DTPM DEVELOPED PATHOGEN ASSAYS
Click on the first letter of the pathogen to jump to that section of the table
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Acinetobacter baumannii | Acinetobacter baumannii, A. seifertii, A. nosocomialis, A. gerneri | RecA | NZ_CP018664 | 72 | 128/98 | 1.02E+08 | 778 | 100% |
| Acremonium (Sarocladium) strictum | Acremonium (Sarocladium) strictum, S bactrocephalum, Sordariomycetes, Hypocreales, Lichtheimia corymbifera, Colletotrichum, Diaporthe eres, Valsa ambiens | ITS Ribosomal | NR_111145.1 | 121 | 239/200 | 1.02E+08 | 599 | 100% |
| Acremonium potronii | Acremonium potronii, A dichromosporum, A fuci, A persicinum, A salmoneum, A sclerotigenum, A zonatum, Emericellopsis maritima, E alkalina, E cladophorae, E phycophila, E pallida, E stolkiae, E nidulans, E atlantica, Mycocitrus zonatus, Hypocreales, Parasarocladium breve, Stilbella fimetaria | ITS Ribosomal | JX535048.1 | 56 | 100/95 | 1.02E+08 | 219 | 100% |
| Adenovirus (RPP) | Adenovirus 3, 4, 4a, 4p. 7, 10, 11, 13, 14, 16, 17, 21, 21a, 34, 35, 40, 48, 50, 51, 55, 71, B3, E4, E4, Human mastadenovirus B, D, E | L3 | NC_011203 | 59 | 100/90 | 1.02E+08 | 1637 | 100% |
| Adenovirus (RPP) | Adenovirus 3, 4, 4a, 4p. 7, 10, 11, 13, 14, 16, 17, 21, 21a, 34, 35, 40, 48, 50, 51, 55, 71, B3, E4, E4, Human mastadenovirus B, D, E | L3 | NC_011203 | 59 | 100/90 | 1.02E+08 | 1637 | 100% |
| Adenovirus spp | Human Adenovirus Type 3, 4, 7, 8, 9, 10, 11, 13, 12, 14, 15, 16, 17, 19, 21, 24, 25-31, 34, 35, 37-39, 40, 41, 43-53, 54-58, 60-67, 81, 55, 56, 83, 86, mastadenovirus A, B, D, E, F | L3 | NC_001454.1 | 98 | 140/125 | 1.02E+08 | 1896 | 100% |
| Aeromonas spp | Aeromonas caviae, A. dhakensis, A. veronii, A. hydrophila, A. media, A. rivipollensis, A. allosaccharophila, A. jandaei, A. australiensis, A. enteropelogenes, A. rivipollensis, A. rivuli, A. taiwanensis, A. encheleia, A. salmonicida, A. schubertii | gyrB | NZ_CP091176 | 131 | 217/187 | 1.02E+08 | 405 | 100% |
| Alternaria species | Alternaria species, Embellisia dennisii, E conoidea, E indefessa, Ulocladium dauci, U capsicum, U oudemansii, U obovoideum, septosporum, Nimbya perpunctulata, N perpunctulata, N celosiae | Alta1 | CM034651 | 84 | 147/110 | 1.02E+08 | 2441 | 100% |
| Aspergillus flavus / oryzae v2.0 | Aspergillus flavus, A oryzae {*aflatoxin biosynthesis gene] | aflC | NC_054693.1 | 67 | 125/120 | 1.02E+08 | 47 | 100% |
| Aspergillus fumigatus | Aspergillus fumigatus, A aculeatus, A arcoverdensis, A aureolus, A brevipes, A botucatensis, A chermesinum, A delicatus, A duricaulis, A felis, A fischeri, A frankstonensis, A fumigatiaffinis, A fumisynnematus, A hiratsukae, A igneus, A laciniosus, A lentulus, A malignus, A marvanovae, A nishimurae, A novofumigatus, A oerlinghausenensis, A parafelis, A pseudofelis, A pseudoviridinutans, A shendaweii, A siamensis, A spinosus, A takakii, A terrus, A tsunodae, A turcosus, A udagawae, A versicolor, A viridinutans, A waksmanii, A wyomingensis, Neosartorya aureola, N coreana, N fischeri, N hiratsukae, N laciniosa, N pseudofischeri, N spathulata, N spinosa, N udagawae, Penicillium chermesinum, P glandicola | ITS Ribosomal | NC_007197 | 101 | 193/181 | 1.02E+08 | 4220 | 100% |
| Aspergillus niger / tubingensis | Aspergillus niger, A tubingensis, A aculeatus, A amstelodami, A awamori, A brasiliensis, A costaricensis, A cristatus, A ficuum, A foetidus, A lacticoffeatus, A luchuensis, A neoniger, A phoenicis, A piperis, A sclerotiorum, A terreus, A welwitschiae, Actinomucor elegans | ITS Ribosomal | CM033103 | 72 | 144/131 | 1.02E+08 | 5186 | 100% |
| Aspergillus terreus | Aspergillus terreus, A alabamensis, A aureoterreus, A citrinoterreus, A elongatus A hortai, A jilinensis, A montoensis, A neoafricanus, A nomius, A pseudoterreus, A temulenta | ITS Ribosomal | LC496504 | 58 | 109/95 | 1.02E+08 | 1318 | 100% |
| Astrovirus | Astrovirus 1-8, (Mamastrovirus 1-3) | orf1b | NC_001943.1 | 85 | 130/105 | 1.02E+08 | 598 | 100% |
