1
|
Ng HK, Chua KH, Kee BP, Chuah KH, Por LY, Puah SM. Genetic variations of penicillin-binding protein 1A: insights into the current status of amoxicillin-based regimens for Helicobacter pylori eradication in Malaysia. J Med Microbiol 2024; 73. [PMID: 38712922 DOI: 10.1099/jmm.0.001832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024] Open
Abstract
Introduction. Resistance towards amoxicillin in Helicobacter pylori causes significant therapeutic impasse in healthcare settings worldwide. In Malaysia, the standard H. pylori treatment regimen includes a 14-day course of high-dose proton-pump inhibitor (rabeprazole, 20 mg) with amoxicillin (1000 mg) dual therapy.Hypothesis/Gap Statement. The high eradication rate with amoxicillin-based treatment could be attributed to the primary resistance rates of amoxicillin being relatively low at 0%, however, a low rate of secondary resistance has been documented in Malaysia recently.Aim. This study aims to investigate the amino acid mutations and related genetic variants in PBP1A of H. pylori, correlating with amoxicillin resistance in the Malaysian population.Methodology. The full-length pbp1A gene was amplified via PCR from 50 genomic DNA extracted from gastric biopsy samples of H. pylori-positive treatment-naïve Malaysian patients. The sequences were then compared with reference H. pylori strain ATCC 26695 for mutation and variant detection. A phylogenetic analysis of 50 sequences along with 43 additional sequences from the NCBI database was performed. These additional sequences included both amoxicillin-resistant strains (n=20) and amoxicillin-sensitive strains (n=23).Results. There was a total of 21 variants of amino acids, with three of them located in or near the PBP-motif (SKN402-404). The percentages of these three variants are as follows: K403X, 2%; S405I, 2% and E406K, 16%. Based on the genetic markers identified, the resistance rate for amoxicillin in our sample remained at 0%. The phylogenetic examination suggested that H. pylori might exhibit unique conserved pbp1A sequences within the Malaysian context.Conclusions. Overall, the molecular analysis of PBP1A supported the therapeutic superiority of amoxicillin-based regimens. Therefore, it is crucial to continue monitoring the amoxicillin resistance background of H. pylori with a larger sample size to ensure the sustained effectiveness of amoxicillin-based treatments in Malaysia.
Collapse
Affiliation(s)
- Heng Kang Ng
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Boon Pin Kee
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kee Huat Chuah
- Department of Medicine, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Lip Yee Por
- Department of Computer System and Technology, Faculty of Computer Science and Information Technology, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| |
Collapse
|
2
|
Šamanić I, Dadić B, Sanader Maršić Ž, Dželalija M, Maravić A, Kalinić H, Vrebalov Cindro P, Šundov Ž, Tonkić M, Tonkić A, Vuković J. Molecular Characterization and Mutational Analysis of Clarithromycin- and Levofloxacin-Resistance Genes in Helicobacter pylori from Gastric Biopsies in Southern Croatia. Int J Mol Sci 2023; 24:14560. [PMID: 37834008 PMCID: PMC10572715 DOI: 10.3390/ijms241914560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Point mutations in the 23S rRNA, gyrA, and gyrB genes can confer resistance to clarithromycin (CAM) and levofloxacin (LVX) by altering target sites or protein structure, thereby reducing the efficacy of standard antibiotics in the treatment of Helicobacter pylori infections. Considering the confirmed primary CAM and LVX resistance in H. pylori infected patients from southern Croatia, we performed a molecular genetic analysis of three target genes (23S rRNA, gyrA, and gyrB) by PCR and sequencing, together with computational molecular docking analysis. In the CAM-resistant isolates, the mutation sites in the 23S rRNA gene were A2142C, A2142G, and A2143G. In addition, the mutations D91G and D91N in GyrA and N481E and R484K in GyrB were associated with resistance to LVX. Molecular docking analyses revealed that mutant H. pylori strains with resistance-related mutations exhibited a lower susceptibility to CAM and LVX compared with wild-type strains due to significant differences in non-covalent interactions (e.g., hydrogen bonds, ionic interactions) leading to destabilized antibiotic-protein binding, ultimately resulting in antibiotic resistance. Dual resistance to CAM and LVX was found, indicating the successful evolution of H. pylori resistance to unrelated antimicrobials and thus an increased risk to human health.
Collapse
Affiliation(s)
- Ivica Šamanić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia; (B.D.); (M.D.); (A.M.)
| | - Blanka Dadić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia; (B.D.); (M.D.); (A.M.)
| | - Željka Sanader Maršić
- Department of Physics, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia;
| | - Mia Dželalija
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia; (B.D.); (M.D.); (A.M.)
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia; (B.D.); (M.D.); (A.M.)
| | - Hrvoje Kalinić
- Department of Compute Science, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia;
| | - Pavle Vrebalov Cindro
- Department of Gastroenterology, University Hospital of Split, 21000 Split, Croatia; (P.V.C.); (Ž.Š.); (A.T.)
| | - Željko Šundov
- Department of Gastroenterology, University Hospital of Split, 21000 Split, Croatia; (P.V.C.); (Ž.Š.); (A.T.)
