Compositions and methods for diagnosing and treating inflammatory bowel disease and related disorders

A method for monitoring the condition of a subject having Crohn's disease, the method comprising:

• (a) contacting a microarray comprising a set of E. coli polypeptides comprising era, ybaN, yhgN, focA, gabT and ycdG, with sera derived from the subject;
• and
• (b) detecting in the subject's sera:
• (i) immunogenic reactivity to era relative to immunogenic reactivity to ybaN;
• (ii) immunogenic reactivity to yhgN relative to immunogenic reactivity to focA;
• and
• (iii) immunogenic reactivity to gabT relative to immunogenic reactivity to ycdG,
• wherein a reduction in the immunogenic reactivity of (i), (ii) and/or (iii) compared to the immunogenic reactivity of (i), (ii) and/or (iii) from an earlier time point identifies an improvement in the subject's condition, and an increase in the immunogenic reactivity of (i), (ii) and/or (iii) compared to the immunogenic reactivity of (i), (ii) and/or (iii) from the earlier time point identifies a worsening in the subject's condition, and
• wherein the microarray further comprises a set of E. coli polypeptides selected from the group consisting of rtn, cadA, lueO, mesJ, mhpF, modC, murA, nrfF, prpE, purK, tpiA, yciD, yejA, ygcE, ygfQ, yhjC, yjfH, yjiJ, yeeF, dgkA, dinI, emrY, folK, fsr, glnD, kch, maoC, msbA, nac, nagE, narI, ppx, prtC, rfaB, secF, secY/prlA, trkG, yafJ, yaiM, ybbC, ycbM, ydaA, ydbD, ydhV, yefI, yeiO, ygjR, yhiN, yjgT, yojl, yphD, yhcP, yhhT, yhiW, aceF, allP, ansP, aqpZ, atoE, brnQ, celD, cobU, codB, cybB, cydB, cydC, dgt, dnaQ, ebgA, emrB, emrD, exuR, fabH, fabZ, fadA, fepD, flhD, glnQ, glpF, gppA, greA, hemY, JW0438, JW1949, lipA, lpxC, malX, malZ, menG, mrdB, murG, mutT, narU, nfrB, nrfE, ompC, oppC, oppF, pbuX, pheP, phsE, pnuC, potC, pssR, ptsH, putP, queA, rfaL, rffG, rocE, rplO, sdhD, secB, sfsA, slyX, sucB, sucD, tauB, thiL, trkH, udk, uidB, virK, yaaH, yabK, yadQ, yaeG, yagG, yagM, yaiV, yajR, ybdS, ybfB, ybfC, ybgE, ybhA, ybhL, ybhM, ybhN, ybhR, ycaD, yccY, yciQ, yciR, yciS, ydcD, yddH, ydeF, ydeZ, ydfO, ydjS, ydjZ, yeaS, yehK, yehY, yejF, yfjY, ygeD, ygfF, yggH, yghK, yghT, ygjQ, yhaH, yhaO, yhbX, yhcO, yhdM, yhdT, yheG, yheU, yhfU, yhhL, yhhS, yhiP, yhiQ, yhjX, yiaL, yiaQ, yibL, yibQ, yicO, yidY, yifE, yigF, yihG, yjeM, yjfF, yjfP, yjfY, yjhB, ymdD, ynaJ, yneC, yneG, ynjC, yoaA, yohG, yphA, yphG, yqcE, and yzgL, or fragments thereof.

A method for monitoring the condition of a subject having Crohn's disease, the method comprising:

• (a) contacting a microarray comprising a set of E. coli polypeptides comprising era, ybaN, yhgN, focA, gabT and ycdG, with sera derived from the subject;
• and
• (b) detecting in the subject's sera:
• (i) immunogenic reactivity to era relative to immunogenic reactivity to ybaN;
• (ii) immunogenic reactivity to yhgN relative to immunogenic reactivity to focA;
• and
• (iii) immunogenic reactivity to gabT relative to immunogenic reactivity to ycdG,
• wherein a reduction in the immunogenic reactivity of (i), (ii) and/or (iii) compared to the immunogenic reactivity of (i), (ii) and/or (iii) from an earlier time point identifies an improvement in the subject's condition, and an increase in the immunogenic reactivity of (i), (ii) and/or (iii) compared to the immunogenic reactivity of (i), (ii) and/or (iii) from the earlier time point identifies a worsening in the subject's condition, and
• wherein the microarray further comprises a set of E. coli polypeptides selected from the group consisting of rpsK, rpsL, sixA, ycfF, yhdN, yjhA, gntU, phnE, rcsC, thiS, ycfA, yfjV, aceB, agaZ, aidA, argB, argC, aroF, aroK, aspA, atpB, baiF, basS, cedA, citB, citG, clpX, cysD, cysJ, cysM, cysW, dgxA, dicC, dinD, ecnB, eno, fadB, fba, fdhE, fecB, fecR, fimB, fimC, fliA, fliS, flxA, folP, frvX, ftn, fumB, gabD, galR, gcpE, glvB, grxA, grxC, gst, hemX, hflX, hisS, hofH, hoxK, hsdM, hycA, hycF, hypC, ibpB, infC, ivbL, lasT, LDR-ABC, LDR-D, lldR, mcrD, metB, metJ, mltB, mviN, narY, nuoE, phbA, phnB, phnG, phnM, ppdB, ptpS, ptsN, purM, radC, rbfA, rbsB, recN, rffD, rpiB, rplP, rplQ, rplT, rpmJ, rpsG, rpsR, selD, slyA, slyD, ssi6, sugE, tdcB, thiF, torA, trmD, ubiG, umuD, vacJ, wcaA, ybbA, ybbQ, ycbF, ycdB, yceD, ycgN, ydfA, ydfD, ydfR, ydhL, ydiL, yedF, yehR, yejG, yejO, yfeC, yfhD, yfiC, yfiD, yfjI, yfjQ, ygbA, ygbD, ygbO, ygcQ, ygeW, ygfY, yhaA, yhaC, yhaN, yhcI, yhcJ, yhfR, yhfV, yhgH, yhgI, yicC, yieF, yieJ, yigK, yihA, yihD, yihK, yiiF, yijD, yijF, yjaI, yjbI, yjbL, yjbQ, yjbR, yjcS, yjeB, yjeJ, yjgF, yjhC, yjhE, yjhF, yjhO, yjiA, yliG, ymfE, yohL, yphC, yrbB, rtn, cadA, lueO, mesJ, mhpF, modC, murA, nrfF, prpE, purK, tpiA, yciD, yejA, ygcE, ygfQ, yhjC, yjfH, yjiJ, yeeF, dgkA, dinI, emrY, folK, fsr, glnD, kch, maoC, msbA, nac, nagE, narI, ppx, prtC, rfaB, secF, secY/prlA, trkG, yafJ, yaiM, ybbC, ycbM, ydaA, ydbD, ydhV, yefI, yeiO, ygjR, yhiN, yjgT, yojl, and yphD, or fragments thereof.