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For: Cheng L, Connor TR, Sirén J, Aanensen DM, Corander J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol 2013;30:1224-8. [PMID: 23408797 PMCID: PMC3670731 DOI: 10.1093/molbev/mst028] [Citation(s) in RCA: 413] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
Number Cited by Other Article(s)
251
León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Francés-Cuesta C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, González Candelas F, Baquero F, Coque TM. Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species. Environ Microbiol 2019;21:3046-3062. [PMID: 31162871 DOI: 10.1111/1462-2920.14702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 05/20/2019] [Accepted: 06/01/2019] [Indexed: 11/29/2022]
252
Ozer EA, Nnah E, Didelot X, Whitaker RJ, Hauser AR. The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages. Genome Biol Evol 2019;11:1780-1796. [PMID: 31173069 PMCID: PMC6690169 DOI: 10.1093/gbe/evz119] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 02/06/2023]  Open
253
Liu T, Sun K, Csorba G, Zhang K, Zhang L, Zhao H, Jin L, Thong VD, Xiao Y, Feng J. Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae). Mol Phylogenet Evol 2019;139:106544. [PMID: 31252069 DOI: 10.1016/j.ympev.2019.106544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
254
Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J. Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Res 2019;47:5539-5549. [PMID: 31076776 PMCID: PMC6582336 DOI: 10.1093/nar/gkz361] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022]  Open
255
Azarian T, Ridgway JP, Yin Z, David MZ. Long-Term Intrahost Evolution of Methicillin Resistant Staphylococcus aureus Among Cystic Fibrosis Patients With Respiratory Carriage. Front Genet 2019;10:546. [PMID: 31244886 PMCID: PMC6581716 DOI: 10.3389/fgene.2019.00546] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/22/2019] [Indexed: 12/29/2022]  Open
256
Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia coli Lineage Sequence Type 648. Antimicrob Agents Chemother 2019;63:AAC.00243-19. [PMID: 30885899 DOI: 10.1128/aac.00243-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/11/2019] [Indexed: 01/10/2023]  Open
257
Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D. Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis. Nat Commun 2019;10:2176. [PMID: 31092817 PMCID: PMC6520353 DOI: 10.1038/s41467-019-09976-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022]  Open
258
Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ, Ho PL, du Plessis M, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, McGee L, Breiman RF, Bentley SD. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine 2019;43:338-346. [PMID: 31003929 PMCID: PMC6557916 DOI: 10.1016/j.ebiom.2019.04.021] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/25/2022]  Open
259
Cox K, McKeown N, Antonini G, Harvey D, Solano E, Van Breusegem A, Thomaes A. Phylogeographic structure and ecological niche modelling reveal signals of isolation and postglacial colonisation in the European stag beetle. PLoS One 2019;14:e0215860. [PMID: 31022224 PMCID: PMC6483211 DOI: 10.1371/journal.pone.0215860] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/09/2019] [Indexed: 12/13/2022]  Open
260
Du Y, Ma J, Yin Z, Liu K, Yao G, Xu W, Fan L, Du B, Ding Y, Wang C. Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis. BMC Genomics 2019;20:283. [PMID: 30975079 PMCID: PMC6458615 DOI: 10.1186/s12864-019-5646-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/27/2019] [Indexed: 02/03/2023]  Open
261
Dorman MJ, Kane L, Domman D, Turnbull JD, Cormie C, Fazal MA, Goulding DA, Russell JE, Alexander S, Thomson NR. The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One. Proc Biol Sci 2019;286:20182025. [PMID: 30966987 PMCID: PMC6501683 DOI: 10.1098/rspb.2018.2025] [Citation(s) in RCA: 14] [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: 09/13/2018] [Accepted: 03/21/2019] [Indexed: 02/01/2023]  Open
262
Peirano G, Matsumura Y, Adams MD, Bradford P, Motyl M, Chen L, Kreiswirth BN, Pitout JDD. Genomic Epidemiology of Global Carbapenemase-Producing Enterobacter spp., 2008-2014. Emerg Infect Dis 2019;24:1010-1019. [PMID: 29774858 PMCID: PMC6004858 DOI: 10.3201/eid2406.171648] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
263