- Department of Internal Medicine, School of Medicine, University of Split, 21000 Split, Croatia
| | - Marija Tonkić
- Department of Medical Microbiology and Parasitology, School of Medicine, University of Split, 21000 Split, Croatia;
| | - Ante Tonkić
- Department of Gastroenterology, University Hospital of Split, 21000 Split, Croatia; (P.V.C.); (Ž.Š.); (A.T.)
- Department of Internal Medicine, School of Medicine, University of Split, 21000 Split, Croatia
| | - Jonatan Vuković
- Department of Gastroenterology, University Hospital of Split, 21000 Split, Croatia; (P.V.C.); (Ž.Š.); (A.T.)
- Department of Internal Medicine, School of Medicine, University of Split, 21000 Split, Croatia
| |
Collapse
|
3
|
Deng R, Liu L, Xie W, Lu W, Liu Z, Wang Y. Prevalence of Helicobacter pylori Antibiotic Resistance in Patients Enrolled in Guangzhou, China. Infect Drug Resist 2023; 16:5033-5038. [PMID: 37554543 PMCID: PMC10406106 DOI: 10.2147/idr.s418482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
PURPOSE Helicobacter pylori (H. pylori) infection is a high-risk factor for the occurrence of gastric cancer. The quadruple therapy has been widely used as the first-line treatment for H. pylori in China. However, the increasing resistance rate to antibiotics has become a major challenge in the treatment of H. pylori. Therefore, there is an urgent need for rapid and cost-effective detection of antibiotic resistance to different antibiotics. To evaluate the prevalence of H. pylori antibiotic resistance in Guangzhou and the diagnostic performance of DOB value of 13C UBT in predicting antibiotic resistance. PATIENTS AND METHODS In this retrospective study, we collected data from 193 H. pylori culture-positive patients in Guangzhou on their DOB values and resistance to antibiotics. We analyzed the antibiotic resistance rate of commonly used antibiotics in quadruple therapy, and the diagnostic efficacy of DOB value was evaluated. RESULTS The resistance rates of clarithromycin (CLA) and levofloxacin (LEV) were 46.1% and 44.0%, respectively. In the age group under 40, the resistance rate of LEV was lower than that of CLA. However, the diagnostic efficacy of DOB value was found to be low and it could not serve as an independent indicator for diagnosing resistance to CLA and LEV. CONCLUSION The high resistance rates of CLA and LEV in H. pylori patients in Guangzhou indicate the urgent need for effective detection methods. The DOB value is not a direct indicator of antibiotic resistance to CLA and LEV. Therefore, it is important to use a combination of diagnostic methods to accurately assess antibiotic resistance in H. pylori infection.
Collapse
Affiliation(s)
- RiHui Deng
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - LiYan Liu
- Shanghai Xinchao Medical Laboratory, Shanghai, People’s Republic of China
| | - WeiKe Xie
- Equipment Management Department, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Weiguo Lu
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Zhihui Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Yang Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| |
Collapse
|
4
|
Alfaray RI, Saruuljavkhlan B, Fauzia KA, Torres RC, Thorell K, Dewi SR, Kryukov KA, Matsumoto T, Akada J, Vilaichone RK, Miftahussurur M, Yamaoka Y. Global Antimicrobial Resistance Gene Study of Helicobacter pylori: Comparison of Detection Tools, ARG and Efflux Pump Gene Analysis, Worldwide Epidemiological Distribution, and Information Related to the Antimicrobial-Resistant Phenotype. Antibiotics (Basel) 2023; 12:1118. [PMID: 37508214 PMCID: PMC10376887 DOI: 10.3390/antibiotics12071118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/15/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
We conducted a global-scale study to identify H. pylori antimicrobial-resistant genes (ARG), address their global distribution, and understand their effect on the antimicrobial resistance (AMR) phenotypes of the clinical isolates. We identified ARG using several well-known tools against extensive bacterial ARG databases, then analyzed their correlation with clinical antibiogram data from dozens of patients across countries. This revealed that combining multiple tools and databases, followed by manual selection of ARG from the annotation results, produces more conclusive results than using a single tool or database alone. After curation, the results showed that H. pylori has 42 ARG against 11 different antibiotic classes (16 genes related to single antibiotic class resistance and 26 genes related to multidrug resistance). Further analysis revealed that H. pylori naturally harbors ARG in the core genome, called the 'Set of ARG commonly found in the Core Genome of H. pylori (ARG-CORE)', while ARG-ACC-the ARG in the accessory genome-are exclusive to particular strains. In addition, we detected 29 genes of potential efflux pump-related AMR that were mostly categorized as ARG-CORE. The ARG distribution appears to be almost similar either by geographical or H. pylori populations perspective; however, some ARG had a unique distribution since they tend to be found only in a particular region or population. Finally, we demonstrated that the presence of ARG may not directly correlate with the sensitive/resistance phenotype of clinical patient isolates but may influence the minimum inhibitory concentration phenotype.
