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Keywords = KPC-Klebsiella pneumoniae

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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
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
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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
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
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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 166
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 443
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
18 pages, 599 KiB  
Article
Mapping Antimicrobial Resistance in Escherichia coli and Klebsiella pneumoniae from Complicated Urinary Tract Infections in Oman: Phenotypic and Genotypic Insights
by Nawal AL Shizawi, Zaaima AL Jabri, Fatima Khan, Hiba Sami, Turkiya AL Siyabi, Zakariya AL Muharrmi, Srinivasa Rao Sirasanagandla and Meher Rizvi
Diagnostics 2025, 15(9), 1062; https://doi.org/10.3390/diagnostics15091062 - 22 Apr 2025
Viewed by 610
Abstract
Background: Mapping the local etiology and susceptibility of common pathogens causing complicated urinary tract infection (cUTI) is important for promoting evidence-based antimicrobial prescribing. Evaluating the prevalence of extended-spectrum beta-lactamase (ESBL), AmpC beta-lactamase (AmpC), and carbapenemase-producing Enterobacterales (CPEs) is equally important as it informs [...] Read more.
Background: Mapping the local etiology and susceptibility of common pathogens causing complicated urinary tract infection (cUTI) is important for promoting evidence-based antimicrobial prescribing. Evaluating the prevalence of extended-spectrum beta-lactamase (ESBL), AmpC beta-lactamase (AmpC), and carbapenemase-producing Enterobacterales (CPEs) is equally important as it informs treatment guidelines and empiric management. Whole genome sequencing (WGS) enhances antimicrobial resistance (AMR) surveillance by complementing phenotypic antimicrobial susceptibility testing, offering deeper insights into resistance mechanisms, transmissions, and evolutions. Integrating it into routine AMR monitoring can significantly improve global efforts to combat antimicrobial resistance. Methods: Antimicrobial susceptibility profiles of isolates from cUTI were collected from patients presenting with Sultan Qaboos University Hospital, Muscat and Suhar Hospital, Suhar, Oman. Automated systems as well as manual methods were used for detection of ESBL, AmpC, and CPE. ESBLs, AmpC β-lactamases, and CPEs were further detected by manual methods: double-disk synergy test for ESBL; disk approximation assay and D69C AmpC detection set for AmpC, and mCIM and KPC/IMP/NDM/VIM/OXA-48 Combo test kit for CPE. WGS was carried out in 11 FOX-resistant E. coli and (22 carbapenem-resistant K. pneumoniae) isolates with varying susceptibilities to identify circulating clades, AMR genes, and plasmids. Bioinformatic analysis was performed using online tools. Results: The susceptibility patterns of E. coli from cUTI were as follows: nitrofurantoin (96%), fosfomycin (100%), fluoroquinolones (44%), aminoglycosides (93%), piperacillin-tazobactam (95%), and carbapenems (98%). In comparison, susceptibility rates of K. pneumoniae were far lower: nitrofurantoin (38%), fosfomycin (89%), aminoglycosides (82%), piperacillin-tazobactam (72%), and carbapenems (83%). K. pneumoniae, however, was more susceptible to fluoroquinolones at 47% in comparison to E. coli. The prevalence of ESBL among E. coli and K. pneumoniae was 37.2% and CRE was 6.2% while the estimated prevalence of AmpC was 5.4%. It was observed that E. coli was the predominant ESBL and AmpC producer, while K. pneumoniae was the major carbapenem-resistant Enterobacterales (CREs) producer. No predominant multi-locus sequence typing (MLST) lineage was observed in AmpC-producing E. coli with nine E. coli MLST lineages being identified from eleven isolates: ST-10, ST-69, ST-77, ST-131, ST-156, ST-167, ST-361, ST-1125, and ST-2520. On the other hand, a less diverse