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17 pages, 3265 KB  
Article
Prevalence and Genomic Characterization of ESBL-Producing Escherichia coli in Livestock and Farmers in Catalonia, Spain
by Marina Serras-Pujol, Noemí Párraga-Niño, Marian Navarro, Anna Vilamala, Emma Puigoriol, Elisenda Arqué, Judit Serra-Pladevall, Luisa Pedro-Botet and Esteban Reynaga
Antibiotics 2026, 15(7), 676; https://doi.org/10.3390/antibiotics15070676 - 9 Jul 2026
Abstract
Background and objectives: Extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae represent an increasing One Health concern because food-producing animals may act as reservoirs of antimicrobial-resistant bacteria with potential transmission to humans. Therefore, this study aimed to assess the prevalence and genomic characteristics of ESBL- [...] Read more.
Background and objectives: Extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae represent an increasing One Health concern because food-producing animals may act as reservoirs of antimicrobial-resistant bacteria with potential transmission to humans. Therefore, this study aimed to assess the prevalence and genomic characteristics of ESBL- and carbapenemase-producing Enterobacteriaceae in livestock and farmers, and to evaluate genomic overlap between animal and human ESBL-producing Escherichia coli to explore potential shared origins and interspecies transmission. Methods: We conducted a cross-sectional study in Osona (Catalonia, Spain), sampling livestock (swine, cattle, poultry, and horses) and farmers. ESBL-, AmpC-, and carbapenemase-producing Enterobacteriaceae were identified and characterized using whole genome sequencing (WGS). Genomic analyses included sequence typing (ST), serotyping, virulence-associated genes, antimicrobial resistance determinants, and plasmid replicon profiling. Results: A total of 945 animals were analysed. ESBL-producing Enterobacteriaceae were predominantly detected in swine, with 63.5% (127/200) of animals testing positive, including four ESBL + AmpC-producing isolates and two carbapenem-resistant Enterobacteriaceae. No ESBL-, AmpC- or carbapenemase-producing isolates were identified in cattle (0/360) or poultry (0/171), and a low prevalence was observed in horses (7.0%, 15/214). A total of 64 farm workers were analysed. ESBL-producing E. coli were detected in 46.7% (7/15) of swine farmers and 8.3% (2/24) of cattle farmers, while no ESBL-producing isolates were found among poultry farmers (0/8) or equine caretakers (0/17). A total of 162 isolates were analyzed by WGS, showing high genetic diversity. Among the 127 Escherichia coli isolates, the most prevalent were ST10 (18/127, 14.2%), followed by ST453 (7/127, 5.5%), ST515 (7/127, 5.5%), and ST10562 (7/127, 5.5%). Virulence-associated gene profiles were heterogeneous, although genes related to stress tolerance and intestinal colonization predominated among ESBL-producing E. coli isolates from swine, including terC (54/127, 42.5%), csgA (41/127, 32.3%), nlpI (41/127, 32.3%), and fimH (39/127, 30.7%). ESBL production among E. coli isolates from swine was primarily mediated by blaCTX-M genes (89/127, 70.1%), with additional contributions from blaSHV (34/127, 26.8%) and blaTEM (40/127, 31.5%). Among swine isolates, IncX1 (100/127, 78.7%), IncFIB(AP001918) (82/127, 64.6%), IncI1-I(Alpha) (69/127, 54.3%), and IncFII (54/127, 42.5%) were the most frequently detected plasmid replicons. Two carbapenem-resistant isolates carrying blaOXA-48 were identified in swine, including E. coli ST58 and K. oxytoca ST145, both associated with IncL plasmids. Conclusions: Swine appear to constitute the primary reservoir of ESBL-producing E. coli. The genomic relatedness observed between animal and human isolates supports shared exposure to a common ecological pool of multidrug-resistant bacteria. The identification of blaOXA-48-producing Enterobacterales associated with IncL plasmids further highlights the public health relevance of livestock-associated antimicrobial resistance. However, the cross-sectional design precludes inference of transmission pathways or transmission directionality. Longitudinal studies are needed to elucidate the dynamics of interspecies transmission. Full article
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14 pages, 3361 KB  
Article
Evolutionary Analysis Reveals a Single Amino Acid in the AAV Entry Receptor (AAVR) of Cats That Disrupts Binding of a Major Phylogenetic Group of AAVs
by Edward E. Large, Isaac Mensah, Godfred Kumi and Michael S. Chapman
Viruses 2026, 18(7), 744; https://doi.org/10.3390/v18070744 - 4 Jul 2026
Viewed by 316
Abstract
Adeno-associated virus (AAV) is a small ssDNA satellite virus that receives wide attention due to its popularity as a safe and effective gene therapy vector. The AAV cell entry receptor (AAVR) for most serotypes is a glycoprotein containing five polycystic kidney disease (PKD) [...] Read more.
