1
|
Yamaoka Y, Saruuljavkhlan B, Alfaray RI, Linz B. Pathogenomics of Helicobacter pylori. Curr Top Microbiol Immunol 2023; 444:117-155. [PMID: 38231217 DOI: 10.1007/978-3-031-47331-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The human stomach bacterium Helicobacter pylori, the causative agent of gastritis, ulcers and adenocarcinoma, possesses very high genetic diversity. H. pylori has been associated with anatomically modern humans since their origins over 100,000 years ago and has co-evolved with its human host ever since. Predominantly intrafamilial and local transmission, along with genetic isolation, genetic drift, and selection have facilitated the development of distinct bacterial populations that are characteristic for large geographical areas. H. pylori utilizes a large arsenal of virulence and colonization factors to mediate the interaction with its host. Those include various adhesins, the vacuolating cytotoxin VacA, urease, serine protease HtrA, the cytotoxin-associated genes pathogenicity island (cagPAI)-encoded type-IV secretion system and its effector protein CagA, all of which contribute to disease development. While many pathogenicity-related factors are present in all strains, some belong to the auxiliary genome and are associated with specific phylogeographic populations. H. pylori is naturally competent for DNA uptake and recombination, and its genome evolution is driven by extraordinarily high recombination and mutation rates that are by far exceeding those in other bacteria. Comparative genome analyses revealed that adaptation of H. pylori to individual hosts is associated with strong selection for particular protein variants that facilitate immune evasion, especially in surface-exposed and in secreted virulence factors. Recent studies identified single-nucleotide polymorphisms (SNPs) in H. pylori that are associated with the development of severe gastric disease, including gastric cancer. Here, we review the current knowledge about the pathogenomics of H. pylori.
Collapse
Affiliation(s)
- Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, 60286, East Java, Indonesia
| | - Bodo Linz
- Division of Microbiology, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
| |
Collapse
|
2
|
Nath AN, Retnakumar RJ, Francis A, Chhetri P, Thapa N, Chattopadhyay S. Peptic Ulcer and Gastric Cancer: Is It All in the Complex Host-Microbiome Interplay That Is Encoded in the Genomes of "Us" and "Them"? Front Microbiol 2022; 13:835313. [PMID: 35547123 PMCID: PMC9083406 DOI: 10.3389/fmicb.2022.835313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
It is increasingly being recognized that severe gastroduodenal diseases such as peptic ulcer and gastric cancer are not just the outcomes of Helicobacter pylori infection in the stomach. Rather, both diseases develop and progress due to the perfect storms created by a combination of multiple factors such as the expression of different H. pylori virulence proteins, consequent human immune responses, and dysbiosis in gastrointestinal microbiomes. In this mini review, we have discussed how the genomes of H. pylori and other gastrointestinal microbes as well as the genomes of different human populations encode complex and variable virulome–immunome interplay, which influences gastroduodenal health. The heterogeneities that are encrypted in the genomes of different human populations and in the genomes of their respective resident microbes partly explain the inconsistencies in clinical outcomes among the H. pylori-infected people.
Collapse
Affiliation(s)
- Angitha N Nath
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - R J Retnakumar
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.,Manipal Academy of Higher Education, Manipal, India
| | - Ashik Francis
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Prakash Chhetri
- Department of Zoology, Biotech Hub, Nar Bahadur Bhandari Degree College, Tadong, India
| | - Namrata Thapa
- Department of Zoology, Biotech Hub, Nar Bahadur Bhandari Degree College, Tadong, India
| | | |
Collapse
|
3
|
Exchanging fluids The sociocultural implications of microbial, cultural, and ethnic admixture in Latin America. Politics Life Sci 2021; 39:56-86. [PMID: 32697057 DOI: 10.1017/pls.2020.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Knowledge of evolutionary influences on patterns of human mating, social interactions, and differential health is increasing, yet these insights have rarely been applied to historical analyses of human population dynamics. The genetic and evolutionary forces behind biases in interethnic mating and in the health of individuals of different ethnic groups in Latin America and the Caribbean since the European colonization of America are still largely ignored. We discuss how historical and contemporary sociocultural interactions and practices are strongly influenced by population-level evolutionary forces. Specifically, we discuss the historical implications of functional (de facto) polygyny, sex-biased admixture, and assortative mating in Latin America. We propose that these three evolutionary mechanisms influenced mating patterns, shaping the genetic and cultural landscape across Latin America and the Caribbean. Further, we discuss how genetic differences between the original populations that migrated at different times into Latin America contributed to their accommodation to and survival in the different local ecologies and interethnic interactions. Relevant medical and social implications follow from the genetic and cultural changes reviewed.
