Table 3

 Microbial tissue phenotypes encountered from control tissues and tissues of patients with inflammatory bowel disease*

DiseasePatientE coli† groupNon-E coliSPATEE coli adhesinsE coli H-typeE coli type 1 fimbriae
APEC, avian pathogenic E coli; ND, E coli not detected; PAI, pathogenicity island; SPATE, serine protease autotransporters; UPEC, uropathogenic E coli.
*A total of 84 biopsy specimens from 47 subjects were used. Data are not shown by site, and were pooled because the correlation between bacterial species and site, within and between subjects, was low (r = 0.22).
†A total of 28 E coli strains and 34 non-E coli were picked and assessed.
‡Identity was determined by sequencing the 16S rDNA between with 27f and 342r.
§Bft1 and Bft2 are enterotoxins produced by Bacteroides fragilis detected from tissue by the nested-PCR method.
¶sfp is a gene cluster of sorbitol-fermenting enterohaemorrhagic E coli O157:H-.
**sfa gene coding for S-fimbriae minor subunit of E coli UTI89.
††Sat gene coding for autotransporter toxin Sat identified in Escherichia fergusonii.
Control41ANDEnterobacter spND
Bacteroides fragilis Bft1§
Control43AB2VatAg43, PAI IH7Bovine
Control48BB2Vat, Pic-likeSfp¶H4APEC
Control50AB2Vat, Sat, PicAg43H1APEC
Control58ND Enterobacter flavescens ND
Control59BND Klebsiella oxytoca ND
Control73AAKlebsiella spNDAIDA-IH12Bovine
Control69ANDEnterococcus spND
Bacteroides fragilis Bft1
Control76ND Escherichia fergusonii SigA, Sat††, SepA
Staphylococcus epidermidis
Staphylococcus capitis
Bacteroides fragilis Bft2§
Control80ND E fergusonii SigA, Sat††, SepA
Klebsiella sp
Control81ND Enterococcus durans ND
Control87NDKlebsiella spND
Control90ANDAIDA-I, Ag43H11Bovine
Control17BDNDAg43H4UPEC
Control88AKlebsiella spNDAIDA-IH21Bovine
CD15BB2Vat, Pic-likeAg43H4APEC
CD79AB2Vat, Sat, PicAg43H1APEC
CD91AB1Acidovorax spNDAIDA-IH21Bovine
CD118ND Staphylococcus auricularis ND
CD120ADEspIPAI I, AIDA-I, Ag43H52Bovine
CD124AND E fergusonii Enterococcus faecium SigA, Sat††, SepA
Bacteroides fragilis Bft1
CD125BND Klebsiella oxytoca ND
CD126CB2NDAIDA-I, Ag43H39Bovine
CD132B2SatAfaE-3, Ag43, AIDA-IH4Bovine
CD137NDKlebsiella spND
CD138ND Staphylococcus aureus ND
Pseudomonas putida
Klebsiella sp
CD146B2VatSfa**, Ag43, PAI IH7APEC
CD149B2Vat, PicSfa, Ag43, PAI IH5APEC
CD128B2 E fergusonii Vat, SigA, Sat††, SepASfaH7UPEC
UC117ADNDAIDA-I, Ag43H18Bovine
UC119AND Enterococcus faecium ND
UC121B1NDNDH10Bovine
UC122ND Enterococcus faecalis ND
Bacteroides fragilis Bft1
UC127AB2 Enterobacter cloacae Vat, Sat, PicF1CH7Bovine
UC130ND Bacillus licheniformis ND
Bacillus pumilus
UC131AB2 E fergusonii Vat, Sat††, Pic, SigA, Sat, SepAAg43, PAI IH10APEC
Bacteroides fragilis Bft2
UC133ANDKlebsiella spND
UC135B2 Klebsiella oxytoca PicAIDA-I, Ag43H31Bovine
UC136B2NDVatAg43, PAI IH7Bovine
UC139DNDNDAIDA-IH6APEC
UC140ANDEnterococcus spND
UC141B2NDNDSfa, Ag43, PAI IH7APEC
UC142B2NDVatAfaE-3, Ag43H5APEC
UC143B2NDSat, Pic-likeAfaE-3, Ag43H4APEC
UC145BB2NDVat, Pic-likeAg43H4Bovine
UC147B2Klebsiella spVatSfa, Ag43H5APEC
UC134ANDKlebsiella spND