Hyseni C, Garrick RC. The role of glacial-interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA. Ecol Evol 2019;9:4621-4636. [PMID: 31031931 PMCID: PMC6476779 DOI: 10.1002/ece3.5065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/27/2019] [Accepted: 02/25/2019] [Indexed: 11/30/2022]  Open
264
Zhang J, Yao J, Hu Z, Jueterbock A, Yotsukura N, Krupnova TN, Nagasato C, Duan D. Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica. Evol Appl 2019;12:791-803. [PMID: 30976310 PMCID: PMC6439492 DOI: 10.1111/eva.12756] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 11/22/2018] [Accepted: 12/09/2018] [Indexed: 01/04/2023]  Open
265
Wailan AM, Coll F, Heinz E, Tonkin-Hill G, Corander J, Feasey NA, Thomson NR. rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. Microb Genom 2019;5. [PMID: 30920366 PMCID: PMC6521585 DOI: 10.1099/mgen.0.000264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
266
Gouliouris T, Raven KE, Moradigaravand D, Ludden C, Coll F, Blane B, Naydenova P, Horner C, Brown NM, Corander J, Limmathurotsakul D, Parkhill J, Peacock SJ. Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment. Genome Res 2019;29:626-634. [PMID: 30898881 PMCID: PMC6442392 DOI: 10.1101/gr.232629.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/14/2019] [Indexed: 12/20/2022]
267
Park CJ, Andam CP. Within-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus. Front Microbiol 2019;10:552. [PMID: 30949149 PMCID: PMC6437091 DOI: 10.3389/fmicb.2019.00552] [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] [Received: 01/04/2019] [Accepted: 03/04/2019] [Indexed: 01/09/2023]  Open
268
van Tonder AJ, Bray JE, Jolley KA, Jansen van Rensburg M, Quirk SJ, Haraldsson G, Maiden MCJ, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Brueggemann AB. Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions. Front Microbiol 2019;10:317. [PMID: 30858837 PMCID: PMC6398412 DOI: 10.3389/fmicb.2019.00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/06/2019] [Indexed: 01/11/2023]  Open
269
Du Z, Ishikawa T, Liu H, Kamitani S, Tadauchi O, Cai W, Li H. Phylogeography of the Assassin Bug Sphedanolestes impressicollis in East Asia Inferred From Mitochondrial and Nuclear Gene Sequences. Int J Mol Sci 2019;20:ijms20051234. [PMID: 30870981 PMCID: PMC6429140 DOI: 10.3390/ijms20051234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 11/29/2022]  Open
270
Genomic Diversity, Virulence, and Antimicrobial Resistance of Klebsiella pneumoniae Strains from Cows and Humans. Appl Environ Microbiol 2019;85:AEM.02654-18. [PMID: 30610074 DOI: 10.1128/aem.02654-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/21/2018] [Indexed: 12/30/2022]  Open
271
Iván Pérez-Quiñonez C, Quiñonez-Velázquez C, García-Rodríguez FJ. Genetic homogeneity of the Pacific thread herring (Opisthonema libertate) (Günther, 1867) in the Eastern Pacific, inferred from mtDNA sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2019;30:517-524. [PMID: 30829095 DOI: 10.1080/24701394.2019.1570173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
272
Kachroo P, Eraso JM, Beres SB, Olsen RJ, Zhu L, Nasser W, Bernard PE, Cantu CC, Saavedra MO, Arredondo MJ, Strope B, Do H, Kumaraswami M, Vuopio J, Gröndahl-Yli-Hannuksela K, Kristinsson KG, Gottfredsson M, Pesonen M, Pensar J, Davenport ER, Clark AG, Corander J, Caugant DA, Gaini S, Magnussen MD, Kubiak SL, Nguyen HAT, Long SW, Porter AR, DeLeo FR, Musser JM. Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis. Nat Genet 2019;51:548-559. [PMID: 30778225 PMCID: PMC8547240 DOI: 10.1038/s41588-018-0343-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022]
273
Nguyen VT, Jamrozy D, Matamoros S, Carrique-Mas JJ, Ho HM, Thai QH, Nguyen TNM, Wagenaar JA, Thwaites G, Parkhill J, Schultsz C, Ngo TH. Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis. J Antimicrob Chemother 2019;74:561-570. [PMID: 30629197 PMCID: PMC6376849 DOI: 10.1093/jac/dky506] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 01/22/2023]  Open
274
Lee RS, Seemann T, Heffernan H, Kwong JC, Gonçalves da Silva A, Carter GP, Woodhouse R, Dyet KH, Bulach DM, Stinear TP, Howden BP, Williamson DA. Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand. J Antimicrob Chemother 2019;73:353-364. [PMID: 29182725 PMCID: PMC5890773 DOI: 10.1093/jac/dkx405] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/08/2017] [Indexed: 12/15/2022]  Open
275
Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP. Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13. Microb Genom 2019;5. [PMID: 30777813 PMCID: PMC6421351 DOI: 10.1099/mgen.0.000252] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
