Antibiotics

20 pages, 6178 KiB

Open AccessArticle

Time Evolution of Bacterial Resistance Observed with Principal Component Analysis

by Claudia P. Barrera Patiño, Mitchell Bonner, Andrew Ramos Borsatto, Jennifer M. Soares, Kate C. Blanco and Vanderlei S. Bagnato

Antibiotics 2025, 14(7), 729; https://doi.org/10.3390/antibiotics14070729 (registering DOI) - 20 Jul 2025

Abstract

Background/Objectives: In recent work, we have demonstrated that principal component analysis (PCA) and Fourier Transformation Infrared (FTIR) spectra are powerful tools for analyzing the changes in microorganisms at the biomolecular level to detect changes in bacteria with resistance to antibiotics. Here biochemical [...] Read more.

Background/Objectives: In recent work, we have demonstrated that principal component analysis (PCA) and Fourier Transformation Infrared (FTIR) spectra are powerful tools for analyzing the changes in microorganisms at the biomolecular level to detect changes in bacteria with resistance to antibiotics. Here biochemical structural changes in Staphylococcus aureus were analyzed over exposure time with the goal of identifying trends inside the samples that have been exposed to antibiotics for increasing amounts of time and developed resistance. Methods: All studied data was obtained from FTIR spectra of samples with induced antibiotic resistance to either Azithromycin, Oxacillin, or Trimethoprim/Sulfamethoxazole following the evolution of this development over four increasing antibiotic exposure periods. Results: The processing and data analysis with machine learning algorithms performed on this FTIR spectral database allowed for the identification of patterns across minimum inhibitory concentration (MIC) values associated with different exposure times and both clusters from hierarchical classification and PCA. Conclusions: The results enable the observation of resistance development pathways for the sake of knowing the present stage of resistance of a bacterial sample. This is carried out via machine learning methods for the purpose of faster and more effective infection treatment in healthcare settings. Full article

(This article belongs to the Section Mechanism and Evolution of Antibiotic Resistance)

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30 pages, 874 KiB

Open AccessReview

Liposome-Encapsulated Antibiotics for the Therapy of Mycobacterial Infections

by Metin Yıldırım and Nejat Düzgüneş

Antibiotics 2025, 14(7), 728; https://doi.org/10.3390/antibiotics14070728 (registering DOI) - 20 Jul 2025

Abstract

About a quarter of the world’s population is infected with Mycobacterium tuberculosis. Growing antibiotic resistance by this microorganism is a major problem in the therapy of the disease. M. avium-M. intracellulare that emerged as a major opportunistic infection of HIV/AIDS continues to [...] Read more.

About a quarter of the world’s population is infected with Mycobacterium tuberculosis. Growing antibiotic resistance by this microorganism is a major problem in the therapy of the disease. M. avium-M. intracellulare that emerged as a major opportunistic infection of HIV/AIDS continues to afflict immunocompromised individuals. We describe the use of liposome-encapsulated antibiotics in the experimental and clinical therapy of mycobacterial infections, as well as recent experimental liposomal vaccines against tuberculosis. Liposome-mediated intravenous or inhalational delivery of antibiotics enhances the antibacterial effects of the drugs, particularly for infections of resident macrophages, where the liposomes are passively targeted. Despite experimental successes of liposomal antibiotics in the treatment of mycobacterial and other bacterial infections, applications of this method to the clinic have been lagging. This review underscores the significance of liposomes in the treatment of mycobacterial infections, encompassing their synthesis methods, limitations, and both preclinical and clinical studies, providing guidance for the development of future therapeutic approaches and innovative antimicrobial strategies. Full article

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18 pages, 586 KiB

Open AccessReview

The Changing Landscape of Antibiotic Treatment: Reevaluating Treatment Length in the Age of New Agents

by Francesca Serapide, Salvatore Rotundo, Luca Gallelli, Caterina Palleria, Manuela Colosimo, Sara Palma Gullì, Gianmarco Marcianò and Alessandro Russo

Antibiotics 2025, 14(7), 727; https://doi.org/10.3390/antibiotics14070727 (registering DOI) - 20 Jul 2025

Abstract

Background: The landscape of antimicrobial therapy is undergoing a profound transformation; the contemporary arsenal of antimicrobials, particularly those with extended half-lives and enhanced tissue penetration, necessitates critically reassessing these traditional paradigms. The growing emphasis on antimicrobial stewardship programs has underscored the importance of [...] Read more.

Background: The landscape of antimicrobial therapy is undergoing a profound transformation; the contemporary arsenal of antimicrobials, particularly those with extended half-lives and enhanced tissue penetration, necessitates critically reassessing these traditional paradigms. The growing emphasis on antimicrobial stewardship programs has underscored the importance of optimizing antimicrobial agents to minimize the development and spread of resistance. Shorter treatment durations, when clinically appropriate, represent a key strategy in this endeavor. Methods: This narrative review provides a comprehensive synthesis of current evidence on the duration of antimicrobial therapy, with a particular focus on the clinical and pharmacological implications of novel agents, including long-acting formulations. Results: We critically examine the pharmacokinetic and pharmacodynamic properties of these agents, evaluate the opportunities and limitations associated with treatment shortening strategies, and underscore the pivotal role of antimicrobial stewardship in optimizing therapeutic outcomes within an increasingly complex and evolving landscape. Conclusions: The future of antimicrobial therapy lies in a personalized approach, where treatment decisions are tailored to the individual patient, but detailed clinical trials are necessary to evaluate these approaches. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Epidemiological Study of Clinically Relevant Pathogens)

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16 pages, 694 KiB

Open AccessArticle

Direct Disk Diffusion Testing and Antimicrobial Stewardship for Gram-Negative Bacteremia in the Context of High Multidrug Resistance

by Wantin Sribenjalux, Pawarit Kulwongroj, Waewta Kuwatjanakul, Lumyai Wonglakorn, Kanuengnit Srisak, Natapong Manomaiwong and Atibordee Meesing

Antibiotics 2025, 14(7), 726; https://doi.org/10.3390/antibiotics14070726 (registering DOI) - 19 Jul 2025

Abstract

Background: Combining direct disk diffusion (DD) testing with antimicrobial stewardship (AMS) may optimize antibiotic use and improve outcomes in patients with Gram-negative bloodstream infections (GNBSIs). Methods: This quasi-experimental study was conducted at Srinagarind Hospital, Khon Kaen University, between 13 September 2022 and 11 [...] Read more.

