Kathryn E Holt (Kathryn Holt)

ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 76

Top Venues

Nature communications

PLoS computational biology

The Journal of antimicrobial chemotherapy

Antimicrobial agents and chemotherapy

Monash University

University of Melbourne (MSC)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Monash University Jan 02 2019

Australia

Professor (Research) :: Dept Infectious Diseases

London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases Apr 16 2018

United Kingdom

Professor of Microbial Systems Genomics :: Department of Pathogen Molecular Biology

University of Melbourne - Dec 31 2018

Australia

Senior Research Fellow :: Department of Biochemistry & Molecular Biology; Bio21 Institute

University of Melbourne

Australia

Research Fellow :: Department of Microbiology and Immunology

Education History

University of Melbourne

Australia

MSC

University of Cambridge

United Kingdom

PHD :: Wellcome Trust Sanger Institute

University of Western Australia

Australia

BSC

Publications

Richael O Mills, Isaac Dadzie, Thanh Le-Viet, David J Baker, Humphrey P K Addy, Samuel A Akwetey, Irene E Donkoh, Elvis Quansah, Prince S Semanshia, Jennifer Morgan, Abraham Mensah, Nana E Adade, Emmanuel O Ampah, Emmanuel Owusu, Philimon Mwintige, Eric O Amoako, Anton Spadar, Kathryn E Holt, Ebenezer Foster-Nyarko
Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. The Journal of antimicrobial chemotherapy 79 (7) (2024)
Jacob Strahilevitz, Yair Motro, Violeta Temper, Diana Merezhko, Oshrat Ayalon, Yehonatan Bar Moshe, Margaret M C Lam, Kathryn E Holt, Moran-Gilad J
In vivo selection of carbapenem resistance during persistent Klebsiella pneumoniae sequence type 395 bloodstream infection due to OmpK36 deletion. Antimicrobial agents and chemotherapy (2024)
Richael O Mills, Isaac Dadzie, Thanh Le-Viet, David J Baker, Humphrey P K Addy, Samuel A Akwetey, Irene E Donkoh, Elvis Quansah, Prince S Semanshia, Jennifer Morgan, Abraham Mensah, Nana E Adade, Emmanuel O Ampah, Emmanuel Owusu, Philimon Mwintige, Eric O Amoako, Anton Spadar, Kathryn E Holt, Ebenezer Foster-Nyarko
Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. The Journal of antimicrobial chemotherapy (2024)
Jacob Strahilevitz, Yair Motro, Violeta Temper, Diana Merezhko, Oshrat Ayalon, Yehonatan Bar Moshe, Margaret M C Lam, Kathryn E Holt, Moran-Gilad J
In vivo selection of carbapenem resistance during persistent Klebsiella pneumoniae sequence type 395 bloodstream infection due to OmpK36 deletion. Antimicrobial agents and chemotherapy 68 (8) (2024)
Megan C Roberts, Kathryn E Holt, Guilherme Del Fiol, Andrea A Baccarelli, Caitlin G Allen
Precision public health in the era of genomics and big data. Nature medicine 30 (7) (2024)
Richael O Mills, Isaac Dadzie, Thanh Le-Viet, David J Baker, Humphrey P K Addy, Samuel A Akwetey, Irene E Donkoh, Elvis Quansah, Prince S Semanshia, Jennifer Morgan, Abraham Mensah, Nana E Adade, Emmanuel O Ampah, Emmanuel Owusu, Philimon Mwintige, Eric O Amoako, Anton Spadar, Kathryn E Holt, Ebenezer Foster-Nyarko
Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. The Journal of antimicrobial chemotherapy 79 (7) (2024)
Megan C Roberts, Kathryn E Holt, Guilherme Del Fiol, Andrea A Baccarelli, Caitlin G Allen
Precision public health in the era of genomics and big data. Nature medicine 30 (7) (2024)
Jacob Strahilevitz, Yair Motro, Violeta Temper, Diana Merezhko, Oshrat Ayalon, Yehonatan Bar Moshe, Margaret M C Lam, Kathryn E Holt, Moran-Gilad J
