1
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Dessenne C, Mariller C, Vidal O, Huvent I, Guerardel Y, Elass-Rochard E, Rossez Y. Glycan-mediated adhesion mechanisms in antibiotic-resistant bacteria. BBA ADVANCES 2025; 7:100156. [PMID: 40207210 PMCID: PMC11979486 DOI: 10.1016/j.bbadva.2025.100156] [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: 11/29/2024] [Revised: 03/10/2025] [Accepted: 03/13/2025] [Indexed: 04/11/2025] Open
Abstract
Bacterial adhesins play a central role in host-pathogen interactions, with many specifically targeting glycans to mediate bacterial colonization, influence infection dynamics, and evade host immune responses. In this review, we focus on bacterial pathogens identified by the World Health Organization as critical threats to public health and in urgent need of new treatments. We summarize glycoconjugate targets identified in the literature across 19 bacterial genera and species. This comprehensive review provides a foundation for the development of innovative therapeutic strategies to effectively combat these pathogens.
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Affiliation(s)
- Clara Dessenne
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Christophe Mariller
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Olivier Vidal
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Isabelle Huvent
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Yann Guerardel
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan
| | - Elisabeth Elass-Rochard
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Yannick Rossez
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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2
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Tourrette E, Torres RC, Svensson SL, Matsumoto T, Miftahussurur M, Fauzia KA, Alfaray RI, Vilaichone RK, Tuan VP, Wang D, Yadegar A, Olsson LM, Zhou Z, Yamaoka Y, Thorell K, Falush D. An ancient ecospecies of Helicobacter pylori. Nature 2024; 635:178-185. [PMID: 39415013 PMCID: PMC11541087 DOI: 10.1038/s41586-024-07991-z] [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: 08/04/2023] [Accepted: 08/23/2024] [Indexed: 10/18/2024]
Abstract
Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer1,2. Numerous H. pylori virulence factors have been identified, showing extensive geographic variation1. Here we identify a 'Hardy' ecospecies of H. pylori that shares the ancestry of 'Ubiquitous' H. pylori from the same region in most of the genome but has nearly fixed single-nucleotide polymorphism differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. Most Hardy strains have a second urease, which uses iron as a cofactor rather than nickel3, and two additional copies of the vacuolating cytotoxin VacA. Hardy strains currently have a limited distribution, including in Indigenous populations in Siberia and the Americas and in lineages that have jumped from humans to other mammals. Analysis of polymorphism data implies that Hardy and Ubiquitous coexisted in the stomachs of modern humans since before we left Africa and that both were dispersed around the world by our migrations. Our results also show that highly distinct adaptive strategies can arise and be maintained stably within bacterial populations, even in the presence of continuous genetic exchange between strains.
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Affiliation(s)
- Elise Tourrette
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Roberto C Torres
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Sarah L Svensson
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | | | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
- Universitas Airlangga, Surabaya, Indonesia
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
- Universitas Airlangga, Surabaya, Indonesia
| | - Ratha-Korn Vilaichone
- Gastroenterology Unit, Department of Medicine and Center of Excellence in Digestive Diseases, Thammasat University, Bangkok, Thailand
| | - Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
- Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Difei Wang
- Cancer Genomics Research Lab, Frederick National Lab for Cancer Research, Rockville, MD, USA
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Lisa M Olsson
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Zhemin Zhou
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan.
- Universitas Airlangga, Surabaya, Indonesia.
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, USA.
- Research center for global and local infectious diseases, Oita University, Yufu, Japan.
| | - Kaisa Thorell
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden.
| | - Daniel Falush
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
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3
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González-Stegmaier R, Aguila-Torres P, Villarroel-Espíndola F. Historical and Molecular Perspectives on the Presence of Helicobacter pylori in Latin America: A Niche to Improve Gastric Cancer Risk Assessment. Int J Mol Sci 2024; 25:1761. [PMID: 38339039 PMCID: PMC10855479 DOI: 10.3390/ijms25031761] [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: 01/16/2024] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Helicobacter pylori (H. pylori) is responsible for causing chronic gastritis, which can cause peptic ulcer and premalignant lesions such as atrophic gastritis, intestinal metaplasia, and dysplasia, with the risk of developing gastric cancer. Recent data describe that H. pylori colonizes the gastric mucosa of more than 50% of the world's population; however, this bacterium has been described as infecting the human population since its prehistory. This review focuses on the populations and subpopulations of H. pylori, differentiated by the polymorphisms present in their constitutive and virulence genes. These genes have spread and associated with different human populations, showing variability depending on their geographical distribution, and have evolved together with the human being. The predominant genotypes worldwide, Latin America and Chile, are described to understand the genetic diversity and pathogenicity of H. pylori in different populations and geographic regions. The high similarity in the sequence of virulence genes between H. pylori strains present in Peruvian and Spanish natives in Latin America suggests a European influence. The presence of cagA-positive strains and vacA s1 m1 allelic variants is observed with greater prevalence in Chilean patients with more severe gastrointestinal diseases and is associated with its geographical distribution. These findings highlight the importance of understanding the genetic diversity of H. pylori in different regions of the world for a more accurate assessment of the risk of associated diseases and their potential impact on health.
