IMPROVING PREVENTION, TRACKING AND TREATMENT OF MAJOR HUMAN BACTERIAL PATHOGENS

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

2022-04-12

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

2022-01-19

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

2021-12-06

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

2021-11-02

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

2021-10-20

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

2021-10-05

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

2021-09-15

Serological assays for SARS-CoV-2 infection are now widely available for use in diagnostic laboratories. Limited data are availabl..

Development of Phylodynamic Methods for Bacterial Pathogens

Danielle J Ingle, Benjamin P Howden, Sebastian Duchene

2021-08-09

Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases..

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

2021-07-28

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

2021-07-01

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

2021-05-01

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

2021-03-16

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

2021-03-02

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

2021-03-01

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

2020-12-01

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

2020-11-09

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

2020-11-01

Antistaphylococcal penicillins such as oxacillin are the key antibiotics in the treatment of invasive methicillin-susceptible Stap..

Serological tests for COVID--19 Serological assays for SARS-CoV-2 present challenges and opportunities

Katherine Bond, Eloise Williams, Benjamin P Howden, Deborah A Williamson

2020-11-01

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

2020-10-15

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

2020-09-01

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

2020-09-01

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

2020-01-01

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

2020-01-01

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

2019-11-01

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

2019-11-01

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

2019-11-01

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

2019-10-01

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

2019-10-01

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

2019-09-05

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

2019-09-01

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

2019-09-01

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

2019-09-01

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

2019-09-01

Improved knowledge of factors that promote outbreaks of enteric pathogens among men who have sex with men (MSM) could enable targe..

The risk of resistance: what are the major antimicrobial resistance threats facing Australia?

Deborah A Williamson, Benjamin P Howden, David L Paterson

2019-08-01

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

2019-07-11

WalKR (YycFG) is the only essential two-component regulator in the human pathogen Staphylococcus aureus. WalKR regulates peptidogl..

Genomics of vancomycin-resistant Enterococcus faecium

Claire Gorrie, Charlie Higgs, Glen Carter, Timothy P Stinear, Benjamin Howden

2019-07-01

Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant public health threat and was listed on the World Healt..

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

2019-05-01

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

2019-05-01

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

2019-03-01

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

2019-01-01

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

2018-12-01

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

2018-11-01

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

2018-10-01

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

2018-08-31

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

2018-08-01

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

2018-07-01

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

2018-04-01

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

2018-03-01

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

2018-02-28

Background: Large-scale genomic studies of within-host evolution during Staphylococcus aureus bacteraemia (SAB) are needed to unde..

Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen

Wei Gao, Benjamin P Howden, Timothy P Stinear

2018-02-01

Enterococci are long-standing members of the human microbiome and they are also widely distributed in nature. However, with the su..

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

2018-02-01

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

2018-02-01

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

2018-02-01

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

2018-01-03

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

2018-01-01

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

2018-01-01

Multidrug-resistant (MDR) and extensively-drug-resistant (XDR) Gram-negative bacteria have emerged as a major threat to human heal..

The Critical Importance of Sampling Fraction to Inferences of Mycobacterium tuberculosis Transmission

Robyn S Lee, Benjamin P Howden

2018-01-01

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

2017-11-01

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

2017-10-01

OBJECTIVES: Vancomycin-intermediate Staphylococcus aureus (VISA) is associated with genetic changes that may also impact upon path..

Current and Emerging Topical Antibacterials and Antiseptics: Agents, Action, and Resistance Patterns.

Deborah A Williamson, Glen P Carter, Benjamin P Howden

2017-07-01

Bacterial skin infections represent some of the most common infectious diseases globally. Prevention and treatment of skin infecti..

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

2017-07-01

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

2017-06-28

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

2017-06-01

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

2017-01-01

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

2016-12-01

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

2016-12-01

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

2016-11-01

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

2016-09-01

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

2016-08-01

Whole-genome sequencing (WGS) provides the highest resolution analysis for comparison of bacterial isolates in public health micro..