IMPROVING PREVENTION, TRACKING AND TREATMENT OF MAJOR HUMAN BACTERIAL PATHOGENS
Grant number: 1105905 | Funding period: 2016 - 2020
This research fellowship will lead to a detailed understanding of the mechanisms by which bacteria become resistant to antibiotics and cause diseases, how bacterial pathogens evolve and spread in the Australian community, and will result in new understanding of the optimal treatment of bacterial diseases and identification of compounds for new antibiotic development.
Related publications (69)
Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis
Norelle L Sherry, Claire L Gorrie, Jason C Kwong, Charlie Higgs, Rhonda L Stuart, Caroline Marshall, Susan A Ballard, Michelle Sait, Tony M Korman, Monica A Slavin, Robyn S Lee, Maryza Graham, Marcel Leroi, Leon J Worth, Hiu Tat Chan, Torsten Seemann, M Lindsay Grayson, Benjamin P Howden
BACKGROUND: Current microbiological methods lack the resolution to accurately identify multidrug-resistant organism (MDRO) transmi..
Feasibility of a refurbished shipping container as a transportable laboratory for rapid SARS-CoV-2 diagnostics.
Stephen Muhi, Nick Tayler, Tuyet Hoang, Jacqueline Prestedge, Jean YH Lee, Susan A Ballard, Nicole Isles, Andrew Wlodek, Arran Greenhalgh, Deborah A Williamson, Benjamin P Howden, Timothy P Stinear
BACKGROUND: Australia's response to the coronavirus disease 2019 (COVID-19) pandemic relies on widespread availability of rapid, a..
Search and Contain: Impact of an Integrated Genomic and Epidemiological Surveillance and Response Program for Control of Carbapenemase-producing Enterobacterales
Courtney R Lane, Judith Brett, Mark Schultz, Claire L Gorrie, Kerrie Stevens, Donna RM Cameron, Siobhan St George, Annaliese van Diemen, Marion Easton, Rhonda L Stuart, Michelle Sait, Anton Y Peleg, Andrew J Stewardson, Allen C Cheng, Denis W Spelman, Mary Jo Waters, Susan A Ballard, Norelle L Sherry, Deborah A Williamson, Finn Romanes
BACKGROUND: Multiresistant organisms (MROs) pose a critical threat to public health. Population-based programs for control of MROs..
Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis
Claire L Gorrie, Anders Goncalves Da Silva, Danielle J Ingle, Charlie Higgs, Torsten Seemann, Timothy P Stinear, Deborah A Williamson, Jason C Kwong, M Lindsay Grayson, Norelle L Sherry, Benjamin P Howden
BACKGROUND: Pairwise single nucleotide polymorphisms (SNPs) are a cornerstone of genomic approaches to the inference of transmissi..
Daptomycin Resistance Occurs Predominantly in vanA-Type Vancomycin-Resistant Enterococcus faecium in Australasia and Is Associated With Heterogeneous and Novel Mutations
Lucy Li, Charlie Higgs, Adrianna M Turner, Yi Nong, Claire L Gorrie, Norelle L Sherry, Kristin H Dyet, Torsten Seemann, Deborah A Williamson, Timothy P Stinear, Benjamin P Howden, Glen P Carter
Healthcare associated infections caused by vancomycin-resistant Enterococcus faecium (VREfm) have a major impact on health outcome..
Viral Genomics to Inform Infection-control Response in Occupational Coronavirus Disease 2019 (COVID-19) Transmission
Naomi CA Whyler, Norelle L Sherry, Courtney R Lane, Torsten Seemann, Patiyan Andersson, Michelle Sait, Maryza Graham, Tony M Korman, Benjamin P Howden, Rhonda L Stuart
Healthcare workers are at increased risk of occupational transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV..
Longitudinal evaluation of laboratory-based serological assays for SARS-CoV-2 antibody detection
KA Bond, E Williams, S Nicholson, S Lim, D Johnson, B Cox, M Putland, E Gardiner, E Tippett, M Graham, F Mordant, M Catton, SR Lewin, K Subbarao, BP Howden, DA Williamson
Serological assays for SARS-CoV-2 infection are now widely available for use in diagnostic laboratories. Limited data are availabl..