| Atopobium vaginae | Atopobium vaginae (Fannyhessea vaginae) | 16S Ribosomal | NR_117757.1 | 66 | 126/121 | 1.02E+08 | 234 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens starting with B
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Bacteroides spp. | Bacteroides fragilis, B. caccae, B. dorei, B. eggerthii, B. faecis, B. finegoldii, B. graminisolvens, B. heparinolyticus, B. intestinalis, B. kribbi, B. koreensis, B. luhongzhouii, B. massiliensis, B. ovatus, B. pyogenes, B. stercoris, B. salyersiae, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. xylanisolvens, B. zhangwenhongii, Phocaeicola massiliensis, P. plebeius, P vulgatus | 16S Ribosomal | AP006841.1 | 112 | 187/179 | 1.02E+08 | 29143 | 100% |
| Bocavirus | Human Bocavirus 1, Primate bocaparvovirus 1 | VP2 | KU557406 | 62 | 124/114 | 1.02E+08 | 643 | 100% |
| Bordetella pertussis V 3.0 | Bordetella pertussis | ptxS1 | CP046994 | 79 | 155/150 | 1.02E+08 | 991 | 100% |
| Bordetella pertussis/holmesii | Bordetella pertussis, holmesii (Bordetella bronchiseptica) | Integrase | CP046994 | 54 | 108/103 | 1.02E+08 | 1059 | 100% |
| BVAB2 | Bacterial Vaginosis Associated Bacteria (BVAB2), Amygdalobacter nucleatus, A. indicium, Oscillospiraceae bacterium | 16S Ribosomal | AY724740.1 | 74 | 148/143 | 1.02E+08 | 56 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with C
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Campylobacter coli | Campylobacter coli | GyrA | NC_022347.1 | 67 | 128/118 | 1.02E+08 | 162 | 100% |
| Campylobacter jejuni | Campylobacter jejuni | GyrA | NZ_CP017863.1 | 72 | 141/132 | 1.02E+08 | 1005 | 100% |
| Campylobacter upsaliensis | Campylobacter upsaliensis, C. vulpis, C. helveticus | GyrA | LR134372.1 | 59 | 118/98 | 1.02E+08 | 9 | 100% |
| Candida albicans | Candida albicans, Candid dubliniensis | Erg11 | NC_032093 | 74 | 142/134 | 1.02E+08 | 363 | 100% |
| Candida albicans | Candida albicans, Candid dubliniensis | Erg11 | NC_032093 | 74 | 142/134 | 1.02E+08 | 363 | 100% |
| Candida albicans | Candida albicans, Candid dubliniensis | Erg11 | NC_032093 | 74 | 142/134 | 1.02E+08 | 363 | 100% |
| Candida parapsilosis | Candida parapsilosis | Erg11 | NW_023503279 | 65 | 130/130 | 1.02E+08 | 502 | 100% |
| Candida parapsilosis | Candida parapsilosis | Erg11 | NW_023503279 | 65 | 130/130 | 1.02E+08 | 502 | 100% |
| Candida parapsilosis | Candida parapsilosis | Erg11 | NW_023503279 | 65 | 130/130 | 1.02E+08 | 502 | 100% |
| Candida tropicalis | Candida tropicalis | Erg11 | NW_003020060 | 70 | 140/134 | 1.02E+08 | 369 | 100% |
| Candida tropicalis | Candida tropicalis | Erg11 | NW_003020060 | 70 | 140/134 | 1.02E+08 | 369 | 100% |
| Candida tropicalis | Candida tropicalis | Erg11 | NW_003020060 | 70 | 140/134 | 1.02E+08 | 369 | 100% |
| Chlamydia pneumoniae [previously Chlamydophila pneumoniae] | Chlamydia pneumoniae [previously known as Chlamydophila pneumoniae] | porin | NC_011216 | 66 | 132/112 | 1.02E+08 | 33 | 100% |
| Chlamydia pneumoniae [previously Chlamydophila pneumoniae] | Chlamydia pneumoniae [previously known as Chlamydophila pneumoniae] | porin | NC_005043 | 66 | 132/112 | 1.02E+08 | 33 | 100% |
| Chlamydia trachomatis | Chlamydia trachomatis | gyrA | NC_021888.1 | 66 | 132 | 1.02E+08 | 296 | 100% |
| Citrobacter freundii & braakii | Citrobacter freundii, C braakii, C arsenatis, C cronae, C europaeus, C pasteurii, C portucalensis, C rodentium, C werkmanii, C youngae [Salmonella entericaay > 100,000 copies may give weak signal] | gyrA | NZ_CP007557 | 64 | 128/123 | 1.02E+08 | 847 | 100% |
| Clostridioides difficile Toxin A | Clostridioides difficile Toxin A, Peptoclostridium difficile | tcbA | KC292104.1 | 124 | 245/236 | 1.02E+08 | 194 | 100% |
| Clostridioides difficile Toxin B | Clostridioides difficile Toxin B | tcbB | KC292179.1 | 92 | 184/152 | 1.02E+08 | 201 | 100% |
