Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche

BMC Genomics

Table 1 List of strains used in this study with corresponding genome information

ID (alt. ID)	child number	Clinical condition	Age at Sampling	Phylogenetic group	Nr. contigs	Median coverage	Colonization Category	Accession Accession Number
EDM1c	1360	Healthy	10 days	B2	712	7,55	early	EMBL:ERS155053
EDM3c	1360	Healthy	1 year	B1	306	12,4	late	EMBL:ERS155049
EDM16c	1870	Healthy	7 days	B1	204	13,75	early	EMBL:ERS155051
EDM70c	1997	Healthy	10 days	B2	562	8,5	early	EMBL:ERS155055
EDM49c	1891	Healthy	4 days	B2	163	14,5	early	EMBL:ERS155056
EDM101c	1891	Healthy	11 days	B2	169	16	early	EMBL:ERS155057
EDM106c	123	Healthy	4 days	B2	585	8	early	EMBL:ERS155058
EDM116c	123	Healthy	1 year	A	864	8,2	late	EMBL:ERS155052
EDM123c	1360	Healthy	4 months	B2	669	8,5	late	EMBL:ERS155054
EDM530c	123	Healthy	2 years	NA	198	17,5	late	EMBL:ERS155050
JEA117c (Trh9)*	117c	Healthy	1 year	B2	284	10,1	late	EMBL:ERS178156
JEA242p (Trh52)*	242p	Diarrhoea	3 years	B2	140	13,2	NC	EMBL:ERS178157
JEA297p (Trh58)*	297p	Diarrhoea	2 years	D	521	11,1	NC	EMBL:ERS178158
JEA179p (Trh39)*	179p	Diarrhoea	4 years	B1	848	7,8	NC	EMBL:ERS178159
JEA160c (Trh12)*	160c	Healthy	2 years	A	188	20,1	late	EMBL:ERS178160
JEA124p (Trh29)*	124p	Diarrhoea	2 years	A	800	8,9	NC	EMBL:ERS178161

c = commensal isolate, isolated from healthy child.
p = pathogenic isolate, isolated from child with diarrhoea.
* Isolation based on positive PCR analysis for intimin gene eae.
NC = not categorized.
The genome assembly statistics are results of Newbler de novo assembly. The colonization categorizations are the ones used for gene enrichment comparison between early and late colonizers. The 10 strains named EDM were isolated from samples originating from the IMPACT study [8, 10, 13]. JEA strains and alternative strain IDs are from [14].

ISSN: 1471-2164