Genetic diversity of bvSP by geography and time.

Different colours were used to represent the various lineages of bvSP: fuchsia for L1, orange for L2a, pink for L2b, green for L3b, and red for L3c. (a) The bvSP in the dataset is classified into five continents based on their isolation regions. The bar graph illustrates the distribution of lineage-specific bvSP across continents, depicted as percentages. (b) The bar graph shows the distribution of bvSP isolated in China by lineage per decade. (c) Geographic distribution of bvSP isolated from China. Doughnut charts in the map show the proportion of lineage types of bvSP collected in the corresponding region, with the total number of isolates in the center.

Phylogenetic tree based on a spatiotemporal Bayesian framework.

The phylogenetic tree was constructed based on cgSNPs, with a spatiotemporal Bayesian framework under a relaxed lognormal clock. The evolutionary time was presented by the length of branches and every hundred years as a period. Different colours were used to represent the various lineages of bvSP: fuchsia for L1, orange for L2a, pink for L2b, green for L3b, and red for L3c. The colour strip on the right side represents the ST type, region of isolation, and number of ARGs carried by the corresponding Salmonella, respectively.

Genomic characteristics of 45 bvSP newly Isolated from Taishun and Yueqing, Zhejiang Province, China.

(a) The phylogenetic tree, constructed using cgSNPs, categorizes the 45 bvSP strains into two distinct lineages (L3c and L2b). The left side of the heatmap displays information on isolation regions, ST types, and sampling times, with various colours indicating different categories as specified on the left side of the heatmap. The right section of the heatmap presents a detailed matrix showing plasmids, ARGs, and cgSNP distances. The presence of a plasmid or ARGs in an isolate is denoted by gray shading, while absence is indicated by light white. In terms of cgSNP distances, darker circles signify a higher probability of transmission between isolate pairs. (b) The average cgSNP distance between bvSP from Taishun and Yueqing. E404 led to an increase in the mean cgSNP distance of bvSP from Taishun. (c) Invasiveness index of bvSP in Taishun and Yueqing. The results show a higher invasiveness index for bvSP isolated from Taishun, indicating that bvSP isolated from Taishun might have greater invasive capabilities among vulnerable hens.

The ARGs carried by S. Gallinarum.

(a) The phylogenetic tree was constructed using cgSNPs, revealing three S. Gallinarum biovars: bvSG, bvSD, and bvSG. Additionally, Salmonella serovar Enteritidis (SE.) is represented by a gray line. Further, bvSP can be subdivided into five lineages: fuchsia (L1), orange (L2a), pink (L2b), green (L3b), and red (L3c). The heatmap on the right indicates the resistome carried by the corresponding Salmonella. (b) The dominant resistome types in different regions of China. The y-axis represents the percentage of each dominant resistome. (c) The average number of resistome carried by bvSP is from different regions of China.

The primary source of resistome is carried by distinct mobilome.

Different font colours denote various mobilome types. Specifically, orange signifies Integrons, red denotes transposons, blue represents plasmids, and green indicates prophages. A black font is utilized to distinguish the categories of resistome. The connecting line between the resistome and the mobilome represents the potential carrying relationship. (a) The mobilome-carried ARGs among bvSP. (b) The average number of ARGs carried by the four MGEs in bvSP. (c-e) The mobilome-carried ARGs among bvSP isolated from the eastern, southern, and northern regions of China.

The HGT frequency of the resistome among bvSP isolated from China.

(a) Workflow for identification of horizontally transferred ARGs in Salmonella. (b) The x-axis represents the resistome of bvSP, while the y-axis represents the corresponding levels of HGT frequency. (c) The overall resistome HGT frequency level of bvSP isolated from various regions of China. (d) The HGT frequency level of specific ARGs carried by bvSP isolated from various regions of China. Deeper colours mean higher HGT frequency. (e) The frequency of horizontal retransmission of the resistome between different regions of China. A higher value indicates more frequent transfer events of resistome between two regions.