2025/03/01 by Jossué Ortiz-Álvarez, Corazón Barrientos-Flores, Claudia Adriana Colín‐Castro +7 · 1 voice
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Infections and bacterial resistance #Fecal contamination and water quality #Bacteriophages and microbial interactions
paper · pdf · doi:10.1093/jambio/lxaf048
openalex publication_date 2025/03/01 · openalex created_date 2025/03/08 · openalex updated_date 2026/08/03
BACKGROUND: Stenotrophomonas maltophilia is the species most frequently identified by clinical microbiology laboratories due to its presence in the main identification systems databases. Phenotypic identification methods are widely used in laboratories, and the misidentification of Stenotrophomonas spp. is highly probable due to the presence of cryptic species. Our aim was to confirm the identity of five cefiderocol-resistant Stenotrophomonas species, initially identified as S. maltophilia, using genome analysis tools, performing comparative and functional analyses of these clinical strains associated with infectious processes. METHODS: Identifications were performed using average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization. Virulence factors, resistance mechanisms, prophages, CRISPR elements, and metabolism elements were identified and annotated. RESULTS: We confirmed the identity of the strains C960 and C2866 as Stenotrophomonas geniculata, and of strain C1657 as Stenotrophomonas indicatrix. The species designation parameters obtained indicated that the strains C4297 and C2852 are novel species. In comparison with the hypothetical proteome of the S. maltophilia complex species analyzed, elements associated with amino acid metabolism, DNA/RNA processing and repair, envelope biogenesis, and intracellular transport are predominant. Elements probably associated with antibiotic resistance, such as efflux pumps, aminoglycoside transferases, and phosphoethanolamine transferases, were identified, and the presence of genes related to capsule formation, iron acquisition, and intracellular survival probably contributes to virulence. CONCLUSIONS: This is the first report of S. geniculata and S. indicatrix as human pathogens. Besides, we proposed two novel species members of Smc: Stenotrophomonas veracruzanensis sp. nov. and Stenotrophomonas mexicanensis sp. nov.