+ + - + - - - - - - - + - + - - - + + - O136:H30 - + - - - - - - - - - + - + - - - - + - O99:H9 - + - - - - - - - - - + + + - - - + + - wzx- Onovel24:H20 - + - - - - - - - - + + + + - - - + + - O140:H21 + - - - - - - - - - - + - + - - - + + - O102:H4 - + - - - - - - - - - + - + - - - . + - O129:H23 - + - - - - - - - - + + + + - - - + + - O17:H18 - + - + + + + - - - + + + + + - - + + - O76:H34 - + - - - - - - - - - + + + - - - + + - O26:H11 + + - + + + - + - + - + - + - + + + + + O129:H23 - + - - - - - - - - + + + + - - - + + - O154:H10 - + - - - - - - - - - + - + - - - + + - O116:H21 + + + - + + + - - - - + - + - - - + + - wzx- Onovel5:H19 - + + + + + + - - - - + - + - - - + + - wzx- Onovel5:H19 - + + + + + + - - - - + - + - - - + + - O87:H7 + + - - - - - - - - - + - + - - - + + - O129:H21 + + + - + + + - - - - + - + - - - + + - O26:H11 + + - + + + - + - + - + - + + + + + + + O26:H11 - + - - - - - - - + - + + + - - - + + - O163:H19 + + + - - - - - + - - + - + - - - + + - O40:H19 + + - - + + + - - - - + - + - - - + + - O22:H21 + + - - + - - - - - - + - + - - - + + - + = gene present, -= gene absent
Autotransporter protein genes= (ehaA, ehaB, epeA and agn43), serine protease gene= (espP), toxins (hlyA, subA, east1 and cdtA), type III translocated gene (espA), iron uptake gene (chuA), invasins genes (fimH, aslA, ibeB and ompA) and adhesins genes= (toxB, eaeA, ecpA, paa and csgA). 
Table S5: Annotation results of antimicrobial resistance for non-O157 E. coli. 

+ = gene present, -= gene absent

Beta-lactams (TEM-105 and TEM-150), streptomycin (aadA1, aadA2 aadA5), sulfonamide ( sul2 and sul3), tetracycline (tetACD), phenicol (cmlA6 and floR), diaminopyrimidine (dfrA12), lincosamides (linG), polymyxin (ugd) and streptogramin (vgaC). 

FLOFigureFigure S2 :

 S2 Figure S1: A flow chart illustrating bacterial characterization. 


Table S1 :

 S1 PCR primer sequences. 


	Gene	Primer sequence (5′ to 3′)	Gene target Product	Reference
				size (bp)	
	ehlyA-F	(F) GCATCATCAAGCGTACGTTCC	hlyA	534	
		(R) AATGAGCCAAGCTGGTTAAGCT			
	eaeA	(F) GACCCGGCACAAGCATAAGC	eaeA	384	(Paton and Paton, 1998)
		(R) CCACCTGCAGCAACAAGAGG			
	stx1	(F) ATAAATCGCCATTCGTTGACTAC	stx1	180	
		(R) AGAACGCCCACTGAGATCATC			
	stx2	(F) GGCACTGTCTGAAACTGCTCC	stx2	255	
		(R) TCGCCAGTTATCTGACATTCTG			
	stx2a	(F) AGATATCGACCCCTCTTGAA	Stx2a	969	(He et al., 2012)
		(R) GTCAACCTTCACTGTAAATG			
	uidA	(F) CTGGTATCAGCGCGAAGTCT	uidA	600	(Anbazhagan et al., 2010)
		(R) AGCGGGTAGATATCACACTC			
	rfbO157	(F) CGGACATCCATGTGATATGG	rfbO157	259	(Morin et al., 2004)
		(R) TTGCCTATGTACAGCTAATCC			
	Streptomycin	(F) TATCCAGCTAAGCGCGAACT	aadA1	447	(Momtaz et al., 2012)
		(R) ATTTGCCGACTACCTTGGTC			
	Chloramphenicol	(F) AGTTGCTCAATGTACCTATAACC	catA1	547	(Van et al., 2008)
		(R) TTGTAATTCATTAAGCATTCTGCC			
	Tetracycline A	(F) GGTTCACTCGAACGACGTCA	tetA	577	
		(R) CTGTCCGACAAGTTGCATGA			(Randall et al., 2004)
	Tetracycline B	(F) CCTCAGCTTCTCAACGCGTG	tetB	634	
		(R) GCACCTTGCTGATGACTCTT			
	Beta-lactams	(F) ATGAGTATTCAACATTTCCGTGTC	blaTEM-1	861	(Haidinger et al., 2003)
		(R) TTACCAATGCTTAATCAGTGAGG			
	Biofilm-related	(F) ACTCTGACTTGACTATTACC	csgA	200	
		(R) AGATGCAGTCTGGTCAAC			(Knobl et al., 2012)
	Biofilm-related	(F) TTTCGATTGTCTGGCTGTATG	crl	250	
		(R) CTTCAGATTCAGCGTCGTC			
	Biofilm-related	(F) TTATCGCCTGAGGTTATCGTTTGC	csgD	501	(Ogasawara et al., 2010)
		(R) TCTTCAGGCTCTATTATTCTTCTGGATAT			
	Biofilm-related	(F) TATCGCCTGGATTACTGGCAAC	rpoS	1900	(Olsen et al., 1993)
		(R) TAGGACGCTGACGTGTCTTATC			
	Biofilm-related	(F) TGCAGAACGGATAAGCCGTGG	fimH	506	(Johnson and Stell, 2000)
		(R) GCAGTCACCTGCCCTCCGGA			
	Biofilm-related	(F) CCGGCGGGCAATGGGTACA	flu	385	(Restieri et al., 2007)
		(R) CAGCTCTCACAATCTGGCGAC			
	Biofilm-related	(F) ATATCGGCTAAAGTGGAACAGGTCC	ehaA a	627	
		(R) TGCTTCCTGGCATTAACTTCACC			(Friedrich et al., 2002)
	Biofilm-related	(F) AGTGCATGACTACTGATTGTGCTG	ehaA b	887	
		(R) CACATTAAACAAACCGCTCTGG			

