Genomic phylogeny, taxonomic classification, genetic landscape, and antibiotic resistance of clinical Stenotrophomonas isolates
Abstract
Background: Stenotrophomonas spp. are increasingly recognized opportunistic pathogens characterized by intrinsic multidrug resistance. Despite recent taxonomic reclassification and the delineation of new species within the S. maltophilia complex (Smc), routine diagnostics often misidentify these species, and their distinctive antibiotic resistance traits and genetic makeup remain underexplored. We aimed to characterize the phylogenomic diversity, genotypic and phenotypic antibiotic resistance traits, virulence markers and horizontally transferrable elements in a large national cohort of clinical Stenotrophomonas isolates.
Methods: We analyzed 323 clinical isolates from the Russian sentinel surveillance program (2002-2021). Analysis included MALDI-TOF MS identification, broth microdilution susceptibility testing to six agents [aztreonam-avibactam, colistin, levofloxacin, minocycline, tigecycline, and trimethoprim-sulfamethoxazole (TMP-SMX)], and long-read Nanopore WGS with hybrid polishing. We performed average nucleotide identity (ANI)-based classification, core- and accessory-genome comparisons, and comprehensive profiling of antibiotic resistance genes (ARGs), virulence factors (VFs), plasmids, and prophages.
Results: While MALDI-TOF MS identified all isolates as S. maltophilia, ANI (≥95% threshold) and core-genome phylogeny revealed 17 distinct species: 52% S. maltophilia sensu stricto, 36.8% across eight other ICNP-named Smc species, and 11.2% within eight "novel"…
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Evidence Hub reads this as a cohort study. Its evidence level is 3 of 5 (Moderate · trial / cohort / secondary analysis). Trials without a large randomized design, cohorts and secondary analyses give moderate evidence.
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