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Abdoh Q, Alnees M, Kharraz L, Ayoub K, Darwish A, Awwad M, Najajra D, Khraim J, Awad W, Sbaih A, Turman S, Abu Hamdeh N. Prevalence of Helicobacter pylori resistance to certain antibiotics at An-Najah University Hospital: a cross-sectional study. Sci Rep 2024; 14:14542. [PMID: 38914675 PMCID: PMC11196700 DOI: 10.1038/s41598-024-63982-0] [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: 12/08/2023] [Accepted: 06/04/2024] [Indexed: 06/26/2024] Open
Abstract
Antibiotic resistance among bacteria is recognized as the primary factor contributing to the failure of treatment. In this research, our objective was to examine the prevalence of antibiotic resistance in H. pylori bacteria in Palestine. We enlisted 91 individuals suffering from dyspepsia, comprising 49 females and 42 males. These participants underwent esophagogastroduodenoscopy procedures with gastric biopsies. These biopsies were subsequently subjected to microbiological assessments and tested for their susceptibility to various antimicrobial drugs. Among the 91 patients, 38 (41.7%) exhibited the presence of H. pylori. Notably, Ciprofloxacin displayed the highest efficacy against H. pylori, followed by Levofloxacin, Moxifloxacin, and Amoxicillin, with resistance rates of 0%, 0%, 2.6%, and 18.4%, respectively. On the contrary, Metronidazole and Clarithromycin demonstrated the lowest effectiveness, with resistance percentages of 100% and 47.4%, respectively. The outcomes of this investigation emphasize that H. pylori strains within the Palestinian patient group exhibit substantial resistance to conventional first-line antibiotics like clarithromycin and metronidazole. However, alternative agents such as fluoroquinolones and amoxicillin remain efficacious choices. Consequently, we recommend favoring quinolone-based treatment regimens for H. pylori infections and adopting a more judicious approach to antibiotic usage among the Palestinian population.
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Affiliation(s)
- Qusay Abdoh
- Faculty of Medicine, An-Najah National University, Nablus, Palestine.
- Division of Gastroenterology, An-Najah National University Hospital, Nablus, Palestine.
| | - Mohammad Alnees
- Faculty of Medicine, An-Najah National University, Nablus, Palestine.
- Global Clinical Scholars Research Training Program, Harvard Medical School Postgraduate Medical Education, Boston, USA.
- Department of Medicine, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine.
| | - Lubna Kharraz
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
| | - Khubaib Ayoub
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
- Department of Internal Medicine, Specialized Araby Hospital, Nablus, Palestine
| | - Abdalaziz Darwish
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
| | - Mahdi Awwad
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
| | - Duha Najajra
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
| | - Jana Khraim
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
| | - Wafaa Awad
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
| | - Aesha Sbaih
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
| | - Safaa Turman
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
| | - Nizar Abu Hamdeh
- Faculty of Medicine, An-Najah National University, Nablus, Palestine
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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.
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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
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Hasanuzzaman M, Bang CS, Gong EJ. Antibiotic Resistance of Helicobacter pylori: Mechanisms and Clinical Implications. J Korean Med Sci 2024; 39:e44. [PMID: 38288543 PMCID: PMC10825452 DOI: 10.3346/jkms.2024.39.e44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024] Open
Abstract
Helicobacter pylori is a pathogenic bacterium associated with various gastrointestinal diseases, including chronic gastritis, peptic ulcers, mucosa-associated lymphoid tissue lymphoma, and gastric cancer. The increasing rates of H. pylori antibiotic resistance and the emergence of multidrug-resistant strains pose significant challenges to its treatment. This comprehensive review explores the mechanisms underlying the resistance of H. pylori to commonly used antibiotics and the clinical implications of antibiotic resistance. Additionally, potential strategies for overcoming antibiotic resistance are discussed. These approaches aim to improve the treatment outcomes of H. pylori infections while minimizing the development of antibiotic resistance. The continuous evolution of treatment perspectives and ongoing research in this field are crucial for effectively combating this challenging infection.
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Affiliation(s)
- Md Hasanuzzaman
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Chang Seok Bang
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Eun Jeong Gong
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, Korea.
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Khangai A, Saruuljavkhlan B, Azzaya D, Gantuya B, Oyuntsetseg K, Akada J, Matsumoto T, Yamaoka Y. Exploring Alternative Treatment Choices for Multidrug-Resistant Clinical Strains of Helicobacter pylori in Mongolia. Microorganisms 2023; 11:2852. [PMID: 38137996 PMCID: PMC10745380 DOI: 10.3390/microorganisms11122852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/24/2023] Open
Abstract
Helicobacter pylori is a pathogen related to severe diseases such as gastric cancer; because of rising antimicrobial-resistant strains, failure to eradicate H. pylori with antibiotics has increased worldwide. Multidrug-resistant H. pylori and gastric cancer is common in Mongolia; therefore, we aimed to explore alternative antimicrobial treatments and the genomes of resistant strains in this country. A total of 361 H. pylori strains isolated from patients in Mongolia were considered. Minimal inhibitory concentrations for two fluoroquinolones (ciprofloxacin and moxifloxacin), rifabutin, and furazolidone were determined via two-fold agar dilution. Genomic mutations in antibiotic-resistant strains were identified by next-generation sequencing using the Illumina Miseq platform and compared with genes from a reference H. pylori strain (26695). The resistance rate of H. pylori strains to quinolones was high (44% to ciprofloxacin and 42% to moxifloxacin), and resistance to rifabutin was low (0.5%); none were resistant to furazolidone. Most quinolone-resistant strains possessed gyrA gene mutations causing amino acid changes (e.g., N87K, A88P, and D91G/Y/N). While one rifabutin-resistant strain had amino acid-substituting mutations in rpoB (D530N and R701C), the other had three novel rpoB mutations; both rifabutin-resistant strains were sensitive to furazolidone. Overall, our findings suggest that rifabutin and/or furazolidone may be an alternative, effective H. pylori treatment in patients who have failed to respond to other treatment regimens.
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Affiliation(s)
- Ayush Khangai
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Japan; (A.K.); (B.S.); (J.A.); (T.M.)
- The Gastroenterology Center, The First Central Hospital of Mongolia, Ulaanbaatar 14210, Mongolia
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Japan; (A.K.); (B.S.); (J.A.); (T.M.)
- Endoscopy Unit, Department of Gastroenterology, Mongolia Japan Hospital of Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (B.G.); (K.O.)
| | - Dashdorj Azzaya
- Department of Gastroenterology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia;
| | - Boldbaatar Gantuya
- Endoscopy Unit, Department of Gastroenterology, Mongolia Japan Hospital of Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (B.G.); (K.O.)
| | - Khasag Oyuntsetseg
- Endoscopy Unit, Department of Gastroenterology, Mongolia Japan Hospital of Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (B.G.); (K.O.)
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Japan; (A.K.); (B.S.); (J.A.); (T.M.)
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Japan; (A.K.); (B.S.); (J.A.); (T.M.)
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Japan; (A.K.); (B.S.); (J.A.); (T.M.)
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60115, Indonesia
- Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University, Yufu 879-5593, Japan
- Department of Medicine-Gastroenterology, Baylor College of Medicine, Houston, TX 77030, USA
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Ng HY, Leung WK, Cheung KS. Antibiotic Resistance, Susceptibility Testing and Stewardship in Helicobacter pylori Infection. Int J Mol Sci 2023; 24:11708. [PMID: 37511471 PMCID: PMC10380565 DOI: 10.3390/ijms241411708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Despite the declining trend of Helicobacter pylori (H. pylori) prevalence around the globe, ongoing efforts are still needed to optimize current and future regimens in view of the increasing antibiotic resistance. The resistance of H. pylori to different antibiotics is caused by different molecular mechanisms, and advancements in sequencing technology have come a far way in broadening our understanding and in facilitating the testing of antibiotic susceptibility to H. pylori. In this literature review, we give an overview of the molecular mechanisms behind resistance, as well as discuss and compare different antibiotic susceptibility tests based on the latest research. We also discuss the principles of antibiotic stewardship and compare the performance of empirical therapies based on up-to-date resistance patterns and susceptibility-guided therapies in providing effective H. pylori treatment. Studies and clinical guidelines should ensure that the treatment being tested or recommended can reliably achieve a pre-agreed acceptable level of eradication rate and take into account the variations in antibiotic resistance across populations. Local, regional and international organizations must work together to establish routine antibiotic susceptibility surveillance programs and enforce antibiotic stewardship in the treatment of H. pylori, so that it can be managed in a sustainable and efficient manner.
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Affiliation(s)
- Ho-Yu Ng
- School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Wai K Leung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Ka-Shing Cheung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
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Fernández-Caso B, Miqueleiz A, Alarcón T. Whole Genome Sequencing for Studying Helicobacter pylori Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:1135. [PMID: 37508231 PMCID: PMC10376898 DOI: 10.3390/antibiotics12071135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Antibiotic resistance (AMR) is an alarming concern worldwide and Helicobacter pylori, one of the most prevalent bacteria, is not an exception. With antibiotics being its primary therapy, increasing resistance leads to a higher rate of treatment failure. Understanding the genomic mechanisms of resistance to clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline, and rifampicin through next-generation sequencing-based molecular tools, such as whole genome sequencing (WGS), can be of great value, not only to direct a patient's treatment, but also to establish and optimize treatment guidelines according to the local epidemiology and to avoid the use of inappropriate antibiotics. WGS approaches allow us to gain insight into the genomic determinants involved in AMR. To this end, different pipelines and platforms are continuously being developed. In this study, we take a more detailed view of the use and progression of WGS for in-depth study of H. pylori's AMR.
