Stenotrophomonas raiganjensis sp. nov., an extensively drug-resistant bacterium isolated from Bombyx mori L., described under the SeqCode.

SeqCode allows a single strain or a high-quality genome to serve as type material, making it compatible with modern genomics and biodiversity governance frameworks, especially for countries such as India. We, therefore, describe a novel bacterium, designated RAC2TS under the SeqCode. RAC2TS was isolated from the hemolymph of infected Bombyx mori L. and characterized using a polyphasic taxonomic approach. While 16S rRNA gene sequence based phylogenetics showed Stenotrophomonas maltophilia NBRC 14161ᵀ to be the closest relative, multilocus sequence analysis (MLSA) based on seven housekeeping genes (atpD, gapA, guaA, mutM, nuoD, ppsA, recA) and genome-based relatedness indices confirmed RAC2TS as a distinct lineage within the genus Stenotrophomonas. Whole-genome analysis identified a 4.6 Mbp genome with 66.5% G + C content; and 4276 coding sequences, including several antimicrobial resistance genes alongside multidrug efflux pump sme operon genes and a single virulence-associated gene, pilG. RAC2TS showed 91-93% average nucleotide identity (ANI) and 41-48% digital DNA-DNA hybridization (dDDH) with closely related taxa. Pangenome analysis revealed an open pangenome (α = 0.257), with 12,623 gene clusters including 229 core genes and 6994 strain-specific genes. Antibiotic susceptibility testing demonstrated extensive drug resistance (XDR) characteristics of RAC2TS. Fatty acid methyl ester (FAME) analysis revealed isoC15:0 (24.56%), anteiso-C15:0 (14.27%), and summed feature 3 (16:1 ω7c/16:1 ω6c; 11.18%) as major components. Combined phenotypic, chemotaxonomic, phylogenomic, and genomic evidence supports the recognition of RAC2TS as a novel species within the genus Stenotrophomonas. Under the SeqCode, we propose the name S. raiganjensis sp. nov. for strain RAC2TS (=MCM-B-1506TS) with the type genome GCA_030658505.2TS.