Rhys Thomas White

Rhys Thomas White
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Rhys verified their affiliation via an institutional email.
Verified
Rhys verified their affiliation via an institutional email.
Institute of Environmental Science and Research | ESR · Health Group

PhD

About

43
Publications
2,273
Reads
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123
Citations
Introduction
I specialise in microbial genomics, particularly phylogenetic analyses, evolution, and characterising mobile genetic elements of pathogens using whole-genome sequencing. With expertise in bioinformatics and fieldwork, I make crucial decisions on bioinformatic approaches and experimental design to advance our understanding of the evolution and spread of pathogens.
Additional affiliations
February 2018 - August 2022
University of Queensland
Position
  • PhD Student
April 2021 - August 2022
University of the Sunshine Coast
Position
  • Bioinformatician
Education
February 2018 - August 2022
University of Queensland
Field of study
  • Microbial Genomics
September 2012 - July 2016
Cardiff University
Field of study
  • Biology

Publications

Publications (43)
Article
Full-text available
Background Klebsiella variicola has been implicated in neonatal intensive care unit (NICU) outbreaks previously and can be misidentified as Klebsiella pneumoniae. An increased incidence of K. pneumoniae bacteremia on the NICU of our institution was notified to the infection prevention and control (IPC) team in May 2024. The four isolates involved d...
Article
Full-text available
Outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) are well described in the neonatal intensive care unit (NICU) setting. Genomics has revolutionized the investigation of such outbreaks; however, to date, this has largely been completed retrospectively and has typically relied on short-read platforms. In 2022, our laboratory establishe...
Article
Full-text available
Objective:To describe an outbreak of sequence type (ST)2 Clostridioides difficile infection (CDI) detected by a recently implemented multilocus sequence type (MLST)-based prospective genomic surveillance system using Oxford Nanopore Technologies (ONT) sequencing. Setting:Hemato-oncology ward of a public tertiary referral centre. Methods:From Februa...
Article
Full-text available
Antibiotic resistance is a significant global public health concern. Uropathogenic Escherichia coli sequence type (ST)131, a widely prevalent multidrug-resistant clone, is frequently associated with bacteraemia. This study investigates third-generation cephalosporin resistance in bloodstream infections caused by E. coli ST131. From 2013-2014 blood...
Article
Full-text available
Pantoea stewartii, a plant pathogen, is primarily transmitted through contaminated seeds and insect vectors, with the corn flea beetle (Chaetocnema pulicaria) being the primary carrier. P. stewartii is a bacterium belonging to the order Enterobacterales and can lead to crop diseases that have a significant economic impact worldwide. Due to its high...
Preprint
Full-text available
Many hospital laboratories have technical capacity to perform whole-genome sequencing but lack bioinformatic expertise to analyse sequence data. Sending isolates to reference laboratories creates delays that can be highly detrimental to outbreak responses. The Wellington Regional Hospital laboratory, which lacks on-site bioinformaticians, implement...
Article
Full-text available
Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract and neonatal infections. Humans, companion animals and the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 has been identified repeatedly among...
Preprint
Full-text available
Background Klebsiella variicola has been implicated in neonatal intensive care unit (NICU) outbreaks previously and can be misidentified as Klebsiella pneumoniae. An increased incidence of K. pneumoniae bacteremia on the NICU of our institution was noticed to the infection prevention and control (IPC) team in May 2024. The four isolates involved di...
Preprint
Full-text available
Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract, and neonatal infections. Humans, companion animals, and the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 has been identified repeatedly amo...
Preprint
Full-text available
Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract, and neonatal infections. Humans, companion animals, and the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 has been identified repeatedly amo...
Preprint
Full-text available
Objectives: Our laboratory began prospective genomic surveillance for healthcare-associated organisms in 2022 using Oxford Nanopore Technologies (ONT) sequencing as a standalone platform. This has permitted the early detection of outbreaks but has been insufficient for single-nucleotide variant (SNV)-level analysis due to lower read accuracy than I...
Article
Full-text available
Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified an uncharacterised transporter of the dietary monosaccharide ʟ-arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full...
Preprint
Full-text available
Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified a novel transporter of the dietary monosaccharide ʟ-arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full competitive...
Article
Full-text available
Chlamydia abortus, an obligate intracellular bacterium, is a major causative agent of reproductive loss in ruminants, with zoonotic potential. Though this pathogen is primarily known to infect livestock, recent studies have detected and isolated genetically distinct avian strains of C. abortus from wild birds globally. Before this study, only five...
Presentation
Full-text available
Chlamydia psittaci is a globally distributed veterinary pathogen with zoonotic potential. Although C. psittaci infections have been reported in various hosts, isolation and culture of Chlamydia is challenging, hampering efforts to produce contemporary global C. psittaci genomes. This is particularly evident in the lack of avian C. psittaci genomes...
Article
Full-text available
