standard fingerprinting’s poor performance when identifying transmission in Beijing and Manila family clusters. Conclusions This study demonstrated that WGS is necessary for epidemiological investigation of TB in Hawaii and the Pacific. Electronic supplementary material The online version of this article (10.1186/s12879-018-3502-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Angela Largen
- Hawaii State Department of Health, Honolulu, HI, USA
| | - Jeffrey T Foster
- University of New Hampshire, Durham, NH, USA.,Present Address: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Lishi Qian
- University of Hawaii at Manoa, Honolulu, HI, USA
| | - Ed Desmond
- California Department of Public Health, Richmond, CA, USA
| | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, HI, USA
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, Honolulu, HI, USA
| | - James T Douglas
- University of Hawaii at Manoa, Honolulu, HI, USA. .,Present Address: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
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15
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Genetic profiling of Mycobacterium bovis strains from slaughtered cattle in Eritrea. PLoS Negl Trop Dis 2018; 12:e0006406. [PMID: 29664901 PMCID: PMC5922621 DOI: 10.1371/journal.pntd.0006406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 04/27/2018] [Accepted: 03/23/2018] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium bovis (M.bovis) is the main causative agent for bovine tuberculosis (BTB) and can also be the cause of zoonotic tuberculosis in humans. In view of its zoonotic nature, slaughterhouse surveillance, potentially resulting in total or partial condemnation of the carcasses and organs, is conducted routinely. Spoligotyping, VNTR profiling, and whole genome sequencing (WGS) of M. bovis isolated from tissues with tuberculosis-like lesions collected from 14 cattle at Eritrea’s largest slaughterhouse in the capital Asmara, were conducted.The 14 M. bovis isolates were classified into three different spoligotype patterns (SB0120, SB0134 and SB0948) and six VNTR profiles. WGS results matched those of the conventional genotyping methods and further discriminated the six VNTR profiles into 14 strains. Furthermore, phylogenetic analysis of the M. bovis isolates suggests two independent introductions of BTB into Eritrea possibly evolving from a common ancestral strain in Europe.This molecular study revealed the most important strains of M. bovis in Eritrea and their (dis)similarities with the strains generally present in East Africa and Europe, as well as potential routes of introduction of M. bovis. Though the sample size is small, the current study provides important information as well as platform for future in-depth molecular studies on isolates from both the dairy and the traditional livestock sectors in Eritrea and the region. This study provides information onthe origin of some of the M. bovis strains in Eritrea, its genetic diversity, evolution and patterns of spread between dairy herds. Such information is essential in the development and implementation of future BTB control strategy for Eritrea. The livestock sector plays a major role in poverty and hunger reduction in the vast majority of Africa, as a source of food, cash income, manure, draught power, transportation, savings, insurance and social status. However, for livestock to play this vital role, the impact of diseases of economic and zoonotic importance need to be reduced. Bovine tuberculosis, mainly caused by Mycobacterium bovis, is such an infectious disease. Slaughterhouse (gross pathology) surveillance, followed by bacterial culture and genotyping, are options to identify the disease-causing agents, their distribution, and enabling trace back of the sources of infections, in order to prevent their re-introduction and spread. Unfortunately, genotyping is by far not generally introduced in the continent. In the present study, tissues with tuberculosis-like lesions were collected from the Asmara municipal slaughterhouse, the largest slaughterhouse in Eritrea, and bacterial culture, classical Mycobacterium tuberculosis complex typing (Spoligotyping and VNTR profiling), as well as whole genome sequencing (WGS) were used to gain insight into the spatial and temporal distribution, genetic diversity and evolution of M. bovis strains circulating in Eritrean dairy cattle. The results revealed (dis)similarities of the Eritrean M. bovis strains with the strains generally present in Africa and Europe, potential routes of introduction to Eritrea and genetic diversity of the M. bovis strains. Future in-depth molecular studies including more samples from dairy cattle as well as cattle and goats from the traditional livestock sector are recommended.
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16
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Jajou R, de Neeling A, van Hunen R, de Vries G, Schimmel H, Mulder A, Anthony R, van der Hoek W, van Soolingen D. Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study. PLoS One 2018; 13:e0195413. [PMID: 29617456 PMCID: PMC5884559 DOI: 10.1371/journal.pone.0195413] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Patients with Mycobacterium tuberculosis isolates sharing identical DNA fingerprint patterns can be epidemiologically linked. However, municipal health services in the Netherlands are able to confirm an epidemiological link in only around 23% of the patients with isolates clustered by the conventional variable number of tandem repeat (VNTR) genotyping. This research aims to investigate whether whole genome sequencing (WGS) is a more reliable predictor of epidemiological links between tuberculosis patients than VNTR genotyping. METHODS VNTR genotyping and WGS were performed in parallel on all Mycobacterium tuberculosis complex isolates received at the Netherlands National Institute for Public Health and the Environment in 2016. Isolates were clustered by VNTR when they shared identical 24-loci VNTR patterns; isolates were assigned to a WGS cluster when the pair-wise genetic distance was ≤ 12 single nucleotide polymorphisms (SNPs). Cluster investigation was performed by municipal health services on all isolates clustered by VNTR in 2016. The proportion of epidemiological links identified among patients clustered by either method was calculated. RESULTS In total, 535 isolates were genotyped, of which 25% (134/535) were clustered by VNTR and 14% (76/535) by WGS; the concordance between both typing methods was 86%. The proportion of epidemiological links among WGS clustered cases (57%) was twice as common than among VNTR clustered cases (31%). CONCLUSION When WGS was applied, the number of clustered isolates was halved, while all epidemiologically linked cases remained clustered. WGS is therefore a more reliable tool to predict epidemiological links between tuberculosis cases than VNTR genotyping and will allow more efficient transmission tracing, as epidemiological investigations based on false clustering can be avoided.
