Publications by authors named "Roger Stephan"

Proteus mirabilis is a Gram-negative bacterium found in the environment and also forms part of the commensal flora in the gastrointestinal tract of both humans and animals. P. mirabilis can cause a wide variety of infections, however it does not harbor any intrinsic β-lactamase genes and as such usually exhibits full susceptibility to β-lactams with the exception of imipenem, to which it is naturally resistant.

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  • Enterohemorrhagic Escherichia coli (EHEC) strains, linked to red meat outbreaks, pose serious global food safety issues, especially since current detection methods often yield false positives due to non-pathogenic strains.
  • This study focused on developing and validating four new hydrolysis probe assays specifically designed to detect pathogenic E. coli serogroups O26, O103, O111, and O121, showing an impressive accuracy of 94.8% in identifying virulent strains.
  • The newly standardized assays offer reliable detection tools for food laboratories worldwide, helping to mitigate waste and financial losses from incorrect positive test results associated with harmless non-pathogenic E. coli.
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  • Foodborne illnesses can lead to serious conditions like liver failure, especially in vulnerable populations such as children and young adults, but they often go unreported due to their self-limiting nature.
  • In a specific case, a 48-year-old woman experienced severe symptoms after eating contaminated rice salad, resulting in metabolic acidosis and liver dysfunction.
  • After treatment in the emergency department, including the use of N-acetylcysteine, her condition improved, and she was discharged nine days later with recovering liver function.
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As the interest in plant-based alternative food products has increased significantly in the last years, it is also important to investigate these products regarding microbiological aspects. The aim of this study was to assess the microbiological quality and the occurrence of selected foodborne pathogens in plant-based meat alternative products (PBMA) collected at retail level in Switzerland. A total of 100 PBMA (84 vegan and 16 vegetarian products) was analyzed qualitatively for the presence of Salmonella, Listeria monocytogenes and quantitatively for Staphylococcus aureus, Bacillus cereus group members, Enterobacteriaceae, and the total viable count.

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Fresh produce is usually consumed raw or minimally processed, making it a potential vehicle for the transmission of antimicrobial-resistant (AMR) microorganisms to humans. The objective of the study was to assess the occurrence of extended-spectrum ß-lactamase (ESBL)- and carbapenemase-producing Enterobacterales (ESBL-E and CPE), respectively, in 118 fresh herbs and 101 bagged salads collected at retail level in Switzerland and to characterize the isolates' phenotypic and genotypic properties using culture-based methods and whole genome sequencing (WGS). Of the fresh herbs, 6/118 contained ESBL-E and 7/118 yielded CPE.

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Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently being challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chromosomes and plasmids. Limited accuracy has hindered its use for investigating pathogen transmission, but recent technology updates have brought significant improvements.

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The objective of this study was to determine the prevalence, molecular epidemiology, and risk factors for gut colonization with extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E), carbapenemase-producing Enterobacterales (CPE), and vancomycin-resistant enterococci (VRE) in healthcare workers (HCWs). In September/October 2022, we performed a cross-sectional study among HCW from 14 institutions in Northeastern Switzerland. HCWs reported risk factors for antimicrobial resistance (covering the last 12-24 months) and provided rectal swabs.

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We traced back a nationwide outbreak of human listeriosis in Switzerland to a persisting production line contamination of a factory producing baker's yeast with Listeria monocytogenes serotype 1/2a sequence type 3141. We used whole-genome sequencing to match clinical isolates to isolates from product samples.

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Methicillin-resistant (MRSA) is of major public health concern due to its resistance to multiple antibiotics. This resistance has been observed in various settings, including hospitals and communities, and has been detected in both animals and humans. Although peridomestic rat species ( spp.

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  • Tumor necrosis factor inhibitors (TNFi), like adalimumab, can increase the risk of tuberculosis (TB) reactivation; however, instances of Mycobacterium bovis infections are rare.
  • A case involved a 78-year-old woman with M. bovis-related disseminated TB, which was initially misdiagnosed as sarcoidosis, and resulted in her death despite a negative TB test (IGRA) before treatment with TNFi.
  • The study emphasizes the need for careful consideration of TB risks in immunosuppressed patients, highlighting the importance of patient history regarding potential exposure to unpasteurized dairy products, even in regions officially free of bovine TB.
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Purpose: We aimed to characterise Yersinia enterocolitica from human clinical specimens in Switzerland using epidemiological, microbiological and whole-genome sequencing (WGS) data.

