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For: Menardo F, Duchêne S, Brites D, Gagneux S. The molecular clock of Mycobacterium tuberculosis. PLoS Pathog 2019;15:e1008067. [PMID: 31513651 PMCID: PMC6759198 DOI: 10.1371/journal.ppat.1008067] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/24/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022]  Open
Number Cited by Other Article(s)
1
Derelle R, von Wachsmann J, Mäklin T, Hellewell J, Russell T, Lalvani A, Chindelevitch L, Croucher NJ, Harris SR, Lees JA. Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis. Genome Res 2024;34:1661-1673. [PMID: 39406504 PMCID: PMC11529842 DOI: 10.1101/gr.279449.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 09/16/2024] [Indexed: 11/01/2024]
2
Wood AJ, Benton CH, Delahay RJ, Marion G, Palkopoulou E, Pooley CM, Smith GC, Kao RR. The utility of whole-genome sequencing to identify likely transmission pairs for pathogens with slow and variable evolution. Epidemics 2024;48:100787. [PMID: 39197305 DOI: 10.1016/j.epidem.2024.100787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/03/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024]  Open
3
Wang L, Lim DR, Phelan JE, Reyes LT, Palparan AG, Sanchez MGC, Asuncion LAA, Tujan MAA, Medado IAP, Daga CMA, Llames JHS, Mitarai S, Murase Y, Morishige Y, Ang CF, Malabad JCM, Montoya JC, Hafalla JC, Campino S, Hibberd ML, Ama CG, Basilio RP, La Paz EMCD, Clark TG. Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines. Sci Rep 2024;14:19602. [PMID: 39179783 PMCID: PMC11344074 DOI: 10.1038/s41598-024-70471-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024]  Open
4
Weimann A, Dinan AM, Ruis C, Bernut A, Pont S, Brown K, Ryan J, Santos L, Ellison L, Ukor E, Pandurangan AP, Krokowski S, Blundell TL, Welch M, Blane B, Judge K, Bousfield R, Brown N, Bryant JM, Kukavica-Ibrulj I, Rampioni G, Leoni L, Harrison PT, Peacock SJ, Thomson NR, Gauthier J, Fothergill JL, Levesque RC, Parkhill J, Floto RA. Evolution and host-specific adaptation of Pseudomonas aeruginosa. Science 2024;385:eadi0908. [PMID: 38963857 DOI: 10.1126/science.adi0908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/02/2024] [Indexed: 07/06/2024]
5
Pereira AC, Lourenço J, Themudo G, Botelho A, Cunha MV. Population structure and history of Mycobacterium bovis European 3 clonal complex reveal transmission across ecological corridors of unrecognized importance in Portugal. Microbiol Spectr 2024;12:e0382923. [PMID: 38771094 PMCID: PMC11218495 DOI: 10.1128/spectrum.03829-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024]  Open
6
Liu Z, Li X, Xiong H, Zhou Q, Yi H, Wu K, Zhou Z, Lu Y, Zhu Y, Zhou L, Zhang M, Gao J, Gao J, Chen S, Wang X, Wang W. Genomic and spatial analysis reveal the transmission dynamics of tuberculosis in areas with high incidence of Zhejiang, China: A prospective cohort study. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024;121:105603. [PMID: 38723983 DOI: 10.1016/j.meegid.2024.105603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/28/2024] [Accepted: 05/05/2024] [Indexed: 05/14/2024]
7
Austin RM, Honap TP, Mann AE, Hübner A, DeGaglia CMS, Warinner C, Zuckerman MK, Hofman CA. Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool. Sci Rep 2024;14:14720. [PMID: 38926415 PMCID: PMC11208530 DOI: 10.1038/s41598-024-64818-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]  Open
8
Bainomugisa A, Pandey S, O'Connor B, Syrmis M, Whiley D, Sintchenko V, Coin LJ, Marais BJ, Coulter C. Sustained transmission over two decades of a previously unrecognised MPT64 negative Mycobacterium tuberculosis strain in Queensland, Australia: a whole genome sequencing study. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024;47:101105. [PMID: 39022748 PMCID: PMC11253042 DOI: 10.1016/j.lanwpc.2024.101105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/09/2024] [Accepted: 05/16/2024] [Indexed: 07/20/2024]