276
Pang R, Xie T, Wu Q, Li Y, Lei T, Zhang J, Ding Y, Wang J, Xue L, Chen M, Wei X, Zhang Y, Zhang S, Yang X. Comparative Genomic Analysis Reveals the Potential Risk of Vibrio parahaemolyticus Isolated From Ready-To-Eat Foods in China. Front Microbiol 2019;10:186. [PMID: 30792709 PMCID: PMC6374323 DOI: 10.3389/fmicb.2019.00186] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/23/2019] [Indexed: 11/13/2022]  Open
277
Asadi A, Montgelard C, Nazarizadeh M, Moghaddasi A, Fatemizadeh F, Simonov E, Kami HG, Kaboli M. Evolutionary history and postglacial colonization of an Asian pit viper (Gloydius halys caucasicus) into Transcaucasia revealed by phylogenetic and phylogeographic analyses. Sci Rep 2019;9:1224. [PMID: 30718614 PMCID: PMC6362119 DOI: 10.1038/s41598-018-37558-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/10/2018] [Indexed: 11/17/2022]  Open
278
Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Res 2019;29:304-316. [PMID: 30679308 PMCID: PMC6360808 DOI: 10.1101/gr.241455.118] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/10/2018] [Indexed: 12/02/2022]
279
Shi P, Cao L, Gong Y, Ma L, Song W, Chen J, Hoffmann AA, Wei S. Independently evolved and gene flow-accelerated pesticide resistance in two-spotted spider mites. Ecol Evol 2019;9:2206-2219. [PMID: 30847105 PMCID: PMC6392376 DOI: 10.1002/ece3.4916] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/20/2018] [Accepted: 12/31/2018] [Indexed: 12/29/2022]  Open
280
Rakotoarivelo AR, Goodman SM, Schoeman MC, Willows-Munro S. Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae). PeerJ 2019;7:e5866. [PMID: 30671293 PMCID: PMC6339777 DOI: 10.7717/peerj.5866] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022]  Open
281
Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella variicola. mBio 2018;9:mBio.02481-18. [PMID: 30563902 PMCID: PMC6299229 DOI: 10.1128/mbio.02481-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
282
Schubert B, Maddamsetti R, Nyman J, Farhat MR, Marks DS. Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings. Nat Microbiol 2018;4:328-338. [PMID: 30510172 DOI: 10.1038/s41564-018-0309-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/26/2018] [Indexed: 11/09/2022]
283
DiLeo MF, Husby A, Saastamoinen M. Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly. Evol Lett 2018;2:544-556. [PMID: 30564438 PMCID: PMC6292703 DOI: 10.1002/evl3.90] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022]  Open
284
Genome-wide analysis of Streptococcus pneumoniae serogroup 19 in the decade after the introduction of pneumococcal conjugate vaccines in Australia. Sci Rep 2018;8:16969. [PMID: 30446692 PMCID: PMC6240094 DOI: 10.1038/s41598-018-35270-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 10/18/2018] [Indexed: 11/09/2022]  Open
285
Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom. mBio 2018;9:mBio.01780-18. [PMID: 30401778 PMCID: PMC6222123 DOI: 10.1128/mbio.01780-18] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
286
Azarian T, Mitchell PK, Georgieva M, Thompson CM, Ghouila A, Pollard AJ, von Gottberg A, du Plessis M, Antonio M, Kwambana-Adams BA, Clarke SC, Everett D, Cornick J, Sadowy E, Hryniewicz W, Skoczynska A, Moïsi JC, McGee L, Beall B, Metcalf BJ, Breiman RF, Ho PL, Reid R, O’Brien KL, Gladstone RA, Bentley SD, Hanage WP. Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci. PLoS Pathog 2018;14:e1007438. [PMID: 30475919 PMCID: PMC6283594 DOI: 10.1371/journal.ppat.1007438] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/06/2018] [Accepted: 10/25/2018] [Indexed: 12/23/2022]  Open
287
Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis. Antimicrob Agents Chemother 2018;62:AAC.00898-18. [PMID: 30150477 PMCID: PMC6201123 DOI: 10.1128/aac.00898-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/18/2018] [Indexed: 12/29/2022]  Open
288
Palma F, Manfreda G, Silva M, Parisi A, Barker DOR, Taboada EN, Pasquali F, Rossi M. Genome-wide identification of geographical segregated genetic markers in Salmonella enterica serovar Typhimurium variant 4,[5],12:i:. Sci Rep 2018;8:15251. [PMID: 30323193 PMCID: PMC6189080 DOI: 10.1038/s41598-018-33266-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/22/2018] [Indexed: 01/18/2023]  Open
289
