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2026
Impacts of mobile genetic elements on antimicrobial resistance genes in gram-negative pathogens: Current insights and genomic approaches
Microbiological Research
2025
Beyond patient contact: combined short- and long read sequencing reveals continuous occurrence of genomically related carbapenemase-producing Enterobacterales and plasmid mobility in a hospital, Germany, 2018 to 2021
Eurosurveillance
2025
Genomics for antimicrobial resistance—progress and future directions
Antimicrobial Agents and Chemotherapy
2025
Manual of Molecular Microbiology
2024
Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes
The Journal of Infectious Diseases
2024
Real-time genomic epidemiologic investigation of a multispecies plasmid-associated hospital outbreak of NDM-5-producing Enterobacterales infections
International Journal of Infectious Diseases
2024
Carbapenemase producing Enterobacterales at a large teaching hospital in Ohio: comparison to state surveillance and retrospective analysis of patient characteristics
Infection Prevention in Practice
2024
High-level nitrofurantoin resistance in a clinical isolate of Klebsiella pneumoniae: a comparative genomics and metabolomics analysis
mSystems
2024
Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care
Journal of Infection
2024
A prospective bacterial whole-genome-sequencing-based surveillance programme for comprehensive early detection of healthcare-associated infection transmission in paediatric oncology patients
Journal of Hospital Infection
2023
Clinical Implementation of Routine Whole-genome Sequencing for Hospital Infection Control of Multi-drug Resistant Pathogens
Clinical Infectious Diseases
2023
Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards
Microbial Genomics
2023
Whole genome sequencing of multidrug resistant Enterobacterales identified in children and their household members within Siem Reap, Cambodia
JAC-Antimicrobial Resistance
2023
Rapid spread of a novel NDM-producing clone of Klebsiella pneumoniae CC147, Northern Italy, February to August 2023
Eurosurveillance
2023
Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids
mSystems
2023
Emergence of KPC-3- and OXA-181-producing ST13 and ST17 Klebsiella pneumoniae in Portugal: genomic insights on national and international dissemination
Journal of Antimicrobial Chemotherapy
2023
Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria
Nature Communications
2022
Antimicrobial Resistance in Rivers: A Review of the Genes Detected and New Challenges
Environmental Toxicology and Chemistry
2022
Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review
Pathogens
2022
Clonal Spread of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 in Chinese Pediatric Patients
Microbiology Spectrum
2022
Whole-genome sequencing surveillance and machine learning for healthcare outbreak detection and investigation: A systematic review and summary
Antimicrobial Stewardship & Healthcare Epidemiology
2022
Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection
Clinical Infectious Diseases
2022
Intestinal Carriage of Extended-Spectrum β-lactamase and Carbapenemase-Producing Enterobacteriaceae in Hemodialysis Patients
Jundishapur Journal of Microbiology
2022
Using Genomics to Understand the Epidemiology of Infectious Diseases in the Northern Territory of Australia
Tropical Medicine and Infectious Disease
2022
Epidemiological characteristics an outbreak of ST11 multidrug-resistant and hypervirulent Klebsiella pneumoniae in Anhui, China
Frontiers in Microbiology
2021
Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis
The Lancet Microbe
2021
Complete Genome Sequences of Klebsiella michiganensis and Citrobacter farmeri, KPC-2-Producers Serially Isolated from a Single Patient
Antibiotics
2021
Presence of carbepenemase-producing Enterobacteriaceae in the River Lambro basin, Italy: might sediment represent an important resistance reservoir?
Journal of Limnology
2021
Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo
Current Protocols
2021
Plasmids shape the diverse accessory resistomes of Escherichia coli ST131
Access Microbiology
2021
Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital
Microbial Genomics
2021
Concordance between epidemiological evaluation of probability of transmission and whole genome sequence relatedness among hospitalized patients acquiring Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae
Clinical Microbiology and Infection
2021
Search and Contain: Impact of an Integrated Genomic and Epidemiological Surveillance and Response Program for Control of Carbapenemase-producing Enterobacterales
Clinical Infectious Diseases
2021
Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care
Microbial Genomics
2021
In Vitro and In Vivo Activity of AS101 against Carbapenem-Resistant Acinetobacter baumannii
Pharmaceuticals
2020
Complete microbial genomes for public health in Australia and the Southwest Pacific
Microbial Genomics
2020
Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital
eLife
2020
Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid
Microbial Genomics
2020
Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital
Journal of Antimicrobial Chemotherapy
2020
Incursions of Candida auris into Australia, 2018
Emerging Infectious Diseases
2020
Toilet drain water as a potential source of hospital room-to-room transmission of carbapenemase-producing Klebsiella pneumoniae
Journal of Hospital Infection
2020
Fine capsule variation affects bacteriophage susceptibility in Klebsiella pneumoniae ST258
The FASEB Journal
2020
A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program
Antibiotics
2020
Rapid detection of carbapenemase producing Enterobacteriaceae direct from blood using real-time PCR
Pathology
2019
The importance of public health genomics for ensuring health security for Australia
Medical Journal of Australia
2019
The risk of resistance: what are the major antimicrobial resistance threats facing Australia?
Medical Journal of Australia
2019
Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing
mSphere
2019
Whole Genome Sequencing detects Inter-Facility Transmission of Carbapenem-resistant Klebsiella pneumoniae
Journal of Infection
2019
Plasmid evolution in carbapenemase‐producing Enterobacteriaceae: a review
Annals of the New York Academy of Sciences
2019
Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors
Microbial Genomics
2019
Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016
Journal of Clinical Microbiology
2019
Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains
Microbial Genomics
2018
From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic
Trends in Microbiology
2018
Extended-spectrum β-lactamase-producing and carbapenemase-producing Enterobacteriaceae
Microbial Genomics
2018
TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data
Microbial Genomics
2018
Complete Genome Sequence of blaIMP–6-Positive Metakosakonia sp. MRY16-398 Isolate From the Ascites of a Diverticulitis Patient
Frontiers in Microbiology
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