Bacterial (gram-negative) 58 Acinetobacter baumannii Aeromonas spp. (bestiarum/caviae/dhakensis/hydrophila/media/popoffii/salmonicida/salmonicida subsp. masoucida/veronii) Anaplasma phagocytophilum Bacteroides fragilis Bordetella parapertussis Bordetella pertussis Bordetella spp. (pertussis/holmesii) Borrelia miyamotoi Borrelia spp. (burgdorferi/hermsii/johnsonii/miyamotoi/parkeri/theileri) Burkholderia cepacia Campylobacter spp. (coli/jejuni/fetus/lari/upsaliensis) Chlamydia trachomatis Chlamydophila pneumoniae Citrobacter spp. (freundii/braakii/koseri) Citrobacter spp. (freundii/koseri) Ehrlichia chaffeensis Ehrlichia ewingii Enterobacter cloacae Enterobacter cloacae/Klebsiella aerogenes Enterohemorrhagic Escherichia coli (EHEC) Enteroinvasive Escherichia coli (EIEC) Enteroinvasive Escherichia coli (EIEC)/Shigella spp. (flexneri/sonnei/dysenteriae) Escherichia coli Fusobacterium necrophorum Fusobacterium nucleatum Haemophilus ducreyi Haemophilus Influenzae Haemophilus influenzae type B Helicobacter pylori Klebsiella (Enterobacter) aerogenes Klebsiella oxytoca Klebsiella pneumoniae Klebsiella spp. (oxytoca/pneumoniae) Klebsiella spp.(aerogenes/oxytoca) Legionella pneumophila Megasphaera type I Megasphaera type II Megasphaera types I and II Moraxella catarrhalis Moraxella lacunata Morganella morganii Neisseria gonorrhoeae Plesiomonas shigelloides Prevotella bivia Proteus mirabilis Proteus spp. (mirabilis/vulgaris) Proteus vulgaris Providentia stuartii Pseudomonas aeruginosa Salmonella enterica serovar Typhimurium Salmonella spp. (typhi/paratyphi) Serratia marcescens Shigella spp. (flexneri/sonnei/dysenteriae) Stenotrophomonas maltophilia Treponema pallidum Vibrio spp. (vulnificus/cholerae) Vibrio vulnificus Yersinia enterocolitica
Resistance marker 35 Class A beta-lactamase resistance (blaKPC) Class A beta-lactamase resistance (blaSHV) Class A beta-lactamase resistance (blaSHV/blaTEM) Class A beta-lactamase resistance (blaTEM) Class A beta-lactamase resistance (cfxA) Class A beta-lactamase resistance (CTX-M-Grp1) Class B beta-lactamase resistance (blaIMP) Class B beta-lactamase resistance (blaIMP/blaVIM) Class B beta-lactamase resistance (blaNDM-1/blaNDM-4/blaNDM-5/blaNDM-7) Class B beta-lactamase resistance (blaVIM) Class C beta-lactamase resistance (ACT/MIR) Class C beta-lactamase resistance (FOX/ACC) Class D beta-lactamase resistance (OXA-48/OXA-51) Class D beta-lactamase resistance (OXA-85) Fluconazole resistance (ERG11) Fluoroquinolone resistance (aac(6')-Ib-cr) Fluoroquinolone resistance (gyrA) Fluoroquinolone resistance (qnrA/qnrB/qnrS) Macrolide lincosamide streptogramin B resistance (ermA/ermB/ermC) Macrolide lincosamide streptogramin B resistance (ermB/ermC) Macrolide resistance (mefA/mefE) Methicillin resistance (mecA) Metronidazole resistance (ntr4Tv/ntr6Tv) Nitrofurantoin resistance (nfsA/nfsB) Sulfonamide resistance (sul1) Sulfonamide resistance (sul1/sul2) Tetracycline resistance (tetB) Tetracycline resistance (tetB/tetM) Tetracycline resistance (tetM) Trimethoprim resistance (dfrA1) Vancomycin resistance (vanA) Vancomycin resistance (vanA/vanB) Vancomycin resistance (vanA/vanM) Vancomycin resistance (vanB) Vancomycin resistance (vanM)
Viral (ssRNA) 32 Enterovirus A71 (EV-A71) Enterovirus A71 and D68 Enterovirus A71 and D68/Human rhinovirus A, B, and C Enterovirus D68 (EV-D68) Hepatitis A virus Hepatitis C virus Human astrovirus types 1, 2, 3, 4, 5, 6, 7, and 8 Human coronavirus 229E Human coronavirus HKU1 Human coronavirus NL63 Human coronavirus OC43 Human immunodeficiency virus 1 (HIV-1) Human immunodeficiency virus 2 (HIV-2) Human metapneumovirus subgroups A and B Human parainfluenza virus 1 Human parainfluenza virus 1 and 2 Human parainfluenza virus 1 and 3 Human parainfluenza virus 2 Human parainfluenza virus 2 and 4 Human parainfluenza virus 3 Human parainfluenza virus 4 Human parechovirus types 1, 3, 4, and 6 Influenza A virus Influenza A virus (H1N1) swl Influenza B virus Influenza C Virus Measles virus Norovirus genogroup I (GI) Norovirus genogroup II (GII) Respiratory syncytial virus (RSV) subgroups A and B Sapovirus genogroup V (GV) SARS-CoV-2
