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  1. Article ; Online: Epidemiology of patients harboring carbapenemase-producing bacteria and comparison with patients with detection of extended-spectrum beta-lactamase-producing Enterobacterales-A retrospective cohort study.

    Vock, Isabelle / Aguilar-Bultet, Lisandra / Goldenberger, Daniel / Ragozzino, Silvio / Kuster, Sabine / Tschudin-Sutter, Sarah

    Infection control and hospital epidemiology

    2023  Volume 44, Issue 12, Page(s) 1959–1965

    Abstract: Objective: We evaluated the epidemiology of carbapenemase-producing bacteria (CPB) in Switzerland by comparing risk factors between patients colonized with CPB and patients colonized with extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE) ...

    Abstract Objective: We evaluated the epidemiology of carbapenemase-producing bacteria (CPB) in Switzerland by comparing risk factors between patients colonized with CPB and patients colonized with extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE).
    Methods: This retrospective cohort study was conducted at the University Hospital Basel in Switzerland. Hospitalized patients with CPB in any sample between January 2008 and July 2019 were included. The ESBL-PE group consisted of hospitalized patients with detection of ESBL-PE from any sample between January 2016 and December 2018. Comparisons of risk factors for acquisition of CPB and ESBL-PE were performed by logistic regression.
    Results: Inclusion criteria were met for 50 patients in the CPB group and 572 in the ESBL-PE group. In the CPB group, 62% had a travel history and 60% had been hospitalized abroad. When comparing the CPB group to the ESBL-PE group, hospitalization abroad (odds ratio [OR], 25.33; 95% confidence interval [CI], 11.07-57.98) and prior antibiotic therapy (OR, 4.76; 95% CI, 2.15-10.55) remained independently associated with CPB colonization. Hospitalization abroad (
    Conclusions: Although CPB still seem to be mainly imported from areas of higher endemicity, local acquisition of CPB is emerging, especially in patients with close and/or frequent contact with healthcare services. This trend resembles the epidemiology of ESBL
    MeSH term(s) Humans ; Retrospective Studies ; Bacteria ; beta-Lactamases ; Escherichia coli ; Klebsiella pneumoniae ; Risk Factors ; Anti-Bacterial Agents/therapeutic use
    Chemical Substances carbapenemase (EC 3.5.2.6) ; beta-Lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents
    Language English
    Publishing date 2023-07-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639378-0
    ISSN 1559-6834 ; 0195-9417 ; 0899-823X
    ISSN (online) 1559-6834
    ISSN 0195-9417 ; 0899-823X
    DOI 10.1017/ice.2023.125
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Cefepime versus carbapenems for treatment of AmpC beta-lactamase-producing Enterobacterales bloodstream infections.

    Herrmann, Julia / Burgener-Gasser, Anne-Valérie / Goldenberger, Daniel / Roth, Jan / Weisser, Maja / Tamma, Pranita D / Tschudin-Sutter, Sarah

    European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

    2023  Volume 43, Issue 2, Page(s) 213–221

    Abstract: Purpose: Cefepime is recommended for treating infections caused by AmpC beta-lactamase-producing Enterobacterales (AmpC-PE), though supporting evidence is limited. Therefore, this study compared outcomes associated with cefepime versus carbapenem ... ...

