DTPM DEVELOPED PATHOGEN ASSAYS

Pathogen Strains Detected by DTPM Developed Assays

On this page you will find a comprehensive list of assays available on the DTPM store. While these assays are not cleared/approved by the FDA for diagnostic purposes, with proper validation your laboratory can run them as LDTs. At this time, only the DTPM Covid-19 Assay has acquired FDA EUA approval.

How to Quick-Search

Utilize your browsers built-in “Find” feature to quickly search the table. Hold the control (CTRL) key and press the F key, this will open a text-input where you can type the text you are searching for. You can also use the menu below to jump to the section of the Pathogens list you are interested in.

Click on the first letter of the pathogen to jump to that section of the table

A
B
C
E
F – H
I – K
L – M
N – O
P
Q – R
S
T – U
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
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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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).

Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf

* If you have inquiries about specific strains, please contact DTPM support.

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