ArticleBMC genomics2017
Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers, 1 of them a synthesis that pooled it.
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68 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data.PLoS computational biology · 2019Pooled it
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- Whole-genome sequencing-based pathogen characterization for streptococcal infection directly from positive blood culture samples.Journal of clinical microbiology · 2026Article
- A mini review of genome-predicted β-lactam susceptibility inFrontiers in cellular and infection microbiology · 2026Review
- Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult.Nature communications · 2025Article
- Machine learning and statistical inference in microbial population genomics.Genome biology · 2025Review
- GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project.Nature communications · 2025Article
- Mitigating antimicrobial resistance by innovative solutions in AI (MARISA): a modified James Lind Alliance analysis.npj antimicrobials and resistance · 2025Article
- Genomic analysis of theMicrobial genomics · 2025Article
- Genomic surveillance of invasiveMicrobial genomics · 2025Article
- Genomic analysis of invasive and non-invasive disease-causingMicrobial genomics · 2025Article
- Prediction of antimicrobial susceptibility of pneumococci based on whole-genome sequencing data: a direct comparison of two genomic tools to conventional antimicrobial susceptibility testing.Journal of clinical microbiology · 2025Article
- Pneumococci Isolated From Children in Community-Based Practice Differ From Isolates Identified by Population- and Laboratory-Based Invasive Disease Surveillance.The Journal of infectious diseases · 2024Article
- A genome-based survey of invasive pneumococci in Norway over four decades reveals lineage-specific responses to vaccination.Genome medicine · 2024Article
8 more citing papers are in PubMed but not listed here.
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11 authors.
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Abstract
backgroundGenomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a penicillin-binding protein (PBP) typing system and two methods (Random Forest (RF) and Mode MIC (MM)) that accurately predicted β-lactam MICs for pneumococcal isolates carrying a characterized PBP sequence type (phenotypic β-lactam MICs known for at least one isolate of this PBP type). This study evaluates the prediction performance for previously uncharacterized (new) PBP types and the probability of encountering new PBP types, both of which impact the overall prediction accuracy.
resultsThe MM and RF methods were used to predict MICs of 4309 previously reported pneumococcal isolates in 2 datasets and the results were compared to the known broth microdilution MICs to 6 β-lactams. Based on a method that specifically evaluated predictions for new PBP types, the RF results were more accurate than MM results for new PBP types and showed percent essential agreement (MICs agree within ±1 dilution) >97%, percent category agreement (interpretive results agree) >93%, major discrepancy (sensitive isolate predicted as resistant) rate < 1.2%, and very major discrepancy (resistant isolate predicted as sensitive) rate < 1.4% for all 6 β-lactams. The identification of new PBP types over time was well approximated by a diminishingly increasing curve (Pearson's r = 0.99) and minimally impacted overall MIC prediction performance.
conclusionsMIC prediction using the RF method could be an accurate alternative of phenotypic susceptibility testing even in the presence of previously uncharacterized PBP types.
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