ArticleFrontiers in microbiology2023
Highly sensitive quantitative phase microscopy and deep learning aided with whole genome sequencing for rapid detection of infection and antimicrobial resistance.
Article in Frontiers in microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 2 of them syntheses that pooled it.
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Who cites it
13 citing papers in PubMed, 2 syntheses or guidelines pooled it, 19 citations in OpenAlex.
- Pooled it
- Pooled it
- Immortal AI, Mortal Life: Long-Term Perspectives on AI and Human Knowledge.Journal of medical Internet research · 2026Article
- Real-time snapping dynamics and nanoscale thickness profiling of salmon keratocyte tunneling nanotubes using partially coherent quantitative phase microscopy.Scientific reports · 2026Article
- Antibiotic resistance inFrontiers in microbiology · 2026Review
- Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours.Nature communications · 2025Article
- Label-free phenotypic antimicrobial susceptibility testing on microfluidic platforms: a review of advances and translation.Mikrochimica acta · 2025Review
- Digital holographic microscopy for rapid bacteria segmentation and counting in microfluidic cartridges: basic considerations and limitations for diagnostic application.Journal of biomedical optics · 2025Article
- Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2024Article
- Tackling the Antimicrobial Resistance "Pandemic" with Machine Learning Tools: A Summary of Available Evidence.Microorganisms · 2024Review
- High space-time bandwidth product imaging in low coherence quantitative phase microscopy.Scientific reports · 2024Article
- Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing.Scientific reports · 2024Article
- Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives.Antibiotics (Basel, Switzerland) · 2023Review
Corrections and comments
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Authors and funding
6 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current state-of-the-art infection and antimicrobial resistance (AMR) diagnostics are based on culture-based methods with a detection time of 48-96 h. Therefore, it is essential to develop novel methods that can do real-time diagnoses. Here, we demonstrate that the complimentary use of label-free optical assay with whole-genome sequencing (WGS) can enable rapid diagnosis of infection and AMR. Our assay is based on microscopy methods exploiting label-free, highly sensitive quantitative phase microscopy (QPM) followed by deep convolutional neural networks-based classification. The workflow was benchmarked on 21 clinical isolates from four WHO priority pathogens that were antibiotic susceptibility tested, and their AMR profile was determined by WGS. The proposed optical assay was in good agreement with the WGS characterization. Accurate classification based on the gram staining (100% recall for gram-negative and 83.4% for gram-positive), species (98.6%), and resistant/susceptible type (96.4%), as well as at the individual strain level (100% sensitivity in predicting 19 out of the 21 strains, with an overall accuracy of 95.45%). The results from this initial proof-of-concept study demonstrate the potential of the QPM assay as a rapid and first-stage tool for species, strain-level classification, and the presence or absence of AMR, which WGS can follow up for confirmation. Overall, a combined workflow with QPM and WGS complemented with deep learning data analyses could, in the future, be transformative for detecting and identifying pathogens and characterization of the AMR profile and antibiotic susceptibility.
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