Publications by authors named "Julian Parkhill"

100Publications

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions.

mBio 2020 Jul 7;11(4). Epub 2020 Jul 7.

Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, University of Oslo, Oslo, Norway.

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http://dx.doi.org/10.1128/mBio.01344-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7343994PMC
July 2020

A decade of advances in transposon-insertion sequencing.

Nat Rev Genet 2020 Sep 12;21(9):526-540. Epub 2020 Jun 12.

Department of Biology, Boston College, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41576-020-0244-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291929PMC
September 2020

A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility.

J Antimicrob Chemother 2020 Jun 8. Epub 2020 Jun 8.

University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.

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http://dx.doi.org/10.1093/jac/dkaa204DOI Listing
June 2020

Defining metrics for whole-genome sequence analysis of MRSA in clinical practice.

Microb Genom 2020 04 31;6(4). Epub 2020 Mar 31.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1099/mgen.0.000354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7276698PMC
April 2020

Mechanisms of β-lactam resistance of Streptococcus uberis isolated from bovine mastitis cases.

Vet Microbiol 2020 Mar 22;242:108592. Epub 2020 Jan 22.

Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK.

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http://dx.doi.org/10.1016/j.vetmic.2020.108592DOI Listing
March 2020

Evaluation of a fully automated bioinformatics tool to predict antibiotic resistance from MRSA genomes.

J Antimicrob Chemother 2020 May;75(5):1117-1122

Department of Medicine, University of Cambridge, Box 157, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK.

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http://dx.doi.org/10.1093/jac/dkz570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7177496PMC
May 2020

Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae.

Plant Biotechnol J 2020 05 3;18(5):1296-1306. Epub 2019 Dec 3.

Plant Science Group, Institute of Molecular, Cell and Systems Biology & School of Life Sciences, University of Glasgow, Glasgow, UK.

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http://dx.doi.org/10.1111/pbi.13294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152609PMC
May 2020

Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae.

Sci Rep 2019 10 11;9(1):14685. Epub 2019 Oct 11.

Microbiotica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1038/s41598-019-51102-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789123PMC
October 2019

Complete Genome Sequence of Pseudomonas aeruginosa Reference Strain PAK.

Microbiol Resour Announc 2019 Oct 10;8(41). Epub 2019 Oct 10.

Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1128/MRA.00865-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6787321PMC
October 2019

Author Correction: Human placenta has no microbiome but can contain potential pathogens.

Nature 2019 Oct;574(7778):E15

Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Biomedical Research Centre, Cambridge, UK.

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http://dx.doi.org/10.1038/s41586-019-1628-yDOI Listing
October 2019

Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study.

Lancet Infect Dis 2019 11 10;19(11):1209-1218. Epub 2019 Sep 10.

Department of Infectious Diseases and Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK; Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, National Institute for Health Research, Imperial College London, London, UK. Electronic address:

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http://dx.doi.org/10.1016/S1473-3099(19)30446-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838661PMC
November 2019

The Genome Sequences of Three sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.

Microbiol Resour Announc 2019 Aug 22;8(34). Epub 2019 Aug 22.

Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom.

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http://dx.doi.org/10.1128/MRA.00778-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706693PMC
August 2019

Human placenta has no microbiome but can contain potential pathogens.

Nature 2019 08 31;572(7769):329-334. Epub 2019 Jul 31.

Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Biomedical Research Centre, Cambridge, UK.

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http://dx.doi.org/10.1038/s41586-019-1451-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697540PMC
August 2019

Genome-wide epistasis and co-selection study using mutual information.

Nucleic Acids Res 2019 10;47(18):e112

Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), Faculty of Science, University of Helsinki, FI-00014 Helsinki, Finland.

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http://dx.doi.org/10.1093/nar/gkz656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765119PMC
October 2019

The impact of antimicrobials on gonococcal evolution.

Nat Microbiol 2019 11 29;4(11):1941-1950. Epub 2019 Jul 29.

