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Search Results (476)

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Keywords = OXA-51 gene

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13 pages, 513 KiB  
Article
Impact of Dietary Inputs on Carbapenem Resistance Gene Dynamics and Microbial Safety During Bioconversion of Agri-Food Waste and Anaerobic Digestate by Hermetia illucens Larvae
by Andrea Marcelli, Alessio Ilari, Vesna Milanović, Ester Foppa Pedretti, Kofi Armah Boakye-Yiadom, Federica Cardinali, Giorgia Rampanti, Andrea Osimani, Cristiana Garofalo and Lucia Aquilanti
Genes 2025, 16(8), 907; https://doi.org/10.3390/genes16080907 - 29 Jul 2025
Viewed by 211
Abstract
Background/Objectives: Hermetia illucens larvae can efficiently convert agri-food residues into high-protein biomass for animal feed and nutrient-rich frass for soil amendment. However, the potential spread of carbapenem resistance genes (CRGs), which confer resistance to last-resort carbapenem antibiotics, and Enterobacteriaceae, common carriers of [...] Read more.
Background/Objectives: Hermetia illucens larvae can efficiently convert agri-food residues into high-protein biomass for animal feed and nutrient-rich frass for soil amendment. However, the potential spread of carbapenem resistance genes (CRGs), which confer resistance to last-resort carbapenem antibiotics, and Enterobacteriaceae, common carriers of these genes and opportunistic pathogens, raises important safety concerns. This study aimed to assess the influence of different agri-food-based diets on Enterobacteriaceae loads and the CRG occurrence during the bioconversion process. Methods: Four experimental diets were formulated from agri-food residues and anaerobic digestate: Diet 1 (peas and chickpea waste), Diet 2 (peas and wheat waste), Diet 3 (onion and wheat waste), and Diet 4 (wheat waste and digestate). Enterobacteriaceae were quantified by viable counts, while five CRGs (blaKPC, blaNDM, blaOXA-48, blaVIM, and blaGES) were detected and quantified using quantitative PCRs (qPCRs). Analyses were performed on individual substrates, formulated diets, larvae (before and after bioconversion), and frass. Results: Plant-based diets sustained moderate Enterobacteriaceae loads. In contrast, the digestate-based diet led to a significant increase in Enterobacteriaceae in both the frass and mature larvae. CRGs were detected only in legume-based diets: blaVIM and blaGES were found in both mature larvae and frass, while blaOXA-48 and blaKPC were found exclusively in either larvae or frass. No CRGs were detected in onion- or digestate-based diets nor in young larvae or diet inputs. Conclusions: The findings suggest that the diet composition may influence the proliferation of Enterobacteriaceae and the persistence of CRGs. Careful substrate selection and process monitoring are essential to minimize antimicrobial resistance risks in insect-based bioconversion systems. Full article
(This article belongs to the Section Microbial Genetics and Genomics)
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20 pages, 2552 KiB  
Article
Environmental Dispersion of Multiresistant Enterobacteriaceae in Aquatic Ecosystems in an Area of Spain with a High Density of Pig Farming
by Javier Díez de los Ríos, Noemí Párraga-Niño, María Navarro, Judit Serra-Pladevall, Anna Vilamala, Elisenda Arqué, María Baldà, Tamar Nerea Blanco, Luisa Pedro-Botet, Óscar Mascaró and Esteban Reynaga
Antibiotics 2025, 14(8), 753; https://doi.org/10.3390/antibiotics14080753 - 25 Jul 2025
Viewed by 301
Abstract
Background: This study aimed to (a) assess the prevalence of multidrug-resistant (MDR) Enterobacteriaceae in the waters of two rivers and wastewater treatment plants (WWTPs) in a region of Catalonia, Spain; (b) genetically characterize the MDR strains; and (c) compare extended-spectrum β-lactamase (ESBL)-producing [...] Read more.
