Supported organisms

Supported pathogen library

Current identification panel, continuously updated. All organisms below are identified from Oxford Nanopore flow cell output data using our adaptive basecalling pipeline.

GRAM+
Staphylococcus aureus
MRSA variant; HAI priority
GRAM+
Streptococcus pneumoniae
Community-acquired pneumonia
GRAM+
Enterococcus faecalis
VRE variant detection
GRAM+
Enterococcus faecium
VRE; hospital-acquired
ANAEROBE
Clostridioides difficile
Toxin gene tcdA/tcdB detection
GRAM+
Listeria monocytogenes
Foodborne / immunocompromised
GRAM−
Klebsiella pneumoniae
KPC + NDM AMR; HAI priority
GRAM−
Acinetobacter baumannii
CRAB; HAI priority pathogen
GRAM−
Pseudomonas aeruginosa
MDR detection
GRAM−
Escherichia coli
ESBL; pathotype typing
GRAM−
Klebsiella oxytoca
AMR gene screen
GRAM−
Enterobacter cloacae
AmpC beta-lactamase
GRAM−
Serratia marcescens
HAI; carbapenem screening
GRAM−
Salmonella spp.
Serovars; AMR profiling
GRAM−
Haemophilus influenzae
Respiratory; type-b detection
GRAM−
Neisseria meningitidis
Serogroup typing
GRAM−
Moraxella catarrhalis
Respiratory; beta-lactamase
AFB
Mycobacterium tuberculosis
rpoB / drug-resistance markers
GRAM+
Streptococcus pyogenes
Group A Strep; emm typing
GRAM−
Stenotrophomonas maltophilia
Immunocompromised host

Panel continuously updated. Contact us for full organism list and validation documentation.

YEAST
Candida auris
Multidrug-resistant; HAI priority
YEAST
Candida albicans
FKS1/2 echinocandin resistance
YEAST
Candida glabrata
Azole / echinocandin screening
MOLD
Aspergillus fumigatus
cyp51A azole resistance
YEAST
Cryptococcus neoformans
Immunocompromised; serotype
RESPIRATORY
Influenza A
Subtype H1/H3; antiviral resistance
RESPIRATORY
Influenza B
Lineage typing; NAI resistance
RESPIRATORY
RSV A/B
Subgroup A and B
RESPIRATORY
SARS-CoV-2
Variant tracking; key mutations
GI
Norovirus GI/GII
Outbreak investigation
RESPIRATORY
Human Metapneumovirus
Pediatric respiratory
Gene Resistance mechanism Relevant organism(s) Clinical note
mecAPBP2a beta-lactam resistanceS. aureus (MRSA)MRSA confirmation
mecCAlternate PBP2a variantS. aureus, coagulase-neg. staphmecA-negative MRSA
blaKPCKlebsiella pneumoniae carbapenemaseK. pneumoniae, E. coli, EnterobacterCRE screen; meropenem resistance
blaNDMNew Delhi metallo-beta-lactamaseK. pneumoniae, A. baumannii, E. coliPan-carbapenem resistance
blaOXA-48OXA-type carbapenemaseK. pneumoniae, EnterobacteralesLow-level carbapenem resistance
blaVIMVerona imipenem-resistant MBLP. aeruginosa, EnterobacteralesCarbapenem resistance
blaSHVSHV beta-lactamase familyK. pneumoniae, E. coliESBL and non-ESBL variants
blaCTX-MCTX-M ESBLE. coli, K. pneumoniaeCommunity + HAI ESBL
vanAD-Ala-D-Lac vancomycin resistanceEnterococcus faecium, E. faecalisVRE high-level resistance
vanBInducible vancomycin resistanceEnterococcus spp.VRE intermediate resistance
mcr-1Plasmid-mediated colistin resistanceE. coli, K. pneumoniaeLast-resort antibiotic resistance
tetMRibosomal protection tetracycline resistanceMultiple speciesTetracycline / doxycycline resistance
aac(6')-IbAminoglycoside acetyltransferaseGram-negativeAmikacin / tobramycin resistance
qnrBQuinolone resistance proteinEnterobacteralesFluoroquinolone resistance
rpoB (variants)RNA polymerase beta-subunitM. tuberculosisRifampicin resistance
inhAEnoyl-ACP reductaseM. tuberculosisIsoniazid resistance
FKS1 hotspots1,3-beta-D-glucan synthaseCandida spp.Echinocandin resistance
cyp51ALanosterol 14-alpha-demethylaseA. fumigatusAzole resistance

AMR validation data available under NDA to qualified laboratory partners. Internal validation data, not published sensitivity/specificity.

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