104 results on '"Cernela N"'
Search Results
2. Antimicrobial resistance patterns and genotypes of Salmonella enterica serovar Hadar strains associated with human infections in Switzerland, 2005–2010
- Author
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CERNELA, N., NÜESCH-INDERBINEN, M., HÄCHLER, H., and STEPHAN, R.
- Published
- 2014
3. Pathogenic Yersinia enterocolitica O:3 isolated from a hunted wild alpine ibex
- Author
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JOUTSEN, S., SARNO, E., FREDRIKSSON-AHOMAA, M., CERNELA, N., and STEPHAN, R.
- Published
- 2013
- Full Text
- View/download PDF
4. Yersinia enterocolitica strains associated with human infections in Switzerland 2001–2010
- Author
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Fredriksson-Ahomaa, M., Cernela, N., Hächler, H., and Stephan, R.
- Published
- 2012
- Full Text
- View/download PDF
5. Yersinia enterocolitica strains associated with human infections in Switzerland 2001-2010
- Author
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Fredriksson-Ahomaa, M., Cernela, N., Hächler, H., Stephan, R., Fredriksson-Ahomaa, M., Cernela, N., Hächler, H., and Stephan, R.
- Abstract
Yersinia enterocolitica infections are common in humans. However, very scarce data are available on the different biotypes and virulence factors of human strains, which has proved to be problematic to assess the clinical significance of the isolated strains. In this study, the presence of the ail gene and distribution of different bio- and serotypes among human Y. enterocolitica strains and their possible relation to the genotype and antimicrobial resistance were studied. In total, 128 Y. enterocolitica strains isolated from human clinical samples in Switzerland during 2001-2010 were characterised. Most (75 out of 128) of the Y. enterocolitica strains belonged to biotypes 2, 3 or 4 and carried the ail gene. One of the 51 strains that belonged to biotype 1A was also ail positive. Most of the ail-positive strains belonged to bioserotype 4/O:3 (47 out of 76) followed by 2/O:9 (22 out of 76). Strains of bioserotype 4/O:3 were dominant among patients between 20 and 40years old and strains of biotype 1A dominate in patients over 40years. Strains belonging to biotypes 2, 3 and 4, which all carried the ail gene, exhibited a high homogeneity with PFGE typing. Y. enterocolitica 2/O:5,27 and 2/O:9 strains showed resistance to amoxicillin/clavulanic acid and cefoxitin, but Y. enterocolitica 4/O:3 strains did not
- Published
- 2018
6. Pathogenic Yersinia enterocolitica O:3 isolated from a hunted wild alpine ibex
- Author
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Joutsen, S, Sarno, E, Fredriksson-Ahomaa, M, Cernela, N, Stephan, Roger, University of Zurich, and Stephan, Roger
- Subjects
570 Life sciences ,biology ,610 Medicine & health ,2725 Infectious Diseases ,10082 Institute of Food Safety and Hygiene ,2713 Epidemiology - Abstract
Occurrence of Yersinia spp. in wild ruminants was studied and the strains were characterized to get more information on the epidemiology of enteropathogenic Yersinia in the wildlife. In total, faecal samples of 77 red deer, 60 chamois, 55 roe deer and 27 alpine ibex were collected during 3 months of the hunting season in 2011. The most frequently identified species was Y. enterocolitica found in 13%, 10%, 4% and 2% of roe deer, red deer, alpine ibex and chamois, respectively. Interestingly, one Y. enterocolitica O:3 strain, isolated from an alpine ibex, carried the important virulence genes located on the virulence plasmid (yadA and virF) and in the chromosome (ail, hreP, myfA and ystA). Most of the Y. enterocolitica strains belonged to biotype 1A of which 14 were ystB positive. Further studies are needed to clarify the importance of alpine ibex as a reservoir of pathogenic Y. enterocolitica
- Published
- 2017
7. Pathogenic Yersinia enterocolitica O:3 isolated from a hunted wild alpine ibex
- Author
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JOUTSEN, S., SARNO, E., FREDRIKSSON-AHOMAA, M., CERNELA, N., STEPHAN, R., JOUTSEN, S., SARNO, E., FREDRIKSSON-AHOMAA, M., CERNELA, N., and STEPHAN, R.
- Abstract
Occurrence of Yersinia spp. in wild ruminants was studied and the strains were characterized to get more information on the epidemiology of enteropathogenic Yersinia in the wildlife. In total, faecal samples of 77 red deer, 60 chamois, 55 roe deer and 27 alpine ibex were collected during 3 months of the hunting season in 2011. The most frequently identified species was Y. enterocolitica found in 13%, 10%, 4% and 2% of roe deer, red deer, alpine ibex and chamois, respectively. Interestingly, one Y. enterocolitica O:3 strain, isolated from an alpine ibex, carried the important virulence genes located on the virulence plasmid (yadA and virF) and in the chromosome (ail, hreP, myfA and ystA). Most of the Y. enterocolitica strains belonged to biotype 1A of which 14 were ystB positive. Further studies are needed to clarify the importance of alpine ibex as a reservoir of pathogenic Y. enterocolitica
- Published
- 2017
8. Salmonella enterica serovar Szentes, a rare serotype causing a 9-month outbreak in 2013 and 2014 in Switzerland
- Author
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Nüesch-Inderbinen, Magdalena, Cernela, N, Althaus, Denise, Hächler, Herbert, Stephan, Roger, University of Zurich, and Stephan, Roger
- Subjects
2404 Microbiology ,570 Life sciences ,biology ,2402 Applied Microbiology and Biotechnology ,610 Medicine & health ,Animal Science and Zoology ,1103 Animal Science and Zoology ,Applied Microbiology and Biotechnology ,Microbiology ,10082 Institute of Food Safety and Hygiene ,1106 Food Science ,Food Science - Published
- 2015
9. Detection of the emerging Shiga toxin-producing Escherichia coli O26:H11/H- sequence type 29 (ST29) clone in human patients and healthy cattle in Switzerland
- Author
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Zweifel, C, Cernela, N, Stephan, Roger, University of Zurich, and Stephan, Roger
- Subjects
1305 Biotechnology ,570 Life sciences ,biology ,2402 Applied Microbiology and Biotechnology ,610 Medicine & health ,2303 Ecology ,10082 Institute of Food Safety and Hygiene ,1106 Food Science - Published
- 2013
10. Development and validation of a PulseNet standardized protocol for sub-typing isolates of Cronobacter species
- Author
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Brengi, S, O'Brien, S B, Pichel, M, Iversen, Carol, Arduino, M, Binsztein, N, Jensen, B, Pagotto, F, Ribot, E, Stephan, Roger, Cernela, N, Cooper, K, Fanning, S, and University of Zurich
- Subjects
2404 Microbiology ,570 Life sciences ,biology ,2402 Applied Microbiology and Biotechnology ,610 Medicine & health ,Animal Science and Zoology ,1103 Animal Science and Zoology ,Applied Microbiology and Biotechnology ,Microbiology ,10082 Institute of Food Safety and Hygiene ,1106 Food Science ,Food Science - Published
- 2012
11. Shiga toxin subtypes associated with Shiga toxin-producing Escherichia coli strains isolated from red deer, roe deer, chamois and ibex
- Author
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Hofer, E, Cernela, N, Stephan, Roger, University of Zurich, and Stephan, Roger
- Subjects
2404 Microbiology ,570 Life sciences ,biology ,2402 Applied Microbiology and Biotechnology ,610 Medicine & health ,Animal Science and Zoology ,1103 Animal Science and Zoology ,Applied Microbiology and Biotechnology ,Microbiology ,10082 Institute of Food Safety and Hygiene ,1106 Food Science ,Food Science - Published
- 2012
12. Evaluation of pet contact as risk factor for carriage of multi-drug resistant staphylococci in nursing home residents
- Author
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Decristophoris, P, De Benedetti, A, Petignat, C, Attinger, M, Guillaume, J, Fiebig, L, Hattendorf, J, Cernela, N, Regula, G, Petrini, O, Zinsstag, J, Schelling, E, and University of Zurich
- Subjects
570 Life sciences ,biology ,610 Medicine & health ,2739 Public Health, Environmental and Occupational Health ,2725 Infectious Diseases ,2719 Health Policy ,10082 Institute of Food Safety and Hygiene ,2713 Epidemiology - Published
- 2012
13. Methicillin-resistant Staphylococcus lentus strains isolated from chicken carcasses and employees of a poultry abattoir