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Affiliation(s)
- Rana Jajou
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Albert de Neeling
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Rianne van Hunen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - Gerard de Vries
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - Henrieke Schimmel
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Arnout Mulder
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Richard Anthony
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Wim van der Hoek
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Dick van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Radboud University Medical Centre, Department of Medical Microbiology, Nijmegen, The Netherlands
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17
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Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev 2017; 30:1015-1063. [PMID: 28855266 PMCID: PMC5608882 DOI: 10.1128/cmr.00016-17] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.
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Affiliation(s)
- Scott Quainoo
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Jordy P M Coolen
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sacha A F T van Hijum
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Heiman F L Wertheim
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
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18
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Fiebig L, Kohl TA, Popovici O, Mühlenfeld M, Indra A, Homorodean D, Chiotan D, Richter E, Rüsch-Gerdes S, Schmidgruber B, Beckert P, Hauer B, Niemann S, Allerberger F, Haas W. A joint cross-border investigation of a cluster of multidrug-resistant tuberculosis in Austria, Romania and Germany in 2014 using classic, genotyping and whole genome sequencing methods: lessons learnt. ACTA ACUST UNITED AC 2017; 22:30439. [PMID: 28106529 PMCID: PMC5404487 DOI: 10.2807/1560-7917.es.2017.22.2.30439] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022]
Abstract
Molecular surveillance of multidrug-resistant tuberculosis (MDR-TB) using 24-loci MIRU-VNTR in the European Union suggests the occurrence of international transmission. In early 2014, Austria detected a molecular MDR-TB cluster of five isolates. Links to Romania and Germany prompted the three countries to investigate possible cross-border MDR-TB transmission jointly. We searched genotyping databases, genotyped additional isolates from Romania, used whole genome sequencing (WGS) to infer putative transmission links, and investigated pairwise epidemiological links and patient mobility. Ten isolates from 10 patients shared the same 24-loci MIRU-VNTR pattern. Within this cluster, WGS defined two subgroups of four patients each. The first comprised an MDR-TB patient from Romania who had sought medical care in Austria and two patients from Austria. The second comprised patients, two of them epidemiologically linked, who lived in three different countries but had the same city of provenance in Romania. Our findings strongly suggested that the two cases in Austrian citizens resulted from a newly introduced MDR-TB strain, followed by domestic transmission. For the other cases, transmission probably occurred in the same city of provenance. To prevent further MDR-TB transmission, we need to ensure universal access to early and adequate therapy and collaborate closely in tuberculosis care beyond administrative borders.
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Affiliation(s)
- Lena Fiebig
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.,These authors contributed equally to this work
| | - Thomas A Kohl
- These authors contributed equally to this work.,Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Odette Popovici
- National Institute of Public Health - National Center for Communicable Diseases Surveillance and Control, Bucharest, Romania
| | | | - Alexander Indra
- Austrian Reference Laboratory for Mycobacteria, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Daniela Homorodean
- Clinical Hospital of Pneumology, Tuberculosis National Reference Laboratory, Cluj-Napoca, Romania
| | | | | | - Sabine Rüsch-Gerdes
- National Reference Center (NRC) for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Beatrix Schmidgruber
- Tuberculosis Patient Service, Health Service of the City of Vienna, Vienna, Austria
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Borstel, Germany
| | - Barbara Hauer
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany.,National Reference Center (NRC) for Mycobacteria, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Borstel, Germany
| | - Franz Allerberger
- Austrian Reference Laboratory for Mycobacteria, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Walter Haas
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
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19
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Genomic Epidemiology of Tuberculosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:79-93. [DOI: 10.1007/978-3-319-64371-7_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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20
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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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21
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Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review. Tuberculosis (Edinb) 2016; 98:77-85. [DOI: 10.1016/j.tube.2016.02.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/22/2016] [Accepted: 02/29/2016] [Indexed: 11/23/2022]
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22
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Hatherell HA, Colijn C, Stagg HR, Jackson C, Winter JR, Abubakar I. Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review. BMC Med 2016; 14:21. [PMID: 27005433 PMCID: PMC4804562 DOI: 10.1186/s12916-016-0566-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/23/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Whole genome sequencing (WGS) is becoming an important part of epidemiological investigations of infectious diseases due to greater resolution and cost reductions compared to traditional typing approaches. Many public health and clinical teams will increasingly use WGS to investigate clusters of potential pathogen transmission, making it crucial to understand the benefits and assumptions of the analytical methods for investigating the data. We aimed to understand how different approaches affect inferences of transmission dynamics and outline limitations of the methods. METHODS We comprehensively searched electronic databases for studies that presented methods used to interpret WGS data for investigating tuberculosis (TB) transmission. Two authors independently selected studies for inclusion and extracted data. Due to considerable methodological heterogeneity between studies, we present summary data with accompanying narrative synthesis rather than pooled analyses. RESULTS Twenty-five studies met our inclusion criteria. Despite the range of interpretation tools, the usefulness of WGS data in understanding TB transmission often depends on the amount of genetic diversity in the setting. Where diversity is small, distinguishing re-infections from relapses may be impossible; interpretation may be aided by the use of epidemiological data, examining minor variants and deep sequencing. Conversely, when within-host diversity is large, due to genetic hitchhiking or co-infection of two dissimilar strains, it is critical to understand how it arose. Greater understanding of microevolution and mixed infection will enhance interpretation of WGS data. CONCLUSIONS As sequencing studies have sampled more intensely and integrated multiple sources of information, the understanding of TB transmission and diversity has grown, but there is still much to be learnt about the origins of diversity that will affect inferences from these data. Public health teams and researchers should combine epidemiological, clinical and WGS data to strengthen investigations of transmission.
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Affiliation(s)
- Hollie-Ann Hatherell
- CoMPLEX, University College London, London, WC1E 6BT, UK. .,Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK.
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK
| | - Helen R Stagg
- Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK
| | - Charlotte Jackson
- Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK
| | - Joanne R Winter
- Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK
| | - Ibrahim Abubakar
- Centre for Infectious Disease Epidemiology, Infection and Population Health, University College London, London, WC1E 6JB, UK.,Medical Research Council Clinical Trials Unit, 125 Kingsway, London, WC2B 6NH, UK
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23
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Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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24
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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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Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes. J Clin Microbiol 2015; 54:333-42. [PMID: 26607978 PMCID: PMC4733179 DOI: 10.1128/jcm.02344-15] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/10/2015] [Indexed: 12/31/2022] Open
Abstract
Whole-genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here we demonstrate that WGS performed prospectively for national epidemiologic surveillance of Listeria monocytogenes has the capacity to be superior to our current approaches using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA), binary typing, and serotyping. Initially 423 L. monocytogenes isolates underwent WGS, and comparisons uncovered a diverse genetic population structure derived from three distinct lineages. MLST, binary typing, and serotyping results inferred in silico from the WGS data were highly concordant (>99%) with laboratory typing performed in parallel. However, WGS was able to identify distinct nested clusters within groups of isolates that were otherwise indistinguishable using our current typing methods. Routine WGS was then used for prospective epidemiologic surveillance on a further 97 L. monocytogenes isolates over a 12-month period, which provided a greater level of discrimination than that of conventional typing for inferring linkage to point source outbreaks. A risk-based alert system based on WGS similarity was used to inform epidemiologists required to act on the data. Our experience shows that WGS can be adopted for prospective L. monocytogenes surveillance and investigated for other pathogens relevant to public health.
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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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Punina NV, Makridakis NM, Remnev MA, Topunov AF. Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015; 9:19. [PMID: 26243131 PMCID: PMC4525730 DOI: 10.1186/s40246-015-0037-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
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Affiliation(s)
- N V Punina
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia.
| | - N M Makridakis
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - M A Remnev
- The Federal State Unitary Enterprise All-Russia Research Institute of Automatics, Moscow, 127055, Russia
| | - A F Topunov
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia
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Coscolla M, Barry PM, Oeltmann JE, Koshinsky H, Shaw T, Cilnis M, Posey J, Rose J, Weber T, Fofanov VY, Gagneux S, Kato-Maeda M, Metcalfe JZ. Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread. J Infect Dis 2015; 212:302-10. [PMID: 25601940 PMCID: PMC4490235 DOI: 10.1093/infdis/jiv025] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/06/2015] [Indexed: 11/12/2022] Open
Abstract
The transcontinental spread of multidrug-resistant (MDR) tuberculosis is poorly characterized in molecular epidemiologic studies. We used genomic sequencing to understand the establishment and dispersion of MDR Mycobacterium tuberculosis within a group of immigrants to the United States. We used a genomic epidemiology approach to study a genotypically matched (by spoligotype, IS6110 restriction fragment length polymorphism, and mycobacterial interspersed repetitive units-variable number of tandem repeat signature) lineage 2/Beijing MDR strain implicated in an outbreak of tuberculosis among refugees in Thailand and consecutive cases within California. All 46 MDR M. tuberculosis genomes from both Thailand and California were highly related, with a median difference of 10 single-nucleotide polymorphisms (SNPs). The Wat Tham Krabok (WTK) strain is a new sequence type distinguished from all known Beijing strains by 55 SNPs and a genomic deletion (Rv1267c) associated with increased fitness. Sequence data revealed a highly prevalent MDR strain that included several closely related but distinct allelic variants within Thailand, rather than the occurrence of a single outbreak. In California, sequencing data supported multiple independent introductions of WTK with subsequent transmission and reactivation within the state, as well as a potential super spreader with a prolonged infectious period. Twenty-seven drug resistance-conferring mutations and 4 putative compensatory mutations were found within WTK strains. Genomic sequencing has substantial epidemiologic value in both low- and high-burden settings in understanding transmission chains of highly prevalent MDR strains.
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Affiliation(s)
- Mireia Coscolla
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute
- University of Basel, Switzerland
| | - Pennan M. Barry
- Division of Communicable Disease Control, Center for Infectious Diseases, California Department of Public Health, Richmond
| | | | | | - Tambi Shaw
- Division of Communicable Disease Control, Center for Infectious Diseases, California Department of Public Health, Richmond
| | - Martin Cilnis
- Division of Communicable Disease Control, Center for Infectious Diseases, California Department of Public Health, Richmond
| | - Jamie Posey
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jordan Rose
- Division of Pulmonary and Critical Care Medicine, Francis J. Curry International Tuberculosis Center, San Francisco General Hospital, University of California
| | - Terry Weber
- Division of Communicable Disease Control, Center for Infectious Diseases, California Department of Public Health, Richmond
| | | | - Sebastien Gagneux
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute
- University of Basel, Switzerland
| | - Midori Kato-Maeda
- Division of Pulmonary and Critical Care Medicine, Francis J. Curry International Tuberculosis Center, San Francisco General Hospital, University of California
| | - John Z. Metcalfe
- Division of Pulmonary and Critical Care Medicine, Francis J. Curry International Tuberculosis Center, San Francisco General Hospital, University of California
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Azé J, Sola C, Zhang J, Lafosse-Marin F, Yasmin M, Siddiqui R, Kremer K, van Soolingen D, Refrégier G. Genomics and Machine Learning for Taxonomy Consensus: The Mycobacterium tuberculosis Complex Paradigm. PLoS One 2015; 10:e0130912. [PMID: 26154264 PMCID: PMC4496040 DOI: 10.1371/journal.pone.0130912] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/25/2015] [Indexed: 11/18/2022] Open
Abstract
Infra-species taxonomy is a prerequisite to compare features such as virulence in different pathogen lineages. Mycobacterium tuberculosis complex taxonomy has rapidly evolved in the last 20 years through intensive clinical isolation, advances in sequencing and in the description of fast-evolving loci (CRISPR and MIRU-VNTR). On-line tools to describe new isolates have been set up based on known diversity either on CRISPRs (also known as spoligotypes) or on MIRU-VNTR profiles. The underlying taxonomies are largely concordant but use different names and offer different depths. The objectives of this study were 1) to explicit the consensus that exists between the alternative taxonomies, and 2) to provide an on-line tool to ease classification of new isolates. Genotyping (24-VNTR, 43-spacers spoligotypes, IS6110-RFLP) was undertaken for 3,454 clinical isolates from the Netherlands (2004-2008). The resulting database was enlarged with African isolates to include most human tuberculosis diversity. Assignations were obtained using TB-Lineage, MIRU-VNTRPlus, SITVITWEB and an algorithm from Borile et al. By identifying the recurrent concordances between the alternative taxonomies, we proposed a consensus including 22 sublineages. Original and consensus assignations of the all isolates from the database were subsequently implemented into an ensemble learning approach based on Machine Learning tool Weka to derive a classification scheme. All assignations were reproduced with very good sensibilities and specificities. When applied to independent datasets, it was able to suggest new sublineages such as pseudo-Beijing. This Lineage Prediction tool, efficient on 15-MIRU, 24-VNTR and spoligotype data is available on the web interface “TBminer.” Another section of this website helps summarizing key molecular epidemiological data, easing tuberculosis surveillance. Altogether, we successfully used Machine Learning on a large dataset to set up and make available the first consensual taxonomy for human Mycobacterium tuberculosis complex. Additional developments using SNPs will help stabilizing it.
