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For: Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol 2015;11:e1004041. [PMID: 25675341 PMCID: PMC4326465 DOI: 10.1371/journal.pcbi.1004041] [Citation(s) in RCA: 607] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/16/2014] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
51
Krisna MA, Jolley KA, Monteith W, Boubour A, Hamers RL, Brueggemann AB, Harrison OB, Maiden MCJ. Development and implementation of a core genome multilocus sequence typing scheme for Haemophilus influenzae. Microb Genom 2024;10:001281. [PMID: 39120932 PMCID: PMC11315579 DOI: 10.1099/mgen.0.001281] [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: 04/22/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]  Open
52
Backman T, Latorre SM, Symeonidi E, Muszyński A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A phage tail-like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria. Science 2024;384:eado0713. [PMID: 38870284 PMCID: PMC11404688 DOI: 10.1126/science.ado0713] [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: 01/16/2024] [Accepted: 04/24/2024] [Indexed: 06/15/2024]
53
Taylor AJ, Yahara K, Pascoe B, Ko S, Mageiros L, Mourkas E, Calland JK, Puranen S, Hitchings MD, Jolley KA, Kobras CM, Bayliss S, Williams NJ, van Vliet AHM, Parkhill J, Maiden MCJ, Corander J, Hurst LD, Falush D, Keim P, Didelot X, Kelly DJ, Sheppard SK. Epistasis, core-genome disharmony, and adaptation in recombining bacteria. mBio 2024;15:e0058124. [PMID: 38683013 PMCID: PMC11237541 DOI: 10.1128/mbio.00581-24] [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: 02/27/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024]  Open
54
Yin Z, Liang J, Zhang M, Chen B, Yu Z, Tian X, Deng X, Peng L. Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;927:172251. [PMID: 38604355 DOI: 10.1016/j.scitotenv.2024.172251] [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: 12/31/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
55
Yamaguchi T, Furuno K, Komori K, Abe T, Sato T, Ogihara S, Aoki K, Ishii Y, Tateda K. Evolutionary dynamics of the novel ST22-PT methicillin-resistant Staphylococcus aureus clone co-harbouring Panton-Valentine leucocidin and duplicated toxic shock syndrome toxin 1 genes. Clin Microbiol Infect 2024;30:779-786. [PMID: 38408643 DOI: 10.1016/j.cmi.2024.02.020] [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: 11/06/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
56
Hayama B, Harada S, Suzuki M, Doi Y, Nomura Y, Aoki K, Takehana K, Akatsuchi T, Enokida T, Takeda K, Seto A, Mitani H, Ohkushi D. Outbreak of Streptococcus pyogenes emm89 ST646 in a head and neck surgical oncology ward. Microbiol Spectr 2024;12:e0426023. [PMID: 38587390 PMCID: PMC11064547 DOI: 10.1128/spectrum.04260-23] [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: 12/20/2023] [Accepted: 03/18/2024] [Indexed: 04/09/2024]  Open
57
Morel-Letelier I, Yuen B, Kück AC, Camacho-García YE, Petersen JM, Lara M, Leray M, Eisen JA, Osvatic JT, Gros O, Wilkins LGE. Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts. PLoS Genet 2024;20:e1011295. [PMID: 38820540 PMCID: PMC11168628 DOI: 10.1371/journal.pgen.1011295] [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: 11/17/2023] [Revised: 06/12/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024]  Open
58
Torrance EL, Burton C, Diop A, Bobay LM. Evolution of homologous recombination rates across bacteria. Proc Natl Acad Sci U S A 2024;121:e2316302121. [PMID: 38657048 PMCID: PMC11067023 DOI: 10.1073/pnas.2316302121] [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: 09/19/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024]  Open
59
