Centre for Infectious Diseases and Microbiology
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Which clinical decisions benefit from automation? A task complexity approach.
International journal of medical informatics Jul, 2003 | Pubmed ID: 12909183
Comparative impact of guidelines, clinical data, and decision support on prescribing decisions: an interactive web experiment with simulated cases.
Journal of the American Medical Informatics Association : JAMIA Jan-Feb, 2004 | Pubmed ID: 14527970
Which clinical decisions benefit from automation? A task complexity approach.
Studies in health technology and informatics , 2002 | Pubmed ID: 15460772
Handheld computer-based decision support reduces patient length of stay and antibiotic prescribing in critical care.
Journal of the American Medical Informatics Association : JAMIA Jul-Aug, 2005 | Pubmed ID: 15802478
Screening for antibiotic resistant Gram-negative bacteria.
The Lancet infectious diseases Jun, 2006 | Pubmed ID: 16728313
A case of urinary tuberculosis due to Mycobacterium bovis subspecies caprae.
Pathology Aug, 2006 | Pubmed ID: 16916737
Genotyping of Mycobacterium tuberculosis in New South Wales: results from 18 months of a statewide trial.
New South Wales public health bulletin May-Jun, 2006 | Pubmed ID: 17036086
Utility of genotyping of Mycobacterium tuberculosis in the contact investigation: a decision analysis.
Tuberculosis (Edinburgh, Scotland) May, 2007 | Pubmed ID: 17161653
Decision complexity affects the extent and type of decision support use.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium , 2006 | Pubmed ID: 17238436
An outbreak of pulmonary tuberculosis in young Australians.
The Medical journal of Australia Mar, 2007 | Pubmed ID: 17391086
Pathogen profiling for disease management and surveillance.
Nature reviews. Microbiology Jun, 2007 | Pubmed ID: 17487146
Point-of-care testing for community-acquired pneumonia: do we have all the answers?
The Medical journal of Australia Jul, 2007 | Pubmed ID: 17605702
Are we measuring the right end-points? Variables that affect the impact of computerised decision support on patient outcomes: a systematic review.
Medical informatics and the Internet in medicine Sep, 2007 | Pubmed ID: 17701828
Comparison of single- and multilocus sequence typing and toxin gene profiling for characterization of methicillin-resistant Staphylococcus aureus.
Journal of clinical microbiology Oct, 2007 | Pubmed ID: 17715374
Is Bordetella pertussis susceptibility to erythromycin changing? MIC trends among Australian isolates 1971-2006.
The Journal of antimicrobial chemotherapy Nov, 2007 | Pubmed ID: 17827145
Are clinicians' information needs and decision support affected by different models of care? Experimental study.
Studies in health technology and informatics , 2007 | Pubmed ID: 17911845
Developing decision support systems in clinical bioinformatics.
Methods in molecular medicine , 2008 | Pubmed ID: 18453098
Biosurveillance of emerging biothreats using scalable genotype clustering.
Journal of biomedical informatics Feb, 2009 | Pubmed ID: 18723122
Genome-wide analysis of single nucleotide polymorphisms in Bordetella pertussis using comparative genomic sequencing.
Research in microbiology Nov-Dec, 2008 | Pubmed ID: 18790049
Decision support systems for antibiotic prescribing.
Current opinion in infectious diseases Dec, 2008 | Pubmed ID: 18988320
The re-emergence of pertussis: implications for diagnosis and surveillance.
New South Wales public health bulletin Jul-Aug, 2008 | Pubmed ID: 19007547
Towards bioinformatics assisted infectious disease control.
BMC bioinformatics , 2009 | Pubmed ID: 19208185
In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles.
BMC bioinformatics , 2009 | Pubmed ID: 19292914
Rapid and accurate typing of Bordetella pertussis targeting genes encoding acellular vaccine antigens using real time PCR and High Resolution Melt analysis.
Journal of microbiological methods Jun, 2009 | Pubmed ID: 19341769
Laboratory-guided detection of disease outbreaks: three generations of surveillance systems.
Archives of pathology & laboratory medicine Jun, 2009 | Pubmed ID: 19492884
Identification of non-tuberculous mycobacteria: utility of the GenoType Mycobacterium CM/AS assay compared with HPLC and 16S rRNA gene sequencing.
Journal of medical microbiology Jul, 2009 | Pubmed ID: 19502366
A new multiplex PCR-based reverse line-blot hybridization (mPCR/RLB) assay for rapid staphylococcal cassette chromosome mec (SCCmec) typing.
Journal of medical microbiology Aug, 2009 | Pubmed ID: 19528184
Rolling circle amplification and multiplex allele-specific PCR for rapid detection of katG and inhA gene mutations in Mycobacterium tuberculosis.
