Genomics for combating antimicrobial resistant bacterial pathogens

Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink

Ashleigh F Porter, Damian FJ Purcell, Benjamin P Howden, Sebastian Duchene

2023-02-03

To investigate genetic signatures of adaptation to the mink host, we characterised the evolutionary rate heterogeneity in mink-ass..

Transiently silent acquired antimicrobial resistance: an emerging challenge in susceptibility testing

Theresa Maria Wagner, Benjamin Peter Howden, Arnfinn Sundsfjord, Kristin Hegstad

2023-01-31

Acquisition and expression of antimicrobial resistance (AMR) mechanisms in bacteria are often associated with a fitness cost. Thus..

Staphylococcus aureus host interactions and adaptation

Benjamin P Howden, Stefano G Giulieri, Tania Wong Fok Lung, Sarah L Baines, Liam K Sharkey, Jean YH Lee, Abderrahman Hachani, Ian R Monk, Timothy P Stinear

2023-01-27

Invasive Staphylococcus aureus infections are common, causing high mortality, compounded by the propensity of the bacterium to dev..

Hidden Resistances: How Routine Whole-Genome Sequencing Uncovered an Otherwise Undetected bla(NDM-1) Gene in Vibrio alginolyticus from Imported Seafood

Jacqueline MM Morris, Karolina Mercoulia, Mary Valcanis, Claire LL Gorrie, Norelle LL Sherry, Benjamin PP Howden

2023-01-05

Vibrio alginolyticus causes vibriosis of marine vertebrates, invertebrates, and humans, and while there have been several reports ..

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, Benjamin P Howden, Torsten Seemann

2023-01-04

Realising the promise of genomics to revolutionise identification and surveillance of antimicrobial resistance (AMR) has been a lo..

New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia

Ashleigh F Porter, Norelle Sherry, Patiyan Andersson, Sandra A Johnson, Sebastian Duchene, Benjamin P Howden

2022-10-01

State-wide genomic epidemiology investigations of COVID-19 in healthcare workers in 2020 Victoria, Australia: Qualitative thematic analysis to provide insights for future pandemic preparedness.

Anne E Watt, Norelle L Sherry, Patiyan Andersson, Courtney R Lane, Sandra Johnson, Mathilda Wilmot, Kristy Horan, Michelle Sait, Susan A Ballard, Christina Crachi, Dianne J Beck, Caroline Marshall, Marion A Kainer, Rhonda Stuart, Christian McGrath, Jason C Kwong, Pauline Bass, Peter G Kelley, Amy Crowe, Stephen Guy

2022-08-01

BACKGROUND: COVID-19 has affected many healthcare workers (HCWs) globally. We performed state-wide SARS-CoV-2 genomic epidemiologi..

Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016

Mark R Davies, Sebastian Duchene, Mary Valcanis, Aaron P Jenkins, Adam Jenney, Varanisese Rosa, Andrew J Hayes, Aneley Getahun Strobel, Liam McIntyre, Jake A Lacey, Elizabeth J Klemm, Vanessa K Wong, Aalisha Sahukhan, Helen Thomson, Andrew Page, Dianna Hocking, Nancy Wang, Litia Tudravu, Eric Rafai, Gordon Dougan

2022-07-01

BACKGROUND: Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not rou..

Genomic characterisation reveals a dominant lineage of SARS-CoV-2 in Papua New Guinea

Theresa Palou, Mathilda Wilmot, Sebastian Duchene, Ashleigh Porter, Janlyn Kemoi, Dagwin Suarkia, Patiyan Andersson, Anne Watt, Norelle Sherry, Torsten Seemann, Michelle Sait, Charlie Turharus, Son Nguyen, Sanmarie Schlebusch, Craig Thompson, Jamie McMahon, Stefanie Vaccher, Chantel Lin, Danoi Esoram, Benjamin P Howden

2022-06-23

The coronavirus disease pandemic has highlighted the utility of pathogen genomics as a key part of comprehensive public health res..

Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

Stefano G Giulieri, Romain Guerillot, Sebastian Duchene, Abderrahman Hachani, Diane Daniel, Torsten Seemann, Joshua S Davis, Steven YC Tong, Bernadette C Young, Daniel J Wilson, Timothy P Stinear, Benjamin P Howden

2022-06-14

During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues and is exposed to new selecti..

Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection

Tania Wong Fok Lung, Daniel Charytonowicz, Kristin G Beaumont, Shivang S Shah, Shwetha H Sridhar, Claire L Gorrie, Andre Mu, Casey E Hofstaedter, David Varisco, Thomas H McConville, Marija Drikic, Brandon Fowler, Andreacarola Urso, Wei Shi, Dario Fucich, Medini K Annavajhala, Ibrahim N Khan, Irina Oussenko, Nancy Francoeur, Melissa L Smith

2022-05-03

K. pneumoniae sequence type 258 (Kp ST258) is a major cause of healthcare-associated pneumonia. However, it remains unclear how it..

AusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic

Tuyet Hoang, Anders Goncalves da Silva, Amy Jennison, Deborah A Williamson, Benjamin P Howden, Torsten Seemann

2022-02-14

The COVID-19 pandemic has driven demand for integrated genomics, resulting in fast-tracked development of AusTrakka, Australia’s p..

Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings

Charlie Higgs, Norelle L Sherry, Torsten Seemann, Kristy Horan, Hasini Walpola, Paul Kinsella, Katherine Bond, Deborah A Williamson, Caroline Marshall, Jason C Kwong, M Lindsay Grayson, Timothy P Stinear, Claire L Gorrie, Benjamin P Howden

2022-01-26

Vancomycin-resistant Enterococcus faecium (VREfm) is a major nosocomial pathogen. Identifying VREfm transmission dynamics permits ..

Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia.

Cheryll M Sia, Sarah L Baines, Mary Valcanis, Darren YJ Lee, Anders Gonçalves da Silva, Susan A Ballard, Marion Easton, Torsten Seemann, Benjamin P Howden, Danielle J Ingle, Deborah A Williamson

2021-12-01

Non-typhoidal Salmonella (NTS) is the second most common cause of foodborne bacterial gastroenteritis in Australia with antimicr..

Genomic Epidemiology and Antimicrobial Resistance Mechanisms of Imported Typhoid in Australia

Danielle J Ingle, Patiyan Andersson, Mary Valcanis, Mathilda Wilmot, Marion Easton, Courtney Lane, Jessica Barden, Anders Goncalves da Silva, Torsten Seemann, Kristy Horan, Susan A Ballard, Norelle L Sherry, Deborah A Williamson, Benjamin P Howden

2021-11-01

Typhoid fever is an invasive bacterial disease of humans that disproportionately affects low- and middle-income countries. Antimic..

Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia

Danielle J Ingle, Rebecca L Ambrose, Sarah L Baines, Sebastian Duchene, Anders Goncalves da Silva, Darren YJ Lee, Miriam Jones, Mary Valcanis, George Taiaroa, Susan A Ballard, Martyn D Kirk, Benjamin P Howden, Jaclyn S Pearson, Deborah A Williamson

2021-08-09

Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emer..

Defective Severe Acute Respiratory Syndrome Coronavirus 2 Immune Responses in an Immunocompromised Individual With Prolonged Viral Replication

Claire L Gordon, Olivia C Smibert, Natasha E Holmes, Kyra YL Chua, Morgan Rose, George Drewett, Fiona James, Effie Mouhtouris, Thi HO Nguyen, Wuji Zhang, Lukasz Kedzierski, Louise C Rowntree, Brendon Y Chua, Leon Caly, Mike G Catton, Julian Druce, Michelle Sait, Torsten Seemann, Norelle L Sherry, Benjamin P Howden

2021-08-02

We describe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific immune responses in a patient with lymphoma and ..

Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study

Courtney R Lane, Norelle L Sherry, Ashleigh F Porter, Sebastian Duchene, Kristy Horan, Patiyan Andersson, Mathilda Wilmot, Annabelle Turner, Sally Dougall, Sandra A Johnson, Michelle Sait, Anders Gonsalves da Silva, Susan A Ballard, Tuyet Hoang, Timothy P Stinear, Leon Caly, Vitali Sintchenko, Rikki Graham, Jamie McMahon, David Smith

2021-07-29

BACKGROUND: A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervise..

Surveillance for SARS-CoV-2 variants of concern in the Australian context

Patiyan Andersson, Norelle L Sherry, Benjamin P Howden

2021-05-31