Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (276)

Search Parameters:
Keywords = Klebsiella pneumoniae KpC4

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
14 pages, 3593 KiB  
Article
Spontaneous Emergence of Cefiderocol Resistance in Klebsiella pneumoniae KPC-163: Genomic and Transcriptomic Insights
by Irene Luu, Vyanka Mezcord, Jenny Escalante, German M. Traglia, Marisel R. Tuttobene, Cecilia Rodriguez, Chun Fu Cheng, Quentin Valle, Rajnikant Sharma, Marcelo E. Tolmasky, Robert A. Bonomo, Gauri Rao, Fernando Pasteran and Maria Soledad Ramirez
Antibiotics 2025, 14(8), 832; https://doi.org/10.3390/antibiotics14080832 - 15 Aug 2025
Viewed by 43
Abstract
Background/Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an urgent public health threat due to its rapid dissemination and resistance to last-line antibiotics. Cefiderocol (FDC), a novel siderophore cephalosporin, targets resistant Gram-negative pathogens by exploiting bacterial iron uptake mechanisms. However, resistance to FDC is emerging [...] Read more.
Background/Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an urgent public health threat due to its rapid dissemination and resistance to last-line antibiotics. Cefiderocol (FDC), a novel siderophore cephalosporin, targets resistant Gram-negative pathogens by exploiting bacterial iron uptake mechanisms. However, resistance to FDC is emerging among Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae strains. This study characterizes a spontaneous FDC-resistant subpopulation (IHC216) derived from a KPC-producing strain (KPNMA216) using comprehensive genomic, transcriptional, and phenotypic analyses. Methods: Given the whole-genome sequencing results, where mutations were identified in genes involved in transcriptional regulation and membrane permeability (ompC) among others, in the present work we further explore their potential implications and conduct a more detailed analysis of the IHC216 genome. A qRT-PCR analysis highlighted significant downregulation of classical siderophore-mediated iron acquisition systems (fepA, cirA, iroN) and upregulation of alternative iron uptake pathways (iucA, fiU), reflecting a switch in iron acquisition strategies. Results: A notable downregulation of blaKPC-163 correlated with restored susceptibility to carbapenems, indicating collateral susceptibility. Altered expressions of pbp2 and pbp3 implicated adaptive changes in cell wall synthesis, potentially affecting FDC resistance mechanisms. Furthermore, enhanced oxidative stress responses via upregulated sodC expression and increased capsule production were observed. Conclusions: These findings underscore the complex interplay of genetic and transcriptional adaptations underlying FDC resistance, highlighting potential therapeutic vulnerabilities. Full article
Show Figures

Figure 1

14 pages, 1033 KiB  
Systematic Review
Resistance of Gram-Negative Bacteria to Cefepime-Enmetazobactam: A Systematic Review
by Matthew E. Falagas, Laura T. Romanos, Dimitrios S. Kontogiannis, Katerina Tsiara and Stylianos A. Kakoullis
Pathogens 2025, 14(8), 777; https://doi.org/10.3390/pathogens14080777 - 6 Aug 2025
Viewed by 423
Abstract
Cefepime-enmetazobactam is a novel β-lactam/β-lactamase inhibitor combination showing good activity against multidrug-resistant (MDR) Gram-negative bacteria producing a variety of β-lactamases. In this systematic review, we aimed to evaluate the available data on resistance to this drug. We performed a thorough search of four [...] Read more.
Cefepime-enmetazobactam is a novel β-lactam/β-lactamase inhibitor combination showing good activity against multidrug-resistant (MDR) Gram-negative bacteria producing a variety of β-lactamases. In this systematic review, we aimed to evaluate the available data on resistance to this drug. We performed a thorough search of four databases (Embase, PubMed, Scopus, and Web of Science), as well as backward citation searching, to identify studies containing data on resistance to cefepime-enmetazobactam. The data were extracted and analyzed according to the breakpoints established by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the Food and Drug Administration (FDA), or the specific breakpoints reported by the authors of the respective studies. Analysis based on the type of lactamases produced by the isolates was also performed. Ten studies reported in vitro susceptibility testing and mechanisms of antimicrobial resistance. The total number of isolates was 15,408. The activity of cefepime-enmetazobactam against β-lactamase-producing isolates was variable. The resistance of the studied extended-spectrum β-lactamase (ESBL)-producing and ampicillin C β-lactamase (AmpC)-producing isolates was low (0–2.8% and 0%, respectively). The resistance was higher among oxacillinase-48 β-lactamase (OXA-48)-producing and Klebsiella pneumoniae carbapenemase (KPC)-producing isolates (3.4–13.2% and 36.7–57.8%, respectively). High resistance was noted among metallo-β-lactamase (MBL)-producing isolates (reaching 87.5% in one study), especially those producing New Delhi metallo-β-lactamase (NDM) and Verona integron-encoded metallo-β-lactamase (VIM), which had the highest rates of resistance. The high activity of cefepime-enmetazobactam against Enterobacterales and selected lactose non-fermenting Gram-negative pathogens, including ESBL-producing and AmpC-producing isolates, makes it a potential carbapenem-sparing agent. The drug should be used after in vitro antimicrobial susceptibility testing in patients with infections caused by OXA-48, KPC, and MBL-producing isolates. Full article
Show Figures