An implementation science approach to evaluating pathogen whole genome sequencing in public health
Angeline S Ferdinand, Margaret Kelaher, Courtney R Lane, Anders Goncalves da Silva, Norelle L Sherry, Susan A Ballard, Patiyan Andersson, Tuyet Hoang, Justin T Denholm, Marion Easton, Benjamin P Howden, Deborah A Williamson
BACKGROUND: Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control syste..
Nonclassical Pathogens as Causative Agents of Proctitis in Men who Have Sex With Men
Eric PF Chow, Darren Lee, Stephanie Bond, Christopher K Fairley, Kate Maddaford, Rebecca Wigan, Glenda Fehler, Sigrid A Lange, Vesna De Petra, Melanie Bissessor, Catriona S Bradshaw, Benjamin P Howden, Jane S Hocking, Deborah A Williamson, Marcus Y Chen
BACKGROUND: This study aimed to identify enteric and sexually acquired rectal pathogens, other than chlamydia and gonorrhea, assoc..
Reflex Detection of Ciprofloxacin Resistance in Neisseria gonorrhoeae by Use of the SpeeDx ResistancePlus GC Assay
Darren YJ Lee, Melinda M Ashcroft, Eric PF Chow, Michelle Sait, Vesna De Petra, Marlene Tschaepe, Sigrid Lange, George Taiaroa, Catriona S Bradshaw, David M Whiley, Christopher K Fairley, Benjamin P Howden, Marcus Y Chen, Shivani Pasricha, Deborah A Williamson
Resistance-guided therapy (RGT) for gonorrhea may reduce unnecessary use of broad-spectrum antibiotics. When reflexed from the Apt..
Genomic Insights Into Last-Line Antimicrobial Resistance in Multidrug-Resistant Staphylococcus and Vancomycin-Resistant Enterococcus
Adrianna M Turner, Jean YH Lee, Claire L Gorrie, Benjamin P Howden, Glen P Carter
Multidrug-resistant Staphylococcus and vancomycin-resistant Enterococcus (VRE) are important human pathogens that are resistant to..
Multi-site assessment of rapid, point-of-care antigen testing for the diagnosis of SARS-CoV-2 infection in a low-prevalence setting: A validation and implementation study
Stephen Muhi, Nick Tayler, Tuyet Hoang, Susan A Ballard, Maryza Graham, Amanda Rojek, Jason C Kwong, Jason A Trubiano, Olivia Smibert, George Drewett, Fiona James, Emma Gardiner, Socheata Chea, Nicole Isles, Michelle Sait, Shivani Pasricha, George Taiaroa, Julie McAuley, Eloise Williams, Katherine B Gibney
BACKGROUND: In Australia, COVID-19 diagnosis relies on RT-PCR testing which is relatively costly and time-consuming. To date, few ..
Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark
Brianna Cheng, Marcel A Behr, Benjamin P Howden, Theodore Cohen, Robyn S Lee
BACKGROUND: Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengt..
Prolonged Outbreak of Multidrug-Resistant Shigella sonnei Harboring bla(CTX-M-27) in Victoria, Australia
Danielle J Ingle, Patiyan Andersson, Mary Valcanis, Jessica Barnden, Anders Goncalves da Silva, Kristy A Horan, Torsten Seemann, Marion Easton, Deborah A Williamson, Norelle L Sherry, Benjamin P Howden
In Australia, cases of shigellosis usually occur in returned travelers from regions of shigellosis endemicity or in men who have s..
An open-label, parallel-group, randomised controlled trial of antiseptic mouthwash versus antibiotics for oropharyngeal gonorrhoea treatment (OMEGA2)
Eric PF Chow, Kate Maddaford, Jane S Hocking, Catriona S Bradshaw, Rebecca Wigan, Marcus Y Chen, Benjamin P Howden, Deborah A Williamson, Christopher K Fairley
New treatments for oropharyngeal gonorrhoea are required to address rising antimicrobial resistance. We aimed to examine the effic..
Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureus
Stefano G Giulieri, Romain Guerillot, Jason C Kwong, Ian R Monk, Ashleigh S Hayes, Diane Daniel, Sarah Baines, Norelle L Sherry, Natasha E Holmes, Peter Ward, Wei Gao, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
Antistaphylococcal penicillins such as oxacillin are the key antibiotics in the treatment of invasive methicillin-susceptible Stap..