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Affiliation(s)
| | - Ana Miqueleiz
- Department of Microbiology, Hospital Universitario de Navarra, 31008 Pamplona, Spain
| | - Teresa Alarcón
- Department of Microbiology, Hospital Universitario La Princesa, 28006 Madrid, Spain
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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.
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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
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Fauzia KA, Aftab H, Miftahussurur M, Waskito LA, Tuan VP, Alfaray RI, Matsumoto T, Yurugi M, Subsomwong P, Kabamba ET, Akada J, Yamaoka Y. Genetic determinants of Biofilm formation of Helicobacter pylori using whole-genome sequencing. BMC Microbiol 2023; 23:159. [PMID: 37264297 PMCID: PMC10234030 DOI: 10.1186/s12866-023-02889-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Infection with Helicobacter pylori as the cause of gastric cancer is a global public health concern. In addition to protecting germs from antibiotics, biofilms reduce the efficacy of H. pylori eradication therapy. The nucleotide polymorphisms (SNPs) related with the biofilm forming phenotype of Helicobacter pylori were studied. RESULTS Fifty-six H. pylori isolate from Bangladeshi patients were included in this cross-sectional study. Crystal violet assay was used to quantify biofilm amount, and the strains were classified into high- and low-biofilm formers As a result, strains were classified as 19.6% high- and 81.4% low-biofilm formers. These phenotypes were not related to specific clades in the phylogenetic analysis. The accessories genes associated with biofilm from whole-genome sequences were extracted and analysed, and SNPs among the previously reported biofilm-related genes were analysed. Biofilm formation was significantly associated with SNPs of alpA, alpB, cagE, cgt, csd4, csd5, futB, gluP, homD, and murF (P < 0.05). Among the SNPs reported in alpB, strains encoding the N156K, G160S, and A223V mutations were high-biofilm formers. CONCLUSIONS This study revealed the potential role of SNPs in biofilm formation and proposed a method to detect mutation in biofilm from whole-genome sequences.
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Affiliation(s)
- Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Hafeza Aftab
- Department of Gastroenterology, Dhaka Medical College and Hospital, Dhaka, 1000, Bangladesh
| | - Muhammad Miftahussurur
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Langgeng Agung Waskito
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
- Department of Physiology and Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, 749000, Vietnam
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
| | - Michiyuki Yurugi
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
| | - Phawinee Subsomwong
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, 036-8562, Aomori, Japan
| | - Evariste Tshibangu Kabamba
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
- Research Center for Infectious Sciences, Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan.
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, 60115, Indonesia.
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, 77030, USA.
- Borneo Medical and Health Research Centre, University Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia.
- The Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu, 879-5593, Oita, Japan.
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Park SY, Lee EH, Kim D, Song YG, Jeong SJ. Novel Mutations Conferring Amoxicillin Resistance in Helicobacter pylori in South Korea. Antibiotics (Basel) 2023; 12:antibiotics12040748. [PMID: 37107110 PMCID: PMC10135067 DOI: 10.3390/antibiotics12040748] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Helicobacter pylori is the primary causative agent of gastritis, gastric ulcers, duodenal ulcers, gastric cancer, and peripheral B-cell lymphoma. H. pylori eradication often fails due to elevated antibiotic resistance. However, no previous studies have thoroughly examined amoxicillin resistance. Here, the objective was to identify clinical strains of H. pylori with amoxicillin resistance and to analyze single-nucleotide polymorphisms (SNPs) associated with amoxicillin resistance. From March 2015 to June 2019, genotypic and phenotypic amoxicillin resistance was analyzed using an E-test and whole-genome sequencing (WGS). Analysis of 368 clinical strains confirmed amoxicillin resistance in 31 strains (resistance rate of 8.7%). The genomes were extracted from nine resistant (<0.125 mg/L) strains, and WGS was performed for genetic analysis. WGS analysis identified SNPs present in pbp1a, pbp2, nhaC, hofH, hofC, and hefC in all nine isolates. Some of these genes may be related to amoxicillin resistance. A total of six SNPs (A69V, V374L, S414R, T503I, A592D, and R435Q) were identified in PBP2 of H-8, the most resistant strain. We predict that these six SNPs are associated with high amoxicillin resistance. Amoxicillin resistance should be considered in the clinical setting for the treatment failure of H. pylori eradication.
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Affiliation(s)
- Soon Young Park
- Division of Infectious Diseases, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Republic of Korea
| | - Eun Hwa Lee
- Division of Infectious Diseases, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Republic of Korea
| | - Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Young Goo Song
- Division of Infectious Diseases, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Republic of Korea
| | - Su Jin Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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10
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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.
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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
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11
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Sholeh M, Khoshnood S, Azimi T, Mohamadi J, Kaviar VH, Hashemian M, Karamollahi S, Sadeghifard N, Heidarizadeh H, Heidary M, Saki M. The prevalence of clarithromycin-resistant Helicobacter pylori isolates: a systematic review and meta-analysis. PeerJ 2023; 11:e15121. [PMID: 37016679 PMCID: PMC10066884 DOI: 10.7717/peerj.15121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/03/2023] [Indexed: 04/06/2023] Open
Abstract
Background Knowledge of global clarithromycin (CLA)-resistant rates of Helicobacter pylori (H. pylori) is crucial for decision of the most appropriate eradication therapies with good clinical outcomes. Therefore, this review and meta-analysis aimed to evaluate the global prevalence of the CLA resistance in H. pylori to provide some guidance for selecting the first-line antibiotics. Method A comprehensive search was performed for relevant literature until April 2021 in PubMed, Embase, and Web of Science databases. Freeman-Tukey double arcsine transformation was performed to estimate the weighted pooled prevalence of resistance. Results The meta-analysis included 248 articles. The prevalence of CLA-resistant H. pylori was 27.53% (95% CI [25.41-29.69]). The heterogeneity between reports was significant (I2 = 97.80%, P < 0.01). The resistance rate increased from 24.28% in 2010-2017 to 32.14% in 2018-2021 (P < 0.01). Iran, with 38 articles, has the most report. Nevertheless, Switzerland, Portugal, and Israel had the highest resistance rates (67.16%, 48.11%, and 46.12%, respectively). The heterogeneity between the continents and the antimicrobial susceptibility methods also interpreted standard guidelines and breakpoints was insignificant (P > 0.05). Conclusion Overall CLA resistance rate was 27.53%, worldwide. The difference in CLA resistance rate among the included studies can be due to several reasons such as differences in antibiotic prescription rates in various geographic areas, use of different breakpoints or inaccurate criteria in performed studies, and the emergence of multidrug-resistant (MDR) strains.
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Affiliation(s)
- Mohammad Sholeh
- Department of Microbiology, Pasteur Institute of Iran, Tehran, Iran
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
- Student Research Committee, Ilam University of Medical Sciences, Ilam, Iran
| | - Taher Azimi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jasem Mohamadi
- Department of Pediatrics, School of Medicine, Emam Khomeini Hospital, Ilam University of Medical Sciences, Ilam, Iran
| | - Vahab Hassan Kaviar
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Marzieh Hashemian
- Department of Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Somayeh Karamollahi
- Department of Microbiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Hedayat Heidarizadeh
- Department of Pediatrics, School of Medicine, Emam Khomeini Hospital, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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12
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Globally Disseminated Multidrug Resistance Plasmids Revealed by Complete Assembly of Multidrug Resistant Escherichia coli and Klebsiella pneumoniae Genomes from Diarrheal Disease in Botswana. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Antimicrobial resistance is a disseminated global health challenge because many of the genes that cause resistance can transfer horizontally between bacteria. Despite the central role of extrachromosomal DNA elements called plasmids in driving the spread of resistance, the detection and surveillance of plasmids remains a significant barrier in molecular epidemiology. We assessed two DNA sequencing platforms alone and in combination for laboratory diagnostics in Botswana by annotating antibiotic resistance genes and plasmids in extensively drug resistant bacteria from diarrhea in Botswana. Long-read Nanopore DNA sequencing and high accuracy basecalling effectively estimated the architecture and gene content of three plasmids in Escherichia coli HUM3355 and two plasmids in Klebsiella pneumoniae HUM7199. Polishing the assemblies with Illumina reads increased base calling precision with small improvements to gene prediction. All five plasmids encoded one or more antibiotic resistance genes, usually within gene islands containing multiple antibiotic and metal resistance genes, and four plasmids encoded genes associated with conjugative transfer. Two plasmids were almost identical to antibiotic resistance plasmids sequenced in Europe and North America from human infection and a pig farm. These One Health connections demonstrate how low-, middle-, and high-income countries collectively benefit from increased whole genome sequencing capacity for surveillance and tracking of infectious diseases and antibiotic resistance genes that can transfer between animal hosts and move across continents.
