This work was supported by the Sanming Project of Medicine in Shenzhen (Grant No. SZSM201510050) and the Guangdong Basic and Applied Basic Research Foundation (Grant No. 2022A1515220023). Research Foundation for Advanced Talents of Guandong Provincial People&#39;s Hospital (No. KJ012021097), and the National Natural Science Foundation of China (81871734, 82072380, 82272423). The funders had no role in the study design, data collection and analysis, the decision to publish, or the preparation of the manuscript.

The present study was conducted in conformity with ethical considerations established by the ethical committee of Guangdong Provincial People&#39;s Hospital, Southern Medical University, Guangzhou, China (Approval Number: KY-Q-2022-384-02). Patients in the age range of 18-60 years old were included in this study. Patients taking antibiotics, antibacterial Chinese medicines, drugs such as proton pump inhibitors (PPI), or H2 receptor antagonists, etc., within 2 weeks prior to testing were not included in this study. Those patients who had received treatment against H.pylori in the past 3 months were also excluded from this study. Those with serious heart, liver, kidney problems, severe neuropathy, or mental illness were also not allowed to participate in this study. There were no pregnant women and lactating mothers included in this study. Details of the supplies (reagents, chemicals, equipment, and software) used in this study are given in the Table of Materials.
1. String test for gastric fluid sampling
<ol>
	<li>Ask the patient to fast overnight before the sample collection.</li>
	<li>The next day, open the string test kit, take the capsule, and hold the loop at the end of the string.</li>
	<li>Tape the string onto the patient&#39;s cheek, and ask them to place the capsule on their tongue near the back of the throat and swallow it with a sip of water.</li>
	<li>Allow the capsule to be dissolved in the patient&#39;s stomach, thus exposing the string within the capsule to absorb gastric mucus.</li>
	<li>Ask a trained assistant to pull out the string carefully 1 h after the patient swallowed the capsule.</li>
	<li>Cut off the lower end of the string (40 cm) soaked in the gastric fluid, place it in the TSE (Tris/saline/EDTA) sample preservation solution, and then send it to the clinical laboratory at room temperature (RT) for the subsequent detection of H. pylori and the determination of the antibiotic resistance profiles using qPCR.</li>
</ol>
2. DNA extraction
<ol>
	<li>Place the specimen-carrying collection tubes on a test tube rack, properly labeled, and vortex them for 10 s.</li>
	<li>Turn the 32-well plate (nucleic acid extraction or purification kit) upside down several times to resuspend the magnetic beads. After a short vortex for 10 s, carefully remove the aluminum foil sealing from the plate.</li>
	<li>Transfer 200 &#181;L of gastric fluid from each sample and H. pylori DNA as a positive control into the separate wells.</li>
	<li>Place the 32-well plate in the corresponding sample slot of the nucleic acid extractor machine for automatic DNA extraction.</li>
	<li>After DNA extraction and confirmation, initiate the antibiotic resistance testing for clarithromycin and levofloxacin through qPCR on the positive samples.</li>
	<li>Place the excessive gastric fluid and extracted DNA samples at &#8722;20 &#176;C for long-term storage and future use.</li>
	<li>Perform all these steps in a biosafety cabinet to avoid any contamination.</li>
</ol>
3. qPCR for the detection of H. pylori and resistance to antibiotics (clarithromycin and levofloxacin)
<ol>
	<li>Perform qPCR for the detection of H. pylori and the suspected antibiotic resistance mutations in its genome.
	<ol>
		<li>Thaw the qPCR reaction mixture (H. pylori nucleic acid detection kit) on ice, and mix it by flicking and spinning to prevent any loss of reagent.</li>
		<li>For each sample on a 32-well plate, mix 20 &#181;L of PCR reaction mixture (genotyping reaction premix [containing the Taq enzyme, deoxyribonucleoside triphosphate, reaction buffer, and magnesium chloride], with ureA forward and reverse primers, and a ureA probe), and 5 &#181;L of the extracted DNA.</li>
		<li>Run the 32-well qPCR plate on the qPCR machine. Program the thermal cycler: the reaction mixture will be first reacted sequentially at 42 &#176;C and 95 &#176;C (both for one cycle) for 2 min each; then, 40 cycles at 95 &#176;C, denaturation for 10 s, and annealing and extension at 58 &#176;C for 45 s.</li>
		<li>Set the fluorescence signal acquisition to FAM (H. pylori) and the data acquisition to the amplification extension period. After the reaction is completed, save the data for future results analysis.</li>
		<li>Analyze the data using specific software for qPCR, as the instrument will automatically select baseline thresholds.</li>
		<li>If the test result for H. pylori is positive, the machine will automatically start drug resistance testing on the sample. Replace the reagent kit with detection reagents for 23S rRNA gene and gyrA gene mutations in the H. Pylori (qPCR) kit. 
		NOTE: The reagent kit (detection reagents for 23S rRNA gene and gyrA gene mutations in Helicobacter pylori [qPCR]) includes the PCR reaction mixture (genotyping reaction premix [containing the Taq enzyme, deoxyribonucleoside triphosphate, reaction buffer, magnesium chloride], primers, and probes). All the negative quality control products are sterile, purified water. The positive quality control product in the H. pylori nucleic acid detection kit is inactivated H. pylori standard beads (ATCC 43504). The strong H. pylori-positive and weak positive quality control products in the kit (detection reagents for 23S rRNA gene and gyrA gene mutations in H. pylori) are the DNA of the inactivated H. pylori strain containing the target gene and the mutant gene. Similarly, based on the actual situation, all diagnostic standards, including the presence of H. pylori infection or drug resistance, are set to CT &#8804; 35 and have a typical S-shaped curve. The concentration of the weak quality control is 1.0 x 103 copies/mL, while the concentration of the strong quality control is 1.0 x 108 copies/mL.</li>
	</ol>
	</li>
</ol>

