ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2017
Whole-Genome Sequencing Accurately Identifies Resistance to Extended-Spectrum β-Lactams for Major Gram-Negative Bacterial Pathogens.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 77 citations in OpenAlex.
- Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages.Clinical microbiology reviews · 2019Pooled it
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- Nanopore sequencing in suitcase lab enables improved detection ofFrontiers in microbiology · 2026Article
- Interpreting antimicrobial resistance from bacterial whole-genome sequencing: prediction tools, database fragmentation, analytical trade-offs, and harmonized reporting.Frontiers in microbiology · 2026Review
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- Genomic Analysis of Two Histamine-Producing Strains Isolated from Yellowfin Tuna.Foods (Basel, Switzerland) · 2025Article
- Comprehensive Assessment of Initial Adaptation of Extended-Spectrum β-Lactamase-Positive ST131 Escherichia coli to Carbapenem Exposure.The Journal of infectious diseases · 2025Article
- One day in Denmark: whole-genome sequence-based analysis of Escherichia coli isolates from clinical settings.The Journal of antimicrobial chemotherapy · 2025Article
- Next-Gen Nano Biosensor Technologies to Monitor Carbapenem Resistance for Personalized Medicine.Indian journal of microbiology · 2025Article
- Detecting antibiotic resistance: classical, molecular, advanced bioengineering, and AI-enhanced approaches.Frontiers in microbiology · 2025Review
- Genomic insights into plasmid-mediated antimicrobial resistance in the bacterium Bhargavaea beijingensis strain PS04.Archives of microbiology · 2023Article
- Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus onMicrobial genomics · 2023Article
- High-level ceftazidime/avibactam resistance in Escherichia coli conferred by the novel plasmid-mediated β-lactamase CMY-185 variant.The Journal of antimicrobial chemotherapy · 2023Article
- Temporal dynamics of genetically heterogeneous extended-spectrum cephalosporin-resistantmSphere · 2023Article
- Comparing antimicrobial resistant genes and phenotypes across multiple sequencing platforms and assays for Enterobacterales clinical isolates.BMC microbiology · 2023Article
- Ceftolozane/tazobactam heteroresistance in cystic fibrosis-relatedJAC-antimicrobial resistance · 2023Article
- Contribution of the Oral and Gastrointestinal Microbiomes to Bloodstream Infections in Leukemia Patients.Microbiology spectrum · 2023Article
- Ultrasensitive and rapid identification of ESRI developer- and piperacillin/tazobactam-resistantEmerging microbes & infections · 2022Article
Corrections and comments
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Authors and funding
13 authors at 7 institutions in 3 countries.
Funding
Abstract
Background: There is marked interest in using DNA-based methods to detect antimicrobial resistance (AMR), with targeted polymerase chain reaction (PCR) approaches increasingly being incorporated into clinical care. Whole-genome sequencing (WGS) could offer significant advantages over targeted PCR for AMR detection, particularly for species where mutations are major drivers of AMR. Methods: Illumina MiSeq WGS and broth microdilution (BMD) assays were performed on 90 bloodstream isolates of the 4 most common gram-negative bacteria causing bloodstream infections in neutropenic patients. The WGS data, including both gene presence/absence and detection of mutations in an array of AMR-relevant genes, were used to predict resistance to 4 β-lactams commonly used in the empiric treatment of neutropenic fever. The genotypic predictions were then compared to phenotypic resistance as determined by BMD and by commercial methods during routine patient care. Results: Of 133 putative instances of resistance to the β-lactams of interest identified by WGS, only 87 (65%) would have been detected by a typical PCR-based approach. The sensitivity, specificity, and positive and negative predictive values for WGS in predicting AMR were 0.87, 0.98, 0.97, and 0.91, respectively. Using BMD as the gold standard, our genotypic resistance prediction approach had a significantly higher positive predictive value compared to minimum inhibitory concentrations generated by commercial methods (0.97 vs 0.92; P = .025). Conclusions: These data demonstrate the potential feasibility of using WGS to guide antibiotic treatment decisions for patients with life-threatening infections for an array of medically important pathogens.
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