Background: Combining direct disk diffusion (DD) testing with antimicrobial stewardship (AMS) may optimize antibiotic use and improve outcomes in patients with Gram-negative bloodstream infections (GNBSIs). Methods: This quasi-experimental study was conducted at Srinagarind Hospital, Khon Kaen University, between 13 September 2022 and 11 April 2023. Patients with GNBSIs were enrolled during two phases: a standard care phase (13 September 2022–2 January 2023) and an intervention phase (16 January 2023–11 April 2023), during which therapy adjustments were guided by DD results interpreted by infectious disease specialists. Results: Among the 141 patients included (68 in the standard care group and 73 in the intervention group), the mean age was 61.7 years, and 60.2% were male. Escherichia coli (36.5%) and Klebsiella pneumoniae (27.6%) were the most frequently isolated pathogens, with intra-abdominal and urinary tract infections being the most common sources. Multidrug-resistant (MDR) organisms were identified in 48.9% of cases. Compared to standard care, the intervention group had a significantly shorter median time to optimal therapy (40.0 vs. 59.1 h, p = 0.037) and a higher proportion of patients receiving optimal therapy within 72 h (86.2% vs. 62.3%, p = 0.002). While 30-day mortality did not differ significantly between groups (17.2% vs. 16.7%, p = 0.98), MDR bacteremia and ICU admission were associated with increased mortality. In contrast, receiving optimal therapy within 72 h was associated with reduced mortality. Conclusion: Direct DD testing combined with AMS significantly reduced the time to optimal antibiotic therapy and decreased inappropriate antibiotic use in GNBSI patients. Achieving optimal therapy within 72 h was associated with a trend toward reduced mortality. Full article

(This article belongs to the Section Antibiotics Use and Antimicrobial Stewardship)

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16 pages, 645 KiB

Open AccessArticle

Antimicrobial-Resistant Staphylococcus spp. Harbored by Hedgehogs (Erinaceus europaeus) in Central Italy

by Fabrizio Bertelloni, Francesca Pauselli, Giulia Cagnoli, Roberto Biscontri, Renato Ceccherelli and Valentina Virginia Ebani

Antibiotics 2025, 14(7), 725; https://doi.org/10.3390/antibiotics14070725 - 18 Jul 2025

Abstract

Background/Objectives: European hedgehogs (Erinaceus europaeus) are present in areas where there is human activity; therefore, they can be a source of pathogens for other animals and humans. Methods: Eighteen hedgehog carcasses were collected and analyzed for Staphylococcus spp. Isolated strains were [...] Read more.

Background/Objectives: European hedgehogs (Erinaceus europaeus) are present in areas where there is human activity; therefore, they can be a source of pathogens for other animals and humans. Methods: Eighteen hedgehog carcasses were collected and analyzed for Staphylococcus spp. Isolated strains were typed and analyzed for exfoliative toxins genes and the phenotypic and genotypic characteristics of antimicrobial resistance. Results: A total of 54 strains were isolated and typed as S. aureus, S. xylosus, S. sciuri, S. pseudintermedius, S. simulans, S. chromogenes, S. epidermidis, S. hyicus, and S. lentus. No strains had the eta and etb genes coding for exfoliative toxins. Overall, 39/54 (72.20%) isolates showed phenotypic resistance to at least one antimicrobial and 21/54 (38.80%) showed more than one resistance. The lowest efficacy was observed for erythromycin, with 40/54 (74.08%) strains classified as intermediate and 6/54 (11.11%) classified as resistant. Among the 29 isolates shown to be penicillin-resistant, 11 (37.93%) were oxacillin-resistant, with a minimum inhibitory concentration (MIC). Among the 54 staphylococcal strains, 2 (3.70%) were resistant to vancomycin, both with an MIC value equal to the maximum concentration of the antibiotic tested (256 μg/mL) and 2 (3.70%) had an intermediate resistance profile with an 8 μg/mL MIC value. No strains had the genes vanA and vanB. Two of the 29 (6.90%) penicillin-resistant strains had the blaZ gene; 8 (27.13%) strains had the mecA gene. Overall, 2/54 (3.70%) isolates were classified as extensively drug-resistant (XDR) and 9/54 (16.66%) were classified as multidrug-resistant (MDR). Conclusions: Hedgehogs can harbor antimicrobial-resistant staphylococci and can be sources of these bacteria for other animals and humans. They can also serve as bioindicators of the pathogens and antimicrobial-resistant bacteria circulating in a given habitat. Full article

(This article belongs to the Collection Staphylococcus— Molecular Pathogenesis, Virulence Regulation and Antibiotics Resistance)

14 pages, 1973 KiB

Open AccessArticle

Exploring the Microbiome of Diabetic Foot Ulcers: A Focus on Cases with a Clinical Worse Outcome

by Laura Soldevila-Boixader, Anna Carrera-Salinas, Isabel Mur, Laura Morata, Alba Rivera, Jordi Bosch, Abelardo Montero-Saez, Jéssica Martínez Castillejo, Natividad Benito, Sara Martí and Oscar Murillo

Antibiotics 2025, 14(7), 724; https://doi.org/10.3390/antibiotics14070724 - 18 Jul 2025

Abstract

Background/Objectives: We evaluated the diabetic foot ulcer (DFU) microbiome in clinical situations identified as risk factors for a worse outcome and explored the roles of the most abundant microorganisms. Methods: A prospective multicenter cohort of diabetic patients with DFU were followed [...] Read more.