Background: This study aimed to (a) assess the prevalence of multidrug-resistant (MDR) Enterobacteriaceae in the waters of two rivers and wastewater treatment plants (WWTPs) in a region of Catalonia, Spain; (b) genetically characterize the MDR strains; and (c) compare extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from environmental and human sources. Methods: A total of 62 samples were collected from the influent and effluent of 31 WWTPs and 29 river water samples from 11 sites. Simultaneously, 382 hospitalized patients were screened for MDR Enterobacteriaceae using rectal swabs. All isolates underwent antibiotic susceptibility testing and whole-genome sequencing. Results: MDR Enterobacteriaceae were detected in 48.4% of WWTP samples, with 18.5% ESBL-producing E. coli and 1.5% (one sample) OXA-48-producing K. pneumoniae in influents, and 12.8% ESBL-producing E. coli in effluents. In river waters, 5.6% of samples contained ESBL-producing E. coli and 1.4% (1 sample) contained VIM-producing Enterobacter cloacae complex strains. Among patients, 10.2% (39/382) carried MDR Gram-negative bacilli, of which 66.7% were ESBL-producing E. coli. In aquatic ecosystems E. coli ST131 (13.3%) and ST162 (13.3%) were the most common strains, while in humans the common were E. coli ST131 (33.3%), ST69 (11.1%) and ST410 (7.4%) in humans. The most frequent environmental antibiotic resistance genes (ARG) were blaCTX-M-15 (24%) and blaTEM-1B (20%), while the most common ARGs were blaTEM-1B (20.4%), blaCTX-M15 (18.4%) and blaCTX-M-27 (14.3%). IncF plasmids were predominant in environmental and human strains. Conclusions: ESBL-producing E. coli and carbapenemase-producing Enterobacteriaceae are present in aquatic environments in the region. Phylogenetic similarities between environmental and clinical strains suggest a possible similar origin. Further studies are necessary to clarify transmission routes and environmental impact. Full article
(This article belongs to the Special Issue A One Health Approach to Antimicrobial Resistance, 2nd Edition)
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16 pages, 1234 KiB  
Article
Genomic Insights of Emerging Multidrug-Resistant OXA-48-Producing ST135 Proteus mirabilis
by Angeliki Mavroidi, Elisavet Froukala, Nick Spanakis, Aikaterini Michelaki, Maria Orfanidou, Vasiliki Koumaki and Athanasios Tsakris
Antibiotics 2025, 14(8), 750; https://doi.org/10.3390/antibiotics14080750 - 25 Jul 2025
Viewed by 296
Abstract
Background/Objectives: Among Enterobacterales, OXA-48-like-producing Proteus mirabilis strains have been scarcely detected. Herein, we characterized a blaOXA-48-harbouring P. mirabilis strain recovered from Greece (Pm GR-1), while phylogenomics and comparative genomics analyses with previously published blaOXA-48 carriers were also assessed. [...] Read more.
Background/Objectives: Among Enterobacterales, OXA-48-like-producing Proteus mirabilis strains have been scarcely detected. Herein, we characterized a blaOXA-48-harbouring P. mirabilis strain recovered from Greece (Pm GR-1), while phylogenomics and comparative genomics analyses with previously published blaOXA-48 carriers were also assessed. Methods: Characterization of Pm GR-1 was performed by the Vitek® Compact and Mass Spectrometry systems, antimicrobial susceptibility testing, detection of beta-lactamases, multilocus-sequence typing (MLST), and whole-genome sequencing (WGS). In silico prediction of mobile genetic elements (MGEs), genomic islands (GIs), antimicrobial resistance genes (ARGs) and virulence factors (VFs), and phylogenetic, core-genome SNP and comparative genomics analyses were executed using bioinformatic tools. Results: Pm GR-1 was isolated from a urine sample of an outpatient in a Greek hospital. It exhibited a multidrug-resistant phenotype, being susceptible only to amikacin and ceftazidime/avibactam. It co-carried several beta-lactamase genes on the chromosome (blaOXA-48, blaCTX-M-14, blaTEM-1) and a plasmid (blaTEM-2) and several other ARGs, but also mutations associated with quinolone resistance in the DNA gyrase and topoisomerase IV subunits. It belonged to the international clone ST135 that has also been detected among OXA-48-producing P. mirabilis strains from Germany and the USA. Pm GR-1 was genetically related to those from Germany, sharing highly similar MGEs, GIs, ARGs and VFs, including the chromosomal blaOXA-48 genetic structure, the O-antigen locus, the flagella locus, the MR/P fimbriae operon, and the urease gene cluster. Conclusions: To our knowledge, this is the first report from Greece of a blaOXA-48-possessing P. mirabilis strain. The emergence of blaOXA-48 among P. mirabilis strains of the international clone ST135 in different geographical regions is worrying. Close monitoring of these strains is required in One Health settings. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)
