Date Published: April 11, 2019
Publisher: Public Library of Science
Author(s): Lester Hiley, Rikki M. A. Graham, Amy V. Jennison, Axel Cloeckaert.
The virulence plasmid pSLT as exemplified by the 94 Kb plasmid in Salmonella Typhimurium strain LT2 is only found in isolates of serovar Typhimurium. While it occurs commonly among such isolates recent genotyping methods have shown that it is mostly confined to certain genotypes. Although pSLT plasmids are capable of self-transmissibility under experimental conditions their confinement to certain host genotypes suggests that in practice they are maintained by vertical rather than by horizontal transmission. This would imply that evolution of the pSLT plasmid proceeds in parallel with evolution of its host. The development of a phylogenetic evolutionary framework for genotypes of S. Typhimurium based on single-nucleotide-polymorphism (SNPs) typing provided an opportunity to test whether the pSLT plasmid coevolves with its host genotype. Accordingly SNPs analysis was applied to the pSLT plasmids from 71 strains S. Typhimurium of Australian and international origins representing most of the genotypes which commonly have a pSLT. The phylogenetic tree showed that pSLT sequences clustered into almost the same groups as the host chromosomes so that each pSLT genotype was associated with a single host genotype. A search for tandem repeats in pSLT plasmids showed that a 9 bp VNTR in the traD gene occurred in the pSLT from all isolates belonging to Clade II but not from isolates belonging to Clade I. Another 9 bp repeat occurred only in three Clade I genotypes with a recent common ancestor. The evidence relating to both of these VNTRs supports the proposition that the pSLT plasmid is only transmitted vertically. Some isolates belonging to one S. Typhimurium genotype were found to have pSLTs which have lost a large block of genes when a resistance gene cassette has been acquired. Examples were found of pSLT plasmids which have recombined with other plasmids to form fusion plasmids sometimes with loss of some pSLT genes. In all cases the underlying genotype of the modified pSLT was the same as the genotype of regular pSLTs with the same host genotype implying that these changes have occurred within the host cell of the pSLT plasmid.
The virulence plasmid of Salmonella enterica serovar Typhimurium (S. Typhimurium), designated pSLT , is, in its most common form, a large, 94Kb, low-copy-number plasmid which belongs to the IncFIIs plasmid incompatibility group  and occurs commonly amongst isolates of S. Typhimurium . The plasmid has an 8-Kb region which encodes the spv genes thought to give a competitive advantage to the host by increasing the growth rate of the bacterium during the systemic phase of disease . In its most common form it does not have any antimicrobial resistance genes but forms of pSLT with resistance genes such as pSal8934B (GenBank Acc. No. NC_019109), pSTU288-1 (NC_021155) and pSTMDT12_L (NC_016861) have been recorded.
This study demonstrates the value of applying the data derived from whole genome sequencing of bacterial isolates towards the understanding of various aspects of plasmid evolution. Genetic characterisation of variants of the pSLT plasmid has provided evidence for co-evolution of pSLT plasmids and their S. Typhimurium hosts for both Australian and international isolates. This supports the proposition that the pSLT plasmid is most likely confined to its host cell since we find no examples of the same pSLT genotype occurring in different host genotypes. As a consequence the pSLT sequences which constitute a pSLT genotype are derived from hosts which all belong to one S. Typhimurium genotype. The study has also provided examples of pSLT plasmids showing large-scale changes under the influence of transposons or IS-elements as well as hybridisation with other plasmids to form fusion plasmids. The evidence indicates that these changes occur within the host cell of the pSLT and are maintained thereafter by vertical transmission.