Publications by authors named "Benjamin P Howden"

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An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance.
Norelle L Sherry, Kristy A Horan, Susan A Ballard, Anders Gonҫalves da Silva, Claire L Gorrie, Mark B Schultz, Kerrie Stevens, Mary Valcanis, Michelle L Sait, Timothy P Stinear

Nat Commun· January 2023

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Genomic and epidemiological characteristics of in Australia, 1991-2022.
Aaliya F Ibrahim, Danielle J Ingle, Jessica R Webb, Benjamin P Howden, Patiyan Andersson

Pathog Glob Health· December 2025

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Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.
Jia Qi Beh, Ryan R Wick, Benjamin P Howden, Christopher H Connor, Jessica R Webb

Antimicrob Agents Chemother· December 2025

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Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference.
Nicola F Müller, Ryan R Wick, Louise M Judd, Deborah A Williamson, Trevor Bedford, Benjamin P Howden

PLoS Pathog· December 2025

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Increased risk of antimicrobial resistance in patients with cirrhosis and hepatic encephalopathy using rifaximin.
Cheng-Hao Kuo, Glen P Carter, Benjamin P Howden, Tsai-Wei Huang, Zhujun Cao

Nat Commun· December 2025

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Human leptospirosis in the central division of Fiji: a retrospective epidemiological study.
Sakopo'Aonga-Ki-Vavau Vaka'uta, Kolosa Matebalavu, Anaseini Ratu, Ramneek Nadan Goundar, Aalisha Sahukhan, Benjamin P Howden

Trans R Soc Trop Med Hyg· November 2025

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Emergence of azithromycin and ciprofloxacin non-susceptible genotype 4.2.2 . Typhi in Fiji.
Ashwini Vinod, Andrew J Hayes, Yogeshni Chandra, Sonika Kaajal Nair, Tashyam Pillay, Benjamin P Howden

Antimicrob Agents Chemother· November 2025

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Therapeutic approach to difficult-to-treat multidrug-resistant enterococcal infections.
Adrianna M Turner, Paul Kinsella, William R Miller, Glen P Carter, Truc T Tran, Benjamin P Howden

Antimicrob Agents Chemother· October 2025

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Population structure and antimicrobial resistance of in Victoria, Australia.
Lamali Sadeesh Kumar, Sarah L Baines, Kylie Hui, Janet Strachan, Norelle L Sherry, Benjamin P Howden

Microb Genom· October 2025

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Communicable diseases genomics network: promoting and harmonising pathogen genomics implementation for public health in Australia.
Chantel Lin, Amy V Jennison, Lex E X Leong, David J Speers, Ella M Meumann, Benjamin P Howden

Lancet Reg Health West Pac· October 2025

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Invasive Streptococcus dysgalactiae subspecies equisimilis compared with Streptococcus pyogenes in Australia, 2011-23, and the emergence of a multi-continent stG62647 lineage: a retrospective clinical and genomic epidemiology study.
Ouli Xie, Leo Featherstone, An N T Nguyen, Andrew J Hayes, Miranda E Pitt, Benjamin P Howden

Lancet Microbe· October 2025

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Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi.
Danielle J Ingle, Jane Hawkey, Martin Hunt, Zamin Iqbal, Jacqueline A Keane, Benjamin P Howden

Genome Med· October 2025

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Selecting candidate Neisseria gonorrhoeae strains for oropharyngeal gonorrhoea human challenge: a genomics-based analysis of clinical isolates.
Eloise Williams, Soo Jen Low, Georgina L Pollock, Mona L Taouk, Jacqueline Prestedge, Benjamin P Howden

Lancet Microbe· September 2025

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Global diversity and evolution of Salmonella enterica serovar Panama: a genomic epidemiology study.
Caisey V Pulford, Blanca M Perez-Sepulveda, Danielle J Ingle, Rebecca J Bengtsson, Rebecca J Bennett, Benjamin P Howden

Lancet Microbe· September 2025

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Autocycler: long-read consensus assembly for bacterial genomes.
Ryan R Wick, Benjamin P Howden, Timothy P Stinear

Bioinformatics· September 2025

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Insights from expert elicitation: prioritising pathogens for genome sequencing for Australian public health response.
Tehzeeb Zulfiqar, Angeline Ferdinand, Danielle Cribb, Patiyan Andersson, Alireza Zahedi, Benjamin P Howden

Lancet Reg Health West Pac· September 2025

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Regulation of airway fumarate by host and pathogen promotes Staphylococcus aureus pneumonia.
Ying-Tsun Chen, Zihua Liu, Dario Fucich, Stefano G Giulieri, Zhe Liu, Benjamin P Howden

Nat Commun· August 2025

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Transposon-directed insertion-site sequencing (TraDIS) analysis of using nanopore sequencing and a WebAssembly analysis platform.
Alexandra L Krause, Wytamma Wirth, Adrianna M Turner, Louise Judd, Lucy Li, Benjamin P Howden

Microbiol Spectr· July 2025

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Global analysis of the genomic diversity, antimicrobial resistance and potential vaccine candidates carried by the major global bovine pathogen .
Adrianna M Turner, Lucy Li, George Taiaroa, Ian R Monk, Peter Mansell, Benjamin P Howden

Microb Genom· July 2025

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Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Typhi.
Danielle J Ingle, Jane Hawkey, Martin Hunt, Zamin Iqbal, Jacqueline A Keane, Benjamin P Howden

bioRxiv· July 2025

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Genomics to understand the global landscape of linezolid resistance in and .
Jia Qi Beh, Diane S Daniel, Louise M Judd, Ryan R Wick, Peter Kelley, Benjamin P Howden

Microb Genom· June 2025

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Distinct adaptation and epidemiological success of different genotypes within serovar Dublin.
Cheryll M Sia, Rebecca L Ambrose, Mary Valcanis, Patiyan Andersson, Susan A Ballard, Benjamin P Howden

Elife· June 2025

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The impact of integrated genomic surveillance on non-typhoidal infection in Australia: an ecological study.
Son Nghiem, Nhung Mai, My Tran, Danielle M Cribb, Liliana Bulfone, Benjamin P Howden

Lancet Reg Health West Pac· June 2025

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Genetic Correlates of Synergy Mechanisms of Daptomycin Plus Fosfomycin in Daptomycin-Susceptible and -Resistant Methicillin-Resistant (MRSA).
Warren E Rose, Selvi C Ersoy, Wessam Abdelhady, Alan R Dominguez, Jedidiah Ndam Muyah Manna, Benjamin P Howden

Microorganisms· June 2025

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A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections.
Stefano G Giulieri, Marcel Leroi, Diane Daniel, Roy Chean, Katherine Bond, Benjamin P Howden

Nat Commun· May 2025

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Regulation of airway fumarate by host and pathogen promotes pneumonia.
Ying-Tsun Chen, Zihua Liu, Dario Fucich, Stefano G Giulieri, Zhe Liu, Benjamin P Howden

bioRxiv· April 2025

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