MLST spectrum (ST-2096, ST-231, ST-147, ST-1770, and ST-111) was observed in the CRE K. pneumoniae. Among the five MLST lineages, ST-2096 (twelve isolates) and ST-147 (seven isolates) predominated. WGS revealed that DHA-1 was the predominant plasmid-mediated AmpC gene in E. coli, while OXA-232 and NDM-5 were the most common carbapenemase genes in K. pneumoniae. All E. coli DHA-1-positive isolates co-harbored the quinolone resistance gene qnrB4 and the sulfonamide resistance gene sul1 while no aminoglycoside resistance genes were detected. The majority of CPE CRE K. pneumoniae carried other β-lactamase genes, such as blaCTX-M-15, blaSHV, and blaTEM; all co-harbored the quinolone resistance gene OqxAB; and 77% carried the aminoglycoside resistance gene armA. Conclusions: Our results suggest that fosfomycin is an excellent empiric choice for treating complicated cystitis caused by both E. coli and K. pneumoniae, while nitrofurantoin is an appropriate choice for E. coli cystitis but not for K. pneumoniae. Aminoglycosides and piperacillin-tazobactam are excellent intravenous alternatives that spare carbapenems. DHA-1 was the predominant AmpC in E. coli, while OXA-232 and NDM-5 were the predominant carbapenemases in K. pneumoniae. In AmpC-producing E. coli, no MLST predominated, suggesting a significant flux in E. coli with lack of stable clades in this region. In contrast, ST-2096 and ST-147 predominated in CRE Klebsiella pneumoniae, suggesting a stable circulation of these in Oman. WGS profiling provides a deeper understanding of the genetic basis of resistance and enhances surveillance and offers comprehensive insights into pathogen evolution and transmission patterns. Full article
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15 pages, 1560 KiB  
Article
Assessment of Phenotypic Tools for Detection of OXA-48, KPC, and NDM in Klebsiella pneumoniae in Oman
by Arwa AL Rujaibi, Zaaima AL Jabri, Amina Al Jardani, Azza AL Rashdi, Azza AL Mamari, Sara AL Sumri, Hiba Sami, Zakariya Al Muharrmi and Meher Rizvi
Diagnostics 2025, 15(8), 949; https://doi.org/10.3390/diagnostics15080949 - 8 Apr 2025
Viewed by 415
Abstract
Background: The alarming increase in carbapenemase-producing Enterobacterales is a matter of grave public health concern. The most ubiquitous carbapenemases, Klebsiella pneumoniae carbapenemase (KPC)-, New Delhi metallo-β-lactamase (NDM)-, and oxacillinase (OXA-48)-like enzymes, belong to the Ambler molecular classes A, B, and D, respectively. [...] Read more.
Background: The alarming increase in carbapenemase-producing Enterobacterales is a matter of grave public health concern. The most ubiquitous carbapenemases, Klebsiella pneumoniae carbapenemase (KPC)-, New Delhi metallo-β-lactamase (NDM)-, and oxacillinase (OXA-48)-like enzymes, belong to the Ambler molecular classes A, B, and D, respectively. KPC- and OXA-48-like enzymes have a serine-based hydrolytic mechanism, while NDMs are metallo-β-lactamases that contain zinc in the active site. For the judicious use of reserve drugs and promoting antimicrobial stewardship, timely detection of carbapenemases is essential. While molecular tools are the gold standard for the detection of these enzymes, many laboratories have limited access to them. This study focused on evaluating in-house tools and commercial phenotypic tests for the detection of OXA-48-, KPC-, and NDM-like enzymes in K. pneumoniae, the predominant extremely drug-resistant pathogen in Oman. Methods: In total, 80 GeneXpert/PCR-confirmed (40 OXA-48 and 20 KPC and NDM each) and 37 whole-genome-sequenced (25 OXA-232 and 6 KPC-2, plus NDM-1 and NDM-5) K. pneumoniae were subjected to screening by temocillin (30 μg disk) (MAST Diagnostica, Germany) and D71C (MASTDISCS®). Isolates resistant to temocillin (<11 mm) and D71C were subjected to four tests: an in-house tool (OXA-48 disk test) and three commercial phenotypic tests: (i) the MASTDISCS® Combi (D72C) (MAST Group Ltd., Bootle, UK); (ii) the MASTDISCS® Combi (D73C) (MAST Group Ltd., UK); and (iii) an immunochromatographic assay (ICT), which is the