Collapse
|
4
|
Gutiérrez-Escobar AJ, Velapatiño B, Borda V, Rabkin CS, Tarazona-Santos E, Cabrera L, Cok J, Hooper CC, Jahuira-Arias H, Herrera P, Noureen M, Wang D, Romero-Gallo J, Tran B, Peek RM, Berg DE, Gilman RH, Camargo MC. Identification of New Helicobacter pylori Subpopulations in Native Americans and Mestizos From Peru. Front Microbiol 2020; 11:601839. [PMID: 33381095 PMCID: PMC7767971 DOI: 10.3389/fmicb.2020.601839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/16/2020] [Indexed: 01/01/2023] Open
Abstract
Region-specific Helicobacter pylori subpopulations have been identified. It is proposed that the hspAmerind subpopulation is being displaced from the Americans by an hpEurope population following the conquest. Our study aimed to describe the genomes and methylomes of H. pylori isolates from distinct Peruvian communities: 23 strains collected from three groups of Native Americans (Asháninkas [ASHA, n = 9], Shimaas [SHIM, n = 5] from Amazonas, and Punos from the Andean highlands [PUNO, n = 9]) and 9 modern mestizos from Lima (LIM). Closed genomes and DNA modification calls were obtained using SMRT/PacBio sequencing. We performed evolutionary analyses and evaluated genomic/epigenomic differences among strain groups. We also evaluated human genome-wide data from 74 individuals from the selected Native communities (including the 23 H. pylori strains donors) to compare host and bacterial backgrounds. There were varying degrees of hspAmerind ancestry in all strains, ranging from 7% in LIM to 99% in SHIM. We identified three H. pylori subpopulations corresponding to each of the Native groups and a novel hspEuropePeru which evolved in the modern mestizos. The divergence of the indigenous H. pylori strains recapitulated the genetic structure of Native Americans. Phylogenetic profiling showed that Orthogroups in the indigenous strains seem to have evolved differentially toward epigenomic regulation and chromosome maintenance, whereas OGs in the modern mestizo (LIM) seem to have evolved toward virulence and adherence. The prevalence of cagA+/vacA s1i1m1 genotype was similar across populations (p = 0.32): 89% in ASHA, 67% in PUNO, 56% in LIM and 40% in SHIM. Both cagA and vacA sequences showed that LIM strains were genetically differentiated (p < 0.001) as compared to indigenous strains. We identified 642 R-M systems with 39% of the associated genes located in the core genome. We found 692 methylation motifs, including 254 population-specific sequences not previously described. In Peru, hspAmerind is not extinct, with traces found even in a heavily admixed mestizo population. Notably, our study identified three new hspAmerind subpopulations, one per Native group; and a new subpopulation among mestizos that we named hspEuropePeru. This subpopulation seems to have more virulence-related elements than hspAmerind. Purifying selection driven by variable host immune response may have shaped the evolution of Peruvian subpopulations, potentially impacting disease outcomes.