In vivo selection of carbapenem resistance during persistent Klebsiella pneumoniae sequence type 395 bloodstream infection due to OmpK36 deletion. Antimicrobial agents and chemotherapy 68 (8) (2024)
Richael O Mills, Isaac Dadzie, Thanh Le-Viet, David J Baker, Humphrey P K Addy, Samuel A Akwetey, Irene E Donkoh, Elvis Quansah, Prince S Semanshia, Jennifer Morgan, Abraham Mensah, Nana E Adade, Emmanuel O Ampah, Emmanuel Owusu, Philimon Mwintige, Eric O Amoako, Anton Spadar, Kathryn E Holt, Ebenezer Foster-Nyarko
Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. The Journal of antimicrobial chemotherapy 79 (7) (2024)
Megan C Roberts, Kathryn E Holt, Guilherme Del Fiol, Andrea A Baccarelli, Caitlin G Allen
Precision public health in the era of genomics and big data. Nature medicine (2024)
Megan C Roberts, Kathryn E Holt, Guilherme Del Fiol, Andrea A Baccarelli, Caitlin G Allen
Precision public health in the era of genomics and big data. Nature medicine 30 (7) (2024)
Richael O Mills, Isaac Dadzie, Thanh Le-Viet, David J Baker, Humphrey P K Addy, Samuel A Akwetey, Irene E Donkoh, Elvis Quansah, Prince S Semanshia, Jennifer Morgan, Abraham Mensah, Nana E Adade, Emmanuel O Ampah, Emmanuel Owusu, Philimon Mwintige, Eric O Amoako, Anton Spadar, Kathryn E Holt, Ebenezer Foster-Nyarko
Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. The Journal of antimicrobial chemotherapy 79 (7) (2024)
Jacob Strahilevitz, Yair Motro, Violeta Temper, Diana Merezhko, Oshrat Ayalon, Yehonatan Bar Moshe, Margaret M C Lam, Kathryn E Holt, Moran-Gilad J
In vivo selection of carbapenem resistance during persistent Klebsiella pneumoniae sequence type 395 bloodstream infection due to OmpK36 deletion. Antimicrobial agents and chemotherapy 68 (8) (2024)
Muhamad Fachrul, Abhilasha Karkey, Mila Shakya, Louise M Judd, Taylor Harshegyi, Kar Seng Sim, Susan Tonks, Sabina Dongol, Rajendra Shrestha, Agus Salim, null null, Stephen Baker, Andrew J Pollard, Chiea Chuen Khor, Christiane Dolecek, Buddha Basnyat, Sarah J Dunstan, Kathryn E Holt, Michael Inouye
Direct inference and control of genetic population structure from RNA sequencing data. Communications biology 6 (1) (2023)
Ryan R Wick, Louise M Judd, Kathryn E Holt
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLoS computational biology 19 (3) (2023)
Ben Vezina, Stephen C Watts, Jane Hawkey, Helena B Cooper, Louise M Judd, Adam W J Jenney, Jonathan M Monk, Kathryn E Holt, Kelly L Wyres
Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models. eLife 12 (2023)
Sydney L Miles, Vincenzo Torraca, Zoe Anne Dyson, Ana Teresa López-Jiménez, Ebenezer Foster-Nyarko, Damián Lobato-Márquez, Claire Jenkins, Kathryn E Holt, Serge Mostowy
Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive Escherichia coli . mBio (2023)
Matthew Silcocks, Xuling Chang, Nguyen Thuy Thuong Thuong, Youwen Qin, Dang Thi Minh Ha, Phan Vuong Khac Thai, Srinivasan Vijay, Do Dang Anh Thu, Vu Thi Ngoc Ha, Hoang Ngoc Nhung, Nguyen Huu Lan, Nguyen Thi Quynh Nhu, David Edwards, Artika Nath, Kym Pham, Nguyen Duc Bang, Tran Thi Hong Chau, Guy Thwaites, A Dorothee Heemskerk, Chiea Chuen Khor, Yik Ying Teo, Michael Inouye, Rick Twee-Hee Ong, Maxine Caws, Kathryn E Holt, Sarah J Dunstan
Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiology spectrum (2023)
Megan E Carey, Zoe Anne Dyson, Silvia Argimón, Louise Cerdeira, Corin Yeats, David Aanensen, Gerald Mboowa, Stephen Baker, Sofonias K Tessema, Anthony Marius Smith, Iruka N Okeke, Kathryn E Holt
Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization. Open forum infectious diseases 10 (Suppl 1) (2023)
Ryan R Wick, Louise M Judd, Kathryn E Holt
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLoS computational biology 19 (3) (2023)
Margaret M C Lam, Kathryn E Holt, Kelly L Wyres
Comment on: MDR carbapenemase-producing Klebsiella pneumoniae of the hypervirulence-associated ST23 clone in Poland, 2009-19. The Journal of antimicrobial chemotherapy (2023)
Ryan R Wick, Louise M Judd, Kathryn E Holt
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLoS computational biology 19 (3) (2023)
Megan E Carey, Zoe Anne Dyson, Danielle J Ingle, Afreenish Amir, Mabel K Aworh, Marie Anne Chattaway, Ka Lip Chew, John A Crump, Nicholas A Feasey, Benjamin Peter Howden, Karen H Keddy, Mailis Maes, Christopher M Parry, Sandra Van Puyvelde, Hattie E Webb, Ayorinde Oluwatobiloba Afolayan, Anna P Alexander, Shalini Anandan, Jason R Andrews, Philip M Ashton, Buddha Basnyat, Ashish Bavdekar, Isaac I Bogoch, John D Clemens, Kesia Esther da Silva, Anuradha De, Joep de Ligt, Paula Lucia Diaz Guevara, Christiane Dolecek, Shanta Dutta, Marthie M Ehlers, Louise K Francois Watkins, Denise O Garrett, Gauri Godbole, Melita A Gordon, Andrew R Greenhill, Chelsey Griffin, Madhu Gupta, Rene S Hendriksen, Robert S Heyderman, Yogesh Hooda, Juan Carlos Hormazabal, Odion O Ikhimiukor, Junaid Iqbal, Jobin John Jacob, Claire Jenkins, Dasaratha Ramaiah Jinka, Jacob John, Gagandeep Kang, Abdoulie Kanteh, Arti Kapil, Abhilasha Karkey, Samuel M Kariuki, Robert A Kingsley, Roshine Mary Koshy, A C Lauer, Myron M Levine, Ravikumar Kadahalli Lingegowda, Stephen P Luby, Grant Austin Mackenzie, Tapfumanei Mashe, Chisomo L Msefula, Ankur Mutreja, Geetha Nagaraj, Savitha Nagaraj, Satheesh Nair, Take K Naseri, Susana Nimarota-Brown, Elisabeth Njamkepo, Iruka N Okeke, Sulochana Putli Bai Perumal, Andrew J Pollard, Agila Kumari Pragasam, Firdausi Qadri, Farah N Qamar, Sadia Isfat Ara Rahman, Savitra Devi Rambocus, David A Rasko, Pallab Ray, Roy Robins-Browne, Temsunaro Rongsen-Chandola, Jean Pierre Rutanga, Samir Kumar Saha, Senjuti Saha, Karnika Saigal, Mohammad Saiful Islam Sajib, Jessica C Seidman, Jivan Shakya, Varun Shamanna, Jayanthi Shastri, Rajeev Shrestha, Sonia Sia, Michael J Sikorski, Ashita Singh, Anthony M Smith, Kaitlin A Tagg, Dipesh Tamrakar, Arif Mohammed Tanmoy, Maria Thomas, Mathew S Thomas, Robert Thomsen, Nicholas R Thomson, Siaosi Tupua, Krista Vaidya, Mary Valcanis, Balaji Veeraraghavan, François-Xavier Weill, Jackie Wright, Gordon Dougan, Silvia Argimón, Jacqueline A Keane, David M Aanensen, Stephen Baker, Kathryn E Holt, null null
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 12 (2023)
Maytham H Hussein, Zetao Sun, Jane Hawkey, Rafah Allobawi, Lousie M Judd, Vincenzo Carbone, Rajnikant Sharma, Varsha Thombare, Mark Baker, Gauri G Rao, Hsin-Hui Shen, Kathryn E Holt, Xukai Jiang
High-level nitrofurantoin resistance in a clinical isolate of Klebsiella pneumoniae: a comparative genomics and metabolomics analysis. mSystems (2023)
Ryan R Wick, Louise M Judd, Kathryn E Holt
Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLoS computational biology 19 (3) (2023)
Jake N Barber, Luke C Nicholson, Laura C Woods, Louise M Judd, Aysha L Sezmis, Jane Hawkey, Kathryn E Holt, Michael J McDonald
Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community. The ISME journal 16 (5) (2022)