Methods: Isolates (n = 149) were collected between January 2019 and December 2023. Epidemiological data was noted and strains were characterized by biochemical and serological typing, antimicrobial susceptibility testing (AST), and WGS-based analysis.

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Introduction: Bovine paratuberculosis (PTB) is a chronic enteric disease caused by subsp. (MAP). Control of PTB is important given its negative economic consequences and the potential zoonotic role of MAP in Crohn's disease in humans.

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Timely and accurate detection and characterization of microbial threats is crucial for effective infection and outbreak management. Additionally, in food production, rapid microbe identification is indispensable for maintaining quality control and hygiene standards. Current methods for typing microbial strains often rely on labor-intensive, time-consuming, and expensive DNA- and sera-serotyping techniques, limiting their applicability in rapid-response scenarios.

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Aims Of The Study: Listeriosis is a notifiable disease in Switzerland. In summer 2022, the Swiss Federal Office of Public Health noticed an increase in reports of listeriosis cases, indicating a possible ongoing outbreak. Here we present the approaches applied for rapidly confirming the outbreak, detecting the underlying source of infection and the measures put in place to eliminate it and contain the outbreak.

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Streptococcus suis is an important pathogen causing severe disease in pigs and humans, giving rise to economic losses in the pig production industry. Out of 65 S. suis isolates collected from diseased pigs in Switzerland between 2019 and 2022, 57 isolates were thoroughly examined by phenotypic and whole genome sequence (WGS) based characterization.

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Study Aims: Although non-toxigenic Vibrio cholerae lack the ctxAB genes encoding cholera toxin, they can cause diarrhoeal disease and outbreaks in humans. In Switzerland, V. cholerae is a notifiable pathogen and all clinical isolates are analysed at the National Reference Laboratory for Enteropathogenic Bacteria and Listeria.

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We describe a case of Salmonella infection caused by a sucrose-fermenting Salmonella enterica Typhimurium sequence type 12 which acquired transposon CTnscr94 carrying the sucrose operon scrKYABR. Sucrose-fermenting Salmonella are particularly challenging for culture-based detection and may lead to failure to detect Salmonella in clinical samples.

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Listeria monocytogenes is an important human pathogen with a high mortality rate. Consumption of contaminated ready-to-eat food is the main mode of transmission to humans. Disinfectant-tolerant L.

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Campylobacter is among the most frequent agents of bacterial gastroenteritis in Europe and is primarily linked to the consumption of contaminated food. The aim of this study was to assess genomic diversity and to identify antimicrobial resistance and virulence genes of 155 Campylobacter isolated from broiler carcasses (neck skin samples) in a large-scale Swiss poultry abattoir over a three-year period. Samples originated from broilers from three different types of farming systems (particularly animal-friendly stabling (PAFS), free-range farms, and organic farms).

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As an international and zoonotic cause of hepatitis, hepatitis E virus (HEV) poses a significant risk to public health. However, the frequency of occurrence and the degree of contamination of food of animal origin require further research. The aim of this study was to develop and validate a highly sensitive quantitative RT-qPCR assay for the detection and quantification of HEV contamination in porcine liver and food.

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Nisin, with its unique mode of action and potent antimicrobial activity, serves as a remarkable inspiration for the design of novel antibiotics. However, peptides possess inherent weaknesses, particularly their susceptibility to proteolytic degradation, such as by trypsin, which limits their broader applications. This led us to speculate that natural variants of nisin produced by underexplored bacterial species can potentially overcome these limitations.

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Nisin is a widely used lantibiotic owing to its potent antimicrobial activity and its food-grade status. Its mode of action includes cell wall synthesis inhibition and pore formation, which are attributed to the lipid II binding and pore-forming domains, respectively. We discovered cesin, a short natural variant of nisin, produced by the psychrophilic anaerobe .

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Here we report the genome sequence of the florfenicol-resistant strain 90_2023 isolated from a raw-meat sausage (Finocchiona) imported from Italy to Switzerland. It has a genome of 2.75 Mbp and harbors 16 antimicrobial resistance genes, including A8, , and a truncated gene on a RepA_N plasmid.

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