KPC/IMP/NDM/VIM/OXA-48 Combo test kit (Medomics, China), for the detection of OXA-48-, KPC-, and NDM-like carbapenemases. Results: Temocillin exhibited good sensitivity and specificity (100% and 97.50%) compared to D71C (70% and 100%). Among the confirmatory tests, the in-house OXA-48 disk test had 92.50% sensitivity and 100% specificity, while the commercial MAST DISC tests D72C, D73C, and ICT had 97.50%, 95.00%, and 100% sensitivity and 100%, 91.67%, and 95% specificity, respectively. Conclusions: The temocillin disk test is a good screening tool. With high sensitivity and specificity, ease of performance, short turnaround time, and low cost, we recommend the ICT format for routine diagnostic use. In resource-constrained centers, the OXA-48 disk test is an excellent alternative with high sensitivity and specificity. Full article
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15 pages, 2612 KiB  
Article
Molecular and Epidemiological Analysis of Carbapenem-Resistant Klebsiella pneumoniae in a Greek Tertiary Hospital: A Retrospective Study
by Alexandra Myari, Petros Bozidis, Efthalia Priavali, Eleni Kapsali, Vasilios Koulouras, Georgia Vrioni and Konstantina Gartzonika
Microbiol. Res. 2025, 16(4), 81; https://doi.org/10.3390/microbiolres16040081 - 4 Apr 2025
Viewed by 392
Abstract
Carbapenemase-producing Klebsiella pneumoniae is responsible for multiple serious infections with high mortality rates. K. pneumoniae carbapenemases (KPCs) are the most commonly isolated carbapenemases worldwide. To study the epidemiological and molecular characteristics of KPC-producing K. pneumoniae (KPC-KP), we conducted a retrospective study at the [...] Read more.
Carbapenemase-producing Klebsiella pneumoniae is responsible for multiple serious infections with high mortality rates. K. pneumoniae carbapenemases (KPCs) are the most commonly isolated carbapenemases worldwide. To study the epidemiological and molecular characteristics of KPC-producing K. pneumoniae (KPC-KP), we conducted a retrospective study at the University General Hospital of Ioannina, Greece. A total of 177 K. pneumoniae clinical strains from the period 2014–2015 were confirmed as KPC producers by polymerase chain reaction (PCR) and were further examined for the presence of blaVIM, blaNDM, blaTEM, blaSHV, and blaCTX-M genes. Using the amplification refractory mutation system (ARMS) method, we identified the presence of the KPC-2 allele in 130 strains and the KPC-9 allele in 47. Strains from both allele groups belonged to the sequence type 258 (ST258). KPC-9 was responsible for a distinct outbreak, considered part of the broader KPC-2 outbreak. Molecular characterization of selected KPC-KP isolates from the period 2021–2022 revealed their continued presence in our hospital. Comparison of the antimicrobial susceptibility profiles of the two alleles showed a statistically significant increase in minimum inhibitory concentration (MIC) for ceftazidime (p = 0.03) and higher resistance to amikacin (p = 0.012) and colistin (p < 0.001) for KPC-9 compared to the KPC-2 allele. The two KPC alleles had similar mortality rates. This study demonstrates the heterogeneity of resistance genes in carbapenem-resistant K. pneumoniae (CR-KP) within a single-hospital setting and underscores the need for immediate containment measures. Full article
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13 pages, 578 KiB  
Review
Plasmid Dissemination in Multispecies Carbapenemase-Producing Enterobacterales Outbreaks Involving Clinical and Environmental Strains: A Narrative Review
by Louis Alglave, Karine Faure and Catherine Mullié
Microorganisms 2025, 13(4), 810; https://doi.org/10.3390/microorganisms13040810 - 2 Apr 2025
Viewed by 366
Abstract
Outbreaks involving carbapenemase-producing enterobacteria (CPE) have become a common occurrence in healthcare settings. While clonal dissemination is firmly established as a cause for these outbreaks, horizontal gene transfers (HGTs) between different species of Enterobacterales found in clinical and environmental isolates are less so. [...] Read more.
