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Keywords = multidrug-resistant strains.

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15 pages, 1274 KB  
Article
Pathogen Profiling in Reverse Total Shoulder Arthroplasty: Virulence Traits of Clinical Isolates Before and After Intraoperative Povidone–Iodine Irrigation
by Enrico Bellato, Fabio Longo, Francesca Menotti, Rebecca Mariani, Lucrezia Massobrio, Valentina Bartolotti, Helena Villavicencio, Narcisa Mandras, Alessandro Bondi, Antonio Curtoni, Filippo Castoldi, Giuliana Banche and Valeria Allizond
Antibiotics 2026, 15(2), 129; https://doi.org/10.3390/antibiotics15020129 - 28 Jan 2026
Abstract
Background/Objectives: Reverse total shoulder arthroplasty (RTSA), a commonly performed procedure in elderly patients with osteoarthritis, is frequently complicated by postoperative infections—primarily caused by Cutibacterium acnes and coagulase-negative staphylococci (CoNS)—which remain a major clinical challenge. While standard antiseptic skin protocols can reduce the [...] Read more.
Background/Objectives: Reverse total shoulder arthroplasty (RTSA), a commonly performed procedure in elderly patients with osteoarthritis, is frequently complicated by postoperative infections—primarily caused by Cutibacterium acnes and coagulase-negative staphylococci (CoNS)—which remain a major clinical challenge. While standard antiseptic skin protocols can reduce the bacterial load at the surgical site, they often fail to achieve complete eradication, particularly with C. acnes, a resident species of the shoulder microbiome. Recent evidence indicates that intraoperative povidone–iodine irrigation is effective in significantly decreasing microbial burden; however, a thorough characterization of the virulence factors of the isolated strains remains essential. Methods: A total of 187 clinical strains isolated immediately after RTSA were characterized with respect to their antibiotic resistance profiles and biofilm-forming capacity, and the impact of intraoperative povidone–iodine irrigation on the reduction in bacteria that express these virulence traits was evaluated. Results: Of the 120 C. acnes isolates, 97.67% were susceptible to the tested antimicrobial agents, while only 3.33% exhibited resistance, specifically to clindamycin. In contrast, 53% of CoNS isolates were classified as susceptible, whereas the remaining 47% demonstrated multidrug resistance. Biofilm production was detected in 24% (29/120) of C. acnes and 39% (25/64) of CoNS isolates, with a statistically significant reduction observed after irrigation only for C. acnes. No association was found between biofilm formation and clindamycin resistance in C. acnes, likely due to the low number of resistant isolates. Conversely, among CoNS, a correlation was observed, with the 17.2% of biofilm-producing strains also exhibiting resistance to antimicrobial agents. Conclusions: Notwithstanding the presence of these virulence factors, povidone–iodine irrigation proved effective in substantially reducing the number of bacterial isolates recovered at the surgical site without selecting for strains with enhanced pathogenicity. Notably, the majority of resistant bacteria were detected prior to intraoperative irrigation. This intraoperative procedure may be a key approach to reducing prosthetic joint infections frequently caused by more virulent pathogens, which are unlikely to be selected following this disinfection strategy. Full article
(This article belongs to the Special Issue Antibiotic Treatment on Surgical Infections)
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24 pages, 1920 KB  
Article
Robust Goat-Derived Enterococcus Isolates with Broad-Spectrum Antipathogenic Activity as Next-Generation Probiotic Candidates
by Mohamed Osman Abdalrahem Essa, Nosiba S. Basher, Layla Ahmed Mohammed Abdelhadi, Nasir A. Ibrahim, Shahab Ur Rehman, Hosameldeen Mohamed Husien, Ahmed A. Saleh and Darong Cheng
Vet. Sci. 2026, 13(2), 120; https://doi.org/10.3390/vetsci13020120 - 27 Jan 2026
Abstract
The rise of multidrug-resistant enteric pathogens and increased demand for antibiotic alternatives have intensified efforts to find reliable, safe, and effective probiotics. This study reports the isolation, characterization, and assessment of the probiotic potential of five Enterococcus strains isolated from the feces of [...] Read more.