Collapse
Affiliation(s)
| | - Billie Velapatiño
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada.,Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Victor Borda
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC/MCTIC), Petrópolis, Brazil
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Eduardo Tarazona-Santos
- Universidad Peruana Cayetano Heredia, Lima, Peru.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Jaime Cok
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | - Mehwish Noureen
- National Institute of Genetics, Mishima, Japan.,Department of Genetics, Graduate School of Life Sciences, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Judith Romero-Gallo
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bao Tran
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Richard M Peek
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Douglas E Berg
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Robert H Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| |
Collapse
|
5
|
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. ISME JOURNAL 2020; 15:78-92. [PMID: 32879462 PMCID: PMC7853065 DOI: 10.1038/s41396-020-00758-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [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.
Collapse
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.
| |
Collapse
|
6
|
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: 0.8] [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.
Collapse
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.
| |
Collapse
|
7
|
Gilbert SF. Evolutionary transitions revisited: Holobiont evo-devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:307-314. [PMID: 31565856 DOI: 10.1002/jez.b.22903] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 08/07/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022]
Abstract
John T. Bonner lists four essential transformations in the evolution of life: the emergence of the eukaryotic cell, meiosis, multicellularity, and the nervous system. This paper analyses the mechanisms for those transitions in light of three of Dr. Bonner's earlier hypotheses: (a) that the organism is its life cycle, (b) that evolution consists of alterations of the life cycle, and (c) that development extends beyond the body and into interactions with other organisms. Using the notion of the holobiont life cycle, this paper attempts to show that these evolutionary transitions can be accomplished through various means of symbiosis. Perceiving the organism both as an interspecies consortium and as a life cycle supports a twofold redefinition of the organism as a holobiont constructed by integrating together the life cycles of several species. These findings highlight the importance of symbiosis and the holobiont development in analyses of evolution.
Collapse
Affiliation(s)
- Scott F Gilbert
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| |
Collapse
|
8
|
Bie M, Wen J, Wang H, Zhou L, Yang L, Pan Y, Luo J, Liu C, Li M, Wang B. Phylogenetic analysis of clinical strains of Helicobacter pylori isolated from patients with gastric diseases in Tibet. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:320. [PMID: 31475190 PMCID: PMC6694268 DOI: 10.21037/atm.2019.05.80] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/28/2019] [Indexed: 08/12/2023]
Abstract
BACKGROUND Helicobacter pylori (H. pylori) is a Gram-negative pathogenic bacterium that causes chronic gastritis and other gastric diseases in humans. In Tibet, China, the infection of H. pylori is an important risk factor that caused gastric cancer. METHODS To understand the characteristics of this pathogen in Tibet, five strains of H. pylori were isolated from three patients' oral cavity or stomach who had either a gastric ulcer or gastritis. We performed genome sequences of these five clinical strains on Illumina Hiseq, and 55,016-63666 SNVs/InDels were identified by comparing to the reference strain of H. pylori 26995. RESULTS The phylogenetic analysis with multi-locus sequence typing (MLST) showed that five Tibetan strains were defined as hpEurope population and their proteins encoded by the cagA gene also presented a western type. Also, the strains that were isolated from the same patients' oral cavity and stomach exhibited homology in molecular evolution. CONCLUSIONS This is the first study to investigate the phylogenetic population structure of the epidemic strains of H. pylori in Tibet, which may improve cognition of Tibetan strains and confirm the homology of the strains from oral cavity and stomach.
