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

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

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
  1. c = commensal isolate, isolated from healthy child.
  2. p = pathogenic isolate, isolated from child with diarrhoea.
  3. * Isolation based on positive PCR analysis for intimin gene eae.
  4. NC = not categorized.
  5. 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].