Supplementary Material (Includes 3 Tables Numbered Table S1 to S3)

Supplementary Material (includes 3 tables numbered table S1 to S3)

Table S1.

Collection of strains used in the study with their origins.

Strain ID Source JM221 Mathewson et al. 1987 17-2 Nataro et al. 1993 255/1-1 JP Girardeau-INRA H10407 Evans et al. 1975 DAEC395 Forestier et al. 1996 DAECT2 Scaletsky et al. 2002 DAEC483 Forestier et al. 1996 DAEC7 Scaletsky et al. 2002 E2539-C1 Tornieporth et al. 1995 EDL1493 Tornieporth et al. 1995 ECOR10 Ochman and Selander 1984 ECOR20 Ochman and Selander 1984 ECOR13 Ochman and Selander 1984 ECOR1 Ochman and Selander 1984 DEC6a Reid et al. 1999 ECOR24 Ochman and Selander 1984 ECOR17 Ochman and Selander 1984 ECOR4 Ochman and Selander 1984 EIEC85b Escobar-Páramo et al. 2003 ECOR23 Ochman and Selander 1984 DAEC5 Scaletsky et al. 2002 DEC9a Reid et al. 1999 DEC8b Reid et al. 1999 55989 Bernier et al. 2002 248/1-2 JP Girardeau-INRA DEC11a Reid et al. 1999 DEC12a Reid et al. 1999 DEC13a Reid et al. 1999 ECOR68 Ochman and Selander 1984 H-19 Smith et al. 1983 DEC10a Reid et al. 1999 469 Yves Germani-Inst.Pasteur TX-1 Tornieporth et al. 1995 ECOR26 Ochman and Selander 1984 ECOR27 Ochman and Selander 1984 11097 Bernier et al. 2002 ECOR45 Ochman and Selander 1984 384P Bernier et al. 2002 DAEC221 Forestier et al. 1996

1 DEC15a Reid et al. 1999 DAECT437 Forestier et al. 1996 ECOR58 Ochman and Selander 1984 ECOR34 Ochman and Selander 1984 11074 Bernier et al. 2002 440 Yves Germani-Inst.Pasteur DEC14a Reid et al. 1999 DAEC126 Forestier et al. 1996 DAECT179 Forestier et al. 1996 ECOR70 Ochman and Selander 1984 DEC7a Reid et al. 1999 SB01-97 Escobar-Páramo et al. 2003 SS92a Escobar-Páramo et al. 2003 SB11-56 Escobar-Páramo et al. 2003 SD01-77 Escobar-Páramo et al. 2003 EDL933 Perna et al. 2001 RIMD0509952 Hayashi et al. 2001 ECOR37 Ochman and Selander 1984 EDL931 Bohm et al. 1992 DEC5d Reid et al. 1999 DEC3a Reid et al. 1999 DEC4a Reid et al. 1999 DAEC218 Forestier et al. 1996 ECOR50 Ochman and Selander 1984 ECOR49 Ochman and Selander 1984 DAEC19 Scaletsky et al. 2002 56390 Bernier et al. 2002 DAECT192 Forestier et al. 1996 ECOR47 Ochman and Selander 1984 ECOR46 Ochman and Selander 1984 DAEC141 Forestier et al. 1996 DAEC162 Forestier et al. 1996 ECOR35 Ochman and Selander 1984 DAEC9 Scaletsky et al. 2002 ECOR40 Ochman and Selander 1984 ECOR41 Ochman and Selander 1984 DAECT14 Scaletsky et al. 2002 042 Nataro et al. 1985 DAECT19 Scaletsky et al. 2002 ECOR60 Ochman and Selander 1984 ECOR59 Ochman and Selander 1984 2348/69 Levine et al. 1978 DEC1a Reid et al. 1999 DEC2a Reid et al. 1999 ECOR51 Ochman and Selander 1984 ECOR52 Ochman and Selander 1984 CFT073 Welch et al. 2002 ECOR57 Ochman and Selander 1984 ECOR62 Ochman and Selander 1984 RS218 Silver et al. 1980

