ArticlePloS one2023
GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
Article in PloS one, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- Genomic and patient epidemiology ofMicrobiology spectrum · 2026Article
- Comparative genomic analyses shed light on the introduction routes of rice-pathogenic Burkholderia gladioli strains into Bangladesh.BMC genomics · 2026Article
- Emergence of OXA-48-producingFrontiers in cellular and infection microbiology · 2026Article
- Genomic epidemiology of Carbapenem-Resistant Enterobacterales in southern Vietnam: dominance ofLe infezioni in medicina · 2026Article
- Genomic diversity and antimicrobial resistance ofMicrobial genomics · 2025Article
- Community-Onset Fungemias: Epidemiology and Genomic Characterization at a Tertiary-Care Hospital in Barcelona, Spain.Journal of fungi (Basel, Switzerland) · 2025Article
- Acquired amphotericin B resistance attributed to a mutatedAntimicrobial agents and chemotherapy · 2025Article
- Typing ofMicroorganisms · 2025Article
- Mechanisms of Cefiderocol Resistance in Carbapenemase-Producing Enterobacterales: Insights from Comparative Genomics.Antibiotics (Basel, Switzerland) · 2025Article
- Characterization ofReports (MDPI) · 2025Article
- Genetic Confirmation of Clonal Spread ofJournal of fungi (Basel, Switzerland) · 2025Article
- Acquired Amphotericin B Resistance Attributed to a MutatedbioRxiv : the preprint server for biology · 2025Article
- Genomic Characterization of Carbapenemase-Producing Enterobacteriaceae from Clinical and Epidemiological Human Samples.Antibiotics (Basel, Switzerland) · 2025Article
- Analyzing Antibiotic Resistance in Bacteria from Wastewater in Pakistan Using Whole-Genome Sequencing.Antibiotics (Basel, Switzerland) · 2024Article
- Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches.Journal of fungi (Basel, Switzerland) · 2024Review
- Accelerating bioinformatics implementation in public health.Microbial genomics · 2023Article
- The role of plasmids in carbapenem resistant E. coli in Alameda County, California.BMC microbiology · 2023Article
- TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization.Frontiers in public health · 2023Article
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Authors and funding
13 authors.
Funding
Abstract
Whole genome sequencing (WGS) of clinical bacterial isolates has the potential to transform the fields of diagnostics and public health. To realize this potential, bioinformatic software that reports identification results needs to be developed that meets the quality standards of a diagnostic test. We developed GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) using k-mer based strategies for identification of bacteria based on WGS reads. GAMBIT incorporates this algorithm with a highly curated searchable database of 48,224 genomes. Herein, we describe validation of the scoring methodology, parameter robustness, establishment of confidence thresholds and the curation of the reference database. We assessed GAMBIT by way of validation studies when it was deployed as a laboratory-developed test in two public health laboratories. This method greatly reduces or eliminates false identifications which are often detrimental in a clinical setting.
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