Outbreaks involving carbapenemase-producing enterobacteria (CPE) have become a common occurrence in healthcare settings. While clonal dissemination is firmly established as a cause for these outbreaks, horizontal gene transfers (HGTs) between different species of Enterobacterales found in clinical and environmental isolates are less so. To gather evidence backing up this hypothesis, a review covering the 2013–2024 period was performed. HGTs between different species of clinical and environmental Enterobacterales were identified in thirteen papers, half of those published within the last three years. A combination of short- and long-read whole genome sequencing (WGS) was predominantly used to identify mobile genetic elements and plasmids. The more frequently reported carbapenemases were KPCs, followed by NDMs and IMPs. Predictably, broad-host-range plasmids were responsible for over 50% of HGTs, with the IncA/C group being in the lead. Klebsiella pneumoniae and Enterobacter cloacae complexes were the most frequent species identified in clinical samples, while Citrobacter freundii dominated environmental ones. Drains and pipework frequently constituted CPE reservoirs in protracted outbreaks, alternating epidemic outbursts with silent phases. Including WGS in a systematic environmental surveillance would help in swiftly identifying those CPE reservoirs and possibly help better control plasmid outbursts by allowing the implementation of adequate infection prevention and control measures. Full article
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17 pages, 2275 KiB  
Article
Identification of a Potential High-Risk Clone and Novel Sequence Type of Carbapenem-Resistant Pseudomonas aeruginosa in Metro Manila, Philippines
by Sherill D. Tesalona, Miguel Francisco B. Abulencia, Maria Ruth B. Pineda-Cortel, Sylvia A. Sapula, Henrietta Venter and Evelina N. Lagamayo
Antibiotics 2025, 14(4), 362; https://doi.org/10.3390/antibiotics14040362 - 1 Apr 2025
Viewed by 565
Abstract
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a significant opportunistic human pathogen, posing a considerable threat to public health due to its antimicrobial resistance and limited treatment options. The incidence of CRPA is high in the Philippines; however, genomic analysis of CRPA in this setting [...] Read more.
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a significant opportunistic human pathogen, posing a considerable threat to public health due to its antimicrobial resistance and limited treatment options. The incidence of CRPA is high in the Philippines; however, genomic analysis of CRPA in this setting is limited. Here, we provide the phenotypic and molecular characterization of 35 non-duplicate CRPA obtained from three tertiary hospitals in Metro Manila, Philippines, from August 2022 to January 2023. Six sequence types (STs), including international high-risk clones ST111 and ST357, were identified. This article highlights the first report in the Philippines on the identification of P. aeruginosa harboring Klebsiella pneumoniae Carbapenemase-2 (KPC-2), coproduced with Verona Integron-encoded Metallo-beta-lactamase-2 (VIM-2) and Oxacillinase-74 (OXA-74). Notably, this is also the first report of KPC in the Philippines identified in P. aeruginosa. New Delhi Metallo-beta-lactamase-7 (NDM-7), coproduced with Cefotaxime-Munich-15 (CTX-M-15) and Temoneira-2 (TEM-2), was also identified from a novel ST4b1c. The relentless identification of NDM in the Philippines’ healthcare setting poses a significant global public health risk. The initial detection of the P. aeruginosa strain harboring KPC exacerbated the situation, indicating the inception of potential dissemination of these resistance determinants within P. aeruginosa in the Philippines. Full article
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16 pages, 249 KiB  
Article
Evaluation of the Microbiological Performance and Potential Clinical Impact of New Rapid Molecular Assays for the Diagnosis of Bloodstream Infections
by Mateo Tićac, Tanja Grubić Kezele, Maja Abram and Marina Bubonja-Šonje
Microorganisms 2025, 13(3), 616; https://doi.org/10.3390/microorganisms13030616 - 7 Mar 2025
Viewed by 707
Abstract
Bloodstream infection (BSI) is a critical medical emergency associated with a high mortality rate. Rapid and accurate identification of the causative pathogen and the results of antimicrobial susceptibility testing are crucial for initiating appropriate antimicrobial therapy. The aim of this study was to [...] Read more.
