Genomic perspective on the bacillus causing paratyphoid B fever

Authors: Jane Hawkey, Lise Frézal, Alicia Tran Dien, Anna Zhukova, Derek Brown, Marie Anne Chattaway, Sandra Simon, Hidemasa Izumiya, Patricia I. Fields, Niall De Lappe, Lidia Kaftyreva, Xuebin Xu, Junko Isobe, Dominique Clermont, Elisabeth Njamkepo, Yukihiro Akeda, Sylvie Issenhuth-Jeanjean, Mariia Makarova, Yanan Wang, Martin Hunt, Brent M. Jenkins, Magali Ravel, Véronique Guibert, Estelle Serre, Zoya Matveeva, Laëtitia Fabre, Martin Cormican, Min Yue, Baoli Zhu, Masatomo Morita, Zamin Iqbal, Carolina Silva Nodari, Maria Pardos de la Gandara, François-Xavier Weill

Source: Nature Communications, Vol 15, Iss 1, Pp 1-17 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/7956e3cfa6a345ad937be87fbbff7d31

Targeted sequencing of Enterobacterales bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies

Authors: Hugh Cottingham, Louise M. Judd, Jessica A. Wisniewski, Ryan R. Wick, Thomas D. Stanton, Ben Vezina, Nenad Macesic, Anton Y. Peleg, Iruka N. Okeke, Kathryn E. Holt, Jane Hawkey

Source: mSystems, Vol 10, Iss 2 (2025)

Subject Terms: Oxford Nanopore, CRISPR-Cas9 enrichment, Klebsiella, Enterobacterales, metagenomics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/a5dadaeb60874b81badeec94c9fa4cc7

Molecular characterization and descriptive analysis of carbapenemase-producing Gram-negative rod infections in Bogota, Colombia

Authors: Elsa D. Ibáñez-Prada, Ingrid G. Bustos, Enrique Gamboa-Silva, Diego F. Josa, Lina Mendez, Yuli V. Fuentes, Cristian C. Serrano-Mayorga, Oscar Baron, Alejandra Ruiz-Cuartas, Edwin Silva, Louise M. Judd, Taylor Harshegyi, Hector F. Africano, Juan Urrego-Reyes, Claudia C. Beltran, Sebastian Medina, Rafael Leal, Andrew J. Stewardson, Kelly L. Wyres, Jane Hawkey, Luis Felipe Reyes

Source: Microbiology Spectrum, Vol 12, Iss 6 (2024)

Subject Terms: antimicrobial resistance, carbapenem resistance, carbapenemase-encoding genes, KPC, sequence analysis, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2165-0497

Access URL: https://doaj.org/article/ce057785c1be4472ba264e236e441dde

Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer

Authors: Nenad Macesic, Jane Hawkey, Ben Vezina, Jessica A. Wisniewski, Hugh Cottingham, Luke V. Blakeway, Taylor Harshegyi, Katherine Pragastis, Gnei Zweena Badoordeen, Amanda Dennison, Denis W. Spelman, Adam W. J. Jenney, Anton Y. Peleg

Source: Nature Communications, Vol 14, Iss 1, Pp 1-12 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/85869f653dc24df6bcd7067f96605c72

High-level nitrofurantoin resistance in a clinical isolate of Klebsiella pneumoniae: a comparative genomics and metabolomics analysis

Authors: Maytham Hussein, Zetao Sun, Jane Hawkey, Rafah Allobawi, Louise M. Judd, Vincenzo Carbone, Rajnikant Sharma, Varsha Thombare, Mark Baker, Gauri G. Rao, Jian Li, Kathryn E. Holt, Tony Velkov

Source: mSystems, Vol 9, Iss 1 (2024)

Subject Terms: nitrofurantoin, Klebsiella pneumoniae, antimicrobial resistance, genomics, metabolomics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/a020996758a44aecb63f2ae7a08f1d44

Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models

Authors: Ben Vezina, Stephen C Watts, Jane Hawkey, Helena B Cooper, Louise M Judd, Adam WJ Jenney, Jonathan M Monk, Kathryn E Holt, Kelly L Wyres

Source: eLife, Vol 12 (2023)

Subject Terms: Klebsiella pneumoniae, software, metabolic modelling, strain-specific, Klebsiella pneumoniae species complex, bacterial, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/87406; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/069d1f508f10446c9f41211db9a4e5c9

A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China

Authors: Shaofu Qiu, Kangkang Liu, Chaojie Yang, Ying Xiang, Kaiyuan Min, Kunpeng Zhu, Hongbo Liu, Xinying Du, Mingjuan Yang, Ligui Wang, Yong Sun, Haijian Zhou, Muti Mahe, Jiayong Zhao, Shijun Li, Deshan Yu, Jane Hawkey, Kathryn E. Holt, Stephen Baker, Juntao Yang, Xuebin Xu, Hongbin Song

Source: Nature Communications, Vol 13, Iss 1, Pp 1-13 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/a60220a5d6084ef9b1913d662e5fd45e

Attributable mortality and excess length of stay associated with third-generation cephalosporin-resistant Enterobacterales bloodstream infections: a prospective cohort study in Suva, Fiji

