Is the Evolution ofSalmonella entericasubsp.entericaLinked to Restriction-Modification Systems?
Salmonella entericasubsp.entericabacteria are highly diverse foodborne pathogens that are subdivided into more than 1,500 serovars. The diversity is believed to result from mutational evolution, as well as intra- and interspecies recombination that potentially could be influenced by restriction-modification (RM) systems. The aim of this study was to investigate whether RM systems were linked to the evolution ofSalmonella entericasubsp.enterica. The study included 221Salmonella entericagenomes, of which 68 werede novosequenced and 153 were public available genomes from ENA. The data set covered 97 different serovars ofSalmonella entericasubsp.entericaand an additional five genomes from four otherSalmonellasubspecies as an outgroup for constructing the phylogenetic trees. The phylogenetic trees were constructed based on multiple alignment of core genes, as well as the presence or absence of pangenes. The topology of the trees was compared to the presence of RM systems, antimicrobial resistance (AMR) genes,Salmonellapathogenicity islands (SPIs), and plasmid replicons. We did not observe any correlation between evolution and the RM systems inS. entericasubsp.enterica. However, sublineage correlations and serovar-specific patterns were observed. Additionally, we conclude that plasmid replicons, SPIs, and AMR were all better correlated to serovars than to RM systems. This study suggests a limited influence of RM systems on the evolution ofSalmonella entericasubsp.enterica, which could be due to the conjugational mode of horizontal gene transfer inSalmonella. Thus, we conclude that other factors must be involved in shaping the evolution of bacteria.IMPORTANCEThe evolution of bacterial pathogens, their plasticity and ability to rapidly change and adapt to new surroundings are crucial for understanding the epidemiology and public health. With the application of genomics, it became clear that horizontal gene transfer played a key role in evolution. To understand the evolution and diversification of pathogens, we need to understand the processes that drive the horizontal gene transfer. Restriction-modification systems are thought to cause rearrangements within the chromosome, as well as act as a barrier to horizontal gene transfer. However, here we show that the correlation between restriction-modification systems and evolution in other bacterial species does not apply toSalmonella entericasubsp.enterica. In summary, from this work, we conclude that other mechanisms might be involved in controlling and shaping the evolution ofSalmonella entericasubsp.enterica.
Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
Louise
L
Roer
Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
Rene S
RS
Hendriksen
Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
Pimlapas
P
Leekitcharoenphon
Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
Oksana
O
Lukjancenko
Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
Rolf Sommer
0000-0002-5050-8668
RS
Kaas
Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark; Section for Microbiology and Diagnostics, Statens Serum Institut, Copenhagen, Denmark.
Henrik
H
Hasman
Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
Frank M
FM
Aarestrup
Salmonella phylogenetic analysis; evolution; next-generation sequencing; restriction-modification systems; whole-genome sequencing