5. Discussion
The present study aimed to comprehensively evaluate temporal trends in the incidence of CRKp, the distribution of its phenotypic categories (KPC, dual carbapenemase, and single-MBL producers) across the overall hospital setting and individual sectors, patterns of resistance to last-line antimicrobial agents, and their impact on patient survival.
The principal findings can be summarized as follows. First, at the hospital-wide level, as well as within the medical sector and ICU, a modest and non–statistically significant increase in CRKp incidence was observed over the seven-year period. This trend was characterized by a pronounced surge peaking in 2021–2022, followed by a decline approaching baseline levels observed in 2019. In contrast, in the surgical sector, the increased incidence observed in 2021 persisted without substantial decline through 2025. Second, the peak in CRKp incidence during 2021–2022 coincided with a corresponding rise in KPC-producing isolates, followed by a marked reduction. This reduction returned KPC levels to those comparable to 2019 in the medical and surgical sectors and to even lower levels in the overall hospital and ICU. This shift was accompanied by an apparent epidemiological replacement of KPC producers by isolates harboring dual carbapenemases (primarily KPC combined with VIM or NDM) and by single-MBL phenotypes, predominantly NDM. Third, resistance to amikacin, gentamicin, and tigecycline followed a similar temporal pattern, with increases around 2021 and partial declines thereafter, although rates did not return to pre-2020 levels. In contrast, resistance to colistin increased steadily throughout the study period. Finally, mortality remained high and tended to be greater among infections caused by MBL-harboring strains compared with KPC producers; however, no statistically significant differences were observed in survival analyses.
Following the emergence of VIM carbapenemase in Greece in 2002 [
8], it predominated in Greek hospitals, including our own, until 2007 [
10], when it was progressively replaced by KPC [
11,
12]. Since then, KPC has remained endemic, accounting for approximately 66.5% of cases, followed by NDM and VIM, while OXA-48-like carbapenemases remain rare [
15,
26]. Surveillance data from the European Centre for Disease Prevention and Control (ECDC) demonstrated an increasing trend in CRKp incidence in Greece from 2019, reaching 73.7% in 2021 [
27]. Our findings are consistent with these data, showing a peak in CRKp incidence in 2021–2022, largely driven by KPC-producing isolates [
26]. Notably, a sharp increase in single-MBL-producing isolates, predominantly NDM, was also observed during the same period.
These increases are likely attributable to the COVID-19 pandemic. During this period (March 2021 to December 2022), our hospital functioned as a mixed facility managing both COVID-19-positive (ICU and part of the medical wards) and non-COVID patients (remaining medical wards and surgical ward). Prolonged hospitalizations, increased ICU admissions, and the widespread use of broad-spectrum antibiotics due to concerns about secondary bacterial infections have been widely associated with increased antimicrobial resistance (AMR) [
28,
29,
30]. In addition, disruptions in infection prevention and control (IPC) practices driven by increased workload—such as reduced adherence to hand hygiene, suboptimal equipment decontamination, inadequate cohorting, and inconsistent use of personal protective equipment—likely facilitated transmission [
31]. The continuous transfer of patients between COVID-19 wards, ICUs, and non-COVID units may have further amplified the spread of resistant organisms. This is supported by our observation that KPC incidence peaked earlier in the ICU (2021) and later in the medical and surgical wards (2022), shaping the overall hospital trend.
After 2022, improved antimicrobial stewardship and stricter IPC measures were associated with a decline in CRKp incidence, although rates remained higher than in 2019. Importantly, KPC ceased to predominate and was progressively replaced by both dual carbapenemase and single-MBL mechanisms. Dual carbapenemase-producing strains have been increasingly reported in Greece since the first description of KPC+VIM in 2009 [
32], followed by additional combinations such as NDM+VIM (2016) [
33], NDM+OXA-48-like (2019) [
34], and KPC+NDM (2022) [
35]. Although typically reported at low prevalence (2.5–7.7%) [
12,
26,
35,
36,
37,
38,
39], higher rates, up to 33%, have been observed during outbreaks [
40]. Similar patterns have also been described in other regions [
41,
42,
43,
44,
45,
46], where the NDM+OXA-48-like combination often predominates [
41,
46].
