Michael Biggel
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View article: Genomic characterization of <i>Klebsiella</i> spp. from bovine mastitis: dissemination of a conserved, highly transmissible <i>lac</i> <sub>acq</sub> <sup>+</sup> <i>fec</i> <sup>+</sup> plasmid drives burden of disease
Genomic characterization of <i>Klebsiella</i> spp. from bovine mastitis: dissemination of a conserved, highly transmissible <i>lac</i> <sub>acq</sub> <sup>+</sup> <i>fec</i> <sup>+</sup> plasmid drives burden of disease Open
Bovine mastitis poses a significant health concern for dairy cattle and a major economic burden on the dairy industry. Klebsiella spp. are important mastitis pathogens, with previous studies identifying lactose-utilization ( lac acq ) and …
View article: Clonal spread of Mycobacterium monacense strains among patients with extrapulmonary mycobacteriosis
Clonal spread of Mycobacterium monacense strains among patients with extrapulmonary mycobacteriosis Open
Background This study presents the phylogenetic and antimicrobial susceptibility characterization of Mycobacterium monacense , a rare nontuberculous mycobacterium (NTM), cultured from clinical extrapulmonary samples. Methods Eight Mycobact…
View article: Insights into recurring multi-country outbreaks of Salmonella Strathcona associated with tomatoes, Europe, 2011 to 2024
Insights into recurring multi-country outbreaks of Salmonella Strathcona associated with tomatoes, Europe, 2011 to 2024 Open
Notifications of Salmonella Strathcona infections increased in Europe in 2023 prompting a multi-country outbreak investigation. We aimed to describe the epidemiology of S . Strathcona infections in 17 European countries 2011–2024, investig…
View article: Occurrence of Selected Foodborne Pathogens on Frozen Berries Collected at Retail Level in Switzerland
Occurrence of Selected Foodborne Pathogens on Frozen Berries Collected at Retail Level in Switzerland Open
Berries are globally appreciated for their health benefits, particularly due to antioxidants, and have grown in popularity over recent decades. However, several foodborne outbreaks-mainly viral, caused by norovirus and hepatitis A-have bee…
View article: Development of shuttle vector-based transformation systems for veterinary and zoonotic chlamydiae
Development of shuttle vector-based transformation systems for veterinary and zoonotic chlamydiae Open
In veterinary medicine, the obligate intracellular bacteria Chlamydia ( C. ) abortus , Chlamydia caviae , and Chlamydia pecorum are known to cause ovine enzootic abortion, conjunctivitis in guinea pigs, and ocular/urogenital disease in koa…
View article: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering
Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering Open
Using a genomic approach we report host-specific strains that serve as carriers of virulence-associated plasmids, indicating an adaptation strategy within distinct R. equi lineages. The existence of shared plasmid profiles between farm ani…
View article: Occurrence and characteristics of extended-spectrum ß-lactamase-producing Escherichia coli in Swiss and imported retail chicken meat
Occurrence and characteristics of extended-spectrum ß-lactamase-producing Escherichia coli in Swiss and imported retail chicken meat Open
The contamination with ESBL-EC in retail chicken meat in Switzerland is moderate; nevertheless, domestic and imported chicken meat is a potential vehicle for MDR ESBL-EC and for genes conferring resistance to clinically important antimicro…
View article: Salmonella in Swiss and Imported Retail Chicken Meat – A Cross-Sectional Study
Salmonella in Swiss and Imported Retail Chicken Meat – A Cross-Sectional Study Open
View article: Describing biosynthetic gene clusters of dairy cattle uterine microbiomes associated with antimetritis properties
Describing biosynthetic gene clusters of dairy cattle uterine microbiomes associated with antimetritis properties Open
Uterine disease perturbs fertility thereby causing economic losses to the dairy enterprise worldwide. About 25-40% of dairy cattle develop metritis postpartum (Sheldon et al., 2009). 16S rRNA amplicon sequencing taxonomic identification of…
View article: Occurrence of <i>Salmonella</i> and presumptive <i>Bacillus cereus</i> in sesame products from Swiss retail stores
Occurrence of <i>Salmonella</i> and presumptive <i>Bacillus cereus</i> in sesame products from Swiss retail stores Open