- Author
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Koller, S, Huber, H, Cernela, N, Stephan, Roger, Zweifel, C, University of Zurich, and Zweifel, C
- Subjects
2308 Management, Monitoring, Policy and Law ,2404 Microbiology ,570 Life sciences ,biology ,610 Medicine & health ,10082 Institute of Food Safety and Hygiene ,1106 Food Science - Published
- 2011
14. Pathogenic Yersinia enterocolitica O:3 isolated from a hunted wild alpine ibex
- Author
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Joutsen, S, Sarno, E, Fredriksson-Ahomaa, M, Cernela, N, Stephan, Roger; https://orcid.org/0000-0003-1002-4762, Joutsen, S, Sarno, E, Fredriksson-Ahomaa, M, Cernela, N, and Stephan, Roger; https://orcid.org/0000-0003-1002-4762
- Abstract
Occurrence of Yersinia spp. in wild ruminants was studied and the strains were characterized to get more information on the epidemiology of enteropathogenic Yersinia in the wildlife. In total, faecal samples of 77 red deer, 60 chamois, 55 roe deer and 27 alpine ibex were collected during 3 months of the hunting season in 2011. The most frequently identified species was Y. enterocolitica found in 13%, 10%, 4% and 2% of roe deer, red deer, alpine ibex and chamois, respectively. Interestingly, one Y. enterocolitica O:3 strain, isolated from an alpine ibex, carried the important virulence genes located on the virulence plasmid (yadA and virF) and in the chromosome (ail, hreP, myfA and ystA). Most of the Y. enterocolitica strains belonged to biotype 1A of which 14 were ystB positive. Further studies are needed to clarify the importance of alpine ibex as a reservoir of pathogenic Y. enterocolitica.
- Published
- 2013
15. Yersinia enterocolitica strains associated with human infections in Switzerland 2001-2010
- Author
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Fredriksson-Ahomaa, M, Cernela, N, Hächler, H, Stephan, Roger; https://orcid.org/0000-0003-1002-4762, Fredriksson-Ahomaa, M, Cernela, N, Hächler, H, and Stephan, Roger; https://orcid.org/0000-0003-1002-4762
- Abstract
Yersinia enterocolitica infections are common in humans. However, very scarce data are available on the different biotypes and virulence factors of human strains, which has proved to be problematic to assess the clinical significance of the isolated strains. In this study, the presence of the ail gene and distribution of different bio- and serotypes among human Y. enterocolitica strains and their possible relation to the genotype and antimicrobial resistance were studied. In total, 128 Y. enterocolitica strains isolated from human clinical samples in Switzerland during 2001-2010 were characterised. Most (75 out of 128) of the Y. enterocolitica strains belonged to biotypes 2, 3 or 4 and carried the ail gene. One of the 51 strains that belonged to biotype 1A was also ail positive. Most of the ail-positive strains belonged to bioserotype 4/O:3 (47 out of 76) followed by 2/O:9 (22 out of 76). Strains of bioserotype 4/O:3 were dominant among patients between 20 and 40 years old and strains of biotype 1A dominate in patients over 40 years. Strains belonging to biotypes 2, 3 and 4, which all carried the ail gene, exhibited a high homogeneity with PFGE typing. Y. enterocolitica 2/O:5,27 and 2/O:9 strains showed resistance to amoxicillin/clavulanic acid and cefoxitin, but Y. enterocolitica 4/O:3 strains did not.
- Published
- 2012
16. Function impairing mutations in blaZ and blaR genes of penicillin susceptible Staphylococcus aureus strains isolated from bovine mastitis
- Author
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Tasara, T., primary, Cernela, N., additional, and Stephan, R., additional
- Published
- 2013
- Full Text
- View/download PDF
17. Antimicrobial resistance patterns and genotypes ofSalmonella entericaserovar Hadar strains associated with human infections in Switzerland, 2005–2010
- Author
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CERNELA, N., primary, NÜESCH-INDERBINEN, M., additional, HÄCHLER, H., additional, and STEPHAN, R., additional
- Published
- 2013
- Full Text
- View/download PDF
18. PathogenicYersinia enterocoliticaO:3 isolated from a hunted wild alpine ibex
- Author
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JOUTSEN, S., primary, SARNO, E., additional, FREDRIKSSON-AHOMAA, M., additional, CERNELA, N., additional, and STEPHAN, R., additional
- Published
- 2012
- Full Text
- View/download PDF
19. Salmonella enterica serotype Kentucky associated with human infections in Switzerland: Genotype and resistance trends 2004–2009
- Author
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Bonalli, M., primary, Stephan, R., additional, Käppeli, U., additional, Cernela, N., additional, Adank, L., additional, and Hächler, H., additional
- Published
- 2012
- Full Text
- View/download PDF
20. Yersinia enterocolitica strains associated with human infections in Switzerland 2001–2010
- Author
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Fredriksson-Ahomaa, M., primary, Cernela, N., additional, Hächler, H., additional, and Stephan, R., additional
- Published
- 2011
- Full Text
- View/download PDF
21. Occurrence of Vibrio spp. in Fish and Shellfish Collected from the Swiss Market
- Author
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SCHÄRER, K., primary, SAVIOZ, S., additional, CERNELA, N., additional, SAEGESSER, G., additional, and STEPHAN, R., additional
- Published
- 2011
- Full Text
- View/download PDF
22. Evaluation of three commercially available real-time PCR based systems for detection of Cronobacter species
- Author
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Fricker-Feer, C., primary, Cernela, N., additional, Bolzan, S., additional, Lehner, A., additional, and Stephan, R., additional
- Published
- 2011
- Full Text
- View/download PDF
23. Fecal Carriage of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Swine and Cattle at Slaughter in Switzerland
- Author
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Geser, N., primary, Stephan, R., additional, Kuhnert, P., additional, Zbinden, R., additional, Kaeppeli, U., additional, Cernela, N., additional, and Haechler, H., additional
- Published
- 2011
- Full Text
- View/download PDF
24. Quinolone resistance mechanisms among extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolated from farm animals in Switzerland.
- Author
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Zurfluh, K., Cernela, N., and Stephan, R.
- Published
- 2015
- Full Text
- View/download PDF
25. Occurrence of Vibrio spp.in Fish and Shellfish Collected from the Swiss Market
- Author
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Scharer, K., Savioz, S., Cernela, N., Saegesser, G., and Stephan, R.
- Abstract
The genus Vibrio includes gram-negative bacteria that inhabit estuarine ecosystems. V. cholerae, V. parahaemolyticus, and V. vulnificuspose a considerable public health threat as agents of sporadic and epidemic foodborne infections associated with the consumption of raw or undercooked contaminated fish or shellfish. In this study, we analyzed 138 fish and shellfish samples collected from the Swiss market (fish fillets [n =102], bivalves [n =34], and squid [n = 2]). Microbiological analysis was done according to International Organization for Standardization method 21872-1/21872-2:2007, using thiosulfate citrate bile sucrose agar and chromID Vibrio agar as selective agar. Presumptive-positive colonies on thiosulfate citrate bile sucrose agar or chromID Vibrio agar were picked and were identified by the API 20E and species-specific PCR systems. V. choleraeisolates were tested further by PCR for the presence of the cholera toxin A subunit gene (ctxA). V. parahaemolyticusisolates were tested by PCR for genes encoding for thermostable direct hemolysin (tdh) and TDH-related hemolysin (trh). V. choleraewas isolated from three samples and V. parahaemolyticusfrom eight samples. None of these strains harbored species-specific virulence factors. Further, V. alginolyticuswas isolated from 40 samples, and V. fluvialiswas isolated from 1 sample. Our study provides, for the first time, data for the assessment of exposure to Vibrio spp. in raw fish and bivalves consumed in Switzerland.