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23 pages, 6061 KiB  
Article
Genomic Insights into Emerging Multidrug-Resistant Chryseobacterium indologenes Strains: First Report from Thailand
by Orathai Yinsai, Sastra Yuantrakul, Punnaporn Srisithan, Wenting Zhou, Sorawit Chittaprapan, Natthawat Intajak, Thanakorn Kruayoo, Phadungkiat Khamnoi, Siripong Tongjai and Kwanjit Daungsonk
Antibiotics 2025, 14(8), 746; https://doi.org/10.3390/antibiotics14080746 - 24 Jul 2025
Viewed by 400
Abstract
Background: Chryseobacterium indologenes, an environmental bacterium, is increasingly recognized as an emerging nosocomial pathogen, particularly in Asia, and is often characterized by multidrug resistance. Objectives: This study aimed to investigate the genomic features of clinical C. indologenes isolates from Maharaj [...] Read more.
Background: Chryseobacterium indologenes, an environmental bacterium, is increasingly recognized as an emerging nosocomial pathogen, particularly in Asia, and is often characterized by multidrug resistance. Objectives: This study aimed to investigate the genomic features of clinical C. indologenes isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand, to understand their mechanisms of multidrug resistance, virulence factors, and mobile genetic elements (MGEs). Methods: Twelve C. indologenes isolates were identified, and their antibiotic susceptibility profiles were determined. Whole genome sequencing (WGS) was performed using a hybrid approach combining Illumina short-reads and Oxford Nanopore long-reads to generate complete bacterial genomes. The hybrid assembled genomes were subsequently analyzed to detect antimicrobial resistance (AMR) genes, virulence factors, and MGEs. Results: C. indologenes isolates were primarily recovered from urine samples of hospitalized elderly male patients with underlying conditions. These isolates generally exhibited extensive drug resistance, which was subsequently explored and correlated with genomic determinants. With one exception, CMCI13 showed a lower resistance profile (Multidrug resistance, MDR). Genomic analysis revealed isolates with genome sizes of 4.83–5.00 Mb and GC content of 37.15–37.35%. Genomic characterization identified conserved resistance genes (blaIND-2, blaCIA-4, adeF, vanT, and qacG) and various virulence factors. Phylogenetic and pangenome analysis showed 11 isolates clustering closely with Chinese strain 3125, while one isolate (CMCI13) formed a distinct branch. Importantly, each isolate, except CMCI13, harbored a large genomic island (approximately 94–100 kb) carrying significant resistance genes (blaOXA-347, tetX, aadS, and ermF). The absence of this genomic island in CMCI13 correlated with its less resistant phenotype. No plasmids, integrons, or CRISPR-Cas systems were detected in any isolate. Conclusions: This study highlights the alarming emergence of multidrug-resistant C. indologenes in a hospital setting in Thailand. The genomic insights into specific resistance mechanisms, virulence factors, and potential horizontal gene transfer (HGT) events, particularly the association of a large genomic island with the XDR phenotype, underscore the critical need for continuous genomic surveillance to monitor transmission patterns and develop effective treatment strategies for this emerging pathogen. Full article
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15 pages, 1416 KiB  
Article
High Prevalence of Virulence and blaOXA Genes Encoding Carbapenemases Among Acinetobacter baumannii Isolates from Hospitalised Patients in Three Regions of Poland
by Magdalena Szemraj, Małgorzata Piechota, Kamila Olszowiec, Jolanta Wicha, Agata Pruss, Monika Sienkiewicz, Małgorzata Witeska, Piotr Szweda and Barbara Kot
Pathogens 2025, 14(8), 731; https://doi.org/10.3390/pathogens14080731 - 24 Jul 2025
Viewed by 374
Abstract
Infections caused by Acinetobacter baumannii are increasing worldwide. We evaluated the antibiotic resistance profile, biofilm production, and the frequency of 12 genes encoding carbapenemases and 13 virulence factors in 90 isolates from patients of three hospitals in various regions of Poland. Antibiotic resistance [...] Read more.