Evaluation of Serological Tests for SARS-CoV-2: Implications for Serology Testing in a Low-Prevalence Setting
Katherine Bond, Suellen Nicholson, Seok Ming Lim, Theo Karapanagiotidis, Eloise Williams, Douglas Johnson, Tuyet Hoang, Cheryll Sia, Damian Purcell, Francesca Mordant, Sharon R Lewin, Mike Catton, Kanta Subbarao, Benjamin P Howden, Deborah A Williamson
BACKGROUND: Robust serological assays are essential for long-term control of the COVID-19 pandemic. Many recently released point-o..
Pandemic printing: a novel 3D-printed swab for detecting SARS-CoV-2
Eloise Williams, Katherine Bond, Nicole Isles, Brian Chong, Douglas Johnson, Julian Druce, Tuyet Hoang, Susan A Ballard, Victoria Hall, Stephen Muhi, Kirsty L Buising, Seok Lim, Dick Strugnell, Mike Catton, Louis B Irving, Benjamin P Howden, Eric Bert, Deborah A Williamson
OBJECTIVES: To design and evaluate 3D-printed nasal swabs for collection of samples for SARS-CoV-2 testing. DESIGN: An iterative d..
Tracking the COVID-19 pandemic in Australia using genomics
Torsten Seemann, Courtney R Lane, Norelle L Sherry, Sebastian Duchene, Anders Goncalves da Silva, Leon Caly, Michelle Sait, Susan A Ballard, Kristy Horan, Mark B Schultz, Tuyet Hoang, Marion Easton, Sally Dougall, Timothy P Stinear, Julian Druce, Mike Catton, Brett Sutton, Annaliese van Diemen, Charles Alpren, Deborah A Williamson
Genomic sequencing has significant potential to inform public health management for SARS-CoV-2. Here we report high-throughput gen..
Comparative Transcriptomic and Functional Assessments o Linezolid-Responsive Small RNA Genes in Staphylococcus aureus
Wei Gao, Romain Guerillot, Ya Hsun Lin, Jai Tree, Marie Beaume, Patrice Francois, Ian R Monk, Torsten Seemann, Jacques Schrenzel, Benjamin P Howden, Timothy P Stinear
Staphylococcus aureus contains a repertoire of at least 50 and possibly 500 small RNAs (sRNAs). The functions of most sRNAs are no..
Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA
Jean YH Lee, Nickala Best, Julie McAuley, Jessica L Porter, Torsten Seemann, Mark B Schultz, Michelle Sait, Nicole Orlando, Karolina Mercoulia, Susan A Ballard, Julian Druce, Thomas Tran, Mike G Catton, Melinda J Pryor, Huanhuan L Cui, Angela Luttick, Sean McDonald, Arran Greenhalgh, Jason C Kwong, Norelle L Sherry
Introduction. The SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes requir..
Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia
Danielle J Ingle, Marion Easton, Mary Valcanis, Torsten Seemann, Jason C Kwong, Nicola Stephens, Glen P Carter, Anders Goncalves da Silva, James Adamopoulos, Sarah L Baines, Kathryn E Holt, Eric PF Chow, Christopher K Fairley, Marcus Y Chen, Martyn D Kirk, Benjamin P Howden, Deborah A Williamson
BACKGROUND: In urban Australia, the burden of shigellosis is either in returning travelers from shigellosis-endemic regions or in ..
Kissing may be an important and neglected risk factor for oropharyngeal gonorrhoea: a cross-sectional study in men who have sex with men
Eric PF Chow, Vincent J Cornelisse, Deborah A Williamson, David Priest, Jane S Hocking, Catriona S Bradshaw, Tim RH Read, Marcus Y Chen, Benjamin P Howden, Christopher K Fairley
OBJECTIVES: A mathematical model suggested that a significant proportion of oropharyngeal gonorrhoea cases are acquired via oropha..
Mining the Methylome Reveals Extensive Diversity in Staphylococcus epidermidis Restriction Modification
Jean YH Lee, Glen P Carter, Sacha J Pidot, Romain Guerillot, Torsten Seemann, Anders Goncalves da Silva, Timothy J Foster, Benjamin P Howden, Timothy P Stinear, Ian R Monk
Staphylococcus epidermidis is a significant opportunistic pathogen of humans. Molecular studies in this species have been hampered..