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Affiliation(s)
- Roxana González-Stegmaier
- Traslational Medicine Laboratory, Instituto Oncológico Fundación Arturo López Pérez, Santiago 7500000, Chile;
| | - Patricia Aguila-Torres
- Laboratorio de Microbiología Molecular, Escuela de Tecnología Médica, Universidad Austral de Chile, Puerto Montt 5480000, Chile;
| | - Franz Villarroel-Espíndola
- Traslational Medicine Laboratory, Instituto Oncológico Fundación Arturo López Pérez, Santiago 7500000, Chile;
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4
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Vital JS, Tanoeiro L, Lopes-Oliveira R, Vale FF. Biomarker Characterization and Prediction of Virulence and Antibiotic Resistance from Helicobacter pylori Next Generation Sequencing Data. Biomolecules 2022; 12:691. [PMID: 35625618 PMCID: PMC9138241 DOI: 10.3390/biom12050691] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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Affiliation(s)
- Joana S. Vital
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
| | - Luís Tanoeiro
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
| | - Ricardo Lopes-Oliveira
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
| | - Filipa F. Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
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5
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Wilkinson DJ, Dickins B, Robinson K, Winter JA. Genomic diversity of Helicobacter pylori populations from different regions of the human stomach. Gut Microbes 2022; 14:2152306. [PMID: 36469575 PMCID: PMC9728471 DOI: 10.1080/19490976.2022.2152306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Individuals infected with Helicobacter pylori harbor unique and diverse populations of quasispecies, but diversity between and within different regions of the human stomach and the process of bacterial adaptation to each location are not yet well understood. We applied whole-genome deep sequencing to characterize the within- and between-stomach region genetic diversity of H. pylori populations from paired antrum and corpus biopsies of 15 patients, along with single biopsies from one region of an additional 3 patients, by scanning allelic diversity. We combined population deep sequencing with more conventional sequencing of multiple H. pylori single colony isolates from individual biopsies to generate a unique dataset. Single colony isolates were used to validate the scanning allelic diversity pipelines. We detected extensive population allelic diversity within the different regions of each patient's stomach. Diversity was most commonly found within non-coding, hypothetical, outer membrane, restriction modification system, virulence, lipopolysaccharide biosynthesis, efflux systems, and chemotaxis-associated genes. Antrum and corpus populations from the same patient grouped together phylogenetically, indicating that most patients were initially infected with a single strain, which then diversified. Single colonies from the antrum and corpus of the same patients grouped into distinct clades, suggesting mechanisms for within-location adaptation across multiple H. pylori isolates from different patients. The comparisons made available by combined sequencing and analysis of isolates and populations enabled comprehensive analysis of the genetic changes associated with H. pylori diversification and stomach region adaptation.
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Affiliation(s)
- Daniel James Wilkinson
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
- School of Science and Technology, Nottingham Trent University, UK
| | - Benjamin Dickins
- School of Science and Technology, Nottingham Trent University, UK
| | - Karen Robinson
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Jody Anne Winter
- School of Science and Technology, Nottingham Trent University, UK
- CONTACT Jody Anne Winter School of Science and Technology, Nottingham Trent University Clifton Campus, Clifton Lane, NottinghamNG118NS, UK
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6
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Miller AK, Williams SM. Helicobacter pylori infection causes both protective and deleterious effects in human health and disease. Genes Immun 2021; 22:218-226. [PMID: 34244666 PMCID: PMC8390445 DOI: 10.1038/s41435-021-00146-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/18/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
Infection with Helicobacter pylori (H. pylori) is necessary but not sufficient for the development of gastric cancer, the third leading cause of cancer death globally. H. pylori infection affects over half of people globally; however, it does not affect populations uniformly. H. pylori infection rates are declining in western industrialized countries but are plateauing in developing and newly industrialized countries where gastric cancer is most prevalent. Despite H. pylori infection being the primary causative agent for gastric cancer, H. pylori infection can also cause other effects, detrimental or beneficial, throughout an individual's life, with the beneficial effects often being seen in childhood and the deleterious effects in adulthood. H. pylori is an ancient bacterium and its likelihood of affecting disease or health is dependent on both human and bacterial genetics that have co-evolved over millennia. In this review, we focus on the impact of infection and its genetic bases in different populations and diseases throughout an individual's lifespan, highlighting the benefits of individualized treatment and argue that universal eradication of H. pylori in its host may cause more harm than good for those infected with H. pylori.