| CMY 1 | blaCMY-1, 8, 8b, 9-11, 19, MOX 1-4, 8, 10, 11 | blaCMY-1 | NG_048768.1 | 67 | 131/111 | 1.02E+08 | 116 | 100% |
| CMY 2 | CMY-2, 4-7, 12-18, 20, 22-25, 27, 30-35, 38, 39, 42-46, 49, 53-62, 64, 69, 71, 73, 77, 80, 86, 94, 95, 96, 99, 102, 106-108, 111, 119, 121, 124-126, 129, 130, 132-134, 138-141, 145-48, 153, 155, 156, 158, 160-167. IcAC2 | blaCMY-2 | AB672503.1 | 58 | 116/106 | 1.02E+08 | 1521 | 100% |
| Coronavirus 229E | Human coronavirus 229, Bat coronavirus | N | NC_011204 | 74 | 148/132 | 100574661 | 241 | 1 |
| Coronavirus 229E | Human coronavirus 229, Bat coronavirus | N | NC_002645 | 74 | 148/132 | 1.02E+08 | 241 | 100% |
| Coronavirus HKU-1 | Human coronavirus HKU-1 | N | NC_011205 | 78 | 147/142 | 100574661 | 143 | 1 |
| Coronavirus HKU-1 | Human coronavirus HKU-1 | N | NC_006577 | 78 | 147/142 | 1.02E+08 | 143 | 100% |
| Coronavirus NL63 | Human coronavirus NL-63 | N | NC_011206 | 67 | 134/129 | 100574661 | 226 | 1 |
| Coronavirus NL63 | Human coronavirus NL-63 | N | NC_005831 | 67 | 134/129 | 1.02E+08 | 226 | 100% |
| Coronavirus OC43 | Human coronavirus OC43, Bovine, Dromedary camel , Canine, Yak, Deer (Water, White-tailed ), Waterbuck, Giraffe, Sable antelope, Porcine, Rabbit | N | NC_011207 | 65 | 130/108 | 100574661 | 955 | 1 |
| Coronavirus OC43 | Human coronavirus OC43, Bovine, Dromedary camel , Canine, Yak, Deer (Water, White-tailed ), Waterbuck, Giraffe, Sable antelope, Porcine, Rabbit | N | NC_006213 | 65 | 130/108 | 1.02E+08 | 955 | 100% |
| Cryptosporidium spp | Cryptosporidium parvum, C. hominis, C. meleagridis, C wrairi, C cuniculus, C. tyzzeri, C. .fayeri, C. erinacei, C. muris, C. xiaoi, C. bovis, C. sciurinum, C. felis, C.myocastoris, C. viatorum, C. suis, C. occultus, C. ubiquitum, C. ratti, C. homai, C. varanii, C. saurophilum, C. apodemi, C. macropodum, C. ditrichi, C. alticolis, C. ryanae, C. canis, C. rubeyi, C. scrofarum, C. ducismarci, C. skunk, C. chipmunk, C. ferret, C. horse, C. mink, C. southern elephant seal, C. kangaroo, C. cervine (deer), C. goose, C. baileyi, C. serpentis, C. testudinis, C. avian, C. andersoni, C. proventriculi, C. fragile, C. galli | 18S | CP044422.1 | 141 | 279/224 | 1.02E+08 | 7272 | 100% |
| CTXM 1 | CTX-M-1, 3, 10, 12, 15, 22, 23, 28, blaFEC-1 | blaCTX-M-1 | NZ_AP024521.1 | 64 | 128/114 | 1.02E+08 | 5823 | 100% |
| CTXM 2 | CTX-M-2, 4, 4L, 5, 6, 7, 20, blaToho-1 | blaCTX-M-2 | CP091665.1 | 57 | 114/107 | 1.02E+08 | 376 | 100% |
| CTXM 25 | CTX-M-25, 26, 39, 41, 78, 89, 91, 94, 100, 152, 160, 185, 205, 217 | blaCTX-M-25 | NG_048974.1 | 59 | 118/101 | 1.02E+08 | 53 | 100% |
| CTXM 8 | CTX-M-8, 40, 63, blaKLUG-1 | blaCTX-M-8 | AB543595.1 | 58 | 113/108 | 1.02E+08 | 84 | 100% |
| CTXM 9 | CTX-M-9, 13, 14, 16, 17, 19, 21, 24, 27, blaTOHO-2, | blaCTX-M-9 | NG_049043.1 | 63 | 123/118 | 1.02E+08 | 2845 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with E
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Enteroaggregative Escherichia coli_aggR | Escherichia coli containing aggR gene | aggR | FN554767.1 | 70 | 134/129 | 1.02E+08 | 79 | 100% |
| Enterobacter cloacae/hormaechei | E faecalis | recG | NZ_CP091198 | 66 | 132/122 | 1.02E+08 | 619 | 100% |
| Enterobacter cloacae/hormaechei | Enterobacter cloacae, E. hormaechei, E. roggenkampii, E. asburiae, E. ludwigii, E. kobei, E. bugandensis | apbC | NZ_CP009756 | 72 | 138/133 | 1.02E+08 | 748 | 100% |
| Enterococcus faecalis | Enterobacter cloacae, E. hormaechei, E. roggenkampii, E. asburiae, E. ludwigii, E. kobei, E. bugandensis | apbC | NZ_CP009756 | 72 | 138/133 | 1.02E+08 | 748 | 100% |
| Enterococcus faecalis | E faecalis | recG | NZ_CP091198 | 66 | 132/122 | 1.02E+08 | 619 | 100% |
| Enterococcus faecalis | E faecalis | recG | NZ_CP091198 | 66 | 132/122 | 1.02E+08 | 619 | 100% |
| Enterococcus faecium | Enterococcus faecium | gyrA | NZ_CP038996.1 | 64 | 128/111 | 1.02E+08 | 618 | 100% |