Rodriguez-Ruiz JP, Xavier BB, Stöhr W, van Heirstraeten L, Lammens C, Finn A, Goossens H, Bielicki JA, Sharland M, Malhotra-Kumar S. High-resolution genomics identifies pneumococcal diversity and persistence of vaccine types in children with community-acquired pneumonia in the UK and Ireland. BMC Microbiol 2024;24:146. [PMID: 38678217 PMCID: PMC11055344 DOI: 10.1186/s12866-024-03300-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: 12/22/2023] [Accepted: 04/11/2024] [Indexed: 04/29/2024]  Open
60
Atre M, Joshi B, Babu J, Sawant S, Sharma S, Sankar TS. Origin, evolution, and maintenance of gene-strand bias in bacteria. Nucleic Acids Res 2024;52:3493-3509. [PMID: 38442257 DOI: 10.1093/nar/gkae155] [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: 08/11/2023] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]  Open
61
Serra Moncadas L, Hofer C, Bulzu PA, Pernthaler J, Andrei AS. Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis. Nat Commun 2024;15:3421. [PMID: 38653968 PMCID: PMC11039613 DOI: 10.1038/s41467-024-47767-7] [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: 07/18/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024]  Open
62
Sterzi L, Nodari R, Di Marco F, Ferrando ML, Saluzzo F, Spitaleri A, Allahverdi H, Papaleo S, Panelli S, Rimoldi SG, Batisti Biffignandi G, Corbella M, Cavallero A, Prati P, Farina C, Cirillo DM, Zuccotti G, Bandi C, Comandatore F. Genetic barriers more than environmental associations explain Serratia marcescens population structure. Commun Biol 2024;7:468. [PMID: 38632370 PMCID: PMC11023947 DOI: 10.1038/s42003-024-06069-w] [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: 11/02/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024]  Open
63
Zhang W, Wang Y, Wang K, Li J, Liu J, Li S, Song L, Liao C, Yang X, Li P, Liu X. Hybrid Sequencing-Based Genomic Analysis of Klebsiella pneumoniae from Urinary Tract Infections Among Inpatients at a Tertiary Hospital in Beijing. Infect Drug Resist 2024;17:1447-1457. [PMID: 38628244 PMCID: PMC11020236 DOI: 10.2147/idr.s448253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/26/2024] [Indexed: 04/19/2024]  Open
64
Briand M, Boccarossa A, Rieux A, Jacques MA, Ganlanon L, Johnson C, Eveillard M, Marsollier L, Marion E. Emergence and spread of Mycobacterium ulcerans at different geographic scales. Microbiol Spectr 2024;12:e0382723. [PMID: 38441471 PMCID: PMC10986537 DOI: 10.1128/spectrum.03827-23] [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: 11/10/2023] [Accepted: 02/10/2024] [Indexed: 04/06/2024]  Open
65
Lyulina AS, Liu Z, Good BH. Linkage equilibrium between rare mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587282. [PMID: 38617331 PMCID: PMC11014483 DOI: 10.1101/2024.03.28.587282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
66
Buultjens AH, Vandelannoote K, Mercoulia K, Ballard S, Sloggett C, Howden BP, Seemann T, Stinear TP. High performance Legionella pneumophila source attribution using genomics-based machine learning classification. Appl Environ Microbiol 2024;90:e0129223. [PMID: 38289130 PMCID: PMC10952463 DOI: 10.1128/aem.01292-23] [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: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 02/08/2024]  Open
67
Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP. Application of phylodynamics to identify spread of antimicrobial-resistant Escherichia coli between humans and canines in an urban environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;916:170139. [PMID: 38242459 DOI: 10.1016/j.scitotenv.2024.170139] [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: 08/29/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
68
Colombi E, Bertels F, Doulcier G, McConnell E, Pichugina T, Sohn KH, Straub C, McCann HC, Rainey PB. Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements. Proc Natl Acad Sci U S A 2024;121:e2309263121. [PMID: 38457521 PMCID: PMC10945833 DOI: 10.1073/pnas.2309263121] [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: 06/01/2023] [Accepted: 01/08/2024] [Indexed: 03/10/2024]  Open
