Table 1 Genome characteristics of the isolates sequenced in this study.

From: Genomic diversity of EPEC associated with clinical presentations of differing severity

Specimen ID	Clinical outcome*	Location	BFP^†	Intimin type^‡	MLST ST (clonal group)	Phylogenomic lineage^§	Phylogroup^§	Draft genome size (Mb)	No. of contigs	Accession no.
100290	LI	The Gambia	+	alpha	236 (6)	EPEC1	B2	5.42	115	JHQV00000000
100343	LI	The Gambia	+	beta	140 (31)	EPEC7	B1	5.07	154	JHQW00000000
100414	LI	The Gambia	+	beta2	ND	EPEC4	B2	5.31	116	JHQX00000000
102550	LI	The Gambia	+	epsilon	555 (NA)	NC	B1	5.17	209	JHQY00000000
103385	LI	The Gambia	+	mu	ND	EPEC8	B2	5.05	149	JHQZ00000000
103573	LI	The Gambia	+	beta	140 (31)	EPEC7	B1	5.15	134	JHRA00000000
203741	LI	Mali	+	beta2	23 (7)	EPEC4	B2	5.05	446	JHRB00000000
300059	LI	Mozambique	+	mu	ND	EPEC8	B2	4.83	122	JHRC00000000
300262	LI	Mozambique	+	mu	ND	EPEC8	B2	4.97	111	JHRD00000000
302014	LI	Mozambique	+	beta	118 (17)	EPEC2	B2	5.23	527	JHRE00000000
302048	LI	Mozambique	+	alpha	ND	EPEC1	B2	5.27	436	JHRF00000000
302053	LI	Mozambique	+	lambda	ND	EPEC9	B2	4.94	420	JHRG00000000
302275	LI	Mozambique	+	mu	ND	EPEC8	B2	5.01	394	JHRH00000000
302662	LI	Mozambique	+	beta	140 (31)	EPEC7	B1	5.13	478	JHRI00000000
303289	LI	Mozambique	+	alpha	ND	EPEC1	B2	5.09	144	JHRJ00000000
400791	LI	Kenya	+	beta	140 (31)	EPEC7	B1	5.32	170	JHRK00000000
401031	LI	Kenya	+	alpha^‡	18 (6)	EPEC1	B2	5.04	170	JHRL00000000
401140	LI	Kenya	+	epsilon	433 (23)	EPEC5	A	5.00	255	JHRM00000000
401150	LI	Kenya	+	beta	140 (31)	EPEC7	B1	5.08	142	JHRN00000000
401264	LI	Kenya	+	mu	ND	EPEC8	B2	5.14	228	JHRO00000000
401954	LI	Kenya	+	beta	118 (17)	EPEC2	B1	5.32	287	JHRP00000000
402290	LI	Kenya	+	beta	140 (31)	EPEC7	B1	5.36	109	JHRQ00000000
702324	LI	Pakistan	+	alpha	228 (5)	EPEC9	B2	5.01	96	JHRR00000000
703533	LI	Pakistan	+	beta	ND	EPEC2	B1	5.30	549	JHRS00000000
100329	NSI	The Gambia	+	ND^‡	169 (23)	EPEC10	A	4.81	390	JHRT00000000
100854	NSI	The Gambia	−	theta	171 (23)	EPEC10	A	4.69	101	JHRU00000000
102536	NSI	The Gambia	+	beta2	23 (7)	EPEC4	B2	5.30	134	JHRV00000000
102598	NSI	The Gambia	+	alpha	236 (6)	EPEC1	B2	5.36	187	JHRW00000000
102929	NSI	The Gambia	−	zeta	535 (28)	NC	B1	5.24	147	JHRX00000000
103578	NSI	The Gambia	+	beta^‡	118 (17)	EPEC2	B1	5.11	376	JHRY00000000
200146	NSI	Mali	+	beta	140 (31)	EPEC7	B1	5.13	125	JHRZ00000000
300075	NSI	Mozambique	+	lambda	ND	EPEC9	B2	4.97	103	JHSA00000000
300214	NSI	Mozambique	+	mu	ND	EPEC8	B2	5.07	104	JHSB00000000
300231	NSI	Mozambique	+	beta2	23 (7)	EPEC4	B2	5.13	79	JHSC00000000
302150	NSI	Mozambique	+	beta2	ND	EPEC4	B2	4.94	286	JHSD00000000
302687	NSI	Mozambique	+	beta^‡	140 (31)	EPEC7	B1	5.00	394	JHSE00000000
302909	NSI	Mozambique	+	lambda	ND	NC	B2	4.79	254	JHSF00000000