- Published
- 2011
- Full Text
- View/download PDF
26. Antimicrobial resistance patterns and genotypes of Salmonella enterica serovar Hadar strains associated with human infections in Switzerland, 2005-2010
- Author
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CERNELA, N., NÜESCH-INDERBINEN, M., HÄCHLER, H., STEPHAN, R., CERNELA, N., NÜESCH-INDERBINEN, M., HÄCHLER, H., and STEPHAN, R.
- Abstract
Salmonella Hadar ranks in the top ten serovars reported from humans in Switzerland. In this study, all 64 S. Hadar strains isolated from different patients from 2005 to 2010 in Switzerland were characterized by (i) assessing phenotypic antimicrobial resistance profiles using the disk diffusion method and (ii) by genotyping using pulsed-field gel electrophoresis (PFGE) in order to evaluate the relationship of the strains. The annual incidences varied between 0·32/100000 in 2005 (highest incidence) and 0·065/100000 in 2007 (lowest incidence). In total 71·8% of the isolates were resistant to nalidixic acid. Although 40·6% of the strains were resistant to the β-lactam antibiotic ampicillin, they remained susceptible to the third-generation cephalosporin cefotaxime. Genotyping revealed a primary cluster consisting of 42 strains, sharing a similarity of >92%, with a subcluster of 18 strains with indistinguishable patterns. Resistance profiles allowed further differentiation within this subcluster providing a link of two strains to an outbreak in Spain
27. Yersinia enterocolitica strains associated with human infections in Switzerland 2001-2010
- Author
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Fredriksson-Ahomaa, M., Cernela, N., Hächler, H., Stephan, R., Fredriksson-Ahomaa, M., Cernela, N., Hächler, H., and Stephan, R.
- Abstract
Yersinia enterocolitica infections are common in humans. However, very scarce data are available on the different biotypes and virulence factors of human strains, which has proved to be problematic to assess the clinical significance of the isolated strains. In this study, the presence of the ail gene and distribution of different bio- and serotypes among human Y. enterocolitica strains and their possible relation to the genotype and antimicrobial resistance were studied. In total, 128 Y. enterocolitica strains isolated from human clinical samples in Switzerland during 2001-2010 were characterised. Most (75 out of 128) of the Y. enterocolitica strains belonged to biotypes 2, 3 or 4 and carried the ail gene. One of the 51 strains that belonged to biotype 1A was also ail positive. Most of the ail-positive strains belonged to bioserotype 4/O:3 (47 out of 76) followed by 2/O:9 (22 out of 76). Strains of bioserotype 4/O:3 were dominant among patients between 20 and 40years old and strains of biotype 1A dominate in patients over 40years. Strains belonging to biotypes 2, 3 and 4, which all carried the ail gene, exhibited a high homogeneity with PFGE typing. Y. enterocolitica 2/O:5,27 and 2/O:9 strains showed resistance to amoxicillin/clavulanic acid and cefoxitin, but Y. enterocolitica 4/O:3 strains did not
28. Pathogenic Yersinia enterocolitica O:3 isolated from a hunted wild alpine ibex
- Author
-
JOUTSEN, S., SARNO, E., FREDRIKSSON-AHOMAA, M., CERNELA, N., STEPHAN, R., JOUTSEN, S., SARNO, E., FREDRIKSSON-AHOMAA, M., CERNELA, N., and STEPHAN, R.
- Abstract
Occurrence of Yersinia spp. in wild ruminants was studied and the strains were characterized to get more information on the epidemiology of enteropathogenic Yersinia in the wildlife. In total, faecal samples of 77 red deer, 60 chamois, 55 roe deer and 27 alpine ibex were collected during 3 months of the hunting season in 2011. The most frequently identified species was Y. enterocolitica found in 13%, 10%, 4% and 2% of roe deer, red deer, alpine ibex and chamois, respectively. Interestingly, one Y. enterocolitica O:3 strain, isolated from an alpine ibex, carried the important virulence genes located on the virulence plasmid (yadA and virF) and in the chromosome (ail, hreP, myfA and ystA). Most of the Y. enterocolitica strains belonged to biotype 1A of which 14 were ystB positive. Further studies are needed to clarify the importance of alpine ibex as a reservoir of pathogenic Y. enterocolitica
29. Salmonella enterica serotype Virchow associated with human infections in Switzerland: 2004-2009
- Author
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Adank Luzius, Cernela Nicole, Käppeli Ursula, Stephan Roger, Bonalli Mario, and Hächler Herbert
- Subjects
Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Salmonellosis is one of the most important foodborne diseases and a major threat to public health. Salmonella serotype Virchow ranks among the top five serovars in Europe. Method A total of 153 strains isolated from different patients from 2004 through 2009 in Switzerland were further characterized by (i) assessing phenotypic antibiotic resistance profiles using the disk diffusion method and (ii) by genotyping using pulsed-field gel electrophoresis (PFGE) after macrorestriction with XbaI in order to evaluate strain relationship. Results The relative frequency of S. Virchow among other Salmonella serovars varied between 4th to 8th rank. The annual incidence ranged from 0.45/100'000 in 2004 to 0.40/100'000 in 2009. A total of 48 strains (32%) were resistant to one to 3 antimicrobials, 54 strains (36%) displayed resistance patterns to more than three antibiotics. No trend was identifiable over the years 2004 to 2009. We found a high prevalence (62%) of nalidixic acid resistant strains, suggesting an equally high rate of decreased fluoroqionolone susceptibility, whereas intermediate resistance to ciprofloxacin was negligible. Two strains were extended spectrum β-lactamase (ESBL) producers. Analysis of PFGE patterns uncovered a predominant cluster (similarity coefficient above 80%) consisting of 104 of the 153 strains. Conclusion The worldwide increase of antibiotic resistances in Salmonella is an emerging public health problem. For Switzerland, no clear trend is identifiable over the years 2004 to 2009 for S. Virchow. Antimicrobial susceptibility and resistance profiles varied considerably within this period. Nevertheless, the situation in Switzerland coincided with findings in other European countries. Genotyping results of this strain collection revealed no evidence for an undetected outbreak within this time period.
- Published
- 2011
- Full Text
- View/download PDF
30. Oxford Nanopore's 2024 sequencing technology for Listeria monocytogenes outbreak detection and source attribution: progress and clone-specific challenges.
- Author
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Biggel M, Cernela N, Horlbog JA, and Stephan R
- Subjects
- Humans, Genome, Bacterial genetics, Nanopore Sequencing methods, Nanopores, High-Throughput Nucleotide Sequencing methods, Listeria monocytogenes genetics, Listeria monocytogenes classification, Listeria monocytogenes isolation & purification, Listeriosis microbiology, Listeriosis epidemiology, Listeriosis diagnosis, Disease Outbreaks, Whole Genome Sequencing
- Abstract
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. To evaluate its readiness for outbreak detection, we selected 78 Listeria monocytogenes isolates from diverse lineages or known epidemiological clusters for sequencing with ONT's V14 Rapid Barcoding Kit and R10.4.1 flow cells. The most accurate of several tested workflows generated assemblies with a median of one error (SNP or indel) per assembly. For 66 isolates, the cgMLST profiles from ONT-only assemblies were identical to those generated from Illumina data. Eight assemblies were of lower quality, with more than 20 erroneous sites each, primarily caused by methylations at the GAAGAC motif (5'-GAAG 6mA C-3'/5'-GT 4mC TTC-3'). This led to inaccurate clustering, failing to group isolates from a persistence-associated clone that carried the responsible restriction-modification system. Out of 50 methylation motifs detected among the 78 isolates, only the GAAGAC motif was linked to substantially increased error rates. Our study shows that most L. monocytogenes genomes assembled from ONT-only data are suitable for high-resolution genotyping, but further improvements of chemistries or basecallers are required for reliable routine use in outbreak and food safety investigations., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
- Full Text
- View/download PDF
31. 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.