2 ECOR64 Ochman and Selander 1984 DAEC18 Scaletsky et al. 2002 EC7372 Pham et al. 1997 DAEC11 Scaletsky et al. 2002 IH11128 Vaisanen-Rhen 1984 DAEC20 Scaletsky et al. 2002 C1845 Bilge et al. 1989 381A Bernier et al. 2002 DAEC213 Forestier et al. 1996 E. fergusonii Lawrence et al. 1991

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6 Table S2

List of the primers used for the sequencing of the six essential genes (trpA to polB) used in the strain phylogenetic analysis as well as those used to generate the specific probes for detecting the presence of the different VFs and to perform their sequences.

Gene Primer sequence Source trpA 5’-ATGGAACGCTACGAATCTCTGTTTGCCC-3’ Escobar-Páramo et al. 2003 5’-TCGCCGCTTTCATCGGTTGTACAAA-3’ trpB 5’-ACAATGACAACATTACTTAACCCCT-3’ Escobar-Páramo et al. 2003 5’-TTTCCCCTCGTGCTTTCAAAATATC-3’ pabB 5’-TTTTACACTCCGGCTATGCCGATCA-3’ Guttman and Dykhuizen

1994 5’-GCTGCGGTTCCAGTTCGTCGATAAT-3’ putP 5’-GCGACGATCCTTTACACCTTTATTG-3’ Escobar-Páramo et al. 2003 5’-CGCATCGGCCTCGGCAAAGCG-3’ icd 5’-GAAAGTAAAGTAGTTGTTCCGG-3’ Escobar-Páramo et al. in

press 5’-GATGATCGCGTCACCAAAYTC-3’ polB 5’-TCAACGCCTGGTTTGCCAACTA-3’ Bjedov et al. 2003 5’-TCCAGTTCTAATGCGCTGGTCA-3’ papC 5’-GACGGCTGTACTGCAGGGTGTGGCG-3’ Le Bouguenec et al., 1992 5’-ATATCCTTTCTGCAGGGATGCAATA-3’ papG 5’-GGGATGAGCGGGCCTTTGAT-3’ Johnson and Brown 1996 5’-CGGGCCCCCAAGTAACTCG-3’ 5’-GGCCTGCAATGGATTTACCTGG-3’ 5’-CCACCAAATGACCATGCCAGAC-3’ sfa/foc 5’-CTCCGGAGAACTGGGTGCATCTTAC-3’ Le Bouguenec et al., 1992 5’-CGGAGGAGTAATTACAAACCTGGCA-3’ sfaS 5’-GTGGATACGACGATTACTGTG-3’ Johnson and Stell 2000 5’-CCGCCAGCATTCCCTGTATTC-3’ focG 5’-CAGCACAGGCAGTGGATACGA-3’ Johnson and Stell 2000 5’-GAATGTCGCCTGCCCATTGCT-3’ iroN 5’-AATCTTACCGGCAATAGCGC-3’ Bonacorsi et al. 2003 5’-GCTATAACGCACGGAGTTAC -3’ hlyCA 5’-AGGTTCTTGGGCATGTATCCT-3’ Bingen et al. 1998 5’-TTGCTTTGCAGACTGCAGTGT-3’ cnf1 5’-CAGTGACCGGATCTCCGTTAT-3’ Picard et al. 2001 5’-CGTGTAATTCTTCTGTACTTCC-3’ hra 5’-CAGAAAACAACCGGTATCAG-3‘ Bingen-Bidois et al. 2002 5’-ACCAAGCATGATGTCATGAC-3’ chuA 5’-GACGAACCAACGGTCAGGAT-3’ Clermont et al. 2000 5’-TGCCGCCAGTACCAAAGACA-3’ iucC 5'-AAACCTGGTTTACGCAACTGT-3' Bingen et al. 1998