Figure 1

26 pages, 477 KiB  
Review
Global Epidemiology and Antimicrobial Resistance of Klebsiella Pneumoniae Carbapenemase (KPC)-Producing Gram-Negative Clinical Isolates: A Review
by Matthew E. Falagas, Christina-Maria Asimotou, Maria Zidrou, Dimitrios S. Kontogiannis and Charalampos Filippou
Microorganisms 2025, 13(7), 1697; https://doi.org/10.3390/microorganisms13071697 - 19 Jul 2025
Viewed by 872
Abstract
Klebsiella pneumoniae carbapenemases (KPCs) are a group of class A β-lactamases of Gram-negative bacteria leading to difficult-to-treat infections. We evaluated the global epidemiology of KPC-producing Gram-negative clinical isolates. A systematic search of six databases (Cochrane Library, Embase, Google Scholar, PubMed, Scopus, and Web [...] Read more.
Klebsiella pneumoniae carbapenemases (KPCs) are a group of class A β-lactamases of Gram-negative bacteria leading to difficult-to-treat infections. We evaluated the global epidemiology of KPC-producing Gram-negative clinical isolates. A systematic search of six databases (Cochrane Library, Embase, Google Scholar, PubMed, Scopus, and Web of Science) was conducted. Extracted data were tabulated and evaluated. After screening 1993 articles, 119 were included in the study. The included studies originated from Asia (n = 49), Europe (n = 29), North America (n = 14), South America (n = 11), and Africa (n = 3); 13 studies were multicontinental. The most commonly reported KPC-producing species were Klebsiella pneumoniae (96 studies) and Escherichia coli (52 studies), followed by Enterobacter cloacae (31), Citrobacter spp. (24), Klebsiella oxytoca (23), Serratia spp. (15), Enterobacter spp. (15), Acinetobacter baumannii complex (13), Providencia spp. (11), Morganella spp. (11), Klebsiella aerogenes (9), Pseudomonas aeruginosa (8), Raoultella spp. (8), Proteus spp. (8), and Enterobacter aerogenes (6). Among the studies with specific blaKPC gene detection, 52/57 (91%) reported the isolation of blaKPC-2 and 26/57 (46%) reported blaKPC-3. The antimicrobial resistance of the studied KPC-producing isolates was the lowest for ceftazidime–avibactam (0–4%). Resistance to polymyxins, tigecycline, and trimethoprim–sulfamethoxazole in the evaluated studies was 4–80%, 0–73%, and 5.6–100%, respectively. Conclusions: The findings presented in this work indicate that KPC-producing Gram-negative bacteria have spread globally across all continents. Implementing proper infection control measures, antimicrobial stewardship programs, and enhanced surveillance is crucial. Full article
(This article belongs to the Special Issue ß-Lactamases, 3rd Edition)
Show Figures

Figure 1

18 pages, 4199 KiB  
Article
Effects of Antibiotic Residues on Fecal Microbiota Composition and Antimicrobial Resistance Gene Profiles in Cattle from Northwestern China
by Wei He, Xiaoming Wang, Yuying Cao, Cong Liu, Zihui Qin, Yang Zuo, Yiming Li, Fang Tang, Jianjun Dai, Shaolin Wang and Feng Xue
Microorganisms 2025, 13(7), 1658; https://doi.org/10.3390/microorganisms13071658 - 14 Jul 2025
Viewed by 393
Abstract
Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the [...] Read more.
Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the antibiotic residues, bacterial community, ARG profiles, and mobile genetic elements (MGEs) in cattle feces from three provinces in western China (Ningxia, Xinjiang, and Inner Mongolia) under grazing modes. The HPLC-MS detection showed that the concentration of tetracycline antibiotics was the highest in all three provinces. Correlation analysis revealed a significant negative correlation between antibiotic residues and the diversity and population abundance of intestinal microbiota. However, the abundance of ARGs was directly proportional to antibiotic residues. Then, the Sankey analysis revealed that the ARGs in the cattle fecal samples were concentrated in 15 human pathogenic bacteria (HPB) species, with 9 of these species harboring multiple drug resistance genes. Metagenomic sequencing revealed that carbapenemase-resistant genes (blaKPC and blaVIM) were also present in considerable abundance, accounting for about 10% of the total ARGs detected in three provinces. Notably, Klebsiella pneumoniae strains carrying blaCTX-M-55 were detected, which had a possibility of IncFII plasmids harboring transposons and IS19, indicating the risk of horizontal transfer of ARGs. This study significantly advances the understanding of the impact of antibiotic residues on the fecal microbiota composition and ARG profiles in grazing cattle from northwestern China. Furthermore, it provides critical insights for the development of rational antibiotic usage strategies and comprehensive public health risk assessments. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
Show Figures

