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Article ; Online: Clostridioides difficile PCR Tcdb Cycle Threshold predicts toxin EIA positivity but not severity of infection.

Mah, Regan / Locher, Kerstin / Steiner, Theodore S / Stefanovic, Aleksandra

2023 Volume 82, Page(s) 102755

Abstract: Background: Diagnosis of Clostridioides difficile Infection (CDI) entails compatible clinical presentation and laboratory findings. We evaluated real-time polymerase chain reaction (qPCR) cycle threshold (C: Methods: Inpatients or emergency ... ...

Abstract	Background: Diagnosis of Clostridioides difficile Infection (CDI) entails compatible clinical presentation and laboratory findings. We evaluated real-time polymerase chain reaction (qPCR) cycle threshold (C Methods: Inpatients or emergency department patients who tested positive for tcdB gene by PCR were evaluated. Patients' stools underwent testing for GDH and TcdA/B by EIA. Medical health records were reviewed for demographic, clinical presentation, laboratory, treatment and outcome data. Severity of CDI was calculated using various severity score indexes. Results: The median C Conclusion: C
MeSH term(s)	Humans ; Bacterial Toxins/genetics ; Bacterial Toxins/analysis ; Clostridioides difficile/genetics ; Clostridioides/genetics ; Immunoenzyme Techniques ; Clostridium Infections/diagnosis ; Real-Time Polymerase Chain Reaction ; Feces/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/analysis
Chemical Substances	Bacterial Toxins ; Bacterial Proteins
Language	English
Publishing date	2023-07-03
Publishing country	England
Document type	Journal Article
ZDB-ID	1237621-8
ISSN	1095-8274 ; 1075-9964
ISSN (online)	1095-8274
ISSN	1075-9964
DOI	10.1016/j.anaerobe.2023.102755
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Article ; Online: Quick versus Quantitative: Evaluation of Two Commercial Real-Time PCR Assays for the Detection of Pneumocystis jirovecii from Bronchoalveolar Lavage Fluids.

Belanger, Corrie R / Locher, Kerstin / Velapatino, Billie / Dufresne, Philippe J / Eckbo, Eric / Charles, Marthe

Microbiology spectrum

2023 Volume 11, Issue 4, Page(s) e0102123

Abstract: Two commercial real-time PCR assays for the detection of Pneumocystis jirovecii were compared, the quantitative RealStar P. jirovecii assay and the qualitative DiaSorin P. jirovecii assay, the latter of which can be used without nucleic acid extraction. ... ...

Abstract	Two commercial real-time PCR assays for the detection of Pneumocystis jirovecii were compared, the quantitative RealStar P. jirovecii assay and the qualitative DiaSorin P. jirovecii assay, the latter of which can be used without nucleic acid extraction. Archived bronchoalveolar lavage (BAL) specimens (
MeSH term(s)	Humans ; Pneumocystis carinii/genetics ; Bronchoalveolar Lavage Fluid ; Real-Time Polymerase Chain Reaction/methods ; Pneumonia, Pneumocystis/diagnosis ; Sensitivity and Specificity
Language	English
Publishing date	2023-06-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01021-23
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Article ; Online: Automated 16S Sequencing Using an R-Based Analysis Module for Bacterial Identification.

Locher, Kerstin / Belanger, Corrie R / Eckbo, Eric / Caza, Melissa / Velapatino, Billie / Charles, Marthe K

Microbiology spectrum

2022 Volume 10, Issue 2, Page(s) e0040822

Abstract: Sanger sequencing of the 16S rRNA gene is routinely used for the identification of bacterial isolates. However, this method is still performed mostly in more-specialized reference laboratories, and traditional protocols can be labor intensive. In this ... ...