Trends and Risk Factors for Antimicrobial-Resistant Neisseria gonorrhoeae, Melbourne, Australia, 2007 to 2018
Deborah A Williamson, Christopher K Fairley, Benjamin P Howden, Marcus Y Chen, Kerrie Stevens, Vesna De Petra, Ian Denham, Eric PF Chow
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major public health problem. Traditionally, AMR surveillance programs..
Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections
Romain Guerillot, Xenia Kostoulias, Liam Donovan, Lucy Li, Glen P Carter, Abderrahman Hachani, Koen Vandelannoote, Stefano Giulieri, Ian R Monk, Mayu Kunimoto, Lora Starrs, Gaetan Burgio, Torsten Seemann, Anton Y Peleg, Timothy P Stinear, Benjamin P Howden
Staphylococcus aureus small-colony variants (SCVs) are associated with unusually chronic and persistent infections despite active ..
Bridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era
Deborah A Williamson, Eric PF Chow, Claire L Gorrie, Torsten Seemann, Danielle J Ingle, Nasra Higgins, Marion Easton, George Taiaroa, Yonatan H Grad, Jason C Kwong, Christopher K Fairley, Marcus Y Chen, Benjamin P Howden
Whole genome sequencing (WGS) has been used to investigate transmission of Neisseria gonorrhoeae, but to date, most studies have n..
Evidence for a new paradigm of gonorrhoea transmission: cross-sectional analysis of Neisseria gonorrhoeae infections by anatomical site in both partners in 60 male couples
Vincent Jasper Cornelisse, Deborah Williamson, Lei Zhang, Marcus Y Chen, Catriona Bradshaw, Jane S Hocking, Jennifer Hoy, Benjamin P Howden, Eric PF Chow, Christopher K Fairley
OBJECTIVE: Gonorrhoea transmission between men is currently thought to occur primarily to and from the urethra. Transmission witho..
Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016
Norelle L Sherry, Courtney R Lane, Jason C Kwong, Mark Schultz, Michelle Sait, Kerrie Stevens, Susan Ballard, Anders Goncalves da Silva, Torsten Seemann, Claire L Gorrie, Timothy P Stinear, Deborah A Williamson, Judith Brett, Annaliese van Diemen, Marion Easton, Benjamin P Howden
Carbapenemase-producing Enterobacterales (CPE) are being increasingly reported in Australia, and integrated clinical and genomic s..
Prevalence of genital and oropharyngeal chlamydia and gonorrhoea among female sex workers in Melbourne, Australia, 2015-2017: need for oropharyngeal testing
Eric PF Chow, Deborah A Williamson, Ria Fortune, Catriona S Bradshaw, Marcus Y Chen, Glenda Fehler, Vesna De Petra, Benjamin P Howden, Christopher K Fairley
OBJECTIVE: The Victorian legislation requires sex workers to have quarterly screening for genital chlamydia and gonorrhoea, but sc..
Risk Factors for Asymptomatic Enteric Pathogen Detection Among Men Who Have Sex With Men
Deborah A Williamson, Eric PF Chow, Darren Lee, Kate Maddaford, Michelle Sait, Marion Easton, Danielle Ingle, Rebecca Wigan, Vesna De Petra, Benjamin P Howden, Christopher K Fairley, Marcus Y Chen
Improved knowledge of factors that promote outbreaks of enteric pathogens among men who have sex with men (MSM) could enable targe..
Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase of Staphylococcus aureus
Ian R Monk, Nausad Shaikh, Stephanie L Begg, Mike Gajdiss, Liam KR Sharkey, Jean YH Lee, Sacha J Pidot, Torsten Seemann, Michael Kuiper, Brit Winnen, Rikki Hvorup, Brett M Collins, Gabriele Bierbaum, Saumya R Udagedara, Jacqueline R Morey, Neha Pulyani, Benjamin P Howden, Megan J Maher, Christopher A McDevitt, Glenn F King
WalKR (YycFG) is the only essential two-component regulator in the human pathogen Staphylococcus aureus. WalKR regulates peptidogl..
Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia
Danielle J Ingle, Anders Goncalves da Silva, Mary Valcanis, Susan A Ballard, Torsten Seemann, Amy Jennison, Ivan Bastian, Rolf Wise, Martyn D Kirk, Benjamin P Howden, Deborah A Williamson
Shiga-toxin-producing Escherichia coli (STEC) infection is an important global cause of foodborne disease. To date however, genomi..
