The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology
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Tanja Stadler | Pieter Moris | Stefan Niemann | Denise Kühnert | Bouke C. de Jong | Conor J. Meehan | Florian Gehre | Matthias Merker | Pauline Lempens | B. D. de Jong | P. Beckert | S. Niemann | Pieter Moris | T. Stadler | C. Meehan | M. Merker | T. Kohl | D. Kühnert | M. Kaswa | Patrick Beckert | Christian Utpatel | F. Gehre | Thomas A. Kohl | Jūlija Pečerska | S. Akter | C. Utpatel | P. Lempens | Jūlija Pečerska | Suriya Akter | Michel K. Kaswa | Patrick Beckert | Christian Utpatel
[1] Stefan Niemann,et al. MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates , 2018, PeerJ.
[2] W. Hanage,et al. Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission , 2018, Microbial genomics.
[3] Stefan Niemann,et al. Harmonized Genome Wide Typing of Tubercle Bacilli Using a Web-Based Gene-By-Gene Nomenclature System , 2018, EBioMedicine.
[4] D. Chin,et al. Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study , 2018, The Lancet. Infectious diseases.
[5] V. Mizrahi,et al. Mycobacterium tuberculosis. , 2018, Trends in microbiology.
[6] Ted Cohen,et al. Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions , 2018, bioRxiv.
[7] Thomas R Rogers,et al. A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study , 2018, The Lancet. Infectious diseases.
[8] Derrick W. Crook,et al. A Quantitative Evaluation of MIRU-VNTR Typing Against Whole-Genome Sequencing for Identifying Mycobacterium tuberculosis Transmission: A Prospective Observational Cohort Study , 2018, bioRxiv.
[9] A. Pain,et al. Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis , 2018, Nature Microbiology.
[10] Victoria Cook,et al. Molecular Epidemiology of Tuberculosis in British Columbia, Canada: A 10-Year Retrospective Study , 2017, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[11] L. Rigouts,et al. Half of rifampicin-resistant Mycobacterium tuberculosis complex isolated from tuberculosis patients in Sub-Saharan Africa have concomitant resistance to pyrazinamide , 2017, PloS one.
[12] L. Rigouts,et al. Genotypic characterization directly applied to sputum improves the detection of Mycobacterium africanum West African 1, under-represented in positive cultures , 2017, PLoS neglected tropical diseases.
[13] T. Clark,et al. Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia , 2017, BMC Infectious Diseases.
[14] S. Niemann,et al. Extent of transmission captured by contact tracing in a tuberculosis high endemic setting , 2017, European Respiratory Journal.
[15] P. Beckert,et al. New Mycobacterium tuberculosis Complex Sublineage, Brazzaville, Congo , 2017, Emerging infectious diseases.
[16] C. Saegerman,et al. Molecular epidemiology of Mycobacterium tuberculosis complex in Brussels, 2010–2013 , 2017, PloS one.
[17] A. Narechania,et al. Transmission of Extensively Drug‐Resistant Tuberculosis in South Africa , 2017, The New England journal of medicine.
[18] B. Tessema,et al. FIND Tuberculosis Strain Bank: a Resource for Researchers and Developers Working on Tests To Detect Mycobacterium tuberculosis and Related Drug Resistance , 2017, Journal of Clinical Microbiology.
[19] J. Gardy,et al. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis , 2017, Annals of the New York Academy of Sciences.
[20] Y. Reddy,et al. Tuberculosis Strain Bank, A Resource For Researchers And Developers Working on Tests To Detect Mycobacterium Tuberculosis and Related Drug Resistance , 2017 .
[21] Stefan Niemann,et al. The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. , 2017, Advances in experimental medicine and biology.
[22] I. Comas. Genomic Epidemiology of Tuberculosis. , 2017, Advances in experimental medicine and biology.
[23] K. Floyd,et al. Population-based resistance of Mycobacterium tuberculosis isolates to pyrazinamide and fluoroquinolones: results from a multicountry surveillance project , 2016, The Lancet. Infectious diseases.
[24] Julian Parkhill,et al. Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study , 2016, PLoS medicine.
[25] S. Niemann,et al. Tracing Mycobacterium tuberculosis transmission by whole genome sequencing in a high incidence setting: a retrospective population-based study in East Greenland , 2016, Scientific Reports.