69
Chen F, Yin Y, Chen H, Wang R, Wang S, Wang H. Global genetic diversity and Asian clades evolution: a phylogeographic study of Staphylococcus aureus sequence type 5. Antimicrob Agents Chemother 2024;68:e0117523. [PMID: 38259089 PMCID: PMC10916392 DOI: 10.1128/aac.01175-23] [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: 09/13/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024]  Open
70
Arizala D, Arif M. Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri. Genome Biol Evol 2024;16:evae032. [PMID: 38385549 PMCID: PMC10946231 DOI: 10.1093/gbe/evae032] [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: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/11/2024] [Indexed: 02/23/2024]  Open
71
Street TL, Sanderson ND, Barker L, Kavanagh J, Cole K, The GonFast Investigators Group, Llewelyn M, Eyre DW. Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing. Microb Genom 2024;10:001208. [PMID: 38529900 PMCID: PMC10995632 DOI: 10.1099/mgen.0.001208] [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: 12/20/2023] [Accepted: 02/10/2024] [Indexed: 03/27/2024]  Open
72
Majander K, Pla-Díaz M, du Plessis L, Arora N, Filippini J, Pezo-Lanfranco L, Eggers S, González-Candelas F, Schuenemann VJ. Redefining the treponemal history through pre-Columbian genomes from Brazil. Nature 2024;627:182-188. [PMID: 38267579 PMCID: PMC10917687 DOI: 10.1038/s41586-023-06965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
73
Wang H, Xia F, Xia Y, Li J, Hu Y, Deng Y, Zou M. Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance. BMC Genomics 2024;25:216. [PMID: 38413855 PMCID: PMC10898099 DOI: 10.1186/s12864-024-10146-z] [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: 08/06/2023] [Accepted: 02/19/2024] [Indexed: 02/29/2024]  Open
74
Backman T, Latorre SM, Symeonidi E, Muszyński A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.17.536465. [PMID: 38352526 PMCID: PMC10862724 DOI: 10.1101/2023.04.17.536465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
75
Luoto J, Keto-Timonen R, Kivistö R. Campylobacter species and genotype distribution in Finnish beef liver - Retail liver juice ideal for isolation and quantification. Int J Food Microbiol 2024;411:110524. [PMID: 38118359 DOI: 10.1016/j.ijfoodmicro.2023.110524] [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: 08/25/2023] [Revised: 10/18/2023] [Accepted: 12/10/2023] [Indexed: 12/22/2023]
76
Liu Z, Good BH. Dynamics of bacterial recombination in the human gut microbiome. PLoS Biol 2024;22:e3002472. [PMID: 38329938 PMCID: PMC10852326 DOI: 10.1371/journal.pbio.3002472] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/14/2023] [Indexed: 02/10/2024]  Open
77
Rafiqullah IM, Varghese R, Hellmann KT, Velmurugan A, Neeravi A, Kumar Daniel JL, Vidal JE, Kompithra RZ, Verghese VP, Veeraraghavan B, Robinson DA. Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India. Microb Genom 2024;10:001191. [PMID: 38315173 PMCID: PMC10926699 DOI: 10.1099/mgen.0.001191] [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: 10/11/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024]  Open
78
Pracser N, Zaiser A, Ying HMK, Pietzka A, Wagner M, Rychli K. Diverse Listeria monocytogenes in-house clones are present in a dynamic frozen vegetable processing environment. Int J Food Microbiol 2024;410:110479. [PMID: 37977080 DOI: 10.1016/j.ijfoodmicro.2023.110479] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
79
McInnes RS, Snaith AE, Dunn SJ, Papangeli M, Hardy KJ, Hussain A, van Schaik W. Integration of vanHAX downstream of a ribosomal RNA operon restores vancomycin resistance in a susceptible Enterococcus faecium strain. NPJ ANTIMICROBIALS AND RESISTANCE 2024;2:2. [PMID: 39843953 PMCID: PMC11702846 DOI: 10.1038/s44259-023-00017-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2025]
