Phenotypic and in silico characterization of carbapenem-resistant Serratia marcescens clinical strains

Background: Serratia marcescens, an opportunistic nosocomial Gram-negative bacterium pathogen, has emerged as an important cause of healthcare-associated infections owing to its acquisition of antimicrobial resistance genes (ARGs) and virulence factor determinants. Methods: Four carbapenem-resistant S. marcescens strains were recovered from patients admitted to different hospitals in 2017 and 2018. We assessed the antimicrobial resistance and virulence context, as well as the genetic similarities of four Brazilian S. marcescens strains, and compared the genomes of these S. marcescens isolates with whole genome data of 428 S. marcescens strains available in the NCBI Reference Sequence. Antimicrobial susceptibility testing was performed by disk diffusion and broth microdilution methods according to CLSI recommendations. Whole genome sequencing was performed using Illumina NextSeq 250-bp paired-end sequencing for two isolates, Sm424 and Sm613, which presented representative phenotypes. Results: The pathogenicity of both sequenced strains was predicted using the Pathogen Finder tool. Both isolates carried efflux system genes (RND, SMR, MFS, ABC-family) and resistance genes (bla_STR-2, aac(6′)-Ic, fos). Virulence factor genes involved in motility, regulation, capsule formation, acid resistance, and acriflavine resistance were also found. The Pathogen Finder tool predicted a > 71% probability of being a human pathogen for Sm424 and Sm613. Conclusion: S. marcescens has shown increased adaptive, resistance, and pathogenic potential, being responsible for different nosocomial infections.