Figure 1

12 pages, 247 KiB  
Article
Restoring Control: Real-World Success with Imipenem–Relebactam in Critical MDR Infections—A Multicenter Observational Study
by Andrea Marino, Giuseppe Pipitone, Emmanuele Venanzi Rullo, Federica Cosentino, Rita Ippolito, Roberta Costa, Sara Bagarello, Ylenia Russotto, Chiara Iaria, Bruno Cacopardo and Giuseppe Nunnari
Pathogens 2025, 14(7), 685; https://doi.org/10.3390/pathogens14070685 - 11 Jul 2025
Viewed by 545
Abstract
Background: Multidrug-resistant (MDR) Gram-negative infections, particularly those caused by carbapenem-resistant Enterobacterales (CRE) and difficult-to-treat Pseudomonas aeruginosa (DTR-Pa), present a growing global healthcare challenge, especially in critically ill populations. Imipenem–relebactam (I/R), a novel β-lactam/β-lactamase inhibitor combination, has shown efficacy in clinical trials, but [...] Read more.
Background: Multidrug-resistant (MDR) Gram-negative infections, particularly those caused by carbapenem-resistant Enterobacterales (CRE) and difficult-to-treat Pseudomonas aeruginosa (DTR-Pa), present a growing global healthcare challenge, especially in critically ill populations. Imipenem–relebactam (I/R), a novel β-lactam/β-lactamase inhibitor combination, has shown efficacy in clinical trials, but real-world data remain limited. Methods: We conducted a multicenter, retrospective–prospective observational study across tertiary-care hospitals in Italy between January 2020 and May 2025. Adult patients (≥18 years) treated with I/R for ≥48 h for suspected or confirmed MDR Gram-negative infections were included. Primary endpoints were clinical success at the end of therapy and 30-day all-cause mortality. Secondary endpoints included microbiological eradication, recurrence, safety, and predictors of treatment failure. Statistical analysis involved descriptive methods and correlation analysis for mortality predictors. Results: Twenty-nine patients were included (median age 66 years; 58.6% ICU admission; 71.4% mechanical ventilation). Clinical success was achieved in 22/29 patients (75.9%), while 30-day mortality was 24.1% (7/29). The most common pathogen was Klebsiella pneumoniae (62.1%), with 41.4% of infections being polymicrobial. Microbiological eradication was confirmed in all the BSIs. Parenteral nutrition (p = 0.016), sepsis at presentation (p = 0.04), candidemia (p = 0.036), and arterial catheter use (p = 0.029) were significantly more frequent in non-survivors. Survivors showed significant reductions in CRP, PCT, and bilirubin at 48 h, while non-survivors did not. Parenteral nutrition (rho = 0.427, p = 0.023), sepsis (rho = 0.378, p = 0.043), and arterial catheter use (rho = 0.384, p = 0.04) were significantly correlated with mortality. Conclusions: In this Italian multicenter cohort of critically ill patients, imipenem–relebactam demonstrated high clinical success and acceptable mortality rates in the treatment of severe MDR Gram-negative infections, particularly those caused by KPC-producing K. pneumoniae. Early biomarker dynamics may aid in monitoring treatment response. Larger prospective studies are needed to confirm these findings and define optimal treatment strategies. Full article
11 pages, 239 KiB  
Article
Carbapenem-Resistant Enterobacteriaceae (CRE) in Children with Cancer: The Impact of Rapid Diagnostics and Targeted Colonization Strategies on Improving Outcomes
by Youssef Madney, Sally Mahfouz, Ahmed Bayoumi, Omayma Hassanain, Omneya Hassanain, Ahmed A. Sayed, Deena Jalal, Maryam Lotfi, May Tolba, Ghada A. Ziad, Mervat Elanany, Mohamed Hashem, Gehad Taha, Lobna Shalaby and Alaa Elhaddad
Microorganisms 2025, 13(7), 1627; https://doi.org/10.3390/microorganisms13071627 - 10 Jul 2025
Viewed by 1152
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) pose an emerging threat, with a high mortality rate among children with cancer. This study aimed to evaluate the impact of routine rectal swab surveillance and rapid PCR-based detection of carbapenemase genes to facilitate the early initiation of appropriate treatment [...] Read more.