- Author
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Uea-Anuwong T, Biggel M, Cernela N, Hung WW, Lugsomya K, Kiu LH, Gröhn YT, Boss S, Stephan R, Nüesch-Inderbinen M, and Magouras I
- Subjects
- Animals, Rats, Hong Kong, Cities, Chickens microbiology, Escherichia coli Infections veterinary, Escherichia coli Infections microbiology, Escherichia coli Infections epidemiology, Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial genetics, Swine, Escherichia coli genetics, beta-Lactamases genetics, Phylogeny, Farms
- Abstract
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 the environment. Peridomestic rats are well adapted to living in proximity to humans and animals in a variety of urban and agricultural environments and may serve as sentinels to identify variations of ESBL-EC within their different habitats. In this study, a set of 221 rats (Rattus norvegicus, R. tanezumi, R. andamanensis, and Niviventer huang) consisting of 104 rats from city areas, 44 from chicken farms, 52 from pig farms, and 21 from stables of horse-riding schools were screened for ESBL-EC. Overall, a total of 134 ESBL-EC were isolated from the caecal samples of 130 (59%) rats. The predominant bla
ESBL genes were blaCTX-M-14 , blaCTX-M-15 , blaCTX-M-55 , and blaCTX-M-65 . Phylogenetic analysis revealed a total of 62 sequence types (STs) and 17 SNP clusters. E. coli ST10 and ST155 were common to ESBL-EC from city areas and chicken farms, and ST44 were found among ESBL-EC from city areas and pig farms. Extra-intestinal pathogenic E. coli (ExPEC) ST69, ST131 and ST1193 were found exclusively among rats from city areas, and avian pathogenic E. coli (APEC) ST177 was restricted to ESBL-EC originating from chicken farms. Phylogenetic analysis showed that the populations of rodent ESBL-EC from city areas, chicken farms and pig farms were genetically different, suggesting a certain degree of partitioning between the human and animal locations. This study contributes to current understanding of ESBL-EC occurring in rats in ecologically diverse locations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2024
- Full Text
- View/download PDF
32. Genetic diversity and antimicrobial susceptibility of Streptococcus suis from diseased Swiss pigs collected between 2019 - 2022.
- Author
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Scherrer S, Biggel M, Schneeberger M, Cernela N, Rademacher F, Schmitt S, and Stephan R
- Subjects
- Animals, Swine, Switzerland epidemiology, Whole Genome Sequencing, Drug Resistance, Bacterial genetics, Virulence genetics, Serogroup, Polymorphism, Single Nucleotide, Streptococcus suis genetics, Streptococcus suis drug effects, Streptococcus suis pathogenicity, Streptococcus suis classification, Streptococcus suis isolation & purification, Swine Diseases microbiology, Genetic Variation, Streptococcal Infections veterinary, Streptococcal Infections microbiology, Anti-Bacterial Agents pharmacology, Microbial Sensitivity Tests
- Abstract
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. The isolates' genomes were sequenced allowing for a comprehensive analysis of their distribution in terms of serovar, sequence type (ST), clonal complex (CC), and classical virulence markers. Antimicrobial resistance (AMR) genes were screened, and phenotypic susceptibility to eight classes of antimicrobial agents was examined. Serovar 6, devoid of any resistance genes, was found to be most prevalent, followed by serovars 1, 3, 1/2, and 9. Thirty STs were identified, with ST1104 being the most prevalent. Serovar 2 and serovar 1/2 were associated with CC1, potentially containing the most virulent variants. Based on single nucleotide polymorphism (SNP) analyses, fifteen isolates belonged to one of seven putative transmission clusters each consisting of two or three isolates. High phenotypic AMR rates were detected for tetracyclines (80%) and macrolides (35%) and associated with the resistance genes tet(O) and erm(B), respectively. In contrast, susceptibility to β-lactam antibiotics and phenicols was high. Determination of phenotypic AMR profiling, including the minimum inhibitory concentrations (MICs) of the tested antimicrobial agents, sets a baseline for future studies. The study provides valuable insights into the genetic diversity and antimicrobial susceptibility of Swiss S. suis isolates, facilitating the identification of emerging clones relevant to public health concerns., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
33. Genomic characteristics of clinical non-toxigenic Vibrio cholerae isolates in Switzerland: a cross-sectional study.
- Author
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Meyer N, Stephan R, Cernela N, Horlbog JA, and Biggel M
- Subjects
- Humans, Cross-Sectional Studies, Phylogeny, Switzerland epidemiology, Genomics, Vibrio cholerae genetics, Cholera epidemiology, Cholera microbiology
- Abstract
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. Up to 20 infections are reported annually. In this study, we investigated the population structure and genetic characteristics of non-toxigenic V. cholerae isolates collected over five years., Methods: V. cholerae isolates were serotyped and non-toxigenic isolates identified using a ctxA-specific PCR. Following Illumina whole-genome sequencing, genome assemblies were screened for virulence and antibiotic resistance genes. Phylogenetic analyses were performed in the context of 965 publicly available V. cholerae genomes., Results: Out of 33 V. cholerae infections reported between January 2017 and January 2022 in Switzerland, 31 were caused by ctxA-negative isolates. These non-toxigenic isolates originated from gastrointestinal (n = 29) or extraintestinal (n = 2) sites. They were phylogenetically diverse and belonged to 29 distinct sequence types. Two isolates were allocated to the lineage L3b, a ctxAB-negative but tcpA-positive clade previously associated with regional outbreaks. The remaining 29 isolates were placed in lineage L4, which is associated with environmental strains. Genes or mutations associated with reduced susceptibility to the first-line antibiotics fluoroquinolones and tetracyclines were identified in 11 and 3 isolates, respectively. One isolate was predicted to be multidrug resistant., Conclusions: V. cholerae infections in Switzerland are rare and predominantly caused by lowly virulent ctxAB-negative and tcpA-negative strains. As V. cholerae is not endemic in Switzerland, cases are assumed to be acquired predominantly during travel. This assumption was supported by the phylogenetic diversity of the analysed isolates.
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- 2024
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34. Whole genome sequence-based characterization of Campylobacter isolated from broiler carcasses over a three-year period in a big poultry slaughterhouse reveals high genetic diversity and a recurring genomic lineage of Campylobacter jejuni.