The rise of multidrug-resistant enteric pathogens and increased demand for antibiotic alternatives have intensified efforts to find reliable, safe, and effective probiotics. This study reports the isolation, characterization, and assessment of the probiotic potential of five Enterococcus strains isolated from the feces of healthy goats aged 7–9 months raised under conventional management. Following an initial screening of 57 lactic acid bacteria, 5 isolates (Enterococcus faecium, E. hirae, E. faecalis, Enterococcus sp., and Streptococcus lutetiensis) were chosen based on their catalase-negative, non-motile, and non-hemolytic characteristics, in addition to their high tolerance to gastric (pH 2.0) and intestinal (pH 8.0, 0.3–1.5% bile salt) stress. In simulated gastric juice, survival rates reached 89.05% (E5) and 85.03% (E3), while in intestinal juice, survival peaked at 78.01% (E4). All strains thrived in 4% NaCl and maintained at least 8 Log10 CFU/mL after 12 h of exposure to 1.5% porcine bile salt. Cell surface hydrophobicity (0.78–93.85%) and auto-aggregation (23–91%) properties were strain-dependent, but exceeded the thresholds required for efficient gut colonization. Co-aggregation assays demonstrated over 45% binding with E. coli and S. typhimurium, suggesting a strong potential to displace pathogens. Cell-free supernatants created inhibition zones measuring 15.02 mm against E. coli and 11.04 mm against S. flexneri, while maintaining activity against methicillin-resistant S. aureus (MRSA). Antibiotic testing indicated that all strains were sensitive to ciprofloxacin and florfenicol. No β-hemolysis or mobile resistance genes were found, supporting the initial safety findings. This study reveals that Enterococcus isolates from goats display a unique combination of gastrointestinal survivability and broad-spectrum antipathogenic activity and, therefore, are promising candidates for the development of next-generation probiotic strains for use in livestock (and, potentially, humans). Further in vivo validation and genome-based safety assessments are warranted. Full article
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31 pages, 1311 KB  
Article
Mapping Escherichia coli in Women with Simple Urinary Tract Infections: Phenotypic ESBL/AmpC Screening and Whole-Genome Insights from Oman
by Aisha Al-Mufarji, Meher Rizvi, Nawal Al-Kindi, Nada Al-Tamtami and Zaaima Al-Jabri
Antibiotics 2026, 15(2), 124; https://doi.org/10.3390/antibiotics15020124 - 27 Jan 2026
Abstract
Background/Objectives: Simple urinary tract infections (sUTIs) are common in women and increasingly affected by multidrug-resistant (MDR) Escherichia coli. Extended-spectrum β-lactamase (ESBL) and AmpC producers restrict oral treatment options and promote carbapenem use. This study aimed to (i) describe the etiology and antimicrobial [...] Read more.
Background/Objectives: Simple urinary tract infections (sUTIs) are common in women and increasingly affected by multidrug-resistant (MDR) Escherichia coli. Extended-spectrum β-lactamase (ESBL) and AmpC producers restrict oral treatment options and promote carbapenem use. This study aimed to (i) describe the etiology and antimicrobial susceptibility of sUTIs in women of reproductive age in Oman, (ii) determine the prevalence of ESBL/AmpC-producing E. coli, (iii) evaluate nitroxoline, fosfomycin, mecillinam, and temocillin against ESBL and non-ESBL E. coli, and (iv) characterize circulating clones and resistance/virulence determinants using whole-genome sequencing (WGS). Methods: In this multicentric study (September 2022–August 2023), 795 uropathogens from 762 women (15–50 years) with sUTI were collected from four Omani hospitals. Identification and susceptibility testing of E. coli (n = 489) and Klebsiella pneumoniae (n = 140) using BD Phoenix and MALDI-TOF MS was performed (CLSI 2022). Thirty ESBL-producing and 82 non-ESBL E. coli underwent phenotypic ESBL/AmpC testing and evaluation of mecillinam, temocillin, nitroxoline, and fosfomycin. WGS was performed on 26 isolates (23 ESBL, 3 wild type) and analyzed for MLST, and SNP phylogeny using ResFinder, CARD, PlasmidFinder, VirulenceFinder. Statistical significance was set at p < 0.05. Results: E. coli (62%) and K. pneumoniae (18%) were the predominant pathogens. E. coli showed high susceptibility to nitrofurantoin (~97%), carbapenems, aminoglycosides, and piperacillin–tazobactam, but reduced susceptibility to cephalosporins, fluoroquinolones, cotrimoxazole, and ampicillin. ESBL prevalence ranged from 38–51%; AmpC producers were rare (4.6%). Mecillinam, nitroxoline, and fosfomycin exhibited 100% activity against both ESBL and non-ESBL isolates; temocillin showed 89.3% activity in ESBL strains. WGS identified 15 sequence types dominated by ST-131, ST-1193, ST-73, and ST-174, with blaCTX-M-15 as the major ESBL genotype. Conclusions: sUTIs in Oman show a high burden of ESBL-producing E. coli. Nitrofurantoin, mecillinam, fosfomycin, temocillin, and nitroxoline would be effective carbapenem-sparing oral options. Continuous phenotypic and genomic surveillance are crucial to guide antimicrobial therapy and stewardship. Full article
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15 pages, 272 KB  
Article
Early Life Antibiotic Exposure and Intestinal Colonization by Enterobacteriaceae upon Admission to a Neonatal Referral Unit: A Case–Control Study
by Sergio Agudelo-Pérez, Gloria Troncoso, Martha Alvarez-Olmos, Maria Pineda, Adriana Moscote and María Paula Molina Pérez
Antibiotics 2026, 15(2), 123; https://doi.org/10.3390/antibiotics15020123 - 27 Jan 2026
Abstract
Background/Objectives: Intestinal colonization by Enterobacteriaceae, including extended-spectrum β-lactamase-producing (ESBL-E) and carbapenemase-producing (E-CPE) strains, is an early marker of multidrug-resistant infections in neonates, particularly those transferred from lower-complexity hospitals. This study aimed to identify factors associated with intestinal Enterobacteriaceae colonization upon admission to a [...] Read more.