9
Dixit A, Ektefaie Y, Kagal A, Freschi L, Karyakarte R, Lokhande R, Groschel M, Tornheim JA, Gupte N, Pradhan NN, Paradkar MS, Deshmukh S, Kadam D, Schito M, Engelthaler DM, Gupta A, Golub J, Mave V, Farhat M. Drug resistance and epidemiological success of modern Mycobacterium tuberculosis lineages in western India. J Infect Dis 2024:jiae240. [PMID: 38819323 DOI: 10.1093/infdis/jiae240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 06/01/2024]  Open
10
Sheinman M, Arndt PF, Massip F. Modeling the mosaic structure of bacterial genomes to infer their evolutionary history. Proc Natl Acad Sci U S A 2024;121:e2313367121. [PMID: 38517978 PMCID: PMC10990148 DOI: 10.1073/pnas.2313367121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/30/2024] [Indexed: 03/24/2024]  Open
11
Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O'Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, van Dorp L. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Med 2024;16:34. [PMID: 38374151 PMCID: PMC10877763 DOI: 10.1186/s13073-024-01289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024]  Open
12
Torres Ortiz A, Grandjean L. Phylogenetic Survival Analysis. Methods Mol Biol 2024;2833:121-128. [PMID: 38949706 DOI: 10.1007/978-1-0716-3981-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
13
Zein-Eddine R, Hak F, Le Meur A, Genestet C, Dumitrescu O, Guyeux C, Senelle G, Sola C, Refrégier G. The paradoxes of Mycobacterium tuberculosis molecular evolution and consequences for the inference of tuberculosis emergence date. Tuberculosis (Edinb) 2023;143S:102378. [PMID: 38012921 DOI: 10.1016/j.tube.2023.102378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 11/29/2023]
14
Pereira AC, Reis AC, Cunha MV. Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal. Emerg Microbes Infect 2023;12:2253340. [PMID: 37640285 PMCID: PMC10484045 DOI: 10.1080/22221751.2023.2253340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
15
Yenew B, Ghodousi A, Diriba G, Tesfaye E, Cabibbe AM, Amare M, Moga S, Alemu A, Dagne B, Sinshaw W, Mollalign H, Meaza A, Tadesse M, Gamtesa DF, Abebaw Y, Seid G, Zerihun B, Getu M, Chiacchiaretta M, Gaudin C, Marceau M, Didelot X, Tolera G, Abdella S, Kebede A, Getahun M, Mehammed Z, Supply P, Cirillo DM. A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex. Nat Commun 2023;14:7519. [PMID: 37980337 PMCID: PMC10657438 DOI: 10.1038/s41467-023-42755-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 10/18/2023] [Indexed: 11/20/2023]  Open
16
Rott P, Grinstead S, Dallot S, Foster ZSL, Daugrois JH, Fernandez E, Kaye CJ, Hendrickson L, Hu X, Adhikari B, Malapi M, Grünwald NJ, Roumagnac P, Mollov D. Genetic Diversity, Evolution, and Diagnosis of Sugarcane Yellow Leaf Virus from 19 Sugarcane-Producing Locations Worldwide. PLANT DISEASE 2023;107:3437-3447. [PMID: 37079008 DOI: 10.1094/pdis-10-22-2405-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
17
Silcocks M, Dunstan SJ. Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history. Commun Biol 2023;6:1037. [PMID: 37833496 PMCID: PMC10575886 DOI: 10.1038/s42003-023-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]  Open
18
Lempens P, Van Deun A, Aung KJM, Hossain MA, Behruznia M, Decroo T, Rigouts L, de Jong BC, Meehan CJ. Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh. Microb Genom 2023;9:001109. [PMID: 37750750 PMCID: PMC10569737 DOI: 10.1099/mgen.0.001109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023]  Open
19
Vargas R, Luna MJ, Freschi L, Marin M, Froom R, Murphy KC, Campbell EA, Ioerger TR, Sassetti CM, Farhat MR. Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A 2023;120:e2301394120. [PMID: 37399390 PMCID: PMC10334774 DOI: 10.1073/pnas.2301394120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/03/2023] [Indexed: 07/05/2023]  Open
20
