Acinetobacter baumannii Yielding Surveillance System
Typing, capsule loci, and epidemiological metadata for every public A. baumannii genome — Pasteur MLST, international clones, KL/OCL capsule types, OXA-51 variants, carbapenemases, plus country, source, host, and collection year. Filter. Verify. Download your accession list.
Pasteur MLST, international clone assignment, OXA-51 variant, and Kaptive capsule typing — each page supports live search, multi-column filtering, row selection, and one-click accession export.
Search and retrieve genomes by antimicrobial resistance, virulence, and plasmid replicon content. Pick genes of interest, switch between match-ANY and match-ALL, and export the accession list for re-downloading genomes.
Interactive dashboards for the whole collection — distribution donuts, rankings, timelines, a crosstab explorer, geographic breakdown, and a literature-curated catalogue of international clones.
Every genome linked to its country of origin, isolation source, host species, and collection year — extracted from NCBI BioSample. Filter by geography and ICU-relevant sources, drop the accessions into your pipeline, and answer questions like "all IC2 from bloodstream infections in West Africa" without writing a single line of code.
Four steps from query to genome download — no installation, no account, no limits.
Pick a typing view (MLST, Capsule), gene-based retrieval (AMR, Virulence, Plasmid), or the Master Table for everything at once.
Combine genotype + geography: e.g. IC2 + KL2 +
OXA-23 + Ghana + blood + 2015–2023.
Click 🧬 Accessions to download a plain-text list of matching genome accession IDs — one per line.
Feed the list to NCBI:
datasets download genome accession --inputfile list.txt
— that's it.
Antimicrobial Resistance Genomic Unified Surveillance · one family, seven ESKAPE pathogens
If you use ABYSS in your research, please cite the typing pipeline and the source dataset:
Typing pipeline: Beckley B, Amarh V, Lopes BS, et al. AcinetoScope: a computational pipeline for rapid, comprehensive Acinetobacter baumannii outbreak investigation and resistance gene tracking. Scientific Reports. 2026. doi:10.1038/s41598-026-70189-y
Gene data: Shelenkov A, Mikhaylova Y, Akimkin V. Genomic Epidemiology Dataset for the Important Nosocomial Pathogenic Bacterium Acinetobacter baumannii. Data. 2024;9(2):22. doi:10.3390/data9020022
Metadata: BioSample records from the NCBI Assembly database — country, isolation source, host, and collection date attributes.