Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Journal of Clinical Microbiology

• Publication date

  2016-08-24

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1128/JCM.00790-16PMID 27558178PMCID PMC5121374
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.

  2016cited by this paper
• Gut Colonization of Healthy Children and Their Mothers With Pathogenic Ciprofloxacin-Resistant Escherichia coli.

  2015cited by this paper
• Genetic testing and FDA regulation: overregulation threatens the emergence of genomic medicine.

  2015cited by this paper
• A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

  2015cited by this paper
• Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes

  2015cited by this paper
• Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

  2015cited by this paper
• Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing.

  2015cited by this paper
• ESCMID guidelines for the management of the infection control measures to reduce transmission of multidrug-resistant Gram-negative bacteria in hospitalized patients.

  2014cited by this paper
• European Society of Clinical Microbiology and Infectious Diseases: update of the treatment guidance document for Clostridium difficile infection.

  2014cited by this paper
• Bacterial Whole-Genome Sequencing Revisited: Portable, Scalable, and Standardized Analysis for Typing and Detection of Virulence and Antibiotic Resistance Genes

  2014influential reference
• Optimizing FDA ’ s Regulatory Oversight of Next Generation Sequencing Diagnostic Tests — Preliminary Discussion

  2014cited by this paper
• European Centre for Disease Prevention and Control.

  2014cited by this paper
• Precise Dissection of an Escherichia coli O157:H7 Outbreak by Single Nucleotide Polymorphism Analysis

  2013cited by this paper
• Updating benchtop sequencing performance comparison

  2013cited by this paper
• Management of Multidrug- resistant organisms in Healthcare settings

  2013cited by this paper
• Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions

  2013cited by this paper
• Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis.

  2013cited by this paper
• Rapid single-colony whole-genome sequencing of bacterial pathogens

  2013cited by this paper
• MLST revisited: the gene-by-gene approach to bacterial genomics

  2013cited by this paper
• Kommission für Krankenhaushygiene und Infektionsprävention (KRINKO) beim Robert Koch Institut

  2013cited by this paper
• Evolution of Enterohemorrhagic Escherichia coli O26 Based on Single-Nucleotide Polymorphisms

  2013cited by this paper
• Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.

  2012cited by this paper
• Healthcare Infection Control Practices Advisory Committee

  2012cited by this paper
• [Hygiene measures for infection or colonization with multidrug-resistant gram-negative bacilli. Commission recommendation for hospital hygiene and infection prevention (KRINKO) at the Robert Koch Institute (RKI)].

  2012cited by this paper
• A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance

  2012cited by this paper
• Assuring the quality of next-generation sequencing in clinical laboratory practice

  2012cited by this paper
• Transforming clinical microbiology with bacterial genome sequencing

  2012cited by this paper
• From genotype to phenotype: can systems biology be used to predict Staphylococcus aureus virulence?

  2012cited by this paper
• Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

  2011cited by this paper
• Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.

  2011cited by this paper
• Epidemiology. Outbreak detectives embrace the genome era.

  2011cited by this paper
• Evolution of MRSA During Hospital Transmission and Intercontinental Spread

  2010cited by this paper
• Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis

  2010cited by this paper
• Faculty Opinions recommendation of Evolution of MRSA during hospital transmission and intercontinental spread.

  2010cited by this paper
• Intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15.

  2007cited by this paper
• Methicillin-resistant Staphylococcus aureus ST398 in Humans and Animals, Central Europe

  2007cited by this paper
• Management of multidrug-resistant organisms in health care settings, 2006.

  2007cited by this paper
• Methicillin-resistant Staphylococcus aureus ST398 in Humans and Animals,

  2007cited by this paper
• European Society of Clinical Microbiology

  2005cited by this paper
• Additional Costs for Preventing the Spread of Methicillin-Resistant Staphylococcus aureus and a Strategy for Reducing These Costs on a Surgical Ward

  2003cited by this paper
• Do physicians examine patients in contact isolation less frequently? A brief report.

  2003cited by this paper
• National Nosocomial Infections Surveillance (NNIS) System Report, data summary from January 1992 through June 2003, issued August 2003.

