About ECLIPSE

🔬 What is ECLIPSE?

ECLIPSE (E. coli Library for Integrated Pathogen Surveillance and Epidemiology) is a comprehensive genomic resource that integrates typing, lineage, and epidemiological metadata for publicly available Escherichia coli genomes into a single, queryable, and user-friendly interface.

E. coli is simultaneously the most-studied organism in molecular biology and one of the most important human pathogens on the planet. It is a commensal, a foodborne pathogen, an extraintestinal pathogen, and one of the major reservoirs of antimicrobial resistance genes. Existing resources present fragments of this picture — a typing database here, a serotype catalogue there, an AMR matrix somewhere else. ECLIPSE brings them together.

🎯 Why ECLIPSE?

E. coli is the leading cause of gram-negative bloodstream infections worldwide and a major driver of the antimicrobial-resistance crisis. A small number of successful clones — most notably ST131-H30 — have spread globally, acquiring extended-spectrum beta-lactamases and carbapenemases along the way. Tracking them requires three things that have historically been hard to combine: typing, lineage context, and epidemiological metadata.

The data exists. Over 431,000 E. coli genomes have been sequenced and publicly deposited. What hasn't existed is a way to actually use it without weeks of setup.

🔒 The retrieval bottleneck

A typical surveillance question — "give me all ST131 isolates from urinary sources in West Africa that carry CTX-M-15" — 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 ECLIPSE changes

ECLIPSE places accession retrieval at the centre of the interface. Filter by genotype, geography, or lineage — 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.

Why it matters: Genomic surveillance belongs to everyone, not just to labs with clusters and bioinformaticians on staff. ECLIPSE exists to close that gap — one accession list at a time.

🗺️ Roadmap — toward complete public E. coli annotation

ECLIPSE is built incrementally toward a single milestone: complete typing annotation of every public E. coli genome in the NCBI Assembly database.

• v0.1 — Metadata foundation LIVE
  431,592 accessions indexed with country, source, host, and year from NCBI BioSample. GCA↔GCF deduplication complete. Geography page live.
• v0.2 — RefSeq typing IN PROGRESS
  RefSeq genomes typed through EcoliTyper — Achtman MLST, Clermont phylogroups, SerotypeFinder (CGE), and CHTyper. Master table, statistics dashboard, and lineages catalogue coming online.
• v0.3 — AMR & virulence modules
  ABRicate-based AMR (CARD, ResFinder, ARG-ANNOT, MEGARes) and virulence (VFDB) modules added. Plasmid replicons via PlasmidFinder.
• v0.5 — Full collection
  All 431,592 genomes typed — RefSeq and GenBank unified in a single master table. Pathotypes inferred from virulence-gene rules.
• v1.0 — Full resource
  All genomes typed · citable Zenodo DOI · frozen, versioned release · peer-reviewed methods manuscript.

📦 Data sources

ECLIPSE combines four publicly available resources into a single integrated view:

1. Genome assemblies — NCBI Assembly

Every genome in ECLIPSE is sourced from the NCBI Assembly database. Accessions are the primary key. Where both a GenBank (GCA_) and RefSeq (GCF_) version exist, the RefSeq version is preferred; assemblies with no RefSeq counterpart are kept as GenBank.

2. 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, environmental, food, and animal categories while preserving the raw submitter strings for provenance. Coverage across the collection: 95% for country, 73% for isolation source, 78% for host, and 92% for collection year.

3. Typing annotations — generated by EcoliTyper

MLST, phylogroup, serotype, and CHTyper annotations were produced with EcoliTyper, the species-optimized typing pipeline built for ECLIPSE. Each module page documents the tool used, the reference database version, and the success rate.

4. Lineage catalogue — curated from the literature

The list of clinically and epidemiologically important sequence types (ST131, ST95, ST73, ST69, ST405, ST1193, ST410, ST648, and others) is curated from published E. coli surveillance literature and is updated as new high-risk clones emerge.

