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k-mer profiling • AMR detection • virulence markers • MLST typing • plasmid replicons

Methodology
24+
AMR Genes
30+
Virulence Factors
8
ESKAPE+ Species
ANALYSIS MODULES

Comprehensive Characterization

Real bioinformatics, not simulations. Every result is traceable to validated methods and citations.

Organism ID

K-mer compositional profiling + GC/size matching. 8 ESKAPE+ Tier 1 priority pathogens.

Assembly Quality

N50/L50/N90, GC analysis, ORF prediction, quality scoring per QUAST standards.

AMR Detection

24+ resistance gene markers. Beta-lactamases, MRSA, VRE, carbapenemases, colistin resistance.

Virulence Factors

30+ virulence markers. Toxins, adhesins, invasion factors, immune evasion, biofilm genes.

MLST Typing

7 MLST schemes with 40+ known STs. Epidemiological context for each clone.

Plasmid Replicons

15+ replicon types. Conjugation assessment, transfer risk, associated resistance.

TARGET DATABASE

Tier 1 Priority Pathogens

WHO priority + ESKAPE pathogens — covering ~80% of hospital-acquired infections

8 Tier 1 Priority Bacterial Pathogens - scientific illustration

E. coli

Escherichia coli

UTI, Sepsis, ESBL

K. pneumoniae

Klebsiella pneumoniae

CRE, hvKp

S. aureus

Staphylococcus aureus

MRSA

P. aeruginosa

Pseudomonas aeruginosa

MDR, CF

A. baumannii

Acinetobacter baumannii

XDR, ICU

E. faecium

Enterococcus faecium

VRE

S. enterica

Salmonella enterica

Typhoid, iNTS

M. tuberculosis

Mycobacterium tuberculosis

MDR-TB, XDR-TB

PATHOGEN ATLAS

Meet the Pathogens

Detailed profiles of each Tier 1 priority pathogen in our detection database

Escherichia coli scientific illustrationGram-negativeWHO Critical
Escherichia coli
Rod-shaped (bacillus), 1–3 µm, flagellated, facultative anaerobe
FlagellatedFacultative anaerobeLactose fermenterESBL-producing
50.6%
GC Content
~5.1 Mb
Genome Size
49–52%
GC Range
Clinical Significance

Leading cause of urinary tract infections (UTIs), neonatal meningitis, and Gram-negative bacteremia. Pathogenic strains include UPEC, ETEC, EHEC (O157:H7), EPEC, and EIEC. Extended-spectrum β-lactamase (ESBL) producing strains are a critical global AMR threat.

Show taxonomy & resistance details
Klebsiella pneumoniae scientific illustrationGram-negativeWHO Critical
Klebsiella pneumoniae
Encapsulated rod, 0.3–1 × 0.6–6 µm, non-motile, facultative anaerobe
Thick capsuleNon-motileMucoid coloniesCRE threat
57.2%
GC Content
~5.5 Mb
Genome Size
56–58.5%
GC Range
Clinical Significance

Major cause of hospital-acquired pneumonia, UTIs, bloodstream infections, and liver abscesses (hypervirulent strains). Carbapenem-resistant K. pneumoniae (CRKP) is one of the most urgent AMR threats worldwide, with mortality rates exceeding 50% in some settings.

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Staphylococcus aureus scientific illustrationGram-positiveWHO High
Staphylococcus aureus
Cocci in grape-like clusters, 0.5–1.5 µm, non-motile, facultative anaerobe
Golden pigmentCoagulase-positiveBiofilm formerMRSA crisis
32.8%
GC Content
~2.87 Mb
Genome Size
32–34%
GC Range
Clinical Significance

Causes a wide spectrum from skin/soft-tissue infections to life-threatening endocarditis, osteomyelitis, pneumonia, and sepsis. Methicillin-resistant S. aureus (MRSA) is a global health crisis affecting both hospital (HA-MRSA) and community (CA-MRSA) settings.

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Pseudomonas aeruginosa scientific illustrationGram-negativeWHO Critical
Pseudomonas aeruginosa
Motile rod, 0.5–0.8 × 1.5–3 µm, polar flagellum, obligate aerobe, oxidase-positive
Pyocyanin producerIntrinsic MDRBiofilm championOxidase-positive
66.2%
GC Content
~6.3 Mb
Genome Size
65–67.5%
GC Range
Clinical Significance

Major opportunistic pathogen in cystic fibrosis, severe burns, ICU infections, and ventilator-associated pneumonia. Notable for intrinsic multi-drug resistance due to efflux pumps and low outer membrane permeability. Carbapenem-resistant strains are a critical WHO priority.

