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Thorell K, Muñoz-Ramírez ZY, Wang D, Sandoval-Motta S, Boscolo Agostini R, Ghirotto S, Torres RC, Falush D, Camargo MC, Rabkin CS. The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes. Nat Commun 2023; 14:8184. [PMID: 38081806 PMCID: PMC10713588 DOI: 10.1038/s41467-023-43562-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.
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Affiliation(s)
- Kaisa Thorell
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Zilia Y Muñoz-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua, Chihuahua, México
| | - Difei Wang
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Santiago Sandoval-Motta
- Instituto Nacional de Medicina Genómica, Ciudad de México, México
- Consejo Nacional de Ciencia y Tecnologia, Cátedras CONACYT, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Roberto C Torres
- Centre for Microbes Development and Health, Institute Pasteur Shanghai, Shanghai, China
| | - Daniel Falush
- Centre for Microbes Development and Health, Institute Pasteur Shanghai, Shanghai, China
| | - M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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2
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Thorpe HA, Tourrette E, Yahara K, Vale FF, Liu S, Oleastro M, Alarcon T, Perets TT, Latifi-Navid S, Yamaoka Y, Martinez-Gonzalez B, Karayiannis I, Karamitros T, Sgouras DN, Elamin W, Pascoe B, Sheppard SK, Ronkainen J, Aro P, Engstrand L, Agreus L, Suerbaum S, Thorell K, Falush D. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nat Commun 2022; 13:6842. [PMID: 36369175 PMCID: PMC9652371 DOI: 10.1038/s41467-022-34475-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck.
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Affiliation(s)
- Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Elise Tourrette
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Filipa F Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Siqi Liu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Teresa Alarcon
- Department of Microbiology, Hospital Universitario La Princesa, Instituto de Investigación Sanitaria Princesa, Madrid, Spain
| | - Tsachi-Tsadok Perets
- Gastroenterology Laboratory, Rabin Medical Center, Petah Tikva, Israel
- Department of Digital Medical Technologies, Holon Institute of Technology, Holon, Israel
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Department of Medicine-Gastroenterology, Baylor College of Medicine, Houston, TX, USA
| | | | - Ioannis Karayiannis
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | | | | | - Wael Elamin
- G42 Healthcare, Abu Dhabi, UAE
- Elrazi University, Khartoum, Sudan
| | - Ben Pascoe
- Department of Biology, University of Oxford, Oxford, UK
| | - Samuel K Sheppard
- Ineos Oxford Institute, Department of Biology, University of Oxford, Oxford, UK
| | - Jukka Ronkainen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Primary Health Care Center, Tornio, Finland
| | | | - Lars Engstrand
- Center for Translational Microbiome Research, Department for Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Lars Agreus
- Division of Family Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Suerbaum
- Department of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
- DZIF German Center for Infection Research, Hannover-Braunschweig and Munich Partner Sites, Munich, Germany
| | - Kaisa Thorell
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Daniel Falush
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
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3
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Akar M, Saticioğlu İB, Karakaya E, Kayman T, Abay S, Solakoğlu T, Vale FF, Aydin F. Two novel sequence types of Helicobacter pylori strains: The first report from Turkey. Helicobacter 2022; 27:e12907. [PMID: 35604361 DOI: 10.1111/hel.12907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/28/2022] [Accepted: 05/07/2022] [Indexed: 12/09/2022]
Affiliation(s)
- Mustafa Akar
- Department of Gastroenterology, University of Health Sciences, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
| | | | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Tuba Kayman
- Department of Medical Microbiology, University of Health Sciences, Şişli Hamidiye Etfal Training and Research Hospital, İstanbul, Turkey
| | - Seçil Abay
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Tevfik Solakoğlu
