A. Underwood

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Commentary: Call for a Quality Standard for Sequence-Based Assays in Clinical Microbiology: Necessity for Quality Assessment of Sequences Used in Microbial Identification and Typing

A. Underwood, Jonathan Green, J. Green, 2010, Journal of Clinical Microbiology.

Distributed under Creative Commons Cc-by 4.0 Most: a Modified Mlst Typing Tool Based on Short Read Sequencing

P. Ashton, T. Dallman, M. Ellington, 2022 .

Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157.

Richard J Ellis, Anthony Underwood, Kathie Grant, 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines

Julian Parkhill, Simon R. Harris, Martin Aslett, 2016, Journal of Clinical Microbiology.

Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria

I. Okeke, D. Aanensen, A. Dalsgaard, 2022, Frontiers in Medicine.

Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy.

N. Loman, M. Pallen, N. Woodford, 2011, The Journal of antimicrobial chemotherapy.

A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus.

A. Kearns, N. Saunders, A. Underwood, 2004, Microbiology.

Rapid detection and evolutionary analysis of Legionella pneumophila serogroup 1 sequence type 47.

T G Harrison, C. Buchrieser, J. Parkhill, 2017, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota

M. Woodward, A. Underwood, L. Petrovska, 2013, Applied and Environmental Microbiology.

Genome analysis following a national increase in Scarlet Fever in England 2014

R. Guy, A. Johnson, Alan P. Johnson, 2017, BMC Genomics.

An ST131 clade and a Phylogroup A clade bearing a novel Escherichia coli O-antigen cluster predominate among bloodstream E. coli isolates from southwest Nigeria hospitals

I. Okeke, D. Aanensen, C. Ihekweazu, 2021, medRxiv.

Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria

I. Okeke, D. Aanensen, C. Ihekweazu, 2021, bioRxiv.

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

Darren L. Smith, Evelien M. Adriaenssens, Gemma L. Kay, 2020, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

Expression and Secretion of a Larval-specific Chitinase (Family 18 Glycosyl Hydrolase) by the Infective Stages of the Parasitic Nematode, Onchocerca volvulus *

S. Sakuda, A. Underwood, A. E. Bianco, 2001, The Journal of Biological Chemistry.

Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of AMR

D. Aanensen, M. Kekre, A. Matimba, 2021, bioRxiv.

Enhanced nasopharyngeal infection and shedding associated with an epidemic lineage of emm3 group A Streptococcus

Ken Smith, M. Holden, A. Efstratiou, 2017, Virulence.

Non-culture detection of Streptococcus agalactiae (Lancefield group B Streptococcus) in clinical samples by real-time PCR.

S. Gharbia, A. Charlett, K. Edwards, 2012, Journal of medical microbiology.

CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

N. Loman, A. Rambaut, D. Aanensen, 2021, Genome biology.

MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

N. Loman, A. Rambaut, D. Aanensen, 2020, bioRxiv.

Large retrospective WGS study describes three major sequence types of S. aureus in India and reveals two novel multi-drug resistant sub-lineages of S. aureus Clonal Complex 22

D. Aanensen, M. Kekre, A. Underwood, 2022, bioRxiv.

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Joshua B. Singer, Darren L. Smith, Shane A. McCarthy, 2021, The Lancet Infectious Diseases.

Identification of a molecular marker for the Y chromosome of Brugia malayi.

A. Underwood, A. E. Bianco, A. Bianco, 1999, Molecular and biochemical parasitology.

Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria's experience.

I. Okeke, D. Aanensen, M. Kekre, 2022, Microbiology.

Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria

I. Okeke, D. Aanensen, M. Kekre, 2022, medRxiv.

Implementing Whole-Genome Sequencing for Ongoing Surveillance of Antimicrobial Resistance: Exemplifying Insights Into Klebsiella pneumoniae

Agnettah M. Olorosa, I. Okeke, N. Wheeler, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs

Agnettah M. Olorosa, I. Okeke, N. Wheeler, 2021, bioRxiv.

Integrating Scalable Genome Sequencing Into Microbiology Laboratories for Routine Antimicrobial Resistance Surveillance

Agnettah M. Olorosa, I. Okeke, N. Wheeler, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

A community-driven resource for genomic epidemiology and 1 antimicrobial resistance prediction of Neisseria gonorrhoeae 2 at Pathogenwatch 3 4

Richard J. Goater, Tatum D. Mortimer, Brian H. Raphael, 2020 .

Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study.

L. Sánchez-Busó, M. Unemo, D. Aanensen, 2022, The Lancet. Microbe.

A community-driven resource for genomic surveillance of Neisseria gonorrhoeae at Pathogenwatch

Yonatan H. Grad, Khalil Abudahab, David M. Aanensen, 2020, bioRxiv.