  2003cited by this paper
• Methicillin-resistant Staphylococcus aureus: psychological impact of hospitalization and isolation in an older adult population.

  2001cited by this paper
• Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms.

  1998cited by this paper
• European society of clinical microbiology

  1984cited by this paper

• Comparative phylogenetic, antimicrobial resistance, and clinical characterization of human spondylodiscitis-associated Staphylococcus pseudintermedius.

  2026cites this paper
• Functional characterization of a novel class A carbapenemase CAE-1 in carbapenem-resistant Pseudomonas aeruginosa clinical isolates

  2026cites this paper
• Prediction of genetic relatedness of Escherichia coli using neighbor typing: a tool for rapid outbreak detection

  2026cites this paper
• Exploring the Utility of MALDI-TOF Mass Spectrometry and Antimicrobial Resistance in Hospital Outbreak Detection.

  2026cites this paper
• Nationwide genomic surveillance of carbapenem- and colistin-resistant Klebsiella pneumoniae bloodstream isolates in Thailand (2020–2024)

  2026cites this paper
• Phylloplane-Adapted Pseudomonas oryzihabitans as a biocontrol agent: omics insights into antibiosis and defense against bacterial blight of pomegranate

  2025cites this paper
• Antimicrobial Resistance in Diverse Ecological Niches—One Health Perspective and Food Safety

  2025cites this paper
• [Antimicrobial Stewardship and Hygiene: Prevention of Multidrug Resistant Pathogens].

  2025cites this paper
• The Impact Of Real-Time Genomic Epidemiology On The Containment Of Nosocomial Outbreaks: A Systematic Review Of Infection Control Outcomes And Medical Laboratory Integration

  2025cites this paper
• High-risk clonal expansion of IMP-producing Enterobacter cloacae complex in regional Japanese healthcare settings

  2025influential citation
• Genome sequencing for prevention of health-care-associated bacterial infections.

  2025cites this paper
• Detecting antibiotic resistance: classical, molecular, advanced bioengineering, and AI-enhanced approaches

  2025cites this paper
• The dark matter of bacterial genomic surveillance—antimicrobial resistance plasmid transmissions in the hospital setting

  2025influential citation
• Transforming antimicrobial resistance mitigation: the genomic revolution in one health and public health

  2025cites this paper
• Integrating whole-genome sequencing into antimicrobial resistance surveillance: methodologies, challenges, and perspectives

  2025cites this paper
• Epidemiology of multidrug resistant E. coli isolates from a German university hospital illustrates dominance of E. coli ST131.

  2025cites this paper
• Antibiotic Stewardship und Hygiene: Prävention multiresistenter Erreger

  2025cites this paper
• Comparison of core genome multi-locus sequencing typing pipelines for hospital outbreak detection of common bacterial pathogens

  2025cites this paper
• Genomics for antimicrobial resistance—progress and future directions

  2025cites this paper
• Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with Nanopore sequencing data

  2025cites this paper
• Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from companion animals and human infections in Europe

  2025cites this paper
• 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

  2025cites this paper
• Development and validation of a core genome multilocus sequence typing scheme for Citrobacter freundii: application in outbreak investigations and comparative analysis across the Citrobacter genus

  2025cites this paper
• Whole-genome sequencing surveillance of vancomycin-resistant Enterococcus faecium (VRE) detects hospital outbreaks and identifies the postanesthesia care unit as a transmission locus

  2025cites this paper
• Microbiological Safety of Donor Human Milk: Comparing Culture-Based Methods for Enterobacterales Detection

  2025cites this paper
• Subspecies typing on the example of klebsiella pneumoniae isolated from patients with pulmonary tuberculosis.

  2025cites this paper
• Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing

  2024cites this paper
• Real-time plasmid transmission detection pipeline

  2024cites this paper
• Methods for cost-efficient, whole genome sequencing surveillance for enhanced detection of outbreaks in a hospital setting

  2024cites this paper
• Comprehensive genomic and plasmid characterization of multidrug-resistant bacterial strains by R10.4.1 nanopore sequencing.