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Affiliation(s)
- Jérôme Azé
- LIRMM UM CNRS, UMR 5506, 860 rue de St Priest, 34095 Montpellier cedex 5, France
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
| | - Jian Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
| | - Florian Lafosse-Marin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
| | - Memona Yasmin
- Pakistan Institute for Engineering and Applied Sciences (PIEAS), Lehtrar Road, Nilore, Islamabad, Pakistan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box # 577, Jhang Road, Faisalabad, Pakistan
| | - Rubina Siddiqui
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box # 577, Jhang Road, Faisalabad, Pakistan
| | - Kristin Kremer
- National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Dick van Soolingen
- National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
- Department of Pulmonary Diseases and Department of Microbiology, Radbout University Nijmegen Medical Centre, University Lung Centre Dekkerswald, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, rue Gregor Mendel, Bât 400, 91405 Orsay cedex, France
- * E-mail:
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30
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Regmi SM, Chaiprasert A, Kulawonganunchai S, Tongsima S, Coker OO, Prammananan T, Viratyosin W, Thaipisuttikul I. Whole genome sequence analysis of multidrug-resistant Mycobacterium tuberculosis Beijing isolates from an outbreak in Thailand. Mol Genet Genomics 2015; 290:1933-41. [DOI: 10.1007/s00438-015-1048-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 04/07/2015] [Indexed: 12/11/2022]
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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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Abstract
Recent advances in DNA sequencing technology have made the whole-genome sequencing of pathogens in a clinically relevant turn-around time both technically and economically feasible. The DNA sequencing of pathogens with epidemic potential offers new and exciting opportunities for high-resolution public health surveillance. This chapter outlines major methods and bioinformatics tools for pathogen genome characterization, the identification of infectious disease clusters, as well as for genomics-guided biosurveillance. Existing challenges are also considered.
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Affiliation(s)
- Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health Pathology West ICPMR, Westmead Hospital C24, Hawkesbury Road and Darcy Road, Westmead, NSW, 2145, Australia,
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Lee RS, Radomski N, Proulx JF, Manry J, McIntosh F, Desjardins F, Soualhine H, Domenech P, Reed MB, Menzies D, Behr MA. Reemergence and amplification of tuberculosis in the Canadian arctic. J Infect Dis 2015; 211:1905-14. [PMID: 25576599 DOI: 10.1093/infdis/jiv011] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 12/19/2014] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Between November 2011 and November 2012, a Canadian village of 933 persons had 50 culture-positive cases of tuberculosis, with 49 sharing the same genotype. METHODS We performed Illumina-based whole-genome sequencing on Mycobacterium tuberculosis isolates from this village, during and before the outbreak. Phylogenetic trees were generated using the maximum likelihood method. RESULTS Three distinct genotypes were identified. Strain I (n = 7) was isolated in 1991-1996. Strain II (n = 8) was isolated in 1996-2004. Strain III (n = 62) first appeared in 2007 and did not arise from strain I or II. Within strain III, there were 3 related but distinct clusters: IIIA, IIIB, and IIIC. Between 2007 and 2010, cluster IIIA predominated (11 of 22 vs 2 of 40; P < .001), whereas in 2011-2012 clusters IIIB (n = 18) and IIIC (n = 20) predominated over cluster IIIA (n = 11). Combined evolutionary and epidemiologic analysis of strain III cases revealed that the outbreak in 2011-2012 was the result of ≥6 temporally staggered events, spanning from 1 reactivation case to a point-source outbreak of 20 cases. CONCLUSIONS After the disappearance of 2 strains of M. tuberculosis in this village, its reemergence in 2007 was followed by an epidemiologic amplification, affecting >5% of the population.