Abstract	Sanger sequencing of the 16S rRNA gene is routinely used for the identification of bacterial isolates. However, this method is still performed mostly in more-specialized reference laboratories, and traditional protocols can be labor intensive. In this study, 99 clinical bacterial isolates were used to validate a fast, simplified, and largely automated protocol for 16S sequencing. The workflow combines real-time PCR of the first 500 bp of the bacterial 16S rRNA gene and amplicon sequencing on an automated, cartridge-based sequence analyzer. Sequence analysis, NCBI BLAST search, and result interpretation were performed using an automated R-based script. The automated workflow and R analysis described here produced results equal to those of manual sequence analysis. Of the 96 sequences with adequate quality, 90 were concordantly identified to the genus (
MeSH term(s)	DNA, Bacterial/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/methods
Chemical Substances	DNA, Bacterial ; RNA, Ribosomal, 16S
Language	English
Publishing date	2022-04-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.00408-22
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Article ; Online: Clostridioides difficile PCR Tcdb Cycle Threshold predicts toxin EIA positivity but not severity of infection

Mah, Regan / Locher, Kerstin / Steiner, Theodore S. / Stefanovic, Aleksandra

Anaerobe. 2023 Aug., v. 82 p.102755-

2023

Abstract: Diagnosis of Clostridioides difficile Infection (CDI) entails compatible clinical presentation and laboratory findings. We evaluated real-time polymerase chain reaction (qPCR) cycle threshold (CT) as a predictor for disease severity and TcdB enzyme ... ...

Abstract	Diagnosis of Clostridioides difficile Infection (CDI) entails compatible clinical presentation and laboratory findings. We evaluated real-time polymerase chain reaction (qPCR) cycle threshold (CT) as a predictor for disease severity and TcdB enzyme immunoassay (EIA) results. Inpatients or emergency department patients who tested positive for tcdB gene by PCR were evaluated. Patients’ stools underwent testing for GDH and TcdA/B by EIA. Medical health records were reviewed for demographic, clinical presentation, laboratory, treatment and outcome data. Severity of CDI was calculated using various severity score indexes. The median CT of cases was 32.05 ± 5.45. The optimal cut-off for predicting toxin EIA positivity and severe CDI based on chart review was 32.6 and 29.8, respectively, with the area under the receiver operator characteristics curve (AUC) of 0.74 and 0.60 respectively. CT value was an acceptable predictor for EIA toxin but less so for clinical severity. Our study potentially supports a diagnostic algorithm including CT value to reduce the number of EIA toxin assays performed.
Keywords	Clostridium difficile ; algorithms ; disease severity ; enzyme immunoassays ; genes ; quantitative polymerase chain reaction ; toxins ; Clostridioides difficile ; Cycle_threshold ; Polymerase_chain_reaction ; EIA_Toxin
Language	English
Dates of publication	2023-08
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	1237621-8
ISSN	1075-9964
ISSN	1075-9964
DOI	10.1016/j.anaerobe.2023.102755
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Evaluation of the Aptima BV and CV/TV assays compared to conventional laboratory based testing methods for the diagnosis of vaginitis.

Caza, Mélissa / Charles, Marthe / Locher, Kerstin / Hoang, Linda / Tucker, Morgan / Mandy, Jeremy / Jewsbury, Heather / Wilmer, Amanda

Diagnostic microbiology and infectious disease

2023 Volume 106, Issue 4, Page(s) 115953

Abstract: Purpose: Vaginitis is caused by bacterial vaginosis (BV), Candida vaginitis (CV) and Trichomonas vaginalis (TV). This retrospective study evaluates the performance of the Aptima CV/TV, and BV assays on the automated Panther system.: Methods: Two ... ...