Infections caused by Acinetobacter baumannii are increasing worldwide. We evaluated the antibiotic resistance profile, biofilm production, and the frequency of 12 genes encoding carbapenemases and 13 virulence factors in 90 isolates from patients of three hospitals in various regions of Poland. Antibiotic resistance survey was performed using the disc-diffusion method, genes encoding resistance to carbapenems and virulence factors were detected with PCR, and biofilm formation was tested using microtiter plates. A total of 52.2% of isolates were resistant to all tested antibiotic groups (penicillins with β-lactamase inhibitors, cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, and trimethoprim plus sulfamethoxazole). Among the genes encoding carbapenem resistance, the blaOXA-23 (68.9%), blaOXA-40 (83.3%), and ISAba-blaOXA-51 (18.9%) were detected. The ompA, ata, and recA genes responsible for biofilm formation, adhesion, and stress response, respectively, occurred in all isolates. Genes responsible for the production of other adhesins (bap—94.4%, espA—4.4%, chop—37.7%), biofilm formation (pbpG—90.0%), production of siderophore (basD—97.7%), toxins (lipA—92.2%, cpaA—1.1%), glycoconjugates (bfmR—84.4%), and inducing host cell death (fhaB—71.1%, abeD—93.3%) were also found. A total of 68.8% of isolates produced biofilm. The isolates from Masovia had more virulence genes than isolates from the other regions; moreover, all isolates from Masovia and West Pomerania were multidrug-resistant (MDR), including resistance to carbapenems. Full article
(This article belongs to the Section Bacterial Pathogens)
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18 pages, 849 KiB  
Article
Antimicrobial Activity of Greek Native Essential Oils Against Escherichia coli O157:H7 and Antibiotic Resistance Strains Harboring pNorm Plasmid, mecA, mcr-1 and blaOXA Genes
by Rafail Fokas, Zoi Anastopoulou and Apostolos Vantarakis
Antibiotics 2025, 14(8), 741; https://doi.org/10.3390/antibiotics14080741 - 24 Jul 2025
Viewed by 929
Abstract
Background/Objectives: The rapid emergence of antibiotic-resistant Escherichia coli in food and clinical environments necessitates new, clean-label antimicrobials. This study assessed eight Greek native essential oils—oregano, thyme, dittany, rosemary, peppermint, lavender, cistus and helichrysum—for activity against six genetically and phenotypically diverse E. coli strains [...] Read more.
