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View article: Diversity of ESBL-producing E. coli in various water and sediment types
Diversity of ESBL-producing E. coli in various water and sediment types Open
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…
View article: MicrobiomePrime: A primer pair selection tool for microbial source tracking validated on a comprehensive collection of animal gut and fecal waste microbiomes
MicrobiomePrime: A primer pair selection tool for microbial source tracking validated on a comprehensive collection of animal gut and fecal waste microbiomes Open
Microbial source tracking (MST) enables identification of fecal contamination sources in water, providing crucial support for water quality management and public health protection. PCR-based detection of host-associated markers remains a c…
View article: High prevalence and clonality of Clostridioides difficile isolates from cryptic clades in household composters and small mammals
High prevalence and clonality of Clostridioides difficile isolates from cryptic clades in household composters and small mammals Open
While our study could not establish the exact direction of C. difficile transmission between compost and mice, it highlights the role of small mammals within the One Health framework of C. difficile transmission pathways.
View article: Longitudinal dynamics of ethanol-resistant microbes and sporulation in the human gut
Longitudinal dynamics of ethanol-resistant microbes and sporulation in the human gut Open
Background A considerable proportion of human gut bacteria use some form of dormancy to survive unfavorable conditions such as oxygen exposure, antibiotic treatment, and inflammation. Dormancy strategies enable persistence, allow recoloniz…
View article: MicrobiomePrime: A primer pair selection tool for microbial source tracking validated on a comprehensive collection of animal gut and fecal waste microbiomes
MicrobiomePrime: A primer pair selection tool for microbial source tracking validated on a comprehensive collection of animal gut and fecal waste microbiomes Open
Identifying primer pairs for use in microbial source tracking (MST) can be challenging. The primer pairs must amplify markers with high sensitivity and specificity for a particular microbiota source, while factors such as melting temperatu…
View article: Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages
Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages Open
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 a…
View article: Limited clonality but widespread plasmid sharing of ESBL-producing E. coli between humans and the environment of northeastern Slovenia
Limited clonality but widespread plasmid sharing of ESBL-producing E. coli between humans and the environment of northeastern Slovenia Open
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 gen…
View article: Distribution of <i>Clostridioides difficile</i> ribotypes and sequence types across humans, animals and food in 13 European countries
Distribution of <i>Clostridioides difficile</i> ribotypes and sequence types across humans, animals and food in 13 European countries Open
Clostridioides difficile is a One Health pathogen found in humans, animals, and the environment, with food representing a potential transmission route. One Health studies are often limited to a single country or selected reservoirs and rib…
View article: Effects of Limosilactobacillus reuteri DSM 17938 in neonates exposed to antibiotics: a randomised controlled trial
Effects of Limosilactobacillus reuteri DSM 17938 in neonates exposed to antibiotics: a randomised controlled trial Open
Perinatal antibiotic exposure potentially leads to gut microbiota dysbiosis, which is associated with functional gastrointestinal disorders (FGIDs). We aimed to investigate the effects of Limosilactobacillus reuteri DSM 17938 supplementati…
View article: Insights into Diversity, Host-Range, and Temporal Stability of<i>Bacteroides</i>and<i>Phocaeicola</i>Prophages
Insights into Diversity, Host-Range, and Temporal Stability of<i>Bacteroides</i>and<i>Phocaeicola</i>Prophages Open
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 …
View article: Using Machine Learning and Natural Language Processing for Unveiling Similarities between Microbial Data
Using Machine Learning and Natural Language Processing for Unveiling Similarities between Microbial Data Open
Microbiota analysis can provide valuable insights in various fields, including diet and nutrition, understanding health and disease, and in environmental contexts, such as understanding the role of microorganisms in different ecosystems. B…
View article: Antimicrobial susceptibility in <i>Clostridioides difficile</i> varies according to European region and isolate source
Antimicrobial susceptibility in <i>Clostridioides difficile</i> varies according to European region and isolate source Open
Objectives Clostridioides difficile epidemiology is evolving with country-associated emerging and resistant ribotypes (RT). Antimicrobial susceptibility testing of C. difficile isolated from clinical and animal samples collected across Eur…
View article: Different sampling strategies for optimal detection of the overall genetic diversity of methicillin-resistant <i>Staphylococcus aureus</i>
