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Number Cited by Other Article(s)
1
Teichmann L, Wenne M, Luitwieler S, Dugar G, Bengtsson-Palme J, ter Kuile B. Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE. PLoS One 2025;20:e0312223. [PMID: 39970152 PMCID: PMC11838884 DOI: 10.1371/journal.pone.0312223] [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: 10/03/2024] [Accepted: 12/27/2024] [Indexed: 02/21/2025]  Open
2
Pham NP, Gingras H, Godin C, Feng J, Groppi A, Nikolski M, Leprohon P, Ouellette M. Holistic understanding of trimethoprim resistance in Streptococcus pneumoniae using an integrative approach of genome-wide association study, resistance reconstruction, and machine learning. mBio 2024;15:e0136024. [PMID: 39120145 PMCID: PMC11389379 DOI: 10.1128/mbio.01360-24] [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: 05/03/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024]  Open
3
Jugas R, Vitkova H. ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing. BMC Bioinformatics 2024;25:233. [PMID: 38982375 PMCID: PMC11234778 DOI: 10.1186/s12859-024-05843-1] [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: 01/31/2024] [Accepted: 06/13/2024] [Indexed: 07/11/2024]  Open
4
Wang Z, Gu D, Hong Y, Hu Y, Gu J, Tang Y, Zhou X, Zhang Y, Jiao X, Li Q. Microevolution of Salmonella 4,[5],12:i:- derived from Salmonella enterica serovar Typhimurium through complicated transpositions. Cell Rep 2023;42:113227. [PMID: 37837619 DOI: 10.1016/j.celrep.2023.113227] [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: 01/24/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 10/16/2023]  Open
5
Long DR, Penewit K, Lo HY, Almazan J, Holmes EA, Bryan AB, Wolter DJ, Lewis JD, Waalkes A, Salipante SJ. In Vitro Selection Identifies Staphylococcus aureus Genes Influencing Biofilm Formation. Infect Immun 2023;91:e0053822. [PMID: 36847490 PMCID: PMC10016075 DOI: 10.1128/iai.00538-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023]  Open
6
Jiang J, Chen L, Chen X, Li P, Xu X, Fowler VG, van Duin D, Wang M. Carbapenemase-Encoding Gene Copy Number Estimator (CCNE): a Tool for Carbapenemase Gene Copy Number Estimation. Microbiol Spectr 2022;10:e0100022. [PMID: 35863018 PMCID: PMC9431437 DOI: 10.1128/spectrum.01000-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/14/2022] [Indexed: 11/20/2022]  Open
7
Jangir PK, Yang Q, Shaw LP, Caballero JD, Ogunlana L, Wheatley R, Walsh T, MacLean RC. Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of resistance to a last-resort antibiotic. eLife 2022;11:e78834. [PMID: 35943060 PMCID: PMC9363117 DOI: 10.7554/elife.78834] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/22/2022] [Indexed: 12/17/2022]  Open
8
Giulieri SG, Guérillot R, Duchene S, Hachani A, Daniel D, Seemann T, Davis JS, Tong SYC, Young BC, Wilson DJ, Stinear TP, Howden BP. Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections. eLife 2022;11:e77195. [PMID: 35699423 PMCID: PMC9270034 DOI: 10.7554/elife.77195] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022]  Open
9
Kapel N, Caballero JD, MacLean RC. Localized pmrB hypermutation drives the evolution of colistin heteroresistance. Cell Rep 2022;39:110929. [PMID: 35675785 PMCID: PMC9189680 DOI: 10.1016/j.celrep.2022.110929] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/02/2021] [Accepted: 05/16/2022] [Indexed: 11/16/2022]  Open
10
Werth BJ, Ashford NK, Penewit K, Waalkes A, Holmes EA, Bryan A, Salipante SJ. OUP accepted manuscript. JAC Antimicrob Resist 2022;4:dlac011. [PMID: 35156034 PMCID: PMC8827560 DOI: 10.1093/jacamr/dlac011] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/19/2022] [Indexed: 11/12/2022]  Open
11
Sicard A, Saponari M, Vanhove M, Castillo AI, Giampetruzzi A, Loconsole G, Saldarelli P, Boscia D, Neema C, Almeida RPP. Introduction and adaptation of an emerging pathogen to olive trees in Italy. Microb Genom 2021;7. [PMID: 34904938 PMCID: PMC8767334 DOI: 10.1099/mgen.0.000735] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
12
Wan Y, Mills E, Leung RC, Vieira A, Zhi X, Croucher NJ, Woodford N, Jauneikaite E, Ellington MJ, Sriskandan S. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microb Genom 2021;7:000702. [PMID: 34860151 PMCID: PMC8767348 DOI: 10.1099/mgen.0.000702] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/01/2021] [Indexed: 01/18/2023]  Open
13
