ABSTRACT
Although the reverse transcriptase polymerase chain reaction (RT-PCR) method has been accepted as the reference method in the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA, it requires special laboratory conditions, complicated and expensive laboratory instruments, competent laboratory staff and long testing duration. Antigen testing methods such as enzyme immunoassay, fluorescent antibody and visually-read immunochromatographic rapid antigen detection (RAD) tests eliminated the above mentioned disadvantages of the RT-PCR. The aim of this study was to determine the performance of a RAD test kit (V-Chek, SGA Ltd, Ankara, Turkey). Two paired nasopharyngeal swabs were collected from each patient, and one of them was used for the RAD test, while the other one (different swab) was used to perform the RT-PCR test. SARS CoV-2 Double Gene RT-PCR kit (Bioeksen, Turkey) was used for RNA amplification on the Light Cycler 480 plate-based RT-PCR instrument (Roche, Switzerland). The SARS-CoV-2 double gene RT-PCR kit targeting the SARS-CoV-2 specific N (nucleocapsid) and Orf1ab gene regions was used for RNA amplification. The human RNaseP gene was used for nucleic acid extraction and inhibition control. The shape of the growth curves was examined and the non-sigmoidal curves were recorded as "negative". Sigmoidal curves with cycle threshold (Ct) <38 were evaluated as "positive". The Ct values of all positive results were recorded. V-Chek RAD test kit uses a colloidal gold enhanced double antibody sandwich type antigen test kit. A SARS-CoV-2 positive specimen produces a distinct color band in the test region, formed by the specific antibody-antigen colored conjugate complex. A positive or negative result is indicated by a colored line appearance on the test region. A colored line appears in the control region, independent of the SARS-CoV-2 presence. The result is visually read 10 minutes after the last drop of the sample liquid is dispensed into the sample well. Specificity and sensitivity values were calculated accepting the RT-PCR results as a standard. Agreement between two different techniques was assessed using Cohen's kappa score. 110 patients were enrolled in this study; 34 (30.9 %) of these patients had positive RT-PCR samples, with the mean of Ct values of 25.8 (95% CI= 24.1-27.5), median of Ct values of 26. In our study population, the overall sensitivity was 61.8% (95% CI= 45.4-78.1), and specificity was 100%. Taking RT-PCR as reference, Cohen's kappa score for the antigen test was 0.691. Fisher's exact test was p<0.001. In conclusion, the RAD kit used in the study determined to be useful for the rapid identification of COVID-19 patients. However, a negative result does not eliminate the possibility of COVID-19 infection and should be confirmed by RT-PCR and clinical findings.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Immunoenzyme Techniques , RNA , Time FactorsABSTRACT
The aim of this study is to evaluate the association between seven important H. pylori virulence factors and antibiotic resistance in patients with gastritis. H. pylori strains isolated from 33 patients with gastritis were examined. Antimicrobial susceptibilities were tested by GenoType® HelicoDR (Hain Life Science, Germany) test kit and RT-PCR. The virulence-factors were determined using conventional PCR. 39% of patients were resistant for clarithromycin and 27% of patients were resistant for fluoroquinolone. 15% of patients were resistant to both clarithromycin and fluoroquinolone. The H. pylori vacA m1/s2 genotype was the most frequent allelic combination. Patients were possessed the vacA s1, m1 (6.1%); s1, m2 (6.1%); s2, m1 (15.1%); and s2, m2 (3.0%) genotypes. 94% of patients with gastritis were positive for H. pylori napA gene. Also, there were no dupA gene-positive gastritis patients. There was no significant correlation between the vacA, cagA, oipA, hpaA, babA, napA, dupA, ureA, ureB virulence genes, clarithromycin, and fluoroquinolone resistance. Herein, we report that the relationship between the H. pylori napA gene and gastritis. Although we found a correlation between H. pylori virulence factor and clinical outcome, there is a need for further studies to enlighten the relation between H. pylori virulence genes and antibiotic resistance.
ABSTRACT
AIM: H. pylori is a bacterial pathogen in the human stomach which infects about 50% of the world population. Untreated infection can lead to various diseases leading to cancer. Some of the H. pylori strains are asymptomatic, but some of them cause more severe diseases. Standard treatment protocol used for the treatment of H. pylori infection is triple therapy, which includes omeprazole as a proton pump inhibitor (PPI) and two antibiotics usually consist of amoxicillin and clarithromycin or metronidazole. In the recent years, because of the increase in the rate of antibiotic resistance, the eradication rate has decreased. MATERIALS AND METHODS: We evaluated 140 patients who applied to a university hospital gastroenterology department and underwent biopsy during endoscopy. In these patients, we analysed floroquinolone and clarithromycin resistance using the GenoType® HelicoDR (Hain Life Science, Germany). We also used the real-time method for clarithromycin resistance. RESULTS: We found the number and rate of floroquinolone resistance as 20 (25.6%) and clarithromycine resistance as 31 (39.7%). With the real-time PCR method, we detected clarithromycine resistance in 26 (33.3%) patients. These results were not statistically significant. Discussion and Conclusion. Our results show similarity to the other studies held in our country. There should be more studies for the policy of eradication through our country.