Goig GA, Menardo F, Salaam-Dreyer Z, Dippenaar A, Streicher EM, Daniels J, Reuter A, Borrell S, Reinhard M, Doetsch A, Beisel C, Warren RM, Cox H, Gagneux S. Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study. THE LANCET. MICROBE 2023;4:e506-e515. [PMID: 37295446 PMCID: PMC10319636 DOI: 10.1016/s2666-5247(23)00110-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/26/2023] [Accepted: 03/01/2023] [Indexed: 06/12/2023]
21
Dubé JY, Behr MA. A nod to the bond between NOD2 and mycobacteria. PLoS Pathog 2023;19:e1011389. [PMID: 37262021 PMCID: PMC10234563 DOI: 10.1371/journal.ppat.1011389] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]  Open
22
Sanders JG, Sprockett DD, Li Y, Mjungu D, Lonsdorf EV, Ndjango JBN, Georgiev AV, Hart JA, Sanz CM, Morgan DB, Peeters M, Hahn BH, Moeller AH. Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. Nat Microbiol 2023;8:1039-1050. [PMID: 37169918 PMCID: PMC10860671 DOI: 10.1038/s41564-023-01388-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
23
Cramer N, Klockgether J, Tümmler B. Microevolution of Pseudomonas aeruginosa in the airways of people with cystic fibrosis. Curr Opin Immunol 2023;83:102328. [PMID: 37116385 DOI: 10.1016/j.coi.2023.102328] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/30/2023]
24
Żukowska L, Zygała-Pytlos D, Struś K, Zabost A, Kozińska M, Augustynowicz-Kopeć E, Dziadek J, Minias A. An overview of tuberculosis outbreaks reported in the years 2011-2020. BMC Infect Dis 2023;23:253. [PMID: 37081448 PMCID: PMC10116450 DOI: 10.1186/s12879-023-08197-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/24/2023] [Indexed: 04/22/2023]  Open
25
Jiang Q, Liu HC, Liu QY, Phelan JE, Tao FX, Zhao XQ, Wang J, Glynn JR, Takiff HE, Clark TG, Wan KL, Gao Q. The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China. Microbiol Spectr 2023;11:e0399122. [PMID: 36912683 PMCID: PMC10101056 DOI: 10.1128/spectrum.03991-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023]  Open
26
López MG, Campos-Herrero MI, Torres-Puente M, Cañas F, Comín J, Copado R, Wintringer P, Iqbal Z, Lagarejos E, Moreno-Molina M, Pérez-Lago L, Pino B, Sante L, García de Viedma D, Samper S, Comas I. Deciphering the Tangible Spatio-Temporal Spread of a 25-Year Tuberculosis Outbreak Boosted by Social Determinants. Microbiol Spectr 2023;11:e0282622. [PMID: 36786614 PMCID: PMC10100973 DOI: 10.1128/spectrum.02826-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023]  Open
27
Ashton PM, Cha J, Anscombe C, Thuong NTT, Thwaites GE, Walker TM. Distribution and origins of Mycobacterium tuberculosis L4 in Southeast Asia. Microb Genom 2023;9:mgen000955. [PMID: 36729036 PMCID: PMC9997747 DOI: 10.1099/mgen.0.000955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/21/2022] [Indexed: 02/03/2023]  Open
28
Sanabria GE, Sequera G, Aguirre S, Méndez J, Dos Santos PCP, Gustafson NW, Godoy M, Ortiz A, Cespedes C, Martínez G, García-Basteiro AL, Andrews JR, Croda J, Walter KS. Phylogeography and transmission of Mycobacterium tuberculosis spanning prisons and surrounding communities in Paraguay. Nat Commun 2023;14:303. [PMID: 36658111 PMCID: PMC9849832 DOI: 10.1038/s41467-023-35813-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023]  Open
29
Pan J, Li X, Zhang M, Lu Y, Zhu Y, Wu K, Wu Y, Wang W, Chen B, Liu Z, Wang X, Gao J. TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data. Bioinformatics 2022;39:6873737. [PMID: 36469333 PMCID: PMC9825751 DOI: 10.1093/bioinformatics/btac785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 10/26/2022] [Accepted: 12/02/2022] [Indexed: 12/11/2022]  Open
30
Goldstein IH, Bayer D, Barilar I, Kizito B, Matsiri O, Modongo C, Zetola NM, Niemann S, Minin VM, Shin SS. Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission. PLoS Comput Biol 2022;18:e1010696. [PMID: 36469509 PMCID: PMC9754595 DOI: 10.1371/journal.pcbi.1010696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 12/15/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022]  Open
