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Article ; Online: Rapid detection of plasmid-mediated AmpC-producers by eazyplex® SuperBug AmpC assay compared to whole-genome sequencing.

Hinić, Vladimira / Seth-Smith, Helena M B / Stammler, Sabrina / Egli, Adrian

2024 Volume 221, Page(s) 106938

Abstract: Current methods for plasmid-mediated AmpC β-lactamase (pAmpC) detection in routine microbiological laboratories are based on various phenotypic tests. Eazyplex®SuperBug AmpC assay is a molecular assay based on isothermal amplification for rapid detection ...

Abstract	Current methods for plasmid-mediated AmpC β-lactamase (pAmpC) detection in routine microbiological laboratories are based on various phenotypic tests. Eazyplex®SuperBug AmpC assay is a molecular assay based on isothermal amplification for rapid detection of the most common pAmpC types from bacterial culture: CMY-2 group, DHA, ACC and MOX. Our aim was to evaluate the diagnostic performance of this assay. The assay was evaluated on 64 clinical isolates of Enterobacterales without chromosomal inducible AmpC, and with phenotypically confirmed AmpC production. The results were confirmed, and isolates further characterized by whole-genome sequencing (WGS). eazyplex®SuperBug AmpC assay correctly detected the two most common pAmpC types CMY-2 group (16/16) and DHA (19/19). Detection of ACC and MOX could not be evaluated on our set of isolates since there was only one isolate harbouring ACC and none with MOX. pAmpC encoding genes could be detected in only eight of 36 investigated Escherichia coli isolates. The remaining 28 E. coli isolates harboured previously described mutations in the bla
MeSH term(s)	beta-Lactamases/genetics ; Plasmids/genetics ; Whole Genome Sequencing/methods ; Bacterial Proteins/genetics ; Humans ; Escherichia coli/genetics ; Escherichia coli/isolation & purification ; Enterobacteriaceae/genetics ; Enterobacteriaceae/isolation & purification ; Enterobacteriaceae/enzymology ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Nucleic Acid Amplification Techniques/methods
Chemical Substances	AmpC beta-lactamases
Language	English
Publishing date	2024-04-19
Publishing country	Netherlands
Document type	Journal Article ; Comparative Study
ZDB-ID	604916-3
ISSN	1872-8359 ; 0167-7012
ISSN (online)	1872-8359
ISSN	0167-7012
DOI	10.1016/j.mimet.2024.106938
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Article ; Online: SARS-CoV-2 in an immunocompromised host: convalescent plasma therapy and viral evolution elucidated by whole genome sequencing.

Seth-Smith, Helena / Vesenbeckh, Silvan / Egli, Adrian / Ott, Sebastian

BMJ case reports

2023 Volume 16, Issue 12

Abstract: The evolution of SARS-CoV-2 within immunocompromised hosts who fail to clear the virus over many months has been proposed as a route to the development of Variants of Concern (VoCs). We present a case of an immunocompromised male patient with a prolonged ...

Abstract	The evolution of SARS-CoV-2 within immunocompromised hosts who fail to clear the virus over many months has been proposed as a route to the development of Variants of Concern (VoCs). We present a case of an immunocompromised male patient with a prolonged SARS-CoV-2 infection. During hospitalisation, 7 weeks after first diagnosis, his condition worsened to require continuous ventilation support. Resolution of symptoms was observed after convalescent plasma therapy. Whole genome sequencing of the virus showed Pango lineage B.1.221. Between the first sample and the second from bronchoalveolar lavage fluid 7 weeks later, we identified eight mutations, including minor variants, which could be used to estimate the chronology of mutations. This suggests an elevated mutation rate, in-host accumulation of mutations and further evidence for sources of VoCs. Prolonged SARS-CoV-2 infections in immunocompromised hosts increase the likelihood of hospital stays and morbidity, and also pose an increased risk to global public health.
MeSH term(s)	Humans ; Male ; SARS-CoV-2/genetics ; COVID-19/therapy ; COVID-19 Serotherapy ; Immunization, Passive ; Whole Genome Sequencing ; Immunocompromised Host ; Mutation ; Genome, Viral
Language	English
Publishing date	2023-12-09
Publishing country	England
Document type	Case Reports ; Journal Article
ISSN	1757-790X
ISSN (online)	1757-790X
DOI	10.1136/bcr-2023-255255
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Article ; Online: Whole-genome-based characterization of

Ghielmetti, Giovanni / Seth-Smith, Helena M B / Roloff, Tim / Cernela, Nicole / Biggel, Michael / Stephan, Roger / Egli, Adrian

Microbial genomics

2023 Volume 9, Issue 2

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) ... ...

