🔬 What is SAURUS?
SAURUS (Staphylococcus aureus Unified Resource for Universal Surveillance) is a comprehensive genomic database that integrates typing, resistance, virulence, and plasmid annotations for publicly available S. aureus genomes into a single, queryable, and user-friendly resource.
It fills a gap in the S. aureus research community: no other single resource combines MLST, spa, SCCmec, agr, capsule, AMR genes, virulence factors, and plasmid replicons with country, isolation source, host, and collection year — all behind an interactive, exportable interface that lets you retrieve genome accessions in seconds.
ARGUS
SAURUS is one resource in ARGUS — a family of independent, open genomic surveillance sites, each dedicated to one of the WHO priority ESKAPE pathogens. Every resource shares the same architecture: accession-first, metadata-integrated, no login, no install, MIT-licensed. Each has its own name, its own DOI, and its own community.
Named for Argus Panoptes — the hundred-eyed giant of Greek myth who never slept — the umbrella is a bet that AMR surveillance has to be unified to be useful, and that the pathogens driving the crisis deserve the same treatment.
Status as of 2026-10-16. SAURUS launched first (S. aureus) and remains the flagship build; ECLIPSE is the second resource. The remaining pathogens are on the roadmap and will ship as their pipelines are built and validated.
🎯 Why SAURUS?
Staphylococcus aureus, and particularly methicillin-resistant S. aureus (MRSA), remains a leading cause of healthcare- and community-associated infections worldwide. Global genomic surveillance is essential for tracking emergent clones, informing infection control, and understanding outbreak dynamics.
The data exists. Over 134,000 S. aureus genomes have been sequenced and publicly deposited. What doesn't exist is a way to actually use it without weeks of setup.
🔒 The retrieval bottleneck
Genomic surveillance generates data faster than researchers can query it. A typical question — "give me all ST5 MRSA blood isolates from the United States that carry mecA and PVL" — requires, in the current ecosystem, that you either:
- Download and re-annotate the entire repository locally (weeks of compute, hundreds of GB, requires a bioinformatics pipeline)
- Write custom scripts to query static TSV archives (days of setup, breaks with every upstream update)
- Manually navigate multiple standalone tools (hours per query, error-prone, doesn't scale to real collections)
None of these options works for a researcher in a low-resource setting with a laptop and an internet connection. None of them works for a clinical microbiologist who needs an answer this afternoon. And none of them produces the one thing every downstream tool actually consumes: a clean accession list.
🦖 What SAURUS changes
SAURUS places accession retrieval at the centre of the interface.
Filter by genotype, geography, or gene content — combine any criteria — and
download a plain-text list ready for
datasets download genome accession --inputfile list.txt.
One click. No scripting. No install. No account.
Filter → export in seconds
Combine ST, CC, spa, SCCmec, agr, capsule, MRSA, country, source, host, year, and up to 5 genes per query. Get the accession list instantly.
One database, eleven modules
MLST · spa · SCCmec (two callers) · capsule · agr · MRSA · AMR · virulence · plasmid · geography · statistics — under a single roof.
Epidemiology, not just genotypes
Country of origin, isolation source, host species, and collection year for all 134,000+ genomes — filterable, sortable, exportable.
Two SCCmec callers, side by side
RPet and CGE run independently. Disagreements are surfaced — not silently resolved — with a dedicated agreement chart.
Zero barrier to entry
No login. No API key. No cost. No rate limit. Runs entirely in your browser over HTTPS. Works on a phone.
Accession-first, always
Every module exports a clean accession list. That's the deliverable downstream pipelines actually consume.
Why it matters: Genomic surveillance belongs to everyone, not just to labs with clusters and bioinformaticians on staff. SAURUS exists to close that gap — one accession list at a time.
🗺️ Roadmap — toward complete public S. aureus annotation
SAURUS is built incrementally toward a single milestone: complete typing annotation of every public S. aureus genome in the NCBI Assembly database.
-
v0.1 — Foundation
LIVE
20K RefSeq genomes · 9 typing and gene modules · lineage catalogue · consistent navigation · accession export -
v0.2 — Epidemiological metadata
LIVE
Country · isolation source · host · collection year, extracted from NCBI BioSample for every genome. Geography page with 4 interactive charts. Country + Source columns and filters added to every typing module. -
v0.2.1 / v0.2.2 — Metadata at scale
LIVE
26K → 134,299 unique genomes. Deduplicated at the numeric-stem level: 7,481 GCF/GCA paired twins removed, 12 GCA version conflicts resolved, 76 spuriously-paired accessions filtered. Verified: zero duplicate accessions, zero duplicate stems, zero GCF/GCA pairs. -
v0.3 — GenBank typing: batch 40K
IN PROGRESS
First 10,000 GenBank (GCA) genomes typed through StaphScope — MLST, spa, SCCmec (CGE + RPet), agr, and capsule. Merged into the existing 26,197-genome typing collection. -
v0.4 — GenBank typing: batches 50K–70K
+ 23,985 additional GCA genomes typed. Brings typing coverage to ~60,000 genomes total — RefSeq and GenBank unified in a single master table. -
v0.5 — Shelenkov GenBank typing
+ 59,741 Shelenkov-unique GCA genomes typed. Shelenkov AMR, virulence, and plasmid annotations carried forward. Brings typing coverage to the full current collection. -
v1.0 — Full resource
All 134,299 genomes typed · cross-module filter UI · citable Zenodo DOI · frozen, versioned release · Database (Oxford) manuscript
📦 Data sources
SAURUS combines two publicly available resources into a single integrated view:
1. Typing annotations (this project)
MLST, spa, SCCmec (CGE + RPet callers), agr, and capsule typing were generated on RefSeq (GCF) genomes using the StaphScope pipeline — a species-optimized computational pipeline for S. aureus genotyping. All accessions are cross-referenced against the current NCBI Assembly database.
