Global distribution of epidemic-related Shiga toxin 2 encoding phages among enteroaggregative Escherichia coli


Table S1:

Information of publicly available genomic data used in the phylogenetic analysis Table S2: 
Comprehensive in silico typing of O86 isolates from Japan and EnteroBase (independent Excel file) 
Table S3: 

Relatedness of key virulence determinants of enteroaggregative

Escherichia coli (EAEC) in Shiga toxin-producing EAEC isolates 

Table S4:

Results of NCBI-BLAST against the Stx2a phage of JE86-ST05 

Table S1 .

 S1 Information of publicly available genomic data used in the phylogenetic analysis 


	Isolate ID	Serotype/Species Pathotype	Phylogenetic group Accession no.	Source	Year Place
	APEC_O1	O1:H7	APEC	a	B2	CP000468	Poultry	-b	USA
	12009	O103:H2	STEC		B1	AP010958	Human	2001 Japan
	2009EL-2071	O104:H4	Stx-EAEC	B1	CP003301	Human	2009 Republic of Georgia
	2009EL-2050	O104:H4	Stx-EAEC	B1	CP003297	Human	2009 Republic of Georgia
	2011C-3493	O104:H4	Stx-EAEC	B1	CP003289	Human	2011 USA
	11128	O111:H8	STEC		B1	AP010960	Human	2001 Japan
	E2348/69	O127:H6	EPEC		B2	FM180568	Human	1969 UK
	Sakai	O157:H7	STEC		E	BA000007	Human	1996 Japan
	MG1655	O16:H48	Commensal	A	CP025268	-	-	USA
	UMN026	O17:H18	ExPEC	D	CU928163	Human	1999 USA
	I-151	O174:H46	STEC		E	SAMN02732277	Human	2005 Germany
	11368	O26:H11	STEC		B1	AP010953	Human	2001 Japan
	042	O44:H18	EAEC		D	FN554766	Human	1983 Peru
	S88	O45:H7	ExPEC	B2	CU928161	Human	1999 France
	536	O6:H31	UPEC	B2	CP000247	Human	1982 Germany
	IAI39	O7:H45	UPEC	F	CU928164	Human	1980s France
	H10407	O78:H11	ETEC		A	FN649414	Human	1973 Bangladesh
	LF82	O83:H1	AIEC		B2	CU651637	Human	-	France
	290590	O86:H27	EAEC		B1	SRR5470218	Human	2016 UK
	300650	O86:H27	EAEC		B1	SRR4788097	Human	2016 UK
	ERS1232417	O86:H32	-		E	ERR1789882	-	-	-
	AMR520-5149	O86:H32	STEC		A	SRR8079366	Livestock	2014 Canada
	AZ-TG60412	O86:H51	-		B1	SRR1186338	Poultry	2013 USA
	C00009219	O86:H51	-		A	ERR296688	-	-	-
	C309	O86:H32	STEC		A	SRR5927204	Wild Animal 2014 USA
	CFS3323	O86:H27	-		B1	ERR3333544	Livestock	2004 Germany
	DRS013916	O86:H27	EAEC		B1	DRR015808	-	-	Japan
	ECO0117	O86:H51	-		B1	ERR439680	Human	2009 UK
	EH3148	O86:H27	Stx-EAEC	B1	Uploaded Reads c	-	2018 Belgium
	FSIS11815123	O86:H32	-		A	SRR8137335	Livestock	2018 USA
	FSIS11919008	O86:H51	-		B1	SRR8754961	Livestock	2019 USA
	KS14_4E	O86:H51	-		B1	DRR103021	Livestock	2013 Japan
	MOD1-EC6197	O86:H27	-		B1	SRR3465496	Wild Animal 2013 USA
	PSU-0601	O86:H51	-		B1	SRR7042103	Wild Animal 1999 USA
	PSU-0715	O86:H51	-		B1	SRR7429964	Livestock	2012 USA
	TM63	O86:H51	-		E	DRR138475	Human	2018 Thailand
	DTU2016_763	O86:H27	-		E	Uploaded Reads	Poultry	2015 Denmark
	DTU2017-803	O86:H27	-		E	ERR2091428	Poultry	2016 Denmark
	DTU2017-855	O86:H51	-		E	ERR2091353	Poultry	2016 Denmark
	ESBL-15/0220	O86:H51	-		B1	ERR2019096	Livestock	2015 Austria
	2012EL-1823B	E. albertii	-		-	CP030783	Human	2012 USA
	b -, not available.								

