Clinical evaluation of a non-purified direct molecular assay for the detection of Clostridioides difficile toxin genes in stool specimens

Hara, Takatoshi; Suzuki, Hiromichi; Oyanagi, Tadatomo; Koyanagi, Norito; Ushiki, Akihito; Kawabata, Nariyoshi; Goto, Miki; Hida, Yukio; Yaguchi, Yuji; Tamai, Kazuya; Notake, Shigeyuki; Kawashima, Yosuke; Sugiyama, Akio; Uemura, Keiichi; Kashiyama, Seiya; Nanmoku, Toru; Suzuki, Satoshi; Yamazaki, Hiroshi; Kimura, Hideki; Kunishima, Hiroyuki; Ohge, Hiroki

doi:10.1371/journal.pone.0234119

Cited by 7 publications

(5 citation statements)

References 30 publications

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“…Application of the GeneXpert assay is usually used to detect the presence of toxigenic C. difficile in hospitalised patients (15). In addition, for this application, the major advantage of this assay is the lower limit of detection for the toxin gene in samples (16). These are the reasons why we selected this assay and tried to apply it with other method as the primary method applied during outbreak.…”

Section: Discusionmentioning

confidence: 99%

Use of tcdC gene sequencing to prevent misidentification of Clostridioides difficile ribotype 176 and 027

Havrilova,

Novakova,

Lucansky

et al. 2024

Medicinski Glasnik

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Aim To compare the sequences of the tcdC gene between Clostridioides difficile (C. difficile) strains identified as PCR ribotype 176 and the reference strain C. difficile PCR ribotype 027 and to evaluate the use of the Xpert C. difficile/Epi assay for their differentiation.&nbsp; Methods A total of 45 strains were grown from storage beads. DNA of sufficient quality and quantity for sequencing was extracted from 9 samples. Single consensus sequences of PCR ribotype 176 strains and PCR ribotype 001, PCR ribotype 070 (a control group) were mapped to a reference genome of strain CDI-01 (PCR ribotype 027).&nbsp; Results Four strains (out of seven; 57%) characterized as PCR ribotype 176 had 100% identity of the tcdC gene with the reference strain. The average length of the tcdC gene in these four strains (PCR ribotype 176) was 643 bp, which is 36 bp shorter than the reference genome. Three strains (PCR ribotype 176) had a percentage identity of the tcdC gene in the range of 99.37-100%. Strains 25 (PCR ribotype 001) and 28 (PCR ribotype 070) had a similarity in the range of 95.39-95.63% as a result of different ribotype to the reference strain.&nbsp; Conclusion PCR ribotype 176 strains have almost the same tcdC gene sequence as PCR ribotype 027, resulting in misidentification of this PCR ribotype by the Xpert C. difficile/Epi assay. Information about presumptive positive results based on deletion in the tcdC gene should be treated with caution or disregarded

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Section: Discusionmentioning

confidence: 99%

Use of tcdC gene sequencing to prevent misidentification of Clostridioides difficile ribotype 176 and 027

Havrilova,

Novakova,

Lucansky

et al. 2024

Medicinski Glasnik

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“…The system automatically prepares reaction mixtures and amplifies and detects target genes in a short time and can analyze up to eight samples and four items at the same time in a single run. GENECUBE ® has been applied for several pathogens, including Mycobacterium tuberculosis [8], M. avium, M. intracellulare, Neisseria gonorrhoeae [9], Chlamydia trachomatis [9], Mycoplasma pneumoniae [7,10], Staphylococcus aureus (nuc and mecA) [11], and the toxin gene of Clostridioides difficile [12].…”

Section: Introductionmentioning

confidence: 99%

A Prospective Evaluation of the Analytical Performance of GENECUBE® HQ SARS-CoV-2 and GENECUBE® FLU A/B