What ECLIPSE adds on top of these

• Unified accession identifier — GCA_XXXXXXXXX.Y format throughout
• Cross-module querying — combine typing filters with metadata filters
• One-click accession export — plain text, TSV, CSV, or JSON
• Ecotype and serogroup classifications for fast screening
• Coverage indicator showing how many typings resolved per genome
• Interactive statistics dashboard with live cross-tabulation

⚙️ Methods & tools

All typing annotations in ECLIPSE are produced by EcoliTyper — a species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. EcoliTyper wraps the following community-standard tools:

• MLST — Multi-locus sequence typing of 7 housekeeping genes (Achtman scheme) mlst (Seemann) + PubMLST
• Phylogroup — Clermont classification (A, B1, B2, C, D, E, F, G) ClermonTyping
• Serotype — O:H serotyping from O-antigen and H-flagellar biosynthesis genes SerotypeFinder (CGE)
• CHTyper — fumC + fimH allele typing for rapid ST131 detection CHTyper
• AMR genes — Resistance determinant presence/absence AMRFinderPlus + ABRicate (CARD, ResFinder, ARG-ANNOT, MEGARes)
• Virulence factors — VFDB gene screening ABRicate + VFDB
• Plasmid replicons — Replicon typing PlasmidFinder (CGE)

The EcoliTyper pipeline is open source and available on GitHub. The ECLIPSE website generator code is available at github.com/bbeckley-hub/eclipse.

🔧 Downstream tools & pipelines

ECLIPSE provides the accession list and the typing context. The next step — phylogenetics, outbreak investigation, pangenome analysis — is done with the tools below. Each is a well-validated, open-source solution that complements ECLIPSE in a standard E. coli workflow.

🔬 Integrated pipelines

• EcoliTyper — The typing pipeline that powers ECLIPSE. Reusable independently on any E. coli assemblies. Python · Beckley
• Bactopia — Complete bacterial genome analysis pipeline. Accepts raw reads or assemblies. Nextflow
• Enterobase — Curated E. coli/Salmonella typing and phylogeny resource from Warwick. Web database
• Pathogenwatch — Rapid genomic surveillance and visual analytics for bacterial pathogens. Web · Sanger

🧬 Extended typing

• chewBBACA — cgMLST and wgMLST allele calling for higher-resolution outbreak tracing. Python · B-UMMI
• PopPUNK — Population-level clustering and lineage assignment. Python · Lees
• SerotypeFinder — The serotyping tool used by EcoliTyper (CGE). Standalone use supported. CGE · DTU
• ClermonTyping — The phylogroup tool used by EcoliTyper. Python · Beghain

🌳 Phylogenetics & recombination

• IQ-TREE 3 — Maximum-likelihood phylogenetics with model selection. C++ · Minh
• Gubbins — Removes recombination from whole-genome alignments before tree inference. Python · Croucher
• ClonalFrameML — Maps recombination events onto a clonal genealogy. C++ · Didelot
• Snippy — Rapid haplotypes and SNP calling against a reference. Perl · Seemann

💊 AMR & virulence confirmation

• AMRFinderPlus — NCBI's curated AMR gene and point-mutation detection. C++ · NCBI
• ABRicate — Mass screening against CARD, ResFinder, VFDB, PlasmidFinder, and others. Perl · Seemann
• CARD — Comprehensive Antibiotic Resistance Database. McMaster
• VFDB — Virulence Factor Database. Cao et al.

📊 Visualization

• Microreact — Interactive phylogeny + metadata visualization. Web · Sanger
• iTOL — Interactive Tree Of Life. Web · Letunic & Bork
• Phandango — Interactive visualization of bacterial phylogenies with metadata layers. JS · Hadfield

👥 The team

ECLIPSE 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.

📚 Citation

📬 Contact & contribute

Found a bug? Have a feature suggestion? Want to collaborate? We'd love to hear from you.

ECLIPSE is released under the MIT License. You are free to use, modify, and redistribute it. Attribution is appreciated.