cUploaded directly to EnteroBase. a APEC, avian pathogenic E. coli ; STEC, Shiga toxin-producing E. coli ; Stx-EAEC, Shiga toxin-producing enteroaggregative E. coli ; EPEC, enteropathogenic E. coli ; ExPEC, extraintestinal pathogenic E. coli ; EAEC, enteroaggregative E. coli ; UPEC, uropathogenic E. coli ; ETEC, enterotoxigenic E. coli ; AIEC, adherent invasive E. coli . 
Table S3 .

 S3 Relatedness of key virulence determinants of enteroaggregative Escherichia coli (EAEC) in Shiga toxin-producing EAEC isolatesSimilarity compared to JE86-ST02 or JE86-ST05: ref, reference; number, similarirty %; ND, not detected under the criteria of > 90% length and > 60% identity. 


	Function	Gene	Encoding replicons	JE86-ST02 JE86-ST05 290590 O86:H27	300650	DRS013916 EH3148	O104:H4 2011C-3493 226 O111:H21
	agg regulator	aggR	pAA	ref	a	100	100	100	100	100	96.2	96.2
		aggA		ref		100	100	100	100	100	ND	b	ND b
	AAF/III	aggB aggC	pAA	ref ref		100 100	100 ND	100 96.3	100 100	99.6 99.8	ND ND		ND ND
		aggD		ref		100	100	100	100	100	ND		ND
		aap		ref		100	100	100	100	100	96.3	96.3
		aatP		ref		100	100	100	100	99.9	95.0	95.0
	dispersin and transporter	aatA aatB	pAA	ref ref		100 100	100 100	100 100	100 100	100 100	95.3 96.2	95.5 96.1
		aatC		ref		100	99.9	100	100	100	96.2	96.2
		aatD		ref		100	100	100	100	100	92.9	92.8
		aaiA		ref		100	100	100	100	100	100	100
		aaiB		ref		100	100	100	100	100	99.9	99.9
		aaiC		ref		100	100	100	100	100	99.8	99.6
		aaiD		ref		100	100	100	100	100	100	100
		aaiE		ref		99.9	99.9	100	100	100	99.9	99.9
		aaiF		ref		100	100	100	100	100	99.9	100
		aaiG		ref		100	100	100	100	100	100	99.9
	T6SS	aaiH	Chromosome	ref		100	100	100	100	100	100	100
		aaiI		ref		100	100	100	100	100	100	100
		aaiJ		ref		100	100	100	100	100	100	100
		aaiK		ref		100	100	100	100	100	99.8	100
		aaiL		ref		100	100	100	100	100	99.9	99.9
		aaiM		ref		100	100	100	100	100	99.8	99.7
		aaiN		ref		100	100	100	100	100	99.9	99.9
		aaiO		ref		100	100	100	100	99.9	99.9	99.9
		pet	Plasmid	ND	ND	ND	ND	ND	ND	ND		ND
		pic	Chromosome	ref		100	100	100	100	100	99.9	99.9
	SPATEs	sat	Chromosome	ref		100	100	100	100	100	ND		99.9
		sigA	Chromosome	ND	ref	ND	ND	ND	ND	98.0	ND
		sepA	pAA	ref		100	100	100	100	100	99.6	ND
		fis	Chromosome	ref		100	100	100	100	100	100	100
	Biofilm	shf	pAA	ref		100	100	100	100	100	98.5	ND
		yafK	Chromosome	ref		100	100	100	100	100	99.5	99.5

b agg operon of AAF/III was absent but the agg operon of the following subtypes is present: O104:H4, AAF/I; O111:H2, AAF/V. a 
e Non-synonymus mutation (V136A) in hypothetical gene. 
f Synonymus mutation in rzpD gene and hypothetical gene.
Keiko Kimata, Kenichi Lee, Masanori Watahiki, Junko Isobe, Makoto Ohnishi, Sunao Iyoda
Global distribution of epidemic-related Shiga toxin 2 encoding phages among enteroaggregative Escherichia coli