Multiple-locus variable-number tandem-repeat analysis of Streptococcus pneumoniae and comparison with multiple loci sequence typing

A. Underwood, B. Pichon, J. Koeck, 2012, BMC Microbiology.

A technique for cloning the telomeres and subtelomeric regions from Pneumocystis carinii.

E. Louis, A. Underwood, R. Borts, 1994, The Journal of eukaryotic microbiology.

Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK.

N. Loman, J. Turton, A. Underwood, 2013, Journal of medical microbiology.

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

William T. Harvey, Scott M Elliott, Robert M. Davies, 2022, Nature Microbiology.

Complete Nucleotide Sequences of Plasmids pEK204, pEK499, and pEK516, Encoding CTX-M Enzymes in Three Major Escherichia coli Lineages from the United Kingdom, All Belonging to the International O25:H4-ST131 Clone

N. Woodford, D. Livermore, A. Carattoli, 2009, Antimicrobial Agents and Chemotherapy.

VNTRDB: a bacterial variable number tandem repeat locus database

Cheng-Yan Kao, Chia-Hung Chang, Yu-Chung Chang, 2006, Nucleic Acids Res..

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Graham W. Taylor, Joshua B. Singer, Darren L. Smith, 2021, Science.

Pneumocystis carinii telomere repeats are composed of TTAGGG and the subtelomeric sequence contains a gene encoding the major surface glycoprotein

J. Stringer, A. Underwood, R. Borts, 1996, Molecular microbiology.

Genetic diversity at the internal transcribed spacer regions of the rRNA operon among isolates of Pneumocystis carinii from AIDS patients with recurrent pneumonia.

R. Miller, A. G. Tsolaki, A. Underwood, 1996, The Journal of infectious diseases.

Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis

Astrid Gall, Paul Kellam, Richard G. Pebody, 2011, Journal of Virology.

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

D. A. Jackson, Graham W. Taylor, William L. Hamilton, 2020, Cell.

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Graham W. Taylor, Joshua B. Singer, Scott M Elliott, 2021, Nature.

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

O. Pybus, E. Holmes, L. du Plessis, 2021, Virus evolution.

Mathematical Modelling of Mycobacterium tuberculosis VNTR Loci Estimates a Very Slow Mutation Rate for the Repeats

Saheer Gharbia, Anthony Underwood, Catherine Arnold, 2008, Journal of Molecular Evolution.

Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005–2010

J. Wain, G. Dougan, J. Parkhill, 2016, Emerging infectious diseases.

Microevolution during the emergence of a monophasic 1 Salmonella Typhimurium epidemic in the United Kingdom 2 3 Running Title : Monophasic Salmonella microevolution 4 5

J. Wain, G. Dougan, J. Parkhill, 2015 .

SARS-CoV-2 evolution during treatment of chronic infection

Graham W. Taylor, William L. Hamilton, Joshua B. Singer, 2021, Nature.

16S rDNA phylogeny and ultrastructural characterization of Wolbachia intracellular bacteria of the filarial nematodes Brugia malayi, B. pahangi, and Wuchereria bancrofti.

J. Archer, M. Taylor, A. Underwood, 1999, Experimental parasitology.

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

William T. Harvey, Graham W. Taylor, William L. Hamilton, 2021, Cell Reports.

The Secreted Larval Acidic Proteins (SLAPs) of Onchocerca spp. are encoded by orthologues of the alt gene family of Brugia malayi and have host protective potential.

D. Pappin, R. Harrison, A. Underwood, 2004, Molecular and biochemical parasitology.

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

Richard J. Goater, I. Okeke, K. Holt, 2021, bioRxiv.

MOP-UP: an online tool for finding strain-specific primers or motifs in DNA or protein alignments.

A. Underwood, J. Green, 2004, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

An Investigation of the Diversity of Strains of Enteroaggregative Escherichia coli Isolated from Cases Associated with a Large Multi-Pathogen Foodborne Outbreak in the UK

T. Dallman, J. Wain, C. Jenkins, 2014, PloS one.

An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals

I. Okeke, D. Aanensen, C. Ihekweazu, 2022, Microbial genomics.

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

William T. Harvey, Scott M Elliott, Kevin R. Cole, 2022, Scientific Reports.

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Graham W. Taylor, Scott M Elliott, Jaime M. Tovar-Corona, 2022, Nature Communications.

Genomic reconstruction of the SARS-CoV-2 epidemic in England

William T. Harvey, William L. Hamilton, Richard J. Goater, 2021, Nature.

SARS-CoV-2 evolution during treatment of chronic infection

Graham W. Taylor, William L. Hamilton, Joshua B. Singer, 2021, Nature.

