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Research: A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland
- Kathy E. Raven,
- Sandra Reuter,
- Rosy Reynolds,
- Hayley J. Brodrick,
- Julie E. Russell,
- M. Estée Török,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. October 2016 26: 1388-1396; Published in Advance August 15, 2016, doi:10.1101/gr.204024.116
...-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001–2011 in the United Kingdom and Ireland (UK&amp;I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
...(IIa) clustered in population 3. Based on analyses of the population structure, population genetics, and recombination, we show that population 3 has recently emerged and expanded throughout Europe to then, possibly from the United Kingdom, reach the United States, where it also expanded. The reason...
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Resource: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
- Sandra Reuter,
- M. Estée Török,
- Matthew T.G. Holden,
- Rosy Reynolds,
- Kathy E. Raven,
- Beth Blane,
- Tjibbe Donker,
- Stephen D. Bentley,
- David M. Aanensen,
- Hajo Grundmann,
- Edward J. Feil,
- Brian G. Spratt,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. February 2016 26: 263-270; Published in Advance December 15, 2015, doi:10.1101/gr.196709.115
...applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) s drawn from England, Northern Ireland...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...1 1Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; 2Genomics and Regulatory Systems Unit & Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan; 3Clinical Genetics Research Program, Centre for Addiction and Mental Health...
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Corrigendum: Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
- Sandra Reuter,
- M. Estée Török,
- Matthew T.G. Holden,
- Rosy Reynolds,
- Kathy E. Raven,
- Beth Blane,
- Tjibbe Donker,
- Stephen D. Bentley,
- David M. Aanensen,
- Hajo Grundmann,
- Edward J. Feil,
- Brian G. Spratt,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. September 2017 27: 1622; doi:10.1101/gr.228155.117
...Genome Research 26: 263–270 (2016) Corrigendum:Buildingagenomic framework forprospectiveMRSAsurveillance in theUnited Kingdom and the Republic of Ireland Sandra Reuter, M. Estée Török, Matthew T.G. Holden, Rosy Reynolds, Kathy E. Raven, Beth Blane, Tjibbe Donker, Stephen D. Bentley, David M...
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Research: Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently
- Sophia David,
- Christophe Rusniok,
- Massimo Mentasti,
- Laura Gomez-Valero,
- Simon R. Harris,
- Pierre Lechat,
- John Lees,
- Christophe Ginevra,
- Philippe Glaser,
- Laurence Ma,
- Christiane Bouchier,
- Anthony Underwood,
- Sophie Jarraud,
- Timothy G. Harrison,
- Julian Parkhill,
- and Carmen Buchrieser
Genome Res. November 2016 26: 1555-1564; Published in Advance September 23, 2016, doi:10.1101/gr.209536.116
...and Carmen Buchrieser 3 , 4 1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA Cambridge, United Kingdom; 2Public Health England, NW9 5HT London, United Kingdom; 3Institut Pasteur, Biologie des Bactéries Intracellulaires, 75015, Paris...
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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...@cau.edu.cnAbstractAlthough CRISPR-Cas-based editing has made significant strides over the past decade, achieving simultaneous homozygous gene editing of multiple targets in primary cells remains a significant challenge. In this study, we optimized a coselection strategy to enhance homozygous gene editing rates in the s of primary...
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Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
- Hamim Zafar,
- Nicholas Navin,
- Ken Chen,
- and Luay Nakhleh
Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
...Fit's error model can be further improved, as the mutated alleles present in multiple copies will be less prone to be affected by allelic dropout. SiCloneFit's error model can be further extended to utilize reference and variant read counts at each mutation site in each cell as the input data instead...
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Method: Leveraging protein language models for accurate multiple sequence alignments
- Claire D. McWhite,
- Isabel Armour-Garb,
- and Mona Singh
Genome Res. July 2023 33: 1145-1153; Published in Advance July 6, 2023, doi:10.1101/gr.277675.123
...@princeton.edu, mona@cs.princeton.eduAbstractMultiple sequence alignment (MSA) is a critical step in the study of protein sequence and function. Typically, MSA algorithms progressively align pairs of sequences and combine these alignments with the aid of a guide tree. These alignment algorithms use scoring systems...
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Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
- Teemu Kallonen,
- Hayley J. Brodrick,
- Simon R. Harris,
- Jukka Corander,
- Nicholas M. Brown,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
...to define whether this MDR phenotype will become more disseminated in ST73 over time. Although previously reported to be present in the United Kingdom and Ireland from 2001 (Day et al. 2016), we observed the appearance of ST69 and ST131 within our sampling framework. We used BEAST to analyze their emergence...
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