Genomic and Molecular Characterization of Clinical Isolates of Enterobacteriaceae Harboring mcr-1 in Colombia, 2002 to 2016

Polymyxins are last-resort antimicrobial agents used to treat infections caused by carbapenem-resistantEnterobacteriaceae . Due to the worldwide dissemination of polymyxin resistance in animal and human isolates, we aimed to characterize polymyxin resistance associated with the presence ofmcr-1 inEnterobacteriaceae and nonfermenter Gram-negative bacilli, using isolates collected retrospectively in Colombia from 2002 to 2016. A total of 5,887 Gram-negative clinical isolates were studied, and 513 were found to be resistant to the polymyxins. Susceptibility to colistin was confirmed by broth microdilution for allmcr-1 -positive isolates, and these were further subjected to whole-genome sequencing (WGS). The localization ofmcr-1 was confirmed by S1 pulsed-field gel electrophoresis (S1-PFGE) and CeuI-PFGE hybridization. Transferability was evaluated by mating assays. A total of 12 colistin-resistant isolates recovered after 2013 harboredmcr-1 , including 8Escherichia coli , 3Salmonella enterica serovar Typhimurium, and 1Klebsiella pneumoniae isolate. E. coli isolates were unrelated by PFGE and belonged to 7 different sequence types (STs) and phylogroups.S . Typhimurium andK. pneumoniae isolates belonged to ST34 and ST307, respectively. Themcr-1 gene was plasmid borne in all isolates but twoE. coli isolates which harbored it on the chromosome. Conjugation ofmcr-1 was successful in 8 of 10 isolates (8.2 × 10−5 to 2.07 × 10−1 cell per recipient). Plasmid sequences showed that themcr-1 plasmids belonged to four different Inc groups (a new IncP-1 variant and the IncFII, IncHI1, and IncH families). Our results indicate thatmcr-1 is circulating in clinical isolates of colistin-resistantEnterobacteriaceae in Colombia and is mainly harbored in transferable plasmids.