Chlamydia psittaci is a globally distributed veterinary pathogen with zoonotic potential. Although C. psittaci infections have been reported in various hosts, isolation and culture of Chlamydia is challenging, hampering efforts to produce contemporary global C. psittaci genomes. This is particularly evident in the lack of avian C. psittaci genomes...
Article
Chlamydia pecorum is a veterinary pathogen associated with abortions and perinatal mortality in sheep. Recent studies investigating foetal and perinatal lamb mortality in sheep from Australia and New Zealand identified C. pecorum clonal sequence type (ST)23 strains in aborted and stillborn lambs. Presently, there is limited genotypic information on...
Poster
Full-text available
Before the 2000s, New Zealand’s surveillance of antibiotic resistance in human pathogens detected less than nine annual cases of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL-E). In 2001, however, the Hawke’s Bay region experienced an increase in ESBL-E associated with clinical infections. Throughout 2001 and 2002, 95 iso...
Poster
Full-text available
Whole-genome sequencing has been critical for Aotearoa New Zealand’s response to the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent behind the coronavirus disease 2019 (COVID-19) pandemic. Early in the pandemic, the rapid and distributed approach to sequencing made possible by Oxford Nanopore Technologies pr...
Article
Full-text available
Chlamydia psittaci is a zoonotic pathogen that infects birds, humans, and other mammals. Notably, recent studies suggested the human-to-human transmission of C. psittaci, and this pathogen also causes equine reproductive loss in Australia. Molecular studies in Australia to date have focused on and described clonal sequence type (ST)24 strains infec...
Presentation
Full-text available
Chlamydia psittaci is an avian pathogen with zoonotic potential. In Australia, C. psittaci has been well reported as a cause of reproductive loss in mares which subsequently have been the source of infection and illness in some in-contact humans. To date, molecular typing studies describe the predominant and clonal C. psittaci sequence type (ST)24...
Article
Full-text available
Chlamydia psittaci is an avian pathogen with zoonotic potential. In Australia, C. psittaci has been well reported as a cause of reproductive loss in mares which subsequently have been the source of infection and illness in some in-contact humans. To date, molecular typing studies describe the predominant and clonal C. psittaci sequence type (ST)24...
Article
Full-text available
Fowl cholera caused by Pasteurella multocida has re-emerged in Australian poultry production since the increasing adoption of free-range production systems. Currently, autogenous killed whole-cell vaccines prepared from the isolates previously obtained from each farm are the main preventative measures used. In this study, we use whole-genome sequen...
Data
The following are available online at https://www.mdpi.com/article/10.3390/pathogens10121543/s1
Presentation
Full-text available
Chlamydia pecorum, an obligate intracellular pathogen, causes significant morbidity and mortality in livestock and the koala (Phascolarctos cinereus). A variety of C. pecorum gene-centric molecular studies have revealed important observations about infection dynamics and genetic diversity in both koala and livestock hosts. In contrast to a variety...
Article
Full-text available
Chlamydia pecorum, an obligate intracellular pathogen, causes significant morbidity and mortality in livestock and the koala (Phascolarctos cinereus). A variety of C. pecorum gene-centric molecular studies have revealed important observations about infection dynamics and genetic diversity in both koala and livestock hosts. In contrast to a variety...
Article
Full-text available
At least 300 million urinary tract infections (UTIs) occur annually worldwide. Uropathogenic Escherichia coli (UPEC) are the leading cause of UTIs. The discovery of antibiotics has revolutionised modern medicine. Yet, overusing antibiotics has accelerated the emergence of antimicrobial resistance (AMR), with UPEC driving the dissemination of AMR gl...
Poster
Full-text available
Introduction. The increasing resistance to third-generation cephalosporins (3GCs) is detrimental to public health, as these antimicrobials are prescribed as empirical therapies for systemic infections caused by Gram-negative bacteria. Uropathogenic Escherichia coli sequence type (ST)131 is a globally disseminated, multidrug-resistant lineage associ...
Preprint
Full-text available
Increasing resistance to third-generation cephalosporins (3GCs) threatens public health, as these antimicrobials are prescribed as empirical therapies for systemic infections caused by Gram-negative bacteria. Resistance to 3GCs in urinary tract infections (UTIs) and bacteraemia is associated with the globally disseminated, multidrug-resistant, urop...
Article
Full-text available
Escherichia coli sequence types 131 (ST131) and 1193 are multidrug-resistant extraintestinal pathogens that have recently spread epidemically among humans and are occasionally isolated from companion animals. This study characterized a nationwide collection of fluoroquinolone-resistant (FQR) E. coli isolates from extraintestinal infections in Austr...
Data
The following are available online at: https://www.frontiersin.org/articles/10.3389/fmicb.2020.01968/full#supplementary-material
Poster
Full-text available
Background: Uropathogenic Escherichia coli (UPEC) are the primary cause of urinary tract infections (UTIs), with >360.8 million global cases in 2016. UTIs have become increasingly difficult to treat due to rising antibiotic resistance. Sequence type (ST)1193 is an emerging fluoroquinolone-resistant UPEC lineage increasingly associated with UTIs. De...
Poster
Full-text available
The global dissemination of fluoroquinolone-resistant (FQr) extra-intestinal pathogenic Escherichia coli (ExPEC) poses an increasing challenge for the management of ExPEC infections. Among the FQr ExPEC, sequence type (ST)1193 is the second most common globally disseminated lineage (after ST131); however, little is known about its evolution. Here,...

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