Lu Yang, Yingbo Shen, Junyao Jiang, Xueyang Wang, Dongyan Shao, Margaret M C Lam, Kathryn E Holt, Bing Shao, Congming Wu, Jianzhong Shen, Timothy R Walsh, Stefan Schwarz, Wang Yang, Zhangqi Shen
Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. Nature food 3 (3) (2022)
Ben Vezina, Lousie M Judd, Fiona K McDougall, Wayne S J Boardman, Michelle L Power, Jane Hawkey, Sylvain Brisse, Jonathan M Monk, Kathryn E Holt, Kelly L Wyres
Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies. Environmental microbiology 24 (9) (2022)
Aasmund Fostervold, Marit Andrea Klokkhammer Hetland, Ragna Bakksjø, Eva Bernhoff, Kathryn E Holt, Ørjan Samuelsen, Gunnar Skov Simonsen, Arnfinn Sundsfjord, Kelly L Wyres, Iren Høyland Löhr, null null
A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307. The Journal of antimicrobial chemotherapy 77 (3) (2022)
Niclas Raffelsberger, Marit Andrea Klokkhammer Hetland, Kristian Svendsen, Lars Småbrekke, Iren Høyland Löhr, Lotte Leonore Eivindsdatter Andreassen, Sylvain Brisse, Kathryn E Holt, Arnfinn Sundsfjord, Ørjan Samuelsen, Kirsten Gravningen
Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity. Gut microbes 13 (1) (2022)
Lu Yang, Yingbo Shen, Junyao Jiang, Xueyang Wang, Dongyan Shao, Margaret M C Lam, Kathryn E Holt, Bing Shao, Congming Wu, Jianzhong Shen, Timothy R Walsh, Stefan Schwarz, Wang Yang, Zhangqi Shen
Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. Nature food 3 (3) (2022)
Kathryn E Holt, David M Aanensen, Mark Achtman
Genomic population structures of microbial pathogens. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 377 (1861) (2022)
Lu Yang, Yingbo Shen, Junyao Jiang, Xueyang Wang, Dongyan Shao, Margaret M C Lam, Kathryn E Holt, Bing Shao, Congming Wu, Jianzhong Shen, Timothy R Walsh, Stefan Schwarz, Wang Yang, Zhangqi Shen
Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. Nature food 3 (3) (2022)
Claire L Gorrie, Mirjana Mirčeta, Ryan R Wick, Louise M Judd, Margaret M C Lam, Ryota Gomi, Iain J Abbott, Nicholas R Thomson, Richard A Strugnell, Nigel F Pratt, Jill S Garlick, Kerrie M Watson, Peter C Hunter, David V Pilcher, Steve A McGloughlin, Denis W Spelman, Kelly L Wyres, Adam W J Jenney, Kathryn E Holt
Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. Nature communications 13 (1) (2022)
Lu Yang, Yingbo Shen, Junyao Jiang, Xueyang Wang, Dongyan Shao, Margaret M C Lam, Kathryn E Holt, Bing Shao, Congming Wu, Jianzhong Shen, Timothy R Walsh, Stefan Schwarz, Wang Yang, Zhangqi Shen
Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. Nature food 3 (3) (2022)
Zoe Anne Dyson, Elisheba Malau, Paul F Horwood, Rebecca Ford, Valentine Siba, Mition Yoannes, William Pomat, Megan Elizabeth Passey, Lousie M Judd, Danielle J Ingle, Deborah A Williamson, Gordon Dougan, Andrew R Greenhill, Kathryn E Holt
Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials. PLoS neglected tropical diseases 16 (3) (2022)
Kenneth Lindstedt, Dorota Julia Buczek, Torunn Pedersen, Erik Hjerde, Niclas Raffelsberger, Yutaka Suzuki, Sylvain Brisse, Kathryn E Holt, Ørjan Samuelsen, Arnfinn Sundsfjord
Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods. Gut microbes 14 (1) (2022)
Ryan R Wick, Kathryn E Holt
Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLoS computational biology 18 (1) (2022)
Jane Hawkey, Ben Vezina, Jonathan M Monk, Lousie M Judd, Taylor Harshegyi, Sebastián López-Fernández, Carla Rodrigues, Sylvain Brisse, Kathryn E Holt, Kelly L Wyres
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality. Genome research 32 (5) (2022)