  2024cites this paper
• NanoCore: core-genome-based bacterial genomic surveillance and outbreak detection in healthcare facilities from Nanopore and Illumina data

  2024cites this paper
• Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection

  2024cites this paper
• Expansion and transmission dynamics of high risk carbapenem-resistant Klebsiella pneumoniae subclones in China: An epidemiological, spatial, genomic analysis.

  2024cites this paper
• Evaluation of a microfluidic-based point-of-care prototype with customized chip for detection of bacterial clusters

  2024cites this paper
• Validation and implementation of whole-genome sequencing-based analytical methods for molecular surveillance and relatedness analysis of Mycobacterium tuberculosis complex isolates at a national reference laboratory

  2024cites this paper
• Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing

  2024cites this paper
• Uncovering the spread of drug-resistant bacteria through next-generation sequencing based surveillance: transmission of extended-spectrum β-lactamase-producing Enterobacterales by a contaminated duodenoscope

  2024cites this paper
• Forensic Microbiology: When, Where and How

  2024cites this paper
• Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors

  2024cites this paper
• Whole Genome Sequencing Applications in Hospital Epidemiology and Infection Prevention

  2024influential citation
• Evaluation of IR Biotyper for carbapenem-resistant Pseudomonas aeruginosa typing and its application potential for the investigation of nosocomial infection

  2023cites this paper
• Active surveillance of carbapenemase-producing Enterobacterales using genomic sequencing for hospital-based infection control interventions

  2023cites this paper
• Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data

  2023cites this paper
• Inter-phylum circulation of a beta-lactamase-encoding gene: a rare but observable event

  2023cites this paper
• Insights into the Evolution of P. aeruginosa Antimicrobial Resistance in a Patient Undergoing Intensive Therapy

  2023cites this paper
• Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST

  2023cites this paper
• Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages

  2023cites this paper
• Scalable genotyping of microbial colonies

  2023cites this paper
• A Prospective Bacterial Whole Genome Sequencing-Based Surveillance Program for Comprehensive Early Detection of Healthcare-Associated Infection Transmission in Pediatric Oncology Patients.

  2023cites this paper
• Evaluation of Fourier Transform Infrared 2 spectroscopy (IR Biotyper) as a complement to 3 Whole genome sequencing (WGS) to characterise 4 Enterobacter cloacae , Citrobacter freundii and 5 Klebsiella pneumoniae isolates recovered from 6 hospital sinks

  2023cites this paper
• Evaluation of Fourier Transform Infrared 2 spectroscopy (IR Biotyper) as a complement to 3 Whole genome sequencing (WGS) to characterise 4 Enterobacter cloacae , Citrobacter freundii and 5 Klebsiella pneumoniae isolates recovered from 6 hospital sinks

  2023cites this paper
• Economic evaluations of whole-genome sequencing for pathogen identification in public health surveillance and health-care-associated infections: a systematic review.

  2023cites this paper
• The Silent Threat: Antimicrobial-Resistant Pathogens in Food-Producing Animals and Their Impact on Public Health

  2023cites this paper
• Discrimination between hypervirulent and non-hypervirulent ribotypes of Clostridioides difficile by MALDI-TOF mass spectrometry and machine learning

  2023influential citation
• Sink Drains in a Neonatal Intensive Care Unit: A Retrospective Risk Assessment and Evaluation

  2023cites this paper
• Vancomycin-sensitive Enterococcus faecium bacteraemia - hospital transmission and mortality in a Danish University Hospital.

  2023cites this paper
• Molecular Characterization of Clinical Linezolid-Resistant Staphylococcus epidermidis in a Tertiary Care Hospital

  2023cites this paper
• Pharyngeal Communities and Antimicrobial Resistance in Pangolins in Gabon

  2023cites this paper
• Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characterise Enterobacter cloacae, Citrobacter freundii and Klebsiella pneumoniae isolates recovered from hospital sinks

  2023cites this paper
• Ancient methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection

  2023cites this paper
• Economic and health impact modelling of a whole genome sequencing-led intervention strategy for bacterial healthcare-associated infections for England and for the USA

  2023cites this paper
• Livestock-associated methicillin-resistant Staphylococcus aureus epidemiology, genetic diversity, and clinical characteristics in an urban region

  2022cites this paper
• Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations

  2022cites this paper
• Single Nucleotide Polymorphism-Based Real-Time PCR Screening Assay for Rapid Tracking of Bacterial Infection Clusters To Complement Whole-Genome Sequencing Efforts during Outbreak Investigations

  2022cites this paper
• Von Basishygiene bis zu aktiver Netzarbeit

  2022cites this paper
• Susceptibility of Burkholderia cepacia Complex to Ceftazidime/Avibactam and Standard Drugs of Treatment for Cystic Fibrosis Patients

  2022cites this paper
• Genomic surveillance uncovers ongoing transmission of carbapenem-resistant Acinetobacter baumannii (CRAB) and identifies actionable routes of transmissions in an endemic setting

  2022cites this paper
• Entwicklung und Fortschritt bei Atemwegsinfektionen

  2022cites this paper
• Molecular Assessment of Staphylococcus Aureus Strains in STAT3 Hyper-IgE Syndrome Patients

  2022cites this paper
• Impact of single-room contact precautions on acquisition and transmission of vancomycin-resistant enterococci on haematological and oncological wards, multicentre cohort-study, Germany, January−December 2016

  2022cites this paper
• Outbreak of MRSA in a Gynecology/Obstetrics Department during the COVID-19 Pandemic: A Cautionary Tale

  2022cites this paper
• Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis

  2022cites this paper
• Curation of the AMRFinderPlus databases: applications, functionality and impact

  2022cites this paper
• Genomic analysis of Staphylococcus aureus from the West African Dwarf (WAD) goat in Nigeria

  2021cites this paper
• Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes

  2021influential citation
• Epidemiological Typing Using WGS

  2021cites this paper
• Global Genomic Characterization of Salmonella enterica Serovar Telelkebir

  2021cites this paper
• Whole-genome sequencing for neonatal intensive care unit outbreak investigations: Insights and lessons learned

  2021cites this paper
• Metagenomics: A field revealing the secrets of the microbial world of wastewater treatment plants

  2021cites this paper
• Combined antibiotic stewardship and infection control measures to contain the spread of linezolid-resistant Staphylococcus epidermidis in an intensive care unit

  2021cites this paper
• The microbiome of the nasopharynx

  2021cites this paper
• AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

  2021cites this paper
• Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing

  2021cites this paper
• Whole Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection.

  2021cites this paper
• Characterization of clinical Ralstonia strains and their taxonomic position

  2021cites this paper
• Reducing the Risk of Transmission of Critical Antimicrobial Resistance Determinants From Contaminated Pork Products to Humans in South-East Asia

  2021cites this paper
• Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

  2021cites this paper
• A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

  2021cites this paper
• Identification of Shiga Toxin-Producing Escherichia coli Outbreaks Using Whole Genome Sequencing.

  2021cites this paper
• An in vitro study on Staphylococcus schweitzeri virulence

  2021cites this paper
• A case of meningitis due to extensively drug-resistant Pseudomonas aeruginosa imported through medical evacuation: Genomic and environmental investigation.

  2021cites this paper
• Using core genome MLST typing for vancomycin-resistant Enterococcus faecium isolates to guide infection control interventions and end an outbreak.

  2021cites this paper
• Prevalence and zoonotic transmission of colistin-resistant and carbapenemase-producing Enterobacterales on German pig farms

  2021cites this paper
• Novel insights into pivotal risk factors for rectal carriage of extended‐spectrum‐β‐lactamase‐producing enterobacterales within the general population in Lower Saxony, Germany

  2021influential citation
• Multiresistant Gram-Negative Pathogens-A Zoonotic Problem.

  2021cites this paper
• Stenotrophomonas maltophilia Infections in Pediatric Patients – Experience at a European Center for Pediatric Hematology and Oncology

  2021cites this paper
• Influence of the Incubator as Direct Patient Environment on Bacterial Colonization of Neonates

  2021cites this paper
• Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of resistome in E. coli

  2020cites this paper
• Strain population structure varies widely across bacterial species and predicts strain colonization in unrelated individuals

  2020cites this paper
• [Hospital hygiene 2.0 : Cross-interface, molecular epidemiological early warning systems for prevention of multidrug-resistant pathogens].

  2020cites this paper