Adeno-associated virus (AAV) is a small ssDNA satellite virus that receives wide attention due to its popularity as a safe and effective gene therapy vector. The AAV cell entry receptor (AAVR) for most serotypes is a glycoprotein containing five polycystic kidney disease (PKD) domains with which AAV interacts. AAV serotypes can be classified into three groups: those that interact primarily with PKD1, those whose interactions with PKD2 are stronger, and AAV4-like serotypes whose transduction is AAVR-independent. A phylogenetic analysis of AAVR and paralog KIAA0319 revealed AAVR amino acid variability in the region of PKD1 that is bound by AAV. We hypothesized that the substitution, in all cat-like animals, of a glutamate at a site that is an arginine (R353) in human AAVR may interfere with the binding of clade H AAVs that interact exclusively with PKD1. Analysis of PKD1 mutations, including ELISA, shows that an R353E substitution of glutamate for arginine affects the binding of the clade H AAVs that interact primarily with PKD1. Full article
(This article belongs to the Special Issue Advances in Parvovirus Research 2024)
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30 pages, 4998 KB  
Article
Epidemiological and Evolutionary Dynamics of Dengue Virus in Saudi Arabia: Insights from Three Decades of Molecular and Serological Surveillance
by Mohamed A. Farrag, Reem M. Aljowaie, Ibrahim M. Aziz, Rawan M. Alshalan, Abdulaziz Abdullah Almosa, Basel Mohammed Alnafjan and Najat A. Y. Marraiki
Int. J. Mol. Sci. 2026, 27(13), 6014; https://doi.org/10.3390/ijms27136014 - 4 Jul 2026
Viewed by 133
Abstract
Dengue fever represents a significant public health challenge in Saudi Arabia, yet comprehensive molecular characterization of circulating serotypes remains limited. This study combines epidemiological and phylogenetic analyses to understand dengue virus (DENV) dynamics in the Kingdom. A systematic review and meta-analysis of dengue [...] Read more.
Dengue fever represents a significant public health challenge in Saudi Arabia, yet comprehensive molecular characterization of circulating serotypes remains limited. This study combines epidemiological and phylogenetic analyses to understand dengue virus (DENV) dynamics in the Kingdom. A systematic review and meta-analysis of dengue epidemiological data from Saudi Arabia (1992–2026) was the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. All available DENV envelope (E) gene sequences from Saudi human cases (1992–2023) were retrieved from GenBank and Global Initiative on Sharing All Influenza Data (GISAID). Phylogenetic trees were constructed using maximum likelihood with 1000 bootstrap replicates and best-fit models. Selection pressure was analyzed using SLAC, FEL, FUBAR, and MEME methods, while glycosylation sites were predicted with NetNGlyc and NetOGlyc. The pooled seroprevalence from 25 studies (n = 32,393) was 40.71% (95% CI: 26.96–56.10%). DENV-2 predominated (80.25%), followed by DENV-1 and DENV-3, with DENV-4 remaining rare (0.42%). Males (67–78%) and adults aged 25–44 years were most affected. Phylogenetic analysis of 50 Saudi isolates showed DENV-1 strains clustered within American–African (1994) and Asian (2004–2011) genotypes, all DENV-2 within the Cosmopolitan genotype, and all DENV-3 within Genotype III (bootstrap support 99–100%). Selection pressure analysis indicated pervasive positive selection in DENV-2, episodic selection across serotypes, and strong purifying selection in the E gene. Several amino acid substitutions with potential functional importance were identified. No DENV-4 E gene sequences from Saudi Arabia are publicly available. Dengue in western Saudi Arabia is characterized by DENV-2 predominance, co-circulation of three serotypes, and multiple introductions. The absence of DENV-4 sequences highlights critical surveillance gaps. Sustained molecular surveillance, expanded genomic sequencing, and data sharing are essential for effective prevention and vaccine preparedness. Full article
(This article belongs to the Section Molecular Microbiology)
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25 pages, 4619 KB  
Article
Antimicrobial Resistance, Serotypes, Virulence Gene Profiles, and Molecular Characterization of Streptococcus suis Isolated from Healthy Pigs in Thailand
by Phirabhat Saengsawang, Pakpoom Tadee, Prapas Patchanee, Watcharapong Mitsuwan, Sumalee Boonmar, Hidenori Kabeya, Nattinee Kittiwan, Ravisa Warin and Ratchadaporn Boripun
Antibiotics 2026, 15(7), 660; https://doi.org/10.3390/antibiotics15070660 - 3 Jul 2026
Viewed by 275
Abstract
Streptococcus suis is an important cause of disease in pigs and an emerging source of severe human infection, with increasing concerns regarding antimicrobial resistance. This study assessed the occurrence and seroprevalence of S. suis in healthy pigs and characterized the antimicrobial susceptibility, serotypes, [...] Read more.