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Affiliation(s)
- Robyn S Lee
- Department of Epidemiology, Biostatistics and Occupational Health Department of McGill International TB Centre The Research Institute of the McGill University Health Centre
| | | | | | - Jeremy Manry
- Department of Medicine Department of Human Genetics, McGill University Department of McGill International TB Centre The Research Institute of the McGill University Health Centre
| | - Fiona McIntosh
- The Research Institute of the McGill University Health Centre
| | | | - Hafid Soualhine
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Pilar Domenech
- The Research Institute of the McGill University Health Centre
| | - Michael B Reed
- Department of McGill International TB Centre The Research Institute of the McGill University Health Centre
| | - Dick Menzies
- The Research Institute of the McGill University Health Centre Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, McGill University Health Centre
| | - Marcel A Behr
- Department of McGill International TB Centre The Research Institute of the McGill University Health Centre
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Sola C, Abadia E, Le Hello S, Weill FX. High-Throughput CRISPR Typing of Mycobacterium tuberculosis Complex and Salmonella enterica Serotype Typhimurium. Methods Mol Biol 2015; 1311:91-109. [PMID: 25981468 DOI: 10.1007/978-1-4939-2687-9_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Spoligotyping was developed almost 18 years ago and still remains a popular first-lane genotyping technique to identify and subtype Mycobacterium tuberculosis complex (MTC) clinical isolates at a phylogeographic level. For other pathogens, such as Salmonella enterica, recent studies suggest that specifically designed spoligotyping techniques could be interesting for public health purposes. Spoligotyping was in its original format a reverse line-blot hybridization method using capture probes designed on "spacers" and attached to a membrane's surface and a PCR product obtained from clustered regularly interspaced short palindromic repeats (CRISPRs). Cowan et al. and Fabre et al. were the first to propose a high-throughput Spoligotyping method based on microbeads for MTC and S. enterica serotype Typhimurium, respectively. The main advantages of the high-throughput Spoligotyping techniques we describe here are their low cost, their robustness, and the existence (at least for MTC) of very large databases that allow comparisons between spoligotypes from anywhere.
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Affiliation(s)
- Christophe Sola
- Microbiology Department, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Rue Gregor Mendel, Building 400, Room 205-208, F-91405, Orsay-Cedex, France,
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Mehaffy C, Guthrie JL, Alexander DC, Stuart R, Rea E, Jamieson FB. Marked microevolution of a unique Mycobacterium tuberculosis strain in 17 years of ongoing transmission in a high risk population. PLoS One 2014; 9:e112928. [PMID: 25405861 PMCID: PMC4236100 DOI: 10.1371/journal.pone.0112928] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/22/2014] [Indexed: 11/18/2022] Open
Abstract
The transmission and persistence of Mycobacterium tuberculosis within high risk populations is a threat to tuberculosis (TB) control. In the current study, we used whole genome sequencing (WGS) to decipher the transmission dynamics and microevolution of M. tuberculosis ON-A, an endemic strain responsible for an ongoing outbreak of TB in an urban homeless/under-housed population. Sixty-one M. tuberculosis isolates representing 57 TB cases from 1997 to 2013 were subjected to WGS. Sequencing data was integrated with available epidemiological information and analyzed to determine how the M. tuberculosis ON-A strain has evolved during almost two decades of active transmission. WGS offers higher discriminatory power than traditional genotyping techniques, dividing the M. tuberculosis ON-A strain into 6 sub-clusters, each defined by unique single nucleotide polymorphism profiles. One sub-cluster, designated ON-ANM (Natural Mutant; 26 isolates from 24 cases) was also defined by a large, 15 kb genomic deletion. WGS analysis reveals the existence of multiple transmission chains within the same population/setting. Our results help validate the utility of WGS as a powerful tool for identifying genomic changes and adaptation of M. tuberculosis.
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Affiliation(s)
- Carolina Mehaffy
- Public Health Ontario, Toronto, Canada
- University of Toronto, Toronto, Canada
- * E-mail:
| | | | | | | | | | - Frances B. Jamieson
- Public Health Ontario, Toronto, Canada
- University of Toronto, Toronto, Canada
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Luo T, Yang C, Peng Y, Lu L, Sun G, Wu J, Jin X, Hong J, Li F, Mei J, DeRiemer K, Gao Q. Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis. Tuberculosis (Edinb) 2014; 94:434-40. [PMID: 24888866 DOI: 10.1016/j.tube.2014.04.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/08/2014] [Accepted: 04/26/2014] [Indexed: 12/19/2022]
Abstract
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has been used to trace the transmission of M. tuberculosis, the causative agent of tuberculosis (TB). Previously published studies using WGS were conducted in developed countries with a low TB burden. We sought to evaluate the relative usefulness of traditional VNTR and SNP typing methods, WGS and epidemiological investigations to study the recent transmission of M. tuberculosis in a high TB burden country. We conducted epidemiological investigations of 42 TB patients whose M. tuberculosis isolates were classified into three clusters based on variable-number tandem repeat (VNTR) typing. We applied WGS to 32 (76.2%) of the 42 strains and calculated the pairwise genomic distances between strains within each cluster. Eighteen (56.3%) of the 32 strains had genomic differences ≥100 SNPs with every other strain, suggesting that direct transmission did not likely occurred. Ten strains were grouped into four WGS-based clusters with genomic distances ≤5 SNPs within each cluster, and confirmed epidemiological links were identified in two of these clusters. Our results indicate that WGS provides reliable resolution for tracing the transmission of M. tuberculosis in high TB burden settings. The high resolution of WGS is particularly useful to confirm or exclude the possibility of direct transmission events defined by traditional typing methods.
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Affiliation(s)
- Tao Luo
- 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 Sciences, Fudan University, Shanghai 200032, China.
| | - Chongguang Yang
- 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 Sciences, Fudan University, Shanghai 200032, China.
| | - Ying Peng
- Tuberculosis (TB) Control Center of Heilongjiang Province, No. 40, Youfang Street, Harbin, Heilongjiang 150030, China.
| | - Liping Lu
- Department of TB Control, Songjiang District of Shanghai Municipal Center for Disease Control and Prevention, 1050 North Xi Lin Road, Shanghai 201620, China.
| | - Guomei Sun
- 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 Sciences, Fudan University, Shanghai 200032, China.
| | - Jie Wu
- Department of TB Control, Shanghai Municipal Centers for Disease Control and Prevention, Shanghai 200336, China.
| | - Xiaoping Jin
- Department of TB Control, Songjiang District of Shanghai Municipal Center for Disease Control and Prevention, 1050 North Xi Lin Road, Shanghai 201620, China.
| | - Jianjun Hong
- Department of TB Control, Songjiang District of Shanghai Municipal Center for Disease Control and Prevention, 1050 North Xi Lin Road, Shanghai 201620, China.
| | - Fabin Li
- Tuberculosis (TB) Control Center of Heilongjiang Province, No. 40, Youfang Street, Harbin, Heilongjiang 150030, China.
| | - Jian Mei
- Department of TB Control, Shanghai Municipal Centers for Disease Control and Prevention, Shanghai 200336, China.
| | - Kathryn DeRiemer
- University of California, Davis, School of Medicine, One Shields Avenue, Davis, CA 95616, USA.
| | - Qian Gao
- 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 Sciences, Fudan University, Shanghai 200032, China.