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Stevens MJA, Stephan R, Horlbog JA, Cernela N, and Nüesch-Inderbinen M
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- Humans, Animals, Poultry microbiology, Abattoirs, Chickens microbiology, Genetic Variation, Genomics, Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial, Campylobacter genetics, Campylobacter jejuni genetics, Campylobacter Infections microbiology, Anti-Infective Agents
- Abstract
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). Campylobacter jejuni (n = 127) and Campylobacter coli (n = 28) were analysed using a whole genome sequencing (WGS) approach (MiniSeq; Illumina). Sequence types (STs) were determined in silico from the WGS data and isolates were assigned into complex types (CTs) using the cgMLST SeqSphere+ scheme. Antimicrobial resistance genes were identified using the Resistance Gene Identifier (RGI), and virulence genes were identified using the virulence factor database (VFDB). A high degree of genetic diversity was observed. Many sequence types (C. jejuni ST19, ST21, ST48, ST50, ST122, ST262 and C. coli ST827) occurred more than once and were distributed throughout the study period, irrespective of the year of isolation and of the broiler farming type. Antimicrobial resistance determinants included bla
OXA and tet(O) genes, as well as the T86I substitution within GyrA. Virulence genes known to play a role in human Campylobacter infection were identified such as the wlaN, cstIII, neuA1, neuB1, and neuC1. Subtyping of the Campylobacter isolates identified the occurrence of a highly clonal population of C. jejuni ST21 that was isolated throughout the three-year study period from carcasses from farms with geographically different locations and different farming systems. The high rate of genetic diversity observed among broiler carcass isolates is consistent with previous studies. The identification of a persisting highly clonal C. jejuni ST21 subtype suggests that the slaughterhouse may represent an environment in which C. jejuni ST21 may survive, however, the ecological reservoir potentially maintaining this clone remains unknown., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)- Published
- 2024
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35. New insights into Bacillus cytotoxicus sources, screening, toxicity, and persistence in food production facilities.
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Etter D, Biggel M, Greutmann M, Cernela N, and Johler S
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- Polymerase Chain Reaction, Plasmids, Bacillus cereus, Enterotoxins genetics, Food Microbiology, Bacillus
- Abstract
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 B. cereus group. The pathogen is mostly found on dehydrated foods containing potato starch or insects. How it enters the food chain or whether it persists in food producing environments is largely unknown. Increased consumption of insects and convenience foods in Europe and the lack of information on the persistence of B. cytotoxicus in food environments and its virulence demand for further characterization. In this study, we aimed to obtain a better understanding of i) the food sources of B. cytotoxicus, ii) screening temperatures needed for its isolation from food matrices, iii) cytotoxicity of the organism, and iv) its ecological niche and potential epidemiological links. To this end, 112 food samples were collected, with a focus on foods exhibiting low water activity. The samples were screened for B. cytotoxicus at 42 °C and at 50 °C. Presumptive isolates were characterized by cytK-1 toxin gene PCR for differentiation of B. cytotoxicus from other B. cereus group members. Vero cell cytotoxicity assays were performed, and selected isolates were sequenced. Our results show that screening at 42 °C might be insufficient for detecting B. cytotoxicus in foods that harbor other less thermophilic Bacillus species. When screening at 50 °C, B. cytotoxicus was detected in 23% of the food samples (n = 26 isolates). The highest prevalence was detected in mashed potato products (82%) and potato flakes (67%). In contrast, a wide range of products not containing any potato ingredients did not yield B. cytotoxicus isolates. All B. cytotoxicus isolates exhibited either low or no detectable cytotoxicity. WGS analysis revealed that a highly toxic isolate is closely related to the French outbreak strain NVH 391-98. In addition, we could show that two isolates sampled 5 years apart from the same production facility only differed by seven SNPs, making it likely that B. cytotoxicus is able to persist in production facilities over a long time. Interestingly, the reoccurring strain possessed an additional plasmid and did not show cytotoxic potential when re-isolated after 5 years., Competing Interests: Declaration of competing interest None, (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)
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- 2024
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36. Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter.
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Nüesch-Inderbinen M, Biggel M, Haussmann A, Treier A, Heyvaert L, Cernela N, and Stephan R
- Abstract
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 oxazolidinone resistance genes., Objective: This study aimed to assess the occurrence of cfr, optrA , and poxtA in florfenicol-resistant isolates from beef cattle and veal calves from different herds in Switzerland., Methods: A total of 618 cecal samples taken from beef cattle and veal calves at slaughter originating from 199 herds were cultured after an enrichment step on a selective medium containing 10 mg/L florfenicol. Isolates were screened by PCR for cfr, optrA , and poxtA which are genes known to confer resistance to oxazolidinones and phenicols. One isolate per PCR-positive species and herd was selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS)., Results: Overall, 105 florfenicol-resistant isolates were obtained from 99 (16%) of the samples, corresponding to 4% of the beef cattle herds and 24% of the veal calf herds. Screening by PCR revealed the presence of optrA in 95 (90%) and poxtA in 22 (21%) of the isolates. None of the isolates contained cfr . Isolates included for AST and WGS analysis were Enterococcus ( E .) faecalis ( n = 14), E. faecium ( n = 12), E. dispar ( n = 1), E. durans ( n = 2), E. gallinarum ( n = 1), Vagococcus ( V .) lutrae ( n = 2), Aerococcus ( A .) urinaeequi ( n = 1), and Companilactobacillus ( C .) farciminis ( n = 1). Thirteen isolates exhibited phenotypic linezolid resistance. Three novel OptrA variants were identified. Multilocus sequence typing identified four E. faecium ST18 belonging to hospital-associated clade A1. There was a difference in the replicon profile among optrA- and poxtA -harboring plasmids, with rep9 (RepA_ N ) plasmids dominating in optrA -harboring E. faecalis and rep2 (Inc18) and rep29 (Rep_3) plasmids in poxtA -carrying E. faecium ., Conclusion: Beef cattle and veal calves are reservoirs for enterococci with acquired linezolid resistance genes optrA and poxtA . The presence of E. faecium ST18 highlights the zoonotic potential of some bovine isolates. The dispersal of clinically relevant oxazolidinone resistance genes throughout a wide variety of species including Enterococcus spp., V. lutrae, A. urinaeequi , and the probiotic C. farciminis in food-producing animals is a public health concern., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Nüesch-Inderbinen, Biggel, Haussmann, Treier, Heyvaert, Cernela and Stephan.)
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- 2023
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37. Emergence of bla SHV-12 and qnrS1 encoded on IncX3 plasmids: Changing epidemiology of extended-spectrum ß-lactamases among Enterobacterales isolated from broilers.
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Nüesch-Inderbinen M, Heyvaert L, Cernela N, Zurfluh K, Biggel M, and Stephan R
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- Animals, Humans, Anti-Bacterial Agents pharmacology, Chickens, Plasmids genetics, beta-Lactamases genetics, Klebsiella pneumoniae genetics, Escherichia coli genetics, Escherichia coli Infections epidemiology, Escherichia coli Infections veterinary
- Abstract
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 bla
ESBL genes via the food chain or within settings where human-animal interfaces exist., Methods: This study assessed the occurrence of ESBL producers among faecal samples of broilers at slaughter. Isolates were characterised by multilocus sequence typing, antimicrobial susceptibility testing, and whole-genome sequencing., Results: The flock prevalence, determined by sampling crates of 100 poultry flocks, was 21%. The predominant blaESBL gene was blaSHV-12 , identified in 92% of the isolates. A variety of Escherichia coli and Klebsiella pneumoniae sequence types (STs) were identified, including extraintestinal pathogenic E. coli ST38, avian pathogenic E. coli ST10, ST93, ST117, and ST155, and nosocomial outbreak clone K. pneumoniae ST20. Whole-genome sequencing was used to characterise a subset of 15 isolates, including 6 E. coli, 4 K. pneumoniae, 1 Klebsiella grimontii, 1 Klebsiella michiganensis, 1 Klebsiella variicola, and 1 Atlantibacter subterranea. Fourteen isolates carried identical or closely related 46338-54929 bp IncX3 plasmids encoding blaSHV-12 and qnrS1. One E. coli isolate carried a 46338 bp IncX3 plasmid, which was integrated chromosomally into ydbD., Conclusions: The blaSHV-12 gene has replaced the previously predominant blaCTX-M-1 in ESBL-producing Enterobacterales from broilers in Switzerland. Broilers may play a role in the dissemination of blaSHV-12 and qnrS1 associated with epidemic IncX3 plasmids, representing a risk to human and animal health., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)- Published
- 2023
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38. High occurrence of Enterococcus faecalis , Enterococcus faecium , and Vagococcus lutrae harbouring oxazolidinone resistance genes in raw meat-based diets for companion animals - a public health issue, Switzerland, September 2018 to May 2020.
