StaphScope: A species-optimized computational pipeline for rapid and accessible Staphylococcus aureus genotyping and surveillance

🦠 StaphScope v1.2.2 – The "ESKAPE from Boring Reports" Edition

Now with 22,638 reasons to love spa typing

Release date: 2026-05-09
Lead developer: Beckley Brown (with caffeine, sarcasm, and a growing hatred for messy tables)
Affiliation: University of Ghana Medical School – where we put the "bio" in "bioinformatics".

"If your MRSA report doesn't make you laugh, you're not using StaphScope right."

🎉 What's New in v1.2.2

We listened to your feedback, read your angry emails, and drank enough coffee to power a small genome assembler. The result? A massive update that turns StaphScope into the Swiss Army knife of S. aureus genomics – with more scrollable lists, colourful citations, and enough filter buttons to make your mouse beg for mercy.

📑 1. Tab‑ocalypse – Reorganised & Renamed

"Where did the 'plasmid' tab go?" – No more confusion.

The tab order now follows the AcinetoScope gospel (because why reinvent the wheel?):

1. Summary
2. Sample Overview
3. FASTA QC
4. MLST
5. spa typing
6. SCCmec
7. MRSA Analysis
8. AMR
9. Virulence
10. BACMET (Biocides & heavy metals – new!)
11. Plasmids
12. Pattern Discovery
13. AI Guide
14. Citation (new – with colours!)
15. Call to Action (new – shameless self‑promotion)
16. Export

No more hunting for your favourite feature. Everything is exactly where you'd expect it – unless you're chaos‑aligned, in which case you can still click randomly.

🧬 2. Gene‑Centric Tables with Scrollable Genome Lists

"I can finally see all 500 samples without zooming out to 10%."

• Each AMR, virulence, and BACMET gene now shows all genomes that carry it – inside a vertically scrollable box (max height 200px).
• No truncation, no horizontal scrolling nightmare. Just clean, wrapped genome tags that you can scan, search, and highlight.
• Works everywhere: AMR tab, Virulence tab, BACMET tab, and – wait for it – all combination tables (ST‑spa, ST‑SCCmec, MRSA combos, triple typing). We finally fixed the "endless comma‑separated string of doom".

🔗 3. Triple Typing Combination (MLST – spa – SCCmec)

"Three is the magic number."

• Want to see which ST‑spa‑SCCmec triplets dominate your collection? Now you can.
• Find it in the Pattern Discovery tab. Each triplet comes with a list of samples (scrollable, of course).
• Perfect for outbreak detectives and clone‑hunters.

🧪 4. BACMET Tab – Biocides & Heavy Metal Resistance

"Because disinfectants and heavy metals are also part of the AMR story."

• BACMET2 genes (qac, mer, ars, cop, sil, etc.) finally get their own shining tab.
• Understand how hospital disinfectants and heavy metals co‑select antibiotic resistance.
• 25+ filter buttons to zoom into quaternary ammonium, mercury, arsenic, copper, chromate, cadmium, zinc – you name it.
• If you don't have BACMET data, we'll politely tell you to go run ABRicate with the bacmet2 database. No hard feelings.

🎨 5. Citation Tab – Now in Technicolor

"My BibTeX never looked so good."

• Each citation (StaphScope, MLST, ABRicate, AMRFinderPlus, SCCmecFinder, spa typing, CARD, ResFinder, VFDB, PlasmidFinder, MEGARes) lives in its own colour‑coded card.
• Hover effects, larger fonts, and a "Suggested acknowledgement" block – because we know you love copy‑pasting.
• Proper BibTeX for every tool. Your thesis's reference section will thank you.
• Updated spa‑type database stats (as of May 2026):
  • 22,638 unique spa types
  • 863 repeat sequences
  • 472,120 total strains
  • 181 countries with strains
  • 961 registered users from 81 countries

🚀 6. Call to Action Tab – ESKAPE Lineup & Shameless Plugs

"One bug report is never enough."

• Meet the ESKAPE rogues' gallery – now spelled correctly:
  • EnteroMark (Enterococcus faecium)
  • StaphScope (you are here)
  • Kleboscope (Klebsiella pneumoniae)
  • Acinetoscope (A. baumannii)
  • Pseudoscope (Pseudomonas aeruginosa)
  • Enteroscope (Enterobacter cloacae)
• Plus EcoliTyper for E. coli (because even non‑ESKAPE bugs deserve love).
• Humorous descriptions, GitHub stars begging, and a call to collaborate. We put the "fun" in "fungus".

🔘 7. Filter Buttons – More Than You'll Ever Need

"We added a button for that."

AMR tab:
mecA, mecC, vanA, vanB, erm, msrA, mphC, tet, aac, aph, ant, dfr, cat, bla, pco – and a clear search button because we're nice.

Virulence tab:
PVL, TSST‑1, enterotoxins, capsule, iron acquisition, ESAT‑6 secretion, SET exotoxins, hemolysins, immune evasion (SCIN, Eap), biofilm (ica), serine protease, adenosine synthase, hyaluronidase, adhesins – 20+ buttons to satisfy your inner click‑aholic.

