ArticleScientific reports2016
Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07626073 (h Can Provide the Detection Results of Pathogen Type and Resistant Gene. This Study is a Prospective Multi Centers Study to Explore Using the New Diagnostic Tool of " RPIP " and the Different Detection Methods of Next Generation Sequencing and Multiplex PC R in Patients With Pneumonia in ICU. Further Compare the Difference of Pathogen Identification and Clinical Impact by Different Diagnostic Methods.), which is not on this map. Cited by 20 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
h Can Provide the Detection Results of Pathogen Type and Resistant Gene. This Study is a Prospective Multi Centers Study to Explore Using the New Diagnostic Tool of " RPIP " and the Different Detection Methods of Next Generation Sequencing and Multiplex PC R in Patients With Pneumonia in ICU. Further Compare the Difference of Pathogen Identification and Clinical Impact by Different Diagnostic Methods.
Who cites it
20 citing papers in PubMed, 60 citations in OpenAlex.
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- Improved targeting of the 16S rDNA nanopore sequencing method enables rapid pathogen identification in bacterial pneumonia in children.Frontiers in cellular and infection microbiology · 2022Article
- RESCRIPt: Reproducible sequence taxonomy reference database management.PLoS computational biology · 2021Article
- Enhancement of Antibiofilm Activity of Ciprofloxacin againstAntibiotics (Basel, Switzerland) · 2021Article
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- A Survey of Antimicrobial Resistance Determinants in Category A Select Agents, Exempt Strains, and Near-Neighbor Species.International journal of molecular sciences · 2020Article
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- Identification of non-invasive biomarkers for chronic atrophic gastritis from serum exosomal microRNAs.BMC cancer · 2019Article
- Evaluation of Targeted Next-Generation Sequencing for Detection of Bovine Pathogens in Clinical Samples.Journal of clinical microbiology · 2018Article
- Detection of 16S rRNA and KPC Genes from Complex Matrix Utilizing a Molecular Inversion Probe Assay for Next-Generation Sequencing.Scientific reports · 2018Article
- Homology-based enzymatic DNA fragment assembly-based illumina sequencing library preparation.Biology methods & protocols · 2018Article
- Circulating exosomal miR-125a-3p as a novel biomarker for early-stage colon cancer.Scientific reports · 2017Article
- Interplay of the Quality of Ciprofloxacin and Antibiotic Resistance in Developing Countries.Frontiers in pharmacology · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antibiotic resistance (AR) is an epidemic of increasing magnitude requiring rapid identification and profiling for appropriate and timely therapeutic measures and containment strategies. In this context, ciprofloxacin is part of the first-line of countermeasures against numerous high consequence bacteria. Significant resistance can occur via single nucleotide polymorphisms (SNP) and deletions within ciprofloxacin targeted genes. Ideally, use of ciprofloxacin would be prefaced with AR determination to avoid overuse or misuse of the antibiotic. Here, we describe the development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant, limits of detection (LOD) for high-throughput pooled sequencing ranged from approximately 300-1800 input genome copies. LODs increased 10-fold in the presence of contaminating human genome DNA. In addition, we show that MIPs can be used as an enrichment step with high resolution melt (HRM) real-time PCR which is a sensitive assay with a rapid time-to-answer. Overall, this technology is a multiplexable upfront enrichment applicable with multiple downstream molecular assays for the detection of targeted genetic regions.
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