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Nüesch-Inderbinen M, Heyvaert L, Treier A, Zurfluh K, Cernela N, Biggel M, and Stephan R
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- Humans, Animals, Enterococcus faecalis, Linezolid pharmacology, Anti-Bacterial Agents pharmacology, Pets, Public Health, Switzerland epidemiology, Drug Resistance, Bacterial genetics, Chloramphenicol pharmacology, Meat, Diet, Microbial Sensitivity Tests, Oxazolidinones pharmacology, Enterococcus faecium, Anti-Infective Agents, Gram-Positive Bacterial Infections epidemiology, Gram-Positive Bacterial Infections veterinary, Gram-Positive Bacterial Infections microbiology
- Abstract
IntroductionEnterococci harbouring genes encoding resistance to florfenicol and the oxazolidinone antimicrobial linezolid have emerged among food-producing animals and meat thereof, but few studies have analysed their occurrence in raw meat-based diets (RMBDs) for pets.AimWe aimed to examine how far RMBDs may represent a source of bacteria with oxazolidinone resistance genes.MethodsFifty-nine samples of different types of RMBDs from 10 suppliers (three based in Germany, seven in Switzerland) were screened for florfenicol-resistant Gram-positive bacteria using a selective culture medium. Isolates were phenotypically and genotypically characterised.ResultsA total of 27 Enterococcus faecalis , Enterococcus faecium , and Vagococcus lutrae isolates were obtained from 24 of the 59 samples. The optrA , poxtA , and cfr genes were identified in 24/27, 6/27 and 5/27 isolates, respectively. Chloramphenicol and linezolid minimum inhibitory concentrations (MICs) ranged from 24.0 mg/L-256.0 mg/L, and 1.5 mg/L-8.0 mg/L, respectively. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoints, 26 of 27 isolates were resistant to chloramphenicol (MICs ≥ 32 mg/L), and two were resistant to linezolid (MICs ≥ 8 mg/L). Multilocus sequence typing analysis of the 17 E. faecalis isolates identified 10 different sequence types (ST)s, with ST593 (n = 4 isolates) and ST207 (n = 2 isolates) occurring more than once, and two novel STs (n = 2 isolates). E. faecium isolates belonged to four different STs (168, 264, 822, and 1846).ConclusionThe high occurrence in our sample of Gram-positive bacteria harbouring genes encoding resistance to the critical antimicrobial linezolid is of concern since such bacteria may spread from companion animals to humans upon close contact between pets and their owners.
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- 2023
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39. Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance.
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Ghielmetti G, Seth-Smith HMB, Roloff T, Cernela N, Biggel M, Stephan R, and Egli A
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- Animals, Humans, Anti-Bacterial Agents pharmacology, Prevalence, Drug Resistance, Bacterial, Poultry microbiology, Tetracycline, Campylobacter jejuni genetics, Gastroenteritis
- Abstract
Campylobacteriosis is the most common cause of acute gastrointestinal bacterial infection in Europe, with most infections linked to the consumption of contaminated food. While previous studies found an increasing rate of antimicrobial resistance (AMR) in Campylobacter spp. over the past decades, the investigation of additional clinical isolates is likely to provide novel insights into the population structure and mechanisms of virulence and drug resistance of this important human pathogen. Therefore, we combined whole-genome sequencing and antimicrobial-susceptibility testing of 340 randomly selected Campylobacter jejuni isolates from humans with gastroenteritis, collected in Switzerland over an 18 year period. In our collection, the most common multilocus sequence types (STs) were ST-257 ( n =44), ST-21 ( n =36) and ST-50 ( n =35); the most common clonal complexes (CCs) were CC-21 ( n =102), CC-257 ( n =49) and CC-48 ( n =33). High heterogeneity was observed among STs, with the most abundant STs recurring over the entire study period, while others were observed only sporadically. Source attribution based on ST assigned more than half of the strains to the 'generalist' category ( n =188), 25 % as 'poultry specialist' ( n =83), and only a few to 'ruminant specialist' ( n =11) or 'wild bird' origin ( n =9). The isolates displayed an increased frequency of AMR from 2003 to 2020, with the highest rates of resistance observed for ciprofloxacin and nalidixic acid (49.8 %), followed by tetracycline (36.9 %). Quinolone-resistant isolates carried chromosomal gyrA mutations T86I (99.4 %) and T86A (0.6 %), whereas tetracycline-resistant isolates carried tet(O ) (79.8 %) or mosaic tetO/32/O (20.2 %) genes. A novel chromosomal cassette carrying several resistance genes, including aph(3')-III , satA and aad (6), and flanked by insertion sequence elements was detected in one isolate. Collectively, our data revealed an increasing prevalence of resistance to quinolones and tetracycline in C. jejuni isolates from Swiss patients over time, linked to clonal expansion of gyrA mutants and acquisition of the tet(O ) gene. Investigation of source attribution suggests that infections are most likely related to isolates from poultry or generalist backgrounds. These findings are relevant to guide future infection prevention and control strategies.
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- 2023
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40. Finding of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in wild game meat originating from several European countries: predominance of Moellerella wisconsensis producing CTX-M-1, November 2021.
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Nüesch-Inderbinen M, Tresch S, Zurfluh K, Cernela N, Biggel M, and Stephan R
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- Humans, Phylogeny, beta-Lactamases genetics, Enterobacteriaceae genetics, Meat microbiology, Europe epidemiology, Escherichia coli, Escherichia coli Infections epidemiology
- Abstract
IntroductionMeat can be a vehicle for food-borne transmission of antimicrobial resistant bacteria and antimicrobial resistance genes. The occurrence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales has been observed in meat from livestock production but has not been well studied in meat from wild game.AimWe aimed to investigate, particularly in central Europe, to what extent ESBL-producing Enterobacterales may be present in wild game meat.MethodsA total of 111 samples of different types of game meat supplied by butchers, hunters, retail stores and a large game-processing establishment in Europe were screened for ESBL-producing Enterobacterales using a selective culture medium. Isolates were genotypically and phenotypically characterised.ResultsThirty-nine samples (35% of the total) yielded ESBL-producing Enterobacterales, with most (35/39) supplied by the game-processing establishment. Isolates included 32 Moellerella wisconsensis , 18 Escherichia coli and one Escherichia marmotae . PCR screening identified bla (n = 31),
CTX-M-1 (n = 8), bla (n = 4),CTX-M-32 (n = 3), bla (n = 1),CTX-M-65 (n = 1), bla (n = 1), andCTX-M-15 (n = 2). Most bla belonged to phylogenetic group A (n = 7) or B1 (n = 9), but several isolates belonged to extraintestinal pathogenicCTX-M-8 (ExPEC) sequence types (ST)58 (n = 4), ST68 (n = 1) and ST540 (n = 1). Whole genome sequencing of six selected isolates localised blaCTX-M-14 (n = 1), blaCTX-M-55 (n = 1), and blaSHV-12 (n = 2). Most E. coli belonged to phylogenetic group A (n = 7) or B1 (n = 9), but several isolates belonged to extraintestinal pathogenic E. coli (ExPEC) sequence types (ST)58 (n = 4), ST68 (n = 1) and ST540 (n = 1). Whole genome sequencing of six selected isolates localised blaCTX-M-1 on megaplasmids in four M. wisconsensis and blaCTX-M-32 on IncN_1 plasmids in one M. wisconsensis and one E. marmotae . Forty-eight isolates (94%) exhibited a multidrug-resistance phenotype.ConclusionWe found a high occurrence of ESBL-producing Enterobacterales in wild game meat, suggesting wildlife habitat pollution and possible microbial contamination events occurring during skinning or cutting carcasses.- Published
- 2022
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41. Nitrite stress increases staphylococcal enterotoxin C transcription and triggers the SigB regulon.