qPCR-Based Rapid, Noninvasive Diagnosis of &lt;em&gt;Helicobacter pylori&lt;/em&gt; Infection and Antibiotic Resistance

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I., Burmistrov, A. I., Maev, I. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Helicobacter+pylori:+Commensal,+symbiont+or+pathogen.">Helicobacter pylori: Commensal, symbiont or pathogen.</a> World Journal of Gastroenterology. 27 (7), 545-560 (2021).</li><li>Thrift, A. P., Wenker, T. N., El-Serag, H. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+burden+of+gastric+cancer:+Epidemiological+trends,+risk+factors,+screening+and+prevention.">Global burden of gastric cancer: Epidemiological trends, risk factors, screening and prevention.</a> Nature Reviews Clinical Oncology. 20 (5), 338-349 (2023).</li><li>Liou, J. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Screening+and+eradication+of+Helicobacter+pylori+for+gastric+cancer+prevention:+The+Taipei+global+consensus.">Screening and eradication of Helicobacter pylori for gastric cancer prevention: The Taipei global consensus.</a> Gut. 69 (12), 2093-2112 (2020).</li><li>IARC Helicobacter pylori Working Group. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Helicobacter Pylori Eradication as A Strategy for Preventing Gastric Cancer. , (2014).</li><li>Vaira, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+stool+antigen+test+for+detection+of+Helicobacter+pylori+after+eradication+therapy.">The stool antigen test for detection of Helicobacter pylori after eradication therapy.</a> Annals of Internal Medicine. 136 (4), 280-287 (2002).</li><li>Laheij, R. 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A., Al-Ouqaili, M. T. S., Majeed, Y. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+Helicobacter+pylori+infection+by+invasive+and+noninvasive+techniques+in+patients+with+gastrointestinal+diseases+from+Iraq:+A+validation+study.">Detection of Helicobacter pylori infection by invasive and noninvasive techniques in patients with gastrointestinal diseases from Iraq: A validation study.</a> PLoS One. 16 (8), e0256393 (2021).</li><li>Chen, Q., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advanced+sensing+strategies+based+on+different+types+of+biomarkers+toward+early+diagnosis+of+H.+pylori.">Advanced sensing strategies based on different types of biomarkers toward early diagnosis of H. pylori.</a> Critical Reviews in Analytical Chemistry. , (2023).</li><li>Hussein, R. A., Al-Ouqaili, M. 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B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+clarithromycin-resistant+Helicobacter+pylori+in+clinical+specimens+by+molecular+methods:+A+review.">Detection of clarithromycin-resistant Helicobacter pylori in clinical specimens by molecular methods: A review.</a> Journal of Global Antimicrobial Resistance. 4, 35-41 (2016).</li><li>Perez-Trallero, E., Montes, M., Alcorta, M., Zubillaga, P., Telleria, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Non-endoscopic+method+to+obtain+Helicobacter+pylori+for+culture.">Non-endoscopic method to obtain Helicobacter pylori for culture.</a> Lancet. 345 (8950), 622-623 (1995).</li><li>DiNardo, A. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+string+test+and+stool+specimens+to+diagnose+pulmonary+tuberculosis.">Use of string test and stool specimens to diagnose pulmonary tuberculosis.</a> International Journal of Infectious Diseases. 41, 50-52 (2015).</li><li>Li, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+hypervirulent+Klebsiella+pneumoniae+isolates+using+the+string+test+in+combination+with+Galleria+mellonella+infectivity.">Identification of hypervirulent Klebsiella pneumoniae isolates using the string test in combination with Galleria mellonella infectivity.</a> European Journal of Clinical Microbiology and Infectious Diseases. 39 (9), 1673-1679 (2020).</li><li>Agbonlahor, D. E., Odugbemi, T. O., Udofia, P. 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H. pylori detection can be performed using both invasive and noninvasive methods13. Commonly used invasive techniques such as histopathology, the rapid urease test, polymerase chain reaction (PCR), and bacterial culturing require endoscopy and biopsy.Serological tests, urea breath tests, and enzyme-linked immunosorbent assays (ELISA) are recommended among the noninvasive procedures14. While noninvasive methods are easy to perform, economical, and more comfortable f...

