Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis

[1]  Anders Gonçalves da Silva,et al.  Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis. , 2021, The Lancet. Microbe.

[2]  V. Sintchenko,et al.  Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study , 2021, The Lancet Public Health.

[3]  D. Paterson,et al.  Budget impact analysis of routinely using whole-genomic sequencing of six multidrug-resistant bacterial pathogens in Queensland, Australia , 2021, BMJ Open.

[4]  J. Kwong,et al.  Pilot study of a combined genomic and epidemiologic surveillance program for hospital-acquired multidrug-resistant pathogens across multiple hospital networks in Australia , 2020, Infection Control & Hospital Epidemiology.

[5]  B. Parcell,et al.  Clinical perspectives in integrating whole-genome sequencing into the investigation of healthcare and public health outbreaks – hype or help? , 2020, The Journal of hospital infection.

[6]  J. Parkhill,et al.  Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance , 2020, Nature microbiology.

[7]  D. Brockmann,et al.  Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital , 2020, PloS one.

[8]  B. Limbago,et al.  Multispecies Outbreak of Verona Integron-Encoded Metallo-ß-Lactamase-Producing Multidrugresistant Bacteria Driven by a Promiscuous Incompatibility Group A/C2. , 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[9]  O. Ng,et al.  The role of hospital environment in transmissions of multidrug-resistant gram-negative organisms , 2020, Antimicrobial Resistance & Infection Control.

[10]  Marta Gwinn,et al.  Pathogen Genomics in Public Health. , 2019, The New England journal of medicine.

[11]  V Mintzer,et al.  Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review. , 2019, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[12]  Mark B. Schultz,et al.  Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016 , 2019, Journal of Clinical Microbiology.

[13]  R. Kolde,et al.  Integration of genomic and clinical data augments surveillance of healthcare-acquired infections , 2019, Infection Control & Hospital Epidemiology.

[14]  F. Balloux,et al.  From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic , 2018, Trends in microbiology.

[15]  Julian Parkhill,et al.  Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens , 2018, Microbiology.

[16]  R. Goering,et al.  Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches. , 2018, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[17]  Evangelos I. Kritsotakis,et al.  Prevalence, incidence burden, and clinical impact of healthcare-associated infections and antimicrobial resistance: a national prevalent cohort study in acute care hospitals in Greece , 2017, Infection and drug resistance.

[18]  Tamara Munzner,et al.  Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory , 2017, bioRxiv.

[19]  A. Suijkerbuijk,et al.  Cost of Nosocomial Outbreak Caused by NDM-1–Containing Klebsiella pneumoniae in the Netherlands, October 2015–January 2016 , 2017, Emerging infectious diseases.

[20]  C. Aibar-Remon,et al.  Impact on Morbidity, Mortality, and Length of Stay of Hospital-Acquired Infections by Resistant Microorganisms , 2017, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[21]  P. François,et al.  Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing. , 2017, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[22]  E. Snitkin,et al.  Whole Genome Sequencing—Implications for Infection Prevention and Outbreak Investigations , 2017, Current Infectious Disease Reports.

[23]  F. Davies,et al.  Counting the cost of an outbreak of carbapenemase-producing Enterobacteriaceae: an economic evaluation from a hospital perspective. , 2017, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[24]  L. Hoang,et al.  Infection control in the new age of genomic epidemiology. , 2017, American journal of infection control.

[25]  A. Mellmann,et al.  Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting , 2016, Journal of Clinical Microbiology.

[26]  S. A. Boers,et al.  Detection of Healthcare-Related Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Transmission Events Using Combined Genetic and Phenotypic Epidemiology , 2016, PloS one.

[27]  A. Mellmann,et al.  Whole-Genome Sequencing Elucidates Epidemiology of Nosocomial Clusters of Acinetobacter baumannii , 2016, Journal of Clinical Microbiology.

[28]  P. Worning,et al.  Multiple hospital outbreaks of vanA Enterococcus faecium in Denmark, 2012-13, investigated by WGS, MLST and PFGE. , 2015, The Journal of antimicrobial chemotherapy.

[29]  A. Kasarskis,et al.  How Next-Generation Sequencing and Multiscale Data Analysis Will Transform Infectious Disease Management , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[30]  Jonas Korlach,et al.  Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae , 2014, Science Translational Medicine.

[31]  G. Smith,et al.  Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. , 2013, JAMA internal medicine.

[32]  Julian Parkhill,et al.  Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study , 2013, The Lancet. Infectious Diseases.

[33]  E. Denamur,et al.  The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. , 2013, Environmental microbiology reports.