80
Grote A, Piscon B, Manson AL, Adani B, Cohen H, Livny J, Earl AM, Gal-Mor O. Persistent Salmonella infections in humans are associated with mutations in the BarA/SirA regulatory pathway. Cell Host Microbe 2024;32:79-92.e7. [PMID: 38211565 PMCID: PMC11410052 DOI: 10.1016/j.chom.2023.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2023] [Accepted: 12/06/2023] [Indexed: 01/13/2024]
81
Steensen K, Séneca J, Bartlau N, Yu XA, Hussain FA, Polz MF. Tailless and filamentous prophages are predominant in marine Vibrio. THE ISME JOURNAL 2024;18:wrae202. [PMID: 39423289 PMCID: PMC11630473 DOI: 10.1093/ismejo/wrae202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 09/05/2024] [Accepted: 10/17/2024] [Indexed: 10/21/2024]
82
Wang X, Feng X. Challenges in estimating effective population sizes from metagenome-assembled genomes. Front Microbiol 2024;14:1331583. [PMID: 38249456 PMCID: PMC10797056 DOI: 10.3389/fmicb.2023.1331583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024]  Open
83
Wang R, Zhang A, Sun S, Yin G, Wu X, Ding Q, Wang Q, Chen F, Wang S, van Dorp L, Zhang Y, Jin L, Wang X, Balloux F, Wang H. Increase in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64. Nat Commun 2024;15:67. [PMID: 38167298 PMCID: PMC10761919 DOI: 10.1038/s41467-023-44351-3] [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: 05/16/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]  Open
84
Carhuaricra-Huaman D, Setubal JC. Step-by-Step Bacterial Genome Comparison. Methods Mol Biol 2024;2802:107-134. [PMID: 38819558 DOI: 10.1007/978-1-0716-3838-5_5] [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: 06/01/2024]
85
Subedi A, Barrera LBTDL, Ivey ML, Egel DS, Kebede M, Kara S, Aysan Y, Minsavage GV, Roberts PD, Jones JB, Goss EM. Population Genomics Reveals an Emerging Lineage of Xanthomonas perforans on Pepper. PHYTOPATHOLOGY 2024;114:241-250. [PMID: 37432099 DOI: 10.1094/phyto-04-23-0128-r] [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: 07/12/2023]
86
Bansal K, Saroha T, Patil PP, Kumar S, Kumar S, Singhal L, Gautam V, Patil PB. Evolutionary trends of carbapenem-resistant and susceptible Acinetobacter baumannii isolates in a major tertiary care setting from North India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024;117:105542. [PMID: 38122920 DOI: 10.1016/j.meegid.2023.105542] [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: 09/28/2023] [Revised: 11/09/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
87
Aguilar-Bultet L, García-Martín AB, Vock I, Maurer Pekerman L, Stadler R, Schindler R, Battegay M, Stadler T, Gómez-Sanz E, Tschudin-Sutter S. Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients. Nat Commun 2023;14:8495. [PMID: 38129423 PMCID: PMC10739949 DOI: 10.1038/s41467-023-44285-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: 04/03/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]  Open
88
Petras JK, Elrod MG, Ty MC, Dawson P, O'Laughlin K, Gee JE, Hanson J, Boutwell C, Ainsworth G, Beesley CA, Saile E, Tiller R, Gulvik CA, Ware D, Sokol T, Balsamo G, Taylor K, Salzer JS, Bower WA, Weiner ZP, Negrón ME, Hoffmaster AR, Byers P. Locally Acquired Melioidosis Linked to Environment - Mississippi, 2020-2023. N Engl J Med 2023;389:2355-2362. [PMID: 38118023 PMCID: PMC10773590 DOI: 10.1056/nejmoa2306448] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
89
Cho ST, Mills EG, Griffith MP, Nordstrom HR, McElheny CL, Harrison LH, Doi Y, Van Tyne D. Evolution of extended-spectrum β-lactamase-producing ST131 Escherichia coli at a single hospital over 15 years. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571174. [PMID: 38168243 PMCID: PMC10760032 DOI: 10.1101/2023.12.11.571174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
90
