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Comprehensive Multi-Database Resistance Gene Assessment

Date: December 1, 2025

Overview

Analyzed 5 E. coli genomes using three different resistance gene databases:

  • CARD (Comprehensive Antibiotic Resistance Database)
  • NCBI (National Center for Biotechnology Information)
  • ResFinder (DTU's resistance gene database)

Genomes Analyzed

  1. NZ_CP107120 / NZ_CP107120.1
  2. NZ_CP107134.1
  3. NZ_CP107164 / NZ_CP107164.1
  4. NZ_CP107178.1
  5. NZ_HG941718 / NZ_HG941718.1

📊 EXTRACTION SUMMARY

Total Proteins Extracted: 43

Database Proteins Extracted Output Directory
CARD 11 results_resistance_genes/
NCBI 16 results_ncbi/
ResFinder 16 results_resfinder/

🔬 GENES FOUND BY DATABASE

CARD Database (11 proteins)

Gene Type Genomes Description
CTX-M-15 ESBL 3 (CP107120, CP107134.1, CP107178.1) Ceftriaxone resistance
OXA-1 Beta-lactamase 3 (CP107120, CP107134.1, CP107178.1) Oxacillin resistance
CMY-59 AmpC 1 (HG941718) Cephalosporin resistance
AAC(6')-Ib-cr Aminoglycoside + Quinolone 3 (CP107120, CP107134.1, CP107178.1) Dual resistance
AAC(3)-IIe Aminoglycoside 1 (CP107120) Gentamicin resistance

NCBI Database (16 proteins)

Gene Type Genomes Description
blaCTX-M-15 ESBL 3 (CP107120.1, CP107134.1, CP107178.1) Ceftriaxone resistance
blaOXA-1 Beta-lactamase 3 (CP107120.1, CP107134.1, CP107178.1) Oxacillin resistance
blaCMY-23 AmpC 1 (HG941718.1) Cephalosporin resistance
blaEC-5 Chromosomal 5 (ALL genomes) Intrinsic E. coli AmpC
aac(6')-Ib-D181Y Aminoglycoside 3 (CP107120.1, CP107134.1, CP107178.1) Gentamicin/Tobramycin resistance
aac(3)-IIe Aminoglycoside 1 (CP107120.1) Gentamicin resistance

Key Finding: NCBI detected blaEC-5 (chromosomal AmpC) in ALL 5 genomes - this is an intrinsic resistance mechanism.

ResFinder Database (16 proteins)

Gene Type Genomes Description
blaCTX-M-15_1 ESBL 3 (CP107120.1, CP107134.1, CP107178.1) Ceftriaxone resistance
blaOXA-1_1 Beta-lactamase 3 (CP107120.1, CP107134.1, CP107178.1) Oxacillin resistance
blaCMY-23_1 AmpC 1 (HG941718.1) Cephalosporin resistance
aac(6')-Ib-cr_1 Aminoglycoside + Quinolone 3 (CP107120.1, CP107134.1, CP107178.1) Dual resistance
aac(3)-IIa_1 Aminoglycoside 1 (CP107120.1) Gentamicin resistance
mdf(A)_1 Efflux pump 5 (ALL genomes) Multidrug resistance

Key Finding: ResFinder detected mdf(A) efflux pump in ALL 5 genomes - chromosomal multidrug efflux.