Remodeling of pSK1 Family Plasmids and Enhanced Chlorhexidine Tolerance in a Dominant Hospital Lineage of Methicillin-Resistant Staphylococcus aureus
Sarah L Baines, Slade O Jensen, Neville Firth, Anders Goncalves da Silva, Torsten Seemann, Glen P Carter, Deborah A Williamson, Benjamin P Howden, Timothy P Stinear
Staphylococcus aureus is a significant human pathogen whose evolution and adaptation have been shaped in part by mobile genetic el..
Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307
Kelly L Wyres, Jane Hawkey, Marit AK Hetland, Aasmund Fostervold, Ryan R Wick, Louise M Judd, Mohammad Hamidian, Benjamin P Howden, Iren H Lohr, Kathryn E Holt
OBJECTIVES: Recent reports indicate the emergence of a new carbapenemase-producing Klebsiella pneumoniae clone, ST307. We sought t..
Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing
Andre Mu, Jason C Kwong, Nicole S Isles, Anders Goncalves da Silva, Mark B Schultz, Susan A Ballard, Courtney R Lane, Glen P Carter, Deborah A Williamson, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail o..
The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study
Robyn S Lee, Anders Goncalves da Silva, Sarah L Baines, Janet Strachan, Susan Ballard, Glen P Carter, Jason C Kwong, Mark B Schultz, Dieter M Bulach, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
BACKGROUND: Vancomycin-resistant Enterococcus faecium (VREfm) represent a major source of nosocomial infection worldwide. In Austr..
Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis
Glen P Carter, James E Ussher, Anders Gonsalves Da Silva, Sarah L Baines, Helen Heffernan, Thomas Riley, Roland Broadbent, Antje van der Linden, Jean Lee, Ian R Monk, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
Coagulase-negative staphylococci (CoNS), such as Staphylococcus capitis, are major causes of bloodstream infections in neonatal in..
Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis
Jean YH Lee, Ian R Monk, Anders Goncalves da Silva, Torsten Seemann, Kyra YL Chua, Angela Kearns, Robert Hill, Neil Woodford, Mette D Bartels, Birgit Strommenger, Frederic Laurent, Magali Dodemont, Ariane Deplano, Robin Patel, Anders R Larsen, Tony M Korman, Timothy P Stinear, Benjamin P Howden
Staphylococcus epidermidis is a conspicuous member of the human microbiome, widely present on healthy skin. Here we show that S. e..
Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq)
Romain Guerillot, Lucy Li, Sarah Baines, Brian Howden, Mark B Schultz, Torsten Seemann, Ian Monk, Sacha J Pidot, Wei Gao, Stefano Giulieri, Anders Goncalves da Silva, Anthony D'Agata, Takehiro Tomita, Anton Y Peleg, Timothy P Stinear, Benjamin P Howden
Mutation acquisition is a major mechanism of bacterial antibiotic resistance that remains insufficiently characterised. Here we pr..
Increasing tolerance of hospital Enterococcus faecium to handwash alcohols
Sacha J Pidot, Wei Gao, Andrew H Buultjens, Ian R Monk, Romain Guerillot, Glen P Carter, Jean YH Lee, Margaret MC Lam, M Lindsay Grayson, Susan A Ballard, Andrew A Mahony, Elizabeth A Grabsch, Despina Kotsanas, Tony M Korman, Geoffrey W Coombs, J Owen Robinson, Anders Goncalves da Silva, Torsten Seemann, Benjamin P Howden, Paul DR Johnson
Alcohol-based disinfectants and particularly hand rubs are a key way to control hospital infections worldwide. Such disinfectants ..
Ceftazidime/avibactam susceptibility by three different susceptibility testing methods in carbapenemase-producing Gram-negative bacteria from Australia
Norelle L Sherry, Sarah L Baines, Benjamin P Howden
Avibactam (AVI) is a novel β-lactamase inhibitor active against class A, class C and some class D β-lactamases. In combination wit..