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13
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Maghami AA, Mobarez AM, Yadegar A, Nikkhah M, Sadeghi A, Esmaeili S. Assessment of Helicobacter pylori positive infected patients according to Clarithromycin resistant 23S rRNA, rpl22 associated mutations and cyp2c19*1, *2, *3 genes pattern in the Early stage of Gastritis. BMC Res Notes 2022; 15:335. [PMID: 36284359 PMCID: PMC9594930 DOI: 10.1186/s13104-022-06227-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Clarithromycin resistant Helicobacter pylori (CAM-R) is the main cause of standard triple therapy eradicating failure. Proton pump inhibitors (PPIs) directly pose bacteriocidic activity and prepare the optimum condition for Clarithromycin’s best function. In counter with Poor metabolizer subjects, Homozygote Extensive Metabolizers have well characterized by treatment failure. Eventually, determination of CAM-R profile and estimation of PPIs metabolization rate support clinicians in better prescription. So, we explored Helicobacter pylori’mutations in 23S rRNA and rpl22 resistant genes, and cyp2c19 *1, *2, *3 allele variations, and PPIs metabolization patterns in patients, consequently the results reported to the physician. Results Sixteen out of 96 patients considered to be CAM-R Helicobacter pylori. A2143C (1/16), rpl22 insertion (16/16), and GTG deletion (2/16) recorded in CAM-R strains. P450 2C19 human genotyping demonstrated that the highest proportion of the H. pylori- positive strains infected patients 43/61(70.49%) categorized in Homozygote extensive metabolizer class. The rest (12/61)19.67% classified as Poor metabolizers, and 6/61(9.83%) distinct from Heterozygote extensive metabolizer group. Proportion of poor metabolizers and Heterozygote extensive metabolizer phenotypes between CAM-R strains mentioned to be 10/16(62.5%), and 6/16(37.5%). Cross points between the most frequently distributed allele in CAM-R strains indicated 81.25% for *2, and w2 for 18.75%. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06227-5.
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Affiliation(s)
- Atena Abedi Maghami
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Al-E Ahmad Exp., Tehran, Iran
| | - Ashraf Mohabati Mobarez
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Al-E Ahmad Exp., Tehran, Iran.
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Nikkhah
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical, Sciences, Tehran, Iran
| | - Saber Esmaeili
- National Reference Laboratory of Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
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14
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Petrosillo N, Granata G. Gram Negatives and Antimicrobial Resistance: Two Faces of the Same Coin. J Clin Med 2022; 11:jcm11195574. [PMID: 36233444 PMCID: PMC9573191 DOI: 10.3390/jcm11195574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Nicola Petrosillo
- Infection Prevention & Control/Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00127 Rome, Italy
- Correspondence:
| | - Guido Granata
- Systemic and Immune Depression-Associated Infection Unit, National Institute for Infectious Diseases “L. Spallanzani”, IRCCS, 00149 Rome, Italy
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15
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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.
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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
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16
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Karbalaei M, Keikha M, Talebi Bezmin Abadi A. Prevalence of Primary Multidrug-resistant Helicobacter pylori in Children: A Systematic Review and Meta-analysis. Arch Med Res 2022; 53:634-640. [PMID: 36089418 DOI: 10.1016/j.arcmed.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/16/2022] [Accepted: 08/25/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND The emergence and global spread of multidrug-resistant Helicobacter pylori (MDR H. pylori) is a major health problem in children, which can increase the risk of serious complications such as gastric cancer. The aim of this study was to determine the prevalence of primary MDR H. pylori in children via a comprehensive systematic literature review and meta-analysis. METHODS All potential studies were collected from international databases like: ISI Web of Science, Embase, PubMed, Google Scholar, and Scopus from 2011-July 24, 2022. Ultimately, primary MDR H. pylori in children was measured as an event rate with corresponding 95% confidence intervals. RESULTS A total of 19 studies met the inclusion criteria. The overall prevalence of primary MDR H. pylori in children was measured at 6.0% (95% CI: 3.1-11.6); There was a significant difference in primary MDR H. pylori resistance rates between Asian populations and Western countries. CONCLUSIONS The global spread of MDR H. pylori strains could significantly limit the options of anti-H. pylori treatment regimens. The frequency of primary MDR H. pylori infection differs between various geographical regions. Thus, drug susceptibility testing and the eradication of H. pylori infection can effectively reduce and control the spread of H. pylori antibiotic resistance throughout the world.
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Affiliation(s)
- Mohsen Karbalaei
- Department of Microbiology and Virology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Masoud Keikha
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Talebi Bezmin Abadi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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17
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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.
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18
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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.
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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
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19
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Li Y, Huang Z, Shang Y, Xie X, Yang R, Chen H, Wang Z, Xue L, Pang R, Zhang J, Ding Y, Chen M, Wang J, Chen J, Wu Q. Exploration of the molecular mechanisms underlying the antibiotic resistance of Helicobacter pylori: A whole-genome sequencing-based study in Southern China. Helicobacter 2022; 27:e12879. [PMID: 35124867 DOI: 10.1111/hel.12879] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND Although antimicrobial resistance (AMR) in Helicobacter pylori is a global threat to human health and the underlying molecular mechanisms have been explored previously, only a few of them are fully elucidated. MATERIALS AND METHODS In the present study, we isolated 54 Helicobacter pylori strains from Southern China and assessed their susceptibility to five antibiotics using the agar dilution assay. Whole-genome sequencing was performed to screen the AMR genotypes of the Helicobacter pylori isolates. RESULTS Our study revealed a high prevalence of resistance to clarithromycin (CLR), levofloxacin (LVX), and metronidazole (MTZ) in the Chinese isolates, 55.56% of which showed multidrug-resistant phenotypes. We screened for the 94 types of previously reported AMR mutations in 12 genes, but only a few of them were related to the AMR phenotype. Furthermore, we discovered four new mutations in the 23S rRNA gene and one mutation in infB related to CLR resistance. Another three mutations in gyrA and one in gyrB were closely correlated with the AMR pattern against LVX. We also demonstrated that the mutations R16C/H in rdxA, V56I in rpsU, and D54A in sodB might contribute to resistance to MTZ, which were previously reported in laboratory experiments but not found in clinical strains. We examined the concordance between the genotype and phenotype of AMR and identified several potential molecular biomarkers for predicting CLR and LVX resistance. CONCLUSIONS Our study explored the molecular mechanisms underlying the antibiotic resistance of Helicobacter pylori isolates from Southern China. We propose further epidemiologic investigations in China.
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Affiliation(s)
- Ying Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhixin Huang
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yanyan Shang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinqiang Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Runshi Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Huizhen Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhi Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jianhui Chen
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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20
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Tran TT, Nguyen AT, Quach DT, Pham DTH, Cao NM, Nguyen UTH, Dang ANT, Tran MA, Quach LH, Tran KT, Le NQ, Ung VV, Vo MNQ, Nguyen DT, Ngo KD, Tran TL, Nguyen VT. Emergence of amoxicillin resistance and identification of novel mutations of the pbp1A gene in Helicobacter pylori in Vietnam. BMC Microbiol 2022; 22:41. [PMID: 35114945 PMCID: PMC8812189 DOI: 10.1186/s12866-022-02463-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
Background Amoxicillin-resistant Helicobacter pylori (H. pylori) strains seem to have increased over time in Vietnam. This threatens the effectiveness of H. pylori eradication therapies with this antibiotic. This study aimed to investigate the prevalence of primary resistance of H. pylori to amoxicillin and to assess its association with pbp1A point mutations in Vietnamese patients. Materials and methods Naive patients who presented with dyspepsia undergoing upper gastrointestinal endoscopy were recruited. Rapid urease tests and PCR assays were used to diagnose H. pylori infection. Amoxicillin susceptibility was examined by E-tests. Molecular detection of the mutant pbp1A gene conferring amoxicillin resistance was carried out by real-time PCR followed by direct sequencing of the PCR products. Phylogenetic analyses were performed using the Tamura-Nei genetic distance model and the neighbor-joining tree building method. Results There were 308 patients (46.1% men and 53.9% women, p = 0.190) with H. pylori infection. The mean age of the patients was 40.5 ± 11.4 years, ranging from 18 to 74 years old. The E-test was used to determine the susceptibility to amoxicillin (minimum inhibitory concentration (MIC) ≤ 0.125 μg/ml) in 101 isolates, among which the rate of primarily resistant strains to amoxicillin was 25.7%. Then, 270 sequences of pbp1A gene fragments were analysed. There were 77 amino acid substitution positions investigated, spanning amino acids 310–596, with the proportion varying from 0.4 to 100%. Seven amino acid changes were significantly different between amoxicillin-sensitive (AmoxS) and amoxicillin-resistant (AmoxR) samples, including Phe366 to Leu (p < 0.001), Ser414 to Arg (p < 0.001), Glu/Asn464–465 (p = 0.009), Val469 to Met (p = 0.021), Phe473 to Val (p < 0.001), Asp479 to Glu (p = 0.044), and Ser/Ala/Gly595–596 (p = 0.001). Phylogenetic analyses suggested that other molecular mechanisms might contribute to amoxicillin resistance in H. pylori in addition to the alterations in PBP1A. Conclusions We reported the emergence of amoxicillin-resistant Helicobacter pylori strains in Vietnam and new mutations statistically associated with this antimicrobial resistance. Additional studies are necessary to identify the mechanisms contributing to this resistance in Vietnam.