31
van Doren TP. Biocultural perspectives of infectious diseases and demographic evolution: Tuberculosis and its comorbidities through history. Evol Anthropol 2022;32:100-117. [PMID: 36436141 DOI: 10.1002/evan.21970] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 06/09/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022]
32
Guellil M, van Dorp L, Inskip SA, Dittmar JM, Saag L, Tambets K, Hui R, Rose A, D’Atanasio E, Kriiska A, Varul L, Koekkelkoren AMHC, Goldina RD, Cessford C, Solnik A, Metspalu M, Krause J, Herbig A, Robb JE, Houldcroft CJ, Scheib CL. Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. SCIENCE ADVANCES 2022;8:eabo4435. [PMID: 35895820 PMCID: PMC9328674 DOI: 10.1126/sciadv.abo4435] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/10/2022] [Indexed: 05/05/2023]
33
Saavedra Cervera B, López MG, Chiner-Oms Á, García AM, Cancino-Muñoz I, Torres-Puente M, Villamayor L, Madrazo-Moya C, Mambuque E, Sequera GV, Respeito D, Blanco S, Augusto O, López-Varela E, García-Basteiro AL, Comas I. Fine-grain population structure and transmission patterns of Mycobacterium tuberculosis in southern Mozambique, a high TB/HIV burden area. Microb Genom 2022;8. [PMID: 35787782 PMCID: PMC9455694 DOI: 10.1099/mgen.0.000844] [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] [Indexed: 12/30/2022]  Open
34
Menardo F. Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis. eLife 2022;11:76780. [PMID: 35762734 PMCID: PMC9239681 DOI: 10.7554/elife.76780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022]  Open
35
Swargam S, Kumari I, Kumar A, Pradhan D, Alam A, Singh H, Jain A, Devi KR, Trivedi V, Sarma J, Hanif M, Narain K, Ehtesham NZ, Hasnain SE, Ahmad S. MycoVarP: Mycobacterium Variant and Drug Resistance Prediction Pipeline for Whole-Genome Sequence Data Analysis. FRONTIERS IN BIOINFORMATICS 2022;1:805338. [PMID: 36303799 PMCID: PMC9580932 DOI: 10.3389/fbinf.2021.805338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022]  Open
36
Ceres KM, Stanhope MJ, Gröhn YT. A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation. Microb Genom 2022;8:mgen000839. [PMID: 35763423 PMCID: PMC9455707 DOI: 10.1099/mgen.0.000839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/29/2022] [Indexed: 11/18/2022]  Open
37
Bainomugisa A, Lavu E, Pandey S, Majumdar S, Banamu J, Coulter C, Marais B, Coin L, Graham SM, du Cros P. Evolution and spread of a highly drug resistant strain of Mycobacterium tuberculosis in Papua New Guinea. BMC Infect Dis 2022;22:437. [PMID: 35524232 PMCID: PMC9077924 DOI: 10.1186/s12879-022-07414-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022]  Open
38
Walter KS, Dos Santos PCP, Gonçalves TO, da Silva BO, da Silva Santos A, de Cássia Leite A, da Silva AM, Figueira Moreira FM, de Oliveira RD, Lemos EF, Cunha E, Liu YE, Ko AI, Colijn C, Cohen T, Mathema B, Croda J, Andrews JR. The role of prisons in disseminating tuberculosis in Brazil: A genomic epidemiology study. LANCET REGIONAL HEALTH. AMERICAS 2022;9. [PMID: 35647574 PMCID: PMC9140320 DOI: 10.1016/j.lana.2022.100186] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Evidence for local and international spread of Mycobacterium avium subspecies paratuberculosis through whole genome sequencing of isolates from the island of Ireland. Vet Microbiol 2022;268:109416. [DOI: 10.1016/j.vetmic.2022.109416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/14/2022] [Accepted: 04/01/2022] [Indexed: 12/18/2022]
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Chiner-Oms Á, López MG, Moreno-Molina M, Furió V, Comas I. Gene evolutionary trajectories in Mycobacterium tuberculosis reveal temporal signs of selection. Proc Natl Acad Sci U S A 2022;119:e2113600119. [PMID: 35452305 PMCID: PMC9173582 DOI: 10.1073/pnas.2113600119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/17/2022] [Indexed: 12/20/2022]  Open
41
