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For: Collins C, Didelot X. A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination. PLoS Comput Biol 2018;14:e1005958. [PMID: 29401456 DOI: 10.1371/journal.pcbi.1005958] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 02/15/2018] [Accepted: 12/30/2017] [Indexed: 11/28/2022]  Open
Number Cited by Other Article(s)
1
Yang Q, Wang X, Han M, Sheng H, Sun Y, Su L, Lu W, Li M, Wang S, Chen J, Cui S, Yang BW. Bacterial genome-wide association studies: exploring the genetic variation underlying bacterial phenotypes. Appl Environ Microbiol 2025:e0251224. [PMID: 40377303 DOI: 10.1128/aem.02512-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2025]  Open
2
Chibani S, Yacoub E, Boujemaa S, Mardassi H, Guglielmini J, Vaysse A, Khadraoui N, Mlik B, Ben Abdelmoumen Mardassi B. A genome-wide investigation of Mycoplasma hominis genes associated with gynecological infections or infertility. Front Microbiol 2025;16:1561378. [PMID: 40371111 PMCID: PMC12075135 DOI: 10.3389/fmicb.2025.1561378] [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: 01/15/2025] [Accepted: 03/18/2025] [Indexed: 05/16/2025]  Open
3
Zein-Eddine R, Le Meur A, Skouloubris S, Jelsbak L, Refrégier G, Myllykallio H. Genome wide analyses reveal the role of mutator phenotypes in Mycobacterium tuberculosis drug resistance emergence. NPJ ANTIMICROBIALS AND RESISTANCE 2025;3:35. [PMID: 40301520 PMCID: PMC12041279 DOI: 10.1038/s44259-025-00107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 04/10/2025] [Indexed: 05/01/2025]
4
Post V, Pascoe B, Hitchings MD, Erichsen C, Fischer J, Morgenstern M, Richards RG, Sheppard SK, Moriarty TF. Methicillin-sensitive Staphylococcus aureus lineages contribute towards poor patient outcomes in orthopaedic device-related infections. Microb Genom 2025;11:001390. [PMID: 40238650 PMCID: PMC12068410 DOI: 10.1099/mgen.0.001390] [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: 04/15/2024] [Accepted: 03/04/2025] [Indexed: 04/18/2025]  Open
5
Bujdoš D, Walter J, O'Toole PW. aurora: a machine learning gwas tool for analyzing microbial habitat adaptation. Genome Biol 2025;26:66. [PMID: 40122838 PMCID: PMC11930000 DOI: 10.1186/s13059-025-03524-7] [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: 02/22/2024] [Accepted: 03/03/2025] [Indexed: 03/25/2025]  Open
6
Tang T, Li R, Li H, Feng H. Adaptive laboratory evolution of Micrococcus luteus and identification of genes associated with radioresistance through genome-wide association study. Sci Rep 2025;15:5614. [PMID: 39955430 PMCID: PMC11830106 DOI: 10.1038/s41598-025-90434-0] [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: 10/20/2024] [Accepted: 02/13/2025] [Indexed: 02/17/2025]  Open
7
Tsoumtsa Meda L, Lagarde J, Guillier L, Roussel S, Douarre PE. Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits. Methods Mol Biol 2025;2852:223-253. [PMID: 39235748 DOI: 10.1007/978-1-0716-4100-2_16] [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]
8
Farzand R, Kimani MW, Mourkas E, Jama A, Clark JL, De Ste Croix M, Monteith WM, Lucidarme J, Oldfield NJ, Turner DPJ, Borrow R, Martinez-Pomares L, Sheppard SK, Bayliss CD. High-throughput phenotype-to-genotype testing of meningococcal carriage and disease isolates detects genetic determinants of disease-relevant phenotypic traits. mBio 2024;15:e0305924. [PMID: 39475240 PMCID: PMC11633189 DOI: 10.1128/mbio.03059-24] [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: 10/04/2024] [Accepted: 10/10/2024] [Indexed: 12/12/2024]  Open
9
Stévenin V, Coipan CE, Duijster JW, van Elsland DM, Voogd L, Bigey L, van Hoek AHAM, Wijnands LM, Janssen L, Akkermans JJLL, Neefjes-Borst A, Franz E, Mughini-Gras L, Neefjes J. Multi-omics analyses of cancer-linked clinical salmonellae reveal bacterial-induced host metabolic shift and mTOR-dependent cell transformation. Cell Rep 2024;43:114931. [PMID: 39488829 DOI: 10.1016/j.celrep.2024.114931] [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: 05/16/2024] [Revised: 09/16/2024] [Accepted: 10/15/2024] [Indexed: 11/05/2024]  Open
10
Dou X, Liu Y, Koutsoumanis K, Song C, Li Z, Zhang H, Yang F, Zhu H, Dong Q. Employing genome-wide association studies to investigate acid adaptation mechanisms in Listeria monocytogenes. Food Res Int 2024;196:115106. [PMID: 39614575 DOI: 10.1016/j.foodres.2024.115106] [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: 06/06/2024] [Revised: 09/13/2024] [Accepted: 09/13/2024] [Indexed: 12/01/2024]