Background/Objectives: Intestinal colonization by Enterobacteriaceae, including extended-spectrum β-lactamase-producing (ESBL-E) and carbapenemase-producing (E-CPE) strains, is an early marker of multidrug-resistant infections in neonates, particularly those transferred from lower-complexity hospitals. This study aimed to identify factors associated with intestinal Enterobacteriaceae colonization upon admission to a level IV neonatal referral unit in Colombia, with a focus on prior antibiotic exposure. Methods: We conducted a retrospective case–control study, including all neonates transferred from peripheral hospitals and screened with rectal swabs at admission. Cases were neonates colonized with Enterobacteriaceae, and controls were non-colonized neonates admitted during the same period. Multivariable logistic regression models were used to evaluate three exposure dimensions: prior antibiotic use (yes/no), number of agents, and the WHO AWaRe classification. A secondary analysis was performed to assess the factors associated with ESBL-E and E-CPE colonization. Results: Among the 435 referred neonates, 87 (20.0%) were colonized, predominantly Klebsiella pneumoniae (53.6%) and Escherichia coli (19.5%). Prior antibiotic use (aOR 3.01; 95% CI 1.47–6.37), exposure to two agents (aOR 4.13; 95% CI 1.94–8.89) and use of AWaRe Access antibiotics (aOR 22.2; 95% CI 5.83–101) were strongly associated with colonization. Longer hospitalization and central catheter use were also associated with greater colonization odds, whereas total parenteral nutrition showed a protective association. In the sub-analysis, Access, Watch, and Reserve antibiotics were independently associated with ESBL-E and E-CPE colonization. Conclusions: Among transferred neonates, prior antibiotic exposure, particularly AWaRe-classified agents, showed the strongest association with intestinal colonization by Enterobacteriaceae, including ESBL-E/CPE phenotypes. Strengthening antimicrobial stewardship in referral facilities and implementing risk-based screening at admission may help reduce colonization and limit the spread of resistance. Full article
(This article belongs to the Special Issue Antimicrobial Stewardship in Neonatal Intensive Care)
18 pages, 3500 KB  
Article
Genomic and Functional Characterization of Lytic Tlsvirus Bacteriophages Targeting Salmonella Infantis Isolated from Poultry Farms in Ecuador
by Sandra Sevilla-Navarro, Ignacio Samuel Gómez-Cano, Ivette Castillo-Beckmann, Santiago Ballaz, Alexis Debut and Esteban Fernández-Moreira
Biology 2026, 15(3), 232; https://doi.org/10.3390/biology15030232 - 26 Jan 2026
Viewed by 35
Abstract
Salmonella is responsible for millions of foodborne illnesses worldwide. The emergence of antibiotic-resistant Salmonella strains necessitates the development of alternatives for controlling this microorganism in the food supply chain. In Ecuador, Salmonella Infantis (S. Infantis) is the most frequently isolated serovar [...] Read more.
Salmonella is responsible for millions of foodborne illnesses worldwide. The emergence of antibiotic-resistant Salmonella strains necessitates the development of alternatives for controlling this microorganism in the food supply chain. In Ecuador, Salmonella Infantis (S. Infantis) is the most frequently isolated serovar in poultry farms, poultry food products, and human infections. The objective of this study was to isolate and characterize lytic bacteriophages against a S. Infantis strain from poultry products in Ecuador to evaluate their potential for biocontrol. Three bacteriophages, GS71, GS156, and GS166, were isolated from chicken feces samples and showed short latent times (5–10 min), burst sizes of 205–231 PFU/cell, and stability up to 50 °C and pH = 10. Despite being isolated at different times and locations, they exhibited high genomic similarity (91.9–98.7%), reflecting the low diversity of Ecuadorian S. Infantis strains. VIRIDIC and phylogenetic analyses placed them within the Tlsvirus genus, showing conserved gene modules for replication, morphogenesis, and lysis. Putative endolysin and depolymerase genes were identified, supporting their anti-biofilm activity against biofilm-forming bacteria. Host range assays showed GS71 and GS166 lysed most S. Infantis field strains, whereas GS156 had a narrower spectrum linked to a unique polynucleotide kinase insertion. TEM confirmed Siphovirus-like morphology with icosahedral capsids (~55 nm) and long non-contractile tails. No genes associated with lysogeny, virulence, or antibiotic resistance were found. These findings support GS71, GS156, and GS166 as safe and effective candidates for bacteriophage cocktails targeting multidrug-resistant S. Infantis in poultry production. Full article
(This article belongs to the Section Microbiology)
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13 pages, 3517 KB  
Article
Extra-Virgin Olive Oil as a Natural Photosensitizer in Photodynamic Therapy Against MDR Candida spp.: In Vitro Study
by Cinzia Casu, Antonia Sinesi, Andrea Butera, Sara Fais, Alessandro Chiesa, Andrea Scribante and Germano Orrù
Optics 2026, 7(1), 10; https://doi.org/10.3390/opt7010010 - 26 Jan 2026
Viewed by 35
Abstract
The growing prevalence of multidrug-resistant (MDR) Candida spp. necessitates the development of new antifungal strategies. Photodynamic therapy (PDT), already widely used in the treatment of various oral infections, is based on the synergistic interaction of three key elements: a photosensitizer capable of selectively [...] Read more.