Abstract	Purpose: Vaginitis is caused by bacterial vaginosis (BV), Candida vaginitis (CV) and Trichomonas vaginalis (TV). This retrospective study evaluates the performance of the Aptima CV/TV, and BV assays on the automated Panther system. Methods: Two hundred forty-two multitest swabs were tested on the CV/TV assay and 422 on the BV assay. Positive and negative percent agreement (PPA, NPA) of the Candida glabrata (CG), Candida species group (CSG), TV and BV targets were calculated using a modified gold standard, with review of Gram smear and the usage of the Allplex Vaginitis Screening Assay to resolve discrepancies. Results: The PPA and NPA were respectively 98.4% and 95.9% for BV, 100% and 95.4% for CSG, 100% and 99% for CG, and 100% and 100% for TV, and when compared to consensus results. Conclusion: The CV/TV and BV assays surpassed the acceptance criteria threshold of 95%, and proved to be an excellent alternative to conventional testing.
MeSH term(s)	Female ; Humans ; Vaginosis, Bacterial/diagnosis ; Vaginosis, Bacterial/microbiology ; Trichomonas vaginalis/genetics ; Trichomonas Vaginitis/diagnosis ; Trichomonas Vaginitis/microbiology ; Retrospective Studies ; Candidiasis, Vulvovaginal/diagnosis ; Candidiasis, Vulvovaginal/microbiology ; Candida ; Candida glabrata
Language	English
Publishing date	2023-04-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2023.115953
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Article ; Online: Retrospective validation of MetaSystems' deep-learning-based digital microscopy platform with assistance compared to manual fluorescence microscopy for detection of mycobacteria.

Desruisseaux, Claudine / Broderick, Conor / Lavergne, Valéry / Sy, Kim / Garcia, Duang-Jai / Barot, Gaurav / Locher, Kerstin / Porter, Charlene / Caza, Mélissa / Charles, Marthe K

Journal of clinical microbiology

2024 Volume 62, Issue 3, Page(s) e0106923

Abstract: This study aimed to validate Metasystems' automated acid-fast bacilli (AFB) smear microscopy scanning and deep-learning-based image analysis module (Neon Metafer) with assistance on respiratory and pleural samples, compared to conventional manual ... ...

Abstract	This study aimed to validate Metasystems' automated acid-fast bacilli (AFB) smear microscopy scanning and deep-learning-based image analysis module (Neon Metafer) with assistance on respiratory and pleural samples, compared to conventional manual fluorescence microscopy (MM). Analytical parameters were assessed first, followed by a retrospective validation study. In all, 320 archived auramine-O-stained slides selected non-consecutively [85 originally reported as AFB-smear-positive, 235 AFB-smear-negative slides; with an overall mycobacterial culture positivity rate of 24.1% (77/320)] underwent whole-slide imaging and were analyzed by the Metafer Neon AFB Module (version 4.3.130) using a predetermined probability threshold (PT) for AFB detection of 96%. Digital slides were then examined by a trained reviewer blinded to previous AFB smear and culture results, for the final interpretation of assisted digital microscopy (a-DM). Paired results from both microscopic methods were compared to mycobacterial culture. A scanning failure rate of 10.6% (34/320) was observed, leaving 286 slides for analysis. After discrepant analysis, concordance, positive and negative agreements were 95.5% (95%CI, 92.4%-97.6%), 96.2% (95%CI, 89.2%-99.2%), and 95.2% (95%CI, 91.3%-97.7%), respectively. Using mycobacterial culture as reference standard, a-DM and MM had comparable sensitivities: 90.7% (95%CI, 81.7%-96.2%) versus 92.0% (95%CI, 83.4%-97.0%) ( Importance: This manuscript presents a full validation of MetaSystems' automated acid-fast bacilli (AFB) smear microscopy scanning and deep-learning-based image analysis module using a probability threshold of 96% including accuracy, precision studies, and evaluation of limit of AFB detection on respiratory samples when the technology is used with assistance. This study is complementary to the conversation started by Tomasello et al. on the use of image analysis artificial intelligence software in routine mycobacterial diagnostic activities within the context of high-throughput laboratories with low incidence of tuberculosis.
MeSH term(s)	Humans ; Retrospective Studies ; Artificial Intelligence ; Deep Learning ; Neon ; Mycobacterium ; Tuberculosis/microbiology ; Microscopy, Fluorescence ; Mycobacterium tuberculosis ; Sputum/microbiology
Chemical Substances	Neon (4VB4Y46AHD)
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.01069-23
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Article ; Online: Approach to Assessment of New Swabs and Viral Transport Media for SARS-CoV-2 Testing.