- Department of Gastroenterology, Faculty of Medicine, Namık Kemal University, Tekirdağ, Turkey
| | - Filipa F Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Fuat Aydin
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
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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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Crowley E, Hussey S. Helicobacter pylori in Childhood. PEDIATRIC GASTROINTESTINAL AND LIVER DISEASE 2021:275-292.e12. [DOI: 10.1016/b978-0-323-67293-1.00027-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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6
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Isaeva GS. Pangenomic studies of Helicobacter pylori: a key to understanding pathogenesis and human history. MINERVA BIOTECNOL 2019. [DOI: 10.23736/s1120-4826.19.02564-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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7
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Ono T, Cruz M, Jiménez Abreu JA, Nagashima H, Subsomwong P, Hosking C, Shiota S, Suzuki R, Yamaoka Y. Comparative study between Helicobacter pylori and host human genetics in the Dominican Republic. BMC Evol Biol 2019; 19:197. [PMID: 31675915 PMCID: PMC6823972 DOI: 10.1186/s12862-019-1526-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/15/2019] [Indexed: 01/06/2023] Open
Abstract
Background Helicobacter pylori, a bacterium that infects the human stomach, has high genetic diversity. Because its evolution is parallel to human, H. pylori is used as a tool to trace human migration. However, there are few studies about the relationship between phylogeography of H. pylori and its host human. Methods We examined both H. pylori DNA and the host mitochondrial DNA and Y-chromosome DNA obtained from a total 119 patients in the Dominican Republic, where human demography consists of various ancestries. DNA extracted from cultured H. pylori were analyzed by multi locus sequence typing. Mitochondrial DNA and Y-chromosome DNA were evaluated by haplogroup analyses. Results H. pylori strains were divided into 2 populations; 68 strains with African group (hpAfrica1) and 51 strains with European group (hpEurope). In Y-chromosomal haplogroup, European origin was dominant, whereas African origin was dominant both in H. pylori and in mtDNA haplogroup. These results supported the hypothesis that mother-to-child infection is predominant in H. pylori infection. The Amerindian type of mtDNA haplogroup was observed in 11.8% of the patients; however, Amerindian type (hspAmerind) of H. pylori was not observed. Although subpopulation type of most hpAfrica1 strains in Central America and South America were hybrid (hspWAfrica/hpEurope), most Dominican Republic hpAfrica1 strains were similar to those of African continent. Conclusions Genetic features of H. pylori, mtDNA, and Y haplogroups reflect the history of colonial migration and slave trade in the Dominican Republic. Discrepancy between H. pylori and the host human genotypes support the hypothesis that adaptability of hspAmerind H. pylori strains are weaker than hpEurope strains. H. pylori strains in the Dominican Republic seem to contain larger proportion of African ancestry compared to other American continent strains.
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Affiliation(s)
- Takaaki Ono
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan.,Criminal Investigation Laboratory, Oita Prefectural Police H.Q, Oita, Japan
| | - Modesto Cruz
- Institute of Microbiology and Parasitology, Faculty of Science, Autonomous University of Santo Domingo, Santo Domingo, Dominican Republic.,Department of Biomedical Research, National Institute of Medicine and Diagnostic Imaging, Santo Domingo, Dominican Republic
| | - José A Jiménez Abreu
- Dominican-Japanese Digestive Disease Center, Dr Luis E. Aybar Health and Hygiene City, Santo Domingo, Dominican Republic
| | - Hiroyuki Nagashima
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan.,Department of Gastroenterology, Hokkaido Cancer Center, Sapporo, Hokkaido, Japan
| | - Phawinee Subsomwong
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Celso Hosking
- Institute of Microbiology and Parasitology, Faculty of Science, Autonomous University of Santo Domingo, Santo Domingo, Dominican Republic
| | - Seiji Shiota
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan. .,Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, USA.
