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Comparative Analyses Suggest Genome Stability and Plasticity in Stenotrophomonas maltophilia
Danny Khar Chen Sum1, Yee Yee Chong1, Joon Liang Tan1,2
1Faculty of Information Science and Technology, Multimedia University, Melaka 75450, Malaysia.
Abstract:
Stenotrophomonas maltophilia (S. maltophilia) is a multidrug-resistant opportunistic pathogen. There are an increasing number of case reports on S. maltophilia 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 S. maltophilia 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 S. maltophilia'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 S. maltophilia population.
Insights
Stenotrophomonas maltophilia (S. maltophilia) infections are a growing public health concern. Mobile genetic elements drive diversity and drug resistance in S. maltophilia populations, impacting genomic stability and plasticity.
Area of Science:
- Microbiology
- Genomics
- Evolutionary Biology
Background:
- Stenotrophomonas maltophilia (S. maltophilia) is an opportunistic pathogen known for multidrug resistance.
- Increasing S. maltophilia infections highlight its public health significance.
- Previous research focused on S. maltophilia pangenomes, antibiotic resistance, and virulence, but neglected mobile genetic elements (MGEs).
Purpose of the Study:
- To investigate the role of MGEs in S. maltophilia population structure, diversity, and evolution.
- To analyze the impact of MGEs on virulence and drug resistance gene distribution.
- To assess evolutionary trends in S. maltophilia core genomes and accessory regions.
Main Methods:
- Downloaded and analyzed 20 S. maltophilia genomes from NCBI.
- Profiled MGEs and their distribution within the genomes.
- Evaluated MGEs' impact on chromosomal rearrangements and linkage disequilibrium in core genomes.
Main Results:
- Catalogued MGEs revealed active horizontal gene transfer in S. maltophilia.
- Virulence and drug resistance genes were identified within and outside MGEs.
- Observed significant chromosomal rearrangements (up to 50% of a genome) attributed to MGEs.
- Detected high levels of linkage disequilibrium in core genomes.
Conclusions:
- MGEs significantly contribute to the plasticity of the accessory genome in S. maltophilia.
- MGEs are implicated in chromosomal instability and the spread of resistance and virulence factors.
- The study elucidates the interplay between core genome stability and accessory genome plasticity in S. maltophilia.