H. pylori is a spiral-shaped, highly motile, gram-negative bacterium that mainly lives in the pylorus region of the stomach1. It&#160;is a common pathogen that infects nearly 50% of the global population2. Most people with H. pylori infection have no clinical manifestations, and most develop different diseases after several years of infection, including chronic gastritis, peptic ulcers, gastric ulcers, and gastric cancer3. In several studies based on different populations, the efficacy of eliminating H. pylori for preventing stomach cancer and precancerous lesions has been demonstrated4,5. Therefore, the World Health Organization (WHO) International Agency for Research on Cancer has advised H. pylori eradication as a preventative measure6.
The use of noninvasive methods to identify H. pylori infection is a key component of treatment for most individuals with asymptomatic dyspepsia. The urea breath test (UBT), H. pylori fecal antigen test (SAT), and serological testing are popular noninvasive techniques. Among these, the UBT is the least intrusive and most accurate procedure available. UBT uses urease, abundantly present in H. pylori, to hydrolyze isotopically labeled urea into ammonia and carbon dioxide (13C or 14C). In contrast, the immunochromatographic assay (ICA)7 is convenient, simple, and noninvasive for sampling. However, the accuracy of the test is affected by several factors, such as the quality of the stool sample, the temperature, and the interval between the sample collection and testing. Another test based on the immune response is the serum H. pylori antibody test, which detects antibodies in a patient&#39;s serum. However, this test is not suitable for post-treatment analysis since the antibodies remain long after the bacteria have been cleared8. Another major drawback is that these methods only diagnose H. pylori infection and do not allow for drug resistance testing to guide sensitivity-based treatment.
For invasive testing methods, gastric biopsy tissue needs to be taken by endoscopy and then subjected to histology, the urease rapid test, and bacterial culture. These testing methods are also very limited due to several factors. Currently, these techniques are limited to elderly patients, patients at high risk for precancerous or malignant disease, and patients who have failed first-line therapy for gastroesophageal reflux disease or H. pylori infection9. Secondly, due to the unique growth characteristics of H. pylori, the success rate of bacterial culture only reaches 50%10. Thus, molecular detection methods offer new hope to overcome the high demands of invasive detection methods and guide sensitivity-based treatment. Among molecular detection methods, quantitative PCR has evolved tremendously in recent years. qPCR, unlike traditional PCR, does not require gel electrophoresis and accurately quantifies DNA/RNA in samples by adding primers and probes at the annealing stage. qPCR kits for the detection of H. pylori infection and drug resistance are now commercially available. Nevertheless, each method has its limitations; therefore, a patient&#39;s clinical diagnosis and treatment should be considered in conjunction with their symptoms, signs, history, other laboratory tests, and response to treatment.
Currently, the primary method of treating H.pylori infections is taking antibiotics, but lately, it is becoming increasingly difficult to treat these infections due to the rise in antibiotic resistance. Subsequently, a significant decline in H. pylori treatment efficacy has been observed globally, making H. pylori eradication a major public health issue11.
Clarithromycin and levofloxacin are the two broad-spectrum antibiotics used to treat infections caused by H.pylori,&#160;but several studies have reported widespread resistance against these two drugs in H.pylori isolates. A2143G, A2142G, and A2142C are three of the numerous point mutations found in the 2.9 kb 23S rRNA gene that result in clarithromycin resistance by preventing the macrolide from binding. At the same time, the mutation loci of the levofloxacin resistance gene are mainly located in the six mutation sites (A260T, C261A, T261G, G271A, G271T, A272G) of the gyrA gene12. The discovery of these resistance mechanisms based on genetic mutations has led to a gradual shift in the detection of H. pylori through cultural-based studies to molecular testing.
Overall, there is an urgent clinical need for a noninvasive, effective, and simultaneous diagnostic method for the detection of H. pylori infections and drug resistance. We adopted a combined string test and qPCR method to overcome the difficulties of sampling and achieve the goal of the simultaneous detection of H. pylori infection and drug resistance using different primer probes.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>23S rRNA and gyrA gene point mutations detection kit (PCR-Fluorescence Probing)</td>
			<td>Hongmed Infagen</td>
			<td></td>
			<td>Detection of Helicobacter pylori resistance to clarithromycin and levofloxacin</td>
		</tr>
		<tr>
			<td>ABI 7500 fluorescence quantitative PCR machine</td>
			<td>Thermo Fisher Scientific</td>
			<td>SEDA 20163220767</td>
			<td>Fluorescent quantitative PCR amplification</td>
		</tr>
		<tr>
			<td>ABI 7500 software</td>
			<td>Thermo Fisher Scientific</td>
			<td></td>
			<td>Data Analysis</td>
		</tr>
		<tr>
			<td>BSC-1500IIA2-X</td>
			<td>BIOBASE</td>
			<td>SEDA 20143222263</td>
			<td>Biosafety cabinet</td>
		</tr>
		<tr>
			<td>DNA extraction kit</td>
			<td>Daan Gene&#160;</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>E-Centrifuge</td>
			<td>WEALTEC</td>
			<td></td>
			<td>Centrifuge the residual liquid off the wall of the tube.</td>
		</tr>
		<tr>
			<td>H. Pylori DNA detection kit (PCR-Fluorescence Probing)&#160;</td>
			<td>Hongmed Infagen</td>
			<td></td>
			<td>Testing for H. pylori infection</td>
		</tr>
		<tr>
			<td>Stream SP96 automated nucleic acid extractor</td>
			<td>Daan Gene</td>
			<td>SEDA 20140104</td>
			<td>For DNA extraction&#160;</td>
		</tr>
		<tr>
			<td>String test kit</td>
			<td>Hongmed Infagen</td>
			<td></td>
			<td>It contains a capsule attached to a string, scissors, cotton swab, and sample preservation tube&#160;</td>
		</tr>
		<tr>
			<td>Ultra-low temperature freezers&#160;(DW-YL450)&#160;</td>
			<td>MELING</td>
			<td>SEDA 20172220091</td>
			<td>-20 &#176;C for storing reagents&#160;</td>
		</tr>
		<tr>
			<td>Vortex-5</td>
			<td>Kylin-bell</td>
			<td></td>
			<td>For mixing reagent&#160;</td>
		</tr>
	</tbody>
</table>