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Whole-genome sequencing of Mycobacterium tuberculosis as an epidemiological marker. THE LANCET RESPIRATORY MEDICINE 2014; 2:251-2. [DOI: 10.1016/s2213-2600(14)70049-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Sintchenko V, Holmes N. Early warning systems augmented by bacterial genomics. MICROBIOLOGY AUSTRALIA 2014. [DOI: 10.1071/ma14012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Clark TG, Mallard K, Coll F, Preston M, Assefa S, Harris D, Ogwang S, Mumbowa F, Kirenga B, O’Sullivan DM, Okwera A, Eisenach KD, Joloba M, Bentley SD, Ellner JJ, Parkhill J, Jones-López EC, McNerney R. Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PLoS One 2013; 8:e83012. [PMID: 24349420 PMCID: PMC3859632 DOI: 10.1371/journal.pone.0083012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Understanding the emergence and spread of multidrug-resistant tuberculosis (MDR-TB) is crucial for its control. MDR-TB in previously treated patients is generally attributed to the selection of drug resistant mutants during inadequate therapy rather than transmission of a resistant strain. Traditional genotyping methods are not sufficient to distinguish strains in populations with a high burden of tuberculosis and it has previously been difficult to assess the degree of transmission in these settings. We have used whole genome analysis to investigate M. tuberculosis strains isolated from treatment experienced patients with MDR-TB in Uganda over a period of four years. METHODS AND FINDINGS We used high throughput genome sequencing technology to investigate small polymorphisms and large deletions in 51 Mycobacterium tuberculosis samples from 41 treatment-experienced TB patients attending a TB referral and treatment clinic in Kampala. This was a convenience sample representing 69% of MDR-TB cases identified over the four year period. Low polymorphism was observed in longitudinal samples from individual patients (2-15 SNPs). Clusters of samples with less than 50 SNPs variation were examined. Three clusters comprising a total of 8 patients were found with almost identical genetic profiles, including mutations predictive for resistance to rifampicin and isoniazid, suggesting transmission of MDR-TB. Two patients with previous drug susceptible disease were found to have acquired MDR strains, one of which shared its genotype with an isolate from another patient in the cohort. CONCLUSIONS Whole genome sequence analysis identified MDR-TB strains that were shared by more than one patient. The transmission of multidrug-resistant disease in this cohort of retreatment patients emphasises the importance of early detection and need for infection control. Consideration should be given to rapid testing for drug resistance in patients undergoing treatment to monitor the emergence of resistance and permit early intervention to avoid onward transmission.
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Affiliation(s)
- Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Mark Preston
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Samuel Assefa
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - David Harris
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Sam Ogwang
- Joint Clinical Research Centre, Kampala, Uganda
| | - Francis Mumbowa
- Joint Clinical Research Centre, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Bruce Kirenga
- Mulago Hospital Tuberculosis Clinic, Mulago Hospital, Kampala, Uganda
| | - Denise M. O’Sullivan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Alphonse Okwera
- Mulago Hospital Tuberculosis Clinic, Mulago Hospital, Kampala, Uganda
| | - Kathleen D. Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Jerrold J. Ellner
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Edward C. Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Pérez-Lago L, Comas I, Navarro Y, González-Candelas F, Herranz M, Bouza E, García-de-Viedma D. Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission. J Infect Dis 2013; 209:98-108. [PMID: 23945373 DOI: 10.1093/infdis/jit439] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND It has been accepted that the infection by Mycobacterium tuberculosis (M. tuberculosis) can be more heterogeneous than considered. The emergence of clonal variants caused by microevolution events leading to population heterogeneity is a phenomenon largely unexplored. Until now, we could only superficially analyze this phenomenon by standard fingerprinting (RFLP and VNTR). METHODS In this study we applied whole genome sequencing for a more in-depth analysis of the scale of microevolution both at the intrapatient and interpatient scenarios. RESULTS We found that the amount of variation accumulated within a patient can be as high as that observed between patients along a chain of transmission. Intrapatient diversity was found both at the extrapulmonary and respiratory sites, meaning that this variability can be transmitted and impact on the inference of transmission events. One of the events studied allowed us to track for a single strain the complete process of (i) interpatient microevolution, (ii) intrapatient respiratory variation, and (iii) isolation of different variants at different infected sites of this patient. CONCLUSIONS Our study adds new data to the understanding of variability in M. tuberculosis in a wide clinical scenario and alerts about the difficulties of establishing thresholds to differentiate relatedness in M. tuberculosis with epidemiological purposes.