Authors: Michael J. Loftus, Tracey E.M.W. Young-Sharma, Sue J. Lee, Shitanjni Wati, Gnei Z. Badoordeen, Luke V. Blakeway, Sally M.H. Byers, Allen C. Cheng, Ben S. Cooper, Hugh Cottingham, Adam W.J. Jenney, Jane Hawkey, Nenad Macesic, Ravi Naidu, Amitesh Prasad, Vinita Prasad, Litia Tudravu, Timoci Vakatawa, Elke van Gorp, Jessica A. Wisniewski, Eric Rafai, Anton Y. Peleg, Andrew J. Stewardson

Source: Journal of Global Antimicrobial Resistance, Vol 30, Iss , Pp 286-293 (2022)

Subject Terms: Bloodstream infection, Enterobacterales, Mortality, Antimicrobial resistance, Fiji, Microbiology, QR1-502

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2213716522001515; https://doaj.org/toc/2213-7165

Access URL: https://doaj.org/article/9e5c3937b73c473fb03a980ad3b100e1

ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting

Authors: Jane Hawkey, Kelly L. Wyres, Louise M. Judd, Taylor Harshegyi, Luke Blakeway, Ryan R. Wick, Adam W. J. Jenney, Kathryn E. Holt

Source: Genome Medicine, Vol 14, Iss 1, Pp 1-13 (2022)

Subject Terms: ESBL, Plasmids, Klebsiella pneumonia, Third-generation cephalosporin resistance, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/9dc4899a1e9347138f68c7c929938c06

Epidemiology and genomic analysis of Klebsiella oxytoca from a single hospital network in Australia

Authors: James Stewart, Louise M. Judd, Adam Jenney, Kathryn E. Holt, Kelly L. Wyres, Jane Hawkey

Source: BMC Infectious Diseases, Vol 22, Iss 1, Pp 1-10 (2022)

Subject Terms: Klebsiella oxytoca, Kleboxymycin, ESBL, Carbapenemase, Genomics, Infectious and parasitic diseases, RC109-216

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2334

Access URL: https://doaj.org/article/ca1b399c9ad6459582933d61857c04e9

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

Authors: Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal

Source: Genome Biology, Vol 22, Iss 1, Pp 1-30 (2021)

Subject Terms: Pan-genome, Genome graph, Accessory genome, Nanopore, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/3bf384fd17904ec49e3cda3805c804b4

Trycycler: consensus long-read assemblies for bacterial genomes

Authors: Ryan R. Wick, Louise M. Judd, Louise T. Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt

Source: Genome Biology, Vol 22, Iss 1, Pp 1-17 (2021)

Subject Terms: Genome assembly, Bacterial genomics, Whole-genome sequencing, Long-read sequencing, Oxford Nanopore sequencing, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/740f7969f10d4909b1310e844a757def

Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients

Authors: Kelly L. Wyres, Jane Hawkey, Mirianne Mirčeta, Louise M. Judd, Ryan R. Wick, Claire L. Gorrie, Nigel F. Pratt, Jill S. Garlick, Kerrie M. Watson, David V. Pilcher, Steve A. McGloughlin, Iain J. Abbott, Nenad Macesic, Denis W. Spelman, Adam W. J. Jenney, Kathryn E. Holt

Source: BMC Infectious Diseases, Vol 21, Iss 1, Pp 1-11 (2021)

Subject Terms: Antimicrobial resistance (AMR), Colonisation, Transmission, Genomic surveillance, Intensive care, Infectious and parasitic diseases, RC109-216

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2334

Access URL: https://doaj.org/article/7661b317e147449c9e877cdf6fa09655

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

Authors: 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 A. Williamson, Kathryn E. Holt

Source: Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/791a5cd8e43b46bfb08ed6884c5a3269

Impact of insertion sequences on convergent evolution of Shigella species.

Authors: Jane Hawkey, Jonathan M Monk, Helen Billman-Jacobe, Bernhard Palsson, Kathryn E Holt

Source: PLoS Genetics, Vol 16, Iss 7, p e1008931 (2020)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/fa085946f3bd4fa687a62184d7bd68e9

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods

Authors: Sebastian Duchene, David A. Duchene, Jemma L. Geoghegan, Zoe A. Dyson, Jane Hawkey, Kathryn E. Holt

Source: BMC Evolutionary Biology, Vol 18, Iss 1, Pp 1-11 (2018)

Subject Terms: Bayesian phylogenetics, Phylodynamics, Molecular clock, Bacterial evolution, Evolution, QH359-425

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12862-018-1210-5; https://doaj.org/toc/1471-2148

Access URL: https://doaj.org/article/e90ec54c3a6a4d4a956dbdb61b0203b5

Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in S. Typhimurium from Australian Food Animal Production

Authors: Ethan R. Wyrsch, Jane Hawkey, Louise M. Judd, Ruth Haites, Kathryn E. Holt, Steven P. Djordjevic, Helen Billman-Jacobe

Source: Microorganisms, Vol 7, Iss 9, p 299 (2019)

Subject Terms: Salmonella, plasmid, antibiotic resistance, AMR, agriculture, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/7/9/299; https://doaj.org/toc/2076-2607

Access URL: https://doaj.org/article/64d1879d1d5f43989cebb773e1964a5c