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
MeSH term(s)	Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; Campylobacter jejuni/genetics ; Prevalence ; Drug Resistance, Bacterial ; Poultry/microbiology ; Tetracycline ; Gastroenteritis
Chemical Substances	Anti-Bacterial Agents ; Tetracycline (F8VB5M810T)
Language	English
Publishing date	2023-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000941
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Article ; Online: Evaluation of the RESIST ACINETO multiplex immunochromatographic assay for detection of OXA-23-like, OXA-40/58-like and NDM carbapenemase production in Acinetobacter baumannii.

Mancini, Stefano / Seth-Smith, Helena M B / Kolesnik-Goldmann, Natalia / Hinic, Vladimira / Roloff, Tim / Imkamp, Frank / Egli, Adrian

The Journal of antimicrobial chemotherapy

2023 Volume 78, Issue 11, Page(s) 2771–2774

MeSH term(s)	Acinetobacter baumannii ; Bacterial Proteins/genetics ; Bacterial Proteins/analysis ; beta-Lactamases/genetics ; beta-Lactamases/analysis ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests
Chemical Substances	carbapenemase (EC 3.5.2.6) ; Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-08-11
Publishing country	England
Document type	Research Support, Non-U.S. Gov't ; Letter
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkad253
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Zs.A 1197: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Description of Pseudoclavibacter triregionum sp. nov. from human blood and Pseudoclavibacter albus comb. nov., and revised classification of the genus Pseudoclavibacter: proposal of Caespitibacter gen. nov., with Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov

Vandamme, Peter / Peeters, Charlotte / Seth-Smith, Helena M. B. / Schmid, Hanna / Cnockaert, Margo / Egli, Adrian / Goldenberger, Daniel

Antonie van Leeuwenhoek. 2022 Apr., v. 115, no. 4 p.461-472

2022

Abstract: We present polyphasic taxonomic data to demonstrate that strain 125703-2019ᵀ, a human blood isolate, represents a novel species within the genus Pseudoclavibacter, and to reclassify the illegitimate Zimmermannella alba Lin et al., 2004 as ... ...

Abstract	We present polyphasic taxonomic data to demonstrate that strain 125703-2019ᵀ, a human blood isolate, represents a novel species within the genus Pseudoclavibacter, and to reclassify the illegitimate Zimmermannella alba Lin et al., 2004 as Pseudoclavibacter albus comb. nov. Upon primary isolation, strain 125703-2019ᵀ could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that it belonged to the genus Pseudoclavibacter. Average nucleotide identity and digital DNA-DNA hybridisation analyses confirmed that it represented a novel species within this genus. A detailed physiological characterisation yielded differential tests between the novel species and its nearest neighbor taxa, which could also be differentiated using MALDI-TOF mass spectrometry. We propose to formally classify this strain into the novel species Pseudoclavibacter triregionum sp. nov., with strain 125703-2019ᵀ (= R-76471ᵀ, LMG 31777ᵀ, CCUG 74796ᵀ) as the type strain. The whole-genome assembly of strain 125703-2019ᵀ has a size of 2.4 Mb and a G + C content of 72.74%. A Pseudoclavibacter pangenome analysis revealed that 667 gene clusters were exclusively present in strain 125703-2019ᵀ. While these gene clusters were enriched in several COG functional categories, this analysis did not reveal functions that explained the occurrence of this species in human infection. Finally, several phylogenetic and phylogenomic analyses demonstrated that the genus Pseudoclavibacter is polyphyletic with Pseudoclavibacter soli and Pseudoclavibacter caeni representing a unique and deeply branching line of descent within the family Microbacteriaceae. We therefore also propose to reclassify both species into the novel genus Caespitibacter gen. nov. as Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov., respectively, and with C. soli comb. nov. as the type species.
Keywords	Microbacteriaceae ; blood ; genes ; human diseases ; humans ; hybridization ; matrix-assisted laser desorption-ionization mass spectrometry ; new genus ; nucleotide sequences ; polyphyly ; sequence analysis
Language	English
Dates of publication	2022-04
Size	p. 461-472.
Publishing place	Springer International Publishing
Document type	Article ; Online
ZDB-ID	214861-4
ISSN	1572-9699 ; 0003-6072
ISSN (online)	1572-9699
ISSN	0003-6072
DOI	10.1007/s10482-022-01712-0
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Article ; Online: Regional spread of an atypical ESBL-producing

Martischang, Romain / Seth-Smith, Helena / Verschuuren, Tess D / Héquet, Delphine / Gaïa, Nadia / François, Patrice / Fluit, Ad C / Kluytmans, Jan A J W / Seiffert, Salome N / Tacconelli, Evelina / Cherkaoui, Abdessalam / Harbarth, Stephan / Egli, Adrian / Kohler, Philipp

Antimicrobial agents and chemotherapy

2024 Volume 68, Issue 2, Page(s) e0092523

Abstract: We describe the inter-regional spread of a novel ESBL- ... ...