The growing prevalence of multidrug-resistant (MDR) Candida spp. necessitates the development of new antifungal strategies. Photodynamic therapy (PDT), already widely used in the treatment of various oral infections, is based on the synergistic interaction of three key elements: a photosensitizer capable of selectively binding to microbial cells, a light source with the appropriate wavelength, and the presence of molecular oxygen. This interaction results in the production of singlet oxygen and reactive oxygen species, responsible for the selective destruction of microorganisms. In recent years, numerous natural compounds have been explored as potential photosensitizers. Olive oil, a cornerstone of the Mediterranean diet, was recently recognized by the U.S. Food and Drug Administration as a medicinal substance thanks to its soothing, immunomodulatory, and antimicrobial properties, which have also been documented in regard to oral administration. Materials and Methods: The aim of this in vitro study was to evaluate the efficacy of activated olive oil as a novel photosensitizer in PDT against Candida species. Oral MDR clinical isolates of C. albicans, C. krusei, and C. glabrata were analyzed using the Kirby–Bauer method according to EUCAST protocols. Six different experimental conditions were considered for each strain: (i) 100 μL of extra-virgin olive oil (EVOO); (ii) 100 μL of EVOO pre-activated with 3% H2O2 (EVOO-H); (iii) 100 μL of EVOO irradiated for 5 min with polarized light (480–3400 nm, 25 W); (iv) 100 μL of EVOO-H subjected to the same polarized light; (v) 100 μL of EVOO irradiated for 5 min with a 660 nm diode laser (100 mW); and (vi) 100 μL of EVOO-H irradiated with the same laser. All plates were incubated at 37 °C for 48 h. Results: The results showed a variable response among the different Candida species. C. glabrata showed sensitivity to all experimental conditions, with a 50% increase in the diameter of the inhibition zone in the presence of polarized light. C. krusei showed no sensitivity under any of the conditions tested. C. albicans showed antifungal activity exclusively when EVOO-H was activated by light. In particular, activation of EVOO and EVOO-H with polarized light resulted in the largest inhibition zones. Conclusions: In conclusion, olive oil, both alone and pre-activated with hydrogen peroxide, can be considered an effective photosensitizer against drug-resistant Candida spp., especially when combined with polarized light. Full article
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16 pages, 939 KB  
Article
Adverse Impact of Gamma-Polyglutamic Acid on the Antimicrobial Efficacy of Cefiderocol and Nanosilver Against Gram-Negative Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii
by Żaneta Binert-Kusztal, Agata Krakowska, Iwona Skiba-Kurek, Przemysław Dorożyński and Tomasz Skalski
Pharmaceutics 2026, 18(2), 157; https://doi.org/10.3390/pharmaceutics18020157 - 25 Jan 2026
Viewed by 129
Abstract
Background/Objectives: Wound infections caused by multidrug-resistant Gram-negative bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii, pose a major clinical challenge. This study evaluated the interactions between gamma-polyglutamic acid (γ-PGA), cefiderocol, and silver nanoparticles (AgNPs) within multilayer wound dressing [...] Read more.