Carbapenem-resistant Enterobacteriaceae (CRE) pose an emerging threat, with a high mortality rate among children with cancer. This study aimed to evaluate the impact of routine rectal swab surveillance and rapid PCR-based detection of carbapenemase genes to facilitate the early initiation of appropriate treatment and assess its effects on outcomes. The study compared two groups of pediatric cancer patients with CRE bloodstream infections: a retrospective cohort of 254 patients from 2013 to 2017, and a prospective cohort of 186 patients from 2020 to 2022, following the implementation of these tools. A rapid diagnostic test in the prospective cohort resulted in the early initiation of proper antibiotics in 85% (165/186) of patients, compared to only 58% (147/254) in the retrospective group. This led to a decrease in the need for ICU admission related to sepsis from CRE and a significant reduction in the 30-day mortality rate (16% vs. 30%, p ≤ 0.01). Genotypic profiling revealed that class B carbapenemases were the most prevalent (69%), with the NDM type being identified in 67% of patients. OXA-48 and KPC enzymes were detected in 59% and 4% of patients, respectively. Multivariate analysis revealed that patients having Klebsiella pneumoniae, NDM genotype carbapenemases, presence of pneumonia, and septic shock requiring ICU admission were predictors of poor outcomes. Rapid diagnostics and targeted colonization lead to the appropriate use of targeted antibiotics, resulting in improved patient outcomes. Understanding carbapenemase-producing microorganisms and administering newer antibiotics may further reduce mortality and enhance treatment strategies for high-risk patients. Full article
(This article belongs to the Special Issue Antimicrobial Resistance: Challenges and Innovative Solutions)
22 pages, 1347 KiB  
Article
The Microbiological Characteristics and Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae Isolated from Clinical Samples
by Mehwish Rizvi, Noman Khan, Ambreen Fatima, Rabia Bushra, Ale Zehra, Farah Saeed and Khitab Gul
Microorganisms 2025, 13(7), 1577; https://doi.org/10.3390/microorganisms13071577 - 4 Jul 2025
Viewed by 690
Abstract
Klebsiella pneumoniae is a major public health concern due to its role in Gram-negative bacteremia, which leads to high mortality and increased healthcare costs. This study characterizes phenotypic and genomic features of K. pneumoniae isolates from clinical samples in Karachi, Pakistan. Among 507 [...] Read more.
Klebsiella pneumoniae is a major public health concern due to its role in Gram-negative bacteremia, which leads to high mortality and increased healthcare costs. This study characterizes phenotypic and genomic features of K. pneumoniae isolates from clinical samples in Karachi, Pakistan. Among 507 isolates, 213 (42%) were carbapenem-resistant based on disk diffusion and MIC testing. Urine (29.7%) and blood (28.3%) were the most common sources, with infections predominantly affecting males (64.7%) and individuals aged 50–70 years. Colistin was the only antibiotic showing consistent activity against these isolates. The whole-genome sequencing of 24 carbapenem-resistant K. pneumoniae (CR-KP) isolates revealed blaNDM-5 (45.8%) as the dominant carbapenemase gene, followed by blaNDM-1 (12.5%) and blaOXA-232 (54.2%). Other detected blaOXA variants included blaOXA-1, blaOXA-4, blaOXA-10, and blaOXA-18. The predominant beta-lactamase gene was blaCTX-M-15 (91.6%), followed by blaCTX-M-163, blaCTX-M-186, and blaCTX-M-194. Sequence types ST147, ST231, ST29, and ST11 were associated with resistance. Plasmid profiling revealed IncR (61.5%), IncL (15.4%), and IncC (7.7%) as common plasmid types. Importantly, resistance was driven not only by acquired genes but also by chromosomal mutations. Porin mutations in OmpK36 and OmpK37 (e.g., P170M, I128M, N230G, A217S) reduced drug influx, while acrR and ramR mutations (e.g., P161R, G164A, P157*) led to efflux pump overexpression, enhancing resistance to fluoroquinolones and tigecycline. These findings highlight a complex resistance landscape driven by diverse carbapenemases and ESBLs, underlining the urgent need for robust antimicrobial stewardship and surveillance strategies. Full article
Show Figures

