ArticleJournal of clinical microbiology2014
Next-generation sequencing for typing and detection of resistance genes: performance of a new commercial method during an outbreak of extended-spectrum-beta-lactamase-producing Escherichia coli.
Article in Journal of clinical microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Epidemic potential of Escherichia coli ST131 and Klebsiella pneumoniae ST258: a systematic review and meta-analysis.BMJ open · 2016Pooled it
- Occurrence and Antimicrobial Susceptibility Pattern of ClinicalAntibiotics (Basel, Switzerland) · 2026Article
- Detection of antimicrobial resistance via state-of-the-art technologies versus conventional methods.Frontiers in microbiology · 2025Review
- Bacteriological diagnosis of osteoarticular infections caused byFrontiers in pediatrics · 2024Review
- Laboratory diagnostics for primary spinal infections in pediatric and adult populations: a narrative review.North American Spine Society journal · 2023Article
- Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria.Diagnostics (Basel, Switzerland) · 2023Review
- Exploring the complex role of gut microbiome in the development of precision medicine strategies for targeting microbial imbalance-induced colon cancer.Folia microbiologica · 2023Review
- Highly multiplexed targeted sequencing strategy for infectious disease surveillance.BMC biotechnology · 2023Article
- Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinicalMicrobial genomics · 2023Article
- The Past, Present, and Future ofDiagnostics (Basel, Switzerland) · 2022Review
- Extended-Spectrum ß-Lactamase-ProducingFrontiers in cellular and infection microbiology · 2022Article
- Beta-Lactamase-ProducingAntibiotics (Basel, Switzerland) · 2020Article
- Extended-spectrum ß-lactamase-producingOne health outlook · 2020Article
- Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci.Antimicrobial resistance and infection control · 2019Article
- Pool deconvolution approach for high-throughput gene mining from Bacillus thuringiensis.Applied microbiology and biotechnology · 2018Article
- Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis.Microorganisms · 2018Article
- AFLP-AFLP in silico-NGS approach reveals polymorphisms in repetitive elements in the malignant genome.PloS one · 2018Article
- Microbiome at the Frontier of Personalized Medicine.Mayo Clinic proceedings · 2017Review
- Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes.Scientific reports · 2016Article
- Comparison of MALDI-TOF MS and AFLP for strain typing of ESBL-producing Escherichia coli.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2016Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) has the potential to provide typing results and detect resistance genes in a single assay, thus guiding timely treatment decisions and allowing rapid tracking of transmission of resistant clones. We evaluated the performance of a new NGS assay (Hospital Acquired Infection BioDetection System; Pathogenica) during an outbreak of sequence type 131 (ST131) Escherichia coli infections in a nursing home in The Netherlands. The assay was performed on 56 extended-spectrum-beta-lactamase (ESBL) E. coli isolates collected during 2 prevalence surveys (March and May 2013). Typing results were compared to those of amplified fragment length polymorphism (AFLP), whereby we visually assessed the agreement of the BioDetection phylogenetic tree with clusters defined by AFLP. A microarray was considered the gold standard for detection of resistance genes. AFLP identified a large cluster of 31 indistinguishable isolates on adjacent departments, indicating clonal spread. The BioDetection phylogenetic tree showed that all isolates of this outbreak cluster were strongly related, while the further arrangement of the tree also largely agreed with other clusters defined by AFLP. The BioDetection assay detected ESBL genes in all but 1 isolate (sensitivity, 98%) but was unable to discriminate between ESBL and non-ESBL TEM and SHV beta-lactamases or to specify CTX-M genes by group. The performance of the hospital-acquired infection (HAI) BioDetection System for typing of E. coli isolates compared well with the results of AFLP. Its performance with larger collections from different locations, and for typing of other species, was not evaluated and needs further study.
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