Streptococcus suis is an important cause of disease in pigs and an emerging source of severe human infection, with increasing concerns regarding antimicrobial resistance. This study assessed the occurrence and seroprevalence of S. suis in healthy pigs and characterized the antimicrobial susceptibility, serotypes, virulence associated genes, and genomic features of colonizing isolates. A total of 58 pigs (13 farm pigs and 45 abattoir pigs) were sampled. Among 176 presumptive isolates recovered by culture, 60 were confirmed as S. suis by polymerase chain reaction (PCR) and were subsequently analyzed. Antimicrobial susceptibility was determined by the disc diffusion method, selected resistance and virulence genes were detected by conventional PCR, and two representative isolates were subjected to whole-genome sequencing (WGS) and comparative genomic analyses. Seroprevalence was determined using an indirect ELISA detecting IgG antibodies against S. suis serotype 2 antigen. S. suis was confirmed in 60/176 presumptive isolates (34.1%), most frequently from nasal swabs and tonsils, whereas no blood isolates were detected. The seropositivity rate was 65.5%. High resistance rates were observed for ceftriaxone, ampicillin, cefepime, clindamycin, and tetracycline, and multidrug resistance was common. Tetracycline- and macrolide-associated resistance genes were frequently detected. Serotypes 2/1⁄2 predominated, whereas major classical invasive virulence genes were not detected, consistent with predominantly colonizing strains. Whole genome sequencing of two representative isolates confirmed species identity and revealed substantial genomic diversity, including a markedly larger genome in a tonsillar isolate, suggesting acquisition of accessory genetic elements. These findings demonstrate that healthy pigs can harbor genetically diverse and antimicrobial resistant S. suis, highlighting the importance of continued surveillance to support antimicrobial stewardship and reduce zoonotic risk. Full article
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10 pages, 3757 KB  
Article
Characterization of Aggregatibacter actinomycetemcomitans Transposon Mutants with Altered Biofilm Formation and Coaggregation Generated by Random Mutagenesis
by Maryam Safar, Maha Al-Sane, Hana Drobiova and Maribasappa Karched
Oral 2026, 6(4), 81; https://doi.org/10.3390/oral6040081 - 3 Jul 2026
Viewed by 132
Abstract
Background/Objectives: Aggregatibacter actinomycetemcomitans is an important periodontal pathogen whose biofilm formation and bacterial aggregation contribute to colonization and persistence within the oral cavity. This study aimed to generate random transposon mutants of A. actinomycetemcomitans and screen for alterations in biofilm- and aggregation-related phenotypes. [...] Read more.
Background/Objectives: Aggregatibacter actinomycetemcomitans is an important periodontal pathogen whose biofilm formation and bacterial aggregation contribute to colonization and persistence within the oral cavity. This study aimed to generate random transposon mutants of A. actinomycetemcomitans and screen for alterations in biofilm- and aggregation-related phenotypes. Methods: A transposon mutagenesis library was created in the serotype d strain SA269 using the EZ-Tn5 transposon system. Transformants were screened in vitro for biofilm formation, autoaggregation, and coaggregation with Fusobacterium nucleatum. Biofilm biomass was quantified using a standardized microtiter plate assay, while aggregation assays were performed by optical density measurements. Results: Among 44 transformants, 12 exhibited a markedly reduced ability to form biofilms compared with the wild-type strain, indicating that disruption of certain loci compromises surface adherence and biofilm biomass accumulation. Five representative mutants were selected for aggregation studies. Three mutants showed reduced autoaggregation, suggesting impaired intraspecies cell–cell interactions, whereas four mutants demonstrated enhanced coaggregation with F. nucleatum, reaching approximately 50% coaggregation after 120 min. These findings indicate that insertional inactivation of genes in A. actinomycetemcomitans can differentially affect biofilm formation, autoaggregation, and interspecies coaggregation. Conclusions: This preliminary study demonstrates the utility of random transposon mutagenesis for identifying mutants with altered adhesion- and biofilm-related phenotypes. Although the disrupted genes were not identified, the mutant library provides a foundation for future molecular characterization of genetic determinants involved in biofilm development and microbial community interactions. Full article
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22 pages, 2133 KB  
Systematic Review
Prevalence and Variability of Clinical Manifestations of Dengue in Peru: A Systematic Review and Meta-Analysis of Observational Studies
by Darwin A. León-Figueroa, Edwin Aguirre-Milachay, Dorothy Luisa Meléndez Morote, Miguel Villegas-Chiroque, Víctor J. Vera-Ponce, Oriana Rivera-Lozada and Mario J. Valladares-Garrido
Viruses 2026, 18(7), 732; https://doi.org/10.3390/v18070732 - 2 Jul 2026
Viewed by 446
Abstract
Dengue remains a major public health challenge in Peru, where recurrent outbreaks show marked variation in clinical presentation. This systematic review and meta-analysis synthesized available evidence to quantify the frequency and variability of dengue manifestations in Peruvian patients and to identify clinically relevant [...] Read more.