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Etter D, Büchel R, Patt T, Biggel M, Tasara T, Cernela N, Stevens MJA, and Johler S
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- Enterotoxins metabolism, Humans, RNA, Messenger, Regulon, Nitrites, Staphylococcal Infections
- Abstract
Staphylococcal food poisoning is a common food intoxication caused by staphylococcal enterotoxins. While growth of Staphylococcus aureus is not inhibited by the meat-curing agent nitrite, we hypothesize that nitrite has an influence on enterotoxin C (SEC) expression. We investigated the influence of 150 mg/l nitrite on SEC expression at mRNA and protein level in seven strains expressing different SEC variants. Additionally, regulatory knockout mutants (Δagr, ΔsarA, and ΔsigB) of high SEC producing strain SAI48 were investigated at mRNA level. Our findings suggest that nitrite effectively increases sec mRNA transcription, but the effects on SEC protein expression are less pronounced. While Δagr mutants exhibited lower sec mRNA transcription levels than wildtype strains, this response was not stress specific. ΔsigB mutants displayed a nitrite stress-specific response. Whole genome sequencing of the strains revealed a defective agr element in one strain (SAI3). In this strain, sec transcription and SEC protein synthesis was not affected by the mutation. Consequently, additional regulatory networks must be at play in SEC expression. Comparison of our findings about SEC with previous experiments on SEB and SED suggest that each SE can respond differently, and that the same stressor can trigger opposing responses in strains that express multiple toxins., (© The Author(s) 2022. Published by Oxford University Press on behalf of FEMS.)
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- 2022
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42. Unraveling the Genotypic and Phenotypic Diversity of the Psychrophilic Clostridium estertheticum Complex, a Meat Spoilage Agent.
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Wambui J, Stevens MJA, Cernela N, and Stephan R
- Abstract
The spoilage of vacuum-packed meat by Clostridium estertheticum complex (CEC), which is accompanied by or without production of copious amounts of gas, has been linked to the acetone-butyrate-ethanol fermentation, but the mechanism behind the variable gas production has not been fully elucidated. The reconstruction and comparison of intra- and interspecies metabolic pathways linked to meat spoilage at the genomic level can unravel the genetic basis for the variable phenotype. However, this is hindered by unavailability of CEC genomes, which in addition, has hampered the determination of genetic diversity and its drivers within CEC. Therefore, the current study aimed at determining the diversity of CEC through comprehensive comparative genomics. Fifty CEC genomes from 11 CEC species were compared. Recombination and gene gain/loss events were identified as important sources of natural variation within CEC, with the latter being pronounced in genomospecies2 that has lost genes related to flagellar assembly and signaling. Pan-genome analysis revealed variations in carbohydrate metabolic and hydrogenases genes within the complex. Variable inter- and intraspecies gas production in meat by C. estertheticum and Clostridium tagluense were associated with the distribution of the [NiFe]-hydrogenase hyp gene cluster whose absence or presence was associated with occurrence or lack of pack distention, respectively. Through comparative genomics, we have shown CEC species exhibit high genetic diversity that can be partly attributed to recombination and gene gain/loss events. We have also shown genetic basis for variable gas production in meat can be attributed to the presence/absence of the hyp gene cluster., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Wambui, Stevens, Cernela and Stephan.)
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- 2022
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43. Targeted Genome Mining Reveals the Psychrophilic Clostridium estertheticum Complex as a Potential Source for Novel Bacteriocins, Including Cesin A and Estercticin A.
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Wambui J, Stevens MJA, Sieber S, Cernela N, Perreten V, and Stephan R
- Abstract
Antimicrobial resistance in pathogenic bacteria is considered a major public health issue necessitating the discovery of alternative antimicrobial compounds. In this regard, targeted genome mining in bacteria occupying under-explored ecological niches has the potential to reveal such compounds, including bacteriocins. In this study, we determined the bacteriocin biosynthetic potential of the psychrophilic Clostridium estertheticum complex (CEC) through a combination of genome mining and phenotypic screening assays. The genome mining was performed in 40 CEC genomes using antiSMASH. The production of bacteriocin-like compounds was phenotypically validated through agar well (primary screening) and disk diffusion (secondary screening) assays using cell free supernatants (CFS) and partially purified extracts, respectively. Stability of four selected CFS against proteolytic enzymes, temperature and pH was determined while one CFS was analyzed by HRMS and MS/MS to identify potential bacteriocins. Twenty novel bacteriocin biosynthetic gene clusters (BBGC), which were classified into eight (six lantibiotics and two sactipeptides) distinct groups, were discovered in 18 genomes belonging to C. estertheticum ( n = 12), C. tagluense ( n = 3) and genomospecies2 ( n = 3). Primary screening linked six BBGC with narrow antimicrobial activity against closely related clostridia species. All four preselected CFS retained activity after exposure to different proteolytic, temperature and pH conditions. Secondary screening linked BBGC1 and BBGC7 encoding a lantibiotic and sactipeptide, respectively, with activity against Bacillus cereus while lantibiotic-encoding BBGC2 and BBGC3 were linked with activity against B. cereus , Staphylococcus aureus (methicillin-resistant), Escherichia coli and Pseudomonas aeruginosa . MS/MS analysis revealed that C. estertheticum CF004 produces cesin A, a short natural variant of nisin, and HRMS indicated the production of a novel sactipeptide named estercticin A. Therefore, we have shown the CEC, in particular C. estertheticum , is a source of novel and stable bacteriocins that have activities against clinically relevant pathogens., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Wambui, Stevens, Sieber, Cernela, Perreten and Stephan.)
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- 2022
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44. Distribution of virulence factors, antimicrobial resistance genes and phylogenetic relatedness among Shiga toxin-producing Escherichia coli serogroup O91 from human infections.
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Nüesch-Inderbinen M, Stevens MJA, Cernela N, Müller A, Biggel M, and Stephan R
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- Anti-Bacterial Agents, Drug Resistance, Bacterial genetics, Humans, Membrane Transport Proteins, Phylogeny, Serogroup, Virulence Factors genetics, Anti-Infective Agents, Escherichia coli Proteins genetics, Shiga-Toxigenic Escherichia coli genetics
- Abstract
Shiga toxin-producing Escherichia coli (STEC) belonging to the serogroup O91 are among the most common non-O157 STEC serogroups associated with human illness in Europe. This study aimed to analyse the virulence factors, antimicrobial resistance genes and phylogenetic relatedness among 48 clinical STEC O91 isolates collected during 2003-2019 in Switzerland. The isolates were subjected to whole genome sequencing using short-read sequencing technologies and a subset of isolates additionally to long-read sequencing. They belonged to O91:H10 (n=6), O91:H14 (n=40), and O91:H21 (n=2). Multilocus sequence typing showed that the O91:H10 isolates all belonged to sequence type (ST)641, while the O91:H14 isolates were assigned to ST33, ST9700, or were non-typeable. Both O91:H21 isolates belonged to ST442. Shiga toxin gene stx1a was the most common Shiga toxin gene subtype among the isolates, followed by stx2b, stx2d and stx2a. All isolates were LEE-negative and carried one or two copies of the IrgA adhesin gene iha. In a subset of long-read sequenced isolates, modules of the Locus of Adhesion and Autoaggregation pathogenicity island (LAA-PAI) carrying iha and other genes such as hes, lesP or agn43 were identified. A large proportion of STEC O91:H14 carried the subtilase cytotoxin gene subA, colicin genes (cba, cea, cib and cma) or microcin genes (mcmA, mchB, mchC and mchF). STEC O91:H14 were further distinguished from STEC O91:H10/H21 by one or more virulence factors found in extraintestinal pathogenic E. coli (ExPEC), including hlyF, iucC/iutA, kpsE and traT. The hlyF gene was identified on a novel mosaic plasmid that was unrelated to hlyF+ plasmids described previously in STEC. Core genome phylogenetic analysis revealed that STEC O91:H10 and STEC O91:H21 were clonally conserved, whereas STEC O91:H14 were clonally diverse. Among three STEC O91:H14 isolates, a number of resistance genes were identified, including genes that mediate resistance to aminoglycosides (aadA, aadA2, aadA9, aadA23, aph(3'')-Ib and aph(6)-Id), chloramphenicol (cmlA), sulphonamides (sul2 and sul3), and trimethoprim (drfA12). Our data contribute to understanding the genetic diversity and differing levels of virulence potential within the STEC O91 serogroup., (Copyright © 2021 The Authors. Published by Elsevier GmbH.. All rights reserved.)
