RESUMEN
OBJECTIVES: K. pneumoniae is a common cause of severe hospital-acquired infections. In the present study, we have characterised the whole-genome of two K. pneumoniae ST437 belonging to the clonal complex CC258. METHODS: The whole-genome sequencing was performed by MiSeq Illumina, with a 2 × 300bp paired-end run. ResFinder 4.4.2 was used to detect acquired antimicrobial resistance genes (ARGs) and chromosomal mutations. Mobile genetic elements (plasmids and ISs) were identified by MobileElementFinder v1.0.3. The genome was also assigned to ST using MLST 2.0.9. Virulence factors were detected using the Virulence Factor Database (VFDB). RESULTS: K. pneumoniae KPNAQ_1/23 and KPNAQ_2/23 strains, isolated from urine samples of hospitalised patients, showed resistance to most antibiotics, including ceftazidime-avibactam, ceftolozane-tazobactam, and meropenem-vaborbactam combinations. Both strains were susceptible only to cefiderocol. Multiple mechanisms of resistance were identified. Resistance to ß-lactams was due to the presence of NDM-5, OXA-232, CTX-M-15, SHV-182 ß-lactamases, and OmpK36 and OmpK37 porin mutations. Resistance to fluoroquinolones was mediated by chromosomal mutations in acrR, oqxAB efflux pumps, and the bifunctional gene aac(6')-Ib-cr. CONCLUSION: The presence of different virulence genes makes these KPNAQ_1/23 and KPNAQ_2/23 high-risk clones.
Asunto(s)
Antibacterianos , Proteínas Bacterianas , Farmacorresistencia Bacteriana Múltiple , Klebsiella pneumoniae , Mutación , Porinas , Secuenciación Completa del Genoma , beta-Lactamasas , Humanos , Farmacorresistencia Bacteriana Múltiple/genética , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/efectos de los fármacos , Porinas/genética , Italia , beta-Lactamasas/genética , Proteínas Bacterianas/genética , Antibacterianos/farmacología , Infecciones por Klebsiella/microbiología , Pruebas de Sensibilidad Microbiana , Factores de Virulencia/genética , Genoma Bacteriano , Tipificación de Secuencias Multilocus , Plásmidos/genéticaRESUMEN
In the present study, we analyzed the genome of two S. enterica strains TS1 and TS2 from stool and blood cultures, respectively, and one strain of C. freundii TS3, isolated from a single hospitalized patient with acute myeloid leukemia. The S. enterica Goldcoast ST358 (O:8 (C2-C3) serogroup), sequenced by the MiSeq Illumina system, showed the presence of ß-lactamase genes (blaVIM-1, blaSHV-12 and blaOXA-10), aadA1, ant(2â³)-Ia, aac(6')-Iaa, aac(6')-Ib3, aac(6')-Ib-cr, qnrVC6, parC(T57S), and several incompatibility plasmids. A wide variety of insertion sequences (ISs) and transposon elements were identified. In C. freundii TS3, these were the blaVIM-1, blaCMY-150, and blaSHV-12, aadA1, aac(6')-Ib3, aac(6')-Ib-cr, mph(A), sul1, dfrA14, ARR-2, qnrVC6, and qnrB38. IncA plasmid isolated from E.coli/K12 transconjugant and C. freundii exhibited a sequence identity >99.9%. The transfer of IncA plasmid was evaluated by conjugation experiments.