Figure 1

15 pages, 916 KiB  
Article
Carbapenem-Resistant Gram-Negative Bacteria in Hospitalized Patients: A Five-Year Surveillance in Italy
by Marcello Guido, Antonella Zizza, Raffaella Sedile, Milva Nuzzo, Laura Isabella Lupo and Pierfrancesco Grima
Infect. Dis. Rep. 2025, 17(4), 76; https://doi.org/10.3390/idr17040076 - 2 Jul 2025
Viewed by 376
Abstract
Background/Objectives: Antibiotic resistance is a significant and escalating challenge that limits available therapeutic options. This issue is further exacerbated by the decreasing number of new antibiotics being developed. Our study aims to describe the epidemiology and pattern of antibiotic resistance in Gram-negative [...] Read more.
Background/Objectives: Antibiotic resistance is a significant and escalating challenge that limits available therapeutic options. This issue is further exacerbated by the decreasing number of new antibiotics being developed. Our study aims to describe the epidemiology and pattern of antibiotic resistance in Gram-negative infections isolated from a cohort of hospitalized patients and to analyze the distribution of infections within the hospital setting. Methods: A retrospective study was conducted on all patients admitted to Vito Fazzi Hospital in Lecce, Italy, who required an infectious disease consultation due to the isolation of Gram-negative bacteria from 1 January 2018 to 31 December 2022. Results: During the study period, 402 isolates obtained from 382 patients (240 men and 142 women) with infections caused by Gram-negative bacteria were identified. Among these isolated, 226 exhibited multidrug resistance, defined as resistance to at least one antimicrobial agent from three or more different classes. In 2018, the percentage of multidrug-resistant isolates peaked at 87.6%, before decreasing to the lowest level (66.2%) in 2021. Overall, of the 402 isolates, 154 (38.3%) displayed resistance to carbapenems, while 73 (18.1%) were resistant to extended-spectrum beta-lactamases (ESBLs). Among the resistant microorganisms, Klebsiella pneumoniae showed the highest resistance to carbapenems, accounting for 85.2% of all resistant strains. Escherichia coli exhibited the greatest resistance to ESBLs, with a rate of 86.7%. Among carbapenem-resistant K. pneumoniae isolates, the following resistance rates were observed: KPC-1 at 98.2%, IMP-1 at 0.9%, VIM-1 at 0.9%, and NDM-1 at 0.9%. Conclusions: Patients with infections caused by multidrug-resistant bacteria have limited treatment options and are therefore at an increased risk of death, complications, and longer hospital stays. Rapid diagnostic techniques and antimicrobial stewardship programs—especially for ESBLs and carbapenemases—can significantly shorten the time needed to identify the infection and initiate appropriate antimicrobial therapy compared to traditional methods. Additionally, enhancing surveillance of antimicrobial resistance within populations is crucial to address this emerging public health challenge. Full article
Show Figures

Figure 1

20 pages, 2497 KiB  
Article
Characterization and Therapeutic Potential of Three Depolymerases Against K54 Capsular-Type Klebsiella pneumoniae
by Yanjun Lu, Chengju Fang, Li Xiang, Ming Yin, Lvxin Qian, Yi Yan, Luhua Zhang and Ying Li
Microorganisms 2025, 13(7), 1544; https://doi.org/10.3390/microorganisms13071544 - 30 Jun 2025
Viewed by 342
Abstract
Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp), a pathogen causing severe nosocomial infections and high mortality rates, is increasingly becoming a serious global public health threat. Capsular polysaccharide (CPS), a major virulence factor of hvKp, can be enzymatically degraded by bacteriophage-derived depolymerases. However, to our [...] Read more.
Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp), a pathogen causing severe nosocomial infections and high mortality rates, is increasingly becoming a serious global public health threat. Capsular polysaccharide (CPS), a major virulence factor of hvKp, can be enzymatically degraded by bacteriophage-derived depolymerases. However, to our knowledge, depolymerases targeting K. pneumoniae K54-type strains have rarely been identified. Here, we identified and characterized three novel capsule depolymerases, Dep_C, Dep_Y, and Dep_Z, derived from three different K. pneumoniae phages, which retained robust activity across a broad pH range (pH 3.0–12.0) and demonstrated thermal stability up to 50 °C. These depolymerases could efficiently digest the CPS of K. pneumoniae K54-serotype strains, significantly inhibit biofilm formation, and remove their mature biofilms. Although no bactericidal activity was detected, these depolymerases rendered host bacteria susceptible to serum complement-mediated killing. We further demonstrate that Dep_C, Dep_Y, and Dep_Z can effectively and significantly prolong the survival time of mice in a pneumonia model infected with K54-type K. pneumoniae and reduce the colonization and virulence of the bacteria in the mice. These findings indicate that depolymerases Dep_C, Dep_Y, and Dep_Z could increase bacterial susceptibility to host immune responses of hvKp to the host through their degradation effect on the CPS. In conclusion, our study demonstrates that the three capsule depolymerases are promising antivirulent agents to combat CR-hvKp infections. Full article
Show Figures