Background/Objectives: We evaluated the diabetic foot ulcer (DFU) microbiome in clinical situations identified as risk factors for a worse outcome and explored the roles of the most abundant microorganisms. Methods: A prospective multicenter cohort of diabetic patients with DFU were followed up for 6 months. We obtained a DFU tissue biopsy for microbiome analysis at the baseline visit. Genomic DNA was extracted (QIAamp DNA Mini Kit, Qiagen, Hilden, Germany) and quantified (QuantiFluor dsDNA System, Promega, Madison, WI, USA), with analysis of bacterial communities focusing on relative abundances (RA) and on alpha and beta diversity. Results: Overall, 59 DFUs were analyzed. DFUs of long duration (≥4 weeks) presented a higher RA of Gammaproteobacteria compared with ulcers of short duration (p = 0.02). Non-infected DFUs had a higher proportion of Actinobacteriota phyla than infected DFUs and, particularly, a higher RA of Corynebacterium genera (means ± SD: 0.063 ± 0.14 vs. 0.028 ± 0.13, respectively; p = 0.03). Regarding the pathogenic role of Staphylococcus aureus, DFUs with low S. aureus bacterial loads (<10⁶ CFU/mL) compared with those with high loads (≥10⁶ CFU/mL) showed a higher Corynebacterium RA (0.045 ± 0.08 vs. 0.003 ± 0.01, respectively; p = 0.01). Conclusions: In clinical situations associated with poor DFU outcomes, we observed a predominance of Gammaproteobacteria in the microbiome of long-duration ulcers and a higher RA of Corynebacterium in non-infected DFUs. An inverse relationship between the predominance of Corynebacterium and the S. aureus bacterial load in DFUs was also noted, which may suggest these commensals have a modulatory role. Further studies should explore the clinical utility of microbiome analysis for DFUs. Full article

(This article belongs to the Special Issue Bone and Joint Infections: The Challenges of Prevention, Diagnosis and Treatment and Opportunities for Future Research)

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22 pages, 591 KiB

Open AccessArticle

Trends in Positive Urine Culture Rates and Antimicrobial Resistance in Non-Hospitalized Children from Western Romania: A Retrospective Observational Study

by Constantin Catalin Marc, Maria Daniela Mot, Monica Licker, Delia Muntean, Daniela Teodora Marti, Ana Alexandra Ardelean, Alina Ciceu, Sergiu Adrian Sprintar, Daniela Adriana Oatis, Alin Gabriel Mihu and Tudor Rares Olariu

Antibiotics 2025, 14(7), 723; https://doi.org/10.3390/antibiotics14070723 - 18 Jul 2025

Abstract

Background: Urinary tract infections (UTIs) are among the most common types of infections during childhood. Limited data are available on the prevalence of UTI in children from Romania, with most being available for hospitalized children. For this reason, we conducted a retrospective observational [...] Read more.

Background: Urinary tract infections (UTIs) are among the most common types of infections during childhood. Limited data are available on the prevalence of UTI in children from Romania, with most being available for hospitalized children. For this reason, we conducted a retrospective observational study in consecutive non-hospitalized children to assess the number of positive UTI samples and the antibacterial resistance of causative pathogens. Methods: This study included 7222 consecutive urine cultures collected from children aged 1 to 18 years who are residents of Arad County, Western Romania. Urine samples were analyzed for leukocyturia and cultures for the presence of monomorphic bacteria. Results: The overall number of positive UTI samples was 10.44%. A higher number of positive UTI samples was observed in females when compared to males and in children aged 6–12 and 12 to 18 years when compared to those aged 1–5 years. The antibiotic susceptibility testing of E. coli isolates revealed high sensitivity to most tested antibacterials. Near-complete susceptibility was observed for fosfomycin (99.71%) and nitrofurantoin (96.01%), while high susceptibility rates were also observed for ciprofloxacin (85.43%) and amoxicillin–clavulanic acid (75.05%). In contrast, high resistance was found for ampicillin (62.28% resistant) and trimethoprim–sulfamethoxazole (36.53% resistant). Conclusions: Given the clinical risks associated with UTI in children, our findings underscore the urgent need for the continued monitoring of multidrug-resistant strains. Our study provides important epidemiological and resistance data to guide empirical treatment and strengthen pediatric antimicrobial resistance surveillance. Future studies should focus on different regions and regularly update resistance patterns to keep treatment and prevention strategies aligned with local conditions. Full article

(This article belongs to the Special Issue Prevalence, Treatment and Antibacterial Resistance of Urinary Tract Infections)

9 pages, 234 KiB

Open AccessArticle

Should Cefoxitin Non-Susceptibility in Ceftriaxone-Susceptible E. coli and K. pneumoniae Prompt Concerns Regarding Plasmid-Mediated AmpC Resistance? A Genomic Characterization and Summary of Treatment Challenges in Singapore

by Jonathan Jinpeng Foo, Ying Ying Ong, Clement Kin Ming Tsui, David C. Lye, De Partha Pratim, Nurhidayah Binte Mohamed Yazid, Swaine L. Chen, Shawn Vasoo and Tat Ming Ng

Antibiotics 2025, 14(7), 722; https://doi.org/10.3390/antibiotics14070722 - 18 Jul 2025

Abstract

Objectives: Plasmid-mediated AmpC beta-lactamases represent a growing clinical concern in Enterobacterales, with challenges in diagnostic approaches, limited data on clinical outcomes, and our incomplete understanding of their regulatory mechanisms warranting the need for further investigation. Methods: This retrospective study examined the genomic [...] Read more.