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Affiliation(s)
- Anna K Miller
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH
| | - Scott M Williams
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH
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7
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Muñoz-Ramirez ZY, Pascoe B, Mendez-Tenorio A, Mourkas E, Sandoval-Motta S, Perez-Perez G, Morgan DR, Dominguez RL, Ortiz-Princz D, Cavazza ME, Rocha G, Queiroz DMM, Catalano M, Palma GZD, Goldman CG, Venegas A, Alarcon T, Oleastro M, Vale FF, Goodman KJ, Torres RC, Berthenet E, Hitchings MD, Blaser MJ, Sheppard SK, Thorell K, Torres J. A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas. THE ISME JOURNAL 2021; 15:78-92. [PMID: 32879462 PMCID: PMC7853065 DOI: 10.1038/s41396-020-00758-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/27/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori is a common component of the human stomach microbiota, possibly dating back to the speciation of Homo sapiens. A history of pathogen evolution in allopatry has led to the development of genetically distinct H. pylori subpopulations, associated with different human populations, and more recent admixture among H. pylori subpopulations can provide information about human migrations. However, little is known about the degree to which some H. pylori genes are conserved in the face of admixture, potentially indicating host adaptation, or how virulence genes spread among different populations. We analyzed H. pylori genomes from 14 countries in the Americas, strains from the Iberian Peninsula, and public genomes from Europe, Africa, and Asia, to investigate how admixture varies across different regions and gene families. Whole-genome analyses of 723 H. pylori strains from around the world showed evidence of frequent admixture in the American strains with a complex mosaic of contributions from H. pylori populations originating in the Americas as well as other continents. Despite the complex admixture, distinctive genomic fingerprints were identified for each region, revealing novel American H. pylori subpopulations. A pan-genome Fst analysis showed that variation in virulence genes had the strongest fixation in America, compared with non-American populations, and that much of the variation constituted non-synonymous substitutions in functional domains. Network analyses suggest that these virulence genes have followed unique evolutionary paths in the American populations, spreading into different genetic backgrounds, potentially contributing to the high risk of gastric cancer in the region.
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Affiliation(s)
- Zilia Y Muñoz-Ramirez
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
- Laboratorio de Bioinformática y Biotecnología Genómica, Escuela Nacional de Ciencias Biológicas, Unidad Profesional Lázaro Cárdenas, Instituto Politécnico Nacional, 11340, Mexico City, Mexico
| | - Ben Pascoe
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK
| | - Alfonso Mendez-Tenorio
- Laboratorio de Bioinformática y Biotecnología Genómica, Escuela Nacional de Ciencias Biológicas, Unidad Profesional Lázaro Cárdenas, Instituto Politécnico Nacional, 11340, Mexico City, Mexico
| | - Evangelos Mourkas
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK
| | - Santiago Sandoval-Motta
- Instituto Nacional de Medicina Genomica, Ciudad de México, México
- Consejo Nacional de Ciencia y Tecnologia, Catedras CONACYT, Ciudad de México, México
| | | | - Douglas R Morgan
- UAB Division of Gastroenterology and Hepatology, The University of Alabama at Birmingham, Birmingham, UK
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University, Nashville, TN, USA
| | - Ricardo Leonel Dominguez
- Western Honduras Gastric Cancer Prevention Initiative Hospital de Occidente Santa Rosa de Copan, Santa Rosa de Copan, Honduras
| | - Diana Ortiz-Princz
- Laboratorio de Microbiología Molecular, Servicio Instituto de Biomedicina MPPS-UCV, Caracas, Venezuela
| | - Maria Eugenia Cavazza
- Laboratorio de Microbiología Molecular, Servicio Instituto de Biomedicina MPPS-UCV, Caracas, Venezuela
| | - Gifone Rocha
- Faculdade de Medicina da UFMG, Belo Horizonte, Brazil
| | | | - Mariana Catalano
- Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPAM, UBA-CONICET), Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Rosa de Copan, Honduras
| | - Gerardo Zerbetto De Palma
- Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini", IQUIFIB UBA-CONICET, Santa Rosa de Copan, Honduras
| | - Cinthia G Goldman
- Facultad de Farmacia y Bioquímica, Cátedra de Física, Universidad de Buenos Aires, C1113AAD, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), C1425FQB, Buenos Aires, Argentina
| | - Alejandro Venegas
- Laboratorio de Patogénesis Microbiana, Centro de Investigación Biomédica, Universidad Diego Portales, Ejército, 141, Santiago, Chile
| | - Teresa Alarcon
- Department of Microbiology, Hospital Universitario La Princesa, Instituto de Investigación Sanitaria Princesa, Madrid, Spain
| | - Monica Oleastro
- Host-Pathogen Interactions Unit, Faculty of Pharmacy, Research Institute for Medicines (iMed-ULisboa), Universidade de Lisboa, Lisboa, Portugal
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Faculty of Pharmacy, Research Institute for Medicines (iMed-ULisboa), Universidade de Lisboa, Lisboa, Portugal
| | - Karen J Goodman
- Division of Gastroenterology, Centre of Excellence for Gastrointestinal Inflammation & Immunity Research, University of Alberta, Edmonton, AB, Canada
| | - Roberto C Torres
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Elvire Berthenet
- Swansea University Medical School, Swansea University, Swansea, UK
| | | | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Samuel K Sheppard
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK
| | - Kaisa Thorell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Javier Torres
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico.
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8
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Baj J, Forma A, Sitarz M, Portincasa P, Garruti G, Krasowska D, Maciejewski R. Helicobacter pylori Virulence Factors-Mechanisms of Bacterial Pathogenicity in the Gastric Microenvironment. Cells 2020; 10:27. [PMID: 33375694 PMCID: PMC7824444 DOI: 10.3390/cells10010027] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
Gastric cancer constitutes one of the most prevalent malignancies in both sexes; it is currently the fourth major cause of cancer-related deaths worldwide. The pathogenesis of gastric cancer is associated with the interaction between genetic and environmental factors, among which infection by Helicobacter pylori (H. pylori) is of major importance. The invasion, survival, colonization, and stimulation of further inflammation within the gastric mucosa are possible due to several evasive mechanisms induced by the virulence factors that are expressed by the bacterium. The knowledge concerning the mechanisms of H. pylori pathogenicity is crucial to ameliorate eradication strategies preventing the possible induction of carcinogenesis. This review highlights the current state of knowledge and the most recent findings regarding H. pylori virulence factors and their relationship with gastric premalignant lesions and further carcinogenesis.
