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

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: bla NDM-1 (N = 65; 44.5%), bla OXA-48 (N = 64; 43.8%), and bla KPC-2 (N = 11; 7.5%). Additionally, six CRKP isolates co-harbored bla NDM-1 and bla OXA-48 (4.1%). This study revealed ten sequence types (STs) and six clonal complexes (CCs), with ST147/CC147/ bla NDM-1 being the most prevalent (N = 44; 29.3%) followed by ST101/CC101/ bla OXA-48 (N = 40; 26.7%). One CRKP isolate, ST101/ bla NDM-1 / bla SHV-1 / bla CTX-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/ bla NDM-1 , suggests a high potential for regional spread of a high-risk clone resistant to last-line antibiotics.