The alarming rate of carbapenem-resistant Klebsiella pneumoniae in Serbia: A deep dive into genomic diversity, resistome, hypervirulence, and expansion of high-risk clone ST147/blaNDM-1

Jovicevic, Milos and Kabic, Jovana and Kekic, Dusan and Brankovic, Milena and Zigmanovic, Anita Sente and Delic, Snezana and Hadnadjev, Mirjana and Trudic, Anika and Blanusa, Ljuban and Trifunovic, Natasa and Jencic, Aleksandra and Ranin, Lazar and Senicic, Stanislava and Boskovic, Lidija and Kintses, Bálint and Stirling, Tamás and Zdravkovic, Marija and Opavski, Natasa and Todorovic, Zoran and Gajic, Ina (2026) The alarming rate of carbapenem-resistant Klebsiella pneumoniae in Serbia: A deep dive into genomic diversity, resistome, hypervirulence, and expansion of high-risk clone ST147/blaNDM-1. MICROBIOLOGICAL RESEARCH, 310. no.-128543. ISSN 0944-5013

Preview

Text JovicevicM_2026.pdf - Published Version Available under License Creative Commons Attribution. Download (6MB) | Preview

Abstract

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging global threat. This study aimed to determine the prevalence of CRKP, the genetic basis of antimicrobial resistance, including beta-lactamase production, efficacy of novel beta-lactam/beta-lactamase inhibitor (BLBLI) combinations, hypervirulence, and genetic diversity of circulating clones in a Serbian hospital setting. From 2022-2023, 2001 K. pneumoniae isolates were collected from 16 hospitals across Serbia. The prevalence of CRKP was 53.4% (N = 1069). Among these, 191 randomly selected CRKP isolates were subjected to expanded antimicrobial susceptibility testing, string test, and carbapenemase production, with 150 further randomly chosen for whole-genome sequencing. Resistance rates to ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam were 50.8% (N = 97), 84.8% (N = 162), and 90.6% (N = 173), respectively. The majority of CRKP isolates (N = 146; 97.3%) harboured carbapenemase-encoding genes: blaNDM-1 (N = 65; 44.5%), blaOXA-48 (N = 64; 43.8%), and blaKPC-2 (N = 11; 7.5%). Additionally, six CRKP isolates co-harbored blaNDM-1 and blaOXA-48 (4.1%). This study revealed ten sequence types (STs) and six clonal complexes (CCs), with ST147/CC147/blaNDM-1 being the most prevalent (N = 44; 29.3%) followed by ST101/CC101/blaOXA-48 (N = 40; 26.7%). One CRKP isolate, ST101/blaNDM-1/ blaSHV-1/blaCTX-M15 was resistant to cefiderocol. The predominant hypervirulence-associated genes were ybt (N = 138; 92%) and iuc (N = 80; 53.3%). According to the genotypic analysis, 75 out of 150 (50.0%) CRKP isolates had iuc and rmpA2/rmpADC genes, whereas 26 (13.6%) strains exhibited the hypermucoviscous phenotype. The emergence of hypervirulent, K. pneumoniae clone ST147/blaNDM-1, suggests a high potential for regional spread of a high-risk clone resistant to last-line antibiotics.

Actions (login required)

View Item