1. Diversity of ESBL-producing E. coli in various water and sediment typesLeon Marič, Maja Rupnik, Sandra Janežič, 2025, izvirni znanstveni članek Povzetek: Antimicrobial resistance is a major global health threat, and aquatic ecosystems serve as critical interfaces between human activity and the environment, providing reservoirs and pathways for the spread of resistant bacteria. In this study, we investigated the prevalence and diversity of ESBL-producing Escherichia coli across multiple aquatic environments in Slovenia by analysing water, sediment, and wastewater treatment plant (WWTP) influent samples collected between June 2023 and April 2024. ESBL-producing E. coli was detected in 93% of WWTP influents, 61% of water, and 35% of sediment samples. From 315 positive samples, 564 isolates were subjected to whole genome sequencing. In total, 134 MLST-sequence types (STs) were identified, with globally prevalent lineages (ST131, ST38, ST10, ST69, ST1193) occurring across regions and sample types. Clonally related isolates occurred in geographically distant sites, and persistent strains were observed over time, suggesting both local persistence and broader dissemination. Fourteen distinct ESBL genes were detected, predominantly plasmid-encoded blaCTX-M-15. Water samples captured the greatest ST diversity, whereas sediment and WWTP influents provided complementary insights. Combining sample types improved detection of overall diversity, with water and sediment or WWTP samples providing the most comprehensive overview. Our findings demonstrate widespread and dynamic dissemination of ESBL-producing E. coli in Slovenian aquatic environments and emphasize the value of integrated sampling strategies for effective surveillance.
Ključne besede: E. coli, ESBL, sediment, water
Objavljeno v DiRROS: 17.12.2025; Ogledov: 129; Prenosov: 70
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2. Sustained circulation of enterovirus D68 in Europe in 2023 and the continued evolution of enterovirus D68 B3-lineages associated with distinct amino acid substitutions in VP1 proteinAurora Hirvonen, Caroline K. Johannesen, Peter Simmonds, Thea K Fischer, Kimberley Benschop, 2025, izvirni znanstveni članek Povzetek: Background Enterovirus D68 (EV-D68) causes respiratory disease ranging from mild to severe and in rare cases a paralytic syndrome, called acute flaccid myelitis (AFM). Since the global EV-D68 outbreak in 2014, the virus has mainly circulated in biennial epidemic cycles with peaks detected during even years. However, following the COVID-19 pandemic, the seasonal pattern of EV-D68 has been characterized by large yearly upsurges. Here, we describe the circulation of EV-D68 in Europe in 2023 and track its genetic evolution. Study design Data was compiled from members of the European Non-Polio Network (ENPEN). This included monthly data on the total number of EV samples tested, EV positive samples, EV-D68 positive samples and cases, and other EV positive samples detected in 2023. Information on sample types and surveillance system was recorded. Sequence data from the VP1 gene was used for phylogenetic and amino acid sequence analysis. Results EV was detected in 13,585 out of 203,622 diagnostic samples tested (6.7 %), of which 402 (3.0 %) were determined as EV-D68, representing 386 cases. EV-D68 infections peaked in October 2023 (136/386; 35.2 %). 267/386 (69.2 %) of EV-D68 cases were captured through clinical EV surveillance, almost all of which (202/204 of positive samples with sample type information) were detected in respiratory specimens. Phylogenetic analysis performed on 99 VP1 sequences revealed a distinct B3-derived lineage with a previously undescribed residue change, D554E, in Europe. Conclusions The study documents sustained circulation of EV-D68 in Europe in 2023, the evolution of B3-derived lineages, and appearance of previously undescribed amino acid substitutions in Europe. This stresses the need for continuous EV-D68 surveillance and harmonization of EV-D68 detection practices towards better data comparability across countries.
Ključne besede: Enterovirus D68 (EV-D68), Europe, Epidemiology, B3-derived, lineages, Surveillance
Objavljeno v DiRROS: 27.06.2025; Ogledov: 555; Prenosov: 358
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3. Limited clonality but widespread plasmid sharing of ESBL-producing E. coli between humans and the environment of northeastern SloveniaLeon Marič, Sandra Janežič, Maja Rupnik, 2025, izvirni znanstveni članek Povzetek: Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is a critical antimicrobial-resistant pathogen. While well-studied in humans and animals, its presence in the environment remains underexplored. This study analyses the genotypes and plasmid composition of ESBL-producing E. coli from human and environmental sources in Northeastern Slovenia. Freshwater and sediment samples were collected bimonthly during one year at ten sites, including rivers, lakes, and wastewater treatment plant (WWTP) influents. Human isolates were collected during the same period and geographic area. Whole-genome sequencing and bioinformatic analyses were conducted to evaluate genetic relatedness, antimicrobial resistance genes, and plasmid composition. Among 414 sequenced isolates (230 human, 184 environmental), 108 multilocus sequence types (MLST-ST) were identified, with 20 STs shared between sources. Core-genome MLST (cgMLST) revealed 59 clonal clusters, six of which included both human and environmental isolates. The dominant ESBL gene was blaCTX−M-15 (59 % of all ESBL isolates), and 54 % of all ESBL isolates carried ESBL genes on plasmids. Plasmid cluster AA474, found across different sources, STs, and locations, was linked to multiple ESBL genes, suggesting a key role in resistance dissemination. Despite shared STs, ESBL genes, and plasmids between humans and the environment, cgMLST analysis indicated limited clonal spread. This suggest that transmission between humans and the environment remains restricted and is more often linked to spread of plasmids than of strains.