Background/Objectives: Wound infections caused by multidrug-resistant Gram-negative bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii, pose a major clinical challenge. This study evaluated the interactions between gamma-polyglutamic acid (γ-PGA), cefiderocol, and silver nanoparticles (AgNPs) within multilayer wound dressing configurations. The primary goal was to clarify the dual role of γ-PGA as a healing promoter and a potential protector of bacterial cells against antimicrobial agents. Methods: Multilayer dressing models were assembled in 96-well plates to simulate vertical stratification of antimicrobial layers4. Bacterial viability was assessed through relative OD600 measurements following incubation with varying concentrations and spatial arrangements of cefiderocol, AgNPs, and γ-PGA. Data were analyzed using generalized linear modeling (GLM) with a gamma distribution and random forest regression to determine the relative importance of each factor in modulating bacterial survival. Results: γ-PGA concentration emerged as the dominant factor influencing bacterial viability, accounting for nearly 100% of variable importance in random forest analysis. Despite high antimicrobial pressure from cefiderocol and AgNPs, bacterial viability stabilized at approximately 40% in the presence of γ-PGA. The vertical positioning of γ-PGA significantly impacted survival; direct physical contact between the polymer and bacteria, particularly at high concentrations, enhanced bacterial persistence in P. aeruginosa and E. coli. Cefiderocol showed strain-specific potency, while AgNPs provided consistent growth inhibition. Conclusions: γ-PGA plays a paradoxical role in wound care by providing moisture retention while simultaneously acting as a cytoprotective agent that reduces antimicrobial efficacy, likely by facilitating biofilm formation. These findings underscore the necessity of optimizing the spatial layering and concentration of biopolymers in advanced dressings. Strategic design is crucial to balance regenerative benefits with maximal antimicrobial control to improve clinical outcomes in chronic wound management. Full article
(This article belongs to the Special Issue Targeted Drug Delivery Strategies for Infectious Diseases)
24 pages, 4164 KB  
Article
Antimicrobial Activity of Acidifying Hyaluronic Acid–Starch Microfiber Dressings Against Clinical Isolates from Chronic Wounds
by Ivana Stará, Petra Moťková, Markéta Vydržalová, Marcela Pejchalová, Ladislav Burgert, Radim Hrdina, Marek Bouška, Martin Adam, Karel Královec and Iveta Brožková
J. Funct. Biomater. 2026, 17(2), 58; https://doi.org/10.3390/jfb17020058 - 23 Jan 2026
Viewed by 204
Abstract
Hyaluronic acid (HA) is a natural biopolymer widely used in wound dressings for its supportive role in the healing process. In this study, we investigated the occurrence of microorganisms in chronic wounds and evaluated the antimicrobial activity of newly synthesized HA–Starch-based materials enriched [...] Read more.
Hyaluronic acid (HA) is a natural biopolymer widely used in wound dressings for its supportive role in the healing process. In this study, we investigated the occurrence of microorganisms in chronic wounds and evaluated the antimicrobial activity of newly synthesized HA–Starch-based materials enriched with acidifying agents. Microbial isolates obtained from chronic wounds were tested for susceptibility using the agar diffusion method. The prepared materials exhibited significant antimicrobial activity against both reference strains and multidrug-resistant clinical isolates. Further characterization by scanning electron microscopy and elemental analysis confirmed uniform microfiber morphology and the expected elemental composition of the fibers. Cytotoxicity assessments performed using the xCELLigence system demonstrated the potential safety of developed materials. Overall, the results indicate that HA–Starch-based materials containing acidifying compounds exhibit strong in vitro antimicrobial activity against chronic-wound isolates, supporting their potential for further evaluation in wound care applications. Full article
(This article belongs to the Section Biomaterials and Devices for Healthcare Applications)
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13 pages, 777 KB  
Article
Antimicrobial Effect of Postbiotics on Multidrug-Resistant Escherichia coli
by Çiğdem Sezer, Nebahat Bilge, Gönül Damla Büyük and Merve Ayyıldız Akın
Foods 2026, 15(2), 384; https://doi.org/10.3390/foods15020384 - 21 Jan 2026
Viewed by 123
Abstract
Pathogens that have developed resistance to antibiotics pose a threat to public health. The primary goal in preventing foodborne infections is to inhibit the growth of and, subsequently, eliminate antibiotic-resistant pathogens at every stage from production to consumption. Escherichia coli, which has acquired [...] Read more.
Pathogens that have developed resistance to antibiotics pose a threat to public health. The primary goal in preventing foodborne infections is to inhibit the growth of and, subsequently, eliminate antibiotic-resistant pathogens at every stage from production to consumption. Escherichia coli, which has acquired resistance to most known antibiotics, is frequently found in chicken meat. In many countries, due to unregulated antibiotic use in poultry farming, poor hygiene in slaughterhouses, or cross-contamination, extended-spectrum beta-lactamase (ESBL)-producing E. coli has been identified as the causative agent in poultry-associated food poisoning. The need for more effective antimicrobial agents against this pathogen, which is resistant to existing antibiotics, has led to increased attention being paid to postbiotics produced by lactic acid bacteria, particularly bacteriocins. This study aimed to determine the antimicrobial effects of postbiotics obtained from kefir-derived Lactiplantibacillus plantarum and Lactococcus lactis against ESBL-positive E. coli. To achieve this, E. coli strains were isolated from raw chicken meat samples collected from the market using culture-based methods, and their antimicrobial resistance profiles were determined using the disk diffusion method. The ESBL positivity of the isolates was assessed using the double-disk synergy test. The antimicrobial activities of the postbiotics against the identified ESBL-positive E. coli strains were tested using the macro-dilution method to determine minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values. ESBL-positive E. coli was detected in 48% of raw chicken meat samples. The antimicrobial effects of postbiotics were examined by disk diffusion, and postbiotics produced by 18 Lb. plantarum strains and 20 Lc. lactis strains showed strong antimicrobial activity. Significant differences in the antimicrobial effects of postbiotics were observed between the two species. Lb. plantarum postbiotics exhibited both bacteriostatic (concentration 60%) and bactericidal (concentration 80%) effects on ESBL-positive E. coli strains, whereas Lc. lactis postbiotics showed only bacteriostatic effects (80% concentration). Postbiotics derived from probiotic bacteria offer promising effects against multidrug-resistant E. coli due to their heat resistance, activity across different pH values, strong antimicrobial effects, affordability, and ease of production. Full article
(This article belongs to the Section Food Microbiology)
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20 pages, 6092 KB  
Article
Antimicrobial Resistance and Comparative Genome Analysis of High-Risk Escherichia coli Strains Isolated from Egyptian Children with Diarrhoea
by Radwa Abdelwahab, Munirah M. Alhammadi, Muhammad Yasir, Ehsan A. Hassan, Entsar H. Ahmed, Nagla H. Abu-Faddan, Enas A. Daef, Stephen J. W. Busby and Douglas F. Browning
Microorganisms 2026, 14(1), 247; https://doi.org/10.3390/microorganisms14010247 - 21 Jan 2026
Viewed by 165
Abstract
Escherichia coli is an important human pathogen that is able to cause a variety of infections, which can result in diarrhoea, urinary tract infections, sepsis, and even meningitis, depending on the pathotype of the infecting strain. Like many Gram-negative bacteria, E. coli is [...] Read more.