Collapse
Affiliation(s)
- Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, Indonesia
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, Indonesia
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Roberto C Torres
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kaisa Thorell
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Selva Rosyta Dewi
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, Indonesia
| | - Kirill A Kryukov
- Biological Networks Laboratory, Department of Informatics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Ratha-Korn Vilaichone
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Thammasat University Hospital, Khlong Nueng 12120, Pathumthani, Thailand
- Center of Excellence in Digestive Diseases, Thammasat University, Thailand Science Research and Innovation Fundamental Fund, Bualuang ASEAN Chair Professorship at Thammasat University, Khlong Nueng 12121, Pathumthani, Thailand
- Department of Medicine, Chulabhorn International College of Medicine (CICM), Thammasat University, Khlong Nueng 12121, Pathumthani, Thailand
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia
| | - Muhammad Miftahussurur
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, Indonesia
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia
- The Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Oita 870-1192, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
5
|
Kim I, Maeng LS, Kim JS, Kim BW, Cheung DY, Kim JI, Park SH. Quantitative multiplex real-time polymerase chain reaction assay for the detection of Helicobacter pylori and clarithromycin resistance. BMC Microbiol 2023; 23:155. [PMID: 37237357 DOI: 10.1186/s12866-023-02868-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Identifying clarithromycin resistance is essential for eradicating Helicobacter pylori (HP). Therefore, we evaluated the performance of Allplex™ H.pylori & ClariR Assay (Allplex™) for diagnosing and detecting clarithromycin resistance in HP. METHODS Subjects who underwent esophagogastroduodenoscopy between April 2020 and August 2021 at Incheon St. Mary's hospital were enrolled in this study. The diagnostic performances of Allplex™ and dual priming oligonucleotide (DPO)-based multiplex polymerase chain reaction (PCR) were compared with sequencing as the gold standard. RESULTS A total of 142 gastric biopsy samples were analyzed. Gene sequencing revealed 124 HP infections, 42 A2143G mutations, 2 A2142G mutations, one dual mutation, and no A2142C mutation. DPO-PCR showed 96.0% sensitivity and 100.0% specificity for HP detection; the corresponding rates for Allplex™ were 99.2% and 100.0%. DPO-PCR showed 88.3% sensitivity and 82.0% specificity for A2143G mutation, and Allplex™ showed 97.6% and 96.0%. The Cohen's Kappa coefficient for overall test results was 0.56 for DPO-PCR and 0.95 for Allplex™. CONCLUSION Allplex™ showed comparable diagnostic performance with direct gene sequencing and non-inferior diagnostic performance to DPO-PCR. Further research is required to confirm whether Allplex™ is an effective diagnostic tool for the eradication of HP.
Collapse
Affiliation(s)
- Ilsoo Kim
- Divison of Gastroenterology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Lee-So Maeng
- Department of Hospital Pathology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joon Sung Kim
- Divison of Gastroenterology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea.
| | - Byung-Wook Kim
- Divison of Gastroenterology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Dae Young Cheung
- Division of Gastroenterology, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin Il Kim
- Division of Gastroenterology, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soo-Heon Park
- Division of Gastroenterology, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| |
Collapse
|
6
|
Feng M, Namanja-Magliano H, Rajagopalan S, Mishra T, Ducati RG, Hirsch BM, Kelly L, Szymczak W, Fajardo JE, Sidoli S, Fiser A, Jacobs WR, Schramm VL. MAT Gain of Activity Mutation in Helicobacter pylori Is Associated with Resistance to MTAN Transition State Analogues. ACS Infect Dis 2023; 9:966-978. [PMID: 36920074 DOI: 10.1021/acsinfecdis.2c00644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Helicobacter pylori is found in the gut lining of more than half of the world's population, causes gastric ulcers, and contributes to stomach cancers. Menaquinone synthesis in H. pylori relies on the rare futalosine pathway, where H. pylori 5'-methylthioadenosine nucleosidase (MTAN) is proposed to play an essential role. Transition state analogues of MTAN, including BuT-DADMe-ImmA (BTDIA) and MeT-DADMe-ImmA (MTDIA), exhibit bacteriostatic action against numerous diverse clinical isolates of H. pylori with minimum inhibitory concentrations (MIC's) of <2 ng/mL. Three H. pylori BTDIA-resistant clones were selected under increasing BTDIA pressure. Whole genome sequencing showed no mutations in MTAN. Instead, resistant clones had mutations in metK, methionine adenosyltransferase (MAT), feoA, a regulator of the iron transport system, and flhF, a flagellar synthesis regulator. The mutation in metK causes expression of a MAT with increased catalytic activity, leading to elevated cellular S-adenosylmethionine. Metabolite analysis and the mutations associated with resistance suggest multiple inputs associated with BTDIA resistance. Human gut microbiome exposed to MTDIA revealed no growth inhibition under aerobic or anaerobic conditions. Transition state analogues of H. pylori MTAN have potential as agents for treating H. pylori infection without disruption of the human gut microbiome or inducing resistance in the MTAN target.