Objectives: Plasmid-mediated AmpC beta-lactamases represent a growing clinical concern in Enterobacterales, with challenges in diagnostic approaches, limited data on clinical outcomes, and our incomplete understanding of their regulatory mechanisms warranting the need for further investigation. Methods: This retrospective study examined the genomic and clinical characteristics of cefoxitin-non-susceptible, ceftriaxone-susceptible Escherichia coli and Klebsiella pneumoniae bloodstream isolates collected from a tertiary hospital in Singapore. Whole-genome sequencing was performed to detect ampC genes, subtypes, and associated regulatory elements. Results: Among 108 cefoxitin-non-susceptible isolates, only 15 (13.9%) harboured plasmid-mediated ampC, suggesting that cefoxitin non-susceptibility alone in ceftriaxone susceptible isolates was not predictive of ampC carriage. All plasmid-ampC isolates were from the bla_DHA-1 subtype and carried ampR, a known transcriptional regulator of inducible beta-lactamase expression. Notably, five non-ampC carrying Klebsiella isolates displayed truncations in ompK35 and ompK36, which could potentially contribute to reduced cefoxitin susceptibility via porin loss. Conclusions: These findings underscore the limited diagnostic utility of cefoxitin susceptibility testing for detecting plasmid-mediated ampC producers and highlight the clinical relevance of regulatory genes such as ampR in mediating inducible resistance. The routine incorporation of molecular diagnostics or genome sequencing may be necessary to improve detection accuracy and inform antimicrobial stewardship strategies. Full article

(This article belongs to the Special Issue Strategies for Combatting Multidrug-Resistant and Extensively Drug-Resistant Bacteria, 2nd Edition)

13 pages, 1371 KiB

Open AccessArticle

Multisite Infections Caused by Carbapenem-Resistant Klebsiella Pneumoniae: Unveiling the Clinical Characteristics and Risk Factors

by Jing Li, Shunjun Wu, Huanhuan Zhang, Xingxing Guo, Wanting Meng, Heng Zhao and Liqiang Song

Antibiotics 2025, 14(7), 721; https://doi.org/10.3390/antibiotics14070721 - 18 Jul 2025

Abstract

Objectives: There is a scarcity of studies on multisite infections (MSIs) caused by carbapenem-resistant Klebsiella pneumoniae (CRKP). The primary objectives of this research were to determine the clinical characteristics of CRKP MSI, and the risk factors of infection and mortality. Methods: [...] Read more.

Objectives: There is a scarcity of studies on multisite infections (MSIs) caused by carbapenem-resistant Klebsiella pneumoniae (CRKP). The primary objectives of this research were to determine the clinical characteristics of CRKP MSI, and the risk factors of infection and mortality. Methods: Patients with a CRKP bloodstream infection (BSI) were enrolled retrospectively between January 2017 and December 2021 in Xijing Hospital, China. The risk factors for CRKP MSI and mortality were evaluated. The demographic data, clinical and microbiological characteristics, therapy and outcomes were analyzed. Results: Among 101 patients, 74.3% (75/101) had a diagnosis of CRKP MSI, while 25.7% (26/101) of CRKP non-MSI. The overall case fatality rate was 42.6% (43/101). Multivariate analysis indicated that previous surgery (OR 3.971, 95% CI 1.504–10.480, p = 0.005) and ICU admission (OR 3.322, 95% CI 1.252–8.816, p = 0.016) were independent risk factors for CRKP MSI. ICU admission (OR 4.765, 95% CI 1.192–19.054, p = 0.027), a Pitt bacteremia score (PBS) > 4 (OR 3.820, 95% CI 1.218–11.983, p = 0.022) and thrombocytopenia (OR 8.650, 95% CI 2.573–29.007, p < 0.001) were independent risk factors for mortality due to CRKP MSI. Conclusions: Our findings confirmed that CRKP MSIs were associated with poorer outcomes. To improve prognosis, early screening of individuals at the highest risk is vital. Full article

(This article belongs to the Special Issue Multidrug-Resistant Gram-Negative Bacteria Infections: Current Epidemiology, Prognosis and Treatment Options)

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21 pages, 1088 KiB

Open AccessReview

Veterinary Clinics as Reservoirs for Pseudomonas aeruginosa: A Neglected Pathway in One Health Surveillance

by George Cosmin Nadăş, Alice Mathilde Manchon, Cosmina Maria Bouari and Nicodim Iosif Fiț

Antibiotics 2025, 14(7), 720; https://doi.org/10.3390/antibiotics14070720 - 17 Jul 2025

Abstract

Pseudomonas aeruginosa is a highly adaptable opportunistic pathogen with significant clinical relevance in both human and veterinary medicine. Despite its well-documented role in hospital-acquired infections in human healthcare settings, its persistence and transmission within veterinary clinics remain underexplored. This review highlights the overlooked [...] Read more.

Pseudomonas aeruginosa is a highly adaptable opportunistic pathogen with significant clinical relevance in both human and veterinary medicine. Despite its well-documented role in hospital-acquired infections in human healthcare settings, its persistence and transmission within veterinary clinics remain underexplored. This review highlights the overlooked status of veterinary facilities as environmental reservoirs and amplification points for multidrug-resistant (MDR) P. aeruginosa, emphasizing their relevance to One Health surveillance. We examine the bacterium’s environmental survival strategies, including biofilm formation, resistance to disinfectants, and tolerance to nutrient-poor conditions that facilitate the long-term colonization of moist surfaces, drains, medical equipment, and plumbing systems. Common transmission vectors are identified, including asymptomatic animal carriers, contaminated instruments, and the hands of veterinary staff. The review synthesizes current data on antimicrobial resistance in environmental isolates, revealing frequent expression of efflux pumps and mobile resistance genes, and documents the potential for zoonotic transmission to staff and pet owners. Key gaps in environmental monitoring, infection control protocols, and genomic surveillance are identified, with a call for standardized approaches tailored to the veterinary context. Control strategies, including mechanical biofilm disruption, disinfectant cycling, effluent monitoring, and staff hygiene training, are evaluated for feasibility and impact. The article concludes with a One Health framework outlining cross-species and environmental transmission pathways. It advocates for harmonized surveillance, infrastructure improvements, and intersectoral collaboration to reduce the risk posed by MDR P. aeruginosa within veterinary clinical environments and beyond. By addressing these blind spots, veterinary facilities can become proactive partners in antimicrobial stewardship and global resistance mitigation. Full article

(This article belongs to the Special Issue Veterinary Microbiology and Antimicrobial Resistance—the One Health Approach)

