bbeckley-hub/EcoliTyper: ECOLITYPER v1.2.0

🧬 ECOLITYPER v1.2.0 – The "We Finally Made It Work (Mostly)" Release (FULL EDITION)

Because a year of debugging, crying over BLAST paths, discovering that *Shigella is just E. coli with an attitude problem, and building an HTML report so detailed it could be a thesis on its own deserves a proper write‑up.*

👨‍💻 The "Who Did This to Themselves?" Credits

• Brown Beckley – Lead developer, chief coffee drinker, and the person who single‑handedly convinced his laptop that running 10 HTML parsers in parallel is "fine".
• Kevin Blake, PhD – For the brilliant PathotypeR logic that we shamelessly ported from R to Python (while keeping the original bugs, but adding new ones of our own).
• The entire E. coli species complex – For being so wonderfully diverse that we needed 27 lineages, 18 serotypes, and 4 hybrid pathotypes just to keep track. You're welcome.

🚀 What's New in This Release? (Spoiler: More Things to Keep You Up at Night)

🔬 Species Confirmation – Because "It Looks Like E. coli" Isn't Good Enough Anymore

We finally added a fastANI‑based species check that compares your assembly against a set of reference genomes (E. coli, Shigella, Klebsiella, Salmonella).

• If it matches E. coli or Shigella with ≥95% ANI → ✅ "E. coli confirmed".
• If it matches Klebsiella with 98% ANI → ❌ "Whoops, that's not our bug".
• If it matches both E. coli and Shigella equally well → 🤷 "Contamination? Or just the usual E. coli identity crisis?"

And yes, we **treat Shigella as E. coli*** because after reading the genomic literature, we realised the only real difference is that *Shigella is E. coli with a PhD in dysentery.

🧬 EcoliLineageDB v2.0 – The "We Found More Nightmares" Update

Remember when we thought ST131 was the only monster under the bed? Cute.

We've added 6 new lineages that have been quietly plotting world domination while you were sleeping:

| ST | Nickname | Why You Should Care (Or Not) | |----|----------|-------------------------------| | ST361 | The Wetland Wanderer | NDM‑5 carrying menace that hangs out in wetlands like it's on vacation, then hops into humans like "surprise, I brought carbapenem resistance!" First identified in 2018, already going global. Because of course it is. | | ST101 | The Turkey Terror | Your Thanksgiving dinner called. It wants its colibacillosis back. This APEC clone has been decimating poultry populations while occasionally reminding humans we're not as special as we think. | | ST38 | Fido's Revenge | Found in dogs, meat products, and apparently your worst nightmares. ESBL‑producing, carbapenemase‑carrying, and living rent‑free in companion animals. Who's a good boy? Not this ST. | | ST141 | The Austrian Import | Emerging ESBL lineage that started in Viennese dogs and thought "hey, humans look like fun." Because zoonosis is just nature's way of keeping us humble. | | ST224 | The Livestock Loiterer | ESBL/MDR clone that treats cows and sheep like a timeshare. Eventually ends up in humans via the food chain. It's not delivery, it's diarrhoea with resistance. | | ST602 | The Mink Menace | First‑ever report of NDM‑5 in farmed minks. Because apparently minks weren't controversial enough already. Plasmid‑mediated – because sharing is caring (unless you're sharing carbapenemase genes). |

🧫 New Serotypes (Because O157:H7 Was Getting Lonely)

| Serotype | What It Does | HUS Risk Level | |----------|--------------|----------------| | O77g:H18 | Caused an HUS outbreak in France from unpasteurised cheese. Yes, cheese. The French finally have something worse than bad wine pairings. | HIGH | | O177:H11 / H25 | Emerging in Italian cattle at slaughter. Because what Italy needed besides COVID, economic crisis, and political drama was another STEC serotype. | MODERATE | | O80:H2 | Hybrid STEC/EPEC causing severe disease in humans AND calves. Efficiency! Why specialise in one pathotype when you can suck at two? | VERY HIGH |

🔄 New Hybrid Pathotypes (Because Monogamy is for Suckers)

We've added 4 hybrid pathotypes that refuse to pick a lane:

• UPEC/EAEC – For when you want a UTI that also makes you question your life choices via diarrhoea.
• aEPEC/ExPEC – Starts in the gut, ends in the bloodstream. It's the scenic route to sepsis!
• STEC/ETEC – Traveller's diarrhoea meets HUS. Your vacation is cancelled. Permanently.
• STEC/EAEC – The O104:H4 special. High HUS rate, adult predilection, and the audacity to exist.

