Characterization of carbapenemase-producing Serratia marcescens and whole-genome sequencing for plasmid typing in a hospital in Madrid, Spain (2016-18)

Objectives: Carbapenemase-producing Enterobacterales (CPE) are increasingly recognized in nosocomial infections, also affecting ICU patients. We aimed to characterize the carbapenemase-producing Serratia marcescens (CPSm) isolates recovered in our hospital in Madrid (Spain) between March 2016 and December 2018. Methods: Overall, 50 isolates from clinical and epidemiological surveillance samples were recovered from 24 patients admitted to the medical ICU and 10 non-ICU-related patients based on their phenotypic resistance. Carbapenemase characterization, antibiotic susceptibility, PFGE clonal relatedness, plasmid characterization, WGS (Illumina-NovaSeq 6000) and phylogenetic analysis were performed. Results: A single isolate was finally considered for each patient, except for Patient 8 that was colonized by two different isolates (n = 35). Isolates were characterized as VIM-1 (n = 29) or OXA-48 producers (n = 6). Up to seven genetic lineages were found by PFGE, with dominance of two clones. Plasmid characterization confirmed that almost all CPSm carried the same similar to 60 kb IncL-OXA-48- or VIM-1-encoding plasmid, which was related to the globally disseminated IncL-pOXA-48a. WGS allowed pLasmid reconstruction with two variants: IncL-pVIM-1 (similar to 65 kb) and IncL-pOXA-48 (similar to 62 kb). bla(OXA-48)-Tn1999 (similar to 5 kb) was the unique antibiotic resistance gene in pOXA-48, whereas pVIM-1 plasmids (similar to 8 kb) harboured a class 1 integron containing 5'-bla(VIM-1) + aacA4 +dfrB1 +aadA1 +catB2+ qacEDelta1 +sul1-3'. Conclusions: Our results confirm the dissemination of CPSm within our institution in both ICU and non-ICU environments, representing two prevalent CPSm clones, and the same IncL-pOXA-48 pLasmid previously described in other Enterobacterales, but containing the bla(VIM)(-1) gene. This also reinforces the relevance of species different from Klebsiella pneumoniae or Escherichia coli in the CPE Landscape and circulating Lineages and plasmids in local CPE epidemiology.