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13 pages, 239 KiB

Open AccessArticle

Extended-Spectrum Beta-Lactamase Production and Carbapenem Resistance in Elderly Urinary Tract Infection Patients: A Multicenter Retrospective Study from Turkey

by Çiğdem Yıldırım, Sema Sarı, Ayşe Merve Parmaksızoğlu Aydın, Aysin Kilinç Toker, Ayşe Turunç Özdemir, Esra Erdem Kıvrak, Sinan Mermer, Hasip Kahraman, Orçun Soysal, Hasan Çağrı Yıldırım and Meltem Isikgoz Tasbakan

Antibiotics 2025, 14(7), 719; https://doi.org/10.3390/antibiotics14070719 - 17 Jul 2025

Abstract

Introduction: Urinary tract infections (UTIs) remain a significant public health issue worldwide, particularly affecting the geriatric population with increased morbidity and mortality. Aging-related immune changes, comorbidities, and urogenital abnormalities contribute to the higher incidence and complexity of UTIs in elderly patients. Antimicrobial resistance, [...] Read more.

Introduction: Urinary tract infections (UTIs) remain a significant public health issue worldwide, particularly affecting the geriatric population with increased morbidity and mortality. Aging-related immune changes, comorbidities, and urogenital abnormalities contribute to the higher incidence and complexity of UTIs in elderly patients. Antimicrobial resistance, especially extended-spectrum beta-lactamase (ESBL) production and carbapenem resistance, poses a major challenge in managing UTIs in this group. Methods: This retrospective, multicenter study included 776 patients aged 65 and older, hospitalized with a diagnosis of urinary tract infection between January 2019 and August 2024. Clinical, laboratory, and microbiological data were collected and analyzed. Urine samples were obtained under sterile conditions and pathogens identified using conventional and automated systems. Antibiotic susceptibility testing was performed according to CLSI standards. Logistic regression analyses were conducted to identify factors associated with ESBL production, carbapenem resistance, and mortality. Results: Among the patients, the median age was 78.9 years, with 45.5% female. ESBL production was detected in 56.8% of E. coli isolates and carbapenem resistance in 1.2%. Klebsiella species exhibited higher carbapenem resistance (37.8%). Independent predictors of ESBL production included the presence of urogenital cancer and antibiotic use within the past three months. Carbapenem resistance was associated with recent hospitalization, absence of kidney stones, and infection with non-E. coli pathogens. Mortality was independently associated with intensive care admission at presentation, altered mental status, Gram-positive infections, and comorbidities such as chronic obstructive pulmonary disease and urinary incontinence. Discussion: Our findings suggest that urinary pathogens and resistance patterns in elderly patients are similar to those in younger adults reported in the literature, highlighting the need for age-specific awareness in empiric therapy. The identification of risk factors for multidrug-resistant organisms emphasizes the importance of targeted antibiotic stewardship, especially in high-risk geriatric populations. Multicenter data contribute to regional understanding of resistance trends, aiding clinicians in optimizing management strategies for elderly patients with UTIs. Conclusions: This study highlights that E. coli and Klebsiella species are the primary causes of UTIs in the elderly, with resistance patterns similar to those seen in younger adults. The findings also contribute important data on risk factors for ESBL production and carbapenem resistance, supported by a robust patient sample. Full article

32 pages, 2479 KiB

Open AccessReview

Fungal Biofilm: An Overview of the Latest Nano-Strategies

by Andrea Giammarino, Laura Verdolini, Giovanna Simonetti and Letizia Angiolella

Antibiotics 2025, 14(7), 718; https://doi.org/10.3390/antibiotics14070718 - 17 Jul 2025

Abstract

Background/Objectives: There is an increasing incidence of fungal infections in conjunction with the rise in resistance to medical treatment. Antimicrobial resistance is frequently associated with virulence factors such as adherence and the capacity of biofilm formation, which facilitates the evasion of the [...] Read more.

Background/Objectives: There is an increasing incidence of fungal infections in conjunction with the rise in resistance to medical treatment. Antimicrobial resistance is frequently associated with virulence factors such as adherence and the capacity of biofilm formation, which facilitates the evasion of the host immune response and resistance to drug action. Novel therapeutic strategies have been developed to overcome antimicrobial resistance, including the use of different type of nanomaterials: metallic (Au, Ag, Fe₃O₄ and ZnO), organic (e.g., chitosan, liposomes and lactic acid) or carbon-based (e.g., quantum dots, nanotubes and graphene) materials. The objective of this study was to evaluate the action of nanoparticles of different synthesis and with different coatings on fungi of medical interest. Methods: Literature research was conducted using PubMed and Google Scholar databases, and the following terms were employed in articles published up to June 2025: ‘nanoparticles’ in combination with ‘fungal biofilm’, ‘Candida biofilm’, ‘Aspergillus biofilm’, ‘Cryptococcus biofilm’, ‘Fusarium biofilm’ and ‘dermatophytes biofilm’. Results: The utilization of nanoparticles was found to exert a substantial impact on the reduction in fungal biofilm, despite the presence of substantial variability in minimum inhibitory concentration (MIC) values attributable to variations in nanoparticle type and the presence of capping agents. It was observed that the MIC values were lower for metallic nanoparticles, particularly silver, and for those synthesized with polylactic acid compared to the others. Conclusions: Despite the limited availability of data concerning the stability and biocompatibility of nanoparticles employed in the treatment of fungal biofilms, it can be posited that these results constitute a significant initial step. Full article

(This article belongs to the Special Issue Methods for Preventing Biofilm Formation and Treat the Infections Caused by Biofilm Formed on Biotics or Abiotic Surfaces)

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15 pages, 636 KiB

Open AccessArticle

High Prevalence of Multidrug-Resistant Bacterial Colonization Among Patients and Healthcare Workers in a Rural Ethiopian Hospital

by Elena Hidalgo, Teresa Alvaredo-Carrillo, Josefina-Marina Gil-Belda, Clara Portela-Pino, Clara Bares-Moreno, Sara Jareño-Moreno, Paula de la Fuente, Lucía Platero and Ramón Pérez-Tanoira

Antibiotics 2025, 14(7), 717; https://doi.org/10.3390/antibiotics14070717 - 17 Jul 2025

Abstract

Background/Objectives: Multidrug-resistant (MDR) bacterial colonization poses a significant risk for subsequent infections, especially within hospital environments. Healthcare workers can inadvertently transmit these MDR bacteria to vulnerable patients, exacerbating the problem. This study aimed to determine the colonization rates of MDR bacteria among patients [...] Read more.