| Enterohemorrhagic Escherichia coli_stx1 | Escherichia coli & Shigella containing Stx1A gene, Stx1A-converting bacteriophage | Stx1A | CP050498.1 | 58 | 116/106 | 1.02E+08 | 444 | 100% |
| Enterohemorrhagic Escherichia coli_stx2 | Escherichia coli & Shigella containing Stx2A gene, Stx2A, C-converting bacteriophage | Stx2A | AM982821.2 | 59 | 115/100 | 1.02E+08 | 1126 | 100% |
| Enteroinvasivve Escherichia coli_ipaH | Escherichia coli & Shigella containing ipaH gene | ipAH | M32063.1 | 58 | 113/105 | 1.02E+08 | 420 | 100% |
| Enterotoxigenic Escherichia coli_elt | Escherichia coli containing elt gene | elt | AB011677.1 | 60 | 120/105 | 1.02E+08 | 112 | 100% |
| Enterotoxigenic Escherichia coli_est | Escherichia coli containing est gene | est | M34916.1 | 64 | 125/121 | 1.02E+08 | 80 | 100% |
| Entertovirus / Rhinovirus (EV/RV)* | Rhino A, B, C: Enterovirus D68, A23, A47, A71, Coxsackievirus A1, A6, A11, A13, A16, A20, A22, Echovirus, Human poliovirus 1, 2, 3, *Pathogens associated with hand, foot, and mouth disease (Coxsackievirus A16, A6, Enterovirus 71) are detected by this assay | Polyprotein | NC_011215 | 114 | 171/98 | 1.02E+08 | 7798 | 100% |
| Entertovirus / Rhinovirus (EV/RV)* | Rhino A, B, C: Enterovirus D68, A23, A47, A71, Coxsackievirus A1, A6, A11, A13, A16, A20, A22, Echovirus, Human poliovirus 1, 2, 3, *Pathogens associated with hand, foot, and mouth disease (Coxsackievirus A16, A6, Enterovirus 71) are detected by this assay | Polyprotein | NC_038308 & NC_038311 | 114 | 171/98 | 1.02E+08 | 7798 | 100% |
| Epidermophyton floccosum | Epidermophyton floccosum, Arthroderma uncinatum | ITS Ribosomal | MH858667.1 | 63 | 126/121 | 1.02E+08 | 166 | 100% |
| ermB | ermB | ermB | MG778119 | 66 | 132/122 | 1.02E+08 | 2690 | 100% |
| Escherichia coli / Shigella | Escherichia coli, O55H7, O157:H7, O10:H32, O104:H4, O121:H19, O178:H19, O6:H16, O169:H41, O25:H16, O27:H7, O128:H27, O114:H49, O15:H11, O6:H16, O127:H6, O4:H5, 025:H1, O8:H28, O170:H18, 085:H1, 0158:H24. Shigellla boydii, S. flexneri, S. dysenteriae | lacY | NC_000913 | 75 | 147/137 | 1.02E+08 | 4629 | 100% |
| Escherichia coli / Shigella | Escherichia coli, O55H7, O157:H7, O10:H32, O104:H4, O121:H19, O178:H19, O6:H16, O169:H41, O25:H16, O27:H7, O128:H27, O114:H49, O15:H11, O6:H16, O127:H6, O4:H5, 025:H1, O8:H28, O170:H18, 085:H1, 0158:H24. Shigellla boydii, S. flexneri, S. dysenteriae | lacY | NC_000913 | 75 | 147/137 | 1.02E+08 | 4629 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with F – H
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| FOX | blaFox-1-10, 12-16 | blaFOX | NG_049098 | 80 | 143/133 | 1.02E+08 | 63 | 100% |
| Fusarium solani | Fusarium solani, F akasia, F ambrosium, F breve, F ensiforme, F euwallaceae, F falciforme, F ferrugineum, F haematococcum, F keratoplasticum, F lateritium, F lichenicola, F metavorans, F neocosmosporiellum, F oblongum, F oxysporum, F paranaense, F perseae, F petroliphilum, F phaseoli, F populicola, F pseudensiforme, F rekanum, F striatum, F suttonianum, F tonkinense, F vanettenii, F waltergamsii, F witzenhausenense, Earliella scabrosa, Ascomycota, Nectria haematococca, N ipomoeae, Neocosmospora vasinfecta, Sordariomycetes | ITS Ribosomal | KY484966.1 | 164 | 319/241 | 1.02E+08 | 10871 | 100% |
| Gardnerella vaginalis | Gardnerella vaginalis | tuf | NZ_NJFH02000002.1 | 60 | 120 | 1.02E+08 | 19 | 100% |
| Giardia spp | Giardia intestinalis, G. microti, G. duodenalis, G. lamblia, G. psittaci | 16S | M54878.1 | 90 | 168/150 | 1.02E+08 | 1088 | 100% |
| Haemophilus ducreyi | Haemophilus ducreyi | gyrA | NZ_CP015434.1 | 61 | 122 | 1.02E+08 | 28 | 100% |
| Haemophilus influenzae | Haemophilus aegyptius | Protein D (hpd) | CP029621 | 67 | 125/120 | 1.02E+08 | 142 | 100% |
| Helicobacter pylori | Helicobacter pylori, H. acinonychis | tuf | CP005490.3 | 58 | 110/95 | 1.02E+08 | 1472 | 100% |
| Herpes simplex 1 | Human herpesvirus 1, Human alphaherpesvirus 1 | DNA polymerase | NC_001806.2 | 111 | 204/194 | 1.02E+08 | 813 | 100% |