    Abstract Purpose: Cefepime is recommended for treating infections caused by AmpC beta-lactamase-producing Enterobacterales (AmpC-PE), though supporting evidence is limited. Therefore, this study compared outcomes associated with cefepime versus carbapenem therapy for bloodstream infections (BSIs) caused by AmpC-PE after phenotypic exclusion of ESBL-co-producing isolates.
    Methods: This retrospective cohort study compared definite cefepime versus carbapenem treatment for AmpC-PE BSI in hospitalized patients of the University Hospital Basel, Switzerland, between 01/2015 and 07/2020. Primary outcomes included in-hospital death, renal impairment and neurologic adverse events; secondary outcomes included length of hospital stay and recurrent infection.
    Results: Two hundred and seventy episodes of AmpC-PE BSI were included, 162, 77 and 31 were treated with a carbapenem, cefepime and other antibiotics, respectively. Patients treated with carbapenems were more likely to be transferred to the ICU on admission and more frequently had central venous catheter as a source of infection. In uni- and multivariable analyses, primary and secondary outcomes did not differ between the two treatment groups, except for more frequent occurrence of neurological adverse events among patients treated with carbapenems and shorter length of hospital stay among survivors treated with cefepime.
    Conclusion: After excluding isolates with phenotypic ESBL-co-production, cefepime was not associated with adverse outcomes compared to carbapenems when used to treat BSIs caused by AmpC-PE. Our study provides evidence to support the use of cefepime as a safe treatment strategy for AmpC-PE BSI, particularly in clinically stable patients without initial renal impairment or increased susceptibility to neurological adverse events.
    MeSH term(s) Humans ; Cefepime/adverse effects ; Anti-Bacterial Agents/adverse effects ; Carbapenems/adverse effects ; Cephalosporins/adverse effects ; Retrospective Studies ; Hospital Mortality ; Enterobacteriaceae Infections/drug therapy ; Enterobacteriaceae Infections/microbiology ; beta-Lactamases ; Sepsis/drug therapy ; Gammaproteobacteria ; Microbial Sensitivity Tests ; Bacterial Proteins
    Chemical Substances Cefepime (807PW4VQE3) ; AmpC beta-lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents ; Carbapenems ; Cephalosporins ; beta-Lactamases (EC 3.5.2.6) ; Bacterial Proteins
    Language English
    Publishing date 2023-11-23
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 603155-9
    ISSN 1435-4373 ; 0934-9723 ; 0722-2211
    ISSN (online) 1435-4373
    ISSN 0934-9723 ; 0722-2211
    DOI 10.1007/s10096-023-04715-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Cutibacterium modestum and “Propionibacterium humerusii” represent the same species that is commonly misidentified as Cutibacterium acnes

    Goldenberger, Daniel / Søgaard, Kirstine K. / Cuénod, Aline / Seth-Smith, Helena / de Menezes, Daniel / Vandamme, Peter / Egli, Adrian

    Antonie van Leeuwenhoek. 2021 Aug., v. 114, no. 8

    2021  

    Abstract: Cutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp. from an implant and investigated this isolate using multiple identification approaches. Correct identification was ... ...

    Abstract Cutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp. from an implant and investigated this isolate using multiple identification approaches. Correct identification was hampered by inconsistent reference data. The isolate was characterised using conventional methods such as Gram stain, MALDI-TOF MS, and antimicrobial susceptibility testing against multiple antimicrobials. Partial 16S rRNA gene sequencing and whole genome sequencing were also performed. In addition, we summarised the available published sequence data and compared prior data to our strain. Conventional phenotypic identification of our isolate resulted in Cutibacterium spp. After analysis of 16S rRNA gene and genome sequences, our isolate was identified as C. modestum, a very recently described species. The 16S rRNA gene analysis was hampered by three incorrect nucleotides within the 16S rRNA gene reference sequence of C. modestum M12ᵀ (accession no. LC466959). We also clearly demonstrate that this novel species is identical to tentatively named “Propionibacterium humerusii”. Retrospective data analysis indicates that C. modestum is a clinically important Cutibacterium species often misidentified as C. acnes. The isolation and identification of Cutibacterium spp. is still a challenge. The correct description of very recently named C. modestum and the availability of a correct 16S rRNA sequence of the type strain may help to clarify the taxonomical uncertainty concerning “P. humerusii”. The novel C. modestum is an additional, clinically important species within the genus Cutibacterium and may represent a new member of the human skin microbiome.
    Keywords anti-infective agents ; antibiotic resistance ; genes ; microbiome ; nucleotide sequences ; nucleotides ; phenotype ; skin (animal) ; uncertainty
    Language English
    Dates of publication 2021-08
    Size p. 1315-1320.
    Publishing place Springer International Publishing
    Document type Article
    ZDB-ID 214861-4
    ISSN 1572-9699 ; 0003-6072
    ISSN (online) 1572-9699
    ISSN 0003-6072
    DOI 10.1007/s10482-021-01589-5
    Database NAL-Catalogue (AGRICOLA)

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  5. 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  Volume 115, Issue 4, Page(s) 461–472

    Abstract: We present polyphasic taxonomic data to demonstrate that strain 125703- ... ...