Lu Yang, Yingbo Shen, Junyao Jiang, Xueyang Wang, Dongyan Shao, Margaret M C Lam, Kathryn E Holt, Bing Shao, Congming Wu, Jianzhong Shen, Timothy R Walsh, Stefan Schwarz, Wang Yang, Zhangqi Shen
Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. Nature food 3 (3) (2022)
Margaret M C Lam, Ryan R Wick, Stephen C Watts, Louise T Cerdeira, Kelly L Wyres, Kathryn E Holt
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature communications 12 (1) (2021)
V Vern Lee, Louise M Judd, Aaron R Jex, Kathryn E Holt, Christopher J Tonkin, Stuart A Ralph
Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites. mSystems 6 (2) (2021)
Jane Hawkey, Kalani Paranagama, Kate S Baker, Rebecca J Bengtsson, François-Xavier Weill, Nicholas R Thomson, Stephen Baker, Louise Cerdeira, Zamin Iqbal, Martin Hunt, Danielle J Ingle, Timothy J Dallman, Claire Jenkins, Deborah Ann Williamson, Kathryn E Holt
Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. Nature communications 12 (1) (2021)
Heyu Lin, David B Ascher, Yoochan Myung, Carl H Lamborg, Steven James Hallam, Caitlin M Gionfriddo, Kathryn E Holt, John W Moreau
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. The ISME journal 15 (6) (2021)
Sadia Isfat Ara Rahman, Zoe Anne Dyson, Elizabeth J Klemm, Farhana Khanam, Kathryn E Holt, Emran Kabir Chowdhury, Gordon Dougan, Firdausi Qadri
Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. PLoS neglected tropical diseases 14 (2) (2020)
Kathryn E Holt, Florent Lassalle, Kelly L Wyres, Ryan R Wick, Rafał J Mostowy
Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. The ISME journal 14 (7) (2020)
Jane Hawkey, Jonathan M Monk, Helen Billman-Jacobe, Bernhard O Palsson, Kathryn E Holt
Impact of insertion sequences on convergent evolution of Shigella species. PLoS genetics 16 (7) (2020)
Qin Qin Huang, Howard H F Tang, Shu Mei Teo, Danny Mok, Scott C Ritchie, Artika P Nath, Marta Brozynska, Agus Salim, Andrew Bakshi, Barbara J Holt, Chiea Chuen Khor, Peter D Sly, Patrick G Holt, Kathryn E Holt, Michael Inouye
Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk. Nature communications 11 (1) (2020)
Kelly L Wyres, Margaret M C Lam, Kathryn E Holt
Population genomics of Klebsiella pneumoniae. Nature reviews. Microbiology 18 (6) (2020)
Caitlin M Gionfriddo, Matthew B Stott, Jean F Power, Jacob M Ogorek, David P Krabbenhoft, Ryan R Wick, Kathryn E Holt, Lin-Xing Chen, Brian C Thomas, Jillian F Banfield, John W Moreau
Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs. Applied and environmental microbiology 86 (15) (2020)
Stephen C Watts, Kathryn E Holt
hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus. Journal of clinical microbiology 57 (6) (2019)
Hao Chung The, Christine Boinett, Duy Pham Thanh, Claire Jenkins, François-Xavier Weill, Benjamin Peter Howden, Mary Valcanis, Niall De Lappe, Martin Cormican, Sonam Wangchuk, Ladaporn Bodhidatta, Carl J Mason, To Nguyen Thi Nguyen, Tuyen Ha Thanh, Vinh Phat Voong, Vu Thuy Duong, Phu Huong Lan Nguyen, Paul Turner, Ryan R Wick, Pieter-Jan Ceyssens, Guy Thwaites, Kathryn E Holt, Nicholas R Thomson, Maia A Rabaa, Stephen Baker
Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nature communications 10 (1) (2019)
Malancha Karmakar, Carlos Henrique Miranda, Kathryn E Holt, Sarah J Dunstan, Justin Denholm, David B Ascher
Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. PloS one 14 (5) (2019)
Mohammad Hamidian, Ryan R Wick, Louise M Judd, Kathryn E Holt, Ruth M Hall
Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece. Microbiology resource announcements 8 (41) (2019)
Louise T Cerdeira, Margaret M C Lam, Kelly L Wyres, Ryan R Wick, Louise M Judd, Ralf Lopes, Rosineide M Ribas, Marcia M Morais, Kathryn E Holt, Nilton Lincopán
Small IncQ1 and Col-Like Plasmids Harboring bla KPC-2 and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258. Antimicrobial agents and chemotherapy 63 (3) (2019)
Danielle N Ingle, Satheesh Nair, Hassan Hartman, Philip M Ashton, Zoe Anne Dyson, Martin Day, Joanne Freedman, Marie A Chattaway, Kathryn E Holt, Timothy J Dallman
Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. PLoS neglected tropical diseases 13 (9) (2019)
Danielle J Ingle, Myron M Levine, Karen L Kotloff, Kathryn E Holt, Roy M Robins-Browne
Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa. Nature microbiology 3 (9) (2018)
Stephen Baker, Nicholas R Thomson, François-Xavier Weill, Kathryn E Holt
Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science (New York, N.Y.) 360 (6390) (2018)
Ryan R Wick, Eva Heinz, Kathryn E Holt, Kelly L Wyres
Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes. Journal of clinical microbiology 56 (6) (2018)
Ola Brønstad Brynildsrud, Caitlin S Pepperell, Philip Suffys, Louis Grandjean, Johana Monteserin, Nadia Debech, Jon Bohlin, Kristian Alfsnes, John O-H Pettersson, Ingerid Kirkeleite, Fatima Fandinho, Marcia Aparecida da Silva, Joao Perdigao, Isabel Portugal, Miguel Viveiros, Taane Clark, Maxine Caws, Sarah J Dunstan, Phan Vuong Khac Thai, Beatriz Lopez, Viviana Ritacco, Andrew Kitchen, Tyler S Brown, Dick van Soolingen, Mary B O'Neill, Kathryn E Holt, Edward J Feil, Barun Mathema, Francois Balloux, Vegard Eldholm
Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. Science advances 4 (10) (2018)
Se Eun Park, Duy Thanh Pham, Christine Boinett, Vanessa K Wong, Gi Deok Pak, Ursula Panzner, Ligia Maria Cruz Espinoza, Vera von Kalckreuth, Justin Im, Heidi Schütt-Gerowitt, John A Crump, Robert F Breiman, Yaw Adu-Sarkodie, Ellis Owusu-Dabo, Raphaël Rakotozandrindrainy, Abdramane Bassiahi Soura, Abraham Aseffa, Nagla Gasmelseed, Karen H Keddy, Jürgen May, Amy Gassama Sow, Peter Aaby, Holly M Biggs, Julian T Hertz, Joel M Montgomery, Leonard Cosmas, Beatrice Olack, Barry Fields, Nimako Sarpong, Tsiriniaina Jean Luco Razafindrabe, Tiana Mirana Raminosoa, Leon Parfait Kabore, Emmanuel Sampo, Mekonnen Teferi, Biruk Yeshitela, Muna Ahmed El Tayeb, Arvinda Sooka, Christian G Meyer, Ralf Krumkamp, Denise Myriam Dekker, Anna Jaeger, Sven Poppert, Adama Tall, Aissatou Niang, Morten Bjerregaard-Andersen, Sandra Valborg Løfberg, Hye Jin Seo, Hyon Jin Jeon, Jessica Fung Deerin, Jinkyung Park, Frank Konings, Mohammad Ali, John D Clemens, Peter Hughes, Juliet Nsimire Sendagala, Tobias Vudriko, Robert Downing, Usman N Ikumapayi, Grant A Mackenzie, Stephen Obaro, Silvia Argimon, David M Aanensen, Andrew Page, Jacqueline A Keane, Sebastian Duchene, Zoe Anne Dyson, Kathryn E Holt, Gordon Dougan, Florian Marks, Stephen Baker
The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Nature communications 9 (1) (2018)
Kathryn E Holt, Paul McAdam, Phan Vuong Khac Thai, Nguyen Thuy Thuong Thuong, Dang Thi Minh Ha, Nguyen Ngoc Lan, Nguyen Huu Lan, Nguyen Thi Quynh Nhu, Hoang Thanh Hai, Vu Thi Ngoc Ha, Guy Thwaites, David J Edwards, Artika P Nath, Kym Pham, David B Ascher, Jeremy Farrar, Chiea Chuen Khor, Yik Ying Teo, Michael Inouye, Maxine Caws, Sarah J Dunstan
Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nature genetics 50 (6) (2018)
Carl D Britto, Zoe Anne Dyson, Sebastian Duchene, Michael J Carter, Meeru Gurung, Dominic F Kelly, David R Murdoch, Imran Ansari, Stephen Thorson, Shrijana Shrestha, Neelam Adhikari, Gordon Dougan, Kathryn E Holt, Andrew J Pollard
Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy. PLoS neglected tropical diseases 12 (4) (2018)
Margaret M C Lam, Kelly L Wyres, Sebastian Duchêne, Ryan R Wick, Louise M Judd, Yunn-Hwen Gan, Chu-Han Hoh, Sophia Archuleta, James Steven Molton, Shirin Kalimuddin, Tse Hsien Koh, Virginie Passet, Sylvain Brisse, Kathryn E Holt
Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. Nature communications 9 (1) (2018)
François-Xavier Weill, Daryl Domman, Elisabeth Njampeko, Cheryl L Tarr, Jean Rauzier, Nizar Fawal, Karen H Keddy, Henrik Salje, Sandra Moore, Asish K Mukhopadhyay, Raymond Bercion, Francisco J Luquero, Antoinette Ngandjio, Mireille Dosso, Elena Monakhova, Benoit Garin, Christiane Bouchier, Carlo Pazzani, Ankur Mutreja, Roland Grunow, Fati Sidikou, Laurence Bonte, Sébastien Breurec, Maria Damian, Berthe-Marie Njanpop-Lafourcade, Guillaume Sapriel, Anne-Laure Page, Monzer Hamze, Myriam Henkens, Goutam Chowdhury, Martin Mengel, Jean-Louis Koeck, Jean-Michel Fournier, Gordon Dougan, Patrick A D Grimont, Julian Parkhill, Kathryn E Holt, Renaud Piarroux, Thandavarayan Ramamurthy, Marie-Laure Quilici, Nicholas R Thomson
Genomic history of the seventh pandemic of cholera in Africa. Science (New York, N.Y.) 358 (6364) (2018)
Ryan R Wick, Lousie M Judd, Kathryn E Holt
Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. PLoS computational biology 14 (11) (2018)
Amandine Perrin, Elise Larsonneur, Ainsley C Nicholson, David J Edwards, Kristin M Gundlach, Anne M Whitney, Christopher A Gulvik, Melissa E Bell, Olaya Rendueles, Jean Cury, Perrine Hugon, Dominique Clermont, Vincent Enouf, Vladimir Loparev, Phalasy Juieng, Timothy Monson, David Warshauer, Lina I Elbadawi, Maroya Spalding Walters, Matthew B Crist, Judith Noble-Wang, Gwen Borlaug, Eduardo P C Rocha, Alexis Criscuolo, Marie Touchon, Jeffrey P Davis, Kathryn E Holt, John R McQuiston, Sylvain Brisse
Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. Nature communications 8 (2017)
Ryan R Wick, Lousie M Judd, Claire L Gorrie, Kathryn E Holt
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS computational biology 13 (6) (2017)
Caitlin M Gionfriddo, Michael T Tate, Ryan R Wick, Mark B Schultz, Adam Zemla, Michael P Thelen, Robyn Schofield, David P Krabbenhoft, Kathryn E Holt, John W Moreau
Microbial mercury methylation in Antarctic sea ice. Nature microbiology 1 (10) (2016)
Danielle J Ingle, Marija Tauschek, David J Edwards, Dianna M Hocking, Derek J Pickard, Kristy I Azzopardi, Thakshila Amarasena, Vicki Bennett-Wood, Jaclyn S Pearson, Boubou Tamboura, Martin Antonio, John B Ochieng, Joseph Oundo, Inácio Mandomando, Shahida Qureshi, Thandavarayan Ramamurthy, Anowar Hossain, Karen L Kotloff, James P Nataro, Gordon Dougan, Myron M Levine, Roy M Robins-Browne, Kathryn E Holt
Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants. Nature microbiology 1 (2016)
Vanessa K Wong, Stephen Baker, Thomas R Connor, Derek Pickard, Andrew J Page, Jayshree Dave, Niamh Murphy, Richard Holliman, Armine Sefton, Michael Millar, Zoe Anne Dyson, Gordon Dougan, Kathryn E Holt, null null
An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature communications 7 (2016)