Bloodstream infection (BSI) is a critical medical emergency associated with a high mortality rate. Rapid and accurate identification of the causative pathogen and the results of antimicrobial susceptibility testing are crucial for initiating appropriate antimicrobial therapy. The aim of this study was to evaluate the performance of a new rapid PCR Molecular Mouse System (MMS) for the identification of Gram-negative bacteria (GNB) and GNB resistance genes directly from a positive blood culture (BC). The validation of these rapid multiplex assays was carried out in a real hospital setting. A total of 80 BSI episodes were included in our study and the results were compared with culture-based methods. BC samples in which GNB had previously been detected microscopically and which originated from different hospital wards were analysed. The MMS GNB identification assay achieved a sensitivity of 98.7% and a specificity of 100% for the covered pathogens. In one BC sample, Klebsiella aerogenes was identified at the family level (Enterobacteriaceae) with MMS. However, in three polymicrobial samples, MMS identified bacteria that were not detected by culture-based methods (Klebsiella pneumoniae, K. aerogenes and Stenotrophomonas maltophilia). MMS also showed excellent overall performance in the detection of GNB resistance markers (100% sensitivity and 100% specificity). The type of extended-spectrum beta-lactamase (ESBL) resistance gene identified correctly with MMS was CTX-M-1/9 (n = 17/20), alone or in combination with SHV-type β-lactamase or with the different types of carbapenemase genes. MMS detected one carbapenemase gene of each type (KPC, NDM and OXA-23) and six OXA-48 genes. In addition, the colistin resistance gene mcr-1 was detected in one positive BC with Escherichia coli (E. coli). The time to result was significantly shorter for MMS than for routine culture methods. A retrospective analysis of the patients’ medical records revealed that a change in empirical antimicrobial therapy would have been made in around half of the patients following the MMS results. These results support the use of MMS as a valuable complement to conventional culture methods for more rapid BSI diagnosis and adjustment of empirical therapy. Full article
(This article belongs to the Special Issue Novel Approaches in the Diagnosis and Control of Emerging Pathogens)
16 pages, 6953 KiB  
Article
Emergence of Tigecycline-Nonsusceptible Carbapenem-Resistant Klebsiella pneumoniae with Metallo-β-Lactamase and Transferable Ceftazidime-Avibactam Resistance in China
by Yajuan Ni, Jiefu Peng, Yawen Xu, Liguo Zhu, Xiao Wang, Hui Jin and Huimin Qian
Pathogens 2025, 14(3), 253; https://doi.org/10.3390/pathogens14030253 - 4 Mar 2025
Viewed by 815
Abstract
In recent years, resistance of Klebsiella pneumoniae to the clinical last-resort drugs carbapenem and tigecycline has intensified, including Metallo-β-Lactamase-producing K. pneumoniae (MBL-KP), which demonstrated resistance to ceftazidime-avibactam (CZA), posing a significant public health threat. This study focused on the carbapenems, CZA, and tigecycline [...] Read more.