    Abstract We present polyphasic taxonomic data to demonstrate that strain 125703-2019
    MeSH term(s) Bacterial Typing Techniques ; DNA, Bacterial/chemistry ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA
    Chemical Substances DNA, Bacterial ; Fatty Acids ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2022-02-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 214861-4
    ISSN 1572-9699 ; 0003-6072
    ISSN (online) 1572-9699
    ISSN 0003-6072
    DOI 10.1007/s10482-022-01712-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: First case of IMP-15-producing

    Goldenberger, Daniel / Vuichard-Gysin, Danielle / Herzog, Kathrin / Hinić, Vladimira / Seth-Smith, Helena / Egli, Adrian

    IDCases

    2020  Volume 22, Page(s) e00933

    Abstract: We report on the first case of ... ...

    Abstract We report on the first case of multiresistant
    Language English
    Publishing date 2020-09-02
    Publishing country Netherlands
    Document type Case Reports
    ZDB-ID 2745454-X
    ISSN 2214-2509
    ISSN 2214-2509
    DOI 10.1016/j.idcr.2020.e00933
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Cutibacterium modestum and "Propionibacterium humerusii" represent the same species that is commonly misidentified as Cutibacterium acnes.

    Goldenberger, Daniel / Søgaard, Kirstine K / Cuénod, Aline / Seth-Smith, Helena / de Menezes, Daniel / Vandamme, Peter / Egli, Adrian

    Antonie van Leeuwenhoek

    2021  Volume 114, Issue 8, Page(s) 1315–1320

    Abstract: Cutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp. from an implant and investigated this isolate using multiple identification approaches. Correct identification was ... ...

    Abstract Cutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp. from an implant and investigated this isolate using multiple identification approaches. Correct identification was hampered by inconsistent reference data. The isolate was characterised using conventional methods such as Gram stain, MALDI-TOF MS, and antimicrobial susceptibility testing against multiple antimicrobials. Partial 16S rRNA gene sequencing and whole genome sequencing were also performed. In addition, we summarised the available published sequence data and compared prior data to our strain. Conventional phenotypic identification of our isolate resulted in Cutibacterium spp. After analysis of 16S rRNA gene and genome sequences, our isolate was identified as C. modestum, a very recently described species. The 16S rRNA gene analysis was hampered by three incorrect nucleotides within the 16S rRNA gene reference sequence of C. modestum M12
    MeSH term(s) Acne Vulgaris ; Humans ; Phylogeny ; Propionibacterium acnes/genetics ; RNA, Ribosomal, 16S/genetics ; Retrospective Studies
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2021-05-07
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 214861-4
    ISSN 1572-9699 ; 0003-6072
    ISSN (online) 1572-9699
    ISSN 0003-6072
    DOI 10.1007/s10482-021-01589-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Evaluation of the clinical relevance of the Biofire

    Søgaard, Kirstine K / Hinic, Vladimira / Goldenberger, Daniel / Gensch, Alexander / Schweitzer, Michael / Bättig, Veronika / Siegemund, Martin / Bassetti, Stefano / Bingisser, Roland / Tamm, Michael / Battegay, Manuel / Weisser, Maja / Stolz, Daiana / Khanna, Nina / Egli, Adrian

    Infection

    2023  Volume 52, Issue 1, Page(s) 173–181

    Abstract: Purpose: Panel PCR tests provide rapid pathogen identification. However, their diagnostic performance is unclear. We assessed the performance of the Biofire: Methods: Setting: University Hospital Basel (February 2019 to July 2020), including ... ...

