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

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

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inferred← citeshttps://doi.org/10.1111/apm.12753openalex-snapshot

Epidemiological characterization of a nosocomial outbreak of extended spectrum β‐lactamaseEscherichia coliST‐131 confirms the clinical value of core genome multilocus sequence typing

inferred← citeshttps://doi.org/10.1111/jam.15399openalex-snapshot

Novel insights into pivotal risk factors for rectal carriage of extended-spectrum-β-lactamase-producing enterobacterales within the general population in Lower Saxony, Germany

inferred← citeshttps://doi.org/10.1111/nyas.13310openalex-snapshot

Challenges and opportunities for whole‐genome sequencing–based surveillance of antibiotic resistance

inferred← citeshttps://doi.org/10.1111/nyas.13672openalex-snapshot

Genomic epidemiology of multidrug‐resistant Gram‐negative organisms

inferred← citeshttps://doi.org/10.1128/aac.00483-19openalex-snapshot

Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates

inferred← citeshttps://doi.org/10.1128/aac.00953-25openalex-snapshot

High-risk clonal expansion of IMP-producing Enterobacter cloacae complex in regional Japanese healthcare settings

inferred← citeshttps://doi.org/10.1128/aac.01071-25openalex-snapshot

Prediction of genetic relatedness of Escherichia coli using neighbor typing: a tool for rapid outbreak detection

inferred← citeshttps://doi.org/10.1128/aac.01082-24openalex-snapshot

Genomics for antimicrobial resistance—progress and future directions

inferred← citeshttps://doi.org/10.1128/aac.01362-25openalex-snapshot

Functional characterization of a novel class A carbapenemase CAE-1 in carbapenem-resistant Pseudomonas aeruginosa clinical isolates

inferred← citeshttps://doi.org/10.1128/aac.01459-23openalex-snapshot

Inter-phylum circulation of a beta-lactamase-encoding gene: a rare but observable event

inferred← citeshttps://doi.org/10.1128/aem.00728-19openalex-snapshot

Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157

inferred← citeshttps://doi.org/10.1128/aem.01454-17openalex-snapshot

Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:H − Isolates from Czech Patients with Novel Plasmid Composition Not Previously Seen in German Isolates

inferred← citeshttps://doi.org/10.1128/cmr.00016-17openalex-snapshot

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis

inferred← citeshttps://doi.org/10.1128/cmr.00135-18openalex-snapshot

Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages

inferred← citeshttps://doi.org/10.1128/cmr.00140-22openalex-snapshot

Integrating whole-genome sequencing into antimicrobial resistance surveillance: methodologies, challenges, and perspectives

inferred← citeshttps://doi.org/10.1128/cmr.00148-22openalex-snapshot

Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages

inferred← citeshttps://doi.org/10.1128/cmr.00177-25openalex-snapshot

Implementation of pathogen genomics in clinical microbiology laboratories

inferred← citeshttps://doi.org/10.1128/genomea.00001-17openalex-snapshot

Genome Sequences of the First WHO Repository of Platelet Transfusion-Relevant Bacterial Reference Strains

inferred← citeshttps://doi.org/10.1128/jcm.00121-25openalex-snapshot

The dark matter of bacterial genomic surveillance—antimicrobial resistance plasmid transmissions in the hospital setting

inferred← citeshttps://doi.org/10.1128/jcm.00180-19openalex-snapshot

Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory

inferred← citeshttps://doi.org/10.1128/jcm.00369-25openalex-snapshot

Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with Nanopore sequencing data

inferred← citeshttps://doi.org/10.1128/jcm.00646-25openalex-snapshot

Comparison of core genome multi-locus sequencing typing pipelines for hospital outbreak detection of common bacterial pathogens

inferred← citeshttps://doi.org/10.1128/jcm.00860-25openalex-snapshot

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

inferred← citeshttps://doi.org/10.1128/jcm.01196-22openalex-snapshot

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

inferred← citeshttps://doi.org/10.1128/jcm.01276-19openalex-snapshot

Genotypic Characterization of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates of Clonal Complex 398 in Pigsty Visitors: Transient Carriage or Persistence?