| Herpes simplex 2 | Human herpesvirus 2, Human alphaherpesvirus 2 | DNA polymerase | NC_001798 | 97 | 194/160 | 1.02E+08 | 437 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with I – K
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Influenza A | H3N2, H1N1, H5N1, H3N2, H1(2009), H7N9 [inquire about other strains] | M1/M2 | NC_011208 | 98 | 161/129 | 1.02E+08 | 54079 | 100% |
| Influenza A | H3N2, H1N1, H5N1, H3N2, H1(2009), H7N9 [inquire about other strains] | M1/M2 | NC_007367 | 98 | 161/129 | 1.02E+08 | 54079 | 100% |
| Influenza B | B/Victoria, B/Yamagata | NEP | NC_011209 | 66 | 126/116 | 1.02E+08 | 7064 | 100% |
| Influenza B | B/Victoria, B/Yamagata | NEP | NC_002211 | 66 | 126/116 | 1.02E+08 | 7064 | 100% |
| Klebsiella aerogenes [previously Enterobacter aerogenes] | Klebsiella aerogenes, Enterobacter aerogenes, Raoultella ornithinolytica, R planticola | Omp35 | NC_015663 | 59 | 118/108 | 1.02E+08 | 142 | 100% |
| Klebsiella oxytoca | Klebsiella oxytoca, K grimontii, K michiganensis, Raoultella terrigena | TonB | NZ_CP033844 | 60 | 117/112 | 1.02E+08 | 179 | 100% |
| Klebsiella pneumoniae | Klebsiella pneumoniae, K variicola, K quasipneumoniae, K africana | gyrA | NC_016845 | 57 | 114/107 | 1.02E+08 | 3189 | 100% |
| Klebsiella pneumoniae | Klebsiella variicola, Klebsiella quasipneumoniae, Klebsiella africana | gyrA | NC_016845 | 57 | 114/105 | 1.02E+08 | 3138 | 100% |
| Klebsiella pneumoniae | Klebsiella variicola, Klebsiella quasipneumoniae, Klebsiella africana | gyrA | NC_016845 | 57 | 114/105 | 1.02E+08 | 3138 | 100% |
| Klebsiella pneumoniae | Klebsiella variicola, Klebsiella quasipneumoniae, Klebsiella africana | gyrA | NC_016845 | 57 | 114/105 | 1.02E+08 | 3138 | 100% |
| Klebsiella pneumoniae | Klebsiella pneumoniae, K variicola, K quasipneumoniae, K africana | gyrA | NC_016845 | 57 | 114/107 | 1.02E+08 | 3189 | 100% |
| KPC | KPC-2-8, 10-35, 142, 167 | blaKPC | CP078006.1 | 58 | 116/111 | 1.02E+08 | 2615 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with L – M
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Lactobacillus crispatus | Lactobacillus crispatus, L. amylolyticus, L. rhamnosus, L. helveticus, L kefiranofaciens, L. panisapium | tuf | NZ_ADGR01000161.1 | 66 | 132/105 | 1.02E+08 | 75 | 100% |
| Lactobacillus iners | Lactobacillus iners, L. heilongjiangensis, L. farciminis, L. crustorum, Companilactobacillus | tuf | ACLN01000003.1 | 62 | 124/102 | 1.02E+08 | 33 | 100% |
| Lactobacillus jensenii | Lactobacillus jensenii, L. mulieris | tuf | ACOY01000024.1 | 57 | 114 | 1.02E+08 | 3 | 100% |
| Legionella pneumophila | Legionella worsleiensis & Legionella fairfieldensis | mip | NZ_CP015941 | 79 | 155/143 | 1.02E+08 | 366 | 100% |
| MecA | mecA | mecA | CP000255 | 81 | 162/128 | 1.02E+08 | 1596 | 100% |
| Megasphaera 1 | Megasphaera 1, M. lornae, Veillonellaceae | 16S Ribosomal | AY738672 | 83 | 160/137 | 1.02E+08 | 458 | 100% |
| Megasphaera 2 | Megasphaera 2, M. hutchinsoni, Veillonellaceae | 16S Ribosomal | AY738697 | 61 | 122/113 | 1.02E+08 | 68 | 100% |
| Metapneumovirus A & B | A2, B2 | F | NC_039199 | 79 | 143/100 | 1.02E+08 | 1624 | 100% |
| Microsporum spp | Microsporum canis, M ferrugineum, M audouinii, Arthroderma otae | ITS Ribosomal | LC317666 | 59 | 118/100 | 1.02E+08 | 965 | 100% |
| Moraxella catarrhalis | Moraxella catarrhalis | UspA1 | CP018059 | 65 | 130 | 1.02E+08 | 31 | 100% |
| Morganella moranii | Morganella moranii | gyrA | CP014026 | 65 | 130/120 | 1.02E+08 | 63 | 100% |
| Morganella moranii | Morganella moranii | gyrA | CP014026 | 65 | 130/120 | 1.02E+08 | 63 | 100% |
| Mycoplasma genitalium | Mycoplasma genitalium | gyrA | NC_000908.2 | 146 | 146 | 1.02E+08 | 8 | 100% |
| Mycoplasma hominis | Micoplasma hominis, Metamycoplasma hominis | KtrB | CP009652 | 79 | 158/153 | 1.02E+08 | 21 | 100% |
| Mycoplasma hominis | Micoplasma hominis, Metamycoplasma hominis | KtrB | CP009652 | 79 | 158/153 | 1.02E+08 | 21 | 100% |