Escherichia coli is an important human pathogen that is able to cause a variety of infections, which can result in diarrhoea, urinary tract infections, sepsis, and even meningitis, depending on the pathotype of the infecting strain. Like many Gram-negative bacteria, E. coli is becoming increasingly resistant to many frontline antibiotics, including third-generation cephalosporins and carbapenems, which are often considered the antibiotics of last resort for these infections. This is particularly the case in Egypt, where multidrug-resistant (MDR) E. coli is highly prevalent. However, in spite of this, few Egyptian MDR E. coli strains have been fully characterised by genome sequencing. Here, we present the genome sequences of ten highly MDR E. coli strains, which were isolated from children who presented with diarrhoea at the Outpatients Clinic of Assiut University Children’s Hospital in Assiut, Egypt. We report that they carry multiple antimicrobial resistance genes, which includes extended spectrum β-lactamase genes, as well as blaNDM and blaOXA carbapenemase genes, likely encoded on IncX3 and IncF plasmids. Many of these strains were also found to be high-risk extra-intestinal pathogenic E. coli (ExPEC) clones belonging to sequence types ST167, ST410, and ST617. Thus, their presence in the Egyptian paediatric population is particularly worrying, and this highlights the need for increased surveillance of high-priority pathogens in this part of the world. Full article
(This article belongs to the Special Issue Bacterial Infections in Clinical Settings, 2nd Edition)
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16 pages, 1577 KB  
Article
Genomic Relationship Between High-Risk Pseudomonas aeruginosa Clone ST244 Serotypes O5 and O12 from Southeastern Brazil
by Kayo Bianco, Thereza Cristina da Costa Vianna, Samara Santanna de Oliveira, Kaylanne Montenegro, Claudia Flores, Ana Paula Alves do Nascimento, Alexander Machado Cardoso and Maysa Mandetta Clementino
Microbiol. Res. 2026, 17(1), 27; https://doi.org/10.3390/microbiolres17010027 - 21 Jan 2026
Viewed by 141
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with nosocomial infections and environmental dissemination. Among its high-risk clones, ST244 is notable for its global distribution and distinctive genomic traits. This study reports whole-genome sequencing of ten ST244 isolates from hospitalized patients and wastewater [...] Read more.
Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with nosocomial infections and environmental dissemination. Among its high-risk clones, ST244 is notable for its global distribution and distinctive genomic traits. This study reports whole-genome sequencing of ten ST244 isolates from hospitalized patients and wastewater in a healthcare complex in Southeastern Brazil. Genomic comparisons revealed a highly conserved clonal group, with nine isolates forming a tight monophyletic cluster based on rMLST, SNP phylogeny, and average nucleotide identity (>99.5%). One isolate showed close phylogenetic proximity to strains from Asia and North America, suggesting international dissemination. Serotype analysis revealed both O5 and O12 variants, indicating intra-lineage antigenic diversity. Resistance profiling identified multidrug-resistant phenotypes carrying carbapenemase genes (blaOXA-494, blaOXA-396) and diverse insertion sequences (ISPa1, ISPa6, ISPa22, ISPa32, and ISPa37), facilitating horizontal gene transfer. Virulence gene analysis showed conserved elements related to adhesion, iron uptake, secretion systems, and quorum sensing, while the cytotoxin gene exoU was absent. These results highlight clonal persistence, possible intra-hospital transmission, and links to globally circulating ST244 sublineages. Our findings underscore the importance of genomic surveillance to track high-risk P. aeruginosa clones at the clinical–environmental interface. Full article
(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)
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21 pages, 3151 KB  
Article
Genomic Insights into Candidozyma auris Clade II: Comparative Phylogenomics and Structural Validation of Fluconazole Resistance Mechanisms
by Sanghak Lee, Kei-Anne Garcia Baritugo, Han-Soo Kim, Hyeyoung Lee, Sook Won Ryu, Soo-Young Kim, Chae Hoon Lee, Young Ree Kim, Jeong Hwan Shin, Jayoung Kim and Gi-Ho Sung
J. Fungi 2026, 12(1), 76; https://doi.org/10.3390/jof12010076 - 20 Jan 2026
Viewed by 330
Abstract
Candidozyma auris (formerly Candida auris) is an emerging multidrug-resistant fungal pathogen with confirmed cases in over 30 countries. Although whole-genome sequencing (WGS) analysis defined distinct clades during characterization of underlying genetic mechanism behind multidrug resistance, Clade II remains under-evaluated. In this study, [...] Read more.
