Stenotrophomonas mexicanensis subsp. fluminensis subsp. nov., a new subspecies isolated from a clinical sample at a hospital in Rio de Janeiro, Brazil, during COVID-19 pandemic.

The genus Stenotrophomonas exhibits wide genetic diversity, and the Stenotrophomonas maltophilia complex (Smc) is formed by multiple cryptic species. In this study, we performed taxonomic characterization of SM006 strain, isolated from lung tissue of an 83-year-old female patient at a hospital in Rio de Janeiro. Initially identified as S. maltophilia by Matrix-Assisted Laser Desorption/Ionization - Time of Flight Mass Spectrometry and 16 S rRNA gene sequencing, the strain was phylogenetically positioned within Smc. Multilocus sequence typing identified a novel allelic profile, leading to the assignment of a new ST-1401 and a new rST (316636). Genomic analysis revealed the presence of resistance genes related to β-lactam, aminoglycoside, and RND family efflux systems, as well as an intact prophage region, indicating evolutionary interaction with phage elements. The Average Nucleotide Identity (96.51%) and digital DNA-DNA hybridization (71.90%) values were close to the limits established for species delimitation, suggesting that SM006 strain belongs to a new subspecies of the recently described Stenotrophomonas mexicanensis. Phylogenomic analyses based on core genes and orthologous proteins confirmed its grouping consistent with S. mexicanensis, but with sufficient divergence to justify its proposal as a new subspecies. Thus, the name Stenotrophomonas mexicanensis subsp. fluminensis subsp. nov. was proposed, with SM006 (= CBAS 932ᵀ = CBP P7452ᵀ) as the type strain. The phenotypic description, including growth characteristics, biochemical results, and antimicrobial susceptibility profile, reinforces its taxonomic distinction. The study highlights the central role of genomic taxonomy in the accurate identification of new taxa and in expanding knowledge about the diversity of the genus Stenotrophomonas.