| Mycoplasma pneumoniae | Mycoplasma pneumoniae | P1 | CP039772 | 61 | 122/111 | 1.02E+08 | 129 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with N – O
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Nakaseomyces glabratus [previously Candida glabrata] | Nakaseomyces glabratus previously known as Candida glabrata | Erg11 | NC_006028 | 64 | 128/128 | 1.02E+08 | 101 | 100% |
| Nakaseomyces glabratus [previously Candida glabrata] | Nakaseomyces glabratus previously known as Candida glabrata | Erg11 | NC_006028 | 64 | 128/128 | 1.02E+08 | 101 | 100% |
| Nakaseomyces glabratus [previously Candida glabrata] | Nakaseomyces glabratus previously known as Candida glabrata | Erg11 | NC_006028 | 64 | 128/128 | 1.02E+08 | 101 | 100% |
| NDM | NDM (1-24) | blaNDM | NG_049326.1 | 56 | 112/107 | 1.02E+08 | 3336 | 100% |
| Neisseria gonorrhoeae | Neisseria gonorrhoeae | gyrA | NZ_LT591897.1 | 64 | 128 | 1.02E+08 | 179 | 100% |
| Neofusicoccum mangiferae | Neofusicoccum mangiferae, N eucalyptorum, N parvum, Botryosphaeria eucalyptorum | ITS Ribosomal | MN519717.1 | 80 | 157/148 | 1.02E+08 | 138 | 100% |
| Neoscytalidium (Scytalidium) dimidiatum | Neoscytalidium (Scytalidium) dimidiatum, N novaehollandiae, N hyalinum, Botryosphaeria dothidea, Macrophomina phaseolina, Aureobasidium melanogenum, A namibiae, Arnium arizonense | BT | KF020895 | 54 | 105/90 | 1.02E+08 | 110 | 100% |
| Norovirus G1 | Norovirus G1 | POL | JX023285.1 | 92 | 130/114 | 1.02E+08 | 1815 | 100% |
| Norovirus G2 | Norovirus G2 | POL | NC_039477.1 | 90 | 135/116 | 1.02E+08 | 13475 | 100% |
| OXA 1 | blaOXA-1, 4 | blaOXA-1 | NC_005327.1 | 60 | 120/112 | 1.02E+08 | 2244 | 100% |
| OXA 2 | blaOXA-2, 3, 21, 32, 46 | blaOXA-2 | NG_049496.1 | 58 | 113/106 | 1.02E+08 | 381 | 100% |
| OXA 48 | blaOXA-48, 48b, 81, 162, 163, 165, 181, 199, 204, 232, 244, 247, 252, 370, 405, 416, 484, 514, 515 | blaOXA-48 | NZ_CP030135.1 | 58 | 116/96 | 1.02E+08 | 1466 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with P
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Parainfluenza virus Type 1 | HPV 1, Human respirovirus 1 | L RNA polymerase | NC_011210 | 74 | 142/132 | 1.02E+08 | 114 | 100% |
| Parainfluenza virus Type 1 | HPV 1, Human respirovirus 1 | L RNA polymerase | NC_003461 | 74 | 142/132 | 1.02E+08 | 114 | 100% |
| Parainfluenza virus Type 2 | Human Rubelavirus 2, Human orthorubelavirus 2 | NP | NC_011213 | 68 | 124 | 1.02E+08 | 83 | 100% |
| Parainfluenza virus Type 2 | Human Rubelavirus 2, Human orthorubelavirus 2 | NP | NC_003443 | 68 | 124 | 1.02E+08 | 83 | 100% |
| Parainfluenza virus Type 3 | HPV 3, Human respirovirus 3 | N | NC_011211 | 75 | 141/131 | 1.02E+08 | 580 | 100% |
| Parainfluenza virus Type 3 | HPV 3, Human respirovirus 3 | N | NC_001796 | 75 | 141/131 | 1.02E+08 | 580 | 100% |
| Parainfluenza virus Type 4 | HPV 4, Human parainfluenza virus 4a & 4b, Human orthorubulavirus 4 | HN | NC_011212 | 118 | 188/141 | 1.02E+08 | 157 | 100% |
| Parainfluenza virus Type 4 | HPV 4, Human parainfluenza virus 4a & 4b, Human orthorubulavirus 4 | HN | NC_021928 | 118 | 188/141 | 1.02E+08 | 157 | 100% |
| Parechovirus | A, 1,3,4,5,6,8,17,19 | 5′ UTR Polyprotein | NC_001897 | 146 | 146/114 | 1.02E+08 | 460 | 100% |
| Proteus mirabilis | Proteus mirabilis | gyrA | NC_010554.1 | 61 | 122 | 1.02E+08 | 143 | 100% |
| Proteus vulgaris | Proteus vulgaris, P columbae, P hauseri, P penneri, P terrae [P mirabilis > 50,0000 copies may give a weak signal] | gyrA | NZ_CP090064.1 | 64 | 128 | 1.02E+08 | 48 | 100% |
| Providencia stuartii | Providencia stuartii | RecA/RadA | CP003488 | 64 | 128 | 1.02E+08 | 20 | 100% |
| Psuedomonas aeruginosa | Psuedomonas aeruginosa, P. alcaligenes, P. balearica, P. citronellolis, P. furukawaii, P. fluorescens, P. guangdongensis, P. jinjuensis, P. knackmussii, P. lalkuanensis, P. multiresinivorans, P. nitroreducens, P. otitidis, P. oryzihabitans, P. stutzeri, P. tohonis, P. paraeruginosa, Stutzerimonas balearica, S. frequens, S. stutzeri | oprL | NC_002516.2 | 60 | 120/90 | 1.02E+08 | 2035 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with Q – R