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8
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Rapid Characterization of Virulence Determinants in Helicobacter pylori Isolated from Non-Atrophic Gastritis Patients by Next-Generation Sequencing. J Clin Med 2019; 8:jcm8071030. [PMID: 31336977 PMCID: PMC6678415 DOI: 10.3390/jcm8071030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 07/09/2019] [Indexed: 02/07/2023] Open
Abstract
Helicobacter pylori is a major human pathogen that causes a wide range of gastrointestinal pathology. Progression of H. pylori induced gastritis to more severe disease has been found to highly correlate with the array of virulence factors expressed by the pathogen. The objective of this study was twofold: first, to characterize the genetic diversity of H. pylori strains isolated from 41 non-atrophic gastritis patients in Switzerland, an issue that has not been investigated to date. And second, to assess the prevalence and sequence variation of H. pylori virulence factors (cagA, vacA, iceA and dupA) and genes encoding outer membrane proteins (OMPs; babA, babB, sabA, sabB, hopZ, hopQ and oipA) by whole genome sequencing (WGS) using an Illumina MiSeq platform. WGS identified high genetic diversity in the analyzed H. pylori strains. Most H. pylori isolates were assigned to hpEurope (95.0%, 39/41), and the remaining ones (5.0%, 2/41) to hpEastAsia, subpopulation hspEAsia. Analysis of virulence factors revealed that 43.9% of the strains were cagA-positive, and the vacA s1 allele was detected in 56.0% of the isolates. The presence of cagA was found to be significantly associated (P < 0.001) with the presence of vacA s1, babA2 and hopQ allele 1 as well as expression of oipA. Moreover, we found an association between the grade of gastritis and H. pylori abundance in the gastric mucosa, respectively and the presence of cagA, vacA s1 and hopQ allele 1. Among our 41 gastritis patients, we identified seven patients infected with H. pylori strains that carried a specific combination of virulence factors (i.e., cagA, vacA s1 allele and babA2 allele), recently implicated in the development of more severe gastrointestinal pathology, like peptic ulcer disease and even gastric cancer. To this end, WGS can be employed for rapid and detailed characterization of virulence determinants in H. pylori, providing valuable insights into the pathogenic capacity of the bacterium. This could ultimately lead to a higher level of personalized treatment and management of patients suffering from H. pylori associated infections.
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9
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Rojas-Rengifo DF, Ulloa-Guerrero CP, Joppich M, Haas R, Del Pilar Delgado M, Jaramillo C, Jiménez-Soto LF. Tryptophan usage by Helicobacter pylori differs among strains. Sci Rep 2019; 9:873. [PMID: 30696868 PMCID: PMC6351589 DOI: 10.1038/s41598-018-37263-6] [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: 04/09/2018] [Accepted: 11/19/2018] [Indexed: 11/14/2022] Open
Abstract
Because of its association with severe gastric pathologies, including gastric cancer, Helicobacter pylori has been subject of research for more than 30 years. Its capacity to adapt and survive in the human stomach can be attributed to its genetic flexibility. Its natural competence and its capacity to turn genes on and off allows H. pylori to adapt rapidly to the changing conditions of its host. Because of its genetic variability, it is difficult to establish the uniqueness of each strain obtained from a human host. The methods considered to-date to deliver the best result for differentiation of strains are Rapid Amplification of Polymorphic DNA (RAPD), Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis. While RAPD analysis is cost-effective, it requires a stable genome for its reliability. MLST and WGS are optimal for strain identification, however, they require analysis of data at the bioinformatics level. Using the StainFree method, which modifies tryptophan residues on proteins using 2, 2, 2, - trichloroethanol (TCE), we observed a strain specific pattern of tryptophan in 1D acrylamide gels. In order to establish the effectiveness of tryptophan fingerprinting for strain identification, we compared the graphic analysis of tryptophan-labelled bands in the gel images with MLST results. Based on this, we find that tryptophan banding patterns can be used as an alternative method for the differentiation of H. pylori strains. Furthermore, investigating the origin for these differences, we found that H. pylori strains alters the number and/or position of tryptophan present in several proteins at the genetic code level, with most exchanges taking place in membrane- and cation-binding proteins, which could be part of a novel response of H. pylori to host adaptation.
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Affiliation(s)
- Diana F Rojas-Rengifo
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia.,Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany
| | - Cindy P Ulloa-Guerrero
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia.,Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany
| | - Markus Joppich
- Lehr- und Forschungseinheit Bioinformatik. Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstr. 17, D-80333, Munich, Germany
| | - Rainer Haas
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany
| | - Maria Del Pilar Delgado
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia
| | - Carlos Jaramillo
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia
| | - Luisa F Jiménez-Soto
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany. .,Ludwig-Maximillians University, Munich, Germany.
