Genomic analysis reveals high intra-species diversity of Shewanella algae

Abstract

Shewanella algae is widely distributed in marine and freshwater habitats, and has been proved to be an emerging marine zoonotic and human pathogen. However, the genomic characteristics and pathogenicity of Shewanella algae are unclear. Here, the whole-genome features of 55 S. algae strains isolated from different sources were described. Pan-genome analysis yielded 2863 (19.4 %) genes shared among all strains. Functional annotation of the core genome showed that the main functions are focused on basic lifestyle such as metabolism and energy production. Meanwhile, the phylogenetic tree of the single nucleotide polymorphisms (SNPs) of core genome divided the 55 strains into three clades, with the majority of strains from China falling into the first two clades. As for the accessory genome, 167 genomic islands (GIs) and 65 phage-related elements were detected. The CRISPR-Cas system with a high degree of confidence was predicted in 23 strains. The GIs carried a suite of virulence genes and mobile genetic elements, while prophages contained several transposases and integrases. Horizontal genes transfer based on homology analysis indicated that these GIs and prophages were parts of major drivers for the evolution and the environmental adaptation of S. algae. In addition, a rich putative virulence-associated gene pool was found. Eight classes of antibiotic-associated resistance genes were detected, and the carriage rate of β-lactam resistance genes was 100 %. In conclusion, S. algae exhibits a high intra-species diversity in the aspects of population structure, virulence-associated genes and potential drug resistance, which is helpful for its evolution in pathogenesis and environmental adaptability.

Keywords: Shewanella algae; diversity; drug resistance; environmental adaptability; genome characteristics; virulence-associated genes.

Fig. 1.

Average nucleotide identity (ANI) values for the whole genomic sequences of the 55  S . algae strains.

Fig. 2.

Pan genome analysis of 55  S . algae strains and dilution curves of core/pan genes. (a): The heatmap based on pan genome sequences. On the top was the cluster of strains, and on the left was the cluster of pan genes. The red colour represented the presence of genes, while the blue colour represented the absence. (b): The dilution curves of core/pan genes.

Fig. 3.

Phylogenetic tree of core genome sequences by maximum-likelihood method. The strains were divided into six clades. The isolation year, regions and sources were shown on the right. Regions were circled in different colours and sources are triangulated (green for environmental sources and red for clinical sources). The robustness of tree topologies was evaluated with 1000 bootstrap replications. The scale represented a nucleotide substitution rate of 0.01 for each site.

Fig. 4.

The collinearity and the phylogeny among Shewanella spp. (a): General comparisons between S. algae JCM 21037^T and S. carassii 08MAS2251^T presented by Mauve software. (b): General comparisons between S. algae JCM 21037^T and S. indica KCTC 23171^T presented by Mauve software. (c): General comparisons between S. algae JCM 21037^T and S. chilikensis KCTC 22540^T presented by Mauve software. The Mauve parameter settings were default. (d): Venn diagram of the shared and unique genes found in S. algae JCM 21037^T and other three Shewanella genomes.

Fig. 5.

The distribution of unique genes in environmental vs. clinical isolates and the gene clusters composition of prophage-related element. (a): The unique genes distribution of environmental strains. (b): The unique genes distribution of clinical strains. (c): The comparison of nucleotide similarity of the prophage-related element in S. algae 18064-CSB-BB and the homologs in E. coli and Salmonella enterica strains. The prophage-related CDSs were represented in yellow, while the insert sequence 1 (IS 1) in emerald green, the transposons in pink, the phage recombination associated CDSs in dark green, the other unnamed mobile elements in orange and the gene clusters in blue.

Fig. 6.

The heatmap of the virulence genes in 55  S . algae strains. On the left, the S. algae strains were divided into three groups (Group 1, Group 2 and Group 3) according to the clustering situation. On the top was the clusters of virulence-related genes, which were marked as Cluster 1 to Cluster 5, respectively. The blue colour indicated the presence of genes while the grey colour indicated the absence.