Collapse
Affiliation(s)
- Mu Feng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Hilda Namanja-Magliano
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Saranathan Rajagopalan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Tanmay Mishra
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Rodrigo G Ducati
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Brett M Hirsch
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Libusha Kelly
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States.,Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Wendy Szymczak
- Department of Pathology, Montefiore-Einstein Medical Center, Bronx, New York 10467, United States
| | - Jorge Eduardo Fajardo
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| |
Collapse
|
7
|
Dascălu RI, Bolocan A, Păduaru DN, Constantinescu A, Mitache MM, Stoica AD, Andronic O. Multidrug resistance in Helicobacter pylori infection. Front Microbiol 2023; 14:1128497. [PMID: 36922977 PMCID: PMC10009102 DOI: 10.3389/fmicb.2023.1128497] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/30/2023] [Indexed: 03/02/2023] Open
Abstract
Helicobacter pylori (Hp), a well-known human pathogen, causes one of the most common chronic bacterial infections and plays an important role in the emergence of chronic progressive gastric inflammation and a variety of gastrointestinal diseases. The prevalence of Hp infection varies worldwide and is indirectly proportional to socio-economic status, especially during childhood. The response to the eradication therapy significantly depends on the antibiotic resistance specific to each geographical region; thus, currently, given the increasing prevalence of antimicrobial resistance (especially to clarithromycin, metronidazole, and levofloxacin), successful treatment for Hp eradication has become a real challenge and a critical issue. The most incriminated factors associated with multidrug resistance (MDR) in Hp proved to be the overuse or the improper use of antibiotics, poor medication adherence, and bacterial-related factors including efflux pumps, mutations, and biofilms. Up to 30% of first-line therapy fails due to poor patient compliance, high gastric acidity, or high bacteremia levels. Hence, it is of great importance to consider new eradication regimens such as vonoprazan-containing triple therapies, quintuple therapies, high-dose dual therapies, and standard triple therapies with probiotics, requiring further studies and thorough assessment. Strain susceptibility testing is also necessary for an optimal approach.
Collapse
Affiliation(s)
| | - Alexandra Bolocan
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,University Emergency Hospital of Bucharest, Bucharest, Romania
| | - Dan Nicolae Păduaru
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,University Emergency Hospital of Bucharest, Bucharest, Romania
| | - Alexandru Constantinescu
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,University Emergency Hospital of Bucharest, Bucharest, Romania
| | | | - Anca Daniela Stoica
- Babeş-Bolyai University, Cluj-Napoca, Romania.,National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Octavian Andronic
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,University Emergency Hospital of Bucharest, Bucharest, Romania.,Research Institute of the University of Bucharest, Bucharest, Romania
| |
Collapse
|
8
|
Ansari S, Yamaoka Y. Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance. Clin Microbiol Rev 2022; 35:e0025821. [PMID: 35404105 PMCID: PMC9491184 DOI: 10.1128/cmr.00258-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite the recent decrease in overall prevalence of Helicobacter pylori infection, morbidity and mortality rates associated with gastric cancer remain high. The antimicrobial resistance developments and treatment failure are fueling the global burden of H. pylori-associated gastric complications. Accurate diagnosis remains the opening move for treatment and eradication of infections caused by microorganisms. Although several reports have been published on diagnostic approaches for H. pylori infection, most lack the data regarding diagnosis from a clinical perspective. Therefore, we provide an intensive, comprehensive, and updated description of the currently available diagnostic methods that can help clinicians, infection diagnosis professionals, and H. pylori researchers working on infection epidemiology to broaden their understanding and to select appropriate diagnostic methods. We also emphasize appropriate diagnostic approaches based on clinical settings (either clinical diagnosis or mass screening), patient factors (either age or other predisposing factors), and clinical factors (either upper gastrointestinal bleeding or partial gastrectomy) and appropriate methods to be considered for evaluating eradication efficacy. Furthermore, to cope with the increasing trend of antimicrobial resistance, a better understanding of its emergence and current diagnostic approaches for resistance detection remain inevitable.