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10
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The Story of Helicobacter pylori: Depicting Human Migrations from the Phylogeography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1149:1-16. [PMID: 31016625 DOI: 10.1007/5584_2019_356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Helicobacter pylori is a spiral-shaped Gram-negative bacterium, which has infected more than half of the human population. Besides its colonisation capability, the genetic diversity of H. pylori is exceptionally well structured and belongs to several distinct genetic populations, depicting various prehistorical human migration events. The evolutionary relationship of H. pylori with its host had been started at least ~100,000 years ago. In addition, the discovery of the ancient H. pylori genome from a European Copper Age glacier mummy, "The Iceman", gave the idea that the second out of Africa migration resulted in the recombinant population of hpEurope at least about 5300 years ago. The advancement of next-generation genome sequencing discovered the prophage of H. pylori and could discriminate the big population of hpEurope into two different subpopulations. In addition, the implementation of the chromopainter/fineSTRUCTURE algorithm to the whole genome analysis of H. pylori provides a finer resolution population genetics of H. pylori; therefore it could also depict the recent migrations within the past 500 years after colonial expansion. This discovery shows that the genetic recombination of H. pylori strains is far more dynamic compared to its human host, but still maintains the similarity to its host, suggesting that H. pylori is a handy tool to reconstruct the human migration both in the past and the recent.
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11
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Vale FF, Lehours P. Relating Phage Genomes to Helicobacter pylori Population Structure: General Steps Using Whole-Genome Sequencing Data. Int J Mol Sci 2018; 19:ijms19071831. [PMID: 29933614 PMCID: PMC6073503 DOI: 10.3390/ijms19071831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/30/2018] [Accepted: 06/15/2018] [Indexed: 12/19/2022] Open
Abstract
The review uses the Helicobacter pylori, the gastric bacterium that colonizes the human stomach, to address how to obtain information from bacterial genomes about prophage biology. In a time of continuous growing number of genomes available, this review provides tools to explore genomes for prophage presence, or other mobile genetic elements and virulence factors. The review starts by covering the genetic diversity of H. pylori and then moves to the biologic basis and the bioinformatics approaches used for studding the H. pylori phage biology from their genomes and how this is related with the bacterial population structure. Aspects concerning H. pylori prophage biology, evolution and phylogeography are discussed.
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Affiliation(s)
- Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal.
| | - Philippe Lehours
- Laboratoire de Bacteriologie, Centre National de Référence des Campylobacters et Hélicobacters, Place Amélie Raba Léon, 33076 Bordeaux, France.
- INSERM U1053-UMR Bordeaux Research in Translational Oncology, BaRITOn, 33000 Bordeaux, France.
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12
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Kabamba ET, Tuan VP, Yamaoka Y. Genetic populations and virulence factors of Helicobacter pylori. INFECTION GENETICS AND EVOLUTION 2018; 60:109-116. [PMID: 29471116 DOI: 10.1016/j.meegid.2018.02.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 12/16/2022]
Abstract
Helicobacter pylori is a bacterium that has infected more than half of the human population worldwide. This bacterium is closely associated with serious human diseases, such as gastric cancer, and identifying and understanding factors that predict bacterial virulence is a priority. In addition, this pathogen shows high genetic diversity and co-evolution with human hosts. H. pylori population genetics, therefore, has emerged as a tool to track human demographic history. As the number of genome sequences available is increasing, studies on the evolution and virulence of H. pylori are gaining momentum. This review article summarizes the most recent findings on H. pylori virulence factors and population genetics.
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Affiliation(s)
- Evariste Tshibangu Kabamba
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593, Japan; Department of Internal Medicine, University of Mbujimayi Faculty of Medicine, Mbujimayi, The Democratic Republic of Congo
| | - Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593, Japan; Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Viet Nam
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593, Japan; Department of Medicine-Gastroenterology, Baylor College of Medicine and Michael E. Debakey Veterans Affairs Medical Center, 2002 Holcombe Blvd., Houston, TX 77030, USA.