Dengue remains a major public health challenge in Peru, where recurrent outbreaks show marked variation in clinical presentation. This systematic review and meta-analysis synthesized available evidence to quantify the frequency and variability of dengue manifestations in Peruvian patients and to identify clinically relevant patterns for early recognition. We systematically searched PubMed, Scopus, Embase, Web of Science, ScienceDirect, Google Scholar, Virtual Health Library, and Scielo for observational studies published between 1993 and January 2025. Two reviewers independently selected studies, extracted data, and assessed methodological quality. Pooled prevalence estimates with 95% confidence intervals (CIs) were calculated using random-effects models. Twenty-eight studies including 4418 patients were analyzed. The most frequent manifestations were fever (95%; 95% CI: 90–98%), headache (86%; 95% CI: 80–91%), malaise (82%; 95% CI: 71–91%), myalgia (69%; 95% CI: 58–79%), arthralgia (64%; 95% CI: 56–73%), and retro-orbital pain (56%; 95% CI: 47–66%). Gastrointestinal symptoms were also common, including nausea/vomiting (40%; 95% CI: 33–48%) and abdominal pain (33%; 95% CI: 21–45%), whereas hemorrhagic and severe manifestations were less frequent, such as hematemesis (6%; 95% CI: 2–10%), petechiae (6%; 95% CI: 2–10%), jaundice (3%; 95% CI: 1–7%), and melena (1%; 95% CI: 0–6%). Heterogeneity was high across most outcomes (I2 generally >90%), suggesting substantial between-study variability. This heterogeneity is likely related to differences in geographic region, outbreak period, circulating serotypes, diagnostic methods, and case severity definitions across studies. These findings highlight a consistent core symptom profile of dengue in Peru while also demonstrating important clinical variability. This information may support earlier clinical suspicion, triage, and surveillance in endemic settings. However, pooled estimates should be interpreted cautiously given the high heterogeneity, moderate methodological rigor of included studies, and lack of individual-level data. Future analyses stratified by region, study period, and diagnostic method are needed to generate more clinically precise estimates. Full article
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22 pages, 400 KB  
Review
The Convergence of Antimicrobial Resistance and Virulence in Streptococcus pneumoniae: A Molecular and Clinical Perspective
by Jorge Almeida, Kenichi Takeshita, Alejandra Ramirez-Villalva, Ana G. Jop Vidal, Pedro Alejandro Fong-Coronado, Javian E. Ervin, Gloria M. Castañeda-Ruelas and Jorge E. Vidal
Microorganisms 2026, 14(7), 1451; https://doi.org/10.3390/microorganisms14071451 - 30 Jun 2026
Viewed by 196
Abstract
Antimicrobial resistance (AMR) and virulence have traditionally been viewed as competing traits in bacterial evolution due to fitness costs. However, Streptococcus pneumoniae has emerged as a paradigm of successful coevolution, with multidrug-resistant clones simultaneously maintaining or enhancing pathogenic potential. This review examines the [...] Read more.
Antimicrobial resistance (AMR) and virulence have traditionally been viewed as competing traits in bacterial evolution due to fitness costs. However, Streptococcus pneumoniae has emerged as a paradigm of successful coevolution, with multidrug-resistant clones simultaneously maintaining or enhancing pathogenic potential. This review examines the molecular mechanisms, epidemiological patterns, and clinical consequences of the convergence between AMR and virulence in Streptococcus pneumoniae. Resistance to β-lactams is driven by mosaic penicillin-binding protein genes (pbp1a, pbp2b, pbp2x), while macrolide resistance is mediated primarily by the erm(B) gene (MLS phenotype) and mef(A/E)–msr(D) genes encoding an efflux system. These determinants are frequently co-localized on integrative and conjugative elements, ICEs, (e.g., Tn916 family) within successful clonal complexes such as CC271/320 and lineages including ST320 and GPSC10. Contrary to the classical fitness cost hypothesis, compensatory epistasis, capsular recombination, metabolic adaptations, and intra-serotype phenotypic variation enable certain clones to combine high-level resistance to β-lactams, macrolides, and tetracyclines with enhanced colonization, biofilm formation, immune evasion, and invasive capacity. Post-pneumococcal conjugate vaccine (PCV) surveillance reveals the persistence and expansion of these high-risk lineages, contributing to treatment-refractory invasive pneumococcal disease (IPD), increased morbidity, and mortality. Although PCVs have reduced vaccine-type resistant strains in some settings, serotype replacement and emerging metabolic genotypes continue to drive adaptation. This review highlights the need for integrated genomic surveillance, novel therapeutics (e.g., omadacycline, lefamulin, endolysins), monoclonal antibodies, and next-generation vaccines targeting both resistance and conserved virulence determinants. A multifaceted strategy combining antimicrobial stewardship, strengthened surveillance, and innovative interventions is essential to curb the evolving threat of resistant and virulent S. pneumoniae. Full article
(This article belongs to the Special Issue Latest Review Papers in Antimicrobial Agents and Resistance 2026)
23 pages, 6274 KB  
Article
FBP1 Is Associated with Attenuated Mitochondrial Injury in Renal Tubular Epithelial Cells of Diabetic Kidney Disease via Modulation of Lactate Metabolism
by Siyi Rao, Mengjie Weng, Yongjie Zhuo, Jiaqun Lin, Danyu You, Jiong Cui, Yi Chen, Xiaohong Zhang and Jianxin Wan
Int. J. Mol. Sci. 2026, 27(13), 5906; https://doi.org/10.3390/ijms27135906 - 30 Jun 2026
Viewed by 135
Abstract
The role of gluconeogenesis in kidney disease has increasingly drawn attention. Fructose-1,6-bisphosphatase 1 (FBP1) is a key rate-limiting enzyme in gluconeogenesis that suppresses glycolysis and reduces lactate production. In this study, we first analyzed public transcriptomic datasets of diabetic kidney disease (DKD) and [...] Read more.