Background/Objectives: The rapid emergence of antibiotic-resistant Escherichia coli in food and clinical environments necessitates new, clean-label antimicrobials. This study assessed eight Greek native essential oils—oregano, thyme, dittany, rosemary, peppermint, lavender, cistus and helichrysum—for activity against six genetically and phenotypically diverse E. coli strains (reference, pNorm, mecA, mcr-1, blaOXA and O157:H7). We aimed to identify oils with broad-spectrum efficacy and clarify the chemical constituents responsible. Methods: Disk-diffusion assays measured inhibition zones at dilutions from 50% to 1.56% (v/v). MIC and MBC values were determined by broth microdilution. GC–MS profiling identified dominant components, and Spearman rank-order correlations (ρ) linked composition to activity. Shapiro–Wilk tests (W = 0.706–0.913, p ≤ 0.002) indicated non-normal data, so strain comparisons used Kruskal–Wallis one-way ANOVA with Dunn’s post hoc and Bonferroni correction. Results: Oregano, thyme and dittany oils—rich in carvacrol and thymol—exhibited the strongest activity, with MIC/MBC ≤ 0.0625% (v/v) against all strains and inhibition zones > 25 mm at 50%. No strain-specific differences were detected (H = 0.30–3.85; p = 0.998–0.571; padj = 1.000). Spearman correlations confirmed that carvacrol and thymol content strongly predicted efficacy (ρ = 0.527–0.881, p < 0.001). Oils dominated by non-phenolic terpenes (rosemary, peppermint, lavender, cistus, helichrysum) showed minimal or no activity. Conclusions: Phenolic-rich EOs maintain potent, strain-independent antimicrobial effects—including against multidrug-resistant and O157:H7 strains—via a multi-target mode that overcomes classical resistance. Their low-dose efficacy and GRAS status support their use as clean-label food preservatives or adjuncts to antibiotics or bacteriophages to combat antimicrobial resistance. Full article
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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 1020
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)
15 pages, 1266 KiB  
Article
Detection of the ST111 Global High-Risk Pseudomonas aeruginosa Clone in a Subway Underpass
by Balázs Libisch, Chioma Lilian Ozoaduche, Tibor Keresztény, Anniek Bus, Tommy Van Limbergen, Katalin Posta and Ferenc Olasz
Curr. Issues Mol. Biol. 2025, 47(7), 532; https://doi.org/10.3390/cimb47070532 - 9 Jul 2025
Viewed by 315
Abstract
P. aeruginosa strain NL201 was cultured from an urban water drain in a populated subway underpass as an environmental isolate for the ST111 global high-risk P. aeruginosa clone. In addition to carrying generally present intrinsic P. aeruginosa antibiotic resistance genes, this serotype O4 [...] Read more.
P. aeruginosa strain NL201 was cultured from an urban water drain in a populated subway underpass as an environmental isolate for the ST111 global high-risk P. aeruginosa clone. In addition to carrying generally present intrinsic P. aeruginosa antibiotic resistance genes, this serotype O4 isolate also carries a set of additional acquired resistance determinants, including aadA2, blaOXA-10, sul1, and an aac(6′)-Ib family gene. The NL201 isolate features the blaPDC-3 allele, which was found to confer significantly higher catalytic efficiency against cefepime and imipenem compared to blaPDC-1, as well as the potent P. aeruginosa virulence factors exoS, exoT, and algD. Serotype O4 isolates of the ST111 global high-risk P. aeruginosa clone have been reported from clinical samples in Canada and the USA, human stool samples in France, and environmental samples (such as cosmetic, hospital drains, and urban water drain) from various European countries. These observations underscore the effective dissemination of the ST111 global high-risk P. aeruginosa clone between different hosts, environments, and habitats, and they warrant targeted investigations from a One Health perspective on the possible routes of its spread and molecular evolution. Full article
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12 pages, 732 KiB  
Article
Bacteremia Outbreak Due to Achromobacter xylosoxidans in Hospitalized COVID-19 Patients
by Magdalini Tsekoura, Georgios Petridis, Konstantinos Koutsouflianiotis, Styliani Pappa, Anna Papa and Konstantina Kontopoulou
Microbiol. Res. 2025, 16(7), 156; https://doi.org/10.3390/microbiolres16070156 - 8 Jul 2025
Viewed by 293
Abstract
Background: Hospitalized COVID-19 patients are particularly vulnerable to secondary bacterial infections, which can significantly worsen clinical outcomes. The aim of the study was to identify the cause of bacteremia in a group of hospitalized COVID-19 patients and find out the source of the [...] Read more.
