TABLE 1.

Pathogens and VMGs targeted with OpenArray plates and organisms used for validationa

Genus (n = 30)SpeciesMarker gene(s) targeted (n = 200)No. of primer sets (n = 220)Strain(s) tested (ATCC)
Designed (n = 200)From literature (n = 20)
Aeromonashydrophilaalt, exeF, tapA, arcV, ascT50
Bacilluscereus, anthracisatxA, capA, lef, cerA, clo, hlyIII, mprF, pagA, plcR9010987
BordetellapertussiscyaC, dnt, ptx, tcfA40BAA-589D
Burkholderiamallei, pseudomalleipilA, pilD, putative outer membrane gene, BPSS140740
Campylobacterjejuni, colihipO, racR, mapA, gyrA, cdtC, cdtB, cdtA, ciaB, cfrA, tonB82700819
Clostridiumperfringens, difficile, botulinumcpe, plc, pfo, cpb2, etx, bontA, ha33, ha70, cdtA, cdtB10012916
CorynebacteriumdiphtheriaedtxR10
CoxiellaburnetiidotA, icmP, icmQ, mip40
Enterococcusfaecalis, faeciumcylA, ace, cylLS, esp, gelE6019433
Escherichiacoli (including Shigella)uidA, stx1, stx2, eae, papG, lucC, ehxA, sfaA, ipaH, mxiH113BAA-460D
FrancisellatularensisacpA, clpB, mglA
Haemophilusinfluenzaelic2A, tbp1, tbp23051907D
HelicobacterpyloricagA, cagE, ureA, virD4, virB9, virB11, ureI, ureB, flaB102700392
Klebsiellapneumoniaenuc, magA, kvgS, kci, kca50
LegionellapneumophilalepB, icmQ, lepA, mip, dotA, icmB, icmR, lspH, lssD9133152
LeptospirainterroganshlyB, lipA, chpI, lipL21, ompL1, chpK, etpK6143642
ListeriamonocytogenesactA, hlyA, inlA, mpl, plcB, lisA, plcA, iap, prfA8115313
Mycobacteriumavium complex, paratuberculosis, tuberculosis, lepraeerp, glnA1, mmpA, mmpB, IS900, mmpC, plcA61
Mycoplasmagenitaliumhww3, p1, p200, p304033530D
Proteusmirabilislpp, uca, zapA, zapD40
PseudomonasaeruginosaexoS, iasA, pcrV, xcpA, popD, popB, las, etA, prfA, pilD1110145
Salmonellaenterica serovars Enterica and TyphimuriumfimA, flicC, fljB, invA, hiA, hiD, invE, prgH, sipB, sipC, spaR, tyv15113311, 19585
SerratiamarcescensflhDC, hasD, lipA, safA40
Staphylococcusaureushly, seA, seC, tsst-1, lukE, lukF, lytS, nuc, seA, tst101700699
Streptococcuspyogenesssa, mtsA, ska, speA, speC5
Vibriocholerae, mimicus, parahaemolyticus, vulnificusace, ompU, tdh, tdhS, tlh, toxR, ctxA, ctxB, mshA, tcpA, zot, trh1, vpl, vvhA, wp, tagA, trh114239315 43996
Yersiniaenterocolitica, pestis, pseudotuberculosiscrp, yopD, yscD, yst, bipA, yadA, yspB, yscN, ail9255075
Cryptosporidiumparvum, hominisgp40, hsp70, COWP gene, cp23, cgd771PRA-67
Giardiaintestinalis, lambliaβ-giardin gene, VSPH71, VSP4177, VSP4173, vsp, VSPH75230888 A-1
  • a The VMGs in bold were only tested in validation sample mixtures prepared to validate the predictive CT equation. Primer sequences are provided in the supplemental material.