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Article ; Online: Adaptation and validation of a quantitative vanA/vanB DNA screening assay on a high-throughput PCR system.

Giersch, Katja / Tanida, Konstantin / Both, Anna / Nörz, Dominik / Heim, Denise / Rohde, Holger / Aepfelbacher, Martin / Lütgehetmann, Marc

Scientific reports

2024 Volume 14, Issue 1, Page(s) 3523

Abstract: Vancomycin resistant enterococci (VRE) are a leading cause of ICU-acquired bloodstream infections in Europe. The bacterial load in enteral colonization may be associated with a higher probability of transmission. Here, we aimed to establish a ... ...

Abstract	Vancomycin resistant enterococci (VRE) are a leading cause of ICU-acquired bloodstream infections in Europe. The bacterial load in enteral colonization may be associated with a higher probability of transmission. Here, we aimed to establish a quantitative vanA/vanB DNA real-time PCR assay on a high-throughput system. Limits of detection (LOD), linear range and precision were determined using serial bacterial dilutions. LOD was 46.9 digital copies (dcp)/ml for vanA and 60.8 dcp/ml for vanB. The assay showed excellent linearity between 4.7 × 10
MeSH term(s)	Humans ; Vancomycin-Resistant Enterococci/genetics ; Predictive Value of Tests ; Real-Time Polymerase Chain Reaction ; DNA ; DNA, Bacterial/genetics ; DNA, Bacterial/analysis ; Bacterial Proteins/genetics ; Gram-Positive Bacterial Infections/microbiology ; Anti-Bacterial Agents
Chemical Substances	DNA (9007-49-2) ; DNA, Bacterial ; Bacterial Proteins ; Anti-Bacterial Agents
Language	English
Publishing date	2024-02-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-54037-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Comparison of two commercial and one in-house real-time PCR assays for the diagnosis of bacterial gastroenteritis.

Tanida, Konstantin / Hahn, Andreas / Frickmann, Hagen

European journal of microbiology & immunology

2020 Volume 10, Issue 4, Page(s) 210–216

Abstract: Introduction: The aim of the study was a comparative evaluation of in-house real-time PCR and commercial real-time PCR (Fast Track Diagnostics (FTD), ampliCube/Mikrogen) targeting enteropathogenic bacteria from stool in preparation of Regulation (EU) ... ...

Abstract	Introduction: The aim of the study was a comparative evaluation of in-house real-time PCR and commercial real-time PCR (Fast Track Diagnostics (FTD), ampliCube/Mikrogen) targeting enteropathogenic bacteria from stool in preparation of Regulation (EU) 2017/746 on in vitro diagnostic medical devices. Methods: Both 241 stool samples from patients and 100 samples from German laboratory control schemes ("Ringversuche") were used to comparatively assess in-house real-time PCR, the FTD bacterial gastroenteritis kit, and the ampliCube gastrointestinal bacterial panels 1&2 either with the in-house PCRs as gold standard and as a test comparison without gold standard applying latent class analysis. Sensitivity, specificity, intra- and inter-assay variation and Cohen's kappa were assessed. Results: In comparison with the gold standard, sensitivity was 75-100% for strongly positive samples, 20-100% for weakly positive samples, and specificity ranged from 96 to 100%. Latent class analysis suggested that sensitivity ranges from 81.2 to 100% and specificity from 58.5 to 100%. Cohen's kappa varied between moderate and nearly perfect agreement, intra- and inter-assay variation was 1-3 to 1-4 Ct values. Conclusion: Acceptable agreement and performance characteristics suggested replaceability of the in-house PCR assays by the commercial approaches.
Language	English
Publishing date	2020-12-05
Publishing country	Hungary
Document type	Journal Article
ZDB-ID	2652327-9
ISSN	2062-8633 ; 2062-509X
ISSN (online)	2062-8633
ISSN	2062-509X
DOI	10.1556/1886.2020.00030
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Article ; Online: Stridor From a Concealed Perforated Aortic Aneurysm.

Tanida, Konstantin H / Wichert, Götz von / Jaganjac, Suad

Deutsches Arzteblatt international

2019 Volume 116, Issue 39, Page(s) 652

MeSH term(s)	Aortic Aneurysm/complications ; Humans ; Respiratory Sounds/etiology
Language	English
Publishing date	2019-09-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2406159-1
ISSN	1866-0452 ; 1866-0452
ISSN (online)	1866-0452
ISSN	1866-0452
DOI	10.3238/arztebl.2019.0652
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Article ; Online: Performance and Hypothetical Impact on Joint Infection Management of the BioFire Joint Infection Panel: a Retrospective Analysis.