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| qnrA 1-9 | qnrA 1-9 | qnrA 1 | NG_050462 | 82 | 146/127 | 1.02E+08 | 454 | 100% |
| qnrB 1 | qnrB 1-3, 6, 13-18, 20, 23, 26, 29, 30, 41-43, 45, 48, 49, 52, 54, 57, 58, 64, 66, 75, 77, 80 | qnrB 1 | NG_050469 | 89 | 160/130 | 1.02E+08 | 1734 | 100% |
| qnrB 5 | qnrB 5, 10, 19, 36, 40, 46, 47, 50, 56, 59, 61, 62, 67, 68, 70, 71, 72 | qnrB 5 | NG_050513 | 85 | 161/131 | 1.02E+08 | 1789 | 100% |
| qnrS | qnrS 1, 3-5, 7-9 | qnrS1 | DQ485529.1 | 66 | 123/118 | 1.02E+08 | 2505 | 100% |
| Respiratory Syncytial Virus A & B | A,B, Human orthopneumovirus | L | NC_011214 | 125 | 214/199 | 1.02E+08 | 5343 | 100% |
| Respiratory Syncytial Virus A & B | A,B, Human orthopneumovirus | L | NC_001781 | 125 | 214/199 | 1.02E+08 | 5343 | 100% |
| Rotavirus | Human Rotavirus A, Bovine rotavirus A, Porcine rotavirus A, Feline rotavirus A, Equine rotavirus A | NSP3 | LC468232 | 76 | 137/112 | 1.02E+08 | 1657 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with S
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Salmonella spp | Salmonella enterica, enteritidis, typhimurium, bongori | enterotoxin (stn) | CP030026 | 131 | 221/201 | 1.02E+08 | 2560 | 100% |
| Scopulariopsis brevicaulis | Scopulariopsis brevicaulis, S alboflavescens, S cordiae, S flava, S insectivora, S stercoraria | ITS Ribosomal | LN850791.1 | 60 | 120/107 | 1.02E+08 | 136 | 100% |
| Serratia spp V2.0 | Serratia marescens, S. bockelmannii, S. entomophila, S. ficaria, S. grimesii, S. liquefaciens, S. nematodiphila, S. odorifera, S. plymuthica,S. proteamaculans, S. quinivorans, S. surfactantfaciens, S. symbiotica, S. ureilytica, S rubidaea | gyrA | NZ_CP027798 | 66 | 120/109 | 1.02E+08 | 1333 | 100% |
| SHV | SHV-1, 2, 2a, 11, 12, 27, 28, 31, 33, 38, 41, 42, 61, 71, 77, 190, 201, 205, 206, 208, 209, 211-228 | blaSHV | CP043859.1 | 71 | 142/127 | 1.02E+08 | 5014 | 100% |
| Staphylococcus aureus | Staphylococcus aureus | acetyl-CoA acetyltransferase | NC_007795 | 59 | 112/107 | 1.02E+08 | 1912 | 100% |
| Staphylococcus aureus | Staphylococcus aureus | acetyl-CoA acetyltransferase | NC_007795 | 59 | 112/107 | 1.02E+08 | 1912 | 100% |
| Staphylococcus aureus | Staphylococcus aureus | acetyl-CoA-acetyltransferase | NC_007795 | 59 | 112/104 | 1.02E+08 | 1969 | 100% |
| Staphylococcus aureus | Staphylococcus aureus | acetyl-CoA-acetyltransferase | NC_007795 | 59 | 112/104 | 1.02E+08 | 1969 | 100% |
| Staphylococcus saprophyticus | Staphylococcus saprophyticus | KtrB | NZ_CP014113 | 66 | 132 | 1.02E+08 | 25 | 100% |
| Streptococcus agalactiae | Streptococcus agalactiae | gyrA | NC_011217 | 72 | 141/136 | 1.02E+08 | 216 | 100% |
| Streptococcus agalactiae | Streptococcus agalactiae | gyrA | CP003919 | 72 | 141/136 | 1.02E+08 | 216 | 100% |
| Streptococcus agalactiae | Streptococcus agalactiae | gyrA | CP003919 | 72 | 141/136 | 1.02E+08 | 216 | 100% |
| Streptococcus dysgalactiae | Streptococcus dysgalactiae | gyrA | NC_011218 | 56 | 112/103 | 1.02E+08 | 62 | 100% |
| Streptococcus dysgalactiae | Streptococcus dysgalactiae | gyrA | AP012976.1 | 56 | 112/103 | 1.02E+08 | 62 | 100% |
| Streptococcus pneumoniae | Streptococcus pneumoniae | lytA | NC_011219 | 60 | 120/110 | 1.02E+08 | 375 | 100% |
| Streptococcus pneumoniae | Streptococcus pneumoniae | lytA | CP003357 | 60 | 120/110 | 1.02E+08 | 375 | 100% |
| Streptococcus pyogenes | Streptococcus pyogenes | gyrA | NC_011220 | 62 | 124/119 | 1.02E+08 | 292 | 100% |
| Streptococcus pyogenes | Streptococcus pyogenes | gyrA | CP014278.2 | 62 | 124/119 | 1.02E+08 | 292 | 100% |
| Sul 1 | sul1 | sul1 | NG_048102.1 | 54 | 108/101 | 1.02E+08 | 8691 | 100% |
| Sul 2 | sul2 | sul2 | NG_048108.1 | 62 | 124/114 | 1.02E+08 | 5963 | 100% |