International journal of medical microbiology : IJMM Dec, 2009 | Pubmed ID: 19604720
Assignment of Reference 5'-end 16S rDNA Sequences and Species-Specific Sequence Polymorphisms Improves Species Identification of Nocardia.
The open microbiology journal , 2009 | Pubmed ID: 19639036
Influenza outbreak during Sydney World Youth Day 2008: the utility of laboratory testing and case definitions on mass gathering outbreak containment.
PloS one , 2009 | Pubmed ID: 19727401
Commonly used molecular epidemiology markers of Streptococcus agalactiae do not appear to predict virulence.
Pathology , 2009 | Pubmed ID: 19900108
Identification of pathogenic Nocardia species by reverse line blot hybridization targeting the 16S rRNA and 16S-23S rRNA gene spacer regions.
Journal of clinical microbiology Feb, 2010 | Pubmed ID: 19955277
Reverse line blot hybridization and DNA sequencing studies of the 16S-23S rRNA gene intergenic spacer regions of five emerging pathogenic Nocardia species.
Journal of medical microbiology May, 2010 | Pubmed ID: 20110385
Bordetella pertussis clones identified by multilocus variable-number tandem-repeat analysis.
Emerging infectious diseases Feb, 2010 | Pubmed ID: 20113564
A PubMed-wide associational study of infectious diseases.
PloS one , 2010 | Pubmed ID: 20224767
Three-year longitudinal study of genotypes of Mycobacterium tuberculosis in a low prevalence population.
Pathology Apr, 2010 | Pubmed ID: 20350221
Rapid identification of methicillin-resistant Staphylococcus aureus transmission in hospitals by use of phage-derived open reading frame typing enhanced by multiplex PCR and reverse line blot assay.
Journal of clinical microbiology Aug, 2010 | Pubmed ID: 20519463
Unexpected diversity of staphylococcal cassette chromosome mec type IV in methicillin-resistant Staphylococcus aureus strains.
Journal of clinical microbiology Oct, 2010 | Pubmed ID: 20686095
secA1 gene sequence polymorphisms for species identification of Nocardia species and recognition of intraspecies genetic diversity.
Journal of clinical microbiology Nov, 2010 | Pubmed ID: 20810768
Insight into evolution of Bordetella pertussis from comparative genomic analysis: evidence of vaccine-driven selection.
Molecular biology and evolution Jan, 2011 | Pubmed ID: 20833694
Editor's choice: Implications of isoniazid resistance in Mycobacterium bovis Bacillus Calmette-Guérin used for immunotherapy in bladder cancer.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Jan, 2011 | Pubmed ID: 21148524
Improved identification of Gordonia, Rhodococcus and Tsukamurella species by 5'-end 16S rRNA gene sequencing.
Pathology Jan, 2011 | Pubmed ID: 21240067
Computational bacterial genome-wide analysis of phylogenetic profiles reveals potential virulence genes of Streptococcus agalactiae.
PloS one , 2011 | Pubmed ID: 21483735
Bug breakfast in the Bulletin: Biosecurity and infectious diseases.
New South Wales public health bulletin May-Jun, 2010 | Pubmed ID: 21604605
Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.
PloS one , 2011 | Pubmed ID: 21687706
Genetic relationships of phage types and single nucleotide polymorphism typing of Salmonella enterica serovar Typhimurium.
Journal of clinical microbiology Jan, 2012 | Pubmed ID: 22205813
Selection and emergence of pertussis toxin promoter ptxP3 allele in the evolution of Bordetella pertussis.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Jan, 2012 | Pubmed ID: 22293463
Improving resolution of public health surveillance for human Salmonella enterica serovar Typhimurium infection: 3 years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA).
BMC infectious diseases Mar, 2012 | Pubmed ID: 22462487
Protocol for a randomised controlled trial examining the impact of a web-based personally controlled health management system on the uptake of influenza vaccination rates.
BMC health services research Apr, 2012 | Pubmed ID: 22462549
Impact of a web-based personally controlled health management system on influenza vaccination and health services utilization rates: a randomized controlled trial.
Journal of the American Medical Informatics Association : JAMIA Sep-Oct, 2012 | Pubmed ID: 22582203
Translational web robots for pathogen genome analysis.
Microbial informatics and experimentation Oct, 2011 | Pubmed ID: 22587672
Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments.
Microbial informatics and experimentation Jan, 2012 | Pubmed ID: 22587938
Prospective genotyping of hospital-acquired methicillin-resistant Staphylococcus aureus isolates by use of a novel, highly discriminatory binary typing system.
Journal of clinical microbiology Nov, 2012 | Pubmed ID: 22895043
Francisella tularensis subspecies holarctica, Tasmania, Australia, 2011.
