Figure 1.
The Core and Accessory Genomes of Bp.
Chromosome 1 is on the left and Chromosome 2 on the right. Both chromosomes are centered around the origin of replication. From outside to inside: Red - Computationally-identified GIs (12 on Chr 1 and 4 on Chr 2) (33); Accessory (Blue) and Core (Yellow) Genes; Internal red - False Discovery Values as assessed by GMM - A red peak indicates high variability in that genomic region (see Methods). Black arrows - Representative examples of novel indels.
Table 1.
Enriched Functions of Core and Accessory Genes in Bp.
Figure 2.
The graph shows the percentage of strains exhibiting either a partial (red) or total (blue) absence of the indel segment (n1–n20). Blue represents the percentage of strains where the entire indel is absent. Red represents strains where the indel is only partially absent.
Table 2.
Novel indels in Bp.
Figure 3.
Unsupervised Accessory Genome Clustering of Bp Isolates.
Clustering diagram of Bp strains on the basis of accessory genome content. The tree is contructed using MultiExperiment Viewer (MeV) version 4, based on the entire 750-gene accessory genome and combined average linkage hierarchical clustering. Clinical (labeled in red), Animal (labeled in blue) and Environmental (labeled in green) strains are indicated. Isolates from Thailand are highlighted in the red broken circle. Three broad clusters/clades are identified which are named C-clinical, A-animal, E-environmental, with the percentage of concordant strains in that cluster. Numbers on branches represent bootstrap values based on 1000 tests. The bootstrapping analysis reveals a clear distinction between the C (clinical) and A/E clusters (non-clinical - animal and environmental) (Bootstrap value = 100).
Figure 4.
Enrichment of Genomic Islands in Clinical Isolates.
Heat map representing absence and presence of GI genes in Clinical, Animal and Environmental isolates. Top row (“Cluster”): AGC clusters corresponding to clinical (left), animal (middle), and environmental (right) isolates. Second row (“Source”) Strains were color-coded according to their original source of isolation, where red = clinical, blue = animal, and green = environmental. Third row: strains highlighted in pink from Thailand. In the heat-map, black indicates gene presence and red indicates gene absence. Locations of the fourteen GIs are depicted on the right.
Table 3.
Concordance of AGC Clusters and MLST Sequence Types.