Comparative Genomics Shows That Mycobacterium ulcerans Migration and Expansion Preceded the Rise of Buruli Ulcer in Southeastern Australia
Andrew H Buultjens, Koen Vandelannoote, Conor J Meehan, Miriam Eddyani, Bouke C de Jong, Janet AM Fyfe, Maria Globan, Nicholas J Tobias, Jessica L Porter, Takehiro Tomita, Ee Laine Tay, Torsten Seemann, Benjamin P Howden, Paul DR Johnson, Timothy P Stinear
Since 2000, cases of the neglected tropical disease Buruli ulcer, caused by infection with Mycobacterium ulcerans, have increased ..
Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study
Jason C Kwong, Eric PF Chow, Kerrie Stevens, Timothy P Stinear, Torsten Seemann, Christopher K Fairley, Marcus Y Chen, Benjamin P Howden
OBJECTIVES: Drug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistan..
Genomic Exploration of Within-Host Microevolution Reveals a Distinctive Molecular Signature of Persistent Staphylococcus aureus Bacteraemia
Stefano Giulieri, Sarah Baines, Romain Guerillot, Torsten Semann, Anders Goncalves da Silva, Mark Schultz, Ruth Massey, Natasha Holmes, Timothy Stinear, Benjamin Howden
Background: Large-scale genomic studies of within-host evolution during Staphylococcus aureus bacteraemia (SAB) are needed to unde..
Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand
Robyn S Lee, Torsten Seemann, Helen Heffernan, Jason C Kwong, Anders Goncalves da Silva, Glen P Carter, Rosemary Woodhouse, Kristin H Dyet, Dieter M Bulach, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
BACKGROUND: Antimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health. No studies to date have examined the..
Increasing Antimicrobial Resistance in Nontyphoidal Salmonella Isolates in Australia from 1979 to 2015
Deborah A Williamson, Courtney R Lane, Marion Easton, Mary Valcanis, Janet Strachan, Mark G Veitch, Martyn D Kirk, Benjamin P Howden
Australia has high and increasing rates of salmonellosis. To date, the serovar distribution and associated antimicrobial resistanc..
Topical Antibiotic Use Coselects for the Carriage of Mobile Genetic Elements Conferring Resistance to Unrelated Antimicrobials in Staphylococcus aureus
Glen P Carter, Mark B Schultz, Sarah L Baines, Anders Goncalves da Silva, Helen Heffernan, Audrey Tiong, Peter H Pham, Ian R Monk, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
Topical antibiotics, such as mupirocin and fusidic acid, are commonly used in the prevention and treatment of skin infections, par..
Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak
Jason C Kwong, Courtney R Lane, Finn Romanes, Anders Goncalves da Silva, Marion Easton, Katie Cronin, Mary Jo Waters, Takehiro Tomita, Kerrie Stevens, Mark B Schultz, Sarah L Baines, Norelle L Sherry, Glen P Carter, Andre Mu, Michelle Sait, Susan A Ballard, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
BACKGROUND: Until recently, Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Austr..
Convergent Evolution Driven by Rifampin Exacerbates the Global Burden of Drug-Resistant &ITStaphylococcus aureus&IT
Romain Guerillot, Anders Goncalves da Silva, Ian Monk, Stefano Giulieri, Takehiro Tomita, Eloise Alison, Jessica Porter, Sacha Pidot, Wei Gao, Anton Y Peleg, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
Mutations in the beta-subunit of bacterial RNA polymerase (RpoB) cause resistance to rifampin (Rifr), a critical antibiotic for tr..
Emerging Gram negative resistance to last-line antimicrobial agents fosfomycin, colistin and ceftazidime-avibactam - epidemiology, laboratory detection and treatment implications
Norelle Sherry, Benjamin Howden
Multidrug-resistant (MDR) and extensively-drug-resistant (XDR) Gram-negative bacteria have emerged as a major threat to human heal..
A Supervised Statistical Learning Approach for Accurate Legionella pneumophila Source Attribution during Outbreaks
Andrew H Buultjens, Kyra YL Chua, Sarah L Baines, Jason Kwong, Wei Gao, Zoe Cutcher, Stuart Adcock, Susan Ballard, Mark B Schultz, Takehiro Tomita, Nela Subasinghe, Glen P Carter, Sacha J Pidot, Lucinda Franklin, Torsten Seemann, Anders Goncalves Da Silva, Benjamin P Howden, Timothy P Stinear
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative ba..