Berinson, Benjamin / Spenke, Laura / Krivec, Lukas / Tanida, Konstantin / Both, Anna / Keller, Johannes / Rolvien, Tim / Christner, Martin / Lütgehetmann, Marc / Aepfelbacher, Martin / Klatte, Till Orla / Rohde, Holger

Journal of clinical microbiology

2023 Volume 61, Issue 8, Page(s) e0059223

Abstract: Pathogen identification is key in septic arthritis. Culture-based techniques are challenging, especially when patients have been pretreated with antibiotics or when difficult-to-culture bacteria are encountered. The BioFire joint infection assay (BJA) is ...

Abstract	Pathogen identification is key in septic arthritis. Culture-based techniques are challenging, especially when patients have been pretreated with antibiotics or when difficult-to-culture bacteria are encountered. The BioFire joint infection assay (BJA) is a multiplex PCR panel which detects 31 of the most prevalent bacterial and fungal pathogens causing septic arthritis. Here, 123 cryoconserved contemporary synovial fluid samples from 120 patients underwent BJA analysis. Results were compared to those of culture-based diagnostics (standard of care [SOC]). Clinical data were collected, and the possible impact of the molecular diagnostic application on patient management was evaluated. Fifteen of 123 synovial fluid cultures grew bacterial pathogens. All on-panel pathogens (9/15) were correctly identified by the BJA. The BJA identified four additional bacterial pathogens in four SOC-negative cases. BJA sensitivity and specificity were 100% (95% confidence interval [CI], 69.2% to 100%) and 100% (95% CI, 96.8% to 100%), respectively. Compared to the SOC, the BJA would have resulted in faster provision of species identification and molecular susceptibility data by 49 h and 99 h, respectively. Clinical data analysis indicates that in BJA-positive cases, faster species ID could have led to timelier optimization of antibiotic therapy. This retrospective study demonstrates high sensitivity and specificity of the BJA to detect on-panel organisms in bacterial arthritis. The usefulness of the BJA in prosthetic-joint infections is limited, as important pathogens (i.e., coagulase negative staphylococci and Cutibacterium acnes) are not covered. Evidence from patient data analysis suggests that the assay might prove valuable for optimizing patient management in acute arthritis related to fastidious organisms or for patients who received antibiotics prior to specimen collection.
MeSH term(s)	Humans ; Retrospective Studies ; Arthritis, Infectious/diagnosis ; Arthritis, Infectious/drug therapy ; Arthritis, Infectious/microbiology ; Bacteria/genetics ; Multiplex Polymerase Chain Reaction/methods
Language	English
Publishing date	2023-07-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.00592-23
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Article: Evaluation of the automated cartridge-based ARIES SARS-CoV-2 Assay (RUO) against automated Cepheid Xpert Xpress SARS-CoV-2 PCR as gold standard.

Tanida, Konstantin / Koste, Lars / Koenig, Christian / Wenzel, Werner / Fritsch, Andreas / Frickmann, Hagen

European journal of microbiology & immunology

2020 Volume 10, Issue 3, Page(s) 156–164

Abstract: Introduction: To evaluate the automated cartridge-based PCR approach ARIES SARS-CoV-2 Assay targeting the ORF-sequence and the N-gene of SARS-CoV-2.: Methods: In line with the suggestions by Rabenau and colleagues, the automated ARIES SARS-CoV-2 ... ...

Abstract	Introduction: To evaluate the automated cartridge-based PCR approach ARIES SARS-CoV-2 Assay targeting the ORF-sequence and the N-gene of SARS-CoV-2. Methods: In line with the suggestions by Rabenau and colleagues, the automated ARIES SARS-CoV-2 Assay was challenged with strongly positive samples, weakly positive samples and negative samples. Further, intra-assay and inter-assay precision as well as the limit-of-detection (lod) were defined with quantified target RNA and DNA. The Cepheid Xpert Xpress SARS-Cov-2 Assay was used as gold standard. Results: Concordance between the ARIES assay and the Cepheid assay was 100% for strongly positive samples and for negative samples, respectively. For weakly positive samples as confirmed applying the Cepheid assay, a relevant minority of 4 out of 15 samples (26.7%) went undetected by the ARIES assay. Intra- and inter-assay precision were satisfactory, while the lod was in the 103 DNA copies/reaction-range, in the 103 virus copies/reaction-range, or in the 103-104 free RNA copies/reaction-range in our hands. Conclusions: The automated ARIES assay shows comparable test characteristics as the Cepheid assay focusing on strongly positive and negative samples but a slightly reduced sensitivity with weakly positive samples. Decisions on diagnostic use should include considerations on the lod.
Keywords	covid19
Language	English
Publishing date	2020-08-17
Publishing country	Hungary
Document type	Journal Article
ZDB-ID	2652327-9
ISSN	2062-8633 ; 2062-509X
ISSN (online)	2062-8633
ISSN	2062-509X
DOI	10.1556/1886.2020.00017
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Article ; Online: High burden of RSV and influenza in patients presenting with suspected pneumonia in the emergency room of a German tertiary hospital in fall of 2022.

