Genomic Epidemiology of Carbapenem- and Colistin-Resistant Klebsiella pneumoniae Isolates From Serbia: Predominance of ST101 Strains Carrying a Novel OXA-48 Plasmid

Abstract

Klebsiella pneumoniae is a major cause of severe healthcare-associated infections and often shows MDR phenotypes. Carbapenem resistance is frequent, and colistin represents a key molecule to treat infections caused by such isolates. Here we evaluated the antimicrobial resistance (AMR) mechanisms and the genomic epidemiology of clinical K. pneumoniae isolates from Serbia. Consecutive non-replicate K. pneumoniae clinical isolates (n = 2,298) were collected from seven hospitals located in five Serbian cities and tested for carbapenem resistance by disk diffusion. Isolates resistant to at least one carbapenem (n = 426) were further tested for colistin resistance with Etest or Vitek2. Broth microdilution (BMD) was performed to confirm the colistin resistance phenotype, and colistin-resistant isolates (N = 45, 10.6%) were characterized by Vitek2 and whole genome sequencing. Three different clonal groups (CGs) were observed: CG101 (ST101, N = 38), CG258 (ST437, N = 4; ST340, N = 1; ST258, N = 1) and CG17 (ST336, N = 1). mcr genes, encoding for acquired colistin resistance, were not observed, while all the genomes presented mutations previously associated with colistin resistance. In particular, all strains had a mutated MgrB, with MgrB C28S being the prevalent mutation and associated with ST101. Isolates belonging to ST101 harbored the carbapenemase OXA-48, which is generally encoded by an IncL/M plasmid that was no detected in our isolates. MinION sequencing was performed on a representative ST101 strain, and the obtained long reads were assembled together with the Illumina high quality reads to decipher the bla OXA-48 genetic background.

High plasmid variability, and the presence of IncFIB, IncQ, IncA/C, IncHI1B, and IncL/M in clinical isolates of Klebsiella pneumoniae with bla KPC and bla NDM from patients at a public hospital in Brazil.

“…The excessive and indiscriminate use of beta-lactam antimicrobials has culminated in the emergence of antibioticresistant K. pneumoniae strains and other carbapenem-resistant Enterobacteria 1,5,6,7 . The development of resistance is related to the production of beta-lactamases which is mediated by conjugative plasmids 8,9,10,11,12 .…”

Emergence of carbapenemase-producing and colistin resistant Klebsiella pneumoniae ST101 high-risk clone in Turkey

“…Carbapenem-resistance among K. pneumoniae isolates makes colistin the last therapeutic option for the treatment. With the rise in consumption of colistin, cases of colistin resistant CRKP isolates are reported globally [1,9,11]. Chromosomal mutations in phoP/phoQ, pmrA/pmrB, mgrB and plasmid-borne mobile colistin resistance genes (mcr-1 to mcr-9) positivity have an important role in increasing colistin resistance in K. pneumoniae [47,10,11].…”

“…Klebsiella pneumoniae is an opportunistic pathogen which can cause different types of healthcare-associated infections. Enhanced use of carbapenems in clinical practice, promoted emergence of carbapenem-resistant K. pneumoniae (CRKP) worldwide in recent years [1]. CRKP has mainly been link to K. pneumoniae carbapenemase (KPC), oxacillinase-48 (OXA-48), and metallo-b-lactamases (MBLs), such as NDM, IMP, and VIM type carbapenemases.…”

“…Dissemination of CRKP is mainly caused by the spread of a few successful clones. Major representatives of these high-risk clonal lineages include sequence type (ST) 11, ST15, ST307, ST17, ST37, ST101, and ST147 strains [1]. ST258 strains are major players in the worldwide spread of KPC-type carbapenemases, and are responsible for 68% of the CRKP outbreaks [12].…”

“…ST258 strains are major players in the worldwide spread of KPC-type carbapenemases, and are responsible for 68% of the CRKP outbreaks [12]. ST101 strains harbor different clinically-relevant resistance determinants, such as carbapenemases of the KPC, OXA-48, VIM, and NDM types [1].…”