Unveiling the resistance: comparative genomic analysis of two novel cefiderocol-resistant Stenotrophomonas species from a referral hospital in Mexico City
Por:
Alvarez, JO, Flores, CB, Castro, CAC, Durán, MH, Zavaleta, MGM, Sotelo, BJM, Pérez, CFH, Sohlenkamp, C, Cendejas, RF, Jácome, LEL
Publicada:
17 mar 2025
Resumen:
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.
Filiaciones:
Alvarez, JO:
Secretaria Ciencia Humanidades Tecnol & Innovac SE, Programa Invest Invest Mexico IIXM, Mexico City 03940, Mexico
Flores, CB:
Clin Especializada Condesa, Mexico City 06140, Mexico
Castro, CAC:
Inst Nacl Rehabil Luis Guillermo Ibarra Ibarra, Lab Microbiol Clin, Div Infectol, Mexico City 14389, Mexico
Durán, MH:
Inst Nacl Rehabil Luis Guillermo Ibarra Ibarra, Lab Microbiol Clin, Div Infectol, Mexico City 14389, Mexico
Zavaleta, MGM:
Inst Nacl Rehabil Luis Guillermo Ibarra Ibarra, Lab Microbiol Clin, Div Infectol, Mexico City 14389, Mexico
Sotelo, BJM:
Inst Nacl Rehabil Luis Guillermo Ibarra Ibarra, Div Infectol, Mexico City 14389, Mexico
Pérez, CFH:
Ctr Nacl Referencia Inocu & Biosegur Agroalimentar, Serv Nacl Sanidad Inocu & Cal Agroalimentaria SENA, Mexico City 55740, Mexico
Sohlenkamp, C:
Univ Nacl Autonoma Mexico, Ctr Ciencias Gen, Cuernavaca 62210, Morelos, Mexico
Cendejas, RF:
Inst Nacl Rehabil Luis Guillermo Ibarra Ibarra, Subdirecc Invest Biomed, Mexico City 14389, Mexico
Jácome, LEL:
Inst Nacl Rehabil Luis Guillermo Ibarra Ibarra, Lab Microbiol Clin, Div Infectol, Mexico City 14389, Mexico
Univ Nacl Autonoma Mexico, Fac Quim, Dept Biol, Circuito Exterior S N, Mexico City 04510, Mexico
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