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Affiliation(s)
- Jacek Baj
- Department of Anatomy, Medical University of Lublin, 20-400 Lublin, Poland;
| | - Alicja Forma
- Chair and Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland;
| | - Monika Sitarz
- Department of Conservative Dentistry with Endodontics, Medical University of Lublin, 20-090 Lublin, Poland;
| | - Piero Portincasa
- Clinica Medica “Augusto Murri”, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Gabriella Garruti
- Section of Endocrinology, Department of Emergency and Organ Transplantations, University of Bari “Aldo Moro” Medical School, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Danuta Krasowska
- Department of Dermatology, Venerology and Paediatric Dermatology of Medical University of Lublin, 20-081 Lublin, Poland;
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9
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Hanafiah A, Lopes BS. Genetic diversity and virulence characteristics of Helicobacter pylori isolates in different human ethnic groups. INFECTION GENETICS AND EVOLUTION 2019; 78:104135. [PMID: 31837482 DOI: 10.1016/j.meegid.2019.104135] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 12/03/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori is the most predominant bacterium in almost 50% of the world's population and colonization causes a persistent inflammatory response leading to chronic gastritis. It shows high genetic diversity and individuals generally harbour a distinct bacterial population. With the advancement of whole-genome sequencing technology, new H. pylori subpopulations have been identified that show admixture between various H. pylori strains. Genotypic variation of H. pylori may be related to the presence of virulence factors among strains and is associated with different outcomes of infection in different individuals. This review summarizes the genetic diversity in H. pylori strain populations and its virulence characteristics responsible for variable outcomes in different ethnic groups.
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Affiliation(s)
- Alfizah Hanafiah
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Bruno S Lopes
- Department of Medical Microbiology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, 0:025 Polwarth Building, Aberdeen AB25 2ZD, United Kingdom.
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10
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Pohl D, Keller PM, Bordier V, Wagner K. Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing. World J Gastroenterol 2019; 25:4629-4660. [PMID: 31528091 PMCID: PMC6718044 DOI: 10.3748/wjg.v25.i32.4629] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/25/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers, mucosa associated tissue lymphoma and gastric adenocarcinoma. In recent years, an alarming increase in antimicrobial resistance and subsequently failing empiric H. pylori eradication therapies have been noted worldwide, also in many European countries. Therefore, rapid and accurate determination of H. pylori’s antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important. Traditionally, detection of H. pylori and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long turn-around-time. Recent advances in diagnostics provide new tools, like real-time polymerase chain reaction (PCR) and line probe assays, to diagnose H. pylori infection and antimicrobial resistance to certain antibiotics, directly from clinical specimens. Moreover, high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen’s genome, thereby allowing identification of resistance mutations and associated antibiotic resistance. In the first part of this review, we will give an overview on currently available diagnostic methods for detection of H. pylori and its drug resistance and their implementation in H. pylori management. The second part of the review focusses on the use of next generation sequencing technology in H. pylori research. To this end, we conducted a literature search for original research articles in English using the terms “Helicobacter”, “transcriptomic”, “transcriptome”, “next generation sequencing” and “whole genome sequencing”. This review is aimed to bridge the gap between current diagnostic practice (histology, rapid urease test, H. pylori culture, PCR and line probe assays) and new sequencing technologies and their potential implementation in diagnostic laboratory settings in order to complement the currently recommended H. pylori management guidelines and subsequently improve public health.
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Affiliation(s)
- Daniel Pohl
- Division of Gastroenterology, University Hospital of Zurich, Zurich 8006, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases, University of Bern, Bern 3010, Switzerland
| | - Valentine Bordier
- Division of Gastroenterology, University Hospital of Zurich, Zurich 8006, Switzerland
| | - Karoline Wagner
- Institute of Medical Microbiology, University of Zurich, Zurich 8006, Switzerland
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11
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Gutiérrez-Escobar AJ, Bravo MM, Acevedo O, Backert S. Molecular evolution of the VacA p55 binding domain of Helicobacter pylori in mestizos from a high gastric cancer region of Colombia. PeerJ 2019; 7:e6634. [PMID: 31119065 PMCID: PMC6507892 DOI: 10.7717/peerj.6634] [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: 09/07/2018] [Accepted: 02/18/2019] [Indexed: 11/20/2022] Open
Abstract
The stomach bacterium Helicobacter pylori is one of the most prevalent pathogens in humans, closely linked with serious diseases such as gastric cancer. The microbe has been associated with its host for more than 100,000 years and escorted modern humans out of Africa. H. pylori is predominantly transmitted within families and dispersed globally, resulting in distinct phylogeographic patterns, which can be utilized to investigate migrations and bioturbation events in human history. Latin America was affected by several human migratory waves due to the Spanish colonisation that drastically changed the genetic load and composition of the bacteria and its host. Genetic evidence indicates that independent evolutionary lines of H. pylori have evolved in mestizos from Colombia and other countries in the region during more than 500 years since colonisation. The vacuolating cytotoxin VacA represents a major virulence factor of the pathogen comprising two domains, p33 and p55, the latter of which is essential for binding to the host epithelial cell. The evolution of the VacA toxin in Colombia has been strongly biased due to the effects of Spanish colonization. However, the variation patterns and microevolution of the p55 domain have not yet been described for this population. In the present study, we determined the genetic polymorphisms and deviations in the neutral model of molecular evolution in the p55 domain of 101 clinical H. pylori isolates collected in Bogotá, a city located in Andean mountains characterized by its high gastric cancer risk and its dominant mestizo population. The microevolutionary patterns of the p55 domain were shaped by recombination, purifying and episodic diversifying positive selection. Furthermore, amino acid positions 261 and 321 in the p55 domain of VacA show a high variability among mestizos clinical subsets, suggesting that natural selection in H. pylori may operate differentially in patients with different gastric diseases.