Collapse
Affiliation(s)
- Mingjiang Bie
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
- Medical College of Tibet University, Lhasa 850000, China
- West China Fourth Hospital of Public Health, Sichuan University, Chengdu 610041, China
- Editorial Board of Journal of Sichuan University (Medical Science Edition), Chengdu 610041, China
| | - Jirui Wen
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hongren Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Linlin Zhou
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Lijun Yang
- Medical College of Tibet University, Lhasa 850000, China
| | - Yongyue Pan
- Medical College of Tibet University, Lhasa 850000, China
| | - Jun Luo
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chao Liu
- Hospital of Chengdu Office, People’s Government of Tibet Autonomous Region, Chengdu 610041, China
| | - Mingyuan Li
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Baoning Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| |
Collapse
|
9
|
Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS, Makharia GK. Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls. Front Microbiol 2019; 10:164. [PMID: 30800106 PMCID: PMC6376745 DOI: 10.3389/fmicb.2019.00164] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/22/2019] [Indexed: 12/12/2022] Open
Abstract
Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed that ecosystem level diversity measures were not significantly different between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific ASVs between pre-disease and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to fecal samples indicating larger disruption of the microbiota at the disease site. The duodenal microbiota of FDR was characterized by significant abundance of ASVs belonging to Parvimonas, Granulicatella, Gemella, Bifidobacterium, Anaerostipes, and Actinomyces genera. The duodenal microbiota of CeD was characterized by higher abundance of ASVs from genera Megasphaera and Helicobacter compared to the FDR microbiota. The CeD and FDR fecal microbiota had reduced abundance of ASVs classified as Akkermansia and Dorea when compared to control group microbiota. In addition, predicted functional metagenome showed reduced ability of gluten degradation by CeD fecal microbiota in comparison to FDRs and controls. The findings of the present study demonstrate differences in ASVs and predicts reduced ability of CeD fecal microbiota to degrade gluten compared to the FDR fecal microbiota. Further research is required to investigate the strain level and active functional profiles of FDR and CeD microbiota to better understand the role of gut microbiome in pathophysiology of CeD.
Collapse
Affiliation(s)
- Rahul Bodkhe
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Sudarshan A Shetty
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Dhiraj P Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Anil K Verma
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Khushbo Bhatia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Asha Mishra
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Gurvinder Kaur
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Pranav Pande
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | | | | | | | - Vineet Ahuja
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
10
|
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: 1.4] [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.
Collapse
|
11
|
Delahay RM, Croxall NJ, Stephens AD. Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements. Mob DNA 2018; 9:5. [PMID: 29416569 PMCID: PMC5785829 DOI: 10.1186/s13100-018-0109-4] [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: 10/13/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
Background The genome of the gastric pathogen Helicobacter pylori is characterised by considerable variation of both gene sequence and content, much of which is contained within three large genomic islands comprising the cag pathogenicity island (cagPAI) and two mobile integrative and conjugative elements (ICEs) termed tfs3 and tfs4. All three islands are implicated as virulence factors, although whereas the cagPAI is well characterised, understanding of how the tfs elements influence H. pylori interactions with different human hosts is significantly confounded by limited definition of their distribution, diversity and structural representation in the global H. pylori population. Results To gain a global perspective of tfs ICE population dynamics we established a bioinformatics workflow to extract and precisely define the full tfs pan-gene content contained within a global collection of 221 draft and complete H. pylori genome sequences. Complete (ca. 35-55kbp) and remnant tfs ICE clusters were reconstructed from a dataset comprising > 12,000 genes, from which orthologous gene complements and distinct alleles descriptive of different tfs ICE types were defined and classified in comparative analyses. The genetic variation within defined ICE modular segments was subsequently used to provide a complete description of tfs ICE diversity and a comprehensive assessment of their phylogeographic context. Our further examination of the apparent ICE modular types identified an ancient and complex history of ICE residence, mobility and interaction within particular H. pylori phylogeographic lineages and further, provided evidence of both contemporary inter-lineage and inter-species ICE transfer and displacement. Conclusions Our collective results establish a clear view of tfs ICE diversity and phylogeographic representation in the global H. pylori population, and provide a robust contextual framework for elucidating the functional role of the tfs ICEs particularly as it relates to the risk of gastric disease associated with different tfs ICE genotypes. Electronic supplementary material The online version of this article (10.1186/s13100-018-0109-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Robin M Delahay
- 1Nottingham 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
| | - Nicola J Croxall
- 1Nottingham 