The role of gluconeogenesis in kidney disease has increasingly drawn attention. Fructose-1,6-bisphosphatase 1 (FBP1) is a key rate-limiting enzyme in gluconeogenesis that suppresses glycolysis and reduces lactate production. In this study, we first analyzed public transcriptomic datasets of diabetic kidney disease (DKD) and validated the findings in 24-week-old BKS-db mice and in high-glucose-induced human renal tubular epithelial (HK-2) cells. We further constructed tubular-specific FBP1 overexpression/knockdown mouse models via adeno-associated virus serotype 9 (AAV-9) and combined pharmacological inhibition of lactate dehydrogenase B (LDHB) to dissect the underlying mechanism. Analysis of public clinical transcriptomic datasets showed that renal tubular FBP1 expression was positively correlated with estimated glomerular filtration rate (eGFR). In vivo, tubular-specific FBP1 overexpression in BKS-db mice reduced 24-h urinary protein and decreased renal lactate accumulation (p < 0.05) compared with diabetic controls. In vitro, high glucose-induced lactate elevation in HK-2 cells was reversed by FBP1 overexpression, while co-treatment with an LDHB inhibitor abolished this protective effect. Our findings suggest that FBP1 represents a potential experimental therapeutic target associated with alleviation of renal lactic acid accumulation and mitochondrial injury in preclinical DKD models. Full article
(This article belongs to the Special Issue Advances in Cell Metabolism in Endocrine Diseases)
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22 pages, 2638 KB  
Article
Antimicrobial Resistance and Comparative Genome Analysis of High-Risk Escherichia coli Strains Isolated from Ventilator-Associated Pneumonia Cases in Egyptian ICUs
by Shaymaa Yusuf, Mona H. Abdel-Rahim, Omnia El-Badawy, Safy Hadiya, Amany G. Thabit, Radwa Abdelwahab, Heba A. Hammad, Shabaan H. Ahmed, Mohamed Samir, Xiaoqiang Liu, Douglas F. Browning and Sherine A. Aly
Microorganisms 2026, 14(7), 1438; https://doi.org/10.3390/microorganisms14071438 - 30 Jun 2026
Viewed by 593
Abstract
Escherichia coli is increasingly recognised as an important cause of ventilator-associated pneumonia (VAP), particularly in intensive care units (ICUs) with high antimicrobial selective pressure. Unlike classical respiratory pathogens, ICU-associated E. coli often originates from the patient’s intestinal microbiota and harbours a complex mobilome [...] Read more.
Escherichia coli is increasingly recognised as an important cause of ventilator-associated pneumonia (VAP), particularly in intensive care units (ICUs) with high antimicrobial selective pressure. Unlike classical respiratory pathogens, ICU-associated E. coli often originates from the patient’s intestinal microbiota and harbours a complex mobilome enriched with antimicrobial resistance determinants. In this study, a total of 200 nosocomial endotracheal aspirate samples were aseptically collected from patients admitted to the Respiratory ICU at Assiut University hospital. Antimicrobial susceptibility testing, serotyping and screening for various virulence and antimicrobial resistance genes (e.g., extended-spectrum β-lactamase (ESBL) and carbapenems genes) were carried out. In total, E. coli isolates were recovered from 54/200 (27%) endotracheal aspirates, with a high prevalence of multidrug resistance (MDR) observed (74.1%). Resistance to β-lactams was common with phenotypic evidence suggestive of ESBL production detected in 64.8% of isolates. Genome sequencing of three MDR E. coli isolates confirmed that they carried multiple antimicrobial resistance genes, which included ESBL genes (e.g., blaCTX-M-15 and blaTEM-1B). Each strain was also found to be high-risk extraintestinal pathogenic E. coli (ExPEC) clones, belonging to either sequence type ST131 or ST405. These findings support an endogenous infection model for VAP, whereby ICU selective pressure favours highly mobile, multidrug-resistant E. coli lineages adapted for extraintestinal survival. The high production of ESBLs and the prevalence of carbapenemase genes highlight the urgent need for molecular surveillance and antimicrobial stewardship strategies for the control of such high-priority pathogens in this part of the world. Full article
(This article belongs to the Special Issue Bacterial Infection and Antimicrobial Resistance)
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12 pages, 289 KB  
Article
Invasive Bacterial Meningitis in Mali: Molecular Detection and Serotype Distribution of Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis
by Fatoumata Kontao, Ibrehima Guindo, Assiya Elkettani, Cheickna Hamallah Dicko, Brehima Zerbo, Hawa Sanogo, Néhémie Nzoyikorea, Klema Marcel Koné, Alou Sanogo, Demba Koita, Mahamadou Abdou, Zahra Aadam, Jalila El Bakkouri, Idrissa Diawara and Ahmed Aziz Bousfiha
Microbiol. Res. 2026, 17(7), 125; https://doi.org/10.3390/microbiolres17070125 - 30 Jun 2026
Viewed by 231
Abstract
Invasive bacterial infections caused by Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis remain a major public health concern. This study aimed to perform the molecular characterization of bacterial strains responsible for meningitis in patients of all ages who met the World [...] Read more.