Background/Objectives: Multidrug-resistant (MDR) bacterial colonization poses a significant risk for subsequent infections, especially within hospital environments. Healthcare workers can inadvertently transmit these MDR bacteria to vulnerable patients, exacerbating the problem. This study aimed to determine the colonization rates of MDR bacteria among patients and healthcare workers in a rural Ethiopian hospital with limited resources. Methods: Between 26 May and 6 June 2024, nasal, rectal, vagino-rectal exudate, and stool samples were collected from patients (n = 78) and healthcare workers (n = 11) at Gambo General Hospital (Oromia Region, Ethiopia). Samples were cultured on chromogenic media selective for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus spp. (VRE), and carbapenemase-producing Enterobacteriaceae (CPE). Bacterial identification was performed using MALDI-TOF mass spectrometry (Bruker), antimicrobial susceptibility testing using the MicroScan WalkAway system (Beckman Coulter), and genotypic characterization with the MDR Direct Flow Chip kit (Vitro). Results: MRSA nasal colonization was detected in 43.3% of patients (13/30; 95% CI: 27.4–60.8%) and 27.3% of healthcare workers (3/11; 95% CI: 6.0–61.0%) (p = 0.73). Rectal (or stool) colonization by MDR bacteria was significantly higher in pediatric patients (85.0%, 17/20; 95% CI: 62.1–96.8%) than in adults (14.3%, 4/28; 95% CI: 5.7–31.5%) (p < 0.001). Notably, a high proportion of pediatric patients harbored Escherichia coli strains co-producing NDM carbapenemase and CTX-M ESBL, and VRE strains were also predominantly isolated in this group. Conclusions: This study reveals a concerningly high prevalence of MRSA and MDR Enterobacteriaceae, especially among children at Gambo Hospital. The VRE prevalence was also substantially elevated compared to other studies. These findings underscore the urgent need for strengthened infection control measures and antimicrobial stewardship programs within the hospital setting. Full article

(This article belongs to the Special Issue Gram-Negative Multidrug-Resistant Pathogens and Their Treatment, 2nd Edition)

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11 pages, 511 KiB

Open AccessArticle

Effects of Antibiotic De-Escalation on Outcomes in Severe Community-Acquired Pneumonia: An Inverse Propensity Score-Weighted Analysis

by Diego Viasus, Gabriela Abelenda-Alonso, Juan Bolivar-Areiza, Carlota Gudiol and Jordi Carratalà

Antibiotics 2025, 14(7), 716; https://doi.org/10.3390/antibiotics14070716 - 17 Jul 2025

Abstract

Objective: This study aimed to assess the effect of antibiotic de-escalation on 30-day mortality, duration of intravenous (IV) antibiotic therapy and length of hospital stay (LOS) in severe community-acquired pneumonia (sCAP). Methods: We performed a retrospective analysis of prospectively collected data [...] Read more.

Objective: This study aimed to assess the effect of antibiotic de-escalation on 30-day mortality, duration of intravenous (IV) antibiotic therapy and length of hospital stay (LOS) in severe community-acquired pneumonia (sCAP). Methods: We performed a retrospective analysis of prospectively collected data from a cohort of adults diagnosed with sCAP and microbiologically confirmed etiology between 1995 to 2022. Two distinct time points of the de-escalation were analyzed: 3 and 6 days post-admission, corresponding, respectively, to the availability of microbiological results and the median time to clinical stability. Inverse propensity score-weighted binary logistic regression was used to adjust for potential confounders. Results: A total of 398 consecutive cases of sCAP were analyzed. No significant differences were observed between the de-escalation and non-de-escalation groups in terms of age, sex, comorbidities, or severity-related variables (such as impaired consciousness, shock, respiratory failure, or multilobar pneumonia). Patients in the de-escalation group had lower rates of leukopenia, bacteremia and empyema, and less need for mechanical ventilation, with variations depending on the timing of de-escalation. After adjusting for confounding factors in an inverse propensity score-weighted analysis, de-escalation within 3 or 6 days after admission was not associated with increased mortality risk (adjusted odds ratio [aOR] 1.48, 95% confidence interval [CI] 0.29–7.4; p = 0.63, and aOR 0.57, 95% CI 0.14–2.31, p = 0.43, respectively). Similar findings were observed for prolonged LOS. However, antibiotic de-escalation was related to a lower risk of prolonged IV antibiotic. Conclusions: Antibiotic de-escalation in microbiologically confirmed sCAP did not negatively impact clinical outcomes, supporting the safety of this strategy for optimizing antibiotic use in this serious infection. Full article

(This article belongs to the Special Issue Therapy of Infectious Diseases Among Children and Adults: The Role of Antibiotics in Daily Practice)

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11 pages, 809 KiB

Open AccessArticle

Antimicrobial Behavior of Surface-Treated Commercially Pure Titanium (CpTi) for Dental Implants in Artificial Saliva—In Vitro Study

by Roshni Bopanna, Neetha J. Shetty, Ashith M. Varadaraj, Himani Kotian, Sameep Shetty and Simran Genescia

Antibiotics 2025, 14(7), 715; https://doi.org/10.3390/antibiotics14070715 - 16 Jul 2025

Abstract

Background/Objectives:Titanium implant surface modifications enhance osseointegration and prevent microbial colonization, improving implant longevity. Antimicrobial coatings, particularly cerium- and bismuth-doped hydroxyapatite (CeHAp and BiHAp), have gained attention for reducing infection-related complications. This study evaluates the antimicrobial activity of CeHAp and BiHAp coatings on [...] Read more.