| Sul 3 | sul3 | sul3 | NG_048120 | 67 | 134/113 | 1.02E+08 | 1068 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with T – U
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| TEM | TEM-1-7, 9, -14, 24, 52, 135, 235, 236, 237, 240 | blaTEM | NC_018106.1 | 94 | 182/170 | 1.02E+08 | 28448 | 100% |
| Treponema pallidum | Treponema pallidum, T paraluiscuniculi | Omp | NZ_LT986434.1 | 63 | 126/121 | 1.02E+08 | 540 | 100% |
| Trichomonas vaginalis | Trichomonas vaginalis | FD | M33717.1 | 88 | 176 | 1.02E+08 | 20 | 100% |
| Trichophyton interdigitale / mentagrophytes | Trichophyton interdigitale, T mentagrophytes, T benhamiae, T equinum, T indotineae, T quinckeanum, T tonsurans, T schoenleinii, T simii, T verrucosum, T violaceum, Arthroderma benhamiae, A simi, A vanbreuseghemii | ITS Ribosomal | NR_144900.1 | 65 | 130/108 | 1.02E+08 | 4066 | 100% |
| Trichophyton rubrum / soudanense | Trichophyton rubrum, T soudanense, T gourvilii, T kuryangei, T raubitschekii, T violaceum, T yaoundei | ITS Ribosomal | NR_131330.1 | 64 | 128/104 | 1.02E+08 | 1873 | 100% |
| Ureaplasma urealyticum | Ureaplasma urealyticum | ureC | NC_011374 | 75 | 150 | 1.02E+08 | 8 | 100% |
| Ureaplasma urealyticum | Ureaplasma urealyticum | ureC | NC_011374 | 75 | 150 | 1.02E+08 | 8 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.
Pathogens Starting with V – Y
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| Van A | vanA | vanA | CP014531.1 | 51 | 102/92 | 1.02E+08 | 536 | 100% |
| Van B | vanB | vanB | AY958220.1 | 63 | 123/101 | 1.02E+08 | 159 | 100% |
| Van C 1 | vanC1 | vanC1 | NG_048345.1 | 60 | 120 | 1.02E+08 | 50 | 100% |
| Van C 2-4 | vanC2, vanC2/3, vanC3, vanC4 | vanC2 | NG_048408.1 | 107 | 190/185 | 1.02E+08 | 58 | 100% |
| Vibrionaceae (Vibrio) V2 spp | V. alginolyticus,V. campbellii, V. cholerae, V. diabolicus, V. harveyi, V. metoecus, V.mimicus, V. neocaledonicus, V. owensii, V. paracholerae, V. vulnificus | RecA | CP053794.1 | 103 | 153/138 | 1.02E+08 | 1934 | 100% |
| VIM | VIM-1-6, 8-12, 14-20, 23-66 | blaVIM | NG_050383.1 | 61 | 122/111 | 1.02E+08 | 1183 | 100% |
| VIM 13 | VIM-13 | blaVIM-13 | NG_050340.1 | 53 | 106 | 1.02E+08 | 6 | 100% |
| VIM 7 | VIM-7 | blaVIM-7 | NC_009739.1 | 56 | 112/102 | 1.02E+08 | 9 | 100% |
| Yersinia enterocolitica_ail | Yersinia enterocolitica_ail | ail | NZ_CP009838.1 | 78 | 156/131 | 1.02E+08 | 37 | 100% |
| Yersinia enterocolitica_inv | Yersinia enterocolitica_inv | invA | NZ_CP009838.1 | 61 | 116/111 | 1.02E+08 | 44 | 100% |
Footnotes:
- The Amplicon is the amplified piece of DNA which contains the Fwd, Rev and Probe sequence. Sequence between the Fwd, Rev and Probe are also included in Amplicon.
- The BLAST Score describes how similar the Amplicon sequence is to aligned sequences in the non-redundant GenBank Database. The range shown as High/Low reflects the highest and lowest scores for a pathogen that would generate a positive response using this assay.
- The number of sequences reviewed reflect the total number sequences in the non-redundant GenBank database on the date of the analysis. This number will change as new sequences are added to the GenBank database.
- Matches reflect the total number of pathogens identified in the BLAST search that would generate a positive ressponse. Statistically these are the number of True Positives (the diagnostic test would indicates the presence of the correct disease) = TP
- False positive (FP) – Test incorrectly detects the presence of pathogen in a sample that does not contain the pathogen. Shown as an incorrect pathogen in the BLAST analysis with a Score within the High/Low range listed for the assay.
True negative (TN) – Test correctly identifies absence of pathogen. Calculated from BLAST data as the (total number of sequences reviewed) – (total number of pathogens correctly detected or TP).
* If you have inquiries about specific strains, please contact DTPM support.