Invasive bacterial infections caused by Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis remain a major public health concern. This study aimed to perform the molecular characterization of bacterial strains responsible for meningitis in patients of all ages who met the World Health Organization case definition for meningitis and had cerebrospinal fluid samples collected between January 2021 and December 2022 at the Clinical Bacteriology Laboratory of the National Public Health Institute of Mali. We conducted a surveillance-based observational study using national surveillance data collected between January 2021 and December 2022. Data were collected continuously and in real time throughout the study. The analysis was cross-sectional and descriptive. Data were obtained from samples received at the laboratory, accompanied by individual clinical notification forms. For each sample, demographic data and additional clinical information, including vaccination status, were collected. Infection was diagnosed by isolating invasive strains through culture, confirmed by real-time triplex PCR, and positive cases were further characterized by real-time triplex PCR for serotyping. Overall, 103 infections were confirmed among the 1000 samples received, corresponding to a positivity rate of 10.3%. S. pneumoniae predominated with 62%, followed by H. influenzae type b with 36% and N. meningitidis serogroup X with 2%. The identified serotypes of pneumococcus were predominantly not covered by existing vaccines, particularly serotype 23A (38.30%), while others, including serotypes 1 (17.02%) and 3 (10.63%), are included in the PCV13 vaccine. The distribution of cases by age and gender shows a predominance of males, accounting for 60.2% of cases (62/103). The 0–5 age group is by far the largest, accounting for 76.7% of cases (79/103), with males representing 58. 22% (46 cases). These findings highlight the importance and the need for continuous monitoring surveillance of circulating strains and strengthening vaccination efforts to improve prevention. Full article
(This article belongs to the Section Medical and Veterinary Microbiology)
17 pages, 4670 KB  
Article
Identification of Ligand-Responsive RNA G-Quadruplexes in the 3′ UTRs of Dengue Virus Serotypes
by Mohammad Jafar Sheikhi, Ayuka Onuma, Yutaro Imachi, Akira Shiraishi, Shoko Mori, Kohtaro Sugahara, Daisuke Miyoshi, Yue Ma, Takayuki Hishiki, Kazuo Nagasawa and Masayuki Tera
Biomolecules 2026, 16(7), 946; https://doi.org/10.3390/biom16070946 - 25 Jun 2026
Viewed by 413
Abstract
Dengue virus (DENV), which comprises four antigenically distinct serotypes (DENV-1 to DENV-4), remains a major global public health concern and continues to expand geographically; however, the structural features of the viral genome remain incompletely understood. Although G-quadruplexes (G4s) have previously been reported in [...] Read more.