Fungal 31 Alternaria spp. (alternata/infectoria) Aspergillus fumigatus Aspergillus niger Aspergillus spp. (fumigatus/flavus/niger/terreus/nidulans) Aspergillus terreus Candida albicans Candida auris Candida dubliniensis Candida glabrata Candida krusei Candida lusitaniae Candida parapsilosis Candida spp. (albicans/tropicalis/parapsilosis/dubliniensis) Candida spp. (albicans/tropicalis/parapsilosis/dubliniensis/krusei/glabrata) Candida tropicalis Cladosporium spp. (cladosporioides/bantiana/sphaerospermum/cladosporioides/herbarum) Coccidioides spp. (posadasii/immitis) Cryptococcus gattii Cryptococcus neoformans Cryptococcus spp. (gattii/neoformans) Curvularia spp. (aeria/affinis/asiatica/clavata/crepinii/fallax/geniculata/lunata/senegalensis/soli/trifolii) Epicoccum spp. (latusicollum/poaceicola/sorghinum/nigrum/purpurascens) Epidermophyton floccosum Fusarium solani Fusarium spp. (solani/moniliforme/oxysporum/arcuatisporum/acuminatum/verticillioides/sulawesiense/sacchari/pernambucanum/luffae/longipes/longifundum/hainanense/graminearum/equiseti/coffeatum/chlamydosporum) Malassezia spp. (furfur/restricta/globosa) Mucor spp. (circinelloides/ramosissimus/spinosus/racemosus/indicus) Pneumocystis jirovecii Trichophyton interdigitale Trichophyton rubrum Trichophyton spp. (rubrum/violaceum)
Bacterial (gram-positive) 31 Actinotignum schaalii Aerococcus urinae Alloiococcus otitis Atopobium vaginae Clostridium difficile (tcdA/tcdB) Corynebacterium amycolatum Corynebacterium urealyticum Cutibacterium (Propionibacterium) acnes Enterococcus faecalis Enterococcus faecium Enterococcus spp. (faecalis/faecium) Lactobacillus spp. (crispatus/reuteri/gasseri/vaginalis/jensenii/iners) Mobiluncus curtisii Mobiluncus mulieris Mobiluncus spp. (curtisii/mulieris) Mycobacterium abscessus Mycobacterium avium Mycobacterium intracellulare Mycobacterium tuberculosis complex spp. (tuberculosis/bovis/africanum/microti/canettii/caprae) Nocardia asteroides Peptostreptococcus spp. (stomatis/magnus/anaerobius) Staphylococcus aureus Staphylococcus epidermidis Staphylococcus haemolyticus Staphylococcus lugdunensis Staphylococcus saprophyticus Staphylococcus spp. (epidermidis/haemolyticus/lugdunensis) Streptococcus agalactiae (Group B) Streptococcus dysgalactiae subsp. equisimilis (Group C/G) Streptococcus pneumoniae Streptococcus pyogenes (Group A)
Viral (dsDNA) 26 Hepatitis B virus Herpes simplex virus (HSV) 1 Herpes simplex virus (HSV) 1 and 2 Herpes simplex virus (HSV) 2 HPV-16 HPV-18 HPV-31 HPV-31,52,58,35,51 HPV-33 HPV-33,56,66 HPV-35 HPV-39 HPV-39,59,68 HPV-45 HPV-51 HPV-52 HPV-56 HPV-58 HPV-59 HPV-66 HPV-68 Human adenovirus type F Human adenovirus types B, C, and E Human gammaherpesvirus 4 (Epstein-Barr, Mono) Monkeypox virus Varicella zoster virus (Human herpesvirus 3)
Parasite 7 Ancylostoma duodenale Blastocystis hominis Cryptosporidium spp. (hominis/parvum/cuniculus) Entamoeba histolytica Enterobius vermicularis Giardia lamblia Necator americanus
Bacterial (mollicute) 6 Mycoplasma genitalium Mycoplasma hominis Mycoplasma pneumoniae Ureaplasma parvum Ureaplasma spp. (urealyticum/parvum) Ureaplasma urealyticum
Bacterial (gram-variable) 5 Bacterial Vaginosis-Associated Bacterium 1 Bacterial Vaginosis-Associated Bacterium 2 Bacterial Vaginosis-Associated Bacterium 2 and 3 Bacterial Vaginosis-Associated Bacterium 3 Gardnerella vaginalis
Protozoa 4 Babesia microti Cyclospora cayetanensis Dientamoeba fragilis Trichomonas vaginalis
Viral (dsRNA) 2 Rotavirus A Rotavirus B
Viral (ssDNA) 1 Human bocavirus types 1 and 3