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
  1. ND, not determined; NC, not classified;
  2. *the clinical outcomes are LI (lethal), NSI (non-lethal symptomatic) and AI (asymptomatic);
  3. 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;
  4. the intimin types of these isolates are truncated and these are the most related intimin types;
  5. §the phylogenomic lineage and phylgroup designations are based on the genome-based phylogeny in Fig. 1.