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For: Marciano DC, Wang C, Hsu TK, Bourquard T, Atri B, Nehring RB, Abel NS, Bowling EA, Chen TJ, Lurie PD, Katsonis P, Rosenberg SM, Herman C, Lichtarge O. Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli. Nat Commun 2022;13:3189. [PMID: 35680894 PMCID: PMC9184624 DOI: 10.1038/s41467-022-30889-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/24/2022] [Indexed: 11/08/2022]  Open
Number Cited by Other Article(s)
1
O'Reilly P, Loiselle G, Darragh R, Slipski C, Bay DC. Reviewing the complexities of bacterial biocide susceptibility and in vitro biocide adaptation methodologies. NPJ ANTIMICROBIALS AND RESISTANCE 2025;3:39. [PMID: 40360746 PMCID: PMC12075810 DOI: 10.1038/s44259-025-00108-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 04/10/2025] [Indexed: 05/15/2025]
2
Yu XQ, Yang H, Feng HZ, Hou J, Tian JQ, Niu SM, You CG, Tao XY, Zhang SP, Wang ZP, He YX. Targeting efflux pumps prevents the multi-step evolution of high-level resistance to fluoroquinolone in Pseudomonas aeruginosa. Microbiol Spectr 2025;13:e0298124. [PMID: 39982069 PMCID: PMC11960432 DOI: 10.1128/spectrum.02981-24] [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: 11/18/2024] [Accepted: 01/08/2025] [Indexed: 02/22/2025]  Open
3
Shibai A, Izutsu M, Kotani H, Furusawa C. Quantitative analysis of relationship between mutation rate and speed of adaptation under antibiotic exposure in Escherichia coli. PLoS Genet 2025;21:e1011627. [PMID: 40153704 PMCID: PMC11975134 DOI: 10.1371/journal.pgen.1011627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 04/07/2025] [Accepted: 02/17/2025] [Indexed: 03/30/2025]  Open
4
Guharajan S, Parisutham V, Brewster RC. A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators. Nucleic Acids Res 2025;53:gkaf058. [PMID: 39921566 PMCID: PMC11806353 DOI: 10.1093/nar/gkaf058] [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: 08/23/2024] [Revised: 01/08/2025] [Accepted: 01/24/2025] [Indexed: 02/10/2025]  Open
5
Lemée P, Charron R, Bridier A. Genomic Pipeline for Analysis of Mutational Events in Bacteria. Methods Mol Biol 2025;2852:211-222. [PMID: 39235747 DOI: 10.1007/978-1-0716-4100-2_15] [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: 09/06/2024]
6
Mahmud Z, Manik MRK, Rahman A, Karim MM, Islam LN. Impact of untreated tannery wastewater in the evolution of multidrug-resistant bacteria in Bangladesh. Sci Rep 2024;14:20379. [PMID: 39223208 PMCID: PMC11369239 DOI: 10.1038/s41598-024-71472-6] [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: 03/06/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]  Open
7
Gupta YD, Bhandary S. Artificial Intelligence for Understanding Mechanisms of Antimicrobial Resistance and Antimicrobial Discovery. ARTIFICIAL INTELLIGENCE AND MACHINE LEARNING IN DRUG DESIGN AND DEVELOPMENT 2024:117-156. [DOI: 10.1002/9781394234196.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
8
Zeng JY, Li W, Su JQ, Wang YZ, Li Y, Yao H. Manure application amplified the co-selection of quaternary ammonium disinfectant and antibiotic on soil antibiotic resistome. JOURNAL OF HAZARDOUS MATERIALS 2024;468:133792. [PMID: 38368685 DOI: 10.1016/j.jhazmat.2024.133792] [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: 10/13/2023] [Revised: 01/17/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
9
Ghoshal M, Bechtel TD, Gibbons JG, McLandsborough L. Adaptive laboratory evolution of Salmonella enterica in acid stress. Front Microbiol 2023;14:1285421. [PMID: 38033570 PMCID: PMC10687551 DOI: 10.3389/fmicb.2023.1285421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023]  Open
10
Shapiro D, Lee K, Asmussen J, Bourquard T, Lichtarge O. Evolutionary Action-Machine Learning Model Identifies Candidate Genes Associated With Early-Onset Coronary Artery Disease. J Am Heart Assoc 2023;12:e029103. [PMID: 37642027 PMCID: PMC10547338 DOI: 10.1161/jaha.122.029103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
11
Manik RK, Mahmud Z, Mishu ID, Hossen MS, Howlader ZH, Nabi AHMN. Multidrug Resistance Profiles and Resistance Mechanisms to β-Lactams and Fluoroquinolones in Bacterial Isolates from Hospital Wastewater in Bangladesh. Curr Issues Mol Biol 2023;45:6485-6502. [PMID: 37623228 PMCID: PMC10453463 DOI: 10.3390/cimb45080409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/26/2023]  Open
12
Wang C, Govindarajan H, Katsonis P, Lichtarge O. ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis. Bioinformatics 2023;39:btad467. [PMID: 37522889 PMCID: PMC10412404 DOI: 10.1093/bioinformatics/btad467] [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: 01/06/2023] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/01/2023]  Open
13
Konecki DM, Hamrick S, Wang C, Agosto MA, Wensel TG, Lichtarge O. CovET: A covariation-evolutionary trace method that identifies protein structure-function modules. J Biol Chem 2023;299:104896. [PMID: 37290531 PMCID: PMC10338321 DOI: 10.1016/j.jbc.2023.104896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]  Open
14
Artificial Intelligence for Antimicrobial Resistance Prediction: Challenges and Opportunities towards Practical Implementation. Antibiotics (Basel) 2023;12:antibiotics12030523. [PMID: 36978390 PMCID: PMC10044311 DOI: 10.3390/antibiotics12030523] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]  Open
15
A Systematic Review on the Occurrence of Antimicrobial-Resistant Escherichia coli in Poultry and Poultry Environments in Bangladesh between 2010 and 2021. BIOMED RESEARCH INTERNATIONAL 2023;2023:2425564. [PMID: 36778056 PMCID: PMC9908353 DOI: 10.1155/2023/2425564] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/26/2022] [Accepted: 01/19/2023] [Indexed: 02/04/2023]
16
Johnstone KF, Herzberg MC. Antimicrobial peptides: Defending the mucosal epithelial barrier. FRONTIERS IN ORAL HEALTH 2022;3:958480. [PMID: 35979535 PMCID: PMC9376388 DOI: 10.3389/froh.2022.958480] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022]  Open
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