Candidozyma auris (formerly Candida auris) is an emerging multidrug-resistant fungal pathogen with confirmed cases in over 30 countries. Although whole-genome sequencing (WGS) analysis defined distinct clades during characterization of underlying genetic mechanism behind multidrug resistance, Clade II remains under-evaluated. In this study, a three-level comparative genomic strategy (Global, Clade, Phenotype) was employed by integration of unbiased genome-wide comparative SNP screening (GATK v4.1.9.0), targeted BLAST profiling (BLAST+ v2.17.0), and in silico protein analysis (ColabFold v1.5.5; DynaMut2 v2.0) for systematic evaluation of mechanisms of antifungal resistance in thirty-nine Clade II C. auris clinical isolates and fourteen reference strains. Global and clade-level analyses confirmed that all the clinical isolates belong to Clade II, according to phylogenetic clustering and mating type locus (MTL) conservation. At the phenotype level, a distinct subclade of fluconazole-resistant mutants was identified to have a heterogenous network of mutations in seven key enzymes associated with cell membrane dynamics and the metabolic stress response. Among these, four core mutations (TAC1B, CAN2, NIC96, PMA1) were confirmed as functional drivers based on strict criteria during multitier in silico protein analysis: cross-species conservation, surface exposure, active site proximity, thermodynamic stability, and protein interface interaction. On the other hand, three high-level fluconazole-resistant clinical isolates (≥128 μg/mL) that lacked these functional drivers were subjected to comprehensive subtractive genomic profiling analysis. The absence of coding mutations in validated resistance drivers, yeast orthologs, and convergent variants suggests that there is an alternative novel non-coding or regulatory mechanism behind fluconazole resistance. These findings highlight Clade II’s evolutionary divergence into two distinct trajectories towards the development of a high level of fluconazole resistance: canonical protein alteration versus regulatory modulation. Full article
(This article belongs to the Special Issue Mycological Research in South Korea)
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13 pages, 1949 KB  
Article
Untargeted LC-HRMS-Based Metabolomic and Antibacterial Potential of Sargassum duplicatum Against Multidrug-Resistant Bacteria
by Feri Susanto, Riyanti, Hamdan Syakuri, Muhammad Nursid, Till F. Schäberle, Ute Mettal, Jae-Suk Choi and Maria Dyah Nur Meinita
Medicina 2026, 62(1), 218; https://doi.org/10.3390/medicina62010218 - 20 Jan 2026
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Abstract
Background/Objectives: The rise in antimicrobial resistance is one of the major challenges to global health systems, which necessitates the development of new antibacterial compounds. The bioactive compounds of brown seaweed Sargassum duplicatum have demonstrated potential antibacterial activity. This study applied metabolomic profiling and [...] Read more.
Background/Objectives: The rise in antimicrobial resistance is one of the major challenges to global health systems, which necessitates the development of new antibacterial compounds. The bioactive compounds of brown seaweed Sargassum duplicatum have demonstrated potential antibacterial activity. This study applied metabolomic profiling and molecular networking in combination with antibacterial screening assays to assess the antimicrobial properties of S. duplicatum extracts against multidrug-resistant bacteria. Methods: Two extraction methods, i.e., maceration and microwave extraction, were used. Therewith, untargeted metabolomic profiling was performed using Liquid Chromatography–High Resolution Mass Spectrometry (LC-HRMS). Molecular networks (MNs) were established and compound dereplication was conducted using the spectral database of the Global Natural Products Social Molecular Networking platform (GNPS). Additionally, antimicrobial assays were conducted against Gram-positive and Gram-negative bacterial strains, including multidrug-resistant bacteria, i.e., methicillin-resistant Staphyloccocus aureus ATCC 33592 (MRSA) and β-lactamase, producing Escherichia coli ATCC 35218 (TEM-1 positive strain). Result: Dereplication resulted in the prediction of six compounds with reported antimicrobial properties, i.e., 13-docosenamide, 9-octadecenamide, pheophorbide A, ouabain, sarmentoside B and AC1L1X1Z. Antibacterial screening of the extracts revealed that the ethyl acetate maceration extracts exhibited the strongest inhibitory activity, with inhibition values between 85 and 98% against S. aureus ATCC 33592. Conclusions: This metabolomics study requires further research to isolate, purify, confirm, and validate the dereplicated compounds that may have potential antibacterial activity. Full article
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17 pages, 1892 KB  
Article
A New Trichlorinated Xanthone and Compounds Isolated from Cladonia skottsbergii with Antimicrobial Properties
by Marvin J. Rositzki, Achara Raksat, Charles J. Simmons, Clifford Smith, Reverend Danette V. Choi, Supakit Wongwiwatthananukit and Leng Chee Chang
Pharmaceuticals 2026, 19(1), 174; https://doi.org/10.3390/ph19010174 - 19 Jan 2026
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Abstract
Background/Objectives: The global rise in multidrug-resistant (MDR) bacteria, particularly methicillin-resistant and methicillin-susceptible Staphylococcus aureus (MRSA and MSSA), continues to pose a major public health challenge, including in Hawaii. This underscores the need to discover new antimicrobial agents from natural sources. Guided by [...] Read more.