Different sampling strategies for optimal detection of the overall genetic diversity of methicillin-resistant <i>Staphylococcus aureus</i> Open
Surveillance schemes for methicillin-resistant Staphylococcus aureus (MRSA) are widely established at the national and international levels. Due to the simple standardization of the protocol, mainly isolates from bloodstream infections are…
View article: New treatment approaches for <i>Clostridioides difficile</i> infections: alternatives to antibiotics and fecal microbiota transplantation
New treatment approaches for <i>Clostridioides difficile</i> infections: alternatives to antibiotics and fecal microbiota transplantation Open
Clostridioides difficile causes a range of debilitating intestinal symptoms that may be fatal. It is particularly problematic as a hospital-acquired infection, causing significant costs to the health care system. Antibiotics, such as vanco…
View article: Rapid Isothermal Detection of Pathogenic <i>Clostridioides difficile</i> Using Recombinase Polymerase Amplification
Rapid Isothermal Detection of Pathogenic <i>Clostridioides difficile</i> Using Recombinase Polymerase Amplification Open
Nosocomial-associated diarrhea due to Clostridioides difficile infection (CDI) is diagnosed after sample precultivation by the detection of the toxins in enzyme immunoassays or via toxin gene nucleic acid amplification. Rapid and direct di…
View article: Carbapenemase and extended-spectrum beta-lactamase-producing bacteria in waters originating from a single landfill in Slovenia
Carbapenemase and extended-spectrum beta-lactamase-producing bacteria in waters originating from a single landfill in Slovenia Open
Groundwater, rainwater, and leachate associated with a single landfill were analysed to detect extended-spectrum beta-lactamase (ESBL)-producing and carbapenemase (CP)-producing bacteria. After cultivation on three commercial selective-dif…
View article: An overview of molecular markers for identification of non-human fecal pollution sources
An overview of molecular markers for identification of non-human fecal pollution sources Open
Identifying primary sources of fecal pollution is important for assessing public health risks and implementing effective remediation strategies. To date, one of the main molecular approaches for identifying sources of fecal pollution relie…
View article: Genomic insights into the safety and bacteriocinogenic potential of isolates from artisanal fermented milk Matsoni
Genomic insights into the safety and bacteriocinogenic potential of isolates from artisanal fermented milk Matsoni Open
Matsoni is a fermented milk common in the Caucasian region. In this study, whole-genome sequencing was performed with the aim of determining the taxonomic position of 25 previously selected candidate Matsoni starter cultures, identifying b…
View article: SARS-CoV-2 molecular epidemiology in Slovenia, January to September 2021
SARS-CoV-2 molecular epidemiology in Slovenia, January to September 2021 Open
Background Sequencing of SARS-CoV-2 PCR-positive samples was introduced in Slovenia in January 2021. Our surveillance programme comprised three complementary schemes: (A) non-targeted sequencing of at least 10% of samples, (B) sequencing o…
View article: Genomic insights into antibiotic resistance and mobilome of lactic acid bacteria and bifidobacteria
Genomic insights into antibiotic resistance and mobilome of lactic acid bacteria and bifidobacteria Open
Lactic acid bacteria (LAB) and Bifidobacterium sp. (bifidobacteria) can carry antimicrobial resistance genes (ARGs), yet data on resistance mechanisms in these bacteria are limited. The aim of our study was to identify the underlying genet…
View article: Gut Microbiome Composition in Patients with Chronic Urticaria: A Review of Current Evidence and Data
Gut Microbiome Composition in Patients with Chronic Urticaria: A Review of Current Evidence and Data Open
Recent studies have linked gut microorganism composition and chronic urticaria (CU); however, the underlying mechanisms responsible for this connection are unknown. Since the human immune system is in homeostasis with microbiota, and the c…
View article: Children gut microbiota exhibits a different composition and metabolic profile after in vitro exposure to Clostridioides difficile and increases its sporulation
Children gut microbiota exhibits a different composition and metabolic profile after in vitro exposure to Clostridioides difficile and increases its sporulation Open
Clostridioides difficile (Clostridium difficile) infection (CDI) is one of the main public health concerns in adults, while children under 2 years of age are often colonized asymptomatically. In both adults and children, CDI is strongly as…
View article: Gut community alterations associated with Clostridioides difficile colonization in hospitalized gastroenterological patients with or without inflammatory bowel disease
Gut community alterations associated with Clostridioides difficile colonization in hospitalized gastroenterological patients with or without inflammatory bowel disease Open
Clostridioides difficile colonization and development of infection commonly occur in inflammatory bowel disease (IBD) patients and can trigger flare-ups. Both conditions are inherently linked to disrupted gut microbiota. This study include…