11
Ayoub H, Kumar MS, Mehta R, Thomas P, Dubey M, Dhanze H, Ajantha GS, Bhilegaonkar KN, Salih HM, Cull CA, Veeranna RP, Amachawadi RG. Exploring genetic determinants of antimicrobial resistance in Brucella melitensis strains of human and animal origin from India. Front Microbiol 2024;15:1474957. [PMID: 39430107 PMCID: PMC11488214 DOI: 10.3389/fmicb.2024.1474957] [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: 08/06/2024] [Accepted: 09/18/2024] [Indexed: 10/22/2024]  Open
12
Schadron T, van den Beld M, Mughini-Gras L, Franz E. Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis. Front Microbiol 2024;15:1460335. [PMID: 39345263 PMCID: PMC11427404 DOI: 10.3389/fmicb.2024.1460335] [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: 07/05/2024] [Accepted: 08/27/2024] [Indexed: 10/01/2024]  Open
13
Xu JT, Lin Y, Cheng T, Deng JY. The rv2820c K114N mutation is related with capreomycin tolerance. Tuberculosis (Edinb) 2024;148:102551. [PMID: 39084000 DOI: 10.1016/j.tube.2024.102551] [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: 02/08/2024] [Revised: 06/17/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
14
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
15
Nair S, Barker CR, Bird M, Greig DR, Collins C, Painset A, Chattaway M, Pickard D, Larkin L, Gharbia S, Didelot X, Ribeca P. Presence of phage-plasmids in multiple serovars of Salmonella enterica. Microb Genom 2024;10:001247. [PMID: 38717818 PMCID: PMC11165635 DOI: 10.1099/mgen.0.001247] [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: 01/05/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024]  Open
16
Roder T, Pimentel G, Fuchsmann P, Stern MT, von Ah U, Vergères G, Peischl S, Brynildsrud O, Bruggmann R, Bär C. Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes. Genome Biol 2024;25:93. [PMID: 38605417 PMCID: PMC11007987 DOI: 10.1186/s13059-024-03233-7] [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: 04/27/2023] [Accepted: 03/29/2024] [Indexed: 04/13/2024]  Open
17
Chitwood MH, Colijn C, Yang C, Crudu V, Ciobanu N, Codreanu A, Kim J, Rancu I, Rhee K, Cohen T, Sobkowiak B. The recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova. Nat Commun 2024;15:2962. [PMID: 38580642 PMCID: PMC10997638 DOI: 10.1038/s41467-024-47282-9] [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: 11/29/2023] [Accepted: 03/26/2024] [Indexed: 04/07/2024]  Open
18
Guerrero-Egido G, Pintado A, Bretscher KM, Arias-Giraldo LM, Paulson JN, Spaink HP, Claessen D, Ramos C, Cazorla FM, Medema MH, Raaijmakers JM, Carrión VJ. bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria. Nat Commun 2024;15:2072. [PMID: 38453959 PMCID: PMC10920822 DOI: 10.1038/s41467-024-46302-y] [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: 07/13/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024]  Open
19
Batisti Biffignandi G, Chindelevitch L, Corbella M, Feil EJ, Sassera D, Lees JA. Optimising machine learning prediction of minimum inhibitory concentrations in Klebsiella pneumoniae. Microb Genom 2024;10:001222. [PMID: 38529944 PMCID: PMC10995625 DOI: 10.1099/mgen.0.001222] [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: 11/23/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024]  Open
20
Padhi AK, Maurya S. Uncovering the secrets of resistance: An introduction to computational methods in infectious disease research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024;139:173-220. [PMID: 38448135 DOI: 10.1016/bs.apcsb.2023.11.004] [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: 03/08/2024]
21
Baker M, Zhang X, Maciel-Guerra A, Babaarslan K, Dong Y, Wang W, Hu Y, Renney D, Liu L, Li H, Hossain M, Heeb S, Tong Z, Pearcy N, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China. Nat Commun 2024;15:206. [PMID: 38182559 PMCID: PMC10770378 DOI: 10.1038/s41467-023-44272-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]  Open
22
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]
23
McTavish KJ, Almeida RND, Tersigni J, Raimundi MK, Gong Y, Wang PW, Gontijo GF, de Souza RM, de Resende MLV, Desveaux D, Guttman DS. Pseudomonas syringae coffee blight is associated with the horizontal transfer of plasmid-encoded type III effectors. THE NEW PHYTOLOGIST 2024;241:409-429. [PMID: 37953378 DOI: 10.1111/nph.19364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/29/2023] [Indexed: 11/14/2023]