BACMET tab:
qac, qacEdelta1, cep, form, mer, ars, arsT, cop, sil, chr, cad, znt, czc, pbr, nik, cor, soxR, cpxR, baeR, emr, sme, norA – plus export and clear. Your fingers will get a workout.

📊 8. Database Summary Cards

• After each gene table (AMR, Virulence, BACMET), you'll see a summary of unique genes and total occurrences per database, plus the top three genes.
• Great for quick "what's hot" insights without scrolling through the whole table.

🧠 9. AI Guide – Smarter Questions

"ChatGPT, what does this 200‑row HTML mean?"

• Example questions you can ask any AI after uploading the JSON or HTML.
• How many samples carry mecA? Which ST‑spa combos dominate? Show me triple typing with >2 isolates.
• We've done the hard work; now let the AI impress you.

🐛 10. Bug Fixes & Performance

• Combination tables (ST‑spa, ST‑SCCmec, MRSA combos, triple typing) now display sample lists as scrollable, wrapped genome tags – no more broken layouts.
• Fixed duplicate method definitions (yes, we had two _generate_amr_section – whoops).
• Genome highlight search works across all tables.
• CSS improvements for mobile (sort of – we tried).
• JSON export now handles sets and defaultdicts without crying.

🧬 11. Lineage Database Expansion

We've added several new clonal complexes and novel sequence types to the built‑in lineage database, making StaphScope even more accurate for epidemiological assignments:

| New Entry | Type | Notes | |-----------|------|-------| | CC49 | Wildlife‑associated | Europe (wild boar, deer) | | CC188 | Rare healthcare | Sporadic MRSA/MSSA | | CC599 | Wildlife‑associated | Europe (MSSA predominant) | | CC692 | Wildlife/environmental | North America | | CC707 | Australian CA‑MRSA | PVL‑positive, related to CC93 | | ST2425, ST2691, ST2963 | Novel STs | Wildlife isolates (Germany, Poland) |

Special thanks to users who contributed to database curation!

📦 Full Changelog (for the nerds)

| Area | Change | |------|--------| | Tabs | Reordered, renamed "Samples" → "Sample Overview", added BACMET, Citation, Call to Action | | Genome lists | Scrollable (max-height:200px, flex-wrap) in all gene and combination tables | | Triple typing | ST‑spa‑SCCmec table under Pattern Discovery | | BACMET | New tab with 25+ filter buttons and detailed info | | Citation tab | Coloured cards with BibTeX for 12+ tools; updated Ridom spa stats | | Call to Action | ESKAPE lineage with humour and GitHub links | | Filter buttons | Expanded to >20 in AMR, >20 in Virulence, >25 in BACMET | | Info boxes | Detailed biology/mechanism for AMR, Virulence, BACMET | | Database summary | Shows unique genes and top genes per database | | Lineage database | Added CC49, CC188, CC599, CC692, CC707, ST2425, ST2691, ST2963 | | spa typing section | Displays current Ridom database statistics (22,638 types, 472k strains, etc.) | | Bug fixes | Combination table sample lists now scrollable; duplicate methods removed; CSS fixes |

⚠️ Upgrading from v1.2.1

• Backup your old staphscope_ultimate_report.html – just in case.
• Replace staphscope_ultimate_reporter.py with the new version.
• Run against the same input directory – the output will be much prettier.
• If you see any issues, clear your browser cache (the CSS changed a lot).
• For those using the lineage database, we've added new entries – update your copy accordingly.

🙏 Acknowledgements & Credits

• Torsten Seemann – for MLST, ABRicate, and generally being a legend.
• Robert Petit (that's puh‑teet, not pet‑it – we had to Google it, don't judge) – for Bactopia, the workflow that inspires us to be better bioinformaticians (while also reminding us how far we have to go). We watch his tutorials on the low, take notes, and dream of one day being half as organised. Robert, if you're reading this: you're a legend, and we're big fans.
• NCBI AMRFinderPlus team – for the most comprehensive resistance gene database.
• CGE (SCCmecFinder, ResFinder, PlasmidFinder) – for keeping us honest.
• VFDB, CARD, MEGARes – for the data that makes our reports useful.
• Ridom (spa.ridom.de) – for maintaining the amazing spa‑type database (22,638 types and counting).
• University of Ghana Medical School – for letting us spend work time on this (don't tell the Dean).
• Coffee, tears, and late nights – the real MVPs.

🍺 Call to Action (yes, again)

If StaphScope saved you even one hour of manual curation, please:

• ⭐ Star the GitHub repo – it helps us stay motivated (and caffeinated).
• 🐛 Report bugs – we promise to laugh, then fix them.
• 🔬 Check out our other ESKAPE tools – because one bug report is never enough.
• 📧 Email brownbeckley94@gmail.com if you want to collaborate or just say hi.

Together we can beat AMR – one genome at a time.

– Brown
🦠🧬💻

If you use this software, please cite it as below.