ArticlemSphere2022
Optimizing Nanopore Sequencing for Rapid Detection of Microbial Species and Antimicrobial Resistance in Patients at Risk of Surgical Site Infections.
Article in mSphere, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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.
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Who cites it
16 citing papers in PubMed, 29 citations in OpenAlex.
- ST8Sia6-dependent glycosylation restrains gut inflammation and pathogenic TCell reports · 2026Article
- Enhancing diabetic foot osteomyelitis diagnosis with metagenomics next-generation sequencing, proof of concept.Diabetic medicine : a journal of the British Diabetic Association · 2026Article
- Laboratory tests for bovine respiratory bacteria and antimicrobial resistance in commercial feedlot cattle: comparing culture, long-read metagenomics, and recombinase polymerase amplification.Frontiers in microbiology · 2026Article
- Wounds and the Microbiota: The Healing Interplay Between Host and Microbial Communities.International journal of molecular sciences · 2025Review
- Comprehensive pathogen identification and antimicrobial resistance prediction from positive blood cultures using nanopore sequencing technology.Genome medicine · 2024Article
- Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.Scientific reports · 2024Article
- Detection of hidden antibiotic resistance through real-time genomics.Nature communications · 2024Article
- Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review.Annals of clinical microbiology and antimicrobials · 2024Review
- NIAID/SMB Workshop on Multiscale Modeling of Infectious and Immune-Mediated Diseases.Bulletin of mathematical biology · 2024Article
- Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle.Frontiers in microbiology · 2024Article
- Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections.Microbial genomics · 2023Article
- Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives.Antibiotics (Basel, Switzerland) · 2023Review
- Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapidFrontiers in microbiology · 2023Article
- The utilization of nanopore targeted sequencing proves to be advantageous in the identification of infections present in deceased donors.Frontiers in microbiology · 2023Article
- Highly sensitive quantitative phase microscopy and deep learning aided with whole genome sequencing for rapid detection of infection and antimicrobial resistance.Frontiers in microbiology · 2023Article
- Neonatal intestinal colonization ofGut microbesArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Surgical site infections (SSI) are a significant burden to patients and health care systems. We evaluated the use of Nanopore sequencing (NS) to rapidly detect microbial species and antimicrobial resistance (AMR) genes present in intraoperative bile aspirates. Bile aspirates from 42 patients undergoing pancreatic head resection were included. Three methods of DNA extraction using mechanical cell lysis or protease cell lysis were compared to determine the optimum method of DNA extraction. The impact of host DNA depletion, sequence run duration, and use of different AMR gene databases was also assessed. To determine clinical value, NS results were compared to standard culture (SC) results. NS identified microbial species in all culture positive samples. Mechanical lysis improved NS detection of cultured species from 60% to 76%, enabled detection of fungal species, and increased AMR predictions. Host DNA depletion improved detection of streptococcal species and AMR correlation with SC. Selection of AMR database influenced the number of AMR hits and resistance profile of 13 antibiotics. AMR prediction using CARD and ResFinder 4.1 correctly predicted 79% and 81% of the bile antibiogram, respectively. Sequence run duration positively correlated with detection of AMR genes. A minimum of 6 h was required to characterize the biliary microbes, resulting in a turnaround time of 14 h. Rapid identification of microbial species and AMR genes can be achieved by NS. NS results correlated with SC, suggesting that NS may be useful in guiding early antimicrobial therapy postsurgery.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.