Locher, Kerstin / Velapatino, Billie / Caza, Mélissa / Li, Lisa / Porter, Charlene / Charles, Marthe

Journal of clinical microbiology

2021 Volume 59, Issue 5

Abstract: In light of the present pandemic of novel coronavirus disease 2019 (COVID-19) and the unprecedented high demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing worldwide, there are shortages of established specimen collection ... ...

Abstract	In light of the present pandemic of novel coronavirus disease 2019 (COVID-19) and the unprecedented high demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing worldwide, there are shortages of established specimen collection devices for respiratory viral testing for diagnostic microbiology laboratories. This creates the need to validate unverified collection devices from manufacturers that may not be a registered supplier for medical devices. As clinical laboratories do not routinely perform quality control of established collection devices, there is a need to have a systematic, robust approach to the assessment of substitute unregistered collection swabs and viral transport media (VTM). A discussion of the aspects requiring consideration when determining the suitability and implementation of new collection devices is presented. These specific assessment criteria include an inspection of device integrity, determination of swab and VTM sterility and
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing/instrumentation ; Clinical Laboratory Techniques ; Humans ; Pandemics ; SARS-CoV-2 ; Specimen Handling/instrumentation
Keywords	covid19
Language	English
Publishing date	2021-04-20
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.01562-20
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Article ; Online: Alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity.

Gauthier, Nick P G / Locher, Kerstin / MacDonald, Clayton / Chorlton, Samuel D / Charles, Marthe / Manges, Amee R

PloS one

2022 Volume 17, Issue 10, Page(s) e0275815

Abstract: Objectives: The COVID-19 pandemic and ensuing public health emergency has emphasized the need to study SARS-CoV-2 pathogenesis. The human microbiome has been shown to regulate the host immune system and may influence host susceptibility to viral ... ...

Abstract	Objectives: The COVID-19 pandemic and ensuing public health emergency has emphasized the need to study SARS-CoV-2 pathogenesis. The human microbiome has been shown to regulate the host immune system and may influence host susceptibility to viral infection, as well as disease severity. Several studies have assessed whether compositional alterations in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection. However, the results of these studies were varied, and many did not account for disease severity. This study aims to examine whether compositional differences in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection status and disease severity. Methods: We performed Nanopore full-length 16S rRNA sequencing on 194 nasopharyngeal swab specimens from hospitalized and community-dwelling SARS-CoV-2-infected and uninfected individuals. Sequence data analysis was performed using the BugSeq 16S analysis pipeline. Results: We found significant beta (PERMANOVA p < 0.05), but not alpha (Kruskal-Wallis p > 0.05) diversity differences in the nasopharyngeal microbiota among our study groups. We identified several differentially abundant taxa associated with SARS-CoV-2 infection status and disease severity using ALDEx2. Finally, we observed a trend towards higher abundance of Enterobacteriaceae in specimens from hospitalized SARS-CoV-2-infected patients. Conclusions: This study identified several alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity. Understanding the role of the microbiome in infection susceptibility and severity may open new avenues of research for disease prevention and treatment.
MeSH term(s)	COVID-19 ; Humans ; Microbiota ; Nasopharynx ; Pandemics/prevention & control ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2 ; Severity of Illness Index
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2022-10-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0275815
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Article ; Online: Diagnostic yield and clinical relevance of expanded germline genetic testing for nearly 7000 suspected HBOC patients.

Henkel, Jan / Laner, Andreas / Locher, Melanie / Wohlfrom, Tobias / Neitzel, Birgit / Becker, Kerstin / Neuhann, Teresa / Abicht, Angela / Steinke-Lange, Verena / Holinski-Feder, Elke

European journal of human genetics : EJHG

2023 Volume 31, Issue 8, Page(s) 925–930

Abstract: Here we report the results of a retrospective germline analysis of 6941 individuals fulfilling the criteria necessary for genetic testing of hereditary breast- and ovarian cancer (HBOC) according to the German S3 or AGO Guidelines. Genetic testing was ... ...