💊 Carbapenemase Updates (Because You Weren't Anxious Enough)

• OXA‑1207 – A new OXA‑48‑like variant discovered in Germany. Because we needed another enzyme that makes carbapenems useless.
• ST602‑NDM‑5 – First report from farmed minks. Yes, minks. What's next, NDM‑5 in hamsters?

🌍 Geographical Shade Throwing

• Ghana confirmed in multiple STs (ST131, ST410, ST648, ST167) – We've found it in humans, livestock, AND environment. The One Health trifecta! 🏆
• ST167 specifically – Isolated from EVERYTHING in Ghana. At this point, ST167 is more Ghanaian than jollof rice.

🖥️ GENIUS E. coli Ultimate Reporter – The "Look Ma, No Excel" Revolution

While the backend modules were busy identifying resistance genes and typing strains, we built a front‑end monster that turns all that data into an interactive HTML report so beautiful it almost makes AMR fun. Here's what we added:

🎨 ASCII Art in Every Module

Yes, every HTML report (FASTA QC, MLST, Serotype, CHTyper, Phylogrouping, AMRfinder, ABRicate, and the Ultimate Reporter) now displays the ECOLITYPER ASCII banner in glowing green. Because science should look like a hacker movie from 1995.

🧬 Pathotype Classification – Finally, a Use for All Those Virulence Genes

We integrated PathotypeR logic directly into the reporter. Now you can see at a glance whether your sample is STEC, EPEC, EHEC, EAEC, ETEC, DAEC, EIEC, or a terrifying hybrid. The sample overview table now includes a Pathotype column with a link back to Kevin Blake's GitHub. Credit where credit is due (even if we did port it from R 😬).

📊 Reordered Tabs – Because Nobody Wants to Scroll Forever

We rearranged the tab order from "random chaos" to a logical flow:

1. Summary
2. Sample Overview (now with species QC columns)
3. FASTA QC
4. MLST
5. Serotype
6. CH Type
7. Phylogroup
8. Pathotype Analysis (new!)
9. AMR
10. Virulence
11. Plasmid & Serotyping Markers (formerly just "Plasmids" – now includes EcoH)
12. Bacmet (biocide & heavy metal resistance)
13. Patterns
14. Database Metrics
15. AI Guide
16. Call to Action (yes, we're begging for GitHub stars)
17. Export

🔍 Genome Highlight Search Bars

In the AMR, Virulence, Plasmid, and Bacmet tabs, you now get two search boxes:

• One to filter rows by gene name (e.g., "blaCTX-M")
• One to highlight genome tags – type a sample name and all matching genome tags light up yellow. No more squinting at long lists of isolates.

🧪 Comprehensive Filter Buttons

• AMR tab: Filter by ESBL (CTX‑M, SHV, TEM), carbapenemases (KPC, NDM, OXA, VIM, IMP), colistin (mcr), quinolone (qnr), aminoglycoside (aac, aph, ant), etc.
• Virulence tab: Filter by Shiga toxins, intimin, CNF1, hemolysin, colibactin, and many more.
• Bacmet tab: Filter by biocides, heavy metals (mercury, arsenic, copper, silver, etc.), stress regulators, efflux pumps.
• Plasmid tab: Filter by IncF, IncI, Col, O‑serotype markers, H‑serotype markers.

All buttons are colour‑coded (because we care about your visual cortex).

📚 Educational Descriptions for Every Tab

Each tab now includes a detailed explanation of why the data matters, what the key genes do, and how to interpret the results. We even added tooltips on gene names – hover over blaCTX-M and a pop‑up tells you it's an ESBL that breaks ceftriaxone. Because memorising 200 gene functions is hard.