303145	NSI	Mozambique	+	lambda	ND	EPEC9	B2	4.84	102	JHSG00000000
400738	NSI	Kenya	+	beta2	23 (7)	EPEC4	B2	5.16	102	JHSH00000000
401091	NSI	Kenya	+	beta	140 (31)	EPEC7	B1	5.09	89	JHSI00000000
401210	NSI	Kenya	−	epsilon^‡	433 (23)	EPEC5	A	4.57	781	JHSJ00000000
401588	NSI	Kenya	+	mu	ND	EPEC8	B2	5.10	100	JHSK00000000
401817	NSI	Kenya	+	mu	ND	EPEC8	B2	4.90	96	JHSL00000000
402310	NSI	Kenya	+	mu	ND	EPEC8	B2	5.11	94	JHSM00000000
402804	NSI	Kenya	+	beta	118 (17)	EPEC2	B1	5.48	135	JHSN00000000
702423	NSI	Pakistan	+	beta	140 (31)	EPEC2	B1	5.40	181	JHSO00000000
702626	NSI	Pakistan	+	beta	140 (31)	EPEC2	B1	5.23	237	JHSP00000000
100100	AI	The Gambia	−	gamma	78 (12)	NC	E	5.27	123	JHSQ00000000
100175	AI	The Gambia	−	epsilon2	254 (43)	NC	B1	4.85	89	JHSR00000000
102132	AI	The Gambia	−	gamma	78 (12)	NC	E	5.28	110	JHSS00000000
102535	AI	The Gambia	+	mu	ND	EPEC8	B2	4.79	97	JHST00000000
103338	AI	The Gambia	T	kappa	933 (NA)	EPEC5	A	4.66	112	JHSU00000000
103447	AI	The Gambia	+	epsilon	555 (NA)	NC	B1	5.09	182	JHSV00000000
200077	AI	Mali	+	eta	20 (NA)	NC	B2	5.09	141	JHSW00000000
300469	AI	Mozambique	+	alpha	228 (5)	EPEC9	B2	4.51	64	JHSX00000000
300847	AI	Mozambique	+	lambda	ND	EPEC9	B2	4.85	385	JHSY00000000
302137	AI	Mozambique	−	zeta	378 (7)	EPEC4	B2	5.10	44	JHSZ00000000
302312	AI	Mozambique	+	alpha	ND	NC	B2	5.15	115	JHTA00000000
303139	AI	Mozambique	+	epsilon	555 (NA)	NC	B1	4.93	150	JHTB00000000
303301	AI	Mozambique	+	alpha	ND	NC	B2	4.91	100	JHTC00000000
303341	AI	Mozambique	−	beta	140 (31)	EPEC7	B1	5.06	86	JHTD00000000
400929	AI	Kenya	+	alpha	236 (6)	EPEC1	B2	5.04	139	JHTE00000000
401195	AI	Kenya	+	alpha^‡	18 (6)	EPEC1	B2	4.89	194	JHTF00000000
401675	AI	Kenya	+	lambda	ND	NC	B2	4.95	125	JHTG00000000
402559	AI	Kenya	+	kappa	8 (3)	NC	B2	4.99	288	JHTH00000000
402981	AI	Kenya	+	beta2	23 (7)	EPEC4	B2	5.17	75	JHTI00000000
403116	AI	Kenya	+	alpha	ND	EPEC1	B2	4.97	108	JHTJ00000000
403341	AI	Kenya	−	beta	140 (31)	EPEC7	B1	5.17	111	JHTK00000000
700283	AI	Pakistan	+	kappa	562 (NA)	NC	B2	4.76	97	JHTL00000000
703450	AI	Pakistan	+	beta	ND	EPEC2	B1	5.52	289	JHTM00000000

ND, not determined; NC, not classified;
^*the clinical outcomes are LI (lethal), NSI (non-lethal symptomatic) and AI (asymptomatic);
^†a ‘+’ indicates that one or more genes of the BFP operon are present, ‘T’ indicates an isolate that has a truncated bfp operon and ‘–’ indicates that no BFP genes were detected;
^‡the intimin types of these isolates are truncated and these are the most related intimin types;
^§the phylogenomic lineage and phylgroup designations are based on the genome-based phylogeny in Fig. 1.

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Table 1 Genome characteristics of the isolates sequenced in this study.

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