ACCIO: An Assembly-Based Tool Enabling Plasmid Detection
Nathan J Raabe1,2,3, Marissa P Griffith1,2, Vatsala Rangachar Srinivasa1,2,3
1Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, 3507 Victoria Street, BST-10 E1000-4A, Pittsburgh, Pennsylvania 15213, USA.
Medrxiv : the Preprint Server for Health Sciences
|November 24, 2025
Summary
ACCIO is a new tool for plasmid epidemiology that overcomes limitations of sequencing data to accurately identify plasmids and their groups. This advances the tracking of antimicrobial resistance genes spread by plasmids.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Plasmids, mobile genetic elements carrying antimicrobial resistance genes, are crucial for tracking disease spread.
- Current plasmid epidemiology faces challenges due to limitations in whole genome sequence data resolution.
- Existing genomic surveillance infrastructure struggles to accurately identify and track complete plasmids.
Purpose of the Study:
- To develop a bioinformatics tool, ACCIO, for accurate plasmid identification and grouping from various sequencing data types.
- To overcome technological and infrastructural barriers in plasmid epidemiology.
- To improve the tracking of plasmid evolution and spread, particularly those carrying antimicrobial resistance genes.
Main Methods:
- ACCIO creates a reference plasmid database for inferring plasmid presence and related groupings in assemblies.
- The tool processes Illumina, Nanopore, and hybrid assemblies.
- Validation involved internal and external datasets, and benchmarking against MOB-suite.
Main Results:
- ACCIO demonstrated high sensitivity and positive predictive value (PPV) across different assembly types (e.g., 100% sensitivity, 92.1% PPV for hybrid assemblies).
- The tool showed consistently high performance on external datasets.
- ACCIO outperformed MOB-suite in plasmid reconstruction and typing across various assembly types and plasmid grouping levels.
Conclusions:
- ACCIO effectively addresses limitations in sequencing technologies for plasmid epidemiology.
- The integrated workflow of ACCIO supports all major sequencing platforms, facilitating broader adoption.
- ACCIO is poised to advance plasmid epidemiology and the surveillance of antimicrobial resistance.
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