Jugas R, Sedlar K, Vitek M, Nykrynova M, Barton V, Bezdicek M, Lengerova M, Skutkova H. CNproScan: Hybrid CNV detection for bacterial genomes. Genomics 2021;113:3103-3111. [PMID: 34224809 DOI: 10.1016/j.ygeno.2021.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 06/13/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
14
Shared and Unique Evolutionary Trajectories to Ciprofloxacin Resistance in Gram-Negative Bacterial Pathogens. mBio 2021;12:e0098721. [PMID: 34154405 PMCID: PMC8262867 DOI: 10.1128/mbio.00987-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
15
Shi L, Qin J, Zheng H, Guo Y, Zhang H, Zhong Y, Yang C, Dong S, Yang F, Wu Y, Zhao G, Song Y, Yang R, Wang P, Cui Y. New Genotype of Yersinia pestis Found in Live Rodents in Yunnan Province, China. Front Microbiol 2021;12:628335. [PMID: 33935990 PMCID: PMC8084289 DOI: 10.3389/fmicb.2021.628335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/24/2021] [Indexed: 12/11/2022]  Open
16
Roe C, Stegger M, Lilje B, Johannesen TB, Ng KL, Sieber RN, Driebe E, Engelthaler DM, Andersen PS. Genomic analyses of Staphylococcus aureus clonal complex 45 isolates does not distinguish nasal carriage from bacteraemia. Microb Genom 2020;6:mgen000403. [PMID: 32667872 PMCID: PMC7641415 DOI: 10.1099/mgen.0.000403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/16/2020] [Indexed: 11/20/2022]  Open
17
Wu L, Wang H, Xia Y, Xi R. CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome. Bioinformatics 2020;36:3890-3891. [DOI: 10.1093/bioinformatics/btaa208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/14/2020] [Accepted: 03/23/2020] [Indexed: 11/14/2022]  Open
18
San JE, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T. Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls. Front Microbiol 2020;10:3119. [PMID: 32082269 PMCID: PMC7002396 DOI: 10.3389/fmicb.2019.03119] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]  Open
19
The Copy Number of the spoVA 2mob Operon Determines Pressure Resistance of Bacillus Endospores. Appl Environ Microbiol 2019;85:AEM.01596-19. [PMID: 31375487 DOI: 10.1128/aem.01596-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 07/27/2019] [Indexed: 12/27/2022]  Open
20
Wardell SJT, Rehman A, Martin LW, Winstanley C, Patrick WM, Lamont IL. A large-scale whole-genome comparison shows that experimental evolution in response to antibiotics predicts changes in naturally evolved clinical Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019;63:AAC.01619-19. [PMID: 31570397 PMCID: PMC6879238 DOI: 10.1128/aac.01619-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 09/23/2019] [Indexed: 12/13/2022]  Open
21
Loss and Gain in the Evolution of the Salmonella enterica Serovar Gallinarum Biovar Pullorum Genome. mSphere 2019;4:4/2/e00627-18. [PMID: 30944215 PMCID: PMC6449608 DOI: 10.1128/msphere.00627-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
22
Desvillechabrol D, Bouchier C, Kennedy S, Cokelaer T. Sequana coverage: detection and characterization of genomic variations using running median and mixture models. Gigascience 2018;7:5091804. [PMID: 30192951 PMCID: PMC6275460 DOI: 10.1093/gigascience/giy110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 08/23/2018] [Indexed: 11/30/2022]  Open
23
Read Depth Analysis to Identify CNV in Bacteria Using CNOGpro. Methods Mol Biol 2018;1833:73-81. [PMID: 30039364 DOI: 10.1007/978-1-4939-8666-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
24
Parallel Evolution of Group B Streptococcus Hypervirulent Clonal Complex 17 Unveils New Pathoadaptive Mutations. mSystems 2017;2:mSystems00074-17. [PMID: 28904998 PMCID: PMC5585690 DOI: 10.1128/msystems.00074-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/10/2017] [Indexed: 12/21/2022]  Open
25
Brynildsrud O, Gulla S, Feil EJ, Nørstebø SF, Rhodes LD. Identifying copy number variation of the dominant virulence factors msa and p22 within genomes of the fish pathogen Renibacterium salmoninarum. Microb Genom 2016;2:e000055. [PMID: 28348850 PMCID: PMC5320689 DOI: 10.1099/mgen.0.000055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/17/2016] [Indexed: 11/24/2022]  Open
26
Perisin M, Vetter M, Gilbert JA, Bergelson J. 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies. ISME JOURNAL 2015;10:1020-4. [PMID: 26359911 DOI: 10.1038/ismej.2015.161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 11/09/2022]
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