Figure 1

17 pages, 2101 KiB  
Article
CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible Klebsiella pneumoniae Clinical Isolates from a Croatian Tertiary Hospital
by Ivana Jurić, Marko Jelić, Manda Markanović, Lucija Kanižaj, Zrinka Bošnjak, Ana Budimir, Tomislav Kuliš, Arjana Tambić-Andrašević, Ivana Ivančić-Baće and Ivana Mareković
Pathogens 2025, 14(6), 604; https://doi.org/10.3390/pathogens14060604 - 19 Jun 2025
Viewed by 620
Abstract
(1) Background: CRISPR-Cas systems provide adaptive immunity against mobile genetic elements (MGEs) carrying antimicrobial resistance (AMR) genes. Carbapenem-resistant (CR) Klebsiella pneumoniae is a major public health concern, and the role of CRISPR-Cas in its resistance is understudied. This study explored CRISPR-Cas associations with [...] Read more.
(1) Background: CRISPR-Cas systems provide adaptive immunity against mobile genetic elements (MGEs) carrying antimicrobial resistance (AMR) genes. Carbapenem-resistant (CR) Klebsiella pneumoniae is a major public health concern, and the role of CRISPR-Cas in its resistance is understudied. This study explored CRISPR-Cas associations with multidrug resistance in clinical K. pneumoniae. (2) Methods: 400 K. pneumoniae isolates (200 CR and 200 carbapenem susceptible (CS)) were analyzed. Carbapenemase genes (blaOXA-48, blaNDM-1, blaKPC-2), cas1, rpoB, and CRISPR1-3 loci were identified by PCR, while only CRISPR loci were sequenced. Genetic relatedness was assessed via PFGE, MLST, and spacer analysis. Statistical analysis utilized chi-squared and Fisher’s exact tests. (3) Results: CRISPR-Cas was present in 15.8% of isolates, mainly subtypes I-E and I-E* (93.3%), with CRISPR3 loci showing the greatest spacer diversity. Clonal complexes ST14/15/101 (CR) and ST35 (CS) were identified. blaOXA-48 was linked to CRISPR-Cas-negative strains, while blaNDM-1 and blaKPC-2 were more frequent in CRISPR-Cas-positive strains (p < 0.0001). Imipenem/relebactam resistance was higher in CRISPR-Cas-negative isolates. (4) Conclusions: K. pneumoniae CRISPR-Cas systems correlate with specific carbapenemase profiles, suggesting pressure against blaOXA-48 acquisition. The coexistence of I-E and I-E* subtypes highlight synergies in targeting MGEs. CRISPR loci could be tools for subtyping organisms following MLST. Full article
Show Figures

Figure 1

18 pages, 2880 KiB  
Article
ESBL-Producing Escherichia coli and Klebsiella pneumoniae Exhibit Divergent Paths During In-Human Evolution Towards Carbapenem Resistance
by Michelle Chioma Kalu, Akanksha Acharya, Peter Jorth and Annie Wong-Beringer
Microorganisms 2025, 13(6), 1387; https://doi.org/10.3390/microorganisms13061387 - 14 Jun 2025
Viewed by 747
Abstract
Treatment of infections caused by ESBL-producing Escherichia coli (EC) and Klebsiella pneumoniae (KP) with carbapenem antibiotics can lead to the development of carbapenem resistance over time through the acquisition of porin mutations and plasmids bearing blaKPC. However, the impact of genetic background [...] Read more.
Treatment of infections caused by ESBL-producing Escherichia coli (EC) and Klebsiella pneumoniae (KP) with carbapenem antibiotics can lead to the development of carbapenem resistance over time through the acquisition of porin mutations and plasmids bearing blaKPC. However, the impact of genetic background and the presence of CRISPR-Cas systems on the evolutionary path towards carbapenem resistance in EC and KP has yet to be investigated. The in-human evolution following repeated carbapenem treatment among ESBL-producing Escherichia coli (EC) and Klebsiella pneumoniae (KP) clinical pairs (n = 45 pairs) was examined to determine the relationship between strain genetic background (MLST, CRISPR-Cas) and the evolved genetic mutations related to resistance, virulence, and metabolism by whole genome sequencing. ST131 and ST258 were predominant among seven distinct STs in EC (70%, 19/27) and 11 STs in KP (33%, 6/18), respectively. Complete CRISPR-Cas systems were present in 22% EC (6/27) and 27.8% (5/18) KP pairs, but none in strains belonging to ST131 or ST258; partial loss of CRISPR-Cas was associated with increased carbapenem resistance. Porin, virulence, and metabolism-related genetic mutations were present on the chromosome in both the EC and KP evolved strains, but their presence was differentially associated with the CRISPR-Cas system. Future research on the role of antibiotic exposure in the species-specific resistance evolution of the Enterobacterales could guide antimicrobial stewardship efforts. Full article
(This article belongs to the Collection Feature Papers in Antimicrobial Agents and Resistance)
Show Figures