    Abstract Purpose: Panel PCR tests provide rapid pathogen identification. However, their diagnostic performance is unclear. We assessed the performance of the Biofire
    Methods: Setting: University Hospital Basel (February 2019 to July 2020), including hospitalized patients with a BAL (± pneumonia). We determined sensitivity and specificity of the PN-panel against standard culture. Using univariate logistic regression, we calculated odds ratios (OR) for pneumonia according to PN-panel and culture status, stratifying by chronic pulmonary disease. We calculated ORs for pneumonia for different pathogens to estimate the clinical relevance.
    Results: We included 840 adult patients, 60% were males, median age was 68 years, 35% had chronic pulmonary disease, 21% had pneumonia, and 36% had recent antibiotic use. In 1078 BAL samples, bacterial pathogens were detected in 36% and 16% with PN-panel and culture, respectively. The overall sensitivity and specificity of the PN-panel was high, whereas the positive predictive value was low. The OR of pneumonia was 1.1 (95% CI 0.7-1.6) for PN-panel-positive only; 2.6 (95% CI 1.3-5.3) for culture-positive only, and 1.6 (95% CI 1.0-2.4) for PN-panel and culture-positive. The detection rate of Haemophilus influenzae, Staphylococcus aureus, and Moraxella catarrhalis in the PN-panel was high but not associated with pneumonia.
    Conclusion: While sensitivity and specificity of PN-panel are high compared to culture, pathogen detection did not correlate well with a pneumonia diagnosis. Patients with culture-positive BAL had the highest OR for pneumonia-thus the impact of the PN-panel on clinical management needs further evaluation in randomized controlled trials.
    MeSH term(s) Male ; Adult ; Humans ; Aged ; Female ; Clinical Relevance ; Pneumonia/diagnosis ; Bacteria ; Anti-Bacterial Agents ; Sensitivity and Specificity
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-08-12
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 185104-4
    ISSN 1439-0973 ; 0300-8126 ; 0173-2129
    ISSN (online) 1439-0973
    ISSN 0300-8126 ; 0173-2129
    DOI 10.1007/s15010-023-02080-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Unexpectedly High False-Positive Rates for

    Zanella, Marie-Céline / Cherkaoui, Abdessalam / Hinic, Vladimira / Renzi, Gesuele / Goldenberger, Daniel / Egli, Adrian / Schrenzel, Jacques

    Frontiers in cellular and infection microbiology

    2021  Volume 11, Page(s) 639658

    Abstract: False-positive results in the diagnostic of meningitis and encephalitis pose important challenges. This study aimed to determine false-positive rates ... ...

    Abstract False-positive results in the diagnostic of meningitis and encephalitis pose important challenges. This study aimed to determine false-positive rates for
    MeSH term(s) Diagnostic Tests, Routine ; Haemophilus influenzae ; Humans ; Meningitis ; Meningoencephalitis ; Retrospective Studies
    Language English
    Publishing date 2021-03-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2021.639658
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Gulosibacter hominis sp. nov.: a novel human microbiome bacterium that may cause opportunistic infections.

    Vandamme, Peter / Peeters, Charlotte / Seth-Smith, Helena M B / Graf, Lukas / Cnockaert, Margo / Egli, Adrian / Goldenberger, Daniel

    Antonie van Leeuwenhoek

    2021  Volume 114, Issue 11, Page(s) 1841–1854

    Abstract: We present genomic, phylogenomic, and phenotypic taxonomic data to demonstrate that three human ear isolates represent a novel species within the genus Gulosibacter. These isolates could not be identified reliably using MALDI-TOF mass spectrometry during ...

    Abstract We present genomic, phylogenomic, and phenotypic taxonomic data to demonstrate that three human ear isolates represent a novel species within the genus Gulosibacter. These isolates could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that they belonged to the genus Gulosibacter. Overall genomic relatedness indices between the draft genome sequences of the three isolates and of the type strains of established Gulosibacter species confirmed that the three isolates represented a single novel Gulosibacter species. A biochemical characterisation yielded differential tests between the novel and established Gulosibacter species, which could also be differentiated using MALDI-TOF mass spectrometry. We propose to formally classify these three isolates into Gulosibacter hominis sp. nov., with 401352-2018
    MeSH term(s) Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Humans ; Microbiota ; Nucleic Acid Hybridization ; Opportunistic Infections ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA
    Chemical Substances DNA, Bacterial ; Fatty Acids ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2021-09-04
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 214861-4
    ISSN 1572-9699 ; 0003-6072
    ISSN (online) 1572-9699
    ISSN 0003-6072
    DOI 10.1007/s10482-021-01644-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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