[26] David J. Edwards,et al. Genome-scale rates of evolutionary change in bacteria , 2016, bioRxiv.
[27] F. Balloux,et al. Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out. , 2016, Trends in microbiology.
[28] Xavier Didelot,et al. Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks , 2016, bioRxiv.
[29] Chao Lu,et al. Retrospective study , 2016, Medicine.
[30] E. Chernyaeva,et al. Next-Generation Sequencing of Mycobacterium tuberculosis , 2016, Emerging infectious diseases.
[31] Hansjakob Furrer,et al. Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country , 2016, Journal of Clinical Microbiology.
[32] Q. Gao,et al. Prevalence and transmission of pyrazinamide resistant Mycobacterium tuberculosis in China. , 2016, Tuberculosis.
[33] Jason Hinds,et al. Clinical use of whole genome sequencing for Mycobacterium tuberculosis , 2016, BMC Medicine.
[34] Joanne R. Winter,et al. Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review , 2016, BMC Medicine.
[35] T. Clark,et al. Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages , 2016, BMC Genomics.
[36] Y. Teo,et al. SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads , 2016, Genome Medicine.
[37] D. Cirillo,et al. Best approaches to drug-resistance surveillance at the country level , 2016, International journal of mycobacteriology.
[38] G. Kaplan,et al. A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings , 2016, PloS one.
[39] A. Stamatakis,et al. Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations , 2016, bioRxiv.
[40] D. Dowdy,et al. The burden of transmitted multi-drug resistance among epidemics of tuberculosis: A transmission model , 2015, The Lancet. Respiratory medicine.
[41] Robyn S Lee,et al. Population genomics of Mycobacterium tuberculosis in the Inuit , 2015, Proceedings of the National Academy of Sciences.
[42] S. Sengstake,et al. Pyrazinamide resistance in Mycobacterium tuberculosis fails to bite? , 2015, Pathogens and disease.
[43] Alexandros Stamatakis,et al. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies , 2015, Systematic biology.
[44] Timothy L. Tickle,et al. Compact graphical representation of phylogenetic data and metadata with GraPhlAn , 2015, PeerJ.
[45] F. Balloux,et al. Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain , 2015, Nature Communications.
[46] S. Guindon,et al. How well can the exponential-growth coalescent approximate constant-rate birth–death population dynamics? , 2015, Proceedings of the Royal Society B: Biological Sciences.
[47] P. Beckert,et al. PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data , 2015, Journal of Clinical Microbiology.
[48] Nalin Rastogi,et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage , 2015, Nature Genetics.
[49] S. Niemann,et al. Mycobacterium tuberculosis Pyrazinamide Resistance Determinants: a Multicenter Study , 2014, mBio.
[50] Emma S McBryde,et al. Construction of a mathematical model for tuberculosis transmission in highly endemic regions of the Asia-Pacific. , 2014, Journal of theoretical biology.
[51] Francesc Coll,et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains , 2014, Nature Communications.
[52] Stefan Niemann,et al. Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach , 2014, Journal of Clinical Microbiology.
[53] Alexandra A. L. Pennhag,et al. Comparison between RFLP and MIRU-VNTR Genotyping of Mycobacterium tuberculosis Strains Isolated in Stockholm 2009 to 2011 , 2014, PloS one.
[54] Dong Xie,et al. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..
[55] Tim E A Peto,et al. Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study , 2014, The Lancet. Respiratory medicine.
[56] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[57] E. Kurbatova,et al. Epidemiology of pyrazinamide-resistant tuberculosis in the United States, 1999-2009. , 2013, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[58] Marc Lipsitch,et al. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug resistant tuberculosis , 2013, Nature Genetics.
[59] Marisa Klopper,et al. Emergence and Spread of Extensively and Totally Drug-Resistant Tuberculosis, South Africa , 2013, Emerging infectious diseases.
[60] Julian Parkhill,et al. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data , 2013, BMC Infectious Diseases.
[61] Stefan Niemann,et al. Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study , 2013, PLoS medicine.
[62] Daniel J. Wilson,et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study , 2013, The Lancet. Infectious diseases.
[63] M. Chase,et al. The mutation rate of mycobacterial repetitive unit loci in strains of M. tuberculosis from cynomolgus macaque infection , 2013, BMC Genomics.