Final report of ENGAGE ‐ Establishing Next Generation sequencing Ability for Genomic analysis in Europe

Alessandra Longo, Yue Tang, Burkhard Malorny, 2018, EFSA Supporting Publications.

Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently

C. Buchrieser, J. Parkhill, S. Harris, 2016, Genome research.

Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents.

T G Harrison, D Harmsen, J Moran-Gilad, 2015, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

N. Loman, A. Rambaut, D. Aanensen, 2021, Genome Biology.

Whole Genome Sequencing for National Surveillance of Shiga Toxin Producing Escherichia coli O 157-- Manuscript Draft

P. Ashton, T. Dallman, J. Wain, 2014 .

High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study

Agnettah M. Olorosa, I. Okeke, D. Aanensen, 2021, bioRxiv.

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch

Richard J. Goater, Jacqueline A. Keane, S. Nair, 2020, Nature Communications.

Emergence of a novel lineage containing a prophage in emm/M3 group A Streptococcus associated with upsurge in invasive disease in the UK

A. Efstratiou, A. Underwood, S. Sriskandan, 2016, Microbial genomics.

Genomic sequence investigation Streptococcus pyogenes clusters in England (2010-2015).

A. Underwood, J. Coelho, R. Tewolde, 2019, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Integration of Genomic and Other Epidemiologic Data to Investigate and Control a Cross-Institutional Outbreak of Streptococcus pyogenes

K. Jolley, N. McCarthy, M. Doumith, 2016, Emerging infectious diseases.

Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak

T. Dallman, J. Wain, G. Dougan, 2012, Journal of Clinical Microbiology.

Overcoming Data Bottlenecks in Genomic Pathogen Surveillance

I. Okeke, D. Aanensen, A. Underwood, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

William T. Harvey, Scott M Elliott, Kevin R. Cole, 2023, Journal of Hospital Infection.

Sustained transmission of high-level azithromycin-resistant Neisseria gonorrhoeae in England: an observational study.

Adrian Wensley, Neil Woodford, Michelle Cole, 2018, The Lancet. Infectious diseases.

Circulation of Third-Generation Cephalosporin Resistant Salmonella Typhi in Mumbai, India

S. Baker, D. Aanensen, M. Kekre, 2021, bioRxiv.

SnapperDB: A database solution for routine sequencing analysis of bacterial isolates

Richard Myers, Aleksey Jironkin, Anthony Underwood, 2017, bioRxiv.

Rapid Identification of Major Escherichia coli Sequence Types Causing Urinary Tract and Bloodstream Infections

J. Wain, N. Woodford, D. Livermore, 2014, Journal of Clinical Microbiology.

Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing

A. Underwood, M. Mentasti, N. Fry, 2013, BMC Microbiology.

Assessment of fluorescent amplified fragment length polymorphism analysis for epidemiological genotyping of Legionella pneumophila serogroup 1.

P. Visca, A. Underwood, D. Jonas, 2005, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis

Aleksey Jironkin, Anthony Underwood, A. Underwood, 2016, BMC Genomics.

Enteroaggregative Escherichia coli Have Evolved Independently as Distinct Complexes within the E. coli Population with Varying Ability to Cause Disease

T. Dallman, J. Wain, I. Okeke, 2014, PloS one.

Virulence Searcher: a tool for searching raw genome sequences from bacterial genomes for putative virulence factors.

S. Gharbia, A. Underwood, A. Mulder, 2005, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

The Impact of Pandemic Influenza H1N1 on Health-Related Quality of Life: A Prospective Population-Based Study

Mark Jit, W. John Edmunds, Anthony Underwood, 2011, PloS one.

Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

William T. Harvey, Scott M Elliott, Robert M. Davies, 2022, Nature Microbiology.

Whole-genome sequencing in the investigation of recurrent invasive group A streptococcus outbreaks in a maternity unit.

A. Underwood, J. Coelho, D. Fowler, 2019, The Journal of hospital infection.

Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline

D. Litt, A. Underwood, C. Sheppard, 2016, PeerJ.

Molecular dissection of carbapenem-resistant Acinetobacter baumannii circulating in Indian hospitals using Whole Genome Sequencing

D. Aanensen, A. Underwood, S. Argimón, 2021, bioRxiv.

Emergence of a novel lineage containing a prophage in emm/M3 group A Streptococcus associated with upsurge in invasive disease in the UK

A. Efstratiou, A. Underwood, S. Sriskandan, 2016, Microbial genomics.

Evolutionary Pathways of the Pandemic Influenza A (H1N1) 2009 in the UK

R. Myers, M. Galiano, M. Zambon, 2011, PloS one.

High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020

I. Okeke, D. Aanensen, A. Dalsgaard, 2023, mSphere.

High genetic diversity and blaNDM-1 prevalence among Acinetobacter baumannii in Nigerian hospitals

I. Okeke, D. Aanensen, A. Dalsgaard, 2023, bioRxiv.

Identification of Legionella spp. by 19 European reference laboratories: results of the European Working Group for Legionella Infections External Quality Assessment Scheme using DNA sequencing of the macrophage infectivity potentiator gene and dedicated online tools.