Pathogen Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1038/s41564-019-0501-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6817357PMC
November 2019

Draft genome sequence of a multidrug-resistant caprine isolate of Staphylococcus cohnii subsp. urealyticus from Tanzania encoding ermB, tet(K), dfrG, fusF and fosD.

J Glob Antimicrob Resist 2019 09 16;18:163-165. Epub 2019 Jul 16.

Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jgar.2019.07.006DOI Listing
September 2019

Complete Whole-Genome Sequence of Haemophilus haemolyticus NCTC 10839.

Microbiol Resour Announc 2019 Jun 20;8(25). Epub 2019 Jun 20.

Culture Collections, Public Health England, London, United Kingdom.

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http://dx.doi.org/10.1128/MRA.00232-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588363PMC
June 2019

Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory.

J Antimicrob Chemother 2019 08;74(8):2153-2156

Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK.

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http://dx.doi.org/10.1093/jac/dkz170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6640301PMC
August 2019

Separating Bacteria by Capsule Amount Using a Discontinuous Density Gradient.

J Vis Exp 2019 01 7(143). Epub 2019 Jan 7.

Wellcome Sanger Institute, Wellcome Genome Campus; Department of Medicine, University of Cambridge;

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http://dx.doi.org/10.3791/58679DOI Listing
January 2019

O-Antigen-Dependent Colicin Insensitivity of Uropathogenic Escherichia coli.

J Bacteriol 2019 02 28;201(4). Epub 2019 Jan 28.

Department of Biochemistry, University of Oxford, Oxford, United Kingdom

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http://dx.doi.org/10.1128/JB.00545-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351738PMC
February 2019

The Capsule Regulatory Network of Defined by density-TraDISort.

mBio 2018 11 20;9(6). Epub 2018 Nov 20.

Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom

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http://dx.doi.org/10.1128/mBio.01863-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247091PMC
November 2018

Correction to: Detecting eukaryotic microbiota with single-cell sensitivity in human tissue.

Microbiome 2018 10 20;6(1):188. Epub 2018 Oct 20.

Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK.

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http://dx.doi.org/10.1186/s40168-018-0576-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6195996PMC
October 2018

Mutations in the MAB_2299c TetR Regulator Confer Cross-Resistance to Clofazimine and Bedaquiline in .

Antimicrob Agents Chemother 2019 01 21;63(1). Epub 2018 Dec 21.

Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France

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http://dx.doi.org/10.1128/AAC.01316-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325171PMC
January 2019

Comparative genomics of Czech vaccine strains of Bordetella pertussis.

Pathog Dis 2018 10 1;76(7). Epub 2018 Oct 1.

Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic.

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https://academic.oup.com/femspd/article/doi/10.1093/femspd/f
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http://dx.doi.org/10.1093/femspd/fty071DOI Listing
October 2018

Detecting eukaryotic microbiota with single-cell sensitivity in human tissue.

Microbiome 2018 09 1;6(1):151. Epub 2018 Sep 1.

Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK.

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https://microbiomejournal.biomedcentral.com/articles/10.1186
Publisher Site
http://dx.doi.org/10.1186/s40168-018-0529-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6119588PMC
September 2018

Arginine-deprivation-induced oxidative damage sterilizes .

Proc Natl Acad Sci U S A 2018 09 24;115(39):9779-9784. Epub 2018 Aug 24.

Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461;

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http://dx.doi.org/10.1073/pnas.1808874115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6166831PMC
September 2018

Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens.

Microbiology 2018 10 27;164(10):1213-1219. Epub 2018 Jul 27.

4​Clinical Microbiology & Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Box 236 Hills Road, Cambridge CB2 0QW, UK.

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http://dx.doi.org/10.1099/mic.0.000700DOI Listing
October 2018

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

Wellcome Open Res 2018 23;3:33. Epub 2018 Mar 23.

Infection Genomics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.14265.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930550PMC
March 2018

Are commercial providers a viable option for clinical bacterial sequencing?

Microb Genom 2018 04 5;4(4). Epub 2018 Apr 5.

1​Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK.

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http://dx.doi.org/10.1099/mgen.0.000173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989584PMC
April 2018