[64] Nigel J. Martin,et al. SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences , 2012, Bioinform..
[65] G. Marks,et al. Contact investigation for tuberculosis: a systematic review and meta-analysis , 2012, European Respiratory Journal.
[66] Caroline O. Buckee,et al. Digital Epidemiology , 2012, PLoS Comput. Biol..
[67] S. Niemann,et al. Evaluation of Mycobacterium tuberculosis Typing Methods in a 4-Year Study in Schleswig-Holstein, Northern Germany , 2011, Journal of Clinical Microbiology.
[68] Steven J. M. Jones,et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. , 2011, The New England journal of medicine.
[69] F. Drobniewski,et al. Molecular Epidemiology of Mycobacterium tuberculosis , 2011 .
[70] P. Small,et al. Strain classification of Mycobacterium tuberculosis: congruence between large sequence polymorphisms and spoligotypes. , 2011, The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.
[71] Adamandia Kapopoulou,et al. TubercuList--10 years after. , 2011, Tuberculosis.
[72] Jeet Sukumaran,et al. DendroPy: a Python library for phylogenetic computing , 2010, Bioinform..
[73] Stefan Niemann,et al. Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies , 2009, PloS one.
[74] Hadley Wickham,et al. ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .
[75] Jeffrey R. Driscoll,et al. Spoligotyping for molecular epidemiology of the Mycobacterium tuberculosis complex. , 2009, Methods in molecular biology.
[76] Falk Hildebrand,et al. Origin, Spread and Demography of the Mycobacterium tuberculosis Complex , 2008, PLoS pathogens.
[77] Nalin Rastogi,et al. Use of cluster-graphs from spoligotyping data to study genotype similarities and a comparison of three indices to quantify recent tuberculosis transmission among culture positive cases in French Guiana during a eight year period , 2008, BMC infectious diseases.
[78] Nalin Rastogi,et al. Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis , 2006, Journal of Clinical Microbiology.
[79] S. Ho,et al. Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.
[80] Jonathan Crabtree,et al. Global Phylogeny of Mycobacterium tuberculosis Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set , 2006, Journal of bacteriology.
[81] O. Pybus,et al. Bayesian coalescent inference of past population dynamics from molecular sequences. , 2005, Molecular biology and evolution.
[82] M. Behr,et al. Sensitivities and Specificities of Spoligotyping and Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing Methods for Studying Molecular Epidemiology of Tuberculosis , 2005, Journal of Clinical Microbiology.
[83] M. Behr,et al. Microevolution of the Direct Repeat Region of Mycobacterium tuberculosis: Implications for Interpretation of Spoligotyping Data , 2002, Journal of Clinical Microbiology.
[84] Claudine Médigue,et al. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. , 2002, Microbiology.
[85] S. Niemann,et al. Epidemiology of Tuberculosis in Hamburg, Germany: Long-Term Population-Based Analysis Applying Classical and Molecular Epidemiological Techniques , 2002, Journal of Clinical Microbiology.
[86] L. O.,et al. A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data , 2002 .
[87] P. Lewis. A likelihood approach to estimating phylogeny from discrete morphological character data. , 2001, Systematic biology.
[88] M. Behr,et al. Predictive value of contact investigation for identifying recent transmission of Mycobacterium tuberculosis. , 1998, American journal of respiratory and critical care medicine.
[89] B. Barrell,et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence , 1998, Nature.
[90] M. Aziz,et al. Guidelines for surveillance of drug resistance in tuberculosis , 2009 .
[91] C. Locht,et al. Identification of novel intergenic repetitive units in a mycobacterial two‐component system operon , 1997, Molecular microbiology.
[92] B. Gicquel,et al. Evaluation of spoligotyping in a study of the transmission of Mycobacterium tuberculosis , 1997, Journal of clinical microbiology.
[93] D van Soolingen,et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology , 1997, Journal of clinical microbiology.
[94] G. Schoolnik,et al. The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods. , 1994, The New England journal of medicine.
[95] J. T. Crawford,et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology , 1993, Journal of clinical microbiology.
[96] J. T. Crawford,et al. IS6110, an IS-like element of Mycobacterium tuberculosis complex , 1990, Nucleic Acids Res..