Emerging infectious diseases Sep, 2012 | Pubmed ID: 22931809
Quantitative estimation of the stability of methicillin-resistant Staphylococcus aureus strain-typing systems by use of Kaplan-Meier survival analysis.
Journal of clinical microbiology Jan, 2013 | Pubmed ID: 23100339
Software for selecting the most informative sets of genomic loci for multi-target microbial typing.
BMC bioinformatics May, 2013 | Pubmed ID: 23635100
The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities.
New South Wales public health bulletin Jul, 2013 | Pubmed ID: 23849021
Potent antimycobacterial activity of the pyridoxal isonicotinoyl hydrazone analog 2-pyridylcarboxaldehyde isonicotinoyl hydrazone: a lipophilic transport vehicle for isonicotinic acid hydrazide.
Molecular pharmacology Feb, 2014 | Pubmed ID: 24243647
Effectiveness of hospital-wide methicillin-resistant Staphylococcus aureus (MRSA) infection control policies differs by ward specialty.
PloS one , 2013 | Pubmed ID: 24340085
Rapid increase in pertactin-deficient Bordetella pertussis isolates, Australia.
Emerging infectious diseases Apr, 2014 | Pubmed ID: 24655754
Pathogen genome bioinformatics.
Methods in molecular biology (Clifton, N.J.) , 2014 | Pubmed ID: 24870136
Improved identification of rapidly growing mycobacteria by a 16S-23S internal transcribed spacer region PCR and capillary gel electrophoresis.
PloS one , 2014 | Pubmed ID: 25013955
Use of the 5' untranslated region and VP1 region to examine the molecular diversity in enterovirus B species.
Journal of medical microbiology Oct, 2014 | Pubmed ID: 25038138
Fluoroquinolone resistance in non-multidrug-resistant tuberculosis-a surveillance study in New South Wales, Australia, and a review of global resistance rates.
International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases Sep, 2014 | Pubmed ID: 25086437
Temporal dynamics of Mycobacterium tuberculosis genotypes in New South Wales, Australia.
BMC infectious diseases Aug, 2014 | Pubmed ID: 25149181
Clinical microbiology informatics.
Clinical microbiology reviews Oct, 2014 | Pubmed ID: 25278581
Investigating genome reduction of Bordetella pertussis using a multiplex PCR-based reverse line blot assay (mPCR/RLB).
BMC research notes Oct, 2014 | Pubmed ID: 25319278
Added value of whole-genome sequencing for management of highly drug-resistant TB.
The Journal of antimicrobial chemotherapy Apr, 2015 | Pubmed ID: 25492392
Delineating community outbreaks of Salmonella enterica serovar Typhimurium by use of whole-genome sequencing: insights into genomic variability within an outbreak.
Journal of clinical microbiology Apr, 2015 | Pubmed ID: 25609719
Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities.
BMC infectious diseases Apr, 2015 | Pubmed ID: 25887164
Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study.
The Lancet. Infectious diseases Aug, 2015 | Pubmed ID: 25936611
The role of pathogen genomics in assessing disease transmission.
BMJ (Clinical research ed.) May, 2015 | Pubmed ID: 25964672
Genome sequencing reveals novel deletions associated with secondary resistance to pyrazinamide in MDR Mycobacterium tuberculosis.
The Journal of antimicrobial chemotherapy Sep, 2015 | Pubmed ID: 25977398
Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing.
Journal of clinical microbiology Aug, 2015 | Pubmed ID: 26019201
Genomic Epidemiology of Clostridium botulinum Isolates from Temporally Related Cases of Infant Botulism in New South Wales, Australia.
Journal of clinical microbiology Sep, 2015 | Pubmed ID: 26109442
Editorial: Laboratory preparedness for Ebolavirus disease.
Pathology Aug, 2015 | Pubmed ID: 26126052
Epidemiology of Peripheral Lymph Node Tuberculosis and Genotyping of M. tuberculosis Strains: A Case-Control Study.
PloS one , 2015 | Pubmed ID: 26177546
Genotype heterogeneity of Mycobacterium tuberculosis within geospatial hotspots suggests foci of imported infection in Sydney, Australia.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 06, 2016 | Pubmed ID: 26187743
Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage.
Journal of clinical microbiology Nov, 2015 | Pubmed ID: 26311853
It Is Not All about Single Nucleotide Polymorphisms: Comparison of Mobile Genetic Elements and Deletions in Listeria monocytogenes Genomes Links Cases of Hospital-Acquired Listeriosis to the Environmental Source.
Journal of clinical microbiology Nov, 2015 | Pubmed ID: 26311854
Pertactin negative Bordetella pertussis demonstrates higher fitness under vaccine selection pressure in a mixed infection model.