Figure 1

14 pages, 1347 KiB  
Article
Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (OXA-23) and Klebsiella pneumoniae (KPC-2) Causing Hospital-Acquired Infections in Dogs
by Isabela Pádua Zanon, João Victor Ferreira Campos, Yasmin Gonçalves de Castro, Isadora Maria Soares de Melo, Flávia Figueira Aburjaile, Bertram Brenig, Vasco Azevedo and Rodrigo Otávio Silveira Silva
Antibiotics 2025, 14(6), 584; https://doi.org/10.3390/antibiotics14060584 - 6 Jun 2025
Viewed by 993
Abstract
Background/Objectives: Antimicrobial resistance is a major global health threat. Among the most problematic pathogens are carbapenem-resistant Acinetobacter baumannii and Klebsiella pneumoniae, which are significant causes of mortality in humans, particularly in the context of nosocomial infections. In companion animals, these bacteria have [...] Read more.
Background/Objectives: Antimicrobial resistance is a major global health threat. Among the most problematic pathogens are carbapenem-resistant Acinetobacter baumannii and Klebsiella pneumoniae, which are significant causes of mortality in humans, particularly in the context of nosocomial infections. In companion animals, these bacteria have been reported mainly as colonizers of healthy animals or, less frequently, in community-acquired infections. However, no confirmed cases of healthcare-associated infections caused by these species have been documented in this population. This study reports the first confirmed fatal cases of infection with carbapenem-resistant A. baumannii and KPC-producing K. pneumoniae in dogs. Methods: Three hospitalized dogs developed infections associated with distinct anatomical devices, including a venous catheter, an endotracheal tube, and a Penrose drain. Bacterial isolation followed by antimicrobial susceptibility testing identified carbapenem-resistant A. baumannii and K. pneumoniae. The isolates were subsequently subjected to additional antimicrobial resistance tests and whole-genome sequencing (WGS). Results: WGS confirmed the presence of the OXA-23 carbapenemase gene in both A. baumannii isolates and the KPC-2 carbapenemase gene was detected in the K. pneumoniae strain. All three strains exhibited resistance to multiple antimicrobial classes, including β-lactams (amoxicillin-clavulanic acid, ampicillin, cephalotin, piperacillin-tazobactam, cefoxitin, ceftiofur, cefotaxime, ertapenem, imipenem and meropenem), aminoglycosides (gentamicin, neomycin), tetracyclines (doxycycline, tetracycline and oxytetracycline), fluoroquinolones (ciprofloxacin, enrofloxacin), and folate pathway antagonists (trimethoprim-sulfamethoxazole). Multilocus sequence typing identified two high-risk clones: K. pneumoniae ST340 (CC258) and A. baumannii ST15 (CC15). Single nucleotide polymorphism analysis confirmed a high degree of genetic similarity between these isolates and strains previously associated with human infections in Brazil. Conclusions: These findings provide the first evidence of fatal, healthcare-associated infections caused by these multidrug-resistant pathogens in dogs and underscore the need to strengthen surveillance and infection control practices in veterinary hospitals. Furthermore, the results raise concerns about the potential of companion animals to act as reservoirs for multidrug-resistant organisms of public health relevance. Full article
Show Figures

Figure 1

8 pages, 636 KiB  
Communication
Integrating an LFA Carbapenemase Detection System into the Laboratory Diagnostic Routine: Preliminary Data and Effectiveness Against Enzyme Variants
by Maddalena Calvo, Gaetano Maugeri, Dafne Bongiorno, Giuseppe Migliorisi and Stefania Stefani
Diagnostics 2025, 15(11), 1434; https://doi.org/10.3390/diagnostics15111434 - 5 Jun 2025
Cited by 1 | Viewed by 513
Abstract
Background/Objectives. Carbapenemase production is the most diffused carbapenem-resistance mechanism among Enterobacterales, with Klebsiella pneumoniae carbapenemase (KPC), Verona-imipenemase (VIM), New-Delhi metallo-β-lactamase (NDM), imipenemase (IMP), and oxacillinase (OXA-48) being reported as the main types within Europe. Particularly, Southern Italy holds a concerningly high [...] Read more.
Background/Objectives. Carbapenemase production is the most diffused carbapenem-resistance mechanism among Enterobacterales, with Klebsiella pneumoniae carbapenemase (KPC), Verona-imipenemase (VIM), New-Delhi metallo-β-lactamase (NDM), imipenemase (IMP), and oxacillinase (OXA-48) being reported as the main types within Europe. Particularly, Southern Italy holds a concerningly high percentage of carbapenemases-producing Enterobacterales diffused among different hospital settings. These strains may colonize critical patients’ gastrointestinal tracts, often causing disseminations and severe complications. Scientific data recently reported carbapenemase variants’ worldwide diffusion and several double-carbapenemases reports. The diagnostic routine needs devices whose detection rates are extended to similar epidemiological conditions, avoiding a lack of specificity and potential negative results. Methods. We planned a retrospective study including carbapenem- and/or ceftazidime/avibactam-resistant Enterobacterales (62) which were tested with the KPC/IMP/NDM/VIM/OXA-48 Combo Test Kit (KINVO, Medomics Medical Technology, Nanjing, Jiangsu, China) based on the lateral flow assay (LFA) method. Results. We compared its results to the phenotypic antimicrobial susceptibility testing (AST) MIC results, obtaining a 100% agreement rate. The LFA kit reported carbapenemases in all the tested strains, also identifying cases of KPC variants and double-carbapenemases production. Conclusions. Our data demonstrated how LFAs may represent a reliable alternative requiring minimum economic and personnel resources along with simple result interpretations. Future studies will be necessary to further investigate the system effectiveness on a larger isolates’ number and a broad carbapenemase variant spectrum. Full article
Show Figures

