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For: Horesh G, Taylor-Brown A, McGimpsey S, Lassalle F, Corander J, Heinz E, Thomson NR. Different evolutionary trends form the twilight zone of the bacterial pan-genome. Microb Genom 2021;7. [PMID: 34559043 PMCID: PMC8715436 DOI: 10.1099/mgen.0.000670] [Citation(s) in RCA: 12] [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] [Indexed: 11/29/2022]  Open
Number Cited by Other Article(s)
1
Thirumoorthy TP, Jacob JJ, Velmurugan A, Teekaraman MP, Shah B, Iyer V, Maheshwari G, Trivedi U, Shah A, Patel P, Gaigawale A, M Y, Sathya Narayanan P, Mutreja A, Carey M, John J, Kang G, Veeraraghavan B. Recent emergence of cephalosporin-resistant Salmonella Typhi in India due to the endemic clone acquiring IncFIB(K) plasmid encoding blaCTX-M-15 gene. Microbiol Spectr 2025;13:e0087524. [PMID: 40208005 PMCID: PMC12054180 DOI: 10.1128/spectrum.00875-24] [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: 04/12/2024] [Accepted: 01/21/2025] [Indexed: 04/11/2025]  Open
2
Piper KR, Souza SSR, Ikhimiukor OO, Workman AA, Martin IW, Andam CP. Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli. BMC Genomics 2025;26:190. [PMID: 39994515 PMCID: PMC11853335 DOI: 10.1186/s12864-025-11367-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 02/14/2025] [Indexed: 02/26/2025]  Open
3
Bouzek H, Srinivasan S, Jones DS, McMahon EF, Strenk SM, Fiedler TL, Fredricks DN, Johnston CD. A Syntenic Pangenome for Gardnerella Reveals Taxonomic Boundaries and Stratification of Metabolic and Virulence Potential across Species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.19.636902. [PMID: 40027674 PMCID: PMC11870614 DOI: 10.1101/2025.02.19.636902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
4
Williams DJ, Hawkins A, Hernandez RE, Mariano G, Mathers K, Buchanan G, Stonier BJ, Inkster T, Leanord A, Chalmers JD, Thomson NR, Holden MTG, Coulthurst SJ. Competitive behaviors in Serratia marcescens are coordinately regulated by a lifestyle switch frequently inactivated in the clinical environment. Cell Host Microbe 2025;33:252-266.e5. [PMID: 39884275 DOI: 10.1016/j.chom.2025.01.001] [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: 07/31/2024] [Revised: 12/02/2024] [Accepted: 01/06/2025] [Indexed: 02/01/2025]
5
Sheng H, Zhao L, Suo J, Yang Q, Cao C, Chen J, Cui G, Fan Y, Ma Y, Huo S, Wu X, Yang T, Cui X, Chen S, Cui S, Yang B. Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken. Food Res Int 2024;197:115299. [PMID: 39577948 DOI: 10.1016/j.foodres.2024.115299] [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: 06/29/2024] [Revised: 10/06/2024] [Accepted: 10/31/2024] [Indexed: 11/24/2024]
6
Foo A, Brettell LE, Nichols HL, 2022 UW-Madison Capstone in Microbiology Students, Medina Muñoz M, Lysne JA, Dhokiya V, Hoque AF, Brackney DE, Caragata EP, Hutchinson ML, Jacobs-Lorena M, Lampe DJ, Martin E, Valiente Moro C, Povelones M, Short SM, Steven B, Xu J, Paustian TD, Rondon MR, Hughes GL, Coon KL, Heinz E. MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies. PLoS Biol 2024;22:e3002897. [PMID: 39546548 PMCID: PMC11633956 DOI: 10.1371/journal.pbio.3002897] [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: 10/26/2023] [Revised: 12/11/2024] [Accepted: 10/11/2024] [Indexed: 11/17/2024]  Open
7