inferred← citeshttps://doi.org/10.1128/jcm.01309-19openalex-snapshot

Origin and Evolution of Hybrid Shiga Toxin-Producing and Uropathogenic Escherichia coli Strains of Sequence Type 141

inferred← citeshttps://doi.org/10.1128/jcm.01714-16openalex-snapshot

Commentary: Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy

inferred← citeshttps://doi.org/10.1128/jcm.01718-16openalex-snapshot

Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis

inferred← citeshttps://doi.org/10.1128/jcm.01873-22openalex-snapshot

Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data

inferred← citeshttps://doi.org/10.1128/jcm.01987-20openalex-snapshot

Establishment and Evaluation of a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Pseudomonas aeruginosa

inferred← citeshttps://doi.org/10.1128/jcm.02198-20openalex-snapshot

Global Epidemiology and Evolutionary History of Staphylococcus aureus ST45

inferred← citeshttps://doi.org/10.1128/jcm.02242-16openalex-snapshot

High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial

inferred← citeshttps://doi.org/10.1128/msphere.00553-17openalex-snapshot

The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification

inferred← citeshttps://doi.org/10.1128/msystems.01080-24openalex-snapshot

NanoCore: core-genome-based bacterial genomic surveillance and outbreak detection in healthcare facilities from Nanopore and Illumina data

inferred← citeshttps://doi.org/10.1128/spectrum.00664-23openalex-snapshot

Pharyngeal Communities and Antimicrobial Resistance in Pangolins in Gabon

inferred← citeshttps://doi.org/10.1128/spectrum.00862-24openalex-snapshot

Evaluation of a microfluidic-based point-of-care prototype with customized chip for detection of bacterial clusters

inferred← citeshttps://doi.org/10.1128/spectrum.02100-24openalex-snapshot

Real-time plasmid transmission detection pipeline

inferred← citeshttps://doi.org/10.1128/spectrum.02230-25openalex-snapshot

Hospital-wide pathogen transmission surveillance combining epidemiological, genetic, and spectroscopic approaches

inferred← citeshttps://doi.org/10.1128/spectrum.03036-22openalex-snapshot

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

inferred← citeshttps://doi.org/10.1136/bmjgh-2019-002244openalex-snapshot

Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

inferred← citeshttps://doi.org/10.1155/2018/1525072openalex-snapshot

Transmission Risk on a Neonatal Intensive Care Unit: Escherichia coli versus Klebsiella pneumoniae

inferred← citeshttps://doi.org/10.1186/s12864-018-4976-3openalex-snapshot

Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany

inferred← citeshttps://doi.org/10.1186/s12864-018-5045-7openalex-snapshot

Attack of the clones: whole genome-based characterization of two closely related enterohemorrhagic Escherichia coli O26 epidemic lineages

inferred← citeshttps://doi.org/10.1186/s12864-021-07702-2openalex-snapshot

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

inferred← citeshttps://doi.org/10.1186/s12866-017-1043-1openalex-snapshot

Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State

inferred← citeshttps://doi.org/10.1186/s13012-019-0930-2openalex-snapshot

Status and potential of bacterial genomics for public health practice: a scoping review

inferred← citeshttps://doi.org/10.1186/s13073-024-01292-wopenalex-snapshot

Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection

inferred← citeshttps://doi.org/10.1186/s13756-017-0206-zopenalex-snapshot

Weekly screening supports terminating nosocomial transmissions of vancomycin-resistant enterococci on an oncologic ward – a retrospective analysis

inferred← citeshttps://doi.org/10.1186/s13756-017-0228-6openalex-snapshot

No nosocomial transmission under standard hygiene precautions in short term contact patients in case of an unexpected ESBL or Q&A E. coli positive patient: a one-year prospective cohort study within three regional hospitals