Background/Objectives:Titanium implant surface modifications enhance osseointegration and prevent microbial colonization, improving implant longevity. Antimicrobial coatings, particularly cerium- and bismuth-doped hydroxyapatite (CeHAp and BiHAp), have gained attention for reducing infection-related complications. This study evaluates the antimicrobial activity of CeHAp and BiHAp coatings on CpTi compared to untreated CpTi in artificial saliva at pH levels of 4.5, 6.5, and 8. Methods: Antibacterial efficacy against Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), and Candida albicans (C. albicans) was assessed using the broth dilution method. Titanium rods coated with test compounds were incubated in inoculated nutrient broth, and microbial inhibition was determined via optical density at 600 nm. A statistical analysis was performed using the Kruskal–Wallis ANOVA test, the median and Interquartile Range were determined for the variables, and a Dwass–Steel–Critchlow–Fligner intergroup pairwise comparison was conducted. Results: The results showed that both the CeHAp and BiHAp coatings demonstrated significant antimicrobial activity against S. aureus (OD = 0.01) at pH 6.5, which was more pronounced than the activity observed against E. coli (OD = 0.05), with the difference being statistically significant (p = 0.001). The least antimicrobial activity was observed against C. albicans (0.21) at pH 8 (p = 0.001). Conclusion: These findings highlight the pH-dependent effectiveness of BiHAp and CeHAp coatings in inhibiting microbial growth. Their application on titanium implants may enhance antimicrobial properties, contributing to improved dental implant success and broader biomedical applications. Full article

(This article belongs to the Section Antimicrobial Materials and Surfaces)

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11 pages, 2797 KiB

Open AccessArticle

Illuminating the Invisible: Green Fluorescent Protein as a Beacon for Antibiotic-Induced Phage Activity in Escherichia coli

by Maria João Silva, Tim Van Den Bossche, Mattias Collin and Rolf Lood

Antibiotics 2025, 14(7), 714; https://doi.org/10.3390/antibiotics14070714 - 16 Jul 2025

Abstract

Background/Objectives: Antibiotic resistance presents an urgent public health threat. By developing a streamlined and effective method for studying bacteriophage induction, this research marks a step further in understanding how antibiotic-resistant genes might spread across different environments. This knowledge is essential for creating strategies [...] Read more.

Background/Objectives: Antibiotic resistance presents an urgent public health threat. By developing a streamlined and effective method for studying bacteriophage induction, this research marks a step further in understanding how antibiotic-resistant genes might spread across different environments. This knowledge is essential for creating strategies to reduce the spread of antimicrobial resistance (AMR), particularly from a One Health perspective. In this study, we develop and validate a Green Fluorescent Protein (GFP)-based method as a proxy for bacteriophage induction. This method screens compounds for their potential to promote bacteriophage induction. Methods: This study utilized a recA-GFP construct in Escherichia coli to measure fluorescence as an indicator of SOS response activation. The experiments involved treating E. coli cultures with varying concentrations of the DNA-damaging chemical mitomycin C and measuring fluorescence over time. Additionally, droplet digital PCR (ddPCR) quantified bacteriophage induction in a lambda phage-carrying E. coli strain, allowing for correlation analysis between the two methods. Results: The recA-driven SOS response depended on both dose and time, with increasing concentrations of mitomycin C leading to higher fluorescence. ddPCR analysis confirmed that mitomycin C induced prophage activation, with gene ratios increasing at higher drug concentrations over time. A strong Spearman correlation (>0.7) was noted between fluorescence and ddPCR results at elevated concentrations and relevant time points, indicating the validity of the GFP-based model as a proxy for bacteriophage induction. Conclusions: The findings demonstrate a strong association between the two methods of measuring phage induction, suggesting that the GFP-based E. coli model is a reliable, cost-effective, and efficient tool for studying phage induction and its potential role in AMR spread. This method could facilitate the screening of environmental samples and specific drugs to evaluate their impact on bacteriophage induction, which opens the door for applications such as screening for antibiotic resistance dissemination. Full article

(This article belongs to the Section Bacteriophages)

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22 pages, 3103 KiB

Open AccessArticle

Genomic and Metabolomic Analysis of the Endophytic Fungus Alternaria alstroemeriae S6 Isolated from Veronica acinifolia: Identification of Anti-Bacterial Properties and Production of Succinic Acid

by Farkhod Eshboev, Alex X. Gao, Akhror Abdurashidov, Kamila Mardieva, Asadali Baymirzaev, Mirzatimur Musakhanov, Elvira Yusupova, Shengying Lin, Meixia Yang, Tina T. X. Dong, Shamansur Sagdullaev, Shakhnoz Azimova and Karl W. K. Tsim

Antibiotics 2025, 14(7), 713; https://doi.org/10.3390/antibiotics14070713 - 16 Jul 2025

Abstract

Background: Endophytic fungi are prolific sources of bioactive metabolites with potential in pharmaceutical and biotechnological applications. Methods: Here, the endophytic fungus, Alternaria alstroemeriae S6, was isolated from Veronica acinifolia (speedwell), and conducted its anti-microbial activities, whole-genome sequencing and metabolome analysis. Results: The ethyl [...] Read more.

Background: Endophytic fungi are prolific sources of bioactive metabolites with potential in pharmaceutical and biotechnological applications. Methods: Here, the endophytic fungus, Alternaria alstroemeriae S6, was isolated from Veronica acinifolia (speedwell), and conducted its anti-microbial activities, whole-genome sequencing and metabolome analysis. Results: The ethyl acetate extract of this fungus exhibited strong anti-bacterial activity and the inhibition zones, induced by the fungal extract at 20 mg/mL, reached 16.25 ± 0.5 mm and 26.5 ± 0.5 mm against Gram-positive and Gram-negative bacteria. To unravel the biosynthetic potential for anti-bacterial compounds, whole-genome sequencing was conducted on A. alstroemeriae S6, resulting in a high-quality assembly of 42.93 Mb encoding 13,885 protein-coding genes. Comprehensive functional genome annotation analyses, including gene ontology (GO) terms, clusters of orthologous groups (COGs), Kyoto encyclopedia of genes and genomes (KEGG), carbohydrate-active enzymes (CAZymes), and antibiotics and secondary metabolites analysis shell (antiSMASH) analyses, were performed. According to the antiSMASH analysis, 58 biosynthetic gene clusters (BGCs), including 16 non-ribosomal peptide synthetases (NRPSs), 21 terpene synthases, 12 polyketide synthetases (PKSs), and 9 hybrids, were identified. In addition, succinic acid was identified as the major metabolite within the fungal extract, while 20 minor bioactive compounds were identified through LC-MS/MS-based molecular networking on a GNPS database. Conclusions: These findings support the biotechnological potential of A. alstroemeriae S6 as an alternative producer of succinic acid, as well as novel anti-bacterial agents. Full article