Abstract	We describe the inter-regional spread of a novel ESBL-producing
MeSH term(s)	Humans ; Escherichia coli Infections/epidemiology ; Switzerland ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Anti-Bacterial Agents ; beta-Lactamases ; Molecular Epidemiology
Chemical Substances	Escherichia coli Proteins ; Anti-Bacterial Agents ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2024-01-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/aac.00925-23
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Zs.A 809: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing.

Muigg, Veronika / Seth-Smith, Helena M B / Adam, Kai-Manuel / Weisser, Maja / Hinić, Vladimira / Blaich, Annette / Roloff, Tim / Heininger, Ulrich / Schmid, Hanna / Kohler, Maurus / Graf, Lukas / Winterflood, Dylan M / Schlaepfer, Pascal / Goldenberger, Daniel

BMC microbiology

2024 Volume 24, Issue 1, Page(s) 14

Abstract: Background: Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot ... ...

Abstract	Background: Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS). Results: We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently. Conclusion: Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.
MeSH term(s)	Bacteria/genetics ; Whole Genome Sequencing ; Corynebacterium/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; RNA, Ribosomal, 16S/genetics ; Bacterial Typing Techniques/methods
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2024-01-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2041505-9
ISSN	1471-2180 ; 1471-2180
ISSN (online)	1471-2180
ISSN	1471-2180
DOI	10.1186/s12866-023-03163-7
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Article: Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings.

Seth-Smith, Helena M B / Egli, Adrian

Frontiers in public health

2019 Volume 7, Page(s) 235

Abstract: Corynebacterium ... ...

Abstract	Corynebacterium diphtheriae
Language	English
Publishing date	2019-08-21
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2711781-9
ISSN	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2019.00235
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Article: S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5.

Hilti, Dominique / Wehrli, Faina / Berchtold, Sabine / Bigler, Susanna / Bodmer, Thomas / Seth-Smith, Helena M B / Roloff, Tim / Kohler, Philipp / Kahlert, Christian R / Kaiser, Laurent / Egli, Adrian / Risch, Lorenz / Risch, Martin / Wohlwend, Nadia

Microorganisms

2024 Volume 12, Issue 2

Abstract: During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex ... ...

Abstract	During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPath
Language	English
Publishing date	2024-02-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms12020321
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Article: Campylobacter jejuni from Canine and Bovine Cases of Campylobacteriosis Express High Antimicrobial Resistance Rates against (Fluoro)quinolones and Tetracyclines

Moser, Sarah / Seth-Smith, Helena / Egli, Adrian / Kittl, Sonja / Overesch, Gudrun

Pathogens. 2020 Aug. 23, v. 9, no. 9

2020

Abstract: Campylobacter (C.) spp. from poultry is the main source of foodborne human campylobacteriosis, but diseased pets and cattle shedding Campylobacter spp. may contribute sporadically as a source of human infection. As fluoroquinolones are one of the drugs ... ...

Abstract	Campylobacter (C.) spp. from poultry is the main source of foodborne human campylobacteriosis, but diseased pets and cattle shedding Campylobacter spp. may contribute sporadically as a source of human infection. As fluoroquinolones are one of the drugs of choice for the treatment of severe human campylobacteriosis, the resistance rates of C. jejuni and C. coli from poultry against antibiotics, including fluoroquinolones, are monitored within the European program on antimicrobial resistance (AMR) in livestock. However, much less is published on the AMR rates of C.jejuni and C. coli from pets and cattle. Therefore, C. jejuni and C. coli isolated from diseased animals were tested phenotypically for AMR, and associated AMR genes or mutations were identified by whole genome sequencing. High rates of resistance to (fluoro)quinolones (41%) and tetracyclines (61.1%) were found in C. jejuni (n = 29/66). (Fluoro)quinolone resistance was associated with the known point mutation in the quinolone resistance-determining region (QRDR) of gyrA, and tetracycline resistance was mostly caused by the tet(O) gene. These high rates of resistance, especially to critically important antibiotics in C. jejuni and C. coli, are worrisome not only in veterinary medicine. Efforts to preserve the efficacy of important antimicrobial treatment options in human and veterinary medicine have to be strengthened in the future.
Keywords	Campylobacter jejuni ; antibiotic resistance ; campylobacteriosis ; cattle ; dogs ; fluoroquinolones ; genes ; human diseases ; humans ; pathogens ; pets ; point mutation ; poultry ; sequence analysis ; tetracyclines ; veterinary medicine
Language	English
Dates of publication	2020-0823
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-light
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens9090691
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