Table 1.
Characterization of the strains used in this study1.
Fig 1.
Unrooted phylogenetic tree generated and AAI values of each strain to AIEC LF82.
Maximum likelihood phylogeny using the 3,101 common concatenated orthologues detected by OrthoFinder. The strains used are described in Table 1. Branches colored blue represent ExPEC, red represent InPEC, and green represent Commensal strains. The red dotted circle indicates that all nodes within have 100% bootstrap support. The grey arrows indicate the strains that clustered together and showed the highest AAI values and proteome coverage to AIEC LF82.
Table 2.
Table of identities of ColV-like plasmids and the identity of their genes to the clusters from p1ColV51551.
Fig 2.
Plasmid comparison using the software BRIG, setting pBEN2908 as the reference strain.
From the innermost to the outermost ring, the following plasmids are shown: p1ColV5155 (NZ_CP005931.1; IMT5155), pAPEC-O1-ColBM (DQ381420.1; APEC O1), pAPEC-1 (CP000836.1; χ7122), and pO83-CORR (CP001856.1; NRG857c). Genes usually present in ColV-like plasmids and the four gene clusters used in Liu et al. for ColV plasmid screening are shown in the figure [85].
Table 3.
Genomic regions (GRs) of BEN2908 with more than 50% coverage to the ExPEC strains from this study and AIEC LF82.
Table 4.
Summary of Genomic Regions (GRs) present in both ExPEC and AIEC strains from this study containing Reported features.
Table 5.
Genomic Regions (GRs) present in both ExPEC and AIEC strains from this study containing Uncharacterized features and their predicted identification.
Fig 3.
Genome comparison using the software BRIG, setting BEN2908 as the reference strain.
From the innermost to the outermost ring, the following strains are shown: APEC IMT5155 and APEC O1 (red tones), NMEC RS218 and IHE3034 (purple tones), UPEC 78-Pyelo and CFT073 (green tones), AIEC LF82 (yellow) and commensal K-12 MG1655 (grey). Genomic regions (GRs) identified by the criteria described in the Methods section are indicated by numbers 1 to 36. The 20 regions marked in orange are common to all strains, except K-12 MG1655.
Fig 4.
Predicted sugar metabolism pathway based on KEGG maps and KEGG Orthology.
ORFs highlighted in purple represent putative novel coding sequences, while those in red correspond to genes located in other regions of the genome. ORFs from GRs 19, 21, 23 appear to be involved in the conversion of different sugars to KDPG, and, after, to Pyruvate and G3P, two important intermediates of glycolytic pathways.
Fig 5.
Predicted dicarboxylate utilization pathway based on KEGG maps and KEGG Orthology.
ORFs highlighted in purple represent putative novel coding sequences. Some ORFs from GR 32 appear to be involved in the conversion of 2-oxoglutarate to succinate, forming a second gene module analogous to the canonical sucABCD from E. coli K-12 MG1655.
Fig 6.
Comparison of operons with gene organization similar to the observed in GRs 6, 29 and 32.