quantitative polymerase chain reaction (qpcr)-based rapid diagnosis of helicobacter pylori infection and antibiotic resistance

Helicobacter pylori is a major human pathogen that&#160;infects approximately half of the global population and is becoming a serious health threat due to its increasing antibiotic resistance. It is the causative agent of chronic active gastritis, peptic ulcer disease, and gastric cancer and has been classified as a Group I Carcinogen by the International Agency for Research on Cancer. Therefore, the rapid and accurate diagnosis of H. pylori and the determination of its antibiotic resistance are important for the efficient eradication of this bacterial pathogen. Currently, H. pylori diagnosis methods mainly include the urea breath test (UBT), the antigen test, the serum antibody test, gastroscopy, the rapid urease test (RUT), and bacterial culture. Among them, the first three detection methods are noninvasive, meaning they are easy tests to conduct. However, bacteria cannot be retrieved through these techniques; thus, drug resistance testing cannot be performed. The last three are invasive examinations, but they are costly, require high skills, and have the potential to cause damage to patients. Therefore, a noninvasive, rapid, and simultaneous method for H. pylori detection and drug resistance testing is very important for efficiently eradicating H. pylori in clinical practice. This protocol aims to present a specific procedure involving the string test in combination with quantitative polymerase chain reaction (qPCR) for the rapid detection of H. pylori infection and antibiotic resistance. Unlike bacterial cultures, this method allows for easy, rapid, noninvasive diagnosis of H. pylori infection status and drug resistance. Specifically, we used qPCR to detect rea for H. pylori infection and mutations in the 23S rRNA and gyrA genes, which encode resistance against clarithromycin and levofloxacin, respectively. Compared to routinely used culturing techniques, this protocol provides a noninvasive, low-cost, and time-saving technique to detect H. pylori infection and determine its antibiotic resistance using qPCR.