🎯 RESISTANCE PROFILE BY GENOME

NZ_CP107120 / CP107120.1 ⚠️ HIGHLY RESISTANT

Beta-lactamases:

  • CTX-M-15 (ESBL) ✓
  • OXA-1 ✓
  • EC-5 (chromosomal) ✓

Aminoglycoside Resistance:

  • AAC(6')-Ib-cr (also quinolone resistance) ✓
  • AAC(3)-IIe / AAC(3)-IIa ✓

Efflux:

  • mdf(A) ✓

Resistance Profile: MDR (Multi-Drug Resistant) - ESBL-producing strain

NZ_CP107134.1 ⚠️ HIGHLY RESISTANT

Beta-lactamases:

  • CTX-M-15 (ESBL) ✓
  • OXA-1 ✓
  • EC-5 (chromosomal) ✓

Aminoglycoside Resistance:

  • AAC(6')-Ib-cr/D181Y ✓

Efflux:

  • mdf(A) ✓

Resistance Profile: MDR - ESBL-producing strain

NZ_CP107164 / CP107164.1 ✅ SUSCEPTIBLE

Beta-lactamases:

  • EC-5 (chromosomal only) ✓

Efflux:

  • mdf(A) ✓

Resistance Profile: Likely susceptible to most antibiotics (only intrinsic resistance)

NZ_CP107178.1 ⚠️ HIGHLY RESISTANT

Beta-lactamases:

  • CTX-M-15 (ESBL) ✓
  • OXA-1 ✓
  • EC-5 (chromosomal) ✓

Aminoglycoside Resistance:

  • AAC(6')-Ib-cr/D181Y ✓

Efflux:

  • mdf(A) ✓

Resistance Profile: MDR - ESBL-producing strain

NZ_HG941718 / HG941718.1 ⚠️ RESISTANT

Beta-lactamases:

  • CMY-23 (AmpC - different from CMY-59 in CARD) ✓
  • EC-5 (chromosomal) ✓

Efflux:

  • mdf(A) ✓

Resistance Profile: AmpC-producing strain (cephalosporin resistance)

❌ REQUESTED GENES NOT FOUND IN ANY DATABASE

Gene Type Status
blaTEM Penicillinase NOT FOUND ❌
blaNDM Carbapenemase (New Delhi Metallo) NOT FOUND ❌
blaKPC Carbapenemase (K. pneumoniae) NOT FOUND ❌
tet(A) Tetracycline efflux NOT FOUND ❌
mcr-1 Colistin/Polymyxin resistance NOT FOUND ❌
gyrA Quinolone target (chromosomal) NOT FOUND ❌
parC Quinolone target (chromosomal) NOT FOUND ❌

Why Are These Missing?

Carbapenemases (blaNDM, blaKPC)

  • These are carbapenem resistance genes typically found in highly resistant clinical isolates
  • Your genomes appear to be ESBL-producers but NOT carbapenem-resistant
  • These genes are rarer and associated with last-line antibiotic failure

blaTEM

  • One of the most common beta-lactamases globally
  • Absence suggests either:
    • These strains acquired different resistance mechanisms (CTX-M, OXA)
    • They are from regions/sources where TEM is less prevalent

tet(A) and mcr-1

  • tet(A): Tetracycline resistance - your strains may be tetracycline susceptible
  • mcr-1: Colistin resistance - critically important, absence is GOOD (colistin is a last-resort drug)

gyrA and parC

  • These are chromosomal genes present in ALL E. coli
  • Resistance databases focus on acquired resistance genes or known resistance mutations
  • Your strains likely have wild-type sequences without resistance-conferring mutations
  • To find these: Extract directly from genomes or use PointFinder for mutation detection

🔍 DATABASE COMPARISON

Overlap & Differences

Finding CARD NCBI ResFinder
CTX-M-15 ✓ ✓ ✓
OXA-1 ✓ ✓ ✓
CMY (AmpC) CMY-59 CMY-23 CMY-23
AAC(6')-Ib AAC(6')-Ib-cr aac(6')-Ib-D181Y aac(6')-Ib-cr_1
AAC(3) AAC(3)-IIe aac(3)-IIe aac(3)-IIa_1
Chromosomal AmpC ❌ blaEC-5 (5/5) ❌
Efflux pump ❌ ❌ mdf(A)_1 (5/5)

Key Insights

  1. CMY Discrepancy: CARD reports CMY-59, but NCBI/ResFinder report CMY-23 in NZ_HG941718

    • This could be:
      • Different variant assignments by databases
      • Sequencing/annotation differences
      • Worth investigating which is correct