Abstract	Here we report the results of a retrospective germline analysis of 6941 individuals fulfilling the criteria necessary for genetic testing of hereditary breast- and ovarian cancer (HBOC) according to the German S3 or AGO Guidelines. Genetic testing was performed by next-generation sequencing using 123 cancer-associated genes based on the Illumina TruSight® Cancer Sequencing Panel. In 1431 of 6941 cases (20.6%) at least one variant was reported (ACMG/AMP classes 3-5). Of those 56.3% (n = 806) were class 4 or 5 and 43.7% (n = 625) were a class 3 (VUS). We defined a 14 gene HBOC core gene panel and compared this to a national and different internationally recommended gene panels (German Hereditary Breast and Ovarian Cancer Consortium HBOC Consortium, ClinGen expert Panel, Genomics England PanelsApp) in regard of diagnostic yield, revealing a diagnostic range of pathogenic variants (class 4/5) from 7.8 to 11.6% depending on the panel evaluated. With the 14 HBOC core gene panel having a diagnostic yield of pathogenic variants (class 4/5) of 10.8%. Additionally, 66 (1%) pathogenic variants (ACMG/AMP class 4 or 5) were found in genes outside the 14 HBOC core gene set (secondary findings) that would have been missed with the restriction to the analysis of HBOC genes. Furthermore, we evaluated a workflow for a periodic re-evaluation of variants of uncertain clinical significance (VUS) for the improvement of clinical validity of germline genetic testing.
MeSH term(s)	Humans ; Female ; Breast Neoplasms/genetics ; Ovarian Neoplasms/genetics ; Genetic Testing ; Genetic Variation
Language	English
Publishing date	2023-05-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1141470-4
ISSN	1476-5438 ; 1018-4813
ISSN (online)	1476-5438
ISSN	1018-4813
DOI	10.1038/s41431-023-01380-2
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Article ; Online: Evaluation of the BioFire® COVID-19 test and Respiratory Panel 2.1 for rapid identification of SARS-CoV-2 in nasopharyngeal swab samples.

Eckbo, Eric J / Locher, Kerstin / Caza, Melissa / Li, Lisa / Lavergne, Valery / Charles, Marthe

Diagnostic microbiology and infectious disease

2020 Volume 99, Issue 3, Page(s) 115260

Abstract: The BioFire® COVID-19 Test and Respiratory Panel 2.1 (RP2.1) are rapid, fully automated assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs. In the case of the RP2.1, an additional 21 viral and ...

Abstract	The BioFire® COVID-19 Test and Respiratory Panel 2.1 (RP2.1) are rapid, fully automated assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs. In the case of the RP2.1, an additional 21 viral and bacterial pathogens can be detected. Both tests have received emergency use authorization from the U.S. Food & Drug Administration and Interim Order authorization from Health Canada for use in clinical laboratories. We evaluated the performance characteristics of these tests in comparison to a laboratory-developed real-time PCR assay targeting the viral RNA-dependent RNA polymerase and E genes. A total of 78 tests were performed using the BioFire COVID-19 Test, including 30 clinical specimens and 48 tests in a limit of detection study; 57 tests were performed using the RP2.1 for evaluation of SARS-CoV-2 detection, including 30 clinical specimens and 27 tests for limit of detection. Results showed 100% concordance between the BioFire assays and the laboratory-developed test for all clinical samples tested, and acceptable performance of both BioFire assays at their stated limits of detection. Conclusively, the BioFire COVID-19 Test and RP2.1 are highly sensitive assays that can be effectively used in the clinical laboratory for rapid SARS-CoV-2 testing.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing/methods ; COVID-19 Testing/standards ; Clinical Laboratory Techniques/methods ; Diagnostic Tests, Routine ; Humans ; Limit of Detection ; Multiplex Polymerase Chain Reaction ; Nasopharynx/virology ; Real-Time Polymerase Chain Reaction/methods ; Reproducibility of Results ; SARS-CoV-2/isolation & purification ; Sensitivity and Specificity
Language	English
Publishing date	2020-11-10
Publishing country	United States
Document type	Evaluation Study ; Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2020.115260
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