Collapse
Affiliation(s)
- Shamshul Ansari
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas, USA
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| |
Collapse
|
9
|
Helicobacter pylori Antibiotic Resistance in the United States Between 2011 and 2021: A Systematic Review and Meta-Analysis. Am J Gastroenterol 2022; 117:1221-1230. [PMID: 35509128 DOI: 10.14309/ajg.0000000000001828] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/29/2022] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Antimicrobial resistance among Helicobacter pylori strains has been rising globally, leading to declining eradication rates. We performed a systematic review and meta-analysis of the resistance patterns of H. pylori strains in the United States between 2011 and 2021. METHODS Ovid MEDLINE, Embase, CINAHL, and Cochrane CENTRAL databases were searched for manuscripts and conference abstracts published between 2011 and 2021 reporting H. pylori antibiotic resistance. A mixed-effects model estimated pooled rates of resistance to clarithromycin, amoxicillin, metronidazole, tetracycline, rifabutin, levofloxacin, or a combination of these, with 95% confidence intervals (CIs). RESULTS A total of 19 studies including 2,660 samples, met inclusion criteria. The pooled rate of resistance to metronidazole was 42.1% (95% CI 27.3%-58.6%), levofloxacin 37.6% (95% CI 26.3%-50.4%), clarithromycin 31.5% (95% CI 23.6%-40.6%), amoxicillin 2.6% (95% CI 1.4%-5.0%), tetracycline 0.87% (95% CI 0.2%-3.8%), rifabutin 0.17% (95% CI 0.00%-10.9%), and dual clarithromycin and metronidazole 11.7% (95% CI 0.1%-94.0%). Considerable data heterogeneity was evident for pooled resistance prevalence rates (I 2 > 50%), with the exception of rifabutin resistance. DISCUSSION Metronidazole, levofloxacin, and clarithromycin resistance rates each exceed 30%; thus, choosing an empiric antibiotic regimen without knowledge of the likely pattern of antibiotic resistance is not appropriate. Resistance to tetracycline, rifabutin, and amoxicillin remains low. Given the scarcity of available data with considerable heterogeneity among studies, continued surveillance, ideally with a more systematic approach to data collection, is an increasingly important goal in H. pylori management.
Collapse
|
10
|
A Survey of Helicobacter pylori Antibiotic-Resistant Genotypes and Strain Lineages by Whole-Genome Sequencing in China. Antimicrob Agents Chemother 2022; 66:e0218821. [PMID: 35652644 PMCID: PMC9211431 DOI: 10.1128/aac.02188-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistance is the most important factor leading to failed Helicobacter pylori eradication therapy, and personalized treatment based on antibiotic susceptibility is becoming increasingly important. To strengthen the understanding of antibiotic genotypic resistance of H. pylori and identify new antibiotic resistance loci, in this study, we identified phenotypic resistance information for 60 clinical isolates and compared the concordance of phenotypic and genotypic resistance using whole-genome sequencing (WGS). Clarithromycin and levofloxacin genotypic resistance was in almost perfect concordance with phenotypic resistance, with kappa coefficients of 0.867 and 0.833, respectively. All strains with the R16H/C mutation and truncation in rdxA were metronidazole resistant, with 100% specificity. For other genes of concern, at least one phenotypically sensitive strain had a previous mutation related to antibiotic resistance. Moreover, we found that the A1378G mutation of HP0399 and the A149G mutation of FabH might contribute to tetracycline resistance and multidrug resistance, respectively. Overall, the inference of resistance to clarithromycin and levofloxacin from genotypic resistance is reliable, and WGS has been very helpful in discovering novel H. pylori resistance loci. In addition, WGS has also enhanced our study of strain lineages, providing new ways to understand resistance information and mechanisms.
Collapse
|
11
|
Biomarker Characterization and Prediction of Virulence and Antibiotic Resistance from Helicobacter pylori Next Generation Sequencing Data. Biomolecules 2022; 12:biom12050691. [PMID: 35625618 PMCID: PMC9138241 DOI: 10.3390/biom12050691] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 02/06/2023] Open
Abstract
The Gram-negative bacterium Helicobacter pylori colonizes c.a. 50% of human stomachs worldwide and is the major risk factor for gastric adenocarcinoma. Its high genetic variability makes it difficult to identify biomarkers of early stages of infection that can reliably predict its outcome. Moreover, the increasing antibiotic resistance found in H. pylori defies therapy, constituting a major human health problem. Here, we review H. pylori virulence factors and genes involved in antibiotic resistance, as well as the technologies currently used for their detection. Furthermore, we show that next generation sequencing may lead to faster characterization of virulence factors and prediction of the antibiotic resistance profile, thus contributing to personalized treatment and management of H. pylori-associated infections. With this new approach, more and permanent data will be generated at a lower cost, opening the future to new applications for H. pylori biomarker identification and antibiotic resistance prediction.