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Raaf N, Amhis W, Saoula H, Abid A, Nakmouche M, Balamane A, Ali Arous N, Ouar-Korichi M, Vale FF, Bénéjat L, Mégraud F. Prevalence, antibiotic resistance, and MLST typing of Helicobacter pylori in Algiers, Algeria. Helicobacter 2017; 22. [PMID: 29035009 DOI: 10.1111/hel.12446] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Helicobacter pylori infection is common in Algeria, but there are few data on the characterization of isolated strains. The aim of this study was to update data on the prevalence of H. pylori in patients submitted to endoscopy, antibiotic resistance, and phylogeography of H. pylori strains isolated in Algiers. MATERIALS AND METHODS This is a prospective study carried out between November 2015 and August 2016. The culture of H. pylori was performed on antral and fundic gastric biopsies of adult patients from 3 hospitals. A real-time PCR using the fluorescence resonance energy transfer (FRET) principle for the detection of H. pylori followed by a melting curve analysis for the detection of mutations associated with resistance to clarithromycin was applied. Differentiation between antral and fundic isolates of the same patient was also determined by RAPD, and an MLST typing was performed for characterization of the phylogeographic group of H. pylori. RESULTS By real-time PCR, the prevalence of H. pylori infection among the 147 patients included was 57%. Culture was positive in only 29% of the cases. Twenty-seven percent of patients had received H. pylori eradication treatment. The primary and secondary resistance rates to clarithromycin were 23% and 36%, respectively, and to metronidazole, 45% and 71%, respectively. Only one isolate was resistant to levofloxacin, and no resistance to amoxicillin, tetracycline, and rifampicin was detected. A double population was present in 14 patients. The MLST analysis classified the 42 H. pylori strains from 38 patients in 2 haplotypes: hpEurope (33) and hpNEAfrica (9). CONCLUSION The prevalence of H. pylori remains high in Algeria but appears to be decreasing in recent years. High resistance to clarithromycin requires increased monitoring of the evolution of antibiotic resistance and adaptation of eradication therapy.
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Affiliation(s)
- Naïma Raaf
- Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université Ferhat Abbas, Setif, Algeria.,Laboratoire Central de Biologie Clinique, EPH Ibn Ziri Bologhine, Algiers, Algeria
| | - Wahiba Amhis
- Laboratoire Central de Biologie Clinique, EPH Ibn Ziri Bologhine, Algiers, Algeria
| | - Houria Saoula
- Service de Gastroentérologie, CHU Lamine Debaghine Bab El Oued, Algiers, Algeria
| | - Ahmed Abid
- Service de Gastroentérologie, CHU Isaad Hassani Beni Messous, Algiers, Algeria
| | - Mhamed Nakmouche
- Service de Gastroentérologie, CHU Lamine Debaghine Bab El Oued, Algiers, Algeria
| | - Abdelmalek Balamane
- Service de Gastroentérologie, CHU Isaad Hassani Beni Messous, Algiers, Algeria
| | - Nassima Ali Arous
- Servive de Médecine interne, EPH Ibn Ziri Bologhine, Algiers, Algeria
| | - Mounira Ouar-Korichi
- Laboratoire des Entérobactéries et autres bactéries apparentées, Institut Pasteur d'Algérie, Algiers, Algeria
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Lucie Bénéjat
- French National Reference Center for Campylobacters and Helicobacters, Laboratoire de Bactériologie, Hôpital Pellegrin, & INSERM U 1053, Université de Bordeaux, Bordeaux, France
| | - Francis Mégraud
- French National Reference Center for Campylobacters and Helicobacters, Laboratoire de Bactériologie, Hôpital Pellegrin, & INSERM U 1053, Université de Bordeaux, Bordeaux, France
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Abstract
As Helicobacter pylori infects half the world's population and displays an extensive intraspecies diversity, genomics is a powerful tool to understand evolution and disease, to identify factors that confer higher risk of severe sequelae, and to find new approaches for therapy both among bacterial and host targets. In line with these objectives, this review article summarizes the major findings in Helicobacter genomics in papers published between April 2016 and March 2017.
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Affiliation(s)
- Kaisa Thorell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Philippe Lehours
- INSERM, Univ. Bordeaux, UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, Bordeaux, France
| | - Filipa F Vale
- Faculty of Pharmacy, Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Universidade de Lisboa, Lisbon, Portugal
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Abstract
The study of Helicobacter pylori genetic variability brought us interesting data on the history of mankind. Based on multilocus sequence typing and more recently on whole-genome sequencing, paleomicrobiology still attracts the attention of global researchers in relation to its ancestor roots and coexistence with humans. Three studies determining the prevalence of virulence factors illustrates the controversial results obtained since 30 years by studies trying to associate prevalence of different virulence markers and clinical outcomes of H. pylori infection. Three articles analyzed the prevalence and risk of multiple (genetically distinct isolates) and mixed (susceptible and resistant isolates) infections. A number of studies confirm that H. pylori prevalence is falling worldwide especially in the developed world and in children but that the level of infection is higher in certain ethnic minorities and in Migrants. There is little new in identifying the mode of H. pylori transmission though intrafamilial spread appears to be important. There have, however, been some interesting papers on the presence of the organism in food, water, and the oral cavity.
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