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Affiliation(s)
- Trung Thien Tran
- Department of Surgery, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Anh Tuan Nguyen
- Molecular Biomedical Center, University Medical Center, Ho Chi Minh City, Vietnam.
| | - Duc Trong Quach
- Department of Internal Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Dao Thi-Hong Pham
- Department of Genetics, University of Science, Vietnam National University Ho Chi Minh, Ho Chi Minh City, Vietnam
| | - Nga Minh Cao
- Department of Microbiology-Parasitology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Uyen Thi-Hong Nguyen
- Department of Genetics, University of Science, Vietnam National University Ho Chi Minh, Ho Chi Minh City, Vietnam
| | - An Nguyen-Thanh Dang
- Department of Genetics, University of Science, Vietnam National University Ho Chi Minh, Ho Chi Minh City, Vietnam
| | - Minh Anh Tran
- Department of Surgery, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Loc Huu Quach
- University Medical Center - Campus 2, Ho Chi Minh City, Vietnam
| | | | - Nhan Quang Le
- Department of Endoscopy, University Medical Center, Ho Chi Minh City, Vietnam
| | - Viet Van Ung
- Department of Endoscopy, University Medical Center, Ho Chi Minh City, Vietnam
| | - Minh Ngoc-Quoc Vo
- Department of Endoscopy, University Medical Center, Ho Chi Minh City, Vietnam
| | - Danh Thanh Nguyen
- Molecular Biomedical Center, University Medical Center, Ho Chi Minh City, Vietnam
| | - Kha Dong Ngo
- Molecular Biomedical Center, University Medical Center, Ho Chi Minh City, Vietnam
| | - Trung Le Tran
- Department of Oral Biology, Yonsei University College of Density, Seoul, South Korea
| | - Vy Thuy Nguyen
- Department of Genetics, University of Science, Vietnam National University Ho Chi Minh, Ho Chi Minh City, Vietnam
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Brincat A, Hofmann M. Automated extraction of genes associated with antibiotic resistance from the biomedical literature. Database (Oxford) 2022; 2022:6520791. [PMID: 35134132 PMCID: PMC9263533 DOI: 10.1093/database/baab077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/21/2021] [Accepted: 11/22/2021] [Indexed: 11/15/2022]
Abstract
Abstract
The detection of bacterial antibiotic resistance phenotypes is important when carrying out clinical decisions for patient treatment. Conventional phenotypic testing involves culturing bacteria which requires a significant amount of time and work. Whole-genome sequencing is emerging as a fast alternative to resistance prediction, by considering the presence/absence of certain genes. A lot of research has focused on determining which bacterial genes cause antibiotic resistance and efforts are being made to consolidate these facts in knowledge bases (KBs). KBs are usually manually curated by domain experts to be of the highest quality. However, this limits the pace at which new facts are added. Automated relation extraction of gene-antibiotic resistance relations from the biomedical literature is one solution that can simplify the curation process. This paper reports on the development of a text mining pipeline that takes in English biomedical abstracts and outputs genes that are predicted to cause resistance to antibiotics. To test the generalisability of this pipeline it was then applied to predict genes associated with Helicobacter pylori antibiotic resistance, that are not present in common antibiotic resistance KBs or publications studying H. pylori. These genes would be candidates for further lab-based antibiotic research and inclusion in these KBs. For relation extraction, state-of-the-art deep learning models were used. These models were trained on a newly developed silver corpus which was generated by distant supervision of abstracts using the facts obtained from KBs. The top performing model was superior to a co-occurrence model, achieving a recall of 95%, a precision of 60% and F1-score of 74% on a manually annotated holdout dataset. To our knowledge, this project was the first attempt at developing a complete text mining pipeline that incorporates deep learning models to extract gene-antibiotic resistance relations from the literature. Additional related data can be found at https://github.com/AndreBrincat/Gene-Antibiotic-Resistance-Relation-Extraction
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Affiliation(s)
- Andre Brincat
- Department of Informatics, TU Dublin , Blanchardstown Campus, Dublin D15 YV78, Ireland
| | - Markus Hofmann
- Department of Informatics, TU Dublin , Blanchardstown Campus, Dublin D15 YV78, Ireland
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Subsomwong P, Doohan D, Fauzia KA, Akada J, Matsumoto T, Yee TT, Htet K, Waskito LA, Tuan VP, Uchida T, Matsuhisa T, Yamaoka Y. Next-Generation Sequencing-Based Study of Helicobacter pylori Isolates from Myanmar and Their Susceptibility to Antibiotics. Microorganisms 2022; 10:microorganisms10010196. [PMID: 35056645 PMCID: PMC8781859 DOI: 10.3390/microorganisms10010196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 02/01/2023] Open
Abstract
Evaluation of Helicobacter pylori resistance to antibiotics is crucial for treatment strategy in Myanmar. Moreover, the genetic mechanisms involved remain unknown. We aimed to investigate the prevalence of H. pylori infection, antibiotic resistance, and genetic mechanisms in Myanmar. One hundred fifty patients from two cities, Mawlamyine (n = 99) and Yangon (n = 51), were recruited. The prevalence of H. pylori infection was 43.3% (65/150). The successfully cultured H. pylori isolates (n = 65) were tested for antibiotic susceptibility to metronidazole, levofloxacin, clarithromycin, amoxicillin, and tetracycline by Etest, and the resistance rates were 80%, 33.8%, 7.7%, 4.6%, and 0%, respectively. In the multidrug resistance pattern, the metronidazole–levofloxacin resistance was highest for double-drug resistance (16/19; 84.2%), and all triple-drug resistance (3/3) was clarithromycin–metronidazole–levofloxacin resistance. Twenty-three strains were subjected to next-generation sequencing to study their genetic mechanisms. Interestingly, none of the strains resistant to clarithromycin had well-known mutations in 23S rRNA (e.g., A2142G, A2142C, and A2143G). New type mutation genotypes such as pbp1-A (e.g., V45I, S/R414R), 23S rRNA (e.g., T248C), gyrA (e.g., D210N, K230Q), gyrB (e.g., A584V, N679H), rdxA (e.g., V175I, S91P), and frxA (e.g., L33M) were also detected. In conclusion, the prevalence of H. pylori infection and its antibiotic resistance to metronidazole was high in Myanmar. The H. pylori eradication regimen with classical triple therapy, including amoxicillin and clarithromycin, can be used as the first-line therapy in Myanmar. In addition, next-generation sequencing is a powerful high-throughput method for identifying mutations within antibiotic resistance genes and monitoring the spread of H. pylori antibiotic-resistant strains.
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Affiliation(s)
- Phawinee Subsomwong
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; (P.S.); (D.D.); (K.A.F.); (J.A.); (T.M.); (L.A.W.); (V.P.T.)
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Dalla Doohan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; (P.S.); (D.D.); (K.A.F.); (J.A.); (T.M.); (L.A.W.); (V.P.T.)
- Department of Public Health and Preventive Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; (P.S.); (D.D.); (K.A.F.); (J.A.); (T.M.); (L.A.W.); (V.P.T.)
- Department of Public Health and Preventive Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
- Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; (P.S.); (D.D.); (K.A.F.); (J.A.); (T.M.); (L.A.W.); (V.P.T.)
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; (P.S.); (D.D.); (K.A.F.); (J.A.); (T.M.); (L.A.W.); (V.P.T.)
| | - Than Than Yee
- Department of GI and HBP Surgery, No. (2) Defense Service General Hospital (1000 Bedded), Nay Pyi Taw 15013, Myanmar;
| | - Kyaw Htet
- Department of GI and HBP Surgery, No. (1) Defense Service General Hospital (1000 Bedded), Mingaladon, Yangon 11021, Myanmar;
| | - Langgeng Agung Waskito
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; (P.S.); (D.D.); (K.A.F.); (J.A.); (T.M.); (L.A.W.); (V.P.T.)
- Department of Public Health and Preventive Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; (P.S.); (D.D.); (K.A.F.); (J.A.); (T.M.); (L.A.W.); (V.P.T.)
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh 749000, Vietnam
| | - Tomohisa Uchida
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan;
| | - Takeshi Matsuhisa
- Department of Gastroenterology, Nippon Medical School Tama Nagayama Hospital, Tama 206-8512, Japan;
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; (P.S.); (D.D.); (K.A.F.); (J.A.); (T.M.); (L.A.W.); (V.P.T.)
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA
- Global Oita Medical Advanced Research Center for Health (GO-MARCH), Yufu 879-5593, Japan
- Correspondence: ; Tel.: +81-(97)-586-5740; Fax: +81-(97)-586-5749
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Hulten KG, Genta RM, Kalfus IN, Zhou Y, Zhang H, Graham DY. Comparison of Culture With Antibiogram to Next-Generation Sequencing Using Bacterial Isolates and Formalin-Fixed, Paraffin-Embedded Gastric Biopsies. Gastroenterology 2021; 161:1433-1442.e2. [PMID: 34293298 PMCID: PMC9047521 DOI: 10.1053/j.gastro.2021.07.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The decline in Helicobacter pylori cure rates emphasizes the need for readily available methods to determine antimicrobial susceptibility. Our aim was to compare targeted next-generation sequencing (NGS) and culture-based H pylori susceptibility testing using clinical isolates and paired formalin-fixed, paraffin-embedded (FFPE) gastric biopsies. METHODS H pylori isolates and FFPE tissues were tested for susceptibility to amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and rifabutin using agar dilution and NGS targeted to 23S rRNA, gyrA, 16S rRNA, pbp1, rpoB and rdxA. Agreement was quantified using κ statistics. RESULTS Paired comparisons included 170 isolates and FFPE tissue for amoxicillin, clarithromycin, metronidazole, and rifabutin and 57 isolates and FFPE tissue for levofloxacin and tetracycline. Agreement between agar dilution and NGS from culture isolates was very good for clarithromycin (κ = 0.90012), good for levofloxacin (κ = 0.78161) and fair for metronidazole (κ = 0.55880), and amoxicillin (κ = 0.21400). Only 1 isolate was resistant to tetracycline (culture) and 1 to rifabutin (NGS). Comparison of NGS from tissue blocks and agar dilution from isolates from the same stomachs demonstrated good accuracy to predict resistance for clarithromycin (94.1%), amoxicillin (95.9%), metronidazole (77%), levofloxacin (87.7%), and tetracycline (98.2%). Lack of resistance precluded comparisons for tetracycline and rifabutin. CONCLUSIONS Compared with agar dilution, NGS reliably determined resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline from clinical isolates and formalin-fixed gastric tissue. Consistency was fair for metronidazole and amoxicillin. Culture-based testing can predict treatment outcomes with clarithromycin and levofloxacin. Studies are needed to compare the relative ability of both methods to predict treatment outcomes for other antibiotics.