In recent years, resistance of Klebsiella pneumoniae to the clinical last-resort drugs carbapenem and tigecycline has intensified, including Metallo-β-Lactamase-producing K. pneumoniae (MBL-KP), which demonstrated resistance to ceftazidime-avibactam (CZA), posing a significant public health threat. This study focused on the carbapenems, CZA, and tigecycline resistance mechanisms of MBL-producing Carbapenem-resistant K. pneumoniae (MBL-CRKP). A retrospective study and genomic epidemiological analysis of Carbapenem-resistant K. pneumoniae (CRKP) strains isolated from Yangzhou City, Jiangsu Province, China, between 2016 and 2023 was conducted. The detection rate of CRKP in Yangzhou City has increased significantly in recent years, with five strains carrying the Metallo-β-Lactamases (MBLs) gene, all of which exhibited resistance to carbapenems and CZA. Two strains even showed reduced susceptibility to tigecycline, with one harboring tmexCD2-toprJ2. Moreover, three CRKP strains carrying both blaKPC-2 and blaNDM-1/blaNDM-29 genes were identified. Plasmids carrying MBL genes can horizontally transfer, leading to the spread of resistance, thus further exacerbating the difficulty of clinical treatment and the spread of resistance. In conclusion, this study not only revealed the resistance of MBL-CRKP strains to clinical last-resort therapeutic drugs but also explored the resistance mechanism and horizontal transfer through genomic analysis. Moreover, this study also suggested that microbial drug resistance surveillance should be conducted from the perspective of “one health” in the future to combat this global health challenge. Full article
(This article belongs to the Section Bacterial Pathogens)
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14 pages, 3373 KiB  
Article
Predicting the Effect of Meropenem Against Klebsiella pneumoniae Using Minimum Inhibitory Concentrations Determined at High Inocula
by Maria V. Golikova, Kamilla N. Alieva, Elena N. Strukova, Julia R. Savelieva, Daria A. Kondratieva, Svetlana A. Dovzhenko, Mikhail B. Kobrin, Vladimir A. Ageevets, Alisa A. Avdeeva and Stephen H. Zinner
Antibiotics 2025, 14(3), 258; https://doi.org/10.3390/antibiotics14030258 - 3 Mar 2025
Viewed by 871
Abstract
Background/Objectives: Assessing antibiotic MICs at high bacterial counts is likely to disclose hidden bacterial resistance and the inoculum effect if present and therefore also reveal potential decreased antibiotic effectiveness. In the current study, we evaluated the predictive potential of MICs determined at high [...] Read more.
Background/Objectives: Assessing antibiotic MICs at high bacterial counts is likely to disclose hidden bacterial resistance and the inoculum effect if present and therefore also reveal potential decreased antibiotic effectiveness. In the current study, we evaluated the predictive potential of MICs determined at high bacterial inocula to evaluate meropenem effectiveness and emergence of resistance in Klebsiella pneumoniae. Methods: Nine carbapenemase-free or carbapenemase-producing K. pneumoniae strains were exposed to meropenem in an in vitro hollow-fiber infection model (HFIM). The treatment effects were correlated with simulated antibiotic ratios of the area under the concentration–time curve (AUC) to the MIC (AUC/MIC) and to MICs determined at high inocula (AUC/MICHI). Results: Based on MICs determined at standard inocula, meropenem effects at different AUC/MIC ratios for both carbapenemase-free and carbapenemase-producing K. pneumoniae strains were stratified and could not be described by a single relationship. In contrast, when AUC/MICHI ratios were used, a single relationship with the antibiotic effect was obtained for all tested strains. Similarly, the emergence of meropenem resistance in HFIM was concordant with AUC/MICHI, but not with AUC/MIC ratios. Conclusions: MICs determined at high bacterial inocula enable the prediction of meropenem effects both for carbapenemase-free and for carbapenemase-producing K. pneumoniae strains. Also, MICs at standard and high inocula can identify carbapenemase-producing strains by revealing the inoculum effect. Full article
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18 pages, 1264 KiB  
Article
Changing Epidemiology of Carbapenemases Among Carbapenem-Resistant Enterobacterales in a Greek Tertiary Care Hospital in Athens, 2020 to 2023
by Vasiliki Koumaki, Eleni Voudanta, Aikaterini Michelaki, Maria Orfanidou, Eleni Vagiakou, Georgia Vrioni and Athanassios Tsakris
Antibiotics 2025, 14(3), 239; https://doi.org/10.3390/antibiotics14030239 - 26 Feb 2025
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Abstract
Background: Carbapenemase-producing Enterobacterales (CPEs) represent a significant global health threat, particularly in the context of nosocomial infections. The current study constitutes a retrospective epidemiological survey that aimed to provide updated data on the prevalence and characteristics of carbapenemases among carbapenem-resistant Enterobacterales (CREs) in [...] Read more.