Background/Objectives: The global rise in multidrug-resistant (MDR) bacteria, particularly methicillin-resistant and methicillin-susceptible Staphylococcus aureus (MRSA and MSSA), continues to pose a major public health challenge, including in Hawaii. This underscores the need to discover new antimicrobial agents from natural sources. Guided by teachings from a Buddhist master regarding the medicinal value of lichens, we investigated the endemic Hawaiian lichen Cladonia skottsbergii. Methods: Specimens of C. skottsbergii were collected from the Lotus Buddhist Monastery in Mountain View, Hawaii. A methanolic extract was prepared and purified using chromatographic techniques, and compound structures were elucidated through spectroscopic analyses and single-crystal X-ray diffraction. The antibacterial activity of the compounds was assessed against Gram-positive strains (MRSA, MSSA) and Gram-negative bacteria (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa). Cytotoxicity was assessed using A549 (non-small cell lung cancer) and Vero E6 (non-tumorigenic) cell lines. Results: Three compounds were isolated: clarosione (1), a newly identified trichlorinated xanthone, and two known metabolites, (S)-usnic acid (2) and perlatolic acid (3). Compounds 2 and 3 demonstrated strong inhibitory effects against MRSA and MSSA. Their minimum inhibitory concentrations (MICs) ranged from 2 to 4 µg/mL, compared with vancomycin (0.5–1 µg/mL). Cytotoxicity testing showed higher sensitivity in A549 cells than in Vero E6 cells, resulting in favorable selectivity indices for the active compounds. Conclusions: In the current study, a new compound, clarosione (1) was discovered. This enhances our understanding of the constituents of C. skottsbergii and its potential antibacterial properties. Lichen-derived compounds may serve as lead candidates for further development, and further study is warranted. Full article
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13 pages, 1806 KB  
Article
Listeria monocytogenes in Jiaxing: Whole-Genome Sequencing Reveals New Threats to Public Health
by Lei Gao, Wenjie Gao, Ping Li, Miaomiao Jia, Xuejuan Liu, Peiyan He, Henghui Wang, Yong Yan and Guoying Zhu
Pathogens 2026, 15(1), 109; https://doi.org/10.3390/pathogens15010109 - 19 Jan 2026
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Abstract
(1) Background: Listeria monocytogenes (Lm) is recognized by the World Health Organization (WHO) as one of the four principal foodborne pathogens. This study aimed to investigate the molecular characteristics of Lm isolates from Jiaxing, China, using whole-genome sequencing (WGS) to enhance our understanding [...] Read more.
(1) Background: Listeria monocytogenes (Lm) is recognized by the World Health Organization (WHO) as one of the four principal foodborne pathogens. This study aimed to investigate the molecular characteristics of Lm isolates from Jiaxing, China, using whole-genome sequencing (WGS) to enhance our understanding of their molecular epidemiology. (2) Methods: A total of 39 foodborne Lm isolates and 7 clinical Lm isolates were analyzed via WGS to identify resistance genes, virulence factors, lineage, sequence type (ST), and clonal complex (CC). Antibiotic susceptibility was assessed using Minimum Inhibitory Concentration (MIC) testing, and serotypes were confirmed via multiplex PCR. (3) Results: We found that 39 food isolates were mainly lineage II (66.67%), with 13 STs; ST8 was the dominant ST, and 2 new types, ST3210 and ST3405, were found. Among the seven clinical isolates, lineage I was dominant (57.14%), and ST87 was the dominant ST. Serotype 1/2a was dominant, accounting for 54.35%, followed by 1/2b, which accounted for 36.96%. The overall antimicrobial resistance rate was 13.04%, with a multidrug resistance rate of 2.17%. All strains harbored LIPI-1 and LIPI-2, and five strains carried LIPI-3 genes: one strain belonged to ST619 of lineage I, two strains belonged to ST224 of lineage I, and two strains belonged to ST11 of lineage II. (4) Conclusions: This study clarified the genotype and serotype characteristics of Listeria monocytogenes in Jiaxing, as well as their molecular characteristics relating to drug resistance and virulence, thus providing a technical basis for improving exposure risk assessment of Listeria monocytogenes. Continuous monitoring, prevention, and control are recommended to further improve regional public health and safety. Full article
(This article belongs to the Section Bacterial Pathogens)
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