Piper KR, Ikhimiukor OO, Souza SSR, Garcia-Aroca T, Andam CP. Evolutionary dynamics of the accessory genomes of Staphylococcus aureus. mSphere 2024;9:e0075123. [PMID: 38501935 PMCID: PMC11036810 DOI: 10.1128/msphere.00751-23] [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: 12/01/2023] [Accepted: 02/24/2024] [Indexed: 03/20/2024]  Open
8
Zepeda-Rivera M, Minot SS, Bouzek H, Wu H, Blanco-Míguez A, Manghi P, Jones DS, LaCourse KD, Wu Y, McMahon EF, Park SN, Lim YK, Kempchinsky AG, Willis AD, Cotton SL, Yost SC, Sicinska E, Kook JK, Dewhirst FE, Segata N, Bullman S, Johnston CD. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche. Nature 2024;628:424-432. [PMID: 38509359 PMCID: PMC11006615 DOI: 10.1038/s41586-024-07182-w] [Citation(s) in RCA: 121] [Impact Index Per Article: 121.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
9
Dong X, Jia H, Yu Y, Xiang Y, Zhang Y. Genomic revisitation and reclassification of the genus Providencia. mSphere 2024;9:e0073123. [PMID: 38412041 PMCID: PMC10964429 DOI: 10.1128/msphere.00731-23] [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: 11/28/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024]  Open
10
Raghuram V, Petit RA, Karol Z, Mehta R, Weissman DB, Read TD. Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577756. [PMID: 38352482 PMCID: PMC10862745 DOI: 10.1101/2024.01.29.577756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
11
Mehrotra T, Konar D, Pragasam AK, Kumar S, Jana P, Babele P, Paul D, Purohit A, Tanwar S, Bakshi S, Das S, Verma J, Talukdar D, Narendrakumar L, Kothidar A, Karmakar SP, Chaudhuri S, Pal S, Jain K, Srikanth CV, Sankar MJ, Atmakuri K, Agarwal R, Gaind R, Ballal M, Kammili N, Bhadra RK, Ramamurthy T, Nair GB, Das B. Antimicrobial resistance heterogeneity among multidrug-resistant Gram-negative pathogens: Phenotypic, genotypic, and proteomic analysis. Proc Natl Acad Sci U S A 2023;120:e2305465120. [PMID: 37549252 PMCID: PMC10434301 DOI: 10.1073/pnas.2305465120] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/07/2023] [Indexed: 08/09/2023]  Open
12
Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity. Microbiol Spectr 2022;10:e0311722. [PMID: 36318042 PMCID: PMC9769869 DOI: 10.1128/spectrum.03117-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
13
Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock. Proc Natl Acad Sci U S A 2022;119:e2211217119. [PMID: 36469788 PMCID: PMC9897428 DOI: 10.1073/pnas.2211217119] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]  Open
14
Cummins EA, Hall RJ, Connor C, McInerney JO, McNally A. Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types. Microb Genom 2022;8:mgen000903. [PMID: 36748558 PMCID: PMC9836092 DOI: 10.1099/mgen.0.000903] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/02/2022] [Indexed: 11/24/2022]  Open
15
Ramamurthy T, Pragasam AK, Taylor-Brown A, Will RC, Vasudevan K, Das B, Srivastava SK, Chowdhury G, Mukhopadhyay AK, Dutta S, Veeraraghavan B, Thomson NR, Sharma NC, Nair GB, Takeda Y, Ghosh A, Dougan G, Mutreja A. Vibrio cholerae O139 genomes provide a clue to why it may have failed to usher in the eighth cholera pandemic. Nat Commun 2022;13:3864. [PMID: 35790755 PMCID: PMC9256687 DOI: 10.1038/s41467-022-31391-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]  Open
16
Cummins EA, Hall RJ, McInerney JO, McNally A. Prokaryote pangenomes are dynamic entities. Curr Opin Microbiol 2022;66:73-78. [PMID: 35104691 DOI: 10.1016/j.mib.2022.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/24/2022]
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