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Acinetobacter baumannii scientific illustrationGram-negativeWHO Critical
Acinetobacter baumannii
Coccobacillus, 1–1.5 × 1.5–2.5 µm, non-motile, strictly aerobic, oxidase-negative
Surface survivalNon-motileDesiccation resistantPan-drug resistant
39.3%
GC Content
~3.95 Mb
Genome Size
38.5–40.5%
GC Range
Clinical Significance

The quintessential nosocomial "superbug". Survives weeks on hospital surfaces. Causes ventilator-associated pneumonia, wound infections, and bloodstream infections in ICU patients. Pan-drug resistant (PDR) strains are increasingly reported, leaving few or no treatment options.

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Enterococcus faecium scientific illustrationGram-positiveWHO High
Enterococcus faecium
Ovoid cocci in pairs/short chains, 0.6–2.5 µm, non-motile, facultative anaerobe
Intrinsic resistantHardy survivorBiofilm formerVRE pathogen
38.2%
GC Content
~3.1 Mb
Genome Size
37.5–39.5%
GC Range
Clinical Significance

Leading cause of vancomycin-resistant enterococcal (VRE) hospital infections. Causes UTIs, endocarditis, intra-abdominal infections, and bloodstream infections. Intrinsically resistant to many antibiotics and readily acquires resistance genes via mobile genetic elements.

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Salmonella enterica scientific illustrationGram-negativeWHO High
Salmonella enterica
Motile rod, 0.7–1.5 × 2–5 µm, peritrichous flagella, facultative anaerobe
2,600+ serovarsIntracellularFood-borneTyphoidal strains
52.2%
GC Content
~4.85 Mb
Genome Size
51–53.5%
GC Range
Clinical Significance

Major food-borne pathogen. Non-typhoidal Salmonella (Typhimurium, Enteritidis) causes gastroenteritis; Typhi/Paratyphi cause typhoid/paratyphoid fever. Invasive non-typhoidal Salmonella (iNTS) causes ~680,000 deaths/year in sub-Saharan Africa. Fluoroquinolone-resistant strains are increasing.

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Mycobacterium tuberculosis scientific illustrationAcid-fastWHO Critical
Mycobacterium tuberculosis
Slender rod, 0.2–0.5 × 1–4 µm, acid-fast, obligate aerobe, very slow-growing (16–20h doubling)
Acid-fastSlow-growingMycolic acid wallMDR/XDR-TB
65.6%
GC Content
~4.41 Mb
Genome Size
65.2–65.8%
GC Range
Clinical Significance

The world’s deadliest bacterial pathogen, causing ~1.3 million deaths/year. Causes pulmonary and extrapulmonary tuberculosis. MDR-TB (resistant to isoniazid + rifampicin) and XDR-TB are major threats. Treatment requires 6–9 months of multi-drug therapy. Unique waxy mycolic acid cell wall.

Show taxonomy & resistance details
PEER-REVIEWED METHODS

Validated Methodology

Same principles as established bioinformatics tools used in clinical and research labs worldwide.

Organism Identification

Method: Compositional analysis: GC content + genome size + tetranucleotide frequency signatures + diagnostic markers

Karlin & Burge (1995) Trends Genet; Ondov et al. (2016) Genome Biol

AMR Gene Detection

Method: Conserved diagnostic marker subsequence search on forward and reverse complement strands

Alcock et al. (2023) CARD; Bortolaia et al. (2020) ResFinder; Feldgarden et al. (2019) AMRFinderPlus

Virulence Factor Detection

Method: Curated VF marker sequence matching with category-based pathogenicity scoring

Liu et al. (2022) VFDB; Joensen et al. (2014) VirulenceFinder

MLST Typing

Method: Conserved primer-region marker detection for MLST loci + allelic profile matching

Jolley et al. (2018) PubMLST; Seemann T — mlst tool

Plasmid Detection

Method: Replicon marker sequence identification on assembled contigs

Carattoli et al. (2014) PlasmidFinder; Robertson & Nash (2018) MOB-suite

Scientific Disclaimer

GenoVox provides computational predictions based on genomic markers. Results are for research purposes. Phenotypic antimicrobial susceptibility testing (AST) is essential for clinical decision-making.

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