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- 2021
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45. Whole Genome Sequence-Based Identification of Clostridium estertheticum Complex Strains Supports the Need for Taxonomic Reclassification Within the Species Clostridium estertheticum .
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Wambui J, Cernela N, Stevens MJA, and Stephan R
- Abstract
Isolates within the Clostridium estertheticum complex (CEC) have routinely been identified through the 16S rRNA sequence, but the high interspecies sequence similarity reduces the resolution necessary for species level identification and often results in ambiguous taxonomic classification. The current study identified CEC isolates from meat juice (MJS) and bovine fecal samples (BFS) and determined the phylogeny of species within the CEC through whole genome sequence (WGS)-based analyses. About 1,054 MJS were screened for CEC using quantitative real-time PCR (qPCR). Strains were isolated from 33 MJS and 34 BFS qPCR-positive samples, respectively. Pan- and core-genome phylogenomics were used to determine the species identity of the isolates. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were used to validate the species identity. The phylogeny of species within the CEC was determined through a combination of these methods. Twenty-eight clostridia strains were isolated from MJS and BFS samples out of which 13 belonged to CEC. At 95% ANI and 70% dDDH thresholds for speciation, six CEC isolates were identified as genomospecies2 ( n =3), Clostridium tagluense ( n =2) and genomospecies3 ( n =1). Lower thresholds of 94% ANI and 58% dDDH were required for the classification of seven CEC isolates into species C. estertheticum and prevent an overlap between species C. estertheticum and Clostridium frigoriphilum . Combination of the two species and abolishment of current subspecies classification within the species C. estertheticum are proposed. These data demonstrate the suitability of phylogenomics to identify CEC isolates and determine the phylogeny within CEC., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Wambui, Cernela, Stevens and Stephan.)
- Published
- 2021
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46. Draft Genome Sequences of Two Clinical Actinobacillus pleuropneumoniae Serotype 19 Strains from Pigs in Switzerland.
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Peterhans S, Stevens MJA, Cernela N, Sidler X, Stephan R, and Scherrer S
- Abstract
Actinobacillus pleuropneumoniae serotype 19 is a very recently described new serotype with a novel type II capsule synthesis locus. Here, we report the draft genome sequences of two Actinobacillus pleuropneumoniae serotype 19 strains with a serogroup 3/6/8/12/15 O-antigen locus that were isolated in 2018 and 2021 from two different pig farms in Switzerland.
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- 2021
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47. High Occurrence of Shiga Toxin-Producing Escherichia coli in Raw Meat-Based Diets for Companion Animals-A Public Health Issue.
- Author
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Treier A, Stephan R, Stevens MJA, Cernela N, and Nüesch-Inderbinen M
- Abstract
Feeding pets raw meat-based diets (RMBDs) is becoming increasingly popular but comes with a risk of pathogenic bacteria, including Shiga toxin-producing Escherichia coli (STEC). In humans, STEC may cause gastrointestinal illnesses, including diarrhea, hemorrhagic colitis (HC), and the hemolytic uremic syndrome (HUS). The aim of this study was to evaluate commercially available RMBDs with regard to the occurrence of STEC. Of 59 RMBD samples, 59% tested positive by real-time PCR for the presence of Shiga toxin genes stx1 and/or stx2 . STECs were recovered from 41% of the 59 samples, and strains were subjected to serotyping and virulence gene profiling, using whole genome sequencing (WGS)-based methods. Of 28 strains, 29% carried stx2a or stx2d , which are linked to STEC with high pathogenic potential. Twenty different serotypes were identified, including STEC O26:H11, O91:H10, O91:H14, O145:H28, O146:H21, and O146:H28, which are within the most common non-O157 serogroups associated with human STEC-related illnesses worldwide. Considering the low infectious dose and potential severity of disease manifestations, the high occurrence of STEC in RMBDs poses an important health risk for persons handling raw pet food and persons with close contact to pets fed on RMBDs, and is of concern in the field of public health.
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- 2021
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48. Environmental dissemination of pathogenic Listeria monocytogenes in flowing surface waters in Switzerland.
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Raschle S, Stephan R, Stevens MJA, Cernela N, Zurfluh K, Muchaamba F, and Nüesch-Inderbinen M
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- Animals, Genetic Variation, Genotype, Listeriosis genetics, Switzerland, Whole Genome Sequencing, Bacterial Proteins genetics, Ecosystem, Genome, Bacterial, Genomic Islands, Listeria monocytogenes pathogenicity, Listeriosis microbiology
- Abstract
Listeria monocytogenes is an opportunistic pathogen that is widely distributed in the environment. The aquatic environment may represent a potential source for the transmission of L. monocytogenes to animals and the food chain. The present study assessed the occurrence of L. monocytogenes in 191 surface water samples from rivers, streams and inland canals throughout Switzerland. Twenty-five (13%) of the surface water samples contained L. monocytogenes. Whole genome sequence (WGS) data were used to characterize the 25 isolates. The isolates belonged to major lineages I and II, with the majority assigned to either serotype 1/2a (48%), or 4b (44%). The predominant CCs identified were the hypervirulent serotype 4b clones CC1 and CC4, and the serotype CC412; all three have been implicated in listeriosis outbreaks and sporadic cases of human and animal infection worldwide. Two (8%) of the isolates belonged to CC6 which is an emerging hypervirulent clone. All isolates contained intact genes associated with invasion and infection, including inlA/B and prfA. The four CC4 isolates all harbored Listeria pathogenicity island 4 (LIPI-4), which confers hypervirulence. The occurrence of L. monocytogenes in river ecosystems may contribute to the dissemination and introduction of clinically highly relevant strains to the food chain.
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- 2021
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49. Correction: Wist et al. Phenotypic and Genotypic Traits of Vancomycin-Resistant Enterococci from Healthy Food-Producing Animals. Microorganisms 2020, 8 , 261.
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Wist V, Morach M, Schneeberger M, Cernela N, Stevens MJA, Zurfluh K, Stephan R, and Nüesch-Inderbinen M
- Abstract
The authors wish to make the following correction to this paper [...].
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- 2021
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50. Draft Genome Sequences of 19 Clinical stx -Harboring Escherichia coli O80:H2 Strains.
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Stevens MJA, Cernela N, Müller A, Nüesch-Inderbinen M, and Stephan R
- Abstract
Shiga toxin-producing Escherichia coli (STEC) O80:H2 is an uncommon hybrid pathotype that has emerged in Switzerland and France. Here, we report the draft genome sequences of 19 stx -harboring Escherichia coli O80:H2 strains isolated between 2003 and 2019 from patients in Switzerland., (Copyright © 2021 Stevens et al.)
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- 2021
- Full Text
- View/download PDF
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