Ključne besede: one health, environment, water, sediment, epidemiology, plasmids, ST1193
Objavljeno v DiRROS: 27.06.2025; Ogledov: 573; Prenosov: 456
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4. Epidemiological and clinical insights into enterovirus circulation in Europe, 2018 - 2023 : a multi-center retrospective surveillance studySten de Schrijver, Emiel Vanhulle, Anne Ingenbleek, Leonidas Alexakis, 2025, izvirni znanstveni članek Povzetek: Background Enteroviruses (EV) cause yearly outbreaks with severe infections, particularly in young children. This study investigates EV circulation, age, and clinical presentations in Europe from 2018 to 2023. Methods Aggregated data were requested from the European Centre for Disease Prevention and Control National Focal Points for Surveillance and European Non-Polio Enterovirus Network. Data included detection month, specimen type, age group, and clinical presentation for the 10 most commonly reported EV types per year. Results Twenty-eight institutions (16 countries) reported 563 654 EV tests during the study period with 33 265 (5.9%) EV positive. Forty-two types were identified (n = 11 605 cases) with echovirus 30 (E30), coxsackievirus A6 (CVA6), EV-D68, E9, E11, CVB5, E18, CVB4, EV-A71, and E6 most frequently reported. E30 declined after 2018/2019, while CVA6, CVB5, E9, E11, and EV-D68 were prevalent both before and after the coronavirus disease 2019 (COVID-19) pandemic, and CVB4 and E18 were prevalent after the pandemic. A shift in seasons (summer to fall) and specimen positivity (feces to respiratory) was observed. Neurological signs predominated among EV-A71, CVB4, CVB5, E6, E9, E11, E18, and E30 (30%–72%). CVB4, CVB5, E9, E11, and E18 were frequently reported among neonates (18%–32%). CVA6 was frequently associated with hand, foot and mouth disease, and EV-D68 with respiratory infections. Paralysis was reported among 22 infections, associated with 10 nonpolio types. Conclusions This study emphasizes the widespread circulation and severity of EV infections in Europe, as well as the (re)emergence of specific types postpandemic. Our findings highlight the need for continuous EV surveillance to monitor variation in circulation, age, and clinical presentations, including paralysis among nonpolio EV infections.
Ključne besede: enterovirus, laboratory detection, surveillance, Europe, epidemiology
Objavljeno v DiRROS: 27.06.2025; Ogledov: 501; Prenosov: 277
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5. Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophagesNejc Stopnišek, Stina Hedžet, Tomaž Accetto, Maja Rupnik, 2025, izvirni znanstveni članek Povzetek: Background Phages are critical components of the gut microbiome, influencing bacterial composition and function as predators, parasites, and modulators of bacterial phenotypes. Prophages, integrated forms of these phages, are prevalent in many bacterial genomes and play a role in bacterial adaptation and evolution. However, the diversity and stability of prophages within gut commensals, particularly in the genera Bacteroides and Phocaeicola, remain underexplored. This study aims to screen and characterize prophages in these genera, providing insights into their diversity, host range, and temporal dynamics in the human gut. Results Using a combination of three bioinformatic tools—Cenote-Taker 3, Vibrant, and PHASTER—we conducted a comprehensive analysis of prophages in Bacteroides and Phocaeicola. Cenote-Taker 3 identified the most diverse set of prophages, with significant overlaps observed between the tools. After clustering high-quality prophages, we identified 22 unique viral operational taxonomic units (vOTUs). Notably, comparisons between prophages identified in isolated bacterial genomes, metaviromes, and large public gut virome databases revealed a broader host range than initially observed in single isolates. Certain prophages were consistent across time points and individuals, suggesting temporal stability. All identified prophages belonged to the Caudoviricetes class and contained genes related to antibiotic resistance, toxin production, and metabolic processes. Conclusions The combined use of multiple prophage detection tools allowed for a more comprehensive assessment of prophage diversity in Bacteroides and Phocaeicola. The identified prophages were not only prevalent but also exhibited broad host ranges and temporal stability. The presence of antibiotic resistance and toxin genes suggests that these prophages may significantly influence bacterial community structure and function in the gut, with potential implications for human health. These findings highlight the importance of using diverse detection tools to accurately assess prophage diversity and dynamics.
Ključne besede: prophage detection, Bacteroides, Phocaeicola, gut microbiome, prophage diversity, Caudoviricetes, antibiotic resistance, phage-bacteria interactions, temporal stability
Objavljeno v DiRROS: 06.03.2025; Ogledov: 843; Prenosov: 643
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