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Mehrotra T, Devi TB, Kumar S, Talukdar D, Karmakar SP, Kothidar A, Verma J, Kumari S, Alexander SM, Retnakumar RJ, Devadas K, Ray A, Mutreja A, Nair GB, Chattopadhyay S, Das B. Antimicrobial resistance and virulence in Helicobacter pylori: Genomic insights. Genomics 2021; 113:3951-3966. [PMID: 34619341 DOI: 10.1016/j.ygeno.2021.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/10/2021] [Accepted: 10/01/2021] [Indexed: 12/26/2022]
Abstract
Microbes evolve rapidly by modifying their genome through mutations or acquisition of genetic elements. Antimicrobial resistance in Helicobacter pylori is increasingly prevalent in India. However, limited information is available about the genome of resistant H. pylori isolated from India. Our pan- and core-genome based analyses of 54 Indian H. pylori strains revealed plasticity of its genome. H. pylori is highly heterogenous both in terms of the genomic content and DNA sequence homology of ARGs and virulence factors. We observed that the H. pylori strains are clustered according to their geographical locations. The presence of point mutations in the ARGs and absence of acquired genetic elements linked with ARGs suggest target modifications are the primary mechanism of its antibiotic resistance. The findings of the present study would help in better understanding the emergence of drug-resistant H. pylori and controlling gastric disorders by advancing clinical guidance on selected treatment regimens.
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Affiliation(s)
- Tanshi Mehrotra
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - T Barani Devi
- Microbiome Laboratory, Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | - Shakti Kumar
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Daizee Talukdar
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Sonali Porey Karmakar
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Akansha Kothidar
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Jyoti Verma
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Shashi Kumari
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Sneha Mary Alexander
- Microbiome Laboratory, Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | - R J Retnakumar
- Microbiome Laboratory, Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | - Krishnadas Devadas
- Department of Gastroenterology, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Animesh Ray
- Department of Medicine, All India Institute of Medical, Science, New Delhi, India
| | - Ankur Mutreja
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India; Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge CB20QQ, United Kingdom
| | - G Balakrish Nair
- Microbiome Laboratory, Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | - Santanu Chattopadhyay
- Microbiome Laboratory, Pathogen Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India.
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India.
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Abstract
Alternate remedies with natural products provides unlimited opportunities for new drug development. These can be either as pure compounds or as standardized set of compounds. The phytochemicals and secondary metabolites are in great demand for screening bioactive compounds and plays an important role towards drug development. Natural products have many advantages over to synthetic chemical drugs. Helicobacter pylori (H. pylori) a Gram-negative bacteria has been classified as Class I carcinogen by World Health Organization in 1994. Current treatment regimens for H. pylori is ‘triple therapy’ administrated for two weeks which includes a combination of two antibiotics like Amoxicillin and Clarithromycin and a proton pump inhibitor (PPI) like Lansoprazole, and for ‘quadruple therapy’ in addition to antibiotics and a PPI, Bismuth is used. Antibiotic resistance can be named as the main factor for failure of treatment of H. pylori infection. The need of the hour is to develop a herbal remedy that could combat the growth of H. pylori. Probiotics can also be used as ‘feasible’ tool for H. pylori infection management. Present review is an attempt to briefly discuss about the pathogenicity, genetic predisposition, perturbation of gut microbiota due to antibiotic treatment and restoration of healthy gut microbiota with phytochemicals and probiotics.
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Shetty V, Lamichhane B, Tay CY, Pai GC, Lingadakai R, Balaraju G, Shetty S, Ballal M, Chua EG. High primary resistance to metronidazole and levofloxacin, and a moderate resistance to clarithromycin in Helicobacter pylori isolated from Karnataka patients. Gut Pathog 2019; 11:21. [PMID: 31110563 PMCID: PMC6513510 DOI: 10.1186/s13099-019-0305-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/02/2019] [Indexed: 12/16/2022] Open
Abstract
Background Due to increased prevalence of H. pylori antimicrobial resistance worldwide and more importantly the resistance patterns vary between different geographical regions, it is important to survey local H. pylori antibiotic resistance profile to provide physicians with more informed drug choices to better treat H. pylori infection. To our knowledge, this is the first study to examine the prevalence of antimicrobial resistance of H. pylori in Karnataka state of South India. Results A total of 113 H. pylori strains were isolated from gastric biopsies and tested: 81.4% were resistant to metronidazole, 54.9% were resistant to levofloxacin, 20.4% were resistant to clarithromycin, 5.3% were resistant to tetracycline and 7.1% were resistant to amoxicillin. Multidrug resistance was detected in 59.3% of total isolated strains, among which 86.6% were resistant to at least both metronidazole and levofloxacin. In this study, 38 out of 113 H. pylori strains had been whole-genome sequenced. Based on the draft genomes, RdxA and/or FrxA inactivation mutations were found to present in 75% of metronidazole-resistant strains. Clarithromycin-resistant strains had mainly A2143G and G2224A mutations in the 23 rRNA gene. While 87.1% levofloxacin-resistant strains had amino acid substitution mutations occurring predominantly at N87 and D91 in GyrA, novel mutations in the same protein including an insertion of five amino acid residues (QDNSV), immediately after the start codon, and a substitution mutation at R295 were identified. Conclusion High primary resistance to metronidazole and levofloxacin, and a modest occurrence of clarithromycin resistance were revealed in H. pylori strains isolated from Karnataka patients. Therefore metronidazole-, levofloxacin- and clarithromycin-based triple therapies are not suitable as first-line treatment in Karnataka. Both amoxicillin and tetracycline can still be used to eradicate H. pylori infection in this region. We also revealed novel mutations in GyrA protein that possibly contribute to H. pylori resistance in levofloxacin, which merit further investigations.
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Affiliation(s)
- Vignesh Shetty
- 1Enteric Diseases Division, Central Research Lab, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Binit Lamichhane
- 2Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA Australia
| | - Chin Yen Tay
- 2Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA Australia.,Shenzhen Dapeng New District Kuichong People Hospital, Shenzhen City, Guangdong Province China
| | - Ganesh C Pai
- 4Department of Gastroenterology & Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Ramachandra Lingadakai
- 5Department of Surgery, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Girisha Balaraju
- 4Department of Gastroenterology & Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Shiran Shetty
- 4Department of Gastroenterology & Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Mamatha Ballal
- 1Enteric Diseases Division, Central Research Lab, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Eng Guan Chua
- 2Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA Australia
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