(This article belongs to the Section Fungi and Their Metabolites)

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Graphical abstract

11 pages, 869 KiB

Open AccessArticle

Species Distribution, Characterization, and Antifungal Susceptibility Patterns of Candida Isolates Causing Oral and Vulvovaginal Candidiasis in Chile

by Francisca Nahuelcura and Eduardo Álvarez Duarte

Antibiotics 2025, 14(7), 712; https://doi.org/10.3390/antibiotics14070712 - 16 Jul 2025

Abstract

Background: Oral candidiasis (OC) and vulvovaginal candidiasis (VVC) are infections caused by species belonging to the genus Candida. In Chile, epidemiological studies on OC/VVC are scarce, leading to an overestimation of the prevalence of C. albicans. Additionally, awareness of the prevalence [...] Read more.

Background: Oral candidiasis (OC) and vulvovaginal candidiasis (VVC) are infections caused by species belonging to the genus Candida. In Chile, epidemiological studies on OC/VVC are scarce, leading to an overestimation of the prevalence of C. albicans. Additionally, awareness of the prevalence of species phenotypically and genotypically similar to C. albicans is lacking. The clinical impact of non-albicans species in cases of OC/VVC is also often underestimated. This study aims to determine the distribution of Candida species, their phenotypic and molecular characteristics, and their antifungal susceptibility patterns in incidents of oral and vulvovaginal candidiasis in Chile. Methods: A descriptive analysis was conducted on 101 isolates of Candida spp. obtained from OC/VVC cases. The identification of Candida species was performed using both phenotypic and molecular techniques. Antifungal susceptibility testing was carried out using the Sensititre YeastOne system. Results: Among the analyzed isolates, 89.1% were identified as C. albicans, while 10.9% were categorized as non-albicans species, including C. dubliniensis, C. glabrata sensu stricto, C. bracarensis, C. tropicalis, C. lusitaniae, and C. parapsilosis sensu stricto. The susceptibility pattern was predominantly susceptible, with only 10.9% of the total strains demonstrating resistance, and low antifungal activity in vitro was observed for Fluconazole, Voriconazole, and Posaconazole. Conclusions: The most prevalent species causing OC/VVC in Chile is C. albicans. This study also presents the first report of C. lusitaniae as a causal agent of VVC in the country. The identification of azole-resistant strains emphasizes the critical role of laboratory diagnosis in VVC cases, thereby preventing potential treatment failures. No resistance was observed in the strains associated with OC. Full article

(This article belongs to the Special Issue Epidemiology, Antifungal Resistance and Therapy in Fungal Infection)

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16 pages, 1988 KiB

Open AccessArticle

Epidemiological Surveillance, Variability, and Evolution of Isolates Belonging to the Spanish Clone of the 4,[5],12:i:- Monophasic Variant of Salmonella enterica Serovar Typhimurium

by Xenia Vázquez, Patricia García, Javier Fernández, Víctor Ladero, Carlos Rodríguez-Lucas, Jürgen J. Heinisch, Rosaura Rodicio and M. Rosario Rodicio

Antibiotics 2025, 14(7), 711; https://doi.org/10.3390/antibiotics14070711 - 16 Jul 2025

Abstract

Background/Objective: The present study focused on the analysis of the Spanish clone belonging to the successful 4,[5],12:i:- monophasic variant of Salmonella enterica serovar Typhimurium. Methods: All isolates of the clone recovered in a Spanish region from human clinical samples between 2008 and 2018 [...] Read more.

Background/Objective: The present study focused on the analysis of the Spanish clone belonging to the successful 4,[5],12:i:- monophasic variant of Salmonella enterica serovar Typhimurium. Methods: All isolates of the clone recovered in a Spanish region from human clinical samples between 2008 and 2018 (N = 14) were investigated using microbiological approaches and genome sequence analysis. In addition, they were compared with isolates from the years 2000 to 2003 (N = 21), which were previously characterized but had not yet been sequenced. Results: Phylogenetic analyses indicate that all isolates are closely related (differing by 1 to 103 SNPs) but belong to two clades termed A and B. With few exceptions, clade A comprised isolates of the first period, also including two “older” control strains, LSP 389/97 and LSP 272/98. Clade B only contained isolates from the second period. Isolates from both periods were resistant to antibiotics and biocides, with almost all resistance genes located on large IncC plasmids, additionally carrying pSLT-derived virulence genes. The number of resistance genes was highly variable, resulting in a total of 22 ABR (antibiotic biocide resistance) profiles. The number of antibiotic resistance genes, but not that of biocide resistance genes, was considerably lower in isolates from the second than from the first period (with averages of 5.5 versus 9.6 genes). Importantly, IS26, which resides in multiple copies within these plasmids, appears to be playing a crucial role in the evolution of resistance, and it was also responsible for the monophasic phenotype, which was associated with four different deletions eliminating the fljAB region. Conclusions: the observed reduction in the number of antibiotic resistance genes could correlate with the loss of adaptive advantage originating from the ban on the use of antibiotics as feed additives implemented in the European Union since 2006, facilitated by the intrinsic instability of the IncC plasmids. Two consecutive IS26 transposition events, which can explain both the clonal relationship of the isolates and their variability, may account for the observed fljAB deletions. Full article

(This article belongs to the Special Issue Genomic Analysis of Antimicrobial Drug-Resistant Bacteria)

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