Gastrointestinal Focused
Molecular Testing Assays
GI TESTING ASSAYS
On this page you will find a comprehensive list of suggested assays available on the DTPM store. While these assays are not certified 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.
ASSAYS SUGGESTED FOR GASTROINTESTINAL TESTING:
| Pathogen | Strain(s) Identified* | Target Gene | GenBank Accession Number | Amplicon1 (base pairs) | BLAST Score2 Range (High/Low) | Sequences3 Reviewed | Matches4 (True Positives) | Specificity5 |
|---|---|---|---|---|---|---|---|---|
| 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% |
| Astrovirus | Astrovirus 1-8, (Mamastrovirus 1-3) | orf1b | NC_001943.1 | 85 | 130/105 | 1.02E+08 | 598 | 100% |
| 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% |
| 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% |
| 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% |
| Enteroaggregative Escherichia coli_aggR | Escherichia coli containing aggR gene | aggR | FN554767.1 | 70 | 134/129 | 1.02E+08 | 79 | 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% |
| 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% |
| Giardia spp | Giardia intestinalis, G. microti, G. duodenalis, G. lamblia, G. psittaci | 16S | M54878.1 | 90 | 168/150 | 1.02E+08 | 1088 | 100% |
| Helicobacter pylori | Helicobacter pylori, H. acinonychis | tuf | CP005490.3 | 58 | 110/95 | 1.02E+08 | 1472 | 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% |
| 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% |
| Salmonella spp | Salmonella enterica, enteritidis, typhimurium, bongori | enterotoxin (stn) | CP030026 | 131 | 221/201 | 1.02E+08 | 2560 | 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% |
| 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).
Specificity = TN / TN + FP
https://lexjansen.com/nesug/nesug10/hl/hl07.pdf
* If you have inquiries about specific strains, please contact DTPM support.
Why Partner with DTPM?
Since 1993, DTPM has been partnering with drug and PCR testing professionals to provide top-tier service, support, and supplies. Our online store has an expansive selection, and we can work with suppliers to ensure you have the products you need to test successfully. Our experienced team can assist you in finding staff, establishing procedures, preparing for CLIA/COLA, and even installing and servicing testing instruments.