Figure 1

13 pages, 263 KiB  
Article
Report of High-Risk Carbapenem-Resistant K. pneumoniae ST307 Clone Producing KPC-2, SHV-106, CTX-M-15, and VEB-1 in Greece
by Maria Chatzidimitriou, Pandora Tsolakidou, Maria Anna Kyriazidi, Sotiris Varlamis, Ilias S. Frydas, Maria Mavridou and Stella Mitka
Antibiotics 2025, 14(6), 567; https://doi.org/10.3390/antibiotics14060567 - 31 May 2025
Viewed by 694
Abstract
Background/Objectives: Klebsiella pneumoniae ST307 is emerging as a significant global high-risk antimicrobial-resistant (AMR) clone with a notable capacity to acquire and disseminate resistance genes. However, there is limited research on the pathogenicity, virulence, and adaptation of ST307 strains and on the clinical characteristics [...] Read more.
Background/Objectives: Klebsiella pneumoniae ST307 is emerging as a significant global high-risk antimicrobial-resistant (AMR) clone with a notable capacity to acquire and disseminate resistance genes. However, there is limited research on the pathogenicity, virulence, and adaptation of ST307 strains and on the clinical characteristics of infected patients. Methods: In this study, a carbapenem-resistant K. pneumoniae (CRKP) ST307 strain named U989 was isolated from a urine culture of a hospitalized patient in Volos, Greece, in July 2024. Whole-genome sequencing was performed to identify resistance genes to β-lactams blaKPC-2, blaCTX-M-15, blaTEM-1B, blaOXA-1, blaOXA-10, blaSHV-106, and blaVEB-1 and resistance genes to other antibiotics. Results: A genomic analysis also revealed the presence of virulence factors such as iutA, clpK1, fyuA, fimH, mrkA, Irp2, and TraT and an IncFiB(pQil)/IncFII(K) replicon, which harbors the blaKPC-2 gene. Additionally, the transposable element Tn4401 was identified as a key vehicle for the mobilization of the blaKPC-2 resistance gene. Finally, this is the report of a high-risk CRKP ST307 clone expressing KPC-2, SHV-106, CTX-M-15, and VEB-1 bla genes in Greece. Conclusions: The coexistence of these resistance genes in addition to aminoglycoside, quinolone, and other resistance genes results in difficult-to-treat infections caused by respective carrier strains, often requiring the use of last-resort antibiotics and contributing to the global challenge of antimicrobial resistance. Full article
16 pages, 248 KiB  
Article
Rapid Syndromic Testing: A Key Strategy for Antibiotic Stewardship in ICU Patients with Pneumonia
by Silvana Vulpie, Monica Licker, Oana Izmendi, Delia Muntean, Diana Lungeanu, Beatrice Sarah Zembrod, Iasmina Maria Hancu, Ovidiu Bedreag, Dorel Sandesc, Romanita Jumanca and Luminita Mirela Baditoiu
Antibiotics 2025, 14(5), 426; https://doi.org/10.3390/antibiotics14050426 - 23 Apr 2025
Viewed by 860
Abstract
Background/Objectives: According to the European Centre for Disease Prevention and Control, improved antimicrobial stewardship programs (ASPs) combined with rapid diagnostic tests could potentially prevent thousands of deaths caused by multidrug-resistant organisms annually. This study aimed to compare the results obtained using the Unyvero [...] Read more.
Background/Objectives: According to the European Centre for Disease Prevention and Control, improved antimicrobial stewardship programs (ASPs) combined with rapid diagnostic tests could potentially prevent thousands of deaths caused by multidrug-resistant organisms annually. This study aimed to compare the results obtained using the Unyvero system/hospital-acquired pneumonia (HPN) panel with those obtained using classic microbiological diagnostic methods to evaluate the potential of introducing this rapid diagnostic test into routine diagnosis and improving local ASPs. Methods: A single-center, observational, cross-sectional, analytical study was performed; it included patients admitted to the intensive care unit (ICU) with the presumptive diagnosis of community- or hospital-acquired pneumonia. One hundred non-repetitive endotracheal aspirates were collected and subjected to analysis using both methods. The concordance between the results obtained via the standard-of-care (SoC) culture and Unyvero was analyzed. Results: Of the results generated using Unyvero/HPN, 51% were fully concordant with those obtained via culture, 48% were partially concordant, and only 1% represented failure. It was also more efficient in identifying multiple organisms in a single sample than the SoC culture (1.32 versus 1.1 per sample). The three most common isolates identified via both methods were Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The most common resistance markers identified with Unyvero were sul1 (41%), tem and ndm (25%), and kpc, imp, vim, and gyrA87 (2% of results). Conclusions: Unyvero/HPN, if associated with appropriate diagnostic stewardship, could be used to manage critically ill patients to ensure an appropriate ASP. Full article
Back to TopTop