Collapse
|
12
|
Li H, Shen Y, Song X, Tang X, Hu R, Marshall BJ, Tang H, Benghezal M. Need for standardization and harmonization of Helicobacter pylori antimicrobial susceptibility testing. Helicobacter 2022; 27:e12873. [PMID: 35151236 DOI: 10.1111/hel.12873] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND AIMS As with other infectious diseases, Helicobacter pylori eradication regimens should be guided by susceptibility testing to achieve excellent success rate, especially in the era of high antibiotic resistance. However, susceptibility testing for H. pylori is rarely performed, which can be partly ascribed to the current lack of standardization of testing methods and the lack of unified consensus on the antibiotic resistance breakpoints. The aim of this review was to call for an international consensus on standardization and harmonization of H. pylori susceptibility testing. METHODS We summarize and compare the advantages and disadvantages of four different phenotypic antimicrobial susceptibility testing (AST) methods (agar dilution, E-test, disk diffusion, and broth microdilution) and the molecular susceptibility testing method for H. pylori. RESULTS The standard phenotypic testing methods and the molecular testing methods have their own advantages and disadvantages. Compared to the standard phenotypic methods, the molecular testing method does not require successful H. pylori culture, and therefore, is much more rapid and convenient for clinical use. However, the currently available molecular testing method is only suitable for detecting clarithromycin and quinolone susceptibility profiles in H. pylori. Although the standard AST is time-consuming, it is currently the only way to test the susceptibility of H. pylori to all the commonly used antibiotics. CONCLUSION To make H. pylori susceptibility testing become a clinical routine, an international consensus on standardization and harmonization of H. pylori AST is needed. Future efforts are needed for optimizing broth culture of H. pylori, and developing commercial AST plates for achieving high throughput and automated susceptibility testing for H. pylori.
Collapse
Affiliation(s)
- Hong Li
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Yalin Shen
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaona Song
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoqiong Tang
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Renwei Hu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Barry James Marshall
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, Australia
| | - Hong Tang
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Mohammed Benghezal
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
13
|
Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
14
|
Mannion A, Dzink-Fox J, Shen Z, Piazuelo MB, Wilson KT, Correa P, Peek RM, Camargo MC, Fox JG. Helicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk Populations. J Clin Microbiol 2021; 59:e03203-20. [PMID: 33692136 PMCID: PMC8091839 DOI: 10.1128/jcm.03203-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/28/2021] [Indexed: 02/07/2023] Open
Abstract
Colombia, South America has one of the world's highest burdens of Helicobacter pylori infection and gastric cancer. While multidrug antibiotic regimens can effectively eradicate H. pylori, treatment efficacy is being jeopardized by the emergence of antibiotic-resistant H. pylori strains. Moreover, the spectrum of and genetic mechanisms for antibiotic resistance in Colombia is underreported. In this study, 28 H. pylori strains isolated from gastric biopsy specimens from a high-gastric-cancer-risk (HGCR) population living in the Andes Mountains in Túquerres, Colombia and 31 strains from a low-gastric-cancer-risk (LGCR) population residing on the Pacific coast in Tumaco, Colombia were subjected to antibiotic susceptibility testing for amoxicillin, clarithromycin, levofloxacin, metronidazole, rifampin, and tetracycline. Resistance-associated genes were amplified by PCR for all isolates, and 29 isolates were whole-genome sequenced (WGS). No strains were resistant to amoxicillin, clarithromycin, or rifampin. One strain was resistant to tetracycline and had an A926G mutation in its 16S rRNA gene. Levofloxacin resistance was observed in 12/59 isolates and was significantly associated with N87I/K and/or D91G/Y mutations in gyrA Most isolates were resistant to metronidazole; this resistance was significantly higher in the LGCR (31/31) group compared to the HGCR (24/28) group. Truncations in rdxA and frxA were present in nearly all metronidazole-resistant strains. There was no association between phylogenetic relationship and resistance profiles based on WGS analysis. Our results indicate H. pylori isolates from Colombians exhibit multidrug antibiotic resistance. Continued surveillance of H. pylori antibiotic resistance in Colombia is warranted in order to establish appropriate eradication treatment regimens for this population.
Collapse
Affiliation(s)
- Anthony Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - JoAnn Dzink-Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | | | | | | | - M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
15
|
Saracino IM, Pavoni M, Zullo A, Fiorini G, Lazzarotto T, Borghi C, Vaira D. Next Generation Sequencing for the Prediction of the Antibiotic Resistance in Helicobacter pylori: A Literature Review. Antibiotics (Basel) 2021; 10:437. [PMID: 33919811 PMCID: PMC8070836 DOI: 10.3390/antibiotics10040437] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Background and aims: Only a few antimicrobials are effective against H. pylori, and antibiotic resistance is an increasing problem for eradication therapies. In 2017, the World Health Organization categorized clarithromycin resistant H. pylori as a "high-priority" bacterium. Standard antimicrobial susceptibility testing can be used to prescribe appropriate therapies but is currently recommended only after the second therapeutic failure. H. pylori is, in fact, a "fastidious" microorganism; culture methods are time-consuming and technically challenging. The advent of molecular biology techniques has enabled the identification of molecular mechanisms underlying the observed phenotypic resistance to antibiotics in H. pylori. The aim of this literature review is to summarize the results of original articles published in the last ten years, regarding the use of Next Generation Sequencing, in particular of the whole genome, to predict the antibiotic resistance in H. pylori.Methods: a literature research was made on PubMed. The research was focused on II and III generation sequencing of the whole H. pylori genome. Results: Next Generation Sequencing enabled the detection of novel, rare and complex resistance mechanisms. The prediction of resistance to clarithromycin, levofloxacin and amoxicillin is accurate; for other antimicrobials, such as metronidazole, rifabutin and tetracycline, potential genetic determinants of the resistant status need further investigation.
