Comparative Analyses Suggest Genome Stability and Plasticity in Stenotrophomonas maltophilia

<i>Stenotrophomonas maltophilia</i> (<i>S. maltophilia</i>) is a multidrug-resistant opportunistic pathogen. There are an increasing number of case reports on <i>S. maltophilia</i> infections in recent years, and the species is becoming a public health concern. Many studies have focused on profiling and pangenome of the species, particularly on their antibiotic resistance and virulence genes. However, there is a lack of studies on mobile genetic elements (MGEs), a subset of pangenome that significantly contributes to the diversity, stability, and plasticity of a population. In this study, 20 genomes of <i>S. maltophilia</i> were downloaded from the NCBI Genome database. The genomes were subjected to profiling of MGEs, their impact on the population structures, and the evaluation of evolutionary trends of the core genomes. The cataloguing of MGEs indicated active horizontal gene transfer events in the <i>S. maltophilia</i>'s population. Multiple virulence and drug resistance genes were predicted within and outside of the MGEs. We observed multiple chromosomal rearrangements in the genomes, most likely caused by MGEs, affecting up to approximately 50% of a single genome sequence. A high number of linkage disequilibrium sites were also predicted in the core genomes. This study provides insights into stability in the core and plasticity in the accessory regions in the <i>S. maltophilia</i> population.