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Affiliation(s)
| | - Robert M. Genta
- Inform Diagnostics, Irving, Texas,Department of Pathology, Baylor College of Medicine, Houston, Texas
| | | | - Yi Zhou
- American Molecular Laboratories, Vernon Hills, Illinois
| | - Hongjun Zhang
- American Molecular Laboratories, Vernon Hills, Illinois
| | - David Y. Graham
- Department of Medicine, Michael E. DeBakey VA Medical Center and Baylor College of Medicine, Houston, Texas
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The Emergence of Multidrug-Resistant Helicobacter pylori in Southeast Asia: A Systematic Review on the Trends and Intervention Strategies Using Antimicrobial Peptides. Antibiotics (Basel) 2021; 10:antibiotics10091061. [PMID: 34572643 PMCID: PMC8465560 DOI: 10.3390/antibiotics10091061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023] Open
Abstract
The emergence of multidrug-resistant H. pylori poses a public healthcare threat, particularly in low- and middle-income countries. Recently, the World Health Organization has classified clarithromycin-resistant H. pylori as high priority in the research and discovery of novel antibiotics. This study was aimed to systematically review the prevalence of primary antibiotic resistance in H. pylori in Southeast Asian countries (SEAC) and to review current studies of antimicrobial peptides against H. pylori. We systematically searched through electronic databases of studies conducted on antimicrobial resistance of H. pylori in SEA countries. Furthermore, we searched articles that conducted studies on antimicrobial peptides, naturally occurring host’s defense molecules, against H. pylori. After a series of screening processes, 15 studies were included in our systematic review. Our analysis revealed that primary resistance of H. pylori to metronidazole, clarithromycin, and levofloxacin were high in SEAC, although the primary resistance to amoxicillin and tetracycline remains low. Multidrug-resistant H. pylori are emerging in SE Asian countries. The antimicrobial peptides show promising antibacterial and antibiofilm activity against drug-resistant H. pylori. The research and discovery of antimicrobial peptides against H. pylori in SEAC will help in limiting the spread of antimicrobial resistance of H. pylori.
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Tshibangu-Kabamba E, Yamaoka Y. Helicobacter pylori infection and antibiotic resistance - from biology to clinical implications. Nat Rev Gastroenterol Hepatol 2021; 18:613-629. [PMID: 34002081 DOI: 10.1038/s41575-021-00449-x] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/31/2021] [Indexed: 02/06/2023]
Abstract
Helicobacter pylori is a major human pathogen for which increasing antibiotic resistance constitutes a serious threat to human health. Molecular mechanisms underlying this resistance have been intensively studied and are discussed in this Review. Three profiles of resistance - single drug resistance, multidrug resistance and heteroresistance - seem to occur, probably with overlapping fundamental mechanisms and clinical implications. The mechanisms that have been most studied are related to mutational changes encoded chromosomally and disrupt the cellular activity of antibiotics through target-mediated mechanisms. Other biological attributes driving drug resistance in H. pylori have been less explored and this could imply more complex physiological changes (such as impaired regulation of drug uptake and/or efflux, or biofilm and coccoid formation) that remain largely elusive. Resistance-related attributes deployed by the pathogen cause treatment failures, diagnostic difficulties and ambiguity in clinical interpretation of therapeutic outcomes. Subsequent to the increasing antibiotic resistance, a substantial drop in H. pylori treatment efficacy has been noted globally. In the absence of an efficient vaccine, enhanced efforts are needed for setting new treatment strategies and for a better understanding of the emergence and spread of drug-resistant bacteria, as well as for improving diagnostic tools that can help optimize current antimicrobial regimens.
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Affiliation(s)
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan. .,Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, USA.
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Cui R, Song Z, Suo B, Tian X, Xue Y, Meng L, Niu Z, Jin Z, Zhang H, Zhou L. Correlation Analysis Among Genotype Resistance, Phenotype Resistance and Eradication Effect of Helicobacter pylori. Infect Drug Resist 2021; 14:1747-1756. [PMID: 34012273 PMCID: PMC8127322 DOI: 10.2147/idr.s305996] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022] Open
Abstract
Background It has not been fully confirmed whether the detection of Helicobacter pylori resistance gene mutation can replace antibiotic drug sensitivity test to guide the clinical individualized treatment. Therefore, we have studied this aspect and discussed the application value of antibiotic sensitivity gene test. Materials and Methods The biopsy specimen of gastric mucosa from the patients examined by endoscopy and positive for rapid urease test were collected continuously for histopathological analysis, H. pylori culture, antibiotic drug sensitivity test (E-test drug sensitivity test), and antibiotic sensitivity gene test (high-throughput nucleotide sequencing). The participants received triple plus bismuth solution eradication treatment (esomeprazole 20 mg, amoxicillin 1000 mg, clarithromycin 500 mg, and bismuth potassium citrate 220 mg, twice daily for 14 days) for follow-up, and the eradication effect was determined. Results The 551/602 subjects, who met the inclusion criteria, were subjected to culture for H. pylori and antibiotic drug sensitivity determination; among them 506 were cultured successfully. The results showed that the resistance rates of H. pylori were 38.9% for clarithromycin and 31.0% for levofloxacin. In 489 H. pylori strains, the mutations were detected in clarithromycin and levofloxacin resistance genes, indicating the genotype resistance. The resistance genes of clarithromycin and levofloxacin were consistent with phenotype resistance with respect to sensitivity (81.2% and 69.7% for clarithromycin and levofloxacin, respectively) and specificity (88.9% and 93.7% for clarithromycin and levofloxacin, respectively). The eradication rate of H. pylori in the clarithromycin-resistant group was significantly lower than that in the sensitive group (ITT: 52.1% vs 85.0%, P < 0.001). Conclusion A correlation was established between the resistance genes of clarithromycin and levofloxacin and their phenotypic resistance and clinical efficacy. The detection of H. pylori resistance genes has a good clinical application prospect.
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Affiliation(s)
- Rongli Cui
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Zhiqiang Song
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Baojun Suo
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Xueli Tian
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Yan Xue
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Lingmei Meng
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Zhanyue Niu
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Zhu Jin
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Hejun Zhang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Liya Zhou
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, People's Republic of China
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Clinical Evaluation of a Real-Time PCR Assay for Simultaneous Detection of Helicobacter pylori and Genotypic Markers of Clarithromycin Resistance Directly from Stool. J Clin Microbiol 2021; 59:JCM.03040-20. [PMID: 33536295 DOI: 10.1128/jcm.03040-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/02/2021] [Indexed: 12/28/2022] Open
Abstract
Helicobacter pylori infection is mainly diagnosed noninvasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empirical, with clarithromycin-based triple therapy recommended where resistance rates are below 15%. Rising rates of clarithromycin resistance, resulting in high clarithromycin-based therapy failure rates, are seen worldwide, but U.S. data are limited. We developed a real-time PCR assay for simultaneous detection of H. pylori and genotypic markers of clarithromycin resistance directly from stool specimens. The assay was validated by testing 524 stool samples using an H. pylori stool antigen test as the reference method for detection accuracy and Sanger sequencing to confirm genotypic susceptibility results. A separate set of 223 antigen-positive stool samples was tested and retrospective medical record review conducted to define clinical utility. PCR resulted in 88.6% and 92.8% sensitivity in the validation and clinical study sets, respectively. Sequencing confirmed correct detection of clarithromycin resistance-associated mutations in all positive validation samples. The PCR-predicted clarithromycin resistance rate was 39% in the clinical data set overall and 31% in treatment-naive patients; the clarithromycin-based triple therapy eradication rate in treatment-naive patients was 62%. The clarithromycin-based triple therapy success was lower when resistance was predicted by PCR (41%) than when no resistance was predicted (70%; P = 0.03). PCR results were positive in 98% of antigen-positive stools from patients tested for eradication. The described PCR assay can accurately and noninvasively diagnose H. pylori, provide genotypic susceptibility, and test for eradication. Our findings support the need for susceptibility-guided therapy in our region if a clarithromycin-based regimen is considered.
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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.
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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.)
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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.
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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.
