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Research: Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla_KPC
- Angela Gomez-Simmonds,
- Medini K. Annavajhala,
- Dwayne Seeram,
- Todd W. Hokunson,
- Heekuk Park,
- and Anne-Catrin Uhlemann
Genome Res. November 2024 34: 1895-1907; Published in Advance October 4, 2024, doi:10.1101/gr.279355.124
.... Plasmid-mediated acquisition of blaKPC occurred in 23%–27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreading blaKPC from ST258 to other clones...
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Resource: Cactus: Algorithms for genome multiple sequence alignment
- Benedict Paten,
- Dent Earl,
- Ngan Nguyen,
- Mark Diekhans,
- Daniel Zerbino,
- and David Haussler
Genome Res. September 2011 21: 1512-1528; Published in Advance June 10, 2011, doi:10.1101/gr.123356.111
...Cactus: Algorithms for genome multiple sequence alignment Benedict Paten 1 , Dent Earl , Ngan Nguyen , Mark Diekhans , Daniel Zerbino and David Haussler 1 Center for Biomolecular Science and Engineering, University...
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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...of the input sequences into a set of synteny blocks—long and conservative genomic regions with respect to micro-rearrangements. However, RACA reconstructs synteny blocks by aligning all input sequences against a single reference . This approach is biased toward the reference and, in some cases, cannot detect...
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Resource: Alignathon: a competitive assessment of whole-genome alignment methods
- Dent Earl,
- Ngan Nguyen,
- Glenn Hickey,
- Robert S. Harris,
- Stephen Fitzgerald,
- Kathryn Beal,
- Igor Seledtsov,
- Vladimir Molodtsov,
- Brian J. Raney,
- Hiram Clawson,
- Jaebum Kim,
- Carsten Kemena,
- Jia-Ming Chang,
- Ionas Erb,
- Alexander Poliakov,
- Minmei Hou,
- Javier Herrero,
- William James Kent,
- Victor Solovyev,
- Aaron E. Darling,
- Jian Ma,
- Cedric Notredame,
- Michael Brudno,
- Inna Dubchak,
- David Haussler,
- and Benedict Paten
Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
....114. Freely available online through the Genome Research Open Access option. 24:2077–2089 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/14; www..org Genome Research 2077 www..org whole- alignment (WGA), this requires the aligner to additionally consider rearrangements, such as inversions...
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Methods: A novel method for multiple alignment of sequences with repeated and shuffled elements
- Benjamin Raphael,
- Degui Zhi,
- Haixu Tang,
- and Pavel Pevzner
Genome Res. November 2004 14: 2336-2346; doi:10.1101/gr.2657504
...-206. Society for Industrial and Applied Mathematics, Philadelphia. ↵ Darling, A.C., Mau, B., Blattner, F.R., and Perna, N.T. 2004 . Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14 : 1394 -1403. ↵ Doolittle, R.F. 1995 . The multiplicity of domains in proteins...
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Methods: Inferring genomic flux in bacteria
- Xavier Didelot,
- Aaron Darling,
- and Daniel Falush
Genome Res. February 2009 19: 306-317; Published in Advance November 17, 2008, doi:10.1101/gr.082263.108
...: 1484 – 1492 . ↵ Cunningham, M.W. ( 2000 ) Pathogenesis of group A streptococcal infections . Clin. Microbiol. Rev. 13 : 470 – 511 . ↵ Darling, A.C. , Mau, B. , Blattner, F.R. , Perna, N.T. ( 2004 ) Mauve: Multiple alignment of conserved genomic sequence with rearrangements . Genome Res. 14 : 1394...
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Resource: Multiple whole-genome alignments without a reference organism
- Inna Dubchak,
- Alexander Poliakov,
- Andrey Kislyuk,
- and Michael Brudno
Genome Res. April 2009 19: 682-689; Published in Advance January 28, 2009, doi:10.1101/gr.081778.108
....R., and Perna, N.T. 2004. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14: 1394–1403. de la Calle-Mustienes, E., Feijoo, C.G., Manzanares, M., Tena, J.J., Rodriguez-Seguel, E., Letizia, A., Allende, M.L., and Gomez-Skarmeta, J.L. 2005. A functional survey...
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Research: Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
- Viola Nolte,
- Ram Vinay Pandey,
- Robert Kofler,
- and Christian Schlötterer
Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
...is frequently referred to as ‘‘NUP98,’’ e.g., in Presgraves et al. (2003). 23:99–110 2013, Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/13; www..org Genome Research 99 www..org genomic conflict (Presgraves 2007; Presgraves and Stephan 2007). While the NUP96 protein is highly conserved...
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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
...more than 324,000 new genes representing more than 12,333 new gene families for this group. The core genome size for the B. cereus s.l. group was ∼1750 genes, with another 2150 genes found in almost every genome constituting the extended core. There was a paucity of genes specific and conserved...
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ARTICLE: Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa
- Craig Winstanley,
- Morgan G.I. Langille,
- Joanne L. Fothergill,
- Irena Kukavica-Ibrulj,
- Catherine Paradis-Bleau,
- François Sanschagrin,
- Nicholas R. Thomson,
- Geoff L. Winsor,
- Michael A. Quail,
- Nicola Lennard,
- Alexandra Bignell,
- Louise Clarke,
- Kathy Seeger,
- David Saunders,
- David Harris,
- Julian Parkhill,
- Robert E.W. Hancock,
- Fiona S.L. Brinkman,
- and Roger C. Levesque
Genome Res. January 2009 19: 12-23; Published in Advance December 1, 2008, doi:10.1101/gr.086082.108
...top hit, then the top hits were considered probable orthologs. In cases where multiple top hits with the same score were identified, gene synteny, from whole alignments obtained with the program Mauve ( Darling et al. 2004 ), was used to identify the most probable ortholog. Orthologs were additionally...
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