Genetic diversity of S. Gallinarum biovar Pullorum (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, red for L3b, and green 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. The total sample size for each bar is indicated at the top. (b) The bar graph shows the distribution of bvSP isolated in China by lineage per decade. The total sample size for each bar is also indicated on the right side. (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 of S. Gallinarum L2b and L3b based on a spatiotemporal Bayesian framework.

The phylogenetic tree on the left was constructed using a reference-mapped multiple core-genome SNPs sequence alignment, with recombination regions detected and removed by Gubbins. The spatiotemporal Bayesian framework was configured with the “GTR” substitution model, 4 Gamma Category Count, “Relaxed Clock Log Normal” model, “Coalescent Bayesian Skyline” tree prior model, and a Markov Chain Monte Carlo (MCMC) chain length of 100,000,000, with sampling every 10,000 iterations. Convergence was assessed using Tracer, ensuring all parameter effective sampling sizes (ESS) exceeded 200. Evolutionary time is represented by the length of the branches. The heatmap on the right displays, respectively, the sequence type (ST), region of isolation, and the number (Num.) of antimicrobial resistance genes (ARGs) carried by the corresponding Salmonella Gallinarum.

Genomic characteristics of 45 newly isolated S. Gallinarum biovar Pullorum (bvSP) strains from Taishun and Yueqing, Zhejiang Province, China.

(a) The phylogenetic tree, constructed using cgSNPs, categorizes the 45 bvSP strains into two distinct lineages (L3b and L2b). On the left side of the heatmap, information on isolation regions, sequence types (ST), and sampling times are displayed, with various colors indicating different categories as specified on the left. The right section of the heatmap presents a detailed matrix showing plasmids, ARGs, and cgSNP distances. The presence of a plasmid or ARG in an isolate is denoted by gray shading, while absence is indicated by white. cgSNPs below five were used as the threshold, with darker circles signifying a higher probability of transmission between isolate pairs. (b) The average cgSNP distance between isolates 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: S. Gallinarum biovar Pullorum (bvSP), S. Gallinarum biovar Duisburg (bvSD), and S. Gallinarum biovar Gallinarum (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), red (L3b), and green (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. The total sample size for each bar is indicated at the top. (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 S. Gallinarum biovar Pullorum (bvSP). (b) The average number of ARGs carried by the four MGEs in bvSP. The unpaired t-test was used to compare the differences between isolates, with P < 0.05 considered statistically significant. (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 S. Gallinarum biovar Pullorum (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 the 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. The colors on the map represent the number of bvSP isolates in each region. Darker colors indicate a higher number of bvSP isolates in that area.