Peculiarities of Diagnostic Reliability—Nested PCR Versus SAT in the Identification of <i>Helicobacter pylori</i>
<i>H. pylori</i> detection via the stool antigen test (SAT) requires 100 times more cells than nested PCR (NPCR) for a 454 bp amplicon, but is significantly more sensitive in identifying positive stool samples. To understand this contradiction, we developed an NPCR assay to amplify a sho...
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2025-06-01
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| author | Barbora Šipková Michaela Abrahamovská Janka Klingová Bianka Prokopová Jana Krčmáriková Iveta Cihová Pavol Sulo |
| author_facet | Barbora Šipková Michaela Abrahamovská Janka Klingová Bianka Prokopová Jana Krčmáriková Iveta Cihová Pavol Sulo |
| author_sort | Barbora Šipková |
| collection | DOAJ |
| description | <i>H. pylori</i> detection via the stool antigen test (SAT) requires 100 times more cells than nested PCR (NPCR) for a 454 bp amplicon, but is significantly more sensitive in identifying positive stool samples. To understand this contradiction, we developed an NPCR assay to amplify a shorter 148 bp segment of the 16S rRNA gene. The assay was extremely sensitive and reliable when adhering to particular rules commonly used in forensic laboratories. The SAT and NPCR for long and short amplicons were compared using stool samples from 208 gastroenterological patients, of which 27.9% were identified as positive according to the SAT and only 6.25% according to the 454 bp NPCR amplicon, but 51.0% in the short 148 bp NPCR. Among 100 asymptomatic volunteers, the prevalence was 35% in the SAT assay and 22% in the long NPCR, but as much as 66.6% of positives were determined in the short 148 bp NPCR. The specificity of the PCR product was determined via DNA sequencing, which confirmed <i>H. pylori</i>’s origin in all NPCR-positive samples. Apparently, the stool contains mostly short fragments of <i>H. pylori</i> DNA, and the most plausible explanation for the SAT/NPCR paradox is the degradation of <i>H. pylori</i> DNA in the digestive system. |
| format | Article |
| id | doaj-art-aa75786b589449f5904313ecde9ca2a7 |
| institution | DOAJ |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj-art-aa75786b589449f5904313ecde9ca2a72025-08-20T03:07:55ZengMDPI AGMicroorganisms2076-26072025-06-01137149810.3390/microorganisms13071498Peculiarities of Diagnostic Reliability—Nested PCR Versus SAT in the Identification of <i>Helicobacter pylori</i>Barbora Šipková0Michaela Abrahamovská1Janka Klingová2Bianka Prokopová3Jana Krčmáriková4Iveta Cihová5Pavol Sulo6Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, SlovakiaDepartment of Biochemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, SlovakiaDepartment of Biochemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, SlovakiaDepartment of Biochemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, SlovakiaSynlab Slovakia s. r. o., Limbova 5, 831 01 Bratislava, SlovakiaDepartment of Track and Field, Faculty of Physical Education and Sports, Comenius University, Nábr. arm. gen. L. Svobodu 9, 814 69 Bratislava, SlovakiaDepartment of Biochemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia<i>H. pylori</i> detection via the stool antigen test (SAT) requires 100 times more cells than nested PCR (NPCR) for a 454 bp amplicon, but is significantly more sensitive in identifying positive stool samples. To understand this contradiction, we developed an NPCR assay to amplify a shorter 148 bp segment of the 16S rRNA gene. The assay was extremely sensitive and reliable when adhering to particular rules commonly used in forensic laboratories. The SAT and NPCR for long and short amplicons were compared using stool samples from 208 gastroenterological patients, of which 27.9% were identified as positive according to the SAT and only 6.25% according to the 454 bp NPCR amplicon, but 51.0% in the short 148 bp NPCR. Among 100 asymptomatic volunteers, the prevalence was 35% in the SAT assay and 22% in the long NPCR, but as much as 66.6% of positives were determined in the short 148 bp NPCR. The specificity of the PCR product was determined via DNA sequencing, which confirmed <i>H. pylori</i>’s origin in all NPCR-positive samples. Apparently, the stool contains mostly short fragments of <i>H. pylori</i> DNA, and the most plausible explanation for the SAT/NPCR paradox is the degradation of <i>H. pylori</i> DNA in the digestive system.https://www.mdpi.com/2076-2607/13/7/1498<i>H. pylori</i>stool antigen testdiagnostic reliabilitynested PCR |
| spellingShingle | Barbora Šipková Michaela Abrahamovská Janka Klingová Bianka Prokopová Jana Krčmáriková Iveta Cihová Pavol Sulo Peculiarities of Diagnostic Reliability—Nested PCR Versus SAT in the Identification of <i>Helicobacter pylori</i> Microorganisms <i>H. pylori</i> stool antigen test diagnostic reliability nested PCR |
| title | Peculiarities of Diagnostic Reliability—Nested PCR Versus SAT in the Identification of <i>Helicobacter pylori</i> |
| title_full | Peculiarities of Diagnostic Reliability—Nested PCR Versus SAT in the Identification of <i>Helicobacter pylori</i> |
| title_fullStr | Peculiarities of Diagnostic Reliability—Nested PCR Versus SAT in the Identification of <i>Helicobacter pylori</i> |
| title_full_unstemmed | Peculiarities of Diagnostic Reliability—Nested PCR Versus SAT in the Identification of <i>Helicobacter pylori</i> |
| title_short | Peculiarities of Diagnostic Reliability—Nested PCR Versus SAT in the Identification of <i>Helicobacter pylori</i> |
| title_sort | peculiarities of diagnostic reliability nested pcr versus sat in the identification of i helicobacter pylori i |
| topic | <i>H. pylori</i> stool antigen test diagnostic reliability nested PCR |
| url | https://www.mdpi.com/2076-2607/13/7/1498 |
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