Background: Hospitalized COVID-19 patients are particularly vulnerable to secondary bacterial infections, which can significantly worsen clinical outcomes. The aim of the study was to identify the cause of bacteremia in a group of hospitalized COVID-19 patients and find out the source of the outbreak to prevent further spread. Methods: Pathogen identification in blood cultures and sensitivity testing were carried out using the automated VITEK2 system. A total of 110 samples were tested; these were collected from patients’ colonization sites and from surfaces, materials and fluids used in the setting. Furthermore, multilocus sequence typing (MLST) and next-generation sequencing (NGS) were employed to characterize the isolates. Results: Achromobacter xylosoxidans was detected in the blood of nine hospitalized patients and in cotton used for disinfection; all isolates presented an identical antibiotic resistance pattern, and all carried the blaOXA-114 gene which is intrinsic to this species. Infection control measures were implemented promptly. With one exception, all patients recovered and were discharged in good health. Conclusions: This outbreak underscores the urgent need for investigation and control of hospital infections, as bacteremia is associated with increased morbidity, mortality, hospitalization time, and cost. It also highlights the importance of close collaboration among healthcare professionals. Full article
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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 603
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
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23 pages, 1347 KiB  
Article
Antibiotic Resistance, Virulence Genes, and Molecular Diversity of Clinical Klebsiella pneumoniae Isolates from Patients of District Hospital in Central Poland
by Barbara Kot, Małgorzata Witeska, Piotr Szweda, Małgorzata Piechota, Elżbieta Kondera, Elżbieta Horoszewicz, Izabela Balak, Ahmer Bin Hafeez and Alicja Synowiec
Pathogens 2025, 14(7), 648; https://doi.org/10.3390/pathogens14070648 - 30 Jun 2025
Viewed by 354
Abstract
In hospital environments, pathogenic bacteria spread easily and acquire virulence and antibiotic resistance genes. The aim of the study was an evaluation of the genetic diversity of 109 K. pneumoniae isolates recovered from patients of a district hospital in central Poland. The frequencies [...] Read more.
In hospital environments, pathogenic bacteria spread easily and acquire virulence and antibiotic resistance genes. The aim of the study was an evaluation of the genetic diversity of 109 K. pneumoniae isolates recovered from patients of a district hospital in central Poland. The frequencies of genes coding for β-lactamases, efflux pumps, and virulence factors were determined. Genotyping of the isolates was performed with ERIC (Enterobacterial Repetitive Intergenic Consensus) and REP (Repetitive Element Sequence Based) PCR techniques, with 21 and 19 genotypes being identified, respectively. The blaSHV-1 (92.7%), blaCTX-M group 1 (83.5%), blaTEM-1 (28.4%), blaNDM-1 (16.5%), blaVEB-1 (11.0%), blaCTX-M group 9 (3.7%), blaKPC (1.8%), blaIMP, blaOXA-48, blaCTX-M group 2, blaCTX-M groups 8, and 25/26 (0% each) and efflux pumps: AcrAB (100%), tolC (93.6%), and mdtk (60.5%), and virulence genes coding: urease subunit ureA (94.5%) endotoxins wabG (92.7%) and uge (64.2%), and siderophore iucB (3.7%) were detected. The blaSHV-1, blaCTX-M group 1, mdtk, tolC, AcrAB (16.5%); blaSHV-1, blaCTX-M group 1, tolC, AcrAB (15.6%), and blaSHV-1, blaCTX-M group 1, blaNDM-1, mdtk, tolC, AcrAB (11.9%) were the most common resistance patterns. The distribution of resistance and virulence genes varied more between hospital wards than between different clinical materials. Hospital’s antibiotic-resistant and virulent K. pneumoniae, able to spread among humans, animals, and in the environment, pose a significant threat to public health. Full article
(This article belongs to the Section Bacterial Pathogens)
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27 pages, 1648 KiB  
Review
Carbapenem Resistance in Acinetobacter baumannii: Mechanisms, Therapeutics, and Innovations
by Joyce de Souza, Helena Regina Salomé D’Espindula, Isabel de Farias Ribeiro, Geiziane Aparecida Gonçalves, Marcelo Pillonetto and Helisson Faoro
Microorganisms 2025, 13(7), 1501; https://doi.org/10.3390/microorganisms13071501 - 27 Jun 2025
Viewed by 1513
Abstract
The global rise of carbapenem-resistant Acinetobacter baumannii (CRAB) strains poses a critical challenge to healthcare systems due to limited therapeutic options and high mortality rates, especially in intensive care settings. This review explores the epidemiological landscape and molecular mechanisms driving carbapenem resistance, including [...] Read more.