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Affiliation(s)
- Andrés J. Gutiérrez-Escobar
- Universidad de Ciencias Aplicadas y Ambientales U.D.C.A. Doctorado en Ciencias Biológicas, Pontificia Universidad Javeriana., Bogotá, Colombia
- Division of Microbiology, Department of Biology, Friedrich Alexander University Erlangen/Nuremberg, Erlangen, Germany
| | - María M. Bravo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Orlando Acevedo
- Grupo de Biofísica y Bioquímica Estructural, Facultad de Ciencias, Pontifica Universidad Javeriana, Bogotá, Colombia
| | - Steffen Backert
- Division of Microbiology, Department of Biology, Friedrich Alexander University Erlangen/Nuremberg, Erlangen, Germany
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12
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Wong C, Zhang S, Adam E, Paszat L, Butel JS. SV40 seroprevalence in two Latin American countries involved in field trials of candidate oral poliovaccines. J Infect 2019; 78:476-483. [PMID: 30965068 DOI: 10.1016/j.jinf.2019.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/10/2018] [Accepted: 04/02/2019] [Indexed: 01/17/2023]
Abstract
OBJECTIVES This study sought to determine SV40 seroprevalence in residents of two Latin American countries, Colombia and Nicaragua, which were sites of prelicensure oral poliovaccine (OPV) trials. METHODS Archival sera were tested for SV40 neutralizing antibody using a virus-specific plaque-reduction assay. Samples included 517 sera from Colombia and 149 sera from Nicaragua. RESULTS Overall SV40 seroprevalence was 22.8% for Colombian subjects and 12.8% for Nicaraguans. Subgroups of Colombian subjects ranged in frequency of SV40 seropositivity from 10.0% to 38.6%. Birth cohorts both older and younger than the age cohort that contained potential OPV vaccinees from both countries had SV40 antibodies. Gender and ethnicity had no significant effects on SV40 seropositivity. CONCLUSIONS Inhabitants of both Colombia and Nicaragua had detectable SV40 neutralizing antibody, including those of ages presumably not recipients of potentially SV40-contaminated OPV. This observation provides support for the concept that transmission of SV40 human infections can occur. Frequency of SV40 antibody positivity was elevated over that reported for the US where there was limited use of contaminated OPV. This investigation indicates also that study results of SV40 infections in humans will reflect whether subject populations had probable exposures to contaminated poliovaccines and to environmental conditions favoring cycles of viral transmission.
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Affiliation(s)
- Connie Wong
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, MS: BCM385, Houston, TX 77030, USA
| | - Shaojie Zhang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, MS: BCM385, Houston, TX 77030, USA
| | - Ervin Adam
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, MS: BCM385, Houston, TX 77030, USA
| | - Lawrence Paszat
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Janet S Butel
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, MS: BCM385, Houston, TX 77030, USA.
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13
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Berthenet E, Yahara K, Thorell K, Pascoe B, Meric G, Mikhail JM, Engstrand L, Enroth H, Burette A, Megraud F, Varon C, Atherton JC, Smith S, Wilkinson TS, Hitchings MD, Falush D, Sheppard SK. A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk. BMC Biol 2018; 16:84. [PMID: 30071832 PMCID: PMC6090961 DOI: 10.1186/s12915-018-0550-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/19/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Helicobacter pylori are stomach-dwelling bacteria that are present in about 50% of the global population. Infection is asymptomatic in most cases, but it has been associated with gastritis, gastric ulcers and gastric cancer. Epidemiological evidence shows that progression to cancer depends upon the host and pathogen factors, but questions remain about why cancer phenotypes develop in a minority of infected people. Here, we use comparative genomics approaches to understand how genetic variation amongst bacterial strains influences disease progression. RESULTS We performed a genome-wide association study (GWAS) on 173 H. pylori isolates from the European population (hpEurope) with known disease aetiology, including 49 from individuals with gastric cancer. We identified SNPs and genes that differed in frequency between isolates from patients with gastric cancer and those with gastritis. The gastric cancer phenotype was associated with the presence of babA and genes in the cag pathogenicity island, one of the major virulence determinants of H. pylori, as well as non-synonymous variations in several less well-studied genes. We devised a simple risk score based on the risk level of associated elements present, which has the potential to identify strains that are likely to cause cancer but will require refinement and validation. CONCLUSION There are a number of challenges to applying GWAS to bacterial infections, including the difficulty of obtaining matched controls, multiple strain colonization and the possibility that causative strains may not be present when disease is detected. Our results demonstrate that bacterial factors have a sufficiently strong influence on disease progression that even a small-scale GWAS can identify them. Therefore, H. pylori GWAS can elucidate mechanistic pathways to disease and guide clinical treatment options, including for asymptomatic carriers.