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Affiliation(s)
- Laura Pérez-Lago
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
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Borgdorff MW, van Soolingen D. The re-emergence of tuberculosis: what have we learnt from molecular epidemiology? Clin Microbiol Infect 2013; 19:889-901. [PMID: 23731470 DOI: 10.1111/1469-0691.12253] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Tuberculosis (TB) has re-emerged over the past two decades: in industrialized countries in association with immigration, and in Africa owing to the human immunodeficiency virus epidemic. Drug-resistant TB is a major threat worldwide. The variable and uncertain impact of TB control necessitates not only better tools (diagnostics, drugs, and vaccines), but also better insights into the natural history and epidemiology of TB. Molecular epidemiological studies over the last two decades have contributed to such insights by answering long-standing questions, such as the proportion of cases attributable to recent transmission, risk factors for recent transmission, the occurrence of multiple Mycobacterium tuberculosis infection, and the proportion of recurrent TB cases attributable to re-infection. M. tuberculosis lineages have been identified and shown to be associated with geographical origin. The Beijing genotype is strongly associated with multidrug resistance, and may have escaped from bacille Calmette-Guérin-induced immunity. DNA fingerprinting has quantified the importance of institutional transmission and laboratory cross-contamination, and has helped to focus contact investigations. Questions to be answered in the near future with whole genome sequencing include identification of chains of transmission within clusters of patients, more precise quantification of mixed infection, and transmission probabilities and rates of progression from infection to disease of various M. tuberculosis lineages, as well as possible variations in vaccine efficacy by lineage. Perhaps most importantly, dynamics in the population structure of M. tuberculosis in response to control measures in high-prevalence areas should be better understood.
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Affiliation(s)
- M W Borgdorff
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, The Netherlands; Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Centre, University of Amsterdam and Centre for Infection and Immunity Amsterdam (CINIMA), Amsterdam, The Netherlands
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Clustering of tuberculosis cases based on variable-number tandem-repeat typing in relation to the population structure of Mycobacterium tuberculosis in the Netherlands. J Clin Microbiol 2013; 51:2427-31. [PMID: 23658260 DOI: 10.1128/jcm.00489-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The population structure of 3,776 Mycobacterium tuberculosis isolates was determined using variable-number tandem-repeat (VNTR) typing. The degree of clonality was so high that a more relaxed definition of clustering cannot be applied. Among recent immigrants with non-Euro-American isolates, transmission is overestimated if based on identical VNTR patterns.
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Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak. PLoS One 2013; 8:e58235. [PMID: 23472164 PMCID: PMC3589338 DOI: 10.1371/journal.pone.0058235] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 02/05/2013] [Indexed: 11/19/2022] Open
Abstract
Rationale Current tools available to study the molecular epidemiology of tuberculosis do not provide information about the directionality and sequence of transmission for tuberculosis cases occurring over a short period of time, such as during an outbreak. Recently, whole genome sequencing has been used to study molecular epidemiology of Mycobacterium tuberculosis over short time periods. Objective To describe the microevolution of M. tuberculosis during an outbreak caused by one drug-susceptible strain. Method and Measurements We included 9 patients with tuberculosis diagnosed during a period of 22 months, from a population-based study of the molecular epidemiology in San Francisco. Whole genome sequencing was performed using Illumina’s sequencing by synthesis technology. A custom program written in Python was used to determine single nucleotide polymorphisms which were confirmed by PCR product Sanger sequencing. Main results We obtained an average of 95.7% (94.1–96.9%) coverage for each isolate and an average fold read depth of 73 (1 to 250). We found 7 single nucleotide polymorphisms among the 9 isolates. The single nucleotide polymorphisms data confirmed all except one known epidemiological link. The outbreak strain resulted in 5 bacterial variants originating from the index case A1 with 0–2 mutations per transmission event that resulted in a secondary case. Conclusions Whole genome sequencing analysis from a recent outbreak of tuberculosis enabled us to identify microevolutionary events observable during transmission, to determine 0–2 single nucleotide polymorphisms per transmission event that resulted in a secondary case, and to identify new epidemiologic links in the chain of transmission.
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Bryant JM, Schürch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, Kremer K, van Hijum SAFT, Siezen RJ, Borgdorff M, Bentley SD, Parkhill J, van Soolingen D. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis 2013; 13:110. [PMID: 23446317 PMCID: PMC3599118 DOI: 10.1186/1471-2334-13-110] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of the rate of change in the genome over relevant timescales is required. METHODS We attempted to estimate a molecular clock by sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years. RESULTS Multiple analyses support an average mutation rate of ~0.3 SNPs per genome per year. However, all analyses revealed a very high degree of variation around this mean, making the confirmation of links proposed by epidemiology, and inference of novel links, difficult. Despite this, in some cases, the phylogenetic context of other strains provided evidence supporting the confident exclusion of previously inferred epidemiological links. CONCLUSIONS This in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies. However, the superior resolution of whole genome sequencing can provide the phylogenetic context to allow the confident exclusion of possible transmission events previously inferred via traditional DNA fingerprinting techniques and epidemiological cluster investigation. Despite the slow generation of variation even at the whole genome level we conclude that the investigation of tuberculosis transmission will benefit greatly from routine whole genome sequencing.
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Affiliation(s)
- Josephine M Bryant
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anita C Schürch
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Henk van Deutekom
- Department of tuberculosis control, Public Health Service, Amsterdam, The Netherlands
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jessica L de Beer
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
| | - Victor de Jager
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands
| | - Kristin Kremer
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
| | - Sacha A F T van Hijum
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands
- NIZO food research, P.O. Box 206710 BA, Ede, The Netherlands
| | - Roland J Siezen
- Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands
| | - Martien Borgdorff
- Department of tuberculosis control, Public Health Service, Amsterdam, The Netherlands
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Stephen D Bentley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Dick van Soolingen
- RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands
- Department of Clinical Microbiology and department of Lung Disease, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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Walker TM, Monk P, Smith EG, Peto TEA. Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing. Clin Microbiol Infect 2013; 19:796-802. [PMID: 23432709 DOI: 10.1111/1469-0691.12183] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The control of tuberculosis depends on the identification and treatment of infectious patients and their contacts, who are currently identified through a combined approach of genotyping and epidemiological investigation. However, epidemiological data are often challenging to obtain, and genotyping data are difficult to interpret without them. Whole genome sequencing (WGS) technology is increasingly affordable, and offers the prospect of identifying plausible transmission events between patients without prior recourse to epidemiological data. We discuss the current approaches to tuberculosis control, and how WGS might advance public health efforts in the future.