Ettemeyer, Marlene / Florey, Maria / Tanida, Konstantin / Jochum, Johannes / Schulze-Sturm, Ulf / Lütgehetmann, Marc / Baehr, Michael / Addo, Marylyn M / Schmiedel, Stefan / Rohde, Holger / Koch, Till

Infection

2023 Volume 51, Issue 5, Page(s) 1569–1575

Abstract: Purpose: Bacterial pneumonia, a major cause of respiratory tract infections (RTI), can be challenging to diagnose and to treat adequately, especially when seasonal viral pathogens co-circulate. The aim of this study was to give a real-world snapshot of ... ...

Abstract	Purpose: Bacterial pneumonia, a major cause of respiratory tract infections (RTI), can be challenging to diagnose and to treat adequately, especially when seasonal viral pathogens co-circulate. The aim of this study was to give a real-world snapshot of the burden of respiratory disease and treatment choices in the emergency department (ED) of a tertiary care hospital in Germany in the fall of 2022. Methods: Anonymized analysis of a quality control initiative that prospectively documented all patients presenting to our ED with symptoms suggestive of RTI from Nov 7th to Dec 18th, 2022. Results: 243 patients were followed at the time of their ED attendance. Clinical, laboratory and radiographic examination was performed in 92% of patients (224/243). Microbiological work-up to identify causative pathogens including blood cultures, sputum or urine-antigen tests were performed in 55% of patients (n = 134). Detection of viral pathogens increased during the study period from 7 to 31 cases per week, while bacterial pneumonias, respiratory tract infections without detection of a viral pathogen and non-infectious etiologies remained stable. A high burden of bacterial and viral co-infections became apparent (16%, 38/243), and co-administration of antibiotic and antiviral treatments was observed (14%, n = 35/243). 17% of patients (41/243) received antibiotic coverage without a diagnosis of a bacterial etiology. Conclusion: During the fall of 2022, the burden of RTI caused by detectable viral pathogens increased unusually early. Rapid and unexpected changes in pathogen distribution highlight the need for targeted diagnostics to improve the quality of RTI management in the ED.
MeSH term(s)	Humans ; Influenza, Human/diagnosis ; Influenza, Human/drug therapy ; Influenza, Human/epidemiology ; Tertiary Care Centers ; Seasons ; Virus Diseases/diagnosis ; Respiratory Tract Infections/drug therapy ; Pneumonia, Bacterial ; Anti-Bacterial Agents/therapeutic use ; Emergency Service, Hospital
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-07-04
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/s15010-023-02069-w
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Zs.A 881: 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: Comparison of Three In-House Real PCR Assays Targeting Kinetoplast DNA, the Small Subunit Ribosomal RNA Gene and the Glucose-6-Phosphate Isomerase Gene for the Detection of Leishmania spp. in Human Serum

Tanida, Konstantin / Balczun, Carsten / Hahn, Andreas / Veit, Alexandra / Nickel, Beatrice / Poppert, Sven / Scheid, Patrick Leander / Hagen, Ralf Matthias / Frickmann, Hagen / Loderstädt, Ulrike / Tannich, Egbert

Pathogens. 2021 June 30, v. 10, no. 7

2021

Abstract: To perform PCR from serum for the diagnosis of visceral leishmaniasis is convenient and much less invasive than the examination of deeper compartments such as bone marrow. We compared three Leishmania-specific real-time PCRs with three different ... ...

