Mobile genetic elements as strain-specific markers: a case study in Shewanella sp. Pdp11

Strain-level identification is a key challenge in microbiology, particularly for monitoring microorganisms of interest such as probiotics. Traditional methods based on 16S rRNA gene sequencing often lack the resolution to discriminate closely related strains. This study investigates the potential of mobile genetic elements (MGEs), including transposons and prophages, as molecular markers for precise strain identification. Shewanella sp. Pdp11, a probiotic strain used in aquaculture, was selected as a model organism. Comparative in silico genome analyses revealed a unique transposon disrupting a phenazine biosynthesis gene, absent from other closely related Shewanella strains, which enabled the design of a highly specific PCR assay. This assay demonstrated a detection limit of 3 × 10 3 cells/mL with no amplification observed in fish intestinal microbiota DNA, indicating strong specificity even within complex bacterial communities. In addition, a complete prophage was characterized in the Pdp11 genome, containing bacterial genes potentially associated with stress tolerance functions; however, this prophage was not applied as a diagnostic marker in the current study due to its structural complexity. The proposed strategy requires prior genome sequence information to identify strain-specific MGEs before PCR marker development . Overall, the results highlight the feasibility of using transposons as genomic resources for developing high-resolution strain identification tools and lay the groundwork for future investigations into their stability and applicability in bacterial traceability systems. Key points • PCR-based method developed to identify bacterial strains specifically. • Transposons identified as useful mobile elements for bacterial identification. • Prophages may serve as an alternative tool for bacterial fingerprinting, though additional gene-level studies are needed.