Detection of rare β-lactamase bla_SCO-1 from a Klebsiella pneumoniae high-risk clone in Peru

Background: The bla_SCO-1 gene, which codes for a carbenicillinase, is an uncommon β-lactamase. To the best of our knowledge, we report the first instance of a Klebsiella pneumoniae clinical high-risk isolate carrying bla_SCO-1 in Peru. Objectives: To characterize a K. pneumoniae clinical isolate carrying bla_SCO-1 in Peru, isolated from a tertiary care hospital in Lima, Peru. Methods: Susceptibility to amoxicillin/clavulanic acid, amoxicillin/sulbactam, piperacillin/tazobactam, aztreonam, ceftriaxone, cefotaxime, ceftazidime, ceftazidime/avibactam, cefepime, imipenem, meropenem, ciprofloxacin, trimethoprim/sulfamethoxazole, gentamicin, amikacin and tigecycline was determined using the Kirby–Bauer disc diffusion method. Detection of bla_SCO-1 was established by Illumina WGS and bioinformatic analyses. All the publicly available genomes from K. pneumoniae carrying bla_SCO-1 from the American continent were downloaded from the NCBI Isolates browser for assessment of phylogenetic comparisons. Results: The isolate showed resistance to all the tested antibiotics except for ceftazidime/avibactam, carbapenems and tigecycline. Illumina WGS showed the presence of bla_SCO-1 and bla_OXA-1, bla_SHV-28, bla_TEM-1, bla_CTX-M-15, as well as genes associated with resistance to quinolones, fosfomycin, aminoglycosides, sulphonamides, trimethoprim and phenicols. Moreover, the isolate was ST307, a high-risk clone of K. pneumoniae usually associated with bla_CTX-M-15 and/or carbapenemases. Notwithstanding, the latter were not found on this isolate. Phylogenetic relationships were established by comparisons with 19 K. pneumoniae genomes carrying bla_SCO-1 from other countries in the Americas, revealing at least three different clades. Conclusions: This study highlights the importance of genomic surveillance of uncommon antimicrobial resistance genes such as bla_SCO-1, which might contribute to further antimicrobial resistance levels in this country.