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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
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Domanovich-Asor T, Motro Y, Khalfin B, Craddock HA, Peretz A, Moran-Gilad J. Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in Helicobacter pylori. Microorganisms 2020; 9:E2. [PMID: 33374988 PMCID: PMC7822022 DOI: 10.3390/microorganisms9010002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) in Helicobacter pylori is increasing and can result in treatment failure and inappropriate antibiotic usage. This study used whole genome sequencing (WGS) to comprehensively analyze the H. pylori resistome and phylogeny in order to characterize Israeli H. pylori. Israeli H. pylori isolates (n = 48) underwent antimicrobial susceptibility testing (AST) against five antimicrobials and WGS analysis. Literature review identified 111 mutations reported to correlate with phenotypic resistance to these antimicrobials. Analysis was conducted via our in-house bioinformatics pipeline targeting point mutations in the relevant genes (pbp1A, 23S rRNA, gyrA, rdxA, frxA, and rpoB) in order to assess genotype-to-phenotype correlation. Resistance rates of study isolates were as follows: clarithromycin 54%, metronidazole 31%, amoxicillin 10%, rifampicin 4%, and levofloxacin 2%. Genotype-to-phenotype correlation was inconsistent; for every analyzed gene at least one phenotypically susceptible isolate was found to have a mutation previously associated with resistance. This was also observed regarding mutations commonly used in commercial kits to diagnose AMR in H. pylori cases. Furthermore, 11 novel point mutations associated with a resistant phenotype were detected. Analysis of a unique set of H. pylori isolates demonstrates that inferring resistance phenotypes from WGS in H. pylori remains challenging and should be optimized further.
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Affiliation(s)
- Tal Domanovich-Asor
- MAGICAL Group, Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (T.D.-A.); (Y.M.); (B.K.); (H.A.C.)
| | - Yair Motro
- MAGICAL Group, Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (T.D.-A.); (Y.M.); (B.K.); (H.A.C.)
| | - Boris Khalfin
- MAGICAL Group, Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (T.D.-A.); (Y.M.); (B.K.); (H.A.C.)
| | - Hillary A. Craddock
- MAGICAL Group, Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (T.D.-A.); (Y.M.); (B.K.); (H.A.C.)
| | - Avi Peretz
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poriyah and Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel;
| | - Jacob Moran-Gilad
- MAGICAL Group, Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (T.D.-A.); (Y.M.); (B.K.); (H.A.C.)
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McDermott PF, Davis JJ. Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring. J Vet Pharmacol Ther 2020; 44:223-237. [PMID: 33010049 DOI: 10.1111/jvp.12913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/25/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022]
Abstract
The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild-type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing, including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics, we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.
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Affiliation(s)
- Patrick F McDermott
- Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - James J Davis
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA.,University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
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Wang YH, Wang FF, Gong XL, Yan LL, Zhao QY, Song YP, Zhao RL, He YJ, Zhou L, Liu DS, Xie Y. Genotype profiles of Helicobacter pylori from gastric biopsies and strains with antimicrobial-induced resistance. Therap Adv Gastroenterol 2020; 13:1756284820952596. [PMID: 33029198 PMCID: PMC7522827 DOI: 10.1177/1756284820952596] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/30/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND AND AIMS The genotypic method could significantly shorten the time needed to obtain antibiotic susceptibility data for Helicobacter pylori. The aim of this study was to explore the profile of H. pylori from gastric biopsies and strains with antibiotic-induced resistance. METHODS A total of 124 gastric biopsies were used to perform gene sequencing and to perform bacterial culture and susceptibility testing. Seven susceptible strains were selected to develop resistance to clarithromycin, levofloxacin, and metronidazole. Four susceptible strains were selected to transfer candidate mutations. The genotype profiles of these groups were analyzed by sequencing analysis. The antibiotic susceptibility of these strains was detected using the E-test method. RESULTS Phenotypic resistance to clarithromycin, levofloxacin, and metronidazole was observed in 35.5%, 40.0%, and 79.8% strains, respectively. Point mutations in 23 S rRNA, gyrA, and rdxA genes were observed in 39.5%, 38.7%, and 86.3% of gastric biopsies, respectively. The A2143G mutation in the 23S rRNA occurs in most clarithromycin-resistant samples. The A2142C point mutation showed a higher efficacy than A2142G and A2143G for inducing clarithromycin resistance. The D91N and N87K mutations in gyrA occurs in most levofloxacin-resistant samples, and double point mutations showed a higher efficacy than single mutations for inducing levofloxacin resistance. Phenotypic resistance and mutations in rdxA lacked consistency. CONCLUSION Genotype-based gastric biopsy analysis was reliable for determining clarithromycin and levofloxacin resistance. A2143G in 23S rRNA and N87K/D91N in the gyrA gene occurred in most resistant strains. Mutations in the rdxA gene were not good indicators of metronidazole resistance.
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Affiliation(s)
| | | | | | - Li-li Yan
- Department of Medical College, Nanchang University, Nanchang, Jiangxi Province, China
| | - Qiao-yun Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Yan-ping Song
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Ru-lin Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Ya-jing He
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Linfu Zhou
- Department of Biochemistry and Molecular Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Dong-sheng Liu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, 17 Yongwai Zheng Street, Nanchang, Jiangxi Province, 330000, China
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O'Connor A, Furuta T, Gisbert JP, O'Morain C. Review - Treatment of Helicobacter pylori infection 2020. Helicobacter 2020; 25 Suppl 1:e12743. [PMID: 32918350 DOI: 10.1111/hel.12743] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review summarizes important studies regarding Helicobacter pylori therapy published from April 2019 to April 2020. The main themes that emerge involve studies assessing antibiotic resistance, and there is also growing momentum behind the utility of vonoprazan as an alternative to proton pump inhibitor (PPI) therapy and also bismuth-based regimens as a first-line regimen. Antibiotic resistance is rising wherever it is being assessed, and clarithromycin resistance in particular has reached a point where it may no longer be a viable therapy without previous testing in many regions of the world. The evidence for the efficacy of a bismuth-based quadruple therapy as a first-line therapy is now very clearly established, and there is substantial evidence that it is the best performing first-line therapy. The utility of vonoprazan as an alternative to PPI therapy, especially in resistant and difficult-to-treat groups, has also been considered in great detail this year, and it may offer an opportunity in the near future to reduce the problem of antibiotic resistance.
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Affiliation(s)
- Anthony O'Connor
- Department of Gastroenterology, Tallaght University Hospital/Trinity College, Dublin, Ireland
| | - Takahisa Furuta
- The Center for Clinical Research, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Colm O'Morain
- Department of Gastroenterology, Tallaght University Hospital/Trinity College, Dublin, Ireland
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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.
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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
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Azzaya D, Gantuya B, Oyuntsetseg K, Davaadorj D, Matsumoto T, Akada J, Yamaoka Y. High Antibiotic Resistance of Helicobacter pylori and Its Associated Novel Gene Mutations among the Mongolian Population. Microorganisms 2020; 8:microorganisms8071062. [PMID: 32708761 PMCID: PMC7409119 DOI: 10.3390/microorganisms8071062] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 12/24/2022] Open
Abstract
Mongolia has a high prevalence of Helicobacter pylori infection and the second highest incidence of gastric cancer worldwide. Thus, investigating the prevalence of antibiotic resistance and its underlying genetic mechanism is necessary. We isolated 361 H. pylori strains throughout Mongolia. Agar dilution assays were used to determine the minimum inhibitory concentrations of five antibiotics; amoxicillin, clarithromycin, metronidazole, levofloxacin, and minocycline. The genetic determinants of antibiotic resistance were identified with next-generation sequencing (NGS) and the CLC Genomics Workbench. The resistance to metronidazole, levofloxacin, clarithromycin, amoxicillin, and minocycline was 78.7%, 41.3%, 29.9%, 11.9% and 0.28%, respectively. Multidrug resistance was identified in 51.3% of the isolates investigated which were further delineated into 9 antimicrobial resistance profiles. A number of known antibiotic resistance mutations were identified including rdxA, frxA (missense, frameshift), gyrA (N87K, A88P, D91G/N/Y), 23S rRNA (A2143G), pbp1A (N562Y), and 16S rRNA (A928C). Furthermore, we detected previously unreported mutations in pbp1A (L610*) and the 23S rRNA gene (A1410G, C1707T, A2167G, C2248T, and C2922T). The degree of antibiotic resistance was high, indicating the insufficiency of standard triple therapy in Mongolia.
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Affiliation(s)
- Dashdorj Azzaya
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu City, Oita 879-5593, Japan; (D.A.); (T.M.); (J.A.)
| | - Boldbaatar Gantuya
- Department of Gastroenterology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (B.G.); (K.O.); (D.D.)
- Endoscopy Unit, Mongolia-Japan Teaching Hospital, Mongolian National University of Medical Sciences, Ulaanbaatar 250573, Mongolia
| | - Khasag Oyuntsetseg
- Department of Gastroenterology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (B.G.); (K.O.); (D.D.)
- Endoscopy Unit, Mongolia-Japan Teaching Hospital, Mongolian National University of Medical Sciences, Ulaanbaatar 250573, Mongolia
| | - Duger Davaadorj
- Department of Gastroenterology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (B.G.); (K.O.); (D.D.)
- Endoscopy Unit, Mongolia-Japan Teaching Hospital, Mongolian National University of Medical Sciences, Ulaanbaatar 250573, Mongolia
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu City, Oita 879-5593, Japan; (D.A.); (T.M.); (J.A.)
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu City, Oita 879-5593, Japan; (D.A.); (T.M.); (J.A.)
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu City, Oita 879-5593, Japan; (D.A.); (T.M.); (J.A.)
- Department of Medicine, Gastroenterology and Hepatology section, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: ; Tel.: +81-97-586-5740; Fax: +81-97-586-5749
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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.