Background: Carbapenemase-producing Enterobacterales (CPEs) represent a significant global health threat, particularly in the context of nosocomial infections. The current study constitutes a retrospective epidemiological survey that aimed to provide updated data on the prevalence and characteristics of carbapenemases among carbapenem-resistant Enterobacterales (CREs) in a Greek tertiary hospital in Athens during and after the COVID-19 pandemic. Results: A total of 2021 non-duplicate CPE clinical isolates were detected. A significant increase in the number of carbapenemase-positive Enterobacterales was revealed during the study period (p < 0.05). KPC remained the predominant carbapenemase type through all four years of the survey, representing 40.7%, 39.9%, 53.5%, and 45.7% of the CPE isolates, respectively. However, a rapid transition from VIM to NDM metal-β-lactamase types was revealed, changing the epidemiological image of carbapenemases in the hospital setting. Notably, among the CPEs, antimicrobial resistance rates were significantly raised in the post-COVID-19 period (2022 and 2023) compared to the first study year (2020) for almost all the tested antibiotics, including those characterized as last-resort antibiotics. Methods: CREs were identified and subjected to screening for the five most prevalent carbapenemase genes [Klebsiella pneumoniae carbapenemase (KPC), Verona integron-borne metallo-β-lactamase (VIM), New Delhi metallo-β-lactamase (NDM), imipenemase (IMP), and oxacillin-hydrolyzing (OXA-48)] using a lateral flow immunoassay, and the CREs recovered from blood cultures were analyzed using a FilmArray system. Their clinical and epidemiological characteristics, as well as their antimicrobial susceptibility profiles, were also subjected to analysis Conclusions: Given this alarming situation, which is exacerbated by the limited treatment options, the development of new, effective antimicrobial agents is needed. The continued monitoring of the changing epidemiology of carbapenemases is also imperative in order to undertake rational public health interventions. Full article
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12 pages, 252 KiB  
Article
Are New β-Lactam/β-Lactamase Inhibitor Combinations Promising Against Carbapenem-Resistant K. pneumoniae Isolates?
by Ayşe Nur Ceylan, Selda Kömeç, Kamuran Şanlı, Beyza Öncel, Mehmet Akif Durmuş and Abdurrahman Gülmez
Pathogens 2025, 14(3), 220; https://doi.org/10.3390/pathogens14030220 - 24 Feb 2025
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Abstract
Background/Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections present a significant clinical challenge due to limited therapeutic options and high transmission potential. This study aimed to identify the resistance genes associated with carbapenemase production in CRKP isolates and evaluate the in vitro activity of ceftazidime/avibactam [...] Read more.