24
Yurtseven A, Buyanova S, Agrawal AA, Bochkareva OO, Kalinina OV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiol 2023;23:404. [PMID: 38124060 PMCID: PMC10731705 DOI: 10.1186/s12866-023-03147-7] [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: 09/12/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]  Open
25
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
26
Liu R, Zou Y, Wang WQ, Chen JH, Zhang L, Feng J, Yin JY, Mao XY, Li Q, Luo ZY, Zhang W, Wang DM. Gut microbial structural variation associates with immune checkpoint inhibitor response. Nat Commun 2023;14:7421. [PMID: 37973916 PMCID: PMC10654443 DOI: 10.1038/s41467-023-42997-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023]  Open
27
Hayati M, Sobkowiak B, Stockdale JE, Colijn C. Phylogenetic identification of influenza virus candidates for seasonal vaccines. SCIENCE ADVANCES 2023;9:eabp9185. [PMID: 37922357 PMCID: PMC10624341 DOI: 10.1126/sciadv.abp9185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 10/05/2023] [Indexed: 11/05/2023]
28
Brenner EP, Sreevatsan S. Global-scale GWAS associates a subset of SNPs with animal-adapted variants in M. tuberculosis complex. BMC Med Genomics 2023;16:260. [PMID: 37875894 PMCID: PMC10598944 DOI: 10.1186/s12920-023-01695-5] [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: 05/10/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023]  Open
29
Coluzzi C, Guillemet M, Mazzamurro F, Touchon M, Godfroid M, Achaz G, Glaser P, Rocha EPC. Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes. Mol Biol Evol 2023;40:msad217. [PMID: 37788575 PMCID: PMC10575684 DOI: 10.1093/molbev/msad217] [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: 07/04/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]  Open
30
Smith EN, van Aalst M, Tosens T, Niinemets Ü, Stich B, Morosinotto T, Alboresi A, Erb TJ, Gómez-Coronado PA, Tolleter D, Finazzi G, Curien G, Heinemann M, Ebenhöh O, Hibberd JM, Schlüter U, Sun T, Weber APM. Improving photosynthetic efficiency toward food security: Strategies, advances, and perspectives. MOLECULAR PLANT 2023;16:1547-1563. [PMID: 37660255 DOI: 10.1016/j.molp.2023.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
31
Eriksson L, Johannesen TB, Stenmark B, Jacobsson S, Säll O, Hedberg ST, Fredlund H, Stegger M, Mölling P. Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis. Microb Genom 2023;9:001124. [PMID: 37874326 PMCID: PMC10634450 DOI: 10.1099/mgen.0.001124] [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: 10/10/2023] [Indexed: 10/25/2023]  Open
32
Trinh P, Clausen DS, Willis AD. happi: a hierarchical approach to pangenomics inference. Genome Biol 2023;24:214. [PMID: 37773075 PMCID: PMC10540326 DOI: 10.1186/s13059-023-03040-6] [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: 05/04/2022] [Accepted: 08/16/2023] [Indexed: 09/30/2023]  Open
33
Giulieri SG, Guérillot R, Holmes NE, Baines SL, Hachani A, Hayes AS, Daniel DS, Seemann T, Davis JS, Van Hal S, Tong SYC, Stinear TP, Howden BP. A statistical genomics framework to trace bacterial genomic predictors of clinical outcomes in Staphylococcus aureus bacteremia. Cell Rep 2023;42:113069. [PMID: 37703880 DOI: 10.1016/j.celrep.2023.113069] [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: 12/01/2022] [Revised: 06/29/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023]  Open
34
Karlsen ST, Rau MH, Sánchez BJ, Jensen K, Zeidan AA. From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry. FEMS Microbiol Rev 2023;47:fuad030. [PMID: 37286882 PMCID: PMC10337747 DOI: 10.1093/femsre/fuad030] [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: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023]  Open
35
Carroll LM, Piacenza N, Cheng RA, Wiedmann M, Guldimann C. A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the USA lost the ability to produce pertussis-like toxin ArtAB. Microb Genom 2023;9:mgen001050. [PMID: 37402177 PMCID: PMC10438809 DOI: 10.1099/mgen.0.001050] [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: 07/27/2022] [Accepted: 05/23/2023] [Indexed: 07/06/2023]  Open
36
Palmieri N, Apostolakos I, Paudel S, Hess M. The genetic network underlying the evolution of pathogenicity in avian Escherichia coli. Front Vet Sci 2023;10:1195585. [PMID: 37415967 PMCID: PMC10321414 DOI: 10.3389/fvets.2023.1195585] [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: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]  Open