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Tshibangu-Kabamba E, Ngoma-Kisoko PDJ, Tuan VP, Matsumoto T, Akada J, Kido Y, Tshimpi-Wola A, Tshiamala-Kashala P, Ahuka-Mundeke S, Mumba Ngoy D, Disashi-Tumba G, Yamaoka Y. Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of Helicobacter pylori Clinical Isolates from the Democratic Republic of Congo. Microorganisms 2020; 8:E887. [PMID: 32545318 PMCID: PMC7356661 DOI: 10.3390/microorganisms8060887] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial susceptibility testing (AST) is increasingly needed to guide the Helicobacter pylori (H. pylori) treatment but remains laborious and unavailable in most African countries. To assess the clinical relevance of bacterial whole genome sequencing (WGS)-based methods for predicting drug susceptibility in African H. pylori, 102 strains isolated from the Democratic Republic of Congo were subjected to the phenotypic AST and next-generation sequencing (NGS). WGS was used to screen for the occurrence of genotypes encoding antimicrobial resistance (AMR). We noted the broad-spectrum AMR of H. pylori (rates from 23.5 to 90.0%). A WGS-based method validated for variant discovery in AMR-related genes (discovery rates of 100%) helped in identifying mutations of key genes statistically related to the phenotypic AMR. These included mutations often reported in Western and Asian populations and, interestingly, several putative AMR-related new genotypes in the pbp1A (e.g., T558S, F366L), gyrA (e.g., A92T, A129T), gyrB (e.g., R579C), and rdxA (e.g., R131_K166del) genes. WGS showed high performance for predicting AST phenotypes, especially for amoxicillin, clarithromycin, and levofloxacin (Youden's index and Cohen's Kappa > 0.80). Therefore, WGS is an accurate alternative to the phenotypic AST that provides substantial decision-making information for public health policy makers and clinicians in Africa, while providing insight into AMR mechanisms for researchers.
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Affiliation(s)
- Evariste Tshibangu-Kabamba
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (V.P.T.); (T.M.); (J.A.); (Y.K.)
- Department of Internal Medicine, Faculty of Medicine, University of Mbujimayi, Mbujimayi, DR Congo;
| | - Patrick de Jesus Ngoma-Kisoko
- Department of Internal Medicine, Gastroenterology and Hepatology Section, Faculty of Medicine, University of Kinshasa, Kinshasa, DR Congo; (P.d.J.N.-K.); (A.T.-W.)
- Department of Gastroenterology and Hepatology, Cinquantenaire’s Hospital, Kinshasa, DR Congo
- Department of Internal Medicine, Gastroenterology and Hepatology Section, General Referential Hospital of Bukavu, DR Congo
| | - Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (V.P.T.); (T.M.); (J.A.); (Y.K.)
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh 70000, Vietnam
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (V.P.T.); (T.M.); (J.A.); (Y.K.)
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (V.P.T.); (T.M.); (J.A.); (Y.K.)
| | - Yasutoshi Kido
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (V.P.T.); (T.M.); (J.A.); (Y.K.)
- Department of Parasitology, Osaka City University, Osaka 545-8585, Japan
| | - Antoine Tshimpi-Wola
- Department of Internal Medicine, Gastroenterology and Hepatology Section, Faculty of Medicine, University of Kinshasa, Kinshasa, DR Congo; (P.d.J.N.-K.); (A.T.-W.)
- Department of Internal Medicine, Gastroenterology and Hepatology Section, Marie-Yvettes Clinics, Kinshasa, DR Congo
| | - Pascal Tshiamala-Kashala
- Department of Internal Medicine, Gastroenterology and Hepatology Section, Astryd Clinics, Kinshasa, DR Congo;
| | - Steve Ahuka-Mundeke
- Department of Virology, National Institute of Biomedical Research, Kinshasa, DR Congo;
| | - Dieudonné Mumba Ngoy
- Department of Parasitology, National Institute of Biomedical Research, Kinshasa, DR Congo;
- Department of Tropical Medicine, School of Medicine, University of Kinshasa, Kinshasa, DR Congo
| | - Ghislain Disashi-Tumba
- Department of Internal Medicine, Faculty of Medicine, University of Mbujimayi, Mbujimayi, DR Congo;
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (V.P.T.); (T.M.); (J.A.); (Y.K.)
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA
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Aumpan N, Vilaichone RK, Gamnarai P, Sanglutong L, Ratanachu-Ek T, Mahachai V, Yamaoka Y. Prevalence and Antibiotic Resistance Patterns of Helicobacter pylori Infection in Koh Kong, Cambodia. Asian Pac J Cancer Prev 2020; 21:1409-1413. [PMID: 32458649 PMCID: PMC7541852 DOI: 10.31557/apjcp.2020.21.5.1409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Gastric cancer, which is the leading cause of cancer mortality in Cambodia, can be prevented by Helicobacter pylori (H. pylori) eradication. There is limited data about H. pylori strains in Cambodia. This study aimed to evaluate H. pylori prevalence and antibiotic resistance in Koh Kong, Cambodia. Methods: 118 Cambodian dyspeptic patients were scheduled to enter this study and 58 were enrolled between July and September 2019. All patients underwent upper GI endoscopy. 3 gastric biopsies were obtained for rapid urease test, H. pylori culture with E-test and GenoType® HelicoDr (Hain Lifescience factory, Germany). 3-mL blood sample was collected for CYP2C19 genotyping. Results: 58 subjects were enrolled (40 females, 18 males, mean age 43.8 years). Overall H. pylori prevalence was 31.0%. Antibiotic resistance rates were 78.6% for metronidazole, 50.0% for fluoroquinolones, and 27.8% for clarithromycin. There was no amoxicillin and tetracycline resistance. More than half of H. pylori strains (57.1%) were multidrug-resistant. Most (35.7%) were resistant to metronidazole and quinolone. Poor, intermediate and rapid metabolizers were 5.5%, 38.9% and 55.6%, respectively. Conclusions: H. pylori infection remains common infection in Cambodia. High prevalence of clarithromycin, metronidazole, levofloxacin and multidrug-resistant H. pylori is still major problems in Cambodia. Treatment regimens without clarithromycin and quinolone such as 14-day bismuth-based quadruple therapy might be an appropriate choice for H. pylori eradication in this particular area.
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Affiliation(s)
- Natsuda Aumpan
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Thammasat University Hospital, Pathumthani, Thailand.,Digestive diseases Research Center (DRC), Thammasat University, Pathumthani, Thailand
| | - Ratha-Korn Vilaichone
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Thammasat University Hospital, Pathumthani, Thailand.,Digestive diseases Research Center (DRC), Thammasat University, Pathumthani, Thailand.,Department of Medicine, Chulabhorn International College of Medicine (CICM) at Thammasat University, Pathumthani, Thailand
| | - Pornpen Gamnarai
- Digestive diseases Research Center (DRC), Thammasat University, Pathumthani, Thailand.,Department of Biochemistry, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Likhasit Sanglutong
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Thammasat University Hospital, Pathumthani, Thailand
| | | | - Varocha Mahachai
- Digestive diseases Research Center (DRC), Thammasat University, Pathumthani, Thailand.,Gastrointestinal and Liver Center, Bangkok Medical Center, Bangkok, Thailand
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
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41
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Yang T, Hu R, Tang X, Shen Y, Tay A, Pi X, Wang G, Debowski AW, Stubbs KA, Benghezal M, Marshall BJ, Li H, Tang H. Susceptibility-guided bismuth quadruple therapies for resistant Helicobacter pylori infections. PRECISION CLINICAL MEDICINE 2020; 3:127-135. [PMID: 35692608 PMCID: PMC8985787 DOI: 10.1093/pcmedi/pbaa010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/11/2020] [Accepted: 03/15/2020] [Indexed: 02/05/2023] Open
Abstract
Increasing Helicobacter pylori resistance to antibiotics has ledthat molecular testing is appropriate as a sub to adoption of seven different bismuth quadruple therapies (BQT) in China without differentiation of first-line or second-line regimens. The objective of this study was to evaluate the efficacy of susceptibility-guided BQT for patients who had experienced previous treatment failures. A total of 133 patients was included and H. pylori was successfully cultured from 101 patients (75.9%) for subsequent antimicrobial susceptibility testing (AST). Based on the AST results, 88 patients completed one of five AST-guided 14-day BQT regimens: esomeprazole and bismuth colloidal pectin, along with either, amoxicillin and clarithromycin (EBAC), amoxicillin and levofloxacin (EBAL), amoxicillin and furazolidone (EBAF), amoxicillin and tetracycline (EBAT), or tetracycline and furazolidone (EBTF). H. pylori eradication rates were 100% for EBAC (5/5), EBAL (13/13), EBAF (14/14), and EBTF (43/43), but 76.9% for EBAT (10/13). The three patients that failed the EBAT regimen were all cured after subsequent treatment with the EBTF regimen. Our study demonstrates the excellent efficacy of the AST-guided BQT for referred H. pylori patients, and that the current EBAT regimen, used in clinics, needs to be optimized. In addition, 57 of the isolates were subjected to whole-genome sequencing. Analysis of the sequences revealed that point mutations in 23S rRNA correlated well with the phenotypic clarithromycin resistance with a concordance of 91.2%, while the concordance between phenotypic levofloxacin resistance and gyrA point mutations was 82.3%. This suggests that molecular testing is appropriate as a substitute for AST as a more rapid and cost-effective method for determining clarithromycin and levofloxacin resistance in Chinese patients.