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Affiliation(s)
- Elvire Berthenet
- Microbiology and Infectious Disease Group, Swansea University Medical School, Swansea University, Swansea, UK
| | - Koji Yahara
- Antimicrobial Resistance Research Centre, National Institute of Infectious Diseases, Toyama, Japan
| | - Kaisa Thorell
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Guillaume Meric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Jane M Mikhail
- Microbiology and Infectious Disease Group, Swansea University Medical School, Swansea University, Swansea, UK
- School of Biosciences, College of Biomedical and Life Sciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Lars Engstrand
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Helena Enroth
- Systems Biology Research Group, School of Biosciences, University of Skövde, Skövde, Sweden
| | - Alain Burette
- Department of Gastroenterology, Centre Hospitalier Interrégional Edith Cavell/Site de la Basilique, Brussels, USA
| | - Francis Megraud
- Laboratoire de Bactériologie, Centre National de Référence des Campylobacters et des Hélicobacters, Place Amélie Raba Léon, 33076, Bordeaux, France
- INSERM, University Bordeaux, UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, 33000, Bordeaux, France
| | - Christine Varon
- INSERM, University Bordeaux, UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, 33000, Bordeaux, France
| | - John C Atherton
- Nottingham Digestive Diseases Centre and National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Sinead Smith
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Thomas S Wilkinson
- Microbiology and Infectious Disease Group, Swansea University Medical School, Swansea University, Swansea, UK
| | - Matthew D Hitchings
- Microbiology and Infectious Disease Group, Swansea University Medical School, Swansea University, Swansea, UK
| | - Daniel Falush
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
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14
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Gutiérrez-Escobar AJ, Méndez-Callejas G, Acevedo O, Bravo MM. Rapid evolution of the Helicobacter pylori AlpA adhesin in a high gastric cancer risk region from Colombia. PeerJ 2018; 6:e4846. [PMID: 29844987 PMCID: PMC5971833 DOI: 10.7717/peerj.4846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/06/2018] [Indexed: 12/13/2022] Open
Abstract
To be able to survive, Helicobacter pylori must adhere to the gastric epithelial cells of its human host. For this purpose, the bacterium employs an array of adhesins, for example, AlpA. The adhesin AlpA has been proposed as a major adhesin because of its critical role in human stomach colonization. Therefore, understanding how AlpA evolved could be important for the development of new diagnostic strategies. However, the genetic variation and microevolutionary patterns of alpA have not been described in Colombia. The study aim was to describe the variation patterns and microevolutionary process of alpA in Colombian clinical isolates of H. pylori. The existing polymorphisms, which are deviations from the neutral model of molecular evolution, and the genetic differentiation of the alpA gene from Colombian clinical isolates of H. pylori were determined. The analysis shows that gene conversion and purifying selection have shaped the evolution of three different variants of alpA in Colombia.
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Affiliation(s)
- Andrés Julián Gutiérrez-Escobar
- Grupo de Investigaciones Biomédicas y Genética Humana Aplicada-GIBGA, Programa de medicina, Universidad de Ciencias Aplicadas y Ambientales U.D.C.A., Bogotá, Colombia.,Doctorado en Ciencias Biológicas, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Gina Méndez-Callejas
- Grupo de Investigaciones Biomédicas y Genética Humana Aplicada-GIBGA, Programa de medicina, Universidad de Ciencias Aplicadas y Ambientales U.D.C.A., Bogotá, Colombia
| | - Orlando Acevedo
- Grupo de Biofísica y Bioquímica Estructural, Facultad de Ciencias, Pontifica Universidad Javeriana, Bogotá, Colombia
| | - Maria Mercedes Bravo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
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15
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In Vivo Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis. Infect Immun 2017; 85:IAI.00031-17. [PMID: 28694295 DOI: 10.1128/iai.00031-17] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 07/07/2017] [Indexed: 12/18/2022] Open
Abstract
Emerging evidence shows that the human microbiota plays a larger role in disease progression and health than previously anticipated. Helicobacter pylori, the causative agent of gastric cancer and duodenal and gastric ulcers, was early associated with gastric disease, but it has also been proposed that the accompanying microbiota in Helicobacter pylori-infected individuals might affect disease progression and gastric cancer development. In this study, the composition of the transcriptionally active microbial community and H. pylori gene expression were determined using metatranscriptomic RNA sequencing of stomach biopsy specimens from individuals with different H. pylori infection statuses and premalignant tissue changes. The results show that H. pylori completely dominates the microbiota not only in infected individuals but also in most individuals classified as H. pylori uninfected using conventional methods. Furthermore, H. pylori abundance is positively correlated with the presence of Campylobacter, Deinococcus, and Sulfurospirillum Finally, we quantified the expression of a large number of Helicobacter pylori genes and found high expression of genes involved in pH regulation and nickel transport. Our study is the first to dissect the viable microbiota of the human stomach by metatranscriptomic analysis, and it shows that metatranscriptomic analysis of the gastric microbiota is feasible and can provide new insights into how bacteria respond in vivo to variations in the stomach microenvironment and at different stages of disease progression.