Table S2 :

 S2 Reference values used to classify isolates as susceptible, intermediate resistant and resistant. 


	Antimicrobial agent	Disk content	S	I	R
	Ampicillin	10 µg	≥ 17	14-16	≤
	Amoxicillin-clavulanate	20/10 µg	≥ 18	14-17	≤
	Ampicillin-sulbactam	10/10 µg	≥ 15	12-14	≤
	Cefepime	30 µg	≥ 25	19-24	≤
	Cefotaxime	30 µg	≥ 26	23-25	≤
	Cefoxitin	30 µg	≥ 18	15-17	≤
	Ceftazidime	30 µg	≥ 21	18-20	≤
	Aztreonam	30 µg	≥ 21	18-20	≤
	Imipenem	10 µg	≥ 23	20-22	≤
	Meropenem	10 µg	≥ 23	20-22	≤
	Gentamicin	10 µg	≥ 15	13-14	≤
	Streptomycin	10 µg	≥ 15	12-14	≤
	Tetracycline	30 µg	≥ 15	12-14	≤
	Nalidixic acid	30 µg	≥ 19	14-18	≤
	Norfloxacin	10 µg	≥ 17	13-16	≤
	Trimethoprim-	1.25/23.75µg	≥ 16	11-15	≤
	sulfamethoxazole				
	Chloramphenicol	30 µg	≥ 18	13-17	≤
	Colistin	10 µg	≥ 17	13-17	≤
	S= Susceptible, I= Intermediate and R= Resistance.			

Table S3 :

 S3 Non-O157 E. coli isolates sequenced in this study. 


	Isolate ID	Serogroup	Number of	Total length	GC (%)	N50
			contigs	(bp)		
	3	O99:H9	116	4686813	50.79	222406
	11	O156:H25	299	5181977	50.43	94802
	12	O108:H2	103	4881051	50.72	186185
	14	O136:H30	128	4564407	50.92	105160
	15	O99:H9	103	4686475	50.78	260468
	22	wzx-Onovel24:H20	94	4964550	50.53	478048
	25	O140:H21	247	5507075	50.47	148987
	30	O102:H4	376	5244869	50.65	87095
	32	O129:H23	203	5501418	50.53	240397
	37	O17:H18	139	5169910	50.45	186852
	38	O76:H34	219	4812816	50.88	114298
	42	O26:H11	494	5526211	50.4	101076
	50	O129:H23	204	5502410	50.52	211833
	56	O154:H10	144	4706567	50.66	96083
	60	O116:H21	195	5081941	50.7	177288
	64	wzx-Onovel5:H19	137	5056230	50.74	161129
	65	wzx-Onovel5:H19	135	5058237	50.74	236278
	67	O87:H7	127	4764651	50.63	195836
	68	O129:H21	171	5105006	50.67	156897
	69	O26:H11	478	5562801	50.4	112464
	72	O26:H11	107	4610054	50.96	161578
	76	O163:H19	303	5171039	50.57	117460
	77	O40:H19	156	4930994	50.7	151142
	80	O22:H21	87	4795733	50.72	185546

Table S4 :

 S4 Annotation of virulence factors for non-O157 E. coli isolates. 


	Isolate ID Serogroup								Virulence factor related genes								
			ehaA ehaB epeA	agn43 espP	hlyA	subA east1 cdtA espA chuA fimH aslA ibeB ompA toxB paa ecpA csgA eaeA
	3	O99:H9	-	+	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	+	+	-
		O156:H25	+	+	-	+	+	+	-	+	-	+	-	+	-	+	-	-	+	+	+	+
		O108:H2																				

Isolate ID


Serogroup

Antimicrobial related genes TEM-105 TEM-150 AadA1 aadA2 aadA5 sul2 sul3 tet(A) tet(C) tet(D) cmlA6 dfrA12 linG floR ugd vgaC