Sesame products such as tahini (tahin) or halva (halwa or helva), originating from Arabic cuisine, are becoming increasingly popular in Switzerland. Pathogens, such as Salmonella, can contaminate sesame products, as evidenced by various pr…
View article: Nanopore- and AI-empowered microbial viability inference
Nanopore- and AI-empowered microbial viability inference Open
Background The ability to differentiate between viable and dead microorganisms in metagenomic data is crucial for various microbial inferences, ranging from assessing ecosystem functions of environmental microbiomes to inferring the virule…
View article: Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital
Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital Open
Our data show a high prevalence of nosocomial acquisition of ESBL-E in a non-ICU setting. The study provides genomic evidence that the endogenous reservoir is the main driver of ESBL-Ec infections underscoring the need for wide implementat…
View article: Oxford Nanopore’s 2024 sequencing technology for <i>Listeria monocytogenes</i> outbreak detection and source attribution: progress and clone-specific challenges
Oxford Nanopore’s 2024 sequencing technology for <i>Listeria monocytogenes</i> outbreak detection and source attribution: progress and clone-specific challenges Open
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 c…
View article: Extended-spectrum ß-lactamase (ESBL)- and Carbapenemase-producing Enterobacterales Isolated from Fresh Herbs and Salads at Retail Level in Switzerland
Extended-spectrum ß-lactamase (ESBL)- and Carbapenemase-producing Enterobacterales Isolated from Fresh Herbs and Salads at Retail Level in Switzerland Open
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…
View article: Development of shuttle vector-based transformation systems for<i>Chlamydia pecorum</i>and<i>Chlamydia caviae</i>
Development of shuttle vector-based transformation systems for<i>Chlamydia pecorum</i>and<i>Chlamydia caviae</i> Open
Chlamydia (C.) abortus , C. caviae and C. pecorum are obligate intracellular, zoonotic pathogens, which have all been associated with community-acquired pneumonia in humans. C. abortus is the causative agent of enzootic ovine abortion in s…
View article: Nanopore- and AI-empowered microbial viability inference
Nanopore- and AI-empowered microbial viability inference Open
The ability to differentiate between viable and dead microorganisms in metagenomic data is crucial for various microbial inferences, ranging from assessing ecosystem functions of environmental microbiomes to inferring the virulence of pote…
View article: Complete genome sequence of the linezolid-resistant clinical <i>Enterococcus faecalis</i> N23-3408 linked to a livestock lineage in Switzerland
Complete genome sequence of the linezolid-resistant clinical <i>Enterococcus faecalis</i> N23-3408 linked to a livestock lineage in Switzerland Open
Here, we report the complete genome of human clinical linezolid-resistant Enterococcus faecalis N23-3408. N23-3408 harbored a 59.5 kb plasmid with antimicrobial resistance genes cat , erm (B), fexA , optrA , tet (L), and tet (M). Closely r…
View article: Genetic diversity and antimicrobial susceptibility of Streptococcus suis from diseased Swiss pigs collected between 2019 – 2022
Genetic diversity and antimicrobial susceptibility of Streptococcus suis from diseased Swiss pigs collected between 2019 – 2022 Open
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 2…
View article: Genomic characteristics of clinical non-toxigenic Vibrio cholerae isolates in Switzerland: a cross-sectional study
Genomic characteristics of clinical non-toxigenic Vibrio cholerae isolates in Switzerland: a cross-sectional study Open
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 a…
View article: Antimicrobial resistance and phylogenetic relatedness of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli in peridomestic rats (Rattus norvegicus and Rattus tanezumi) linked to city areas and animal farms in Hong Kong
Antimicrobial resistance and phylogenetic relatedness of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli in peridomestic rats (Rattus norvegicus and Rattus tanezumi) linked to city areas and animal farms in Hong Kong Open
Extended-spectrum β-lactamase-producing Escherichia (E.) coli (ESBL-EC) in the clinical setting have emerged as a major threat to public and animal health. Wildlife, including Rattus spp. may serve as reservoirs and spreaders of ESBL-EC in…
View article: <i>Chlamydia suis</i>displays high transformation capacity with complete cloning vector integration into the chromosomal<i>rrn-nqrF</i>plasticity zone