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Affiliation(s)
- T M Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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Comparative study of IS6110 restriction fragment length polymorphism and variable-number tandem-repeat typing of Mycobacterium tuberculosis isolates in the Netherlands, based on a 5-year nationwide survey. J Clin Microbiol 2013; 51:1193-8. [PMID: 23363841 DOI: 10.1128/jcm.03061-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a detailed evaluation on discriminatory power and agreement with findings in a cluster investigation was performed on 3,975 tuberculosis cases during the period of 2004 to 2008. The level of discrimination of the two typing methods did not differ substantially: RFLP typing yielded 2,733 distinct patterns compared to 2,607 in VNTR typing. The global concordance, defined as isolates labeled unique or identically distributed in clusters by both methods, amounted to 78.5% (n = 3,123). Of the remaining 855 cases, 12% (n = 479) of the cases were clustered only by VNTR, 7.7% (n = 305) only by RFLP typing, and 1.8% (n = 71) revealed different cluster compositions in the two approaches. A cluster investigation was performed for 87% (n = 1,462) of the cases clustered by RFLP. For the 740 cases with confirmed or presumed epidemiological links, 92% were concordant with VNTR typing. In contrast, only 64% of the 722 cases without an epidemiological link but clustered by RFLP typing were also clustered by VNTR typing. We conclude that VNTR typing has a discriminatory power equal to IS6110 RFLP typing but is in better agreement with findings in a cluster investigation performed on an RFLP-clustering-based cluster investigation. Both aspects make VNTR typing a suitable method for tuberculosis surveillance systems.
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Abstract
Recent years have witnessed an increased appreciation of the extent and relevance of strain-to-strain variation in Mycobacterium tuberculosis. This paradigm shift can largely be attributed to an improved understanding of the global population structure of this organism, and to the realisation that the various members of the M. tuberculosis complex (MTBC) harbour more genetic diversity than previously realised. Moreover, many studies using experimental models of infection have demonstrated that MTBC diversity translates into significant differences in immunogenecity and virulence . However, linking these experimental phenotypes to relevant clinical phenotypes has been difficult, and to date, largely unsuccessful. Nevertheless, emerging high-throughput technologies, in particular next-generation sequencing , offer new opportunities, and have already lead to important new insights. Given the complexity of the host-pathogen interaction in tuberculosis, systems approaches will be key to define the role of MTBC diversity in the fight against one of humankind's most important pathogens.
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Stucki D, Gagneux S. Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database. Tuberculosis (Edinb) 2012; 93:30-9. [PMID: 23266261 DOI: 10.1016/j.tube.2012.11.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 11/25/2012] [Indexed: 12/12/2022]
Abstract
Recent advances in DNA sequencing have led to the discovery of thousands of single nucleotide polymorphisms (SNPs) in clinical isolates of Mycobacterium tuberculosis complex (MTBC). This genetic variation has changed our understanding of the differences and phylogenetic relationships between strains. Many of these mutations can serve as phylogenetic markers for strain classification, while others cause drug resistance. Moreover, SNPs can affect the bacterial phenotype in various ways, which may have an impact on the outcome of tuberculosis (TB) infection and disease. Despite the importance of SNPs for our understanding of the diversity of MTBC populations, the research community currently lacks a comprehensive, well-curated and user-friendly database dedicated to SNP data. First attempts to catalogue and annotate SNPs in MTBC have been made, but more work is needed. In this review, we discuss the biological and epidemiological relevance of SNPs in MTBC. We then review some of the analytical challenges involved in processing SNP data, and end with a list of features, which should be included in a new SNP database for MTBC.
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Affiliation(s)
- David Stucki
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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Walker TM, Ip CLC, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TEA. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. THE LANCET. INFECTIOUS DISEASES 2012; 13:137-46. [PMID: 23158499 PMCID: PMC3556524 DOI: 10.1016/s1473-3099(12)70277-3] [Citation(s) in RCA: 661] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Background Tuberculosis incidence in the UK has risen in the past decade. Disease control depends on epidemiological data, which can be difficult to obtain. Whole-genome sequencing can detect microevolution within Mycobacterium tuberculosis strains. We aimed to estimate the genetic diversity of related M tuberculosis strains in the UK Midlands and to investigate how this measurement might be used to investigate community outbreaks. Methods In a retrospective observational study, we used Illumina technology to sequence M tuberculosis genomes from an archive of frozen cultures. We characterised isolates into four groups: cross-sectional, longitudinal, household, and community. We measured pairwise nucleotide differences within hosts and between hosts in household outbreaks and estimated the rate of change in DNA sequences. We used the findings to interpret network diagrams constructed from 11 community clusters derived from mycobacterial interspersed repetitive-unit–variable-number tandem-repeat data. Findings We sequenced 390 separate isolates from 254 patients, including representatives from all five major lineages of M tuberculosis. The estimated rate of change in DNA sequences was 0·5 single nucleotide polymorphisms (SNPs) per genome per year (95% CI 0·3–0·7) in longitudinal isolates from 30 individuals and 25 families. Divergence is rarely higher than five SNPs in 3 years. 109 (96%) of 114 paired isolates from individuals and households differed by five or fewer SNPs. More than five SNPs separated isolates from none of 69 epidemiologically linked patients, two (15%) of 13 possibly linked patients, and 13 (17%) of 75 epidemiologically unlinked patients (three-way comparison exact p<0·0001). Genetic trees and clinical and epidemiological data suggest that super-spreaders were present in two community clusters. Interpretation Whole-genome sequencing can delineate outbreaks of tuberculosis and allows inference about direction of transmission between cases. The technique could identify super-spreaders and predict the existence of undiagnosed cases, potentially leading to early treatment of infectious patients and their contacts. Funding Medical Research Council, Wellcome Trust, National Institute for Health Research, and the Health Protection Agency.
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Affiliation(s)
- Timothy M Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
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