7 5’-ACCCGTCTGCAAATCATGGAT-3’ afaBC/daaC 5’-GCTGGGCAGCAAACTGATAACTCTC-3’ Le Bouguenec et al., 1992 5’-CATCAAGCTGTTTGTTCGTCCGCCG-3’ afaD 5’-GAAAGCGGTAAGCTGAAGGC-3’ This study 5’-CCGGTGAAATAAATACTCTC-3’ M030 5'-GATCAGCGCCACAATTAC-3' Blanc-Potard et al. 2002 5'-CAGTGGAGTCTGCTGCTC-3' AA 5’-CTGGCGAAAGACTGTATCAT-3’ Baudry et al. 1990 5’-CAATGTATAGAAATCCGCTGTT-3’ eaeA 5’-GCAAATTTAGGTGCGGGTCAGCGTT-3’ Germani et al. 1997 5’-GGCTCAATTTGCTGAGACCACGGTT-3’ bfpA 5’-CAATGGTGCTTGCGCTTGCT-3’ Tornieporth et al. 1995 5’-GCCGCTTTATCCAACCTGGT-3’ ST 5’-TCTGTATTGTCTTTTTCACC-3’ Tornieporth et al. 1995 5’-TTAATAGCACCCGGTACAAGC-3’ LT 5’-GCGACAAATTATACCGTGCT-3’ Tornieporth et al. 1995 5’-CCGAATTCTGTTATATATGT-3’ stx1 5’-GAAGAGTCCGTGGGATTACG-3’ Pollard et al. 1990 5’-AGCGATGCAGCTATTAATAA-3’ stx2 5’-TTAACCACACCCACGGCAGT-3’ Pollard et al. 1990 5’-GCTCTGGATGCATCTCTGGT-3’ ehxA 5’-ACGATGTGGTTTATTCTGGA-3’ Schmidt et al. 1995 5’-CTTCACGTCACCATACATAT-3’ ipaB 5’-GGACGCAATTCAGGATATCAAGGAG-3’ Escobar-Páramo et al. 2003 5’-GCCCCAAGTATTTTCCCAACACAAC-3’

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11 Table S3: Extraintestinal virulence genotypes of studied strains and their PAI-like content

Strains Phylo sfa/focD Adhesin iroN iucC papC papG hlyC cnf1 hra PAI-like type* group E type allele A

17-2 A - - + + II + - - PAI ICFT073 ECOR24 A - - + + II + - + PAI ICFT073 DEC9a A - - - - - + - + 248/1-2 B1 - + - + - - - +

ECOR58 B1 + foc + ------PAI III536 DAECT179 C - - + + III + + + PAI IIJ96 DEC7a C - - - - - + - - ECOR50 D - - + + II - - + ECOR49 D - - + + II - - - ECOR46 D - - - + III - - + DAEC162 D - - - + - - - - ECOR40 D - - + + II - - - ECOR41 D - - + + II - - -

ECOR60 B2 + foc + - + III + + + PAI III536 + PAI IIJ96 ECOR51 B2 + foc + + + III + + + PAI III536 + PAI IIJ96 ECOR52 B2 + foc + - + III + + + PAI III536 + PAI IIJ96 CFT073 B2 + foc + + + II + - - PAI III536 + PAI ICFT073 ECOR57 B2 + foc + + + II - - - PAI III536 ECOR62 B2 - + + + II - - -

RS218 B2 + sfa + - + III + + + PAI III536 + PAI IIJ96 ECOR64 B2 + foc + ------PAI III536 EC7372 B2 - - + + II + - - PAI ICFT073

* PAI-like types were defined by simultaneous identification of different characteristic virulence factors such as sfa/foc and iroN (PAI III536); papGII, hly and iucC (PAI ICFT073); and hly, cnf1 and hra with or without pap (PAI IIJ96) (Bonacorsi et al. 2003)