Searching journal content for articles similar to MacAlasdair et al. 31 (7): 1258.

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  1. Method: Microbial strain-level population structure and genetic diversity from metagenomes
    • Duy Tin Truong,
    • Adrian Tett,
    • Edoardo Pasolli,
    • Curtis Huttenhower,
    • and Nicola Segata
    Genome Res. April 2017 27: 626-638; Published in Advance February 6, 2017, doi:10.1101/gr.216242.116
    .... prausnitzii) are likely the results of more plastic s subject to recombination and lateral gene exchange. This has been described in a few specific cases such as oral neisseriae (Donati et al. 2016), but the relative ease withwhich thousands ofmetas can nowbe obtained compared to isolate (Browne et al. 2016...
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  2. Research: Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis
    • Michael E. Zwick,
    • Sandeep J. Joseph,
    • Xavier Didelot,
    • Peter E. Chen,
    • Kimberly A. Bishop-Lilly,
    • Andrew C. Stewart,
    • Kristin Willner,
    • Nichole Nolan,
    • Shannon Lentz,
    • Maureen K. Thomason,
    • Shanmuga Sozhamannan,
    • Alfred J. Mateczun,
    • Lei Du,
    • and Timothy D. Read
    Genome Res. August 2012 22: 1512-1524; Published in Advance May 29, 2012, doi:10.1101/gr.134437.111
    ...was estimated to be 2.91 (similar to an earlier estimate of 2.41 based on 13 s) (Didelot et al. 2009), which is an intermediate level compared to the extremes of recombinogenic speciesNeisseria meningitidis and clonal Staphylococcus aureus (r/m of 13.6 and 0.2, respectively) (Didelot et al. 2009; Vos...
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  3. LETTER: A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?
    • Xavier Didelot,
    • Mark Achtman,
    • Julian Parkhill,
    • Nicholas R. Thomson,
    • and Daniel Falush
    Genome Res. January 2007 17: 61-68; Published in Advance November 7, 2006, doi:10.1101/gr.5512906
    ...within human populations in Neisseria meningitidis ( Linz et al. 2000 ; Zhu et al. 2001 ), but in general the role of recombination in the evolution of other phenotypic adaptations remains unclear, and its extent has not been quantified at the genomic level. Indeed, it has even been suggested...
  4. Method: Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
    • Gerry Tonkin-Hill,
    • Rebecca A. Gladstone,
    • Anna K. Pöntinen,
    • Sergio Arredondo-Alonso,
    • Stephen D. Bentley,
    • and Jukka Corander
    Genome Res. January 2023 33: 129-140; Published in Advance January 20, 2023, doi:10.1101/gr.277340.122
    ...naturally transformable species such as Streptococcus pneumoniae and Neisseria meningitidis have very high rates of homologous recombination (Dubnau 1999). In other species such as Salmonella enterica, horizontal exchange is generally restricted to the movement of MGEs (Harris et al. 2010). Although HGT...
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  5. LETTER: The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis
    • Thierry Wirth,
    • Giovanna Morelli,
    • Barica Kusecek,
    • Alex van Belkum,
    • Cindy van der Schee,
    • Axel Meyer,
    • and Mark Achtman
    Genome Res. November 2007 17: 1647-1656; Published in Advance September 25, 2007, doi:10.1101/gr.6122607
    ...( Maynard Smith et al. 1993 ; Feil and Spratt 2001 ). The frequency of recombination is extremely variable, resulting in population structures that range from panmixia in Helicobacter pylori ( Falush et al. 2001 ; Linz et al. 2007 ) and Neisseria meningitidis ( Feil et al. 2001 ) to absolute clonality...
  6. Method: Fast and flexible bacterial genomic epidemiology with PopPUNK
    • John A. Lees,
    • Simon R. Harris,
    • Gerry Tonkin-Hill,
    • Rebecca A. Gladstone,
    • Stephanie W. Lo,
    • Jeffrey N. Weiser,
    • Jukka Corander,
    • Stephen D. Bentley,
    • and Nicholas J. Croucher
    Genome Res. February 2019 29: 304-316; Published in Advance January 24, 2019, doi:10.1101/gr.241455.118
    ...-wide collections listed in Table 1 (Fig. 4; Supplemental Fig. S8). Species known to exchange sequence through homologous recombination at similar frequencies to S. pneumoniae, such as Neisseria meningitidis (Fig. 4), exhibited a similar distribution of pairwise genetic distances. The group of within...
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  7. Perspective: On the origin of prokaryotic species
    • W. Ford Doolittle and
    • Olga Zhaxybayeva
    Genome Res. May 2009 19: 744-756; doi:10.1101/gr.086645.108
    ...-locus sequence typing (MLST), first developed to characterize (‘‘type’’) strains of Neisseria meningitidis and other pathogens (Maiden et al. 1998), has now come to be the dominant method for analysis of population structure with prokaryotes of all kinds (in which context it is more commonly called MLSA...
  8. LETTER: Chlamydia trachomatis: Genome sequence analysis of lymphogranuloma venereum isolates
    • Nicholas R. Thomson,
    • Matthew T.G. Holden,
    • Caroline Carder,
    • Nicola Lennard,
    • Sarah J. Lockey,
    • Pete Marsh,
    • Paul Skipp,
    • C. David O’Connor,
    • Ian Goodhead,
    • Halina Norbertzcak,
    • Barbara Harris,
    • Doug Ormond,
    • Richard Rance,
    • Michael A. Quail,
    • Julian Parkhill,
    • Richard S. Stephens,
    • and Ian N. Clarke
    Genome Res. January 2008 18: 161-171; Published in Advance November 21, 2007, doi:10.1101/gr.7020108
    ...a rectal swab of a 49-yr-old MSM who was HIV positive and Hepatitis C negative. He attended a London Genital and Urinary Medicine (GUM) clinic in January 2006 showing clinical signs of proctitis. The rectal sample tested positive for C. trachomatis (negative for Neisseria gonorrhoeae ) using a conventional...
  9. LETTER: The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403
    • Alexander Bolotin,
    • Patrick Wincker,
    • Stéphane Mauger,
    • Olivier Jaillon,
    • Karine Malarme,
    • Jean Weissenbach,
    • S. Dusko Ehrlich,
    • and Alexei Sorokin
    Genome Res. May 1, 2001 11: 731-753; Published in Advance April 11, 2001, doi:10.1101/gr.169701
    ...,020 were required for the of Neisseria meningitidis ( Tettelin et al. 2000 ), which is of a similar size. Diagnostic sequence allowed us to identify all L. lactis genes that encode proteins sufficiently similar to those present in the databases. However, the elevated error rate, estimated to be ∼1%, did...
  10. LETTER: Widespread balancing selection and pathogen-driven selection at blood group antigen genes
    • Matteo Fumagalli,
    • Rachele Cagliani,
    • Uberto Pozzoli,
    • Stefania Riva,
    • Giacomo P. Comi,
    • Giorgia Menozzi,
    • Nereo Bresolin,
    • and Manuela Sironi
    Genome Res. February 2009 19: 199-212; Published in Advance November 7, 2008, doi:10.1101/gr.082768.108
    .... 2000 ), and respiratory viruses ( Raza et al. 1991 ); yet secretor subjects also display advantages compared to nonsecretors, such as lower susceptibility to urinary tract and Candida infections, and increased protection against Neisseria meningitis and Streptococcus ( Haverkorn and Goslings 1969...
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