Thorell K, Muñoz-Ramírez ZY, Wang D, Sandoval-Motta S, Boscolo Agostini R, Ghirotto S, Torres RC, Falush D, Camargo MC, Rabkin CS. The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes. Nat Commun 2023;14:8184. [PMID: 38081806 DOI: 10.1038/s41467] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/13/2023] [Indexed: 09/17/2024]  Open
91
Thorell K, Muñoz-Ramírez ZY, Wang D, Sandoval-Motta S, Boscolo Agostini R, Ghirotto S, Torres RC, Falush D, Camargo MC, Rabkin CS. The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes. Nat Commun 2023;14:8184. [PMID: 38081806 PMCID: PMC10713588 DOI: 10.1038/s41467-023-43562-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]  Open
92
Liu X, Yan Z, Ye L, Wang K, Li J, Lin Y, Liao C, Liu Y, Li P, Du M. Genomic epidemiological investigation of an outbreak of Serratia marcescens neurosurgical site infections associated with contaminated haircutting toolkits in a hospital barber shop. J Hosp Infect 2023;142:58-66. [PMID: 37774927 DOI: 10.1016/j.jhin.2023.09.013] [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: 07/19/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
93
Mosquera-Rendón J, Moreno-Herrera CX, Robledo J, Hurtado-Páez U. Genome-Wide Association Studies (GWAS) Approaches for the Detection of Genetic Variants Associated with Antibiotic Resistance: A Systematic Review. Microorganisms 2023;11:2866. [PMID: 38138010 PMCID: PMC10745584 DOI: 10.3390/microorganisms11122866] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 12/24/2023]  Open
94
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: 1.5] [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
95
Obolski U, Swarthout TD, Kalizang'oma A, Mwalukomo TS, Chan JM, Weight CM, Brown C, Cave R, Cornick J, Kamng'ona AW, Msefula J, Ercoli G, Brown JS, Lourenço J, Maiden MC, French N, Gupta S, Heyderman RS. The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi. Nat Commun 2023;14:7477. [PMID: 37978177 PMCID: PMC10656543 DOI: 10.1038/s41467-023-43160-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/02/2023] [Indexed: 11/19/2023]  Open
96
Salamzade R, McElheny CL, Manson AL, Earl AM, Shaikh N, Doi Y. Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic Escherichia coli among children in the United States. mSphere 2023;8:e0018423. [PMID: 37581436 PMCID: PMC10597468 DOI: 10.1128/msphere.00184-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/15/2023] [Indexed: 08/16/2023]  Open
97
Molteni C, Forni D, Cagliani R, Bravo IG, Sironi M. Evolution and diversity of nucleotide and dinucleotide composition in poxviruses. J Gen Virol 2023;104. [PMID: 37792576 DOI: 10.1099/jgv.0.001897] [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: 10/06/2023]  Open
98
Monteith W, Pascoe B, Mourkas E, Clark J, Hakim M, Hitchings MD, McCarthy N, Yahara K, Asakura H, Sheppard SK. Contrasting genes conferring short- and long-term biofilm adaptation in Listeria. Microb Genom 2023;9:001114. [PMID: 37850975 PMCID: PMC10634452 DOI: 10.1099/mgen.0.001114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023]  Open
99
Lassalle F, Al-Shalali S, Al-Hakimi M, Njamkepo E, Bashir IM, Dorman MJ, Rauzier J, Blackwell GA, Taylor-Brown A, Beale MA, Cazares A, Al-Somainy AA, Al-Mahbashi A, Almoayed K, Aldawla M, Al-Harazi A, Quilici ML, Weill FX, Dhabaan G, Thomson NR. Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen. Nat Microbiol 2023;8:1787-1798. [PMID: 37770747 PMCID: PMC10539172 DOI: 10.1038/s41564-023-01472-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
100
Kozhar O, Sitz RA, Woyda R, Legg L, Ibarra Caballero JR, Pearse IS, Abdo Z, Stewart JE. Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America. Sci Rep 2023;13:14852. [PMID: 37684300 PMCID: PMC10491777 DOI: 10.1038/s41598-023-41976-8] [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: 03/09/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]  Open
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