<i>Chlamydia suis</i>displays high transformation capacity with complete cloning vector integration into the chromosomal<i>rrn-nqrF</i>plasticity zone Open
Chlamydia , comprising several human and zoonotic pathogens, is a genus of the conserved bacterial phylum Chlamydiota. Their obligate intracellular niche serves as a barrier for natural genetic exchange via horizontal gene transfer (HGT), …
View article: New insights into Bacillus cytotoxicus sources, screening, toxicity, and persistence in food production facilities
New insights into Bacillus cytotoxicus sources, screening, toxicity, and persistence in food production facilities Open
Bacillus cytotoxicus is a thermotolerant member of the Bacillus cereus group. It has been linked to rare, but at times fatal cases of diarrheal disease and might be missed at routine diagnostic screening temperatures commonly used for the …
View article: Completely assembled genome sequence of the florfenicol-resistant <i>Enterococcus faecalis</i> strain 90_2023 isolated from a raw sausage imported from Italy to Switzerland
Completely assembled genome sequence of the florfenicol-resistant <i>Enterococcus faecalis</i> strain 90_2023 isolated from a raw sausage imported from Italy to Switzerland Open
Here we report the genome sequence of the florfenicol-resistant Enterococcus faecalis 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 antimicrobia…
View article: Dissemination of ESBL-producing E. coli ST131 through wastewater and environmental water in Switzerland
Dissemination of ESBL-producing E. coli ST131 through wastewater and environmental water in Switzerland Open
View article: Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter
Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter Open
Background Linezolid is a critically important oxazolidinone antibiotic used in human medicine. Although linezolid is not licensed for use in food-producing animals, the use of florfenicol in veterinary medicine co-selects for oxazolidinon…
View article: Complete Genome Sequence of the Extensively Drug-Resistant Extended-Spectrum β-Lactamase-Producing Proteus mirabilis Isolate HK294, Obtained from Poultry Feces in Hong Kong
Complete Genome Sequence of the Extensively Drug-Resistant Extended-Spectrum β-Lactamase-Producing Proteus mirabilis Isolate HK294, Obtained from Poultry Feces in Hong Kong Open
Here, we report the complete genome sequence of Proteus mirabilis isolate HK294, recovered from pooled poultry feces in Hong Kong in 2022. The chromosome contained 32 antimicrobial resistance genes, including the extended-spectrum β-lactam…
View article: Strain diversity in Mycobacterium avium subsp. paratuberculosis-positive bovine fecal samples collected in Switzerland
Strain diversity in Mycobacterium avium subsp. paratuberculosis-positive bovine fecal samples collected in Switzerland Open
Paratuberculosis or Johne’s disease is a chronic intestinal disease in domestic and wild ruminants. It affects global dairy economy and is caused by Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to anal…
View article: Draft Genome Sequences of Four Escherichia albertii Isolates from Hunted Wild Boars in Switzerland
Draft Genome Sequences of Four Escherichia albertii Isolates from Hunted Wild Boars in Switzerland Open
Here, we report the genome sequences of four Escherichia albertii isolates that were recovered from hunted wild boars in Switzerland in 2022 and 2023. The genome sizes of KBWS15i, KBWS35i, KBWS50i, and KBSW171i were 4.4 Mbp, 4.5 Mbp, 4.5 M…
View article: Draft Genome Sequence of Pseudomonas carnis Strain 23-145, Causing Blue Discolorations on Rabbit Carcasses
Draft Genome Sequence of Pseudomonas carnis Strain 23-145, Causing Blue Discolorations on Rabbit Carcasses Open
Here, we report the genome sequence of Pseudomonas carnis strain 23-145, which was recovered from a rabbit carcass with blue discolorations. The strain harbored two trpABCDF loci involved in tryptophan biosynthesis, which is characteristic…
View article: Emergence of blaSHV-12 and qnrS1 encoded on IncX3 plasmids: Changing epidemiology of extended-spectrum ß-lactamases among Enterobacterales isolated from broilers
Emergence of blaSHV-12 and qnrS1 encoded on IncX3 plasmids: Changing epidemiology of extended-spectrum ß-lactamases among Enterobacterales isolated from broilers Open
Objectives: The occurrence of extended-spectrum ß-lactamase (ESBL)-producing Enterobacterales in broilers represents a risk to public health because of the possibility of transmission of ESBL producers and/or blaESBL genes via the food cha…