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<p><i>Stenotrophomonas maltophilia</i> is an opportunistic Gram-negative pathogen whose genome evolution is shaped in part by mobile genetic elements, including prophages. Here, we analyzed 320 <i>S. maltophilia</i> genomes and identified 880 intact prophages, ranging from 4,557 to 68,546&#xa0;bp with GC contents of 49.98–67.22%. Prophage prevalence varied across multilocus sequence types (MLST), with ST14 exhibiting the highest prophage intensity (mean intact prophages per genome), indicating lineage-specific differences in prophage acquisition and retention. Taxonomic classification revealed <i>Caudoviricetes</i> as the dominant class (739/880, 84.0%), followed by <i>Faserviricetes</i> (141/880, 16.0%). Functional annotation identified prophage structural genes and virulence-associated homologs, including <i>clpC</i> (<i>n</i> = 15), <i>clpP</i> (<i>n</i> = 37), <i>phoP</i> (<i>n</i> = 15), <i>pilZ</i> (<i>n</i> = 2), and <i>fpvA</i> (<i>n</i> = 1), with only one intact prophage carrying <i>tet(C)</i>. These findings highlight extensive prophage diversity, dominated by <i>Caudoviricetes</i>, and reveal lineage-specific variation in prophage carriage, providing genome-scale insights into their composition and potential role in <i>S. maltophilia</i> genome evolution.</p>

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Genome-wide comparative and taxonomic characterization of prophages in Stenotrophomonas maltophilia

  • 期刊论文

  • 发表日期：

    2026年3月30日

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  • Afia Anjum,
  • Zuhayr Mahtab,
  • Sattajith Roy,
  • Jarin Tabassum,
  • Ishrat Jabeen,
  • Sohidul Islam,
  • Sabbir R. Shuvo

摘要

Stenotrophomonas maltophilia is an opportunistic Gram-negative pathogen whose genome evolution is shaped in part by mobile genetic elements, including prophages. Here, we analyzed 320 S. maltophilia genomes and identified 880 intact prophages, ranging from 4,557 to 68,546 bp with GC contents of 49.98–67.22%. Prophage prevalence varied across multilocus sequence types (MLST), with ST14 exhibiting the highest prophage intensity (mean intact prophages per genome), indicating lineage-specific differences in prophage acquisition and retention. Taxonomic classification revealed Caudoviricetes as the dominant class (739/880, 84.0%), followed by Faserviricetes (141/880, 16.0%). Functional annotation identified prophage structural genes and virulence-associated homologs, including clpC (n = 15), clpP (n = 37), phoP (n = 15), pilZ (n = 2), and fpvA (n = 1), with only one intact prophage carrying tet(C). These findings highlight extensive prophage diversity, dominated by Caudoviricetes, and reveal lineage-specific variation in prophage carriage, providing genome-scale insights into their composition and potential role in S. maltophilia genome evolution.