Abstract	To perform PCR from serum for the diagnosis of visceral leishmaniasis is convenient and much less invasive than the examination of deeper compartments such as bone marrow. We compared three Leishmania-specific real-time PCRs with three different molecular targets (kinetoplast DNA, the small subunit-ribosomal RNA-(ssrRNA-)gene, the glucose-6-phosphate isomerase-(gpi-)gene) regarding their sensitivity and specificity in human serum. Residual sera from previous diagnostic assessments at the German National Reference Center for Tropical Pathogens Bernhard Nocht Institute for Tropical Medicine Hamburg and the Swiss Tropical and Public Health Institute were used. The sensitivities of kinetoplast DNA-PCR, ssrRNA-gene PCR, and gpi-PCR were 93.3%, 73.3%, and 33.3%, respectively, with 15 initial serum samples from visceral leishmaniasis patients, as well as 9.1%, 9.1%, and 0.0%, respectively, with 11 follow-up serum samples taken at various time points following anti-leishmanial therapy. Specificity was 100.0% in all assays as recorded with 1.137 serum samples from deployed soldiers and migrants without clinical suspicion of visceral leishmaniasis. Kinetoplast-DNA PCR from serum was confirmed as a sensitive and specific approach for the diagnosis of visceral leishmaniasis. The results also indicate the suitability of serum PCR for diagnostic follow-up after therapy, in particular regarding therapeutic failure in case of persisting positive PCR results.
Keywords	Leishmania ; blood serum ; bone marrow ; genes ; glucose 6-phosphate ; glucose-6-phosphate isomerase ; humans ; kinetoplast DNA ; medicine ; public health ; ribosomal RNA ; therapeutics ; visceral leishmaniasis
Language	English
Dates of publication	2021-0630
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens10070826
Database	NAL-Catalogue (AGRICOLA)

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Article: Comparative Assessment of In-House Real-Time PCRs Targeting Enteric Disease-Associated Microsporidia in Human Stool Samples [Erratum: February 2022, v.11(2)]

Tanida, Konstantin / Hahn, Andreas / Eberhardt, Kirsten Alexandra / Tannich, Egbert / Landt, Olfert / Kann, Simone / Feldt, Torsten / Sarfo, Fred Stephen / Di Cristanziano, Veronica / Frickmann, Hagen / Loderstädt, Ulrike

Pathogens. 2021 May 26, v. 10, no. 6

2021

Abstract: Microsporidiosis is an infection predominantly occurring in immunosuppressed patients and infrequently also in travelers. This study was performed to comparatively evaluate the diagnostic accuracy of real-time PCR assays targeting microsporidia with ... ...

Abstract	Microsporidiosis is an infection predominantly occurring in immunosuppressed patients and infrequently also in travelers. This study was performed to comparatively evaluate the diagnostic accuracy of real-time PCR assays targeting microsporidia with etiological relevance in the stool of human patients in a latent class analysis-based test comparison without a reference standard with perfect accuracy. Thereby, two one-tube real-time PCR assays and two two-tube real-time PCR assays targeting Enterocytozoon bieneusi and Encephalocytozoon spp. were included in the assessment with reference stool material (20), stool samples from Ghanaian HIV-positive patients (903), and from travelers, migrants and Colombian indigenous people (416). Sensitivity of the assays ranged from 60.4% to 97.4% and specificity from 99.1% to 100% with substantial agreement according to Cohen’s kappa of 79.6%. Microsporidia DNA was detected in the reference material and the stool of the HIV patients but not in the stool of the travelers, migrants, and the Colombian indigenous people. Accuracy-adjusted prevalence was 5.8% (n = 78) for the study population as a whole. In conclusion, reliable detection of enteric disease-associated microsporidia in stool samples by real-time PCR could be demonstrated, but sensitivity between the compared microsporidia-specific real-time PCR assays varied.
Keywords	DNA ; Enterocytozoon bieneusi ; feces ; humans ; indigenous peoples ; microsporidiosis ; quantitative polymerase chain reaction ; reference standards
Language	English
Dates of publication	2021-0526
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens10060656
Database	NAL-Catalogue (AGRICOLA)

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Article: Correction: Tanida et al. Comparative Assessment of In-House Real-Time PCRs Targeting Enteric Disease-Associated Microsporidia in Human Stool Samples.

Pathogens (Basel, Switzerland)

2022 Volume 11, Issue 2

Abstract: In the original publication [ ... ]. ...

Abstract	In the original publication [...].
Language	English
Publishing date	2022-02-17
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11020256
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Article: Epidemiology of Plasmids in

Pankok, Frederik / Taudien, Stefan / Dekker, Denise / Thye, Thorsten / Oppong, Kwabena / Wiafe Akenten, Charity / Lamshöft, Maike / Jaeger, Anna / Kaase, Martin / Scheithauer, Simone / Tanida, Konstantin / Frickmann, Hagen / May, Jürgen / Loderstädt, Ulrike

Antibiotics (Basel, Switzerland)

2022 Volume 11, Issue 5

Abstract: Little information is available on the local epidemiology of mobile genetic elements such as plasmids harboring acquired beta-lactamase genes in Western African Ghana. In the present study, we screened for plasmids in ... ...

Abstract	Little information is available on the local epidemiology of mobile genetic elements such as plasmids harboring acquired beta-lactamase genes in Western African Ghana. In the present study, we screened for plasmids in three
Language	English
Publishing date	2022-05-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2681345-2
ISSN	2079-6382
ISSN	2079-6382
DOI	10.3390/antibiotics11050689
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