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Affiliation(s)
- Tiankuo Yang
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Renwei Hu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoqiong Tang
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yalin Shen
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Alfred Tay
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands 6009, Australia
| | - Xuenan Pi
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Chengdu 610041, China
| | - Gang Wang
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Chengdu 610041, China
| | - Aleksandra W Debowski
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands 6009, Australia
- School of Molecular Sciences, University of Western Australia, Nedlands 6009, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, Nedlands 6009, Australia
| | - Mohammed Benghezal
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Barry J Marshall
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands 6009, Australia
| | - Hong Li
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hong Tang
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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42
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Saranathan R, Levi MH, Wattam AR, Malek A, Asare E, Behin DS, Pan DH, Jacobs WR, Szymczak WA. Helicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing. J Clin Microbiol 2020; 58:e01591-19. [PMID: 31801839 PMCID: PMC7041580 DOI: 10.1128/jcm.01591-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022] Open
Abstract
The emergence of drug resistance in Helicobacter pylori has resulted in a greater need for susceptibility-guided treatment. While the alleles associated with resistance to clarithromycin and levofloxacin have been defined, there are limited data regarding the molecular mechanisms underlying resistance to other antimicrobials. Using H. pylori isolates from 42 clinical specimens, we compared phenotypic and whole-genome sequencing (WGS)-based detection of resistance. Phenotypic resistance correlated with the presence of alleles of 23S rRNA (A2142G/A2143G) for clarithromycin (kappa coefficient, 0.84; 95% confidence interval [CI], 0.67 to 1.0) and gyrA (N87I/N87K/D91Y/D91N/D91G/D99N) for levofloxacin (kappa coefficient, 0.90; 95% CI, 0.77 to 1.0). Phenotypic resistance to amoxicillin in three isolates correlated with mutations in pbp1, pbp2, and/or pbp3 within coding regions near known amoxicillin binding motifs. All isolates were phenotypically susceptible to tetracycline, although four bore a mutation in 16S rRNA (A926G). For metronidazole, nonsense mutations and R16H substitutions in rdxA correlated with phenotypic resistance (kappa coefficient, 0.76; 95% CI, 0.56 to 0.96). Previously identified mutations in the rpoB rifampin resistance-determining region (RRDR) were not present, but 14 novel mutations outside the RRDR were found in rifampin-resistant isolates. WGS also allowed for strain lineage determination, which may be important for future studies in associating precise MICs with specific resistance alleles. In summary, WGS allows for broad analyses of H. pylori isolates, and our findings support the use of WGS for the detection of clarithromycin and levofloxacin resistance. Additional studies are warranted to better define mutations conferring resistance to amoxicillin, tetracycline, and rifampin, but combinatorial analyses for rdxA gene truncations and R16H mutations have utility for determining metronidazole resistance.
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Affiliation(s)
- Rajagopalan Saranathan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Michael H Levi
- Department of Pathology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Alice R Wattam
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, Virginia, USA
| | - Adel Malek
- Provincial Public Health Laboratory, Eastern Health Microbiology Services, St. John's, New Foundland and Labrador, Canada
| | - Emmanuel Asare
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Pathology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Daniel S Behin
- Department of Medicine, Division of Gastroenterology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Debra H Pan
- Department of Pediatrics, Division of Gastroenterology and Nutrition, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Wendy A Szymczak
- Department of Pathology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
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43
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Shimazawa R, Ikeda M. Regulatory perspectives on next-generation sequencing and complementary diagnostics in Japan. Expert Rev Mol Diagn 2020; 20:601-610. [DOI: 10.1080/14737159.2020.1728256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rumiko Shimazawa
- Department of Clinical Pharmacology, Tokai University School of Medicine, Isehara, Japan
| | - Masayuki Ikeda
- Department of Medical Informatics, Kagawa University Hospital, Takamatsu, Japan
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44
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Ansari S, Yamaoka Y. Helicobacter pylori Virulence Factors Exploiting Gastric Colonization and its Pathogenicity. Toxins (Basel) 2019; 11:E677. [PMID: 31752394 PMCID: PMC6891454 DOI: 10.3390/toxins11110677] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/15/2019] [Accepted: 11/16/2019] [Indexed: 02/07/2023] Open
Abstract
Helicobacter pylori colonizes the gastric epithelial cells of at least half of the world's population, and it is the strongest risk factor for developing gastric complications like chronic gastritis, ulcer diseases, and gastric cancer. To successfully colonize and establish a persistent infection, the bacteria must overcome harsh gastric conditions. H. pylori has a well-developed mechanism by which it can survive in a very acidic niche. Despite bacterial factors, gastric environmental factors and host genetic constituents together play a co-operative role for gastric pathogenicity. The virulence factors include bacterial colonization factors BabA, SabA, OipA, and HopQ, and the virulence factors necessary for gastric pathogenicity include the effector proteins like CagA, VacA, HtrA, and the outer membrane vesicles. Bacterial factors are considered more important. Here, we summarize the recent information to better understand several bacterial virulence factors and their role in the pathogenic mechanism.
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Affiliation(s)
- Shamshul Ansari
- Department of Microbiology, Chitwan Medical College and Teaching Hospital, Bharatpur 44200, Chitwan, Nepal;
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Idaigaoka, Hasama-machi, Yufu, Oita 879-5593, Japan
- Global Oita Medical Advanced Research Center for Health, Idaigaoka, Hasama-machi, Yufu, Oita 879-5593, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, 2002 Holcombe Blvd., Houston, TX 77030, USA
- Borneo Medical and Health Research Centre, Universiti Malaysia Sabah, Kota Kinabaru, Sabah 88400, Malaysia
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45
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Prevalence of Infection and Antibiotic Susceptibility of Helicobacter pylori: An Evaluation in Public and Private Health Systems of Southern Chile. Pathogens 2019; 8:pathogens8040226. [PMID: 31717523 PMCID: PMC6963584 DOI: 10.3390/pathogens8040226] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 12/21/2022] Open
Abstract
Helicobacter pylori colonizes half of the human population. Age, ethnicity, and socioeconomic status are factors that influence the prevalence of the infection. This is important in southern Chile, one of the most unequal regions in the world, where a significant difference in the health access of the population occurs due to the existence of two competing health systems. Moreover, in the last few years, current protocols of H. pylori eradication have shown high rates of resistance with reduced therapeutic efficacy. This study reported the epidemiology of infection and attempted to identify divergent points among the population beneficiaries of the two health care schemes in southern Chile. Biopsies from public (n = 143) and private (n = 86) health systems were studied. At the same time, clinical and sociodemographic factors were evaluated. H. pylori strains were obtained from gastric biopsies for culture and molecular testing. Antibiotic susceptibility was determined by the agar dilution method. Differences about ethnicity, rural residence, and education (p ≤ 0.05) were observed between beneficiaries of the two health systems. The prevalence of H. pylori was 45%, with no significant differences regardless of the socioeconomic conditions. The only identified risk factor associated with H. pylori infection was Mapuche ethnicity (OR (odds ratio) = 2.30). H. pylori showed high resistance rates, particularly against clarithromycin (40%), levofloxacin (43.1%), and metronidazole (81.8%). This study highlighted the importance of Mapuche ancestry as a risk factor in southern Chile and emphasized the need to search for new eradication strategies as well as further studies evaluating therapeutic efficacy.
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Singh A, Singh PK, Sharma AK, Singh NK, Sonah H, Deshmukh R, Sharma TR. Understanding the Role of the WRKY Gene Family under Stress Conditions in Pigeonpea ( Cajanus Cajan L.). PLANTS 2019; 8:plants8070214. [PMID: 31295921 PMCID: PMC6681228 DOI: 10.3390/plants8070214] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/26/2022]
Abstract
Pigeonpea (Cajanus cajan L.), a protein-rich legume, is a major food component of the daily diet for residents in semi-arid tropical regions of the word. Pigeonpea is also known for its high level of tolerance against biotic and abiotic stresses. In this regard, understanding the genes involved in stress tolerance has great importance. In the present study, identification, and characterization of WRKY, a large transcription factor gene family involved in numerous biological processes like seed germination, metabolism, plant growth, biotic and abiotic stress responses was performed in pigeonpea. A total of 94 WRKY genes identified in the pigeonpea genome were extensively characterized for gene-structures, localizations, phylogenetic distribution, conserved motif organizations, and functional annotation. Phylogenetic analysis revealed three major groups (I, II, and III) of pigeonpea WRKY genes. Subsequently, expression profiling of 94 CcWRKY genes across different tissues like root, nodule, stem, petiole, petal, sepal, shoot apical meristem (SAM), mature pod, and mature seed retrieved from the available RNAseq data identified tissue-specific WRKY genes with preferential expression in the vegetative and reproductive stages. Gene co-expression networks identified four WRKY genes at the center of maximum interaction which may play a key role in the entire WRKY regulations. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) expression analysis of WRKY genes in root and leaf tissue samples from plants under drought and salinity stress identified differentially expressed WRKY genes. The study will be helpful to understand the evolution, regulation, and distribution of the WRKY gene family, and additional exploration for the development of stress tolerance cultivars in pigeonpea and other legumes crops.
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Affiliation(s)
- Akshay Singh
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
- Dr. A. P. J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh 226031, India
| | | | - Ajay Kumar Sharma
- Meerut Institute of Engineering and Technology, Meerut, Uttar Pradesh 250005, India
| | | | - Humira Sonah
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India.
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