Dengue virus (DENV), which comprises four antigenically distinct serotypes (DENV-1 to DENV-4), remains a major global public health concern and continues to expand geographically; however, the structural features of the viral genome remain incompletely understood. Although G-quadruplexes (G4s) have previously been reported in coding regions of DENV, their presence within the 3′ untranslated region (3′ UTR) has not been experimentally characterized. Here, we focused on selected guanine-rich motifs within the 3′ UTRs of DENV-1 to DENV-4 and investigated their ability to form RNA G4 structures. Using bioinformatic analysis, we identified comparable G-rich regions in the 3′ UTRs of the four serotypes, with serotype-dependent differences in conservation. We then examined the propensity of the selected putative quadruplex-forming sequences (PQSs) to adopt G4 structures using circular dichroism spectroscopy, UV melting analysis, 1H NMR spectroscopy, ligand-binding analysis, and reverse transcription stop (RT-stop) assays. Our results provided in vitro evidence that the 3′ UTR oligonucleotides from DENV-1 to DENV-4 are capable of forming ligand-responsive G4 structures, with serotype-dependent differences in conservation, stability, and conformational homogeneity. In addition, reverse transcription (RT)-stop analysis revealed ligand-dependent arrest at the corresponding PQS sites in the presence of the G4 ligand 6OTD, which stabilizes G4 structures. These findings suggest the DENV 3′ UTR as an additional source of ligand-responsive RNA G4-forming elements and support future studies on their possible roles in DENV RNA regulation. Full article
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9 pages, 234 KB  
Case Report
Fulminant Hepatitis Due to Enterovirus E25 Systemic Infection in a Pediatric Patient
by Silvia Garattini, Lorenza Romani, Luana Coltella, Tommaso Alterio, Stefania Mercadante, Costanza Tripiciano, Maia De Luca, Sara Chiurchiù, Laura Cursi, Francesca Ippolita Calò Carducci, Cristina Russo, Carlo Federico Perno, Alberto Villani, Andrea Pietrobattista, Stefania Bernardi and Laura Lancella
Pathogens 2026, 15(7), 666; https://doi.org/10.3390/pathogens15070666 - 25 Jun 2026
Viewed by 217
Abstract
Pediatric acute liver failure (PALF) is a rare but life-threatening condition characterized by rapid clinical deterioration and high mortality. Viral infections represent a major etiology of PALF, although the causative agent remains unidentified in a substantial proportion of cases. Human Enteroviruses (EVs) are [...] Read more.
Pediatric acute liver failure (PALF) is a rare but life-threatening condition characterized by rapid clinical deterioration and high mortality. Viral infections represent a major etiology of PALF, although the causative agent remains unidentified in a substantial proportion of cases. Human Enteroviruses (EVs) are typically associated with self-limiting illnesses; however, they may rarely cause severe systemic disease, including fulminant hepatitis, particularly in neonates and young children. We describe the case of a 4-year-old previously healthy male who presented with acute fulminant hepatitis secondary to systemic Echovirus 25 (E25) infection, with concomitant Epstein–Barr virus (EBV) co-infection of recent onset. The diagnosis was established through multiplex PCR on cerebrospinal fluid, blood, stool, and nasopharyngeal aspirate, with serotype confirmation by the Italian National Institute of Health. The patient required intensive supportive care including therapeutic plasma exchange (TPE), continuous kidney replacement therapy (CKRT), and intravenous immunoglobulins (IGIV). Despite initial clinical deterioration and placement on the liver transplant list, the patient achieved complete hepatic recovery and was discharged after fourteen days of hospitalization without requiring transplantation. This case highlights the importance of prompt virological workup including enterovirus PCR in children presenting with acute liver failure of undetermined etiology and supports the use of extracorporeal therapies as a bridge to recovery. Full article
(This article belongs to the Section Viral Pathogens)
21 pages, 988 KB  
Technical Note
Rapid Detection and Quantification of Salmonella in Chicken Carcass Rinse Using Point-of-Use Filtration-Isothermal Diagnostic Test
by Anitha Sathish Kumar, Rajeev Shrestha, Loïc Deblais and Gireesh Rajashekara
Poultry 2026, 5(4), 45; https://doi.org/10.3390/poultry5040045 - 24 Jun 2026
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Abstract
Poultry meat producers face pressure to ensure both safety and efficiency as food systems expand in scale and complexity. However, existing diagnostic tools often force a trade-off between speed, accuracy, and cost, leaving limited options for real-time, on-site pathogen detection. This study evaluated [...] Read more.
Poultry meat producers face pressure to ensure both safety and efficiency as food systems expand in scale and complexity. However, existing diagnostic tools often force a trade-off between speed, accuracy, and cost, leaving limited options for real-time, on-site pathogen detection. This study evaluated the performance of a novel point-of-use rapid diagnostic tool combining filtration and lyophilized isothermal amplification for detecting and semi-quantifying Salmonella in chicken carcass rinse samples. Targeted DNA (invA) was amplified at 65 °C for 60 min, and fluorescence was measured over time. Salmonella was successfully detected in all spiked samples (1.0- to 7.5-log10 CFU/mL; n = 57). An association was observed between the isothermal detection speed data and Salmonella load in the sample (r2 = 0.90; p < 0.001), particularly at concentrations ≥ 1.5-log10 CFU/mL. Repeatable data were obtained across three operators and samples of multiple origins (Georgia, Illinois, Nebraska; 0.16-log10; 95%CI: 0.11–0.21). Importantly, complete inclusivity for all tested Salmonella serotypes (n = 46/46) and exclusivity against non-target organisms (n = 0/37) was validated in this study. In conclusion, the technological combination of filtration and lyophilized isothermal amplification enabled the point-of-use detection and quantification of Salmonella in chicken carcass samples within 60 min and minimal lab infrastructure. Full article
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20 pages, 7105 KB  
Article
Dengue Virus NS5 Target Discovery: A Comprehensive in Silico Exploration of Novel Druggable Sites for Pan-Serotype Antiviral Design
by João Trigueiro-Louro, Vanessa Correia, Inara dos Santos Ali, Bulbul Ahmed and Helena Rebelo-de-Andrade
Int. J. Mol. Sci. 2026, 27(12), 5639; https://doi.org/10.3390/ijms27125639 - 22 Jun 2026
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Abstract
Dengue is the most common vector-borne viral disease worldwide, posing an increasing global health threat. Despite its high burden, no approved antiviral treatments or widely applicable vaccines exist, and patient management remains limited to supportive care, underscoring the urgent need for antiviral development. [...] Read more.