To our knowledge, this is the first study demonstrating a progressive replacement of long-standing endemic KPC by single-MBL (primarily NDM) and dual carbapenemase-producing strains (mainly KPC+VIM and, to a lesser extent, KPC+NDM). At this point, it is worth noting that the co-presence of
blaKPC-2 and
blaVIM-1 has been reported in highly drug-resistant ST39
K. pneumoniae isolates from 2018 and 2019 [
47]. Furthermore, a surveillance study by Tryfinopoulou et al. (2022) demonstrated that among 310 CRKp isolates collected from 15 Greek hospitals, all isolates carrying multiple carbapenemase genes, including
blaKPC-2 with either
blaVIM-1 or
blaNDM, belonged to the ST39 lineage. This clone was shown to spread rapidly both within and between hospitals and has therefore been characterized as a high-risk clone [
37]. In the present study, molecular typing was not performed, and thus assignment of isolates to specific clones was not feasible. Consequently, it remains unclear whether the dual carbapenemase-producing isolates observed here belong to the ST39 lineage, which could potentially explain their progressive dissemination in our hospital from 2022 onwards, or whether they represent the emergence of a novel clone. Nevertheless, irrespective of their clonal background, MBL-harboring strains (either single or dual) exhibited a highly drug-resistant phenotype and were associated with infections that are increasingly difficult to treat.
From a therapeutic perspective, KPC-producing isolates are generally managed with β-lactam antibiotics combined with newer β-lactamase inhibitors, whereas MBL-harboring isolates require more complex regimens, such as ceftazidime/avibactam plus aztreonam or aztreonam/avibactam [
48]. In our hospital, until 2018, last-line agents, including aminoglycosides, colistin, tigecycline, and fosfomycin, constituted the only available treatment options for CRKp infections. Ceftazidime/avibactam was introduced into routine clinical use in 2019 under strict restriction policies to preserve its efficacy. It was administered only in cases of confirmed infection caused by KPC-producing isolates susceptible to ceftazidime/avibactam, or empirically in patients with septic shock known to be colonized with KPC [
49,
50].
Aztreonam availability in Greece has been inconsistent, with only intermittent access, while aztreonam/avibactam is not routinely available and can be obtained only through special request procedures. As a result, last-resort antibiotics continued to be widely used throughout the study period, both empirically and as targeted therapy, reflecting the limited availability of effective treatment options, particularly against MBL-producing organisms. Despite these therapeutic constraints, mortality was only marginally higher among infections caused by MBL-harboring strains compared with KPC-producing isolates, and Kaplan–Meier analysis did not demonstrate a statistically significant difference between groups. This finding, consistent with previous studies [
49,
50], together with the observed early mortality in our cohort, may reflect either suboptimal initial antimicrobial therapy across all CRKp phenotypes or the poor baseline clinical status of patients with severe underlying disease and multiple comorbidities.
The changing epidemiology of CRKp, characterized by the progressive replacement of KPC by MBL-harboring strains (predominantly dual carbapenemase producers) suggests ongoing genetic exchange and selective antimicrobial pressure driving this evolution. Of particular concern is the potential horizontal transfer of MDR plasmids to other Enterobacterales, such as
E. coli, as well as the dissemination of resistance genes into the community, similar to what has been previously observed with ESBLs. Moreover, evidence indicates that certain
K. pneumoniae strains, including hospital-associated pathogens, can persist and proliferate across diverse ecological niches, such as the gastrointestinal tract of animals and environmental reservoirs like soil [
51,
52]. These environments facilitate genetic exchange with other bacterial species. Taken together, these characteristics highlight
K. pneumoniae as a critical target for sentinel surveillance, particularly for the early detection of emerging antimicrobial resistance genes within Gram-negative pathogens [
53].
Collectively, these findings underscore the urgent need to strengthen antimicrobial stewardship and, above all, to reinforce infection prevention and control measures [
52]. In the context of rotating hospital admissions, limited isolation capacity, and the endemic presence of MDR pathogens, strict adherence to hand hygiene is of paramount importance. This should be complemented by consistent implementation of contact precautions, potentially applied universally, as if all patients were colonized with MDR organisms. However, such an approach may impose additional strain on an already understaffed healthcare system and further complicate routine clinical practice.
The main strength of the present study lies in its extended observation period of seven years, including three years following the official end of the COVID-19 pandemic, providing a comprehensive view of carbapenemase dynamics and epidemiological shifts. Nevertheless, several limitations should be acknowledged. The lack of detailed clinical data beyond survival outcomes limits the ability to characterize patient comorbidities and risk factors. Additionally, the absence of molecular typing precludes identification of circulating K. pneumoniae clones. Finally, the single-center design may limit generalizability; however, data from a large tertiary-care hospital are likely to reflect broader national trends, as supported by WHONET Greece surveillance data.