inferred← citeshttps://doi.org/10.1186/s13756-017-0276-yopenalex-snapshot

Evaluation of a Stenotrophomonas maltophilia bacteremia cluster in hematopoietic stem cell transplantation recipients using whole genome sequencing

inferred← citeshttps://doi.org/10.1186/s13756-018-0394-1openalex-snapshot

Hospital acquired vancomycin resistant enterococci in surgical intensive care patients – a prospective longitudinal study

inferred← citeshttps://doi.org/10.1186/s13756-019-0604-5openalex-snapshot

Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci

inferred← citeshttps://doi.org/10.1186/s13756-020-00820-8openalex-snapshot

A nosocomial cluster of vancomycin resistant enterococci among COVID-19 patients in an intensive care unit

inferred← citeshttps://doi.org/10.1186/s13756-020-00845-zopenalex-snapshot

Donor-derived vancomycin-resistant enterococci transmission and bloodstream infection after intestinal transplantation

inferred← citeshttps://doi.org/10.1186/s13756-021-00970-3openalex-snapshot

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

inferred← citeshttps://doi.org/10.1186/s13756-021-00987-8openalex-snapshot

Genomic analysis of Staphylococcus aureus from the West African Dwarf (WAD) goat in Nigeria

inferred← citeshttps://doi.org/10.1186/s13756-023-01359-0openalex-snapshot

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

inferred← citeshttps://doi.org/10.1186/s13756-024-01386-5openalex-snapshot

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

inferred← citeshttps://doi.org/10.12688/f1000research.39214.1openalex-snapshot

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

inferred← citeshttps://doi.org/10.1371/journal.pone.0198103openalex-snapshot

High prevalence of MRSA and multi-resistant gram-negative bacteria in refugees admitted to the hospital—But no hint of transmission

inferred← citeshttps://doi.org/10.1371/journal.pone.0235160openalex-snapshot

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

inferred← citeshttps://doi.org/10.1371/journal.ppat.1006024openalex-snapshot

Dynamic in vivo mutations within the ica operon during persistence of Staphylococcus aureus in the airways of cystic fibrosis patients

inferred← citeshttps://doi.org/10.1556/1886.2018.00002openalex-snapshot

Molecular epidemiology of multidrug-resistant bacteria isolated from Libyan and Syrian patients with war injuries in two Bundeswehr hospitals in Germany

inferred← citeshttps://doi.org/10.2174/9789815313628125010008openalex-snapshot

Antibiotic Resistant Infections

inferred← citeshttps://doi.org/10.2217/fmb-2024-0043openalex-snapshot

Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing

inferred← citeshttps://doi.org/10.2807/1560-7917.es.2017.22.21.30541openalex-snapshot

Ongoing haemolytic uraemic syndrome (HUS) outbreak caused by sorbitol-fermenting (SF) Shiga toxin-producing Escherichia coli (STEC) O157, Germany, December 2016 to May 2017

inferred← citeshttps://doi.org/10.2807/1560-7917.es.2022.27.2.2001876openalex-snapshot

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

inferred← citeshttps://doi.org/10.2807/1560-7917.es.2025.30.23.2400590openalex-snapshot

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

inferred← citeshttps://doi.org/10.29074/ascls.119.001750openalex-snapshot

Next Generation Sequencing for Outbreak Investigation in the Clinical Microbiology Laboratory

inferred← citeshttps://doi.org/10.31744/pg.108723openalex-snapshot

Estudo da colonização intestinal como fator de risco para infecção e disseminação de enterobactérias resistentes aos carbapenêmicos no ambiente hospitalar