The global rise of carbapenem-resistant Acinetobacter baumannii (CRAB) strains poses a critical challenge to healthcare systems due to limited therapeutic options and high mortality rates, especially in intensive care settings. This review explores the epidemiological landscape and molecular mechanisms driving carbapenem resistance, including the production of diverse beta-lactamases (particularly OXA-type enzymes), porin loss, efflux pump overexpression, and mutations in antibiotic targets. Emerging treatment strategies are discussed, such as the use of new beta-lactam–beta-lactamase inhibitor combinations (e.g., sulbactam–durlobactam), siderophore cephalosporins, next-generation polymyxins, as well as novel agents like zosurabalpin and rifabutin (BV100). Alternative approaches—including phage therapy, antimicrobial peptides, CRISPR-based gene editing, and nanoparticle-based delivery systems—are also evaluated for their potential to bypass traditional resistance mechanisms. Furthermore, advances in artificial intelligence and multi-omics integration are highlighted as tools for identifying novel drug targets and predicting resistance profiles. Together, these innovations represent a multifaceted strategy to overcome CRAB infections, yet their successful implementation requires further clinical validation and coordinated surveillance efforts. This analysis highlights the urgent need for continued investment in innovative treatments and effective resistance monitoring to limit the spread of CRAB and protect the effectiveness of last-line antibiotics. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)
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21 pages, 2764 KiB  
Article
First Report of Stenotrophomonas maltophilia from Canine Dermatological Infections: Unravelling Its Antimicrobial Resistance, Biofilm Formation, and Virulence Traits
by Ria Rajeev, Porteen Kannan, Sureshkannan Sundaram, Sandhya Bhavani Mohan, Sivachandiran Radjendirane, Chaudhary Jeetendrakumar Harnathbhai, Anbazhagan Subbaiyan, Viswanathan Naveenkumar, Nithya Quintoil Mohanadasse, Wilfred Ruban Savariraj, Charley A. Cull and Raghavendra G. Amachawadi
Antibiotics 2025, 14(7), 639; https://doi.org/10.3390/antibiotics14070639 - 23 Jun 2025
Viewed by 537
Abstract
Background/Objectives: The present study was aimed at documenting S. maltophilia occurrence in dogs with skin ailments, investigating its virulence, biofilm-forming ability, antimicrobial susceptibility, and zoonotic potential to inform preventive and therapeutic strategies against multidrug resistant S. maltophilia infections. Methods: Skin swabs [...] Read more.
Background/Objectives: The present study was aimed at documenting S. maltophilia occurrence in dogs with skin ailments, investigating its virulence, biofilm-forming ability, antimicrobial susceptibility, and zoonotic potential to inform preventive and therapeutic strategies against multidrug resistant S. maltophilia infections. Methods: Skin swabs (n = 300) were collected from dogs with dermatological ailments. Isolation was performed using selective media and confirmed with molecular methods, validated by MALDI Biotyper. Antimicrobial susceptibility testing and efflux activity assessment were conducted. Resistance genes related to sulfonamides, quinolones, and β-lactams were screened. Virulence was assessed by biofilm formation, motility, and virulence gene profiling. Results: In total, 15 S. maltophilia (5%) isolates were identified. All 15 isolates were susceptible to trimethoprim-sulfamethoxazole, enrofloxacin, gatifloxacin, levofloxacin, minocycline, and tigecycline, but resistant to cefpodoxime and aztreonam. The following resistance genes qnr (93.3%), blaOXA-48 (46.7%), blaKPC (33.3%), blaNDM (33.3%), blaCTX-M (20%), blaSHV (20%), and blaTEM (6.7%) were detected. All 15 isolates displayed high efflux activity. Overall, 9 isolates (60%) were strong biofilm producers, and 6 (40%) were moderate. Virulence genes such as virB, motA, rmlA, and fliC were present in all 15 isolates, with others varying in frequency. All isolates exhibited swimming motility. Heat map clustering showed diverse profiles, with no identical isolate patterns. Correlation analysis indicated positive associations between several antimicrobial resistance and virulence genes. Conclusions: This study underscores the zoonotic potential of S. maltophilia from dogs, advocating for a One Health approach to mitigate infection risks and limit the spread of virulent multidrug resistant pathogens. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Infections in Veterinary Settings)
