Why the discovery of adherent-invasive Escherichia coli molecular markers is so challenging?

Table 2 Review of studies in which the prevalence of particular virulence genes has been examined according to the adherent-invasive Escherichia coli pathotype

Ref.	AIEC	Non-AIEC	Genes studied
Darfeuille-Michaud et al[1], 2004	26	0	afaD, eae, ipaC, tia
Martinez-Medina et al[11], 2009	22	38	afa/draBC, bfpA, cdtB,cnf1, eae, eltA, est, fimAvMT78, fimH, hlyA, ibeA, ipaH, iucD, neuC, papC, pCDV432, sfa/focDE, stx1, stx2
Martinez-Medina et al[26], 2009	27	59	afa/draBC, bfpA, bmaE, cdtB, cnf1, cvaC, eae, eltA, est, fimA, fimAvMT78, fimH, focG, gafD, hlyA, ibeA ,ipaH, iroN, iucD, kpsMII, kpsMIII, malX, neuC, papC, papGI, papGII, papGIII alleles,pCDV432, sat, sfa/focDE, sfaS, stx1, stx2, traT, usp
Martinez-Medina et al[37], 2011	49	134	afa/draBC, astA, bmaE, chuA, cnf, csgA, cvaB, cvaC, eaI, eitA, eitC, etsB, etsC, fimC, focG, fyuA, gafD, gimB, hlyA, hlyF, hra, ibeA, iha, ireA, iroN, irp2, iss, iucD, iutA, kpsMTII, malX, mat, neuC, nfaE, ompA, ompT, papC, papEF, papGI, papGII, papGII/III, papGIII, pic, pks, sat, sfa/foc, sfaS, sitA, sitD (chr.), sitD (epis.), tia, traT, tsh, vat
Chassaing et al[5], 2011	249		lpfA
Conte et al[16], 2014	27	0	afa/draBC, aggR, cnf1, cvaC, fimH, focG, fyuA, gafD, hlyA, ibeA, iutA, kpsMT1, kpsMT5, kpsMTII, kpsMTIII, nfaE, pAA, PAI1, papA, papC, papEF, papG alleles, sfa/focDE, traT
Vazeille et al[39], 2016	35	103	lpfA + gipA
Céspedes et al[13], 2017	15	37	afa/draBC, aufA, cdtB, chuA, cnf1, cvaC, eaaA, eatA, ecNA144, espC, espP, fhuD, fimAvMT78 , fimH, gipA, hlyA, ibeA, irp2, neuC, papC, pet, pic, ratA, sat, sepA, sfa/focDE, sigA, tsh, vat
Dogan et al[40], 2018	19	57	afaC, chuA, cnf1, colV, focG, fyuA, gsp, hcp, ibeA, iss, kpsMII, lpfA, malX, papC, pduC, pmt1, ratA, sfaDE, traC
Camprubí-Font et al[38], 2019	48	56	afa/draBC, bmaE, csgA, fimC, focG, gafD, hra, iha, mat, nfaE, papC, papEF, papGII/III, papGI, papGII, papGIII, sfa/foc, sfaS, tsh, chuA, eitA, eitC, fyuA, ireA, iroN, irp2, iucD, iutA, sitA, sitD, (epis.), sitD (chr.), iss, neuC, kpsMTII, ompA, ompT, traT, astA, cnf, sat, vat, hlyA, hlyF, ibeA, gimB, tia, malX, pic, pks, eaI, cvaB, cvaC, etsB, etsC, lpfA141, lpfA154, fimH, chiA, astA, cnf, sat, vat
Camprubí-Font et al[46], 2019	13	30	ompA, ompC, ompF

Genes associated with pathotype or origin of isolation are highlighted in bold.

¹Pathogenicity island described in a virulent uropathogen. AIEC: Adherent-invasive Escherichia coli; CD: Crohn’s disease patients; UC: Ulcerative colitis patients.