inferred← citeshttps://doi.org/10.3238/arztebl.2018.0822openalex-snapshot

New Microbiological Techniques in the Diagnosis of Bloodstream Infections

inferred← citeshttps://doi.org/10.3238/arztebl.m2021.0184openalex-snapshot

Multiresistant Gram-Negative Pathogens

inferred← citeshttps://doi.org/10.3343/alm.2019.39.6.530openalex-snapshot

Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems

inferred← citeshttps://doi.org/10.3389/fgene.2020.563975openalex-snapshot

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

inferred← citeshttps://doi.org/10.3389/fimmu.2019.02552openalex-snapshot

High Nuclease Activity of Long Persisting Staphylococcus aureus Isolates Within the Airways of Cystic Fibrosis Patients Protects Against NET-Mediated Killing

inferred← citeshttps://doi.org/10.3389/fmicb.2017.01914openalex-snapshot

Epidemiology of Extended-Spectrum β-Lactamase-Producing E. coli and Vancomycin-Resistant Enterococci in the Northern Dutch–German Cross-Border Region

inferred← citeshttps://doi.org/10.3389/fmicb.2018.01494openalex-snapshot

A Sporadic Four-Year Hospital Outbreak of a ST97-IVa MRSA With Half of the Patients First Identified in the Community

inferred← citeshttps://doi.org/10.3389/fmicb.2020.00230openalex-snapshot

Antibiotic Treatment and Age Are Associated With Staphylococcus aureus Carriage Profiles During Persistence in the Airways of Cystic Fibrosis Patients

inferred← citeshttps://doi.org/10.3389/fmicb.2020.01049openalex-snapshot

A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa

inferred← citeshttps://doi.org/10.3389/fmicb.2020.01729openalex-snapshot

Comparison of Whole Genome (wg-) and Core Genome (cg-) MLST (BioNumericsTM) Versus SNP Variant Calling for Epidemiological Investigation of Pseudomonas aeruginosa

inferred← citeshttps://doi.org/10.3389/fmicb.2021.689015openalex-snapshot

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

inferred← citeshttps://doi.org/10.3389/fmicb.2021.704152openalex-snapshot

Global Genomic Characterization of Salmonella enterica Serovar Telelkebir

inferred← citeshttps://doi.org/10.3389/fmicb.2022.875775openalex-snapshot

Livestock-associated methicillin-resistant Staphylococcus aureus epidemiology, genetic diversity, and clinical characteristics in an urban region

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1068872openalex-snapshot

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

inferred← citeshttps://doi.org/10.3389/fmicb.2025.1673343openalex-snapshot

Detecting antibiotic resistance: classical, molecular, advanced bioengineering, and AI-enhanced approaches

inferred← citeshttps://doi.org/10.3389/fmicb.2026.1735075openalex-snapshot

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

inferred← citeshttps://doi.org/10.3389/fonc.2021.752037openalex-snapshot

Stenotrophomonas maltophilia Infections in Pediatric Patients – Experience at a European Center for Pediatric Hematology and Oncology

inferred← citeshttps://doi.org/10.3390/antibiotics12030483openalex-snapshot

Insights into the Evolution of P. aeruginosa Antimicrobial Resistance in a Patient Undergoing Intensive Therapy

inferred← citeshttps://doi.org/10.3390/antibiotics14050443openalex-snapshot

Antimicrobial Resistance in Diverse Ecological Niches—One Health Perspective and Food Safety

inferred← citeshttps://doi.org/10.3390/antibiotics9050246openalex-snapshot

A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program

inferred← citeshttps://doi.org/10.3390/ijerph20176692openalex-snapshot

Sink Drains in a Neonatal Intensive Care Unit: A Retrospective Risk Assessment and Evaluation

inferred← citeshttps://doi.org/10.3390/jcm5090083openalex-snapshot

Advances in the Microbiome: Applications to Clostridium difficile Infection

inferred← citeshttps://doi.org/10.3390/microorganisms10040689openalex-snapshot

Outbreak of MRSA in a Gynecology/Obstetrics Department during the COVID-19 Pandemic: A Cautionary Tale

inferred← citeshttps://doi.org/10.3390/microorganisms11071805openalex-snapshot

Molecular Characterization of Clinical Linezolid-Resistant Staphylococcus epidermidis in a Tertiary Care Hospital

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