Dengue is the most common vector-borne viral disease worldwide, posing an increasing global health threat. Despite its high burden, no approved antiviral treatments or widely applicable vaccines exist, and patient management remains limited to supportive care, underscoring the urgent need for antiviral development. The NS5 protein is a prime antiviral target, owing to its crucial role in viral replication, high conservation across dengue virus (DENV) serotypes and lack of a human orthologue. We conducted a comprehensive sequence-to-structure analysis to identify conserved druggable regions within NS5, integrating large-scale sequence analysis with structural characterization across all four DENV serotypes. We identified four highly promising Consensus Druggable Pockets within the NS5 dimer—CDP1d, CDP3d, CDP5d and CDP12d—that overlap functionally critical regions, alongside 149 new potential hot spot residues. Domain-specific analysis revealed that MTase offers more densely conserved targets, whereas RdRp provides broader druggable surfaces, revealing complementary features for pharmacological modulation. Several identified pockets spatially overlap known inhibitor binding sites, and preliminary docking analyses support their capacity to accommodate small molecules, reinforcing their therapeutic relevance as candidate targets. Collectively, these findings provide a robust framework for the rational design of pan-serotype anti-DENV NS5 antivirals with an enhanced barrier to resistance. Full article
(This article belongs to the Section Molecular Informatics)
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21 pages, 3088 KB  
Article
An Efficient TetR/TetO-Integrated Packaging System for Fowl Adenovirus 4 Vector Carrying Toxic Transgene
by Qian-Wen Ma, Zhi Li, Zhi-Chao Zhang, Xiao-Juan Guo, Xiao-Hui Zou, Tao Hung and Zhuo-Zhuang Lu
Methods Protoc. 2026, 9(3), 100; https://doi.org/10.3390/mps9030100 - 22 Jun 2026
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Abstract
Adenoviral vectors are widely used for gene therapy and vaccine development. To circumvent pre-existing immunity against commonly used human adenovirus type 5, vectors based on rare human serotype or animal adenoviruses have attracted increasing interest. Previously, we constructed vectors based on fowl adenovirus [...] Read more.
Adenoviral vectors are widely used for gene therapy and vaccine development. To circumvent pre-existing immunity against commonly used human adenovirus type 5, vectors based on rare human serotype or animal adenoviruses have attracted increasing interest. Previously, we constructed vectors based on fowl adenovirus 4 (FAdV-4) and replaced the knob of FAdV-4 fiber2 with that of FAdV-1 fiber1 to generate FAdV4-CF1K vectors with enhanced transduction efficiency in human cells. In this study, we aimed to modify the packaging system to efficiently produce FAdV-4 vectors carrying transgenes toxic to viral replication. Chicken LMH cells failed to form colonies at low seeding densities. We collected used medium from LMH cell cultures and used it as a supplement to adapt LMH cells, generating the colony-competent subclone LMH-C3532. A lentiviral vector encoding a codon-optimized tetracycline repressor (tetR) was transduced into LMH-C3532 to establish a tetR-integrated cell line, LMH-tetR24. An adenoviral plasmid, pKFAV4-CF1K-CtG, was constructed in which a tetracycline operator (tetO)-bearing CMV promoter controlled GFP expression. The SwaI-flanked GFP in this plasmid was replaced with the HA gene from an H5N1 influenza virus to generate pKFAV4-CF1K-CtHA. Linearized adenoviral plasmids were transfected into LMH-tetR24 cells, and recombinant FAdV4-CF1K-CtG and FAdV4-CF1K-CtHA viruses were successfully rescued, amplified, and purified. When infected with FAdV4-CF1K-CtG at various multiplicities of infection (MOI), the progeny virus yield from LMH-tetR24 cells was 4–10 times higher than that from LMH-C3532 cells. For FAdV4-CF1K-CtHA, the yield difference between the two cell lines was even more pronounced, reaching 3–4 orders of magnitude. Overexpression of HA in LMH-C3532 cells negatively affected FAdV4-CF1K-CtHA replication, resulting in smaller and fewer plaques. In conclusion, by separately integrating tetR into packaging cells and TetO into the adenoviral plasmid, we established a system that can be routinely used to package FAdV-4 vectors. Notably, this system facilitates the propagation of FAdV-4 vectors carrying toxic transgenes. Full article
(This article belongs to the Section Molecular and Cellular Biology)
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