Integrated genomic analysis of Stenotrophomonas maltophilia: resistome, virulence-associated genes, predicted mobile genetic elements, and core-genome phylogeny

Abstract

Background Stenotrophomonas maltophilia is an emerging opportunistic pathogen characterized by intrinsic multidrug resistance and broad ecological distribution. However, its genomic characteristics across publicly available clinical, environmental, and animal isolates remain incompletely defined. Objective This study aimed to characterize the taxonomic distribution, antimicrobial resistance genes (ARGs), virulence-associated genes (VAGs), sequence types (STs), predicted mobile genetic elements (MGEs), orthogroup-occupancy patterns, and core-genome sequence variation of publicly available S. maltophilia isolates. Methods A total of 3,343 high-quality Stenotrophomonas candidate genomes obtained from NCBI were subjected to average nucleotide identity (ANI)-based taxonomic verification using the NCBI Prokaryotic Genome Annotation Pipeline. Of these, 1,584 genomes unambiguously assigned to S. maltophilia were retained for genomic analyses. ARGs were identified using a custom BLASTN-based nucleotide screen validated against AMRFinderPlus, and VAGs, multi-locus sequence types (MLST), and predicted MGEs were characterized using complementary bioinformatic approaches. Source-stratified analyses used the 1,054 genomes with resolved isolation-source metadata. Pangenome composition and lineage-specific core-genome phylogenetic relationships were evaluated separately for 95 ST4 and 113 ST5 genomes. Results S. maltophilia represented 1,584 of the 3,343 candidate genomes (47.4%). Country-level metadata were resolved for 1,044 genomes, representing 35 countries, whereas 540 had missing or unresolved geographic information. Among the 1,054 source-resolved genomes, 856 (81.2%) were human-derived, 154 (14.6%) were environmental, and 44 (4.2%) were animal-derived. The custom ARG screen identified 12,215 loci representing 67 ARG designations, while 38 non-redundant VAGs were detected. The efflux-associated genes emrA, emrB, emrC, and smeF, together with the intrinsic β-lactamase gene blaL1, were widely distributed, whereas acquired carbapenemase genes were uncommon. Source-associated differences were limited to selected ARGs and VAGs rather than broad changes in ARG or VAG burden. Among 1,388 typeable genomes, 234 STs were identified, with ST5, ST4, ST31, ST162, and ST115 being the most frequently represented. A total of 1,140 predicted ARG–MGE co-localization events were identified; predicted plasmid-associated contigs represented the largest category of ARG–MGE co-localization events, accounting for 898 events (78.8%), although these computational assignments did not establish confirmed plasmid carriage or transferability. In the pangenome comparison, ST4 showed a larger rare-gene and strain-specific orthogroup component, whereas ST5 showed greater core-genome sequence separation according to retained variable-site counts and pairwise SNP-distance metrics. ST4 had higher proportions of strain-specific orthogroups (3.4% versus 1.3%) and unassigned genes (2.7% versus 0.8%), whereas the shell-plus-cloud proportions were similar between ST4 and ST5 (46.7% versus 46.2%). ST5 had a higher orthogroup-assignment rate (99.2% versus 97.3%) and a higher proportion of orthogroups meeting the ≥ 99% core threshold (52.4% versus 49.8%). Core-genome analyses showed a higher pre-recombination variable-site density in ST5 than in ST4 (4.54 versus 3.50 sites/kb), more retained variable sites after recombination filtering (3,269 versus 2,295), and a higher median pairwise SNP distance (127 versus 108 SNPs). Conclusion This analysis of publicly available S. maltophilia genomes identified widely distributed intrinsic resistance determinants, uncommon acquired carbapenemases, selected source-associated gene differences, and frequent computational co-localization of ARGs with sequences predicted to be plasmid-associated. ST4 contained a larger strain-specific and unassigned-gene component, whereas ST5 showed greater core-genome sequence separation according to variable-site density and pairwise SNP-distance metrics. These findings support continued genomic surveillance across clinical, environmental, and animal sources while emphasizing the need for epidemiologically representative sampling, complete genome assemblies, and experimental validation of predicted ARG mobility.