Cardona PJ, Català M, Prats C. The Origin and Maintenance of Tuberculosis Is Explained by the Induction of Smear-Negative Disease in the Paleolithic. Pathogens 2022;11:pathogens11030366. [PMID: 35335692 PMCID: PMC8955375 DOI: 10.3390/pathogens11030366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/05/2022] [Accepted: 03/15/2022] [Indexed: 12/05/2022]  Open
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Wollenberg KR, Jeffrey BM, Harris MA, Gabrielian A, Hurt DE, Rosenthal A. Patterns of genomic interrelatedness of publicly available samples in the TB portals database. Tuberculosis (Edinb) 2022;133:102171. [PMID: 35101846 PMCID: PMC8997244 DOI: 10.1016/j.tube.2022.102171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 10/19/2022]
43
Malyarchuk AB, Andreeva TV, Kuznetsova IL, Kunizheva SS, Protasova MS, Uralsky LI, Tyazhelova TV, Gusev FE, Manakhov AD, Rogaev EI. Genomics of Ancient Pathogens: First Advances and Prospects. BIOCHEMISTRY. BIOKHIMIIA 2022;87:242-258. [PMID: 35526849 PMCID: PMC8916790 DOI: 10.1134/s0006297922030051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/08/2022] [Accepted: 01/21/2022] [Indexed: 11/23/2022]
44
Yang C, Sobkowiak B, Naidu V, Codreanu A, Ciobanu N, Gunasekera KS, Chitwood MH, Alexandru S, Bivol S, Russi M, Havumaki J, Cudahy P, Fosburgh H, Allender CJ, Centner H, Engelthaler DM, Menzies NA, Warren JL, Crudu V, Colijn C, Cohen T. Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis. PLoS Med 2022;19:e1003933. [PMID: 35192619 PMCID: PMC8903246 DOI: 10.1371/journal.pmed.1003933] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/08/2022] [Accepted: 01/31/2022] [Indexed: 11/19/2022]  Open
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Guyeux C, Senelle G, Refrégier G, Bretelle-Establet F, Cambau E, Sola C. Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage. Epidemiol Infect 2022;150:1-25. [PMID: 35042579 PMCID: PMC8931808 DOI: 10.1017/s0950268822000048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022]  Open
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Torres Ortiz A, Coronel J, Vidal JR, Bonilla C, Moore DAJ, Gilman RH, Balloux F, Kon OM, Didelot X, Grandjean L. Genomic signatures of pre-resistance in Mycobacterium tuberculosis. Nat Commun 2021;12:7312. [PMID: 34911948 PMCID: PMC8674244 DOI: 10.1038/s41467-021-27616-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022]  Open
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van Tonder AJ, Thornton MJ, Conlan AJK, Jolley KA, Goolding L, Mitchell AP, Dale J, Palkopoulou E, Hogarth PJ, Hewinson RG, Wood JLN, Parkhill J. Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial. PLoS Pathog 2021;17:e1010075. [PMID: 34843579 PMCID: PMC8659364 DOI: 10.1371/journal.ppat.1010075] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 12/09/2021] [Accepted: 10/29/2021] [Indexed: 11/18/2022]  Open
48
Ruis C, Bryant JM, Bell SC, Thomson R, Davidson RM, Hasan NA, van Ingen J, Strong M, Floto RA, Parkhill J. Dissemination of Mycobacterium abscessus via global transmission networks. Nat Microbiol 2021;6:1279-1288. [PMID: 34545208 PMCID: PMC8478660 DOI: 10.1038/s41564-021-00963-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023]
49
Boom WH, Schaible UE, Achkar JM. The knowns and unknowns of latent Mycobacterium tuberculosis infection. J Clin Invest 2021;131:136222. [PMID: 33529162 DOI: 10.1172/jci136222] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
50
Calland JK, Pascoe B, Bayliss SC, Mourkas E, Berthenet E, Thorpe HA, Hitchings MD, Feil EJ, Corander J, Blaser MJ, Falush D, Sheppard SK. Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages. PLoS Genet 2021;17:e1009829. [PMID: 34582435 PMCID: PMC8500405 DOI: 10.1371/journal.pgen.1009829] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/08/2021] [Accepted: 09/20/2021] [Indexed: 11/20/2022]  Open
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