Author Spotlight: Detection and Treatment of Helicobacter pylori Infection 

Quantitative Polymerase Chain Reaction (qPCR)-Based Rapid Diagnosis of Helicobacter pylori Infection and Antibiotic Resistance

Detection of H. pylori infection and antibiotic resistance in stomach fluid by qPCR 
We performed qPCR for the detection of H. pylori infection by amplifying the ureA gene and determined its antibiotic resistance profile by targeting point mutations in the 23S rRNA gene and gyrA gene (Table 1). The quality control CT values in all three groups of the qPCR experiments were within the recommended range, indicating that the samples were all in a norm...

Watch this Scientific Journal Video about Detection and Treatment of Helicobacter pylori Infection at JoVE.com

The protocol presents a noninvasive method for the rapid diagnosis of Helicobacter pylori stomach infections through the string test and determines its antibiotic resistance to clarithromycin and levofloxacin using quantitative polymerase chain reaction (qPCR).

Helicobacter pylori is a major human pathogen that&#160;infects approximately half of the global population and is becoming a serious health threat due to ...

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Gastric Fluid Sampling, DNA Extraction, and qPCR for H. pylori Detection and its Antibiotic Resistance

Gastric Fluid Sampling, DNA Extraction, and qPCR for H. pylori Detection and its Antibiotic Resistance  

To begin, instruct the patient to fast overnight before the sample collection. The next day, open the string test kit. Take the capsule and hold the loop at the end of the string.Tape the string onto the patient's cheek. Then guide the patient to place the capsule on their tongue near the back of the throat and swallow it with a sip of water. After the capsule has been dissolved in the patient's stomach for an hour instruct a trained assistant to carefully pull out the string from the patient.Next place the end soaked in the gastric fluid in a TSE sample preservation solution and cut off the lower end of the string. Place the labeled specimen carrying collection tubes on a test tube rack and vortex for 10 seconds. Turn the 32 well plate upside down several times to resuspend the magnetic beads, vortex for 10 seconds.Then carefully remove the aluminum foil ceiling from the plate. Transfer 200 microliters of gastric fluid from each sample and helicobacter pylori DNA as a positive control into the separate wells. Place the 32 well plate in the corresponding sample slot of the nucleic acid extractor machine for automatic DNA extraction, after DNA extraction and confirmation.Place the excess gastric fluid and extracted DNA samples at minus 20 degrees Celsius until use, thaw the qPCR reaction mixture on ice and mix it by flicking and spinning to avoid reagent loss For each sample in a 32 well plate, mix 20 microliters of the PCR reaction mixture with urea forward and reverse primers, a urea probe and five microliters of the extracted DNA. Place the plate on the qPCR machine and set the thermal cycler program. Set the fluorescent signal acquisition to FAM the data acquisition, to the amplification extension period and start the run, upon completion of the reaction.Save the data for analysis. Analyze the data with specialized software for qPCR as the instrument automatically selects baseline thresholds. If the test results for h.pylori are positive replace the reagent kit with detection reagents for 23S rRNA gene and gyrA gene mutation in the h. pylori kit and start the drug resistance testing on the sample. This study shows the detection of h.pylori and its antibiotic resistance in stomach fluid by qPCR. Among h. pylori positive samples.S2 had CT values within the detection range indicating dual resistance to clarithromycin and Levofloxacin. The S3 CT values were within the detection for h. pylori infection and Levofloxacin resistance, but not for clarithromycin resistance, indicating levofloxacin resistance.Similarly, S4 had detectable CT values for h. pylori infection and clarithromycin resistance but not for levofloxacin resistance suggesting clarithromycin resistance. The S5 had detectable CT values only for h.pylori infection indicating sensitivity to both antibiotics and allowing treatment with either drug.

2.5K Views.  Southern Medical University.  The protocol presents a noninvasive method for the rapid diagnosis of Helicobacter pylori stomach infections through the string test and determines its antibiotic resistance to clarithromycin and levofloxacin using quantitative polymerase chain reaction (qPCR).

qPCR-Based Rapid, Noninvasive Diagnosis of Helicobacter pylori Infection and Antibiotic Resistance

Summary