Background/Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections present a significant clinical challenge due to limited therapeutic options and high transmission potential. This study aimed to identify the resistance genes associated with carbapenemase production in CRKP isolates and evaluate the in vitro activity of ceftazidime/avibactam (CZA) and meropenem/vaborbactam (MEV), among other β-lactam/β-lactamase inhibitor combinations. Methods: Between October 2021 and June 2022, a total of 504 CRKP isolates were grown from patient samples in intensive care units. When duplicate patient samples were removed, the remaining 89 isolates were included in the study. Bacterial identification and antimicrobial susceptibility testing were per-formed using MALDI-TOF, Phoenix M50, and disk diffusion methods, following EUCAST guidelines. PCR analyses identified carbapenemase genes such as OXA-48, NDM, and KPC. Results: The most prevalent carbapenemase gene was OXA-48 (79.8%), followed by NDM (21.4%) and KPC (17.9%). The susceptibility rate to CZA was 82.0%, significantly higher than MEV (10.1%). All isolates were resistant to piperacillin/tazobactam and ceftolozane/tazobactam. Among MEV-resistant isolates, most carried the OXA-48 gene, while NDM was common in CZA-resistant isolates. Conclusions: CZA demonstrates high efficacy against OXA-48-producing CRKP, making it a viable treatment option in settings where OXA-48 predominates. The limited activity of MEV in this study underscores the need for molecular surveillance of resistance mechanisms to guide empirical therapy. Full article
12 pages, 258 KiB  
Article
Outbreak of High-Risk Clone ST323 Klebsiella pneumoniae Resistant to Ceftazidime–Avibactam Due to Acquisition of blaVEB-25 and to Cefiderocol Due to Mutated fiu Gene
by Irene Galani, Ilias Karaiskos, Maria Souli, Vassiliki Papoutsaki, Aikaterini Gkoufa, Anastasia Antoniadou and Helen Giamarellou
Antibiotics 2025, 14(3), 223; https://doi.org/10.3390/antibiotics14030223 - 21 Feb 2025
Cited by 1 | Viewed by 896
Abstract
Background/Objectives: The incidence of Ceftazidime/Avibactam (CZA)-resistant Klebsiella pneumoniae isolate co-producing Klebsiella pneumoniae carbapenemase 2 (KPC-2) and Vietnamese extended-spectrum β-lactamase 25 (VEB-25) has been on the rise in Greece over the past five years. This study investigates the isolation of ST323 K. pneumoniae isolates [...] Read more.
Background/Objectives: The incidence of Ceftazidime/Avibactam (CZA)-resistant Klebsiella pneumoniae isolate co-producing Klebsiella pneumoniae carbapenemase 2 (KPC-2) and Vietnamese extended-spectrum β-lactamase 25 (VEB-25) has been on the rise in Greece over the past five years. This study investigates the isolation of ST323 K. pneumoniae isolates co-resistant to CZA and cefiderocol (FDC) from colonized and infected patients in a single hospital in Athens. Methods: CZA-resistant K. pneumoniae strains were isolated from 5 ICU patients from 27 December 2023 to 22 January 2024. Antimicrobial susceptibility was tested against a panel of agents. Whole-genome sequencing of the isolates was carried out to identify the acquired resistance genes and mutations that were associated with CZA and FDC resistance. Results: The K. pneumoniae isolates belonged to ST323 and harbored blaKPC-2 and blaVEB-25. The isolates had a minimum inhibitory concentration (MIC) of >256 mg/L for CZA and 32 mg/L for FDC, due to the disrupted catecholate siderophore receptor Fiu. blaVEB-25 was located on an IncC non-conjugative plasmid and on a ~14 kb multidrug resistance (MDR) region comprising 15 further acquired resistance genes. Transformation studies showed that the blaVEB-25-carrying plasmid provided resistance to most of the β-lactams tested, including CZA. The isolates remained susceptible to carbapenems, imipenem/relebactam, and meropenem/vaborbactam. The plasmid harbored the citrate-dependent iron (III) uptake system (fecIRABCDE), which increased the MIC of FDC from ≤0.08 mg/L to 2 mg/L. Conclusions: The blaVEB-25 gene was associated with IncC plasmids which are important contributors to the spread of key antibiotic resistance genes. Strict infection control measures must be elaborated upon to prevent the spread of extensively drug-resistant organisms such as those described here. Full article
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