A. Underwood, R. Ratcliff, B. Afshar, 2007, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

Graham W. Taylor, William L. Hamilton, Joshua B. Singer, 2021, Nature.

External Quality Assessment of a DNA Sequence-Based Scheme for Epidemiological Typing of Legionella pneumophila by an International Network of Laboratories

A. Underwood, B. Afshar, N. Fry, 2007, Journal of Clinical Microbiology.

BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness

T. Peto, D. Crook, D. Wyllie, 2017, BMC Bioinformatics.

A one health approach for enhancing the integration of Salmonella enterica surveillance in Colombia

D. Aanensen, A. Underwood, S. Argimón, 2023, medRxiv.

High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom

A. Witney, N. Woodford, J. Turton, 2015, Journal of Clinical Microbiology.

Single-nucleotide polymorphism-based differentiation and drug resistance detection in Mycobacterium tuberculosis from isolates or directly from sputum.

S. Gharbia, C. Arnold, A. Underwood, 2005, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Typing of Legionella pneumophila and its Role in Elucidating the Epidemiology of Legionnaires’ Disease

A. Underwood, B. Afshar, N. Fry, 2006 .

Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines

Agnettah M. Olorosa, I. Okeke, D. Aanensen, 2021, bioRxiv.

Phylocanvas.gl: A WebGL-powered JavaScript library for large tree visualisation

D. Aanensen, A. Underwood, C. Yeats, 2021 .

Extension of the Legionella pneumophila sequence-based typing scheme to include strains carrying a variant of the N-acylneuraminate cytidylyltransferase gene.

C. Lück, A. Underwood, N. Kozak-Muiznieks, 2014, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Genome analysis following a national increase in Scarlet Fever in England 2014

R. Guy, Alan P. Johnson, A. Underwood, 2017, BMC Genomics.

P864 Complete nucleotide sequence of pEK499, a multidrug-resistance plasmid from the UK's most prevalent Escherichia coli strain with CTX-M-15 β-lactamase

N. Woodford, D. Livermore, M. Ellington, 2007 .

snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing

Ali Al-Shahib, Anthony Underwood, A. Underwood, 2013, BMC Bioinformatics.

Pandemic (H1N1) 2009 influenza in the UK: clinical and epidemiological findings from the first few hundred (FF100) cases

T. Dallman, R. Myers, P. White, 2010, Epidemiology and Infection.

Evolution of short sequence repeats in Mycobacterium tuberculosis.

S. Gharbia, C. Arnold, A. Underwood, 2006, FEMS microbiology letters.

Revolutionising Public Health Reference Microbiology using Whole Genome Sequencing: Salmonella as an exemplar

Anthony Underwood, Catherine Arnold, Kathie Grant, 2015, bioRxiv.

Pandemic ( H 1 N 1 ) 2009 influenza in the UK : clinical and epidemiological findings from the first few hundred ( FF 100 ) cases

T. Dallman, R. Pebody, R. Myers, 2010 .

Evolutionary clues from comparative analysis of Mycobacterium tuberculosis variable-number tandem repeat sequences within genetic families.

S. Gharbia, C. Arnold, A. Underwood, 2007, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Whole-Genome Sequencing and Epidemiological Analysis Do Not Provide Evidence for Cross-transmission of Mycobacterium abscessus in a Cohort of Pediatric Cystic Fibrosis Patients

K. Harris, A. Underwood, D. Kenna, 2014, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

of Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity

D. A. Jackson, Graham W. Taylor, William L. Hamilton, 2021 .

A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch

Richard J. Goater, Tatum D. Mortimer, Brian H. Raphael, 2021, Genome Medicine.

SnapperDB: A database solution for routine sequencing analysis of bacterial isolates

P. Ashton, T. Dallman, H. Hartman, 2017, bioRxiv.

Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak

T. Dallman, J. Wain, G. Dougan, 2012, Journal of Clinical Microbiology.

Revealed by Whole-Genome Analysis H1N1/2009 Influenza Virus Lineages Evolutionary Dynamics of Local Pandemic

O. Pybus, R. Pebody, R. Myers, 2012 .

BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness

Oriol Mazariegos-Canellas, Anthony Underwood, David W. Eyre, 2017, BMC Bioinformatics.