2. Gene presence/absence (Shelenkov et al. 2025)
Antimicrobial resistance genes, virulence factors, and plasmid replicons were sourced from the Shelenkov et al. (2025) S. aureus genomic dataset published in BMC Genomic Data. The original matrices were re-processed into long-format TSVs (accession × gene) to enable interactive retrieval in SAURUS.
3. Epidemiological metadata (NCBI BioSample)
Country of origin, isolation source, host species, and collection year were extracted from NCBI BioSample records attached to each assembly. Source values were normalised into broad clinical and environmental categories (blood, nasal/screening, skin/wound, food, respiratory, …) while preserving the raw submitter strings for provenance. Coverage across the collection: ~85% for country, ~65% for isolation source, ~80% for host, ~80% for collection year.
What SAURUS adds on top of these
- Unified accession identifier —
GCA_XXXXXXXXX.Yformat throughout - Interactive gene retrieval — pick up to 5 genes, match ANY or ALL
- Cross-module querying — combine typing filters with gene filters
- One-click accession export — plain text, TSV, CSV, or JSON
- MRSA consensus call — resolves CGE / RPet disagreements
- Clonal complex (CC) column across all typing views
- Prevalence & co-occurrence views — statistical context for every gene
⚙️ Methods & tools
Every typing module in SAURUS is built on a well-validated, community-standard tool:
- MLST — Multi-locus sequence typing of 7 housekeeping genes mlst (Seemann) + PubMLST
- spa typing — Protein A repeat region characterisation spaTyper + Ridom SpaServer
- SCCmec CGE — Cassette type via gene-level detection SCCmecFinder
- SCCmec RPet — Cassette type + subtype via reference mapping sccmec (Petit)
- Capsule typing — cap5 / cap8 serotype determination BLAST
- agr typing — Accessory gene regulator classification agrVATE
- AMR genes — Resistance determinant presence/absence ABRicate + CARD / ResFinder / NCBI / ARG-ANNOT / MEGARes
- Virulence factors — VFDB gene screening ABRicate + VFDB
- Plasmid replicons — Replicon typing ABRicate + PlasmidFinder
- Lineage catalogue — literature-curated clonal complex reference custom
All computation is reproducible and open source. The StaphScope pipeline is available on GitHub, and the SAURUS website generator code is available on GitHub.
🔧 Downstream tools & pipelines
SAURUS provides the accession list and the typing context. The next step — phylogenetics, outbreak investigation, pangenome analysis — is done with the tools below. Each entry is a well-validated, open-source solution that complements SAURUS in a standard S. aureus workflow.
🔬 Integrated pipelines
🧬 Extended typing
🌳 Phylogenetics & recombination
🔬 Outbreak investigation
📊 Pangenome & comparative genomics
💊 AMR & virulence confirmation
🎨 Visualization & reporting
All tools listed above are open-source and actively maintained. If you use them alongside SAURUS, please cite each tool directly in addition to citing SAURUS.
👥 The team
University of Ghana Medical School
& Department of Biochemistry and Biotechnology, KNUST
University of Ghana Medical School
SAURUS is an independent, unfunded project born out of a need for open, accessible genomic surveillance tools in low- and middle-income settings. We welcome collaborations, bug reports, and feature suggestions.
⭐ Support SAURUS
SAURUS is an independent, unfunded project built on a shared HPC cluster and GitHub Pages. If you find it useful in your research, there are three easy ways to help it reach more people.
Every star, issue, and citation makes the next release easier to justify. Thank you for using SAURUS.
📚 Citation
If you use SAURUS in your research, please cite both the underlying pipeline and the source gene dataset:
When possible, please also cite the underlying typing tools credited in the Methods section above (mlst, spaTyper, SCCmecFinder, sccmec, agrVATE, ABRicate, AMRFinderPlus, and their reference databases).
🙏 Acknowledgements
SAURUS would not be possible without the open-source community. We are deeply grateful to the developers, curators, and maintainers of:
- StaphScope — the typing pipeline this resource is built on
- Torsten Seemann — for
mlstandABRicate - Robert A. Petit III — for
sccmecand contributions toagrVATE - Center for Genomic Epidemiology (DTU) — for
SCCmecFinder - NCBI — for the
datasetsCLI,AMRFinderPlus, and the Assembly database - PubMLST & Ridom — for allele and spa-type reference databases
- Shelenkov, Slavokhotova, Yunusova et al. — for publishing the gene dataset openly
- The open-source community — Python, pandas, and every library we rely on
📬 Contact & contribute
Found a bug? Have a feature suggestion? Want to collaborate? We'd love to hear from you.
SAURUS is released under the MIT License. You are free to use, modify, and redistribute it. Attribution is appreciated.