Emergence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacterales in Spain studied by WGS.

ABSTRACT The emergence of 16S rRNA methyltransferases (RMTs) in gram-negative pathogens bearing other clinically relevant resistance mechanisms, such as carbapenemase-producing Enterobacterales (CPE), is becoming an alarming concern. We investigated the prevalence, antimicrobial susceptibility, resistance mechanisms, molecular epidemiology, and genetic support of RMTs in CPE isolates from Spain. The study included a collection of 468 CPE isolates recovered during 2018 from 32 participating Spanish hospitals. MICs were determined using the broth microdilution method, the agar dilution method (fosfomycin) or MIC gradient strips (plazomicin). All isolates were subjected to hybrid whole-genome sequencing. Sequence types (STs), core-genome phylogenetic relatedness, horizontally acquired resistance mechanisms, plasmid analysis and genetic environment of RMTs was in silico determined from WGS data in all RMT-positive isolates. Among the 468 CPE isolates evaluated, 24 (5.13%) isolates recovered from 9 different hospitals spanning 5 different Spanish regions showed resistance to all aminoglycosides and were positive for an RMT: 21 RmtF, 2 AmrA and 1 RmtC. All the RMT-producers showed high-level resistance to all aminoglycosides, including plazomicin, and in most of cases exhibited an extensively drug-resistant (XDR) susceptibility profile. The RMT-positive isolates showed low genetic diversity and were global clones of K. pneumoniae (ST147, ST101, ST395) or E. cloacae (ST93) species bearing blaOXA-48, blaNDM-1 or blaVIM-1 carbapenemase genes. RMTs were in 5 different multidrug-resistant plasmids and linked to efficient mobile elements. Our findings highlight that RMTs are emerging among clinical CPE isolates from Spain and their spread should be monitored to preserve the clinical utility of aminoglycosides and plazomicin in the future.