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16
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Gutiérrez-Escobar AJ, Trujillo E, Acevedo O, Bravo MM. Phylogenomics of Colombian Helicobacter pylori isolates. Gut Pathog 2017; 9:52. [PMID: 28912838 PMCID: PMC5594506 DOI: 10.1186/s13099-017-0201-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/03/2017] [Indexed: 12/27/2022] Open
Abstract
Background During the Spanish colonisation of South America, African slaves and Europeans arrived in the continent with their corresponding load of pathogens, including Helicobacter pylori. Colombian strains have been clustered with the hpEurope population and with the hspWestAfrica subpopulation in multilocus sequence typing (MLST) studies. However, ancestry studies have revealed the presence of population components specific to H. pylori in Colombia. The aim of this study was to perform a thorough phylogenomic analysis to describe the evolution of the Colombian urban H. pylori isolates. Results A total of 115 genomes of H. pylori were sequenced with Illumina technology from H. pylori isolates obtained in Colombia in a region of high risk for gastric cancer. The genomes were assembled, annotated and underwent phylogenomic analysis with 36 reference strains. Additionally, population differentiation analyses were performed for two bacterial genes. The phylogenetic tree revealed clustering of the Colombian strains with hspWestAfrica and hpEurope, along with three clades formed exclusively by Colombian strains, suggesting the presence of independent evolutionary lines for Colombia. Additionally, the nucleotide diversity of horB and vacA genes from Colombian isolates was lower than in the reference strains and showed a significant genetic differentiation supporting the hypothesis of independent clades with recent evolution. Conclusions The presence of specific lineages suggest the existence of an hspColombia subtype that emerged from a small and relatively isolated ancestral population that accompanied crossbreeding of human population in Colombia. Electronic supplementary material The online version of this article (doi:10.1186/s13099-017-0201-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrés Julián Gutiérrez-Escobar
- Grupo de Investigaciones Biomédicas y Genética Humana Aplicada, Programa de Medicina, Universidad de Ciencias Aplicadas y Ambientales, Calle 222 55-37, Bogotá, Colombia.,Programa de Doctorado en Ciencias Biológicas, Universidad Javeriana, Carrera 7 40-62, Bogotá, Colombia
| | - Esperanza Trujillo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Calle 1 9-85, Bogotá, Colombia
| | - Orlando Acevedo
- Grupo de Biofísica y Bioquímica Estructural, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7 40-62, Bogotá, Colombia
| | - María Mercedes Bravo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Calle 1 9-85, Bogotá, Colombia
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17
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Muñoz-Ramírez ZY, Mendez-Tenorio A, Kato I, Bravo MM, Rizzato C, Thorell K, Torres R, Aviles-Jimenez F, Camorlinga M, Canzian F, Torres J. Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway. Front Cell Infect Microbiol 2017; 7:50. [PMID: 28293542 PMCID: PMC5328995 DOI: 10.3389/fcimb.2017.00050] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/10/2017] [Indexed: 12/21/2022] Open
Abstract
Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk.
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Affiliation(s)
- Zilia Y Muñoz-Ramírez
- Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional Ciudad de México, Mexico
| | - Alfonso Mendez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional Ciudad de México, Mexico
| | - Ikuko Kato
- Department of Oncology and of Pathology, Wayne State University School of Medicine Detroit, MI, USA
| | - Maria M Bravo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerologia Bogota, Colombia
| | - Cosmeri Rizzato
- Dipartmento di Ricerca Traslazionale e Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa Pisa, Italy
| | - Kaisa Thorell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Stockholm, Sweden
| | - Roberto Torres
- Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional Ciudad de México, Mexico
| | | | - Margarita Camorlinga
- Unidad de Investigacion en Enfermedades Infecciosas, IMSS Ciudad de México, Mexico
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Javier Torres
- Unidad de Investigacion en Enfermedades Infecciosas, IMSS Ciudad de México, Mexico
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18
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Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, Mendez A, Rizzato C, Bravo MM, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D. Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas. PLoS Genet 2017; 13:e1006546. [PMID: 28231283 PMCID: PMC5322909 DOI: 10.1371/journal.pgen.1006546] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/19/2016] [Indexed: 12/13/2022] Open
Abstract
For the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach-dwelling bacterium Helicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence of H. pylori isolated in North, Central and South America, we found evidence for admixture between H. pylori of European and African origin throughout the Americas, without substantial input from pre-Columbian (hspAmerind) bacteria. In the US, strains of African and European origin have remained genetically distinct, while in Colombia and Nicaragua, bottlenecks and rampant genetic exchange amongst isolates have led to the formation of national gene pools. We found three outer membrane proteins with atypical levels of Asian ancestry in American strains, as well as alleles that were nearly fixed specifically in South American isolates, suggesting a role for the ethnic makeup of hosts in the colonization of incoming strains. Our results show that new H. pylori subpopulations can rapidly arise, spread and adapt during times of demographic flux, and suggest that differences in transmission ecology between high and low prevalence areas may substantially affect the composition of bacterial populations. Helicobacter pylori is one of the best studied examples of an intimate association between bacteria and humans, due to its ability to colonize the stomach for decades and to transmit from generation to generation. A number of studies have sought to link diversity in H. pylori to human migrations but there are some discordant signals such as an “out of Africa” dispersal within the last few thousand years that has left a much stronger signal in bacterial genomes than in human ones. In order to understand how such discrepancies arise, we have investigated the evolution of H. pylori during the recent colonization of the Americas. We find that bacterial populations evolve quickly and can spread rapidly to people of different ethnicities. Distinct new bacterial subpopulations have formed in Colombia from a European source and in Nicaragua and the US from African sources. Genetic exchange between bacterial populations is rampant within Central and South America but is uncommon within North America, which may reflect differences in prevalence. Our results also suggest that adaptation of bacteria to particular human ethnic groups may be confined to a handful of genes involved in interaction with the immune system.