  2. AAC(6')-Ib Variants:

    • CARD: AAC(6')-Ib-cr (emphasizes quinolone resistance)
    • NCBI: aac(6')-Ib-D181Y (emphasizes mutation)
    • ResFinder: aac(6')-Ib-cr_1 (matches CARD)
    • Same gene, different naming conventions

  3. NCBI Advantage: Detects chromosomal blaEC-5 (intrinsic AmpC)

  4. ResFinder Advantage: Detects mdf(A) efflux pump (intrinsic resistance)

  5. CARD Advantage: Most consistent naming, clinical focus

📂 OUTPUT LOCATIONS

results_resistance_genes/    - CARD database extractions (11 files)
results_ncbi/                 - NCBI database extractions (16 files)
results_resfinder/            - ResFinder database extractions (16 files)
results_5genomes/             - Efflux pumps and regulators (20 files)

Total: 63 protein sequence files

🎯 CLINICAL SIGNIFICANCE

High-Risk Strains (3/5)

  • NZ_CP107120, NZ_CP107134.1, NZ_CP107178.1
  • ESBL-producing (CTX-M-15)
  • Multi-drug resistant
  • Expected resistance:
    • ✓ 3rd-generation cephalosporins (Ceftriaxone, Cefotaxime)
    • ✓ Penicillins
    • ✓ Aminoglycosides (Gentamicin, Tobramycin)
    • ✓ Potentially fluoroquinolones (via AAC(6')-Ib-cr)
    • ❌ Carbapenems (likely still effective)
    • ❌ Colistin (likely still effective)

Moderate-Risk Strain (1/5)

  • NZ_HG941718
  • AmpC-producing (CMY-23)
  • Expected resistance:
    • ✓ Cephalosporins
    • ✓ Penicillins
    • ❌ Carbapenems (likely still effective)

Low-Risk Strain (1/5)

  • NZ_CP107164
  • Only intrinsic resistance
  • Likely susceptible to most antibiotics

💡 RECOMMENDATIONS

For Missing Genes:

  1. To find gyrA/parC mutations:

    • Use PointFinder or similar mutation detection tools
    • Extract genes directly from assemblies and sequence specific codons
    • Check positions: gyrA S83L/D87N, parC S80I

  2. To find carbapenemases (blaNDM, blaKPC):

    • Analyze different clinical isolates (ICU, bloodstream infections)
    • Look for strains from high-prevalence regions (India for NDM)
    • These genomes appear to be pre-carbapenem era or non-carbapenem-resistant

  3. To find blaTEM:

    • Analyze older clinical isolates or hospital strains
    • Very common globally, absence is unusual for clinical MDR strains

  4. For tetracycline and colistin resistance:

    • Current strains likely susceptible
    • Colistin susceptibility is clinically beneficial (last-resort drug)

For Further Analysis:

  1. Resolve CMY variant discrepancy (CMY-23 vs CMY-59)
  2. Phenotypic testing to confirm predicted resistance profiles
  3. Plasmid analysis to understand horizontal gene transfer potential
  4. Efflux pump expression studies for marA, acrAB-tolC complex

✅ CONCLUSION

  • Successfully extracted 43 resistance genes from 5 E. coli genomes across 3 databases
  • 3/5 genomes are ESBL-producers with multi-drug resistance (CTX-M-15)
  • 1/5 genome is AmpC-producer (CMY-23)
  • 1/5 genome is susceptible (only intrinsic resistance)
  • Carbapenemases NOT detected - good news for treatment options
  • mcr-1 NOT detected - colistin remains a viable last-resort option
  • Chromosomal quinolone resistance genes (gyrA/parC) require different analysis approach

These genomes represent ESBL-producing hospital-associated E. coli strains with multi-drug resistance but preserved carbapenem and colistin susceptibility.