Vancomycin-intermediate Staphylococcus aureus isolates are attenuated for virulence when compared with susceptible progenitors
DR Cameron, Y-H Lin, S Trouillet-Assant, V Tafani, X Kostoulias, E Mouhtouris, N Skinner, K Visvanathan, SL Baines, B Howden, IR Monk, F Laurent, TP Stinear, BP Howden, AY Peleg
OBJECTIVES: Vancomycin-intermediate Staphylococcus aureus (VISA) is associated with genetic changes that may also impact upon path..
Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring bla(CTX-M-9)
Sarah J Sparham, Jason C Kwong, Mary Valcanis, Marion Easton, Darren J Trott, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
Antimicrobial resistance in non-typhoidal Salmonella is a critical problem globally, with the emergence of resistance to third-gen..
A multicentre double-blind randomised controlled trial evaluating the efficacy of daily use of antibacterial mouthwash against oropharyngeal gonorrhoea among men who have sex with men: the OMEGA (Oral Mouthwash use to Eradicate GonorrhoeA) study protocol
Eric PF Chow, Sandra Walker, Jane S Hocking, Catriona S Bradshaw, Marcus Y Chen, Sepehr N Tabrizi, Benjamin P Howden, Matthew G Law, Kate Maddaford, Tim RH Read, David A Lewis, David M Whiley, Lei Zhang, Andrew E Grulich, John M Kaldor, Vincent J Cornelisse, Samuel Phillips, Basil Donovan, Anna M McNulty, David J Templeton
BACKGROUND: Gonorrhoea is one of the most common sexually transmissible infections in men who have sex with men (MSM). Gonorrhoea ..
Target-Specific Assay for Rapid and Quantitative Detection of Mycobacterium chimaera DNA
Enrique Zozaya-Valdes, Jessica L Porter, John Coventry, Janet AM Fyfe, Glen P Carter, Anders Goncalves da Silva, Mark B Schultz, Torsten Seemann, Paul DR Johnson, Andrew J Stewardson, Ivan Bastian, Sally A Roberts, Benjamin P Howden, Deborah A Williamson, Timothy P Stinear
Mycobacterium chimaera is an opportunistic environmental mycobacterium belonging to the Mycobacterium avium-M. intracellulare comp..
A phylogenomic framework for assessing the global emergence and evolution of clonal complex 398 methicillin-resistant Staphylococcus aureus
Anders Goncalves da Silva, Sarah L Baines, Glen P Carter, Helen Heffernan, Nigel P French, Xiaoyun Ren, Torsten Seemann, Dieter Bulach, Jason Kwong, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
Distinct clones of methicillin-resistant Staphylococcus aureus (MRSA) have emerged as important causes of infection in individuals..
Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium
Glen P Carter, Andrew H Buultjens, Susan A Ballard, Sarah L Baines, Takehiro Tomita, Janet Strachan, Paul DR Johnson, John K Ferguson, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
BACKGROUND: Enterococcus faecium is a major nosocomial pathogen causing significant morbidity and mortality worldwide. Assessment ..
Genomic Insights into a Sustained National Outbreak of Yersinia pseudotuberculosis
Deborah A Williamson, Sarah L Baines, Glen P Carter, Anders Goncalves da silva, Xiaoyun Ren, Jill Sherwood, Muriel Dufour, Mark B Schultz, Nigel P French, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
In 2014, a sustained outbreak of yersiniosis due to Yersinia pseudotuberculosis occurred across all major cities in New Zealand (N..
Use of bacterial whole-genome sequencing to understand and improve the management of invasive Staphylococcus aureus infections
Stefano G Giulieri, Natasha E Holmes, Timothy P Stinear, Benjamin P Howden
Management of invasive Staphylococcus aureus infections is complex. Dramatic improvements in bacterial whole genome sequencing (WG..
Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis
Jean YH Lee, Ian R Monk, Sacha J Pidot, Siddarth Singh, Kyra YL Chua, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage is frequently multidrug-resistant an..
NGMASTER: in silico multi-antigen sequence typing for Neisseria gonorrhoeae
Jason C Kwong, Anders Goncalves da Silva, Kristin Dyet, Deborah A Williamson, Timothy P Stinear, Benjamin P Howden, Torsten Seemann
Whole-genome sequencing (WGS) provides the highest resolution analysis for comparison of bacterial isolates in public health micro..