Table 3 Number of gene clusters identified using LS-BSR that are significantly correlated with one clinical outcome when compared to another clinical outcome.

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

Clinical outcomes* No. of genomes No. of gene clusters
   Lineage-specific LS-BSR ≥ 0.9 EPEC-specific LS-BSR ≥ 0.8
   <0.005 <0.05 <0.005 <0.05
All genomes
LI vs AI
 Total 47 20 367 12 198
 LI 24 19 227 11 134
 AI 23 1 140 1 64
LI vs NSI
 Total 47 1 111 0 39
 LI 24 0 31 0 14
 NSI 23 1 80 0 25
NSI vs AI
 Total 46 7 118 4 67
 NSI 23 5 63 1 27
 AI 23 2 55 3 40
Typical EPEC genomes only
LI vs AI
 Total 41 11 238 2 134
 LI 24 11 167 2 96
 AI 17 0 71 0 38
LI vs NSI
 Total 44 0 39 0 7
 LI 24 0 9 0 5
 NSI 20 0 30 0 2
NSI vs AI
 Total 37 7 176 0 87
 NSI 20 4 89 0 24
 AI 17 3 87 0 63
  1. *Clinical outcomes are classified as lethal (LI), non-lethal symptomatic (NSI) and asymptomatic (AI);
  2. as part of a lineage-specific gene comparison, genes with ≥90% nucleotide identity were grouped together into gene clusters, and the gene clusters were identified as more prevalent in genomes of one clinical outcome over another by the percentage of genomes of each group that contained the gene cluster with significant similarity (LS-BSR ≥ 0.9);
  3. as part of an EPEC pathovar-specific comparison, genes with ≥80% nucleotide similarity were grouped together into gene clusters and the gene clusters were identified as more prevalent in genomes of one clinical outcome over another by the percentage of genomes of each group that contained the gene cluster with significant similarity (LS-BSR ≥ 0.8) that were not present in three previously characterized E. coli commensal genomes (K-12, SE11, HS).