Elisabeth Njamkepo, Nizar Fawal, Alicia Tran-Dien, Jane Hawkey, Nancy Strockbine, Claire Jenkins, Kaisar A Talukder, Raymond Bercion, Konstantin Kuleshov, Renáta Kolínská, Julie E Russell, Lidia Kaftyreva, Marie Accou-Demartin, Andreas Karas, Olivier Vandenberg, Alison E Mather, Carl J Mason, Andrew J Page, Thandavarayan Ramamurthy, Chantal Bizet, Andrzej Gamian, Isabelle Carle, Amy Gassama Sow, Christiane Bouchier, Astrid Louise Wester, Monique Lejay-Collin, Marie-Christine Fonkoua, Simon Le Hello, Martin J Blaser, Cecilia Jernberg, Corinne Ruckly, Audrey Mérens, Anne-Laure Page, Martin Aslett, Peter Roggentin, Angelika Fruth, Erick Denamur, Malabi Venkatesan, Hervé Bercovier, Ladaporn Bodhidatta, Chien-Shun Chiou, Dominique Clermont, Bianca Colonna, Svetlana Egorova, Gururaja P Pazhani, Analia V Ezernitchi, Ghislaine Guigon, Simon R Harris, Hidemasa Izumiya, Agnieszka Korzeniowska-Kowal, Anna Lutyńska, Malika Gouali, Francine Grimont, Céline Langendorf, Monika Marejková, Lorea A M Peterson, Guillermo Perez-Perez, Antoinette Ngandjio, Alexander Podkolzin, Erika Souche, Mariia Makarova, German A Shipulin, Changyun Ye, Helena Žemličková, Mária Herpay, Patrick A D Grimont, Julian Parkhill, Philippe Sansonetti, Kathryn E Holt, Sylvain Brisse, Nicholas R Thomson, François-Xavier Weill
Global phylogeography and evolutionary history of Shigella dysenteriae type 1. Nature microbiology 1 (2016)
Tze Peng Lim, Rick Twee-Hee Ong, Pei-Yun Hon, Jane Hawkey, Kathryn E Holt, Tse Hsien Koh, Micky Lo-Ngah Leong, Jocelyn Qi-Min Teo, Thean Yen Tan, Mary Mah-Lee Ng, Li Yang Hsu
Multiple Genetic Mutations Associated with Polymyxin Resistance in Acinetobacter baumannii. Antimicrobial agents and chemotherapy 59 (12) (2015)
Mohammad Hamidian, Jane Hawkey, Kathryn E Holt, Ruth M Hall
Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1. Genome announcements 3 (6) (2015)
Yu Wan, Claire L Gorrie, Adam Jenney, Mirjana Mirceta, Kathryn E Holt
Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1. Genome announcements 3 (5) (2015)
Vanessa K Wong, Stephen Baker, Derek J Pickard, Julian Parkhill, Andrew J Page, Nicholas A Feasey, Robert A Kingsley, Nicholas R Thomson, Jacqueline A Keane, François-Xavier Weill, David J Edwards, Jane Hawkey, Simon R Harris, Alison E Mather, Amy K Cain, James Hadfield, Peter J Hart, Nga Tran Vu Thieu, Elizabeth J Klemm, Dafni A Glinos, Robert F Breiman, Conall H Watson, Samuel Kariuki, Melita A Gordon, Robert S Heyderman, Chinyere Okoro, Jan Jacobs, Octavie Lunguya, W John Edmunds, Chisomo Msefula, Jose A Chabalgoity, Mike Kama, Kylie Jenkins, Shanta Dutta, Florian Marks, Josefina Campos, Corinne Thompson, Stephen Obaro, Calman A MacLennan, Christiane Dolecek, Karen H Keddy, Anthony M Smith, Christopher M Parry, Abhilasha Karkey, E Kim Mulholland, James I Campbell, Sabina Dongol, Buddha Basnyat, Muriel Dufour, Don Bandaranayake, Take Toleafoa Naseri, Shalini Pravin Singh, Mochammad Hatta, Paul Newton, Robert S Onsare, Lupeoletalalei Isaia, David Dance, Viengmon Davong, Guy Thwaites, Lalith Wijedoru, John A Crump, Elizabeth De Pinna, Satheesh Nair, Eric J Nilles, Duy Pham Thanh, Paul Turner, Sona Soeng, Mary Valcanis, Joan Powling, Karolina Dimovski, Geoff Hogg, Jeremy Farrar, Kathryn E Holt, Gordon Dougan
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nature genetics 47 (6) (2015)

Kathryn E Holt.css-eqlu8i{font-size:small;padding-left:4px;} (Kathryn Holt)

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Kathryn E Holt (Kathryn Holt)