Collapse
Affiliation(s)
- Ilaria Maria Saracino
- Microbiology Unit, Department of Specialized, Experimental, and Diagnostic Medicine, IRCCS St. Orsola Polyclinic, University of Bologna, 40138 Bologna, Italy; (I.M.S.); (T.L.)
| | - Matteo Pavoni
- Department of Medical and Surgical Sciences, IRCCS St. Orsola Polyclinic, University of Bologna, 40138 Bologna, Italy; (M.P.); (G.F.); (C.B.)
| | - Angelo Zullo
- Gastroenterology and Digestive Endoscopy, ‘Nuovo Regina Margherita’ Hospital, 00153 Rome, Italy;
| | - Giulia Fiorini
- Department of Medical and Surgical Sciences, IRCCS St. Orsola Polyclinic, University of Bologna, 40138 Bologna, Italy; (M.P.); (G.F.); (C.B.)
| | - Tiziana Lazzarotto
- Microbiology Unit, Department of Specialized, Experimental, and Diagnostic Medicine, IRCCS St. Orsola Polyclinic, University of Bologna, 40138 Bologna, Italy; (I.M.S.); (T.L.)
| | - Claudio Borghi
- Department of Medical and Surgical Sciences, IRCCS St. Orsola Polyclinic, University of Bologna, 40138 Bologna, Italy; (M.P.); (G.F.); (C.B.)
| | - Dino Vaira
- Department of Medical and Surgical Sciences, IRCCS St. Orsola Polyclinic, University of Bologna, 40138 Bologna, Italy; (M.P.); (G.F.); (C.B.)
| |
Collapse
|
16
|
Helicobacter pylori type 4 secretion systems as gastroduodenal disease markers. Sci Rep 2021; 11:4584. [PMID: 33633144 PMCID: PMC7907105 DOI: 10.1038/s41598-021-83862-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/01/2021] [Indexed: 12/20/2022] Open
Abstract
Although the type 4 secretion system of the integrating and conjugative elements (tfs ICE) is common in Helicobacter pylori, its clinical association with the cag pathogenicity island (cagPAI) have not yet been well-investigated. In this study, Vietnamese patient H. pylori samples (46 duodenal ulcer (DU), 51 non-cardia gastric cancer (NCGC), 39 chronic gastritis (CG)) were fully sequenced using next-generation sequencing and assembled into contigs. tfs3, tfs4, and cagPAI genes were compared with the public database. Most (94%) H. pylori strains possessed a complete cagPAI, which was the greatest risk factor for clinical outcomes, while the prevalences of tfs3 and tfs4 were 45% and 77%, respectively. Complete tfs3 and tfs4 were found in 18.3% and 17.6% of strains, respectively. The prevalence of H. pylori strains with complete tfs3 ICE in DU patients was significantly higher than that in NCGC patients (30.4% vs 11.7%, P < 0.05). In addition, the prevalence of strains with complete tfs3 ICE and cagPAI was significantly higher in DU patients than that in NCGC (28.4% vs 9.8%, P = 0.038) and CG patients (28.2% vs 7.7%, P = 0.024). cagPAI and complete tfs3 increased the risk of DU compared to NCGC (OR = 3.56, 95%CI: 1.1–14.1, P = 0.038) and CG (OR = 4.64, 95%CI: 1.1–27.6, P = 0.024). A complete cluster of tfs3 ICE was associated with gastroduodenal diseases in Vietnam. However, there was a low prevalence of the dupA/complete dupA cluster (15.4%) in the Vietnam strains. The prevalence of cagPAI in Vietnam strains was significantly higher than in US (P = 0.01) and Indonesia (P < 0.0001); the prevalence of the dupA cluster was also higher in the Vietnam strains than in the Indonesian strains (P < 0.05). In addition, the prevalence of ctkA, an accessory gene of tfs3, was significantly different between Vietnam and US strains (28% vs 2%, P = 0.0002). In summary, the acquisition of tfs3/4 ICE was common in H. pylori strains in patients with gastroduodenal disease in Vietnam, and the complete cluster of tfs3 ICE was a reliable marker for the severity of disease in the H. pylori infected population.