Song W, Cao LJ, Li BY, Gong YJ, Hoffmann AA, Wei SJ. Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest. BMC Evol Biol 2018;18:152. [PMID: 30314450 PMCID: PMC6186135 DOI: 10.1186/s12862-018-1269-z] [Citation(s) in RCA: 21] [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: 03/09/2018] [Accepted: 09/27/2018] [Indexed: 11/10/2022]  Open
290
Thiele EA, Eberhard ML, Cotton JA, Durrant C, Berg J, Hamm K, Ruiz-Tiben E. Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations. PLoS Negl Trop Dis 2018;12:e0006747. [PMID: 30286084 PMCID: PMC6191157 DOI: 10.1371/journal.pntd.0006747] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/16/2018] [Accepted: 08/11/2018] [Indexed: 02/08/2023]  Open
291
Lee JYH, Monk IR, Gonçalves da Silva A, Seemann T, Chua KYL, Kearns A, Hill R, Woodford N, Bartels MD, Strommenger B, Laurent F, Dodémont M, Deplano A, Patel R, Larsen AR, Korman TM, Stinear TP, Howden BP. Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis. Nat Microbiol 2018;3:1175-1185. [PMID: 30177740 PMCID: PMC6660648 DOI: 10.1038/s41564-018-0230-7] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/27/2018] [Indexed: 01/19/2023]
292
Smet A, Yahara K, Rossi M, Tay A, Backert S, Armin E, Fox JG, Flahou B, Ducatelle R, Haesebrouck F, Corander J. Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence. THE ISME JOURNAL 2018;12:2518-2531. [PMID: 29942073 PMCID: PMC6154992 DOI: 10.1038/s41396-018-0199-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/29/2018] [Accepted: 03/20/2018] [Indexed: 12/17/2022]
293
Marcelletti S, Scortichini M. Some strains that have converged to infect Prunus spp. trees are members of distinct Pseudomonas syringae genomospecies and ecotypes as revealed by in silico genomic comparison. Arch Microbiol 2018;201:67-80. [PMID: 30229267 DOI: 10.1007/s00203-018-1573-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/06/2018] [Accepted: 09/13/2018] [Indexed: 11/29/2022]
294
New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam. mBio 2018;9:mBio.01056-18. [PMID: 30181247 PMCID: PMC6123440 DOI: 10.1128/mbio.01056-18] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
295
Cleary DW, Devine VT, Morris DE, Osman KL, Gladstone RA, Bentley SD, Faust SN, Clarke SC. Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae. Microb Genom 2018;4. [PMID: 30080135 PMCID: PMC6202451 DOI: 10.1099/mgen.0.000209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
296
Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J. RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Wellcome Open Res 2018;3:93. [PMID: 30345380 PMCID: PMC6178908 DOI: 10.12688/wellcomeopenres.14694.1] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2018] [Indexed: 12/04/2022]  Open
297
Mendoza-Ramírez M, Gutiérrez-Rodríguez J, Poteaux C, Ornelas-García P, Zaldívar-Riverón A. Late Pleistocene genetic diversification and demographic expansion in the widely distributed neotropical ant Neoponera villosa (Ponerinae). Mitochondrial DNA A DNA Mapp Seq Anal 2018;30:296-306. [PMID: 30044161 DOI: 10.1080/24701394.2018.1493469] [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: 10/28/2022]
298
Shen Y, Zhou H, Xu J, Wang Y, Zhang Q, Walsh TR, Shao B, Wu C, Hu Y, Yang L, Shen Z, Wu Z, Sun Q, Ou Y, Wang Y, Wang S, Wu Y, Cai C, Li J, Shen J, Zhang R, Wang Y. Anthropogenic and environmental factors associated with high incidence of mcr-1 carriage in humans across China. Nat Microbiol 2018;3:1054-1062. [PMID: 30038311 PMCID: PMC6198934 DOI: 10.1038/s41564-018-0205-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 06/22/2018] [Indexed: 12/24/2022]
299
Invasion of the assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae) to Japan: Source estimation inferred from mitochondrial and nuclear gene sequences. Int J Biol Macromol 2018;118:1565-1573. [PMID: 29981333 DOI: 10.1016/j.ijbiomac.2018.06.191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/21/2018] [Accepted: 06/30/2018] [Indexed: 11/21/2022]
300
Raghwani J, Redd AD, Longosz AF, Wu CH, Serwadda D, Martens C, Kagaayi J, Sewankambo N, Porcella SF, Grabowski MK, Quinn TC, Eller MA, Eller LA, Wabwire-Mangen F, Robb ML, Fraser C, Lythgoe KA. Evolution of HIV-1 within untreated individuals and at the population scale in Uganda. PLoS Pathog 2018;14:e1007167. [PMID: 30052678 PMCID: PMC6082572 DOI: 10.1371/journal.ppat.1007167] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 08/08/2018] [Accepted: 06/20/2018] [Indexed: 12/15/2022]  Open
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