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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
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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
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11 pages, 257 KiB  
Article
Antibiotic Resistance Profiles of Diarrhoeagenic Enterobacterales in Bioko Island, Equatorial Guinea
by Úrsula-Eva Eñeso Efuá, Silvia Herrera-León, Fátima Patabobe, Pascual Erasmo Owono and Agustín Benito
Acta Microbiol. Hell. 2025, 70(2), 24; https://doi.org/10.3390/amh70020024 - 10 Jun 2025
Viewed by 966
Abstract
Acute diarrhoeal disease caused by antibiotic-resistant diarrhoeagenic bacteria is a significant global public health issue, particularly in low- and middle-income countries. This study provides the first molecular characterisation of antimicrobial resistance profiles, including the detection of CTX-M-15 and CTX-M-55 extended-spectrum beta-lactamases (ESBLs), among [...] Read more.
Acute diarrhoeal disease caused by antibiotic-resistant diarrhoeagenic bacteria is a significant global public health issue, particularly in low- and middle-income countries. This study provides the first molecular characterisation of antimicrobial resistance profiles, including the detection of CTX-M-15 and CTX-M-55 extended-spectrum beta-lactamases (ESBLs), among diarrhoeagenic Enterobacterales in Bioko Island, Equatorial Guinea, offering novel epidemiological insights into an understudied region. This study investigated the antibiotic resistance profiles of pathogenic bacteria isolated from diarrhoeal samples on Bioko Island. A total of 153 clinical isolates were collected between 1 February and 30 May 2014, and antimicrobial susceptibility testing was performed at Loeri Comba Polyclinic (Malabo) using the Kirby–Bauer method. The molecular characterisation of β-lactamase-associated genes was performed on different isolates of diarrhoeagenic pathotypes—144 Escherichia coli, 7 Salmonella enterica, and 2 Shigella flexneri—at the National Centre for Microbiology (Majadahonda, Spain). High resistance rates were detected against ampicillin (98%), tetracycline (93.5%), sulfonamides (94.8%), sulfamethoxazole–trimethoprim (88.2%), and cefotaxime (78.8%), while moderate rates of resistance were noted for ciprofloxacin (26.7%), and all isolates remained susceptible to imipenem. Of the isolates, 107 (69.9%) produced either single or multiple β-lactamases. Among these, 73 (68.2%) harbored classical β-lactamases, specifically TEM and OXA-1 types, representing 47.7% of the total sample. Additionally, 34 (31.8%) of the isolates were identified as producers of extended-spectrum β-lactamases (ESBLs), specifically CTX-M enzymes. Sequencing identified CTX-M-15 and CTX-M-55 variants. The predominant ESBL-producing bacteria were enteroaggregative Escherichia coli (56.2%), followed by enteropathogenic and enterotoxigenic E. coli. These findings confirm the circulation of multidrug-resistant diarrhoeagenic Enterobacterales in Equatorial Guinea, raising concerns about limited treatment options due to widespread resistance to multiple antibiotic classes, including third-generation cephalosporins and quinolones. The most important conclusion drawn from this study is that a high percentage of diarrhoeagenic bacteria have an antibiotic resistance and multi-resistance profile, especially to beta-lactams and other groups of antibiotics such as tetracyclines and sulphonamides. There is also a moderate prevalence of isolates carrying ESBLs on Bioko Island, Equatorial Guinea, which could indicate the inappropriate use of antimicrobials. Full article
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