et al. 2021

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Background Molecular tests are the mainstay of detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, their accessibility can be limited by the long examination time and inability to evaluate multiple samples at once. Objective This study evaluated the analytical performance of the newly developed rapid molecular assays GENECUBE ® HQ SARS-CoV-2 and GENECUBE ® FLU A/B. Method This prospective study was conducted between 14 December 2020 and 9 January 2021 at a polymerase chain reaction (PCR) center. Samples were collected from the nasopharynx with flocked swabs. Molecular tests were performed with the GENECUBE ® system and reference reverse transcription (RT)-PCR, and the results of the two assays were compared. Result Among 1065 samples, 81 (7.6%) were positive for SARS-CoV-2 on the reference RT-PCR. Three showed discordance between GENECUBE ® HQ SARS-CoV-2 and the reference RT-PCR; the total, positive, and negative samples of concordance for the two assays were 99.7%, 100%, and 99.7%, respectively. All discordant cases were positive with GENECUBE ® HQ SARS-CoV-2 and negative with the reference RT-PCR. SARS-CoV-2 was detected in all three samples using another molecular assay for SARS-CoV-2. For GENECUBE ® FLU A/B, the total, positive, and negative samples of concordance for the two assays were 99.5%, 100%, and 99.1%. ConclusionThe GENECUBE ® HQ SARS-CoV-2 and GENECUBE ® FLU A/B demonstrated sufficient analytical performance to detect SARS-CoV-2 and influenza virus A/B.

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“…The system automatically prepares reaction mixtures and amplifies and detects target genes in a short time, which, in a single run, can analyze up to eight samples and four items at the same time. GENECUBE ® has been applied for several pathogens, including Mycobacterium tuberculosis [8], M. avium, M. intracellulare, Neisseria gonorrhoeae [9], Chlamydia trachomatis [9], Mycoplasma pneumoniae [7,10], Staphylococcus aureus (nuc and mecA) [11] and the toxin gene of Clostridiodes difficile [12].…”

Section: Introductionmentioning

confidence: 99%

A prospective evaluation of the analytical performance of GENECUBE^® HQ SARS-CoV-2 and GENECUBE^® FLU A/B

Kiyasu

Akashi

Sugiyama

et al. 2021

Preprint

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Background: Molecular tests are the mainstay for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, their accessibility can be limited by the long examination time and inability to evaluate multiple samples at once. This study evaluated the analytical performance of the newly developed rapid molecular assays GENECUBE® HQ SARS-CoV-2 and the GENECUBE® FLU A/B. Method: This prospective study was conducted between December 14, 2020, and January 9, 2021, at a polymerase chain reaction (PCR) center. Samples were collected from the nasopharynx with flocked swabs. Molecular tests were performed with the GENECUBE® system and reference reverse transcription (RT)-PCR, and the results of the two assays were compared. Result: Among 1065 samples, 81 (7.6%) were positive for SARS-CoV-2 on the reference RT-PCR. Three showed discordance between GENECUBE® HQ SARS-CoV-2 and the reference RT-PCR; the total, positive and negative samples of concordance for the two assays were 99.7%, 100%, and 99.7%, respectively. All discordant cases were positive for GENECUBE® HQ SARS-CoV-2 and negative for the reference RT-PCR. SARS-CoV-2 was detected from all three samples by another molecular assay for SARS-CoV-2. For the GENECUBE® FLU A/B, the total, positive and negative samples of concordance for the two assays were 99.5%, 100%, and 99.1%. Conclusion: The GENECUBE® HQ SARS-CoV-2 and GENECUBE® FLU A/B demonstrated sufficient analytical performance to detect SARS-CoV-2 and influenza virus A/B.

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Clinical evaluation of a non-purified direct molecular assay for the detection of Clostridioides difficile toxin genes in stool specimens

Cited by 7 publications

References 30 publications

Use of tcdC gene sequencing to prevent misidentification of Clostridioides difficile ribotype 176 and 027

Use of tcdC gene sequencing to prevent misidentification of Clostridioides difficile ribotype 176 and 027

A Prospective Evaluation of the Analytical Performance of GENECUBE® HQ SARS-CoV-2 and GENECUBE® FLU A/B

A prospective evaluation of the analytical performance of GENECUBE^® HQ SARS-CoV-2 and GENECUBE^® FLU A/B

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Clinical evaluation of a non-purified direct molecular assay for the detection of Clostridioides difficile toxin genes in stool specimens

Cited by 7 publications

References 30 publications

Use of tcdC gene sequencing to prevent misidentification of Clostridioides difficile ribotype 176 and 027

Use of tcdC gene sequencing to prevent misidentification of Clostridioides difficile ribotype 176 and 027

A Prospective Evaluation of the Analytical Performance of GENECUBE® HQ SARS-CoV-2 and GENECUBE® FLU A/B

A prospective evaluation of the analytical performance of GENECUBE® HQ SARS-CoV-2 and GENECUBE® FLU A/B

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Product

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A prospective evaluation of the analytical performance of GENECUBE^® HQ SARS-CoV-2 and GENECUBE^® FLU A/B