Vaccine Nov, 2015 | Pubmed ID: 26432908
Antibiotic susceptibility of diverse Mycobacterium abscessus complex strains in New South Wales, Australia.
Pathology Dec, 2015 | Pubmed ID: 26517625
Genomic dissection of Australian Bordetella pertussis isolates from the 2008-2012 epidemic.
The Journal of infection Apr, 2016 | Pubmed ID: 26826518
Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing.
PloS one , 2016 | Pubmed ID: 26938641
Concordance of four commercial enzyme immunoassay and three immunoblot formats for the detection of Lyme borreliosis antibodies in human serum: the two-tier approach remains.
Pathology Apr, 2016 | Pubmed ID: 27020501
dfrA thyA Double Deletion in para-Aminosalicylic Acid-Resistant Mycobacterium tuberculosis Beijing Strains.
Antimicrobial agents and chemotherapy Jun, 2016 | Pubmed ID: 27021327
Nontoxic Metal-Cyclam Complexes, a New Class of Compounds with Potency against Drug-Resistant Mycobacterium tuberculosis.
Journal of medicinal chemistry Jun, 2016 | Pubmed ID: 27214150
Better colonisation of newly emerged Bordetella pertussis in the co-infection mouse model study.
Vaccine 07, 2016 | Pubmed ID: 27346304
Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014.
BMC microbiology Sep, 2016 | Pubmed ID: 27629541
SnpFilt: A pipeline for reference-free assembly-based identification of SNPs in bacterial genomes.
Computational biology and chemistry 12, 2016 | Pubmed ID: 27647159
Whole Genome Sequencing Demonstrates Limited Transmission within Identified Mycobacterium tuberculosis Clusters in New South Wales, Australia.
PloS one , 2016 | Pubmed ID: 27737005
16S-23S Internal Transcribed Spacer Region PCR and Sequencer-Based Capillary Gel Electrophoresis has Potential as an Alternative to High Performance Liquid Chromatography for Identification of Slowly Growing Nontuberculous Mycobacteria.
PloS one , 2016 | Pubmed ID: 27749897
Transmission of multi-drug resistant tuberculosis in Mongolia is driven by Beijing strains of Mycobacterium tuberculosis resistant to all first-line drugs.
Tuberculosis (Edinburgh, Scotland) Dec, 2016 | Pubmed ID: 27865397
Evolution of Variable Number Tandem Repeats and Its Relationship with Genomic Diversity in Salmonella Typhimurium.
Frontiers in microbiology , 2016 | Pubmed ID: 28082952
Assignment of recA reference sequence types for enhanced identification of the Burkholderia cepacia complex.
Pathology Jun, 2012 | Pubmed ID: 28193343
Characterisation of the Bordetella pertussis secretome under different media.
Journal of proteomics Mar, 2017 | Pubmed ID: 28242451
Genomic heterogeneity of Salmonella enterica serovar Typhimurium bacteriuria from chronic infection.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Jul, 2017 | Pubmed ID: 28279807
Francisella tularensis ssp. holarctica in Ringtail Possums, Australia.
Emerging infectious diseases 07, 2017 | Pubmed ID: 28628459
Drug resistance and Mycobacterium tuberculosis strain diversity in TB/HIV co-infected patients in Ho Chi Minh city, Vietnam.
Journal of global antimicrobial resistance Sep, 2017 | Pubmed ID: 28743648
Comparative genomics of Australian and international isolates of Salmonella Typhimurium: correlation of core genome evolution with CRISPR and prophage profiles.
Scientific reports Aug, 2017 | Pubmed ID: 28851865
Genome sequencing links persistent outbreak of legionellosis in Sydney to an emerging clone of Legionella pneumophila ST211.
Applied and environmental microbiology Dec, 2017 | Pubmed ID: 29247056
Chayanika Biswas*,1,
Sharon C-A. Chen*,1,2,3,
Catriona Halliday1,2,
Elena Martinez1,
Rebecca J. Rockett1,
Qinning Wang1,
Verlaine J. Timms1,
Rajat Dhakal1,
Rosemarie Sadsad1,
Karina J. Kennedy4,
Geoffrey Playford4,5,
Deborah J. Marriott6,
Monica A. Slavin7,
Tania C. Sorrell1,3,
Vitali Sintchenko1,2,3
1Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital,
2Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR,
3Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney,
4Department of Microbiology and Infectious Diseases, Canberra Hospital and Health Services, Australian National University Medical School,
5Infection Management Services, Australian National University Medical School,
6Department of Microbiology and Infectious Diseases, St. Vincent's Hospital,
7Department of Infectious Diseases, Peter MacCallum Cancer Centre