N
Nicholas J. Croucher
Researcher at Imperial College London
Publications - 131
Citations - 11969
Nicholas J. Croucher is an academic researcher from Imperial College London. The author has contributed to research in topics: Population & Genome. The author has an hindex of 48, co-authored 120 publications receiving 9820 citations. Previous affiliations of Nicholas J. Croucher include Harvard University & Wellcome Trust Sanger Institute.
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Journal ArticleDOI
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
Nicholas J. Croucher,Andrew J. Page,Thomas R. Connor,Aidan Delaney,Jacqueline A. Keane,Stephen D. Bentley,Julian Parkhill,Simon R. Harris +7 more
TL;DR: Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity.
Journal ArticleDOI
Rapid Pneumococcal Evolution in Response to Clinical Interventions
Nicholas J. Croucher,Simon R. Harris,Christophe Fraser,Michael A. Quail,John Burton,Mark van der Linden,Lesley McGee,Anne von Gottberg,Jae-Hoon Song,Kwan Soo Ko,Bruno Pichon,Stephen Baker,Christopher M. Parry,Lotte Lambertsen,Dea Shahinas,Dylan R. Pillai,Timothy J. Mitchell,Gordon Dougan,Alexander Tomasz,Keith P. Klugman,Keith P. Klugman,Keith P. Klugman,Julian Parkhill,William P. Hanage,William P. Hanage,Stephen D. Bentley +25 more
TL;DR: How genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales is detailed.
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Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.
Claudio U. Köser,Claudio U. Köser,Matthew T. G. Holden,Matthew J. Ellington,Edward J. P. Cartwright,Edward J. P. Cartwright,Nicholas M. Brown,Nicholas M. Brown,Amanda Ogilvy-Stuart,Li Yang Hsu,Claire Chewapreecha,Nicholas J. Croucher,Simon R. Harris,Mandy Sanders,Mark C. Enright,Gordon Dougan,Stephen D. Bentley,Julian Parkhill,Louise Fraser,Jason Betley,Ole Schulz-Trieglaff,Geoffrey Paul Smith,Sharon J. Peacock +22 more
TL;DR: Whole-genome sequencing can provide clinically relevant data within a time frame that can influence patient care and the need for automated data interpretation and the provision of clinically meaningful reports represent hurdles to clinical implementation.
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Evidence for several waves of global transmission in the seventh cholera pandemic
Ankur Mutreja,Dong Wook Kim,Dong Wook Kim,Nicholas R. Thomson,Thomas R. Connor,Jehee Lee,Jehee Lee,Samuel Kariuki,Nicholas J. Croucher,Seon Young Choi,Seon Young Choi,Simon R. Harris,Michael Lebens,Swapan Kumar Niyogi,Eun Jin Kim,Thandavarayan Ramamurthy,Jongsik Chun,James L. N. Wood,John D. Clemens,Cecil Czerkinsky,G. Balakrish Nair,Jan Holmgren,Julian Parkhill,Gordon Dougan +23 more
TL;DR: It is shown here that the seventh pandemic has spread from the Bay of Bengal in at least three independent but overlapping waves with a common ancestor in the 1950s, and several transcontinental transmission events are identified.
Journal ArticleDOI
Phandango: an interactive viewer for bacterial population genomics
James Hadfield,Nicholas J. Croucher,Richard Goater,Khalil Abudahab,David M. Aanensen,David M. Aanensen,Simon R. Harris +6 more
TL;DR: Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner.