Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes

Abstract

Plasmids play important roles in bacterial genome diversification. In the Serratia marcescens complex (SMC), a notable contribution of plasmids to genome diversification was also suggested by our recent analysis of >600 draft genomes. As accurate analyses of plasmids in draft genomes are difficult, in this study we analysed 142 closed genomes covering the entire complex, 67 of which were obtained in this study, and identified 132 plasmids (1.9–244.4 kb in length) in 77 strains. While the average numbers of plasmids in clinical and non-clinical strains showed no significant difference, strains belonging to clade 2 (one of the two hospital-adapted lineages) contained more plasmids than the others. Pangenome analysis revealed that of the 28 954 genes identified, 12.8 % were plasmid-specific, and 1.4 % were present in plasmids or chromosomes depending on the strain. In the latter group, while transposon-related genes were most prevalent (31.4 % of the function-predicted genes), genes related to antimicrobial resistance and heavy metal resistance accounted for a notable proportion (22.7 %). Mash distance-based clustering separated the 132 plasmids into 23 clusters and 50 singletons. Most clusters/singletons showed notably different GC contents compared to those of host chromosomes, suggesting their recent or relatively recent appearance in the SMC. Among the 23 clusters, 17 were found in only clinical or only non-clinical strains, suggesting the possible preference of their distribution on the environmental niches of host strains. Regarding the host strain phylogeny, 16 clusters were distributed in two or more clades, suggesting their interclade transmission. Moreover, for many plasmids, highly homologous plasmids were found in other species, indicating the broadness of their potential host ranges, beyond the genus, family, order, class or even phylum level. Importantly, highly homologous plasmids were most frequently found in Klebsiella pneumoniae and other species in the family Enterobacteriaceae , suggesting that this family, particularly K. pneumoniae , is the main source for plasmid exchanges with the SMC. These results highlight the power of closed genome-based analysis in the investigation of plasmids and provide important insights into the nature of plasmids distributed in the SMC.

Effects of phage variation on Shiga toxin 2 (Stx2) production and the virulence of Stx-producingEscherichia coli

“…All-to-all phage genome comparison was performed for the three sets of genomes (the entire genomes of 83 Stx phages, the entire genomes of 54 Stx2 phages, and the early regions of 54 Stx2 phages) using Mash v2.0 [37] with default parameters to generate pairwise Mash distance matrices. Based on each matrix, Stx phages and the early regions of Stx phages were clustered with a cutoff of 0.05 as previously described [51]. The amino acid sequences of CI and Q encoded by each Stx2 phage were aligned with the proteins from phages lambda, Sp5, and 933W by MUSCLE in MEGA v10.1.8 [52], and dendrograms were generated based on these alignments using the UPGMA algorithm in MEGA v10.1.8.…”