Surveillance of carbapenemase-producing Klebsiella pneumoniae in Russia, Belarus and Kazakhstan

Klebsiella pneumoniae is a versatile human pathogen and a common cause of nosocomial infections. Its clinical significance over the last years has been propelled by its remarkable ability to acquire virulence and antibiotic resistance determinants. Carbapenemase-producing Klebsiella pneumoniae (CPKp) represent one of the most serious public health threats as they are resistant to most currently available antibiotics. This project was carried out by a consortium of research institutions and was aimed at gaining an in-depth knowledge of the molecular epidemiology and evolution of CPKp in Russia and neighbor countries. The clinical isolates included in this project and accompanying metadata (e.g. clinical and patient related data, resistance phenotypes etc.) were collected as part of the sentinel AMR surveillance program, Monitoring of Antimicrobial Resistance at Hospitals (MARatHOn), that included over 90 hospitals across Russia (https://doi.org/10.3389/fmicb.2021.620002), and from participating centers in Belarus and Kazakhstan, in 2012-2018. All isolates were non-duplicate (one isolate per patient/case of infections) and were selected for whole genome sequencing (WGS) to represent the most diverse geographic areas, phenotypic patterns of antibiotic resistance (as was determined by means of broth microdilution susceptibility testing in the central laboratory), and types of carbapenemase genes carried (as was detected by means of real-time PCR screening). Short-read paired-end WGS was performed on Illumina platforms and was used to construct draft genome assemblies of all isolates. For a subset of isolates, long-read sequencing on MinION (Oxford Nanopore Technologies) was added to produce hybrid genome assemblies. Consent to the submission of WGS results was obtained from all members of the research consortium. This project will explore the population structure of CPKp in Russia and neighbor countries and will gain the insights into the role of high-risk international clones and plasmids in spreading resistance and virulence genes. The results of the project will be published shortly.