37
Mehta RS, Petit RA, Read TD, Weissman DB. Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes. BMC Bioinformatics 2023;24:243. [PMID: 37296404 PMCID: PMC10251594 DOI: 10.1186/s12859-023-05363-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]  Open
38
Donegan MA, Coletta-Filho HD, Almeida RPP. Parallel host shifts in a bacterial plant pathogen suggest independent genetic solutions. MOLECULAR PLANT PATHOLOGY 2023;24:527-535. [PMID: 36992605 DOI: 10.1111/mpp.13316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 05/18/2023]
39
Papudeshi B, Rusch DB, VanInsberghe D, Lively CM, Edwards RA, Bashey F. Host Association and Spatial Proximity Shape but Do Not Constrain Population Structure in the Mutualistic Symbiont Xenorhabdus bovienii. mBio 2023:e0043423. [PMID: 37154562 DOI: 10.1128/mbio.00434-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]  Open
40
Key FM, Khadka VD, Romo-González C, Blake KJ, Deng L, Lynn TC, Lee JC, Chiu IM, García-Romero MT, Lieberman TD. On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis. Cell Host Microbe 2023;31:593-603.e7. [PMID: 37054679 PMCID: PMC10263175 DOI: 10.1016/j.chom.2023.03.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/14/2023] [Accepted: 03/10/2023] [Indexed: 04/15/2023]
41
Demirjian C, Vailleau F, Berthomé R, Roux F. Genome-wide association studies in plant pathosystems: success or failure? TRENDS IN PLANT SCIENCE 2023;28:471-485. [PMID: 36522258 DOI: 10.1016/j.tplants.2022.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/28/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
42
Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes. Appl Environ Microbiol 2023;89:e0172722. [PMID: 36695629 PMCID: PMC9972950 DOI: 10.1128/aem.01727-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
43
Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates. mSphere 2023;8:e0049522. [PMID: 36794931 PMCID: PMC10117131 DOI: 10.1128/msphere.00495-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]  Open
44
Oggenfuss U, Croll D. Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen. PLoS Pathog 2023;19:e1011130. [PMID: 36787337 PMCID: PMC9970103 DOI: 10.1371/journal.ppat.1011130] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/27/2023] [Accepted: 01/18/2023] [Indexed: 02/15/2023]  Open
45
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: 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: 08/20/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023]  Open
46
Didelot X. Phylogenetic Analysis of Bacterial Pathogen Genomes. Methods Mol Biol 2023;2674:87-99. [PMID: 37258962 DOI: 10.1007/978-1-0716-3243-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Martinez-Zurita A, Cuomo CA. Genome-Wide Identification of Variants Associated with Antifungal Drug Resistance. Methods Mol Biol 2023;2658:81-103. [PMID: 37024697 DOI: 10.1007/978-1-0716-3155-3_7] [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] [Indexed: 04/08/2023]
48
Joyce LR, Youngblom MA, Cormaty H, Gartstein E, Barber KE, Akins RL, Pepperell CS, Palmer KL. Comparative Genomics of Streptococcus oralis Identifies Large Scale Homologous Recombination and a Genetic Variant Associated with Infection. mSphere 2022;7:e0050922. [PMID: 36321824 PMCID: PMC9769543 DOI: 10.1128/msphere.00509-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]  Open
49
dessouky YE, Elsayed SW, Abdelsalam NA, Saif NA, Álvarez-Ordóñez A, Elhadidy M. Genomic insights into zoonotic transmission and antimicrobial resistance in Campylobacter jejuni from farm to fork: a one health perspective. Gut Pathog 2022;14:44. [PMID: 36471447 PMCID: PMC9721040 DOI: 10.1186/s13099-022-00517-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/08/2022] [Indexed: 12/09/2022]  Open
50
Rodrigues RA, Pizauro LJL, Varani ADM, de Almeida CC, Silva SR, Cardozo MV, MacInnes JI, Kropinski AM, Melo PDC, Ávila FA. Comparative genomics study of Staphylococcus aureus isolated from cattle and humans reveals virulence patterns exclusively associated with bovine clinical mastitis strains. Front Microbiol 2022;13:1033675. [PMID: 36419431 PMCID: PMC9676464 DOI: 10.3389/fmicb.2022.1033675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/17/2022] [Indexed: 12/08/2023]  Open
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