🤖 AI Guide – Ethically Use Large Language Models to Write Your Paper

We added a whole section that teaches you how to upload your JSON data to ChatGPT, Claude, or Gemini and ask it to draft your manuscript, thesis, or public health report – with ethical guardrails. Includes example prompts, a step‑by‑step workflow, and a warning about AI hallucinations (Galileo did not discover IncF plasmids).

🌍 Call to Action – "Star Us or We'll Send ST167 to Your Lab"

A beautiful, inspiring, slightly guilt‑tripping section that explains the ESCAPE AMR project (formerly ESKAPE), breaks down the acronym into a global call to action, and begs you to ⭐ the GitHub repo. We even added a pun about escaping the AMR crisis. You're welcome.

📁 Separate CSV Exports for Everything

You can now export:

• Sample overview (with species and pathotype)
• AMR genes (gene‑centric)
• Virulence genes (gene‑centric)
• Plasmid & serotyping markers
• Bacmet genes
• Pathotype sample details

All via one‑click buttons in the Export tab.

🧩 Integration of Species QC into Sample Overview

The FASTA QC module now writes FASTA_QC_summary.tsv with columns: Best Species, ANI (%), E. coli / Shigella Confirmed, Contamination Suspected. The Ultimate Reporter parses that TSV and adds those four columns to the Sample Overview table. No more switching between reports to figure out if a sample is really E. coli.

📊 Database Statistics (The "Before You Ask" Section)

| Item | Before | After | Change | |------|--------|-------|--------| | Lineages | 21 | 27 | +6 (growth mindset) | | Serotypes | 14 | 18 | +4 (variety is the spice of… HUS) | | Phylogroups | 8 | 8 | (still 8, physics hasn't changed) | | Pathotypes | 16 | 20 | +4 hybrids (commitment issues) | | Carbapenemase STs | now includes ST602 (mink edition) | | | | HTML tabs | 12 | 17 | +5 (more clicking, more fun) | | Filter buttons | 12 | >100 | we lost count, honestly |

🧪 Performance Improvements (The "We Didn't Break It, We Made It Faster")

• Concurrent processing in ABRicate, AMRfinder, CHTyper, Phylogrouping, and SerotypeFinder – uses all available CPU cores (or as many as you allow).
• MAXIMUM SPEED MODE – automatically detects RAM and cores and goes brrrr.
• Parallel parsing of HTML reports – because waiting for 50 samples to load one by one is so 2024.

🙏 Acknowledgments (The Extended Cut)

• To the French for reminding us that cheese can kill (O77g:H18 outbreak).
• To Italian cattle for their dedication to emerging serotypes.
• To Ghanaian researchers for proving ST167 is everywhere.
• To the minks… just… the minks.
• To Kevin Blake for the original PathotypeR logic that saved us from reinventing the wheel (we only bent it a little).
• To the developers of fastANI, ABRicate, AMRfinderPlus, ezClermont, CHTyper, SerotypeFinder, MLST, and BioPython – we stand on the shoulders of giants (and occasionally step on their toes).
• To every user who opened a GitHub issue instead of rage‑quitting – you are the real MVPs.

📧 Contact & Support

Brown Beckley – brownbeckley94@gmail.com
University of Ghana Medical School – Department of Medical Biochemistry

If you find a bug, it's probably not a bug, it's just E. coli being E. coli.

🚨 DISCLAIMER

This database and pipeline are for educational and research purposes only. If you use it to diagnose your own UTI, that's between you and your urologist. The author is not responsible for any anxiety, insomnia, or sudden urge to autoclave everything you own.

Last updated: 2026‑05‑15 (or whenever the next superbug emerges, whichever comes first)

⭐ If this pipeline saved you from publishing wrong ST assignments, consider starring it on GitHub. Your PI will never know you copied the references.

Now go forth and type those E. coli genomes – and may your N50 be high and your contamination be low! 🧬💥