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Affiliation(s)
- Kaisa Thorell
- Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Koji Yahara
- Dept. of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Elvire Berthenet
- Medical Microbiology and Infectious Disease group, Swansea University, Swansea, Wales, United Kingdom
| | - Daniel J. Lawson
- Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Jane Mikhail
- Medical Microbiology and Infectious Disease group, Swansea University, Swansea, Wales, United Kingdom
| | - Ikuko Kato
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, United States of America
| | - Alfonso Mendez
- Instituto Politecnico Nacional, ENCB, Mexico City, Mexico
| | - Cosmeri Rizzato
- Dipartimento di Ricerca Traslazionale e Nuove Tecnologie in Medicina e Chirurgia, Universitá di Pisa, Pisa, Italy
| | - María Mercedes Bravo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogota, Colombia
| | - Rumiko Suzuki
- Dept. of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Yoshio Yamaoka
- Dept. of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico City, Mexico
| | - Samuel K. Sheppard
- Milner Center for Evolution, Dept. of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Daniel Falush
- Milner Center for Evolution, Dept. of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- * E-mail:
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19
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Karlsson R, Thorell K, Hosseini S, Kenny D, Sihlbom C, Sjöling Å, Karlsson A, Nookaew I. Comparative Analysis of Two Helicobacter pylori Strains using Genomics and Mass Spectrometry-Based Proteomics. Front Microbiol 2016; 7:1757. [PMID: 27891114 PMCID: PMC5104757 DOI: 10.3389/fmicb.2016.01757] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/19/2016] [Indexed: 12/20/2022] Open
Abstract
Helicobacter pylori, a gastroenteric pathogen believed to have co-evolved with humans over 100,000 years, shows significant genetic variability. This motivates the study of different H. pylori strains and the diseases they cause in order to identify determinants for disease evolution. In this study, we used proteomics tools to compare two H. pylori strains. Nic25_A was isolated in Nicaragua from a patient with intestinal metaplasia, and P12 was isolated in Europe from a patient with duodenal ulcers. Differences in the abundance of surface proteins between the two strains were determined with two mass spectrometry-based methods, label-free quantification (MaxQuant) or the use of tandem mass tags (TMT). Each approach used a lipid-based protein immobilization (LPITM) technique to enrich peptides of surface proteins. Using the MaxQuant software, we found 52 proteins that differed significantly in abundance between the two strains (up- or downregulated by a factor of 1.5); with TMT, we found 18 proteins that differed in abundance between the strains. Strain P12 had a higher abundance of proteins encoded by the cag pathogenicity island, while levels of the acid response regulator ArsR and its regulatory targets (KatA, AmiE, and proteins involved in urease production) were higher in strain Nic25_A. Our results show that differences in protein abundance between H. pylori strains can be detected with proteomic approaches; this could have important implications for the study of disease progression.
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Affiliation(s)
- Roger Karlsson
- Nanoxis Consulting ABGothenburg, Sweden; Department of Infectious Diseases, Sahlgrenska Academy, University of GothenburgGothenburg, Sweden
| | - Kaisa Thorell
- Department of Microbiology and Immunology, University of GothenburgGothenburg, Sweden; Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden
| | - Shaghayegh Hosseini
- Department of Biology and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Diarmuid Kenny
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
| | - Åsa Sjöling
- Department of Microbiology and Immunology, University of Gothenburg Gothenburg, Sweden
| | | | - Intawat Nookaew
- Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden; Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little RockAR, USA
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20
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Abstract
The development of high-throughput whole genome sequencing (WGS) technologies is changing the face of microbiology, facilitating the comparison of large numbers of genomes from different lineages of a same organism. Our aim was to review the main advances on Helicobacter pylori "omics" and to understand how this is improving our knowledge of the biology, diversity and pathogenesis of H. pylori. Since the first H. pylori isolate was sequenced in 1997, 510 genomes have been deposited in the NCBI archive, providing a basis for improved understanding of the epidemiology and evolution of this important pathogen. This review focuses on works published between April 2015 and March 2016. Helicobacter "omics" is already making an impact and is a growing research field. Ultimately these advances will be translated into a routine clinical laboratory setting in order to improve public health.
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Affiliation(s)
- Elvire Berthenet
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Sam Sheppard
- Departments of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Instituto de Medicina Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal
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