Collapse
|
17
|
Camorlinga-Ponce M, Gómez-Delgado A, Aguilar-Zamora E, Torres RC, Giono-Cerezo S, Escobar-Ogaz A, Torres J. Phenotypic and Genotypic Antibiotic Resistance Patterns in Helicobacter pylori Strains From Ethnically Diverse Population in México. Front Cell Infect Microbiol 2021; 10:539115. [PMID: 33643927 PMCID: PMC7905308 DOI: 10.3389/fcimb.2020.539115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori strains carry a range of mutations in genes that confer antimicrobial resistance and restrict the available options to treat the infection. Latin America is a region that conserve a large number of indigenous communities relatively isolated that practice a traditional medicine without consumption of drugs. We hypothesized that rates of antibiotic resistance are lower in these communities. Recent progress in whole-genome sequencing has allowed the study of drug susceptibility by searching for the known mutations associated with antibiotic resistance. The aim of this work was to study trends of antibiotic resistance over a 20-year period in Mexican H. pylori strains and to compare susceptibility between strains from Mexican mestizos and from indigenous population; we also aimed to learn the prevalence of mutational patterns in genes gyrA, gyrB, rdxA, frxA, rpsU, omp11, dppA, and 23S rRNA and its association with phenotypic tests. Resistance to clarithromycin, metronidazole, amoxicillin and levofloxacin was determined in167 H. pylori isolates by E-test, and the occurrence of mutational patterns in specific genes was determined by whole genome sequencing (WGS). The trend of resistance over 20 years in mestizo isolates showed significant resistant increase for clarithromycin and levofloxacin to frequencies that banned its clinical use. Resistance in H. pylori isolates of native communities was lower for all antibiotics tested. Phenotypic resistance showed good to moderate correlation with genotypic tests. Genetic methods for characterizing antibiotic resistance require further validation in each population.
Collapse
Affiliation(s)
- Margarita Camorlinga-Ponce
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Alejandro Gómez-Delgado
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Emmanuel Aguilar-Zamora
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico.,Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Roberto C Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Silvia Giono-Cerezo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Antonio Escobar-Ogaz
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| |
Collapse
|
18
|
Abstract
New imaging techniques are still the topic of many evaluations for both the diagnosis of Helicobacter pylori gastritis and the detection of early gastric cancer. Concerning invasive tests, there were studies on the reuse of the rapid urease test material for other tests, and a novel fluorescent method to be used for histology but with limited sensitivity. Progress occurred essentially in the molecular methods area, especially next-generation sequencing which is applied to detect both H pylori and the mutations associated with antibiotic resistance. For non-invasive tests, a few studies have been published on the validity of breath collection bags, the shortening of the testing time, the performance of different analysers or the added value of citric acid in the protocol. The accuracy of serological immunochromatographic tests is also improving. Multiplex serology detecting antibodies to certain proteins allows confirmation of a current infection. Dried blood spots can be used to collect and store blood without a loss of accuracy. Finally, the serum antibody titer can be useful in predicting the risk of gastric cancer. Several stool antigen tests were evaluated with good results, and a novel test using immunomagnetic beads coated with monoclonal antibodies is potentially interesting. PCR detection in stools can also be effective but needs an efficient DNA extraction method. The use of easyMAG® (bioMérieux) combined with Amplidiag® H pylori + ClariR (Mobidiag) appears to be powerful.
Collapse
Affiliation(s)
- Gauri Godbole
- Gastrointestinal Pathogens Unit, National Infection Service, Public Health England, London, UK
| | - Francis Mégraud
- Inserm U1053 Bariton, University of Bordeaux, Bordeaux, France.,National Reference Centre for Campylobacters and Helicobacters, Bacteriology Laboratory, Pellegrin Hospital, Bordeaux, France
| | - Emilie Bessède
- Inserm U1053 Bariton, University of Bordeaux, Bordeaux, France.,National Reference Centre for Campylobacters and Helicobacters, Bacteriology Laboratory, Pellegrin Hospital, Bordeaux, France
| |
Collapse
|
19
|
Genotypic and Phenotypic Resistance to Clarithromycin in Helicobacter pylori Strains. J Clin Med 2020; 9:jcm9061930. [PMID: 32575584 PMCID: PMC7356929 DOI: 10.3390/jcm9061930] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
Background: The increasing prevalence of antimicrobial resistance, together with the lack of novel treatment options, negatively affects successful eradication of Helicobacter pylori. The aim of this study was to investigate genetic mutations in the 23S rRNA genes, which is associated with clarithromycin resistance, and to determine the clinical impact of genotype on phenotypic antimicrobial resistance. Methods: A total of 46 H. pylori strains were obtained from 13 patients, before and after unsuccessful eradication with clarithromycin-based triple therapy. The phenotypic resistance of each H. pylori strain was determined by minimum inhibitory concentration against clarithromycin using the serial two-fold agar dilution method. The genomic sequences of 23S rRNA genes were identified through next-generation sequencing, and nucleotide variants were determined based on comparison with genome sequences of the reference strain H. pylori 26695. Results: Clarithromycin resistance was found in 9 of 13 subjects before treatment and all subjects after unsuccessful eradication. Whole-genome sequencing of the 23S rRNA genes detected 42 mutations on 40 nonidentical loci, including 2147A>G (formerly 2143A>G) and 2146A>G (formerly 2142A>G). All strains with clarithromycin-resistant phenotype had either 2147A>G or 2146A>G mutation. When comparing genotype and phenotype for clarithromycin resistance, there was a significant association between 2147A>G mutation and clarithromycin-resistant phenotype. Conclusions: All clarithromycin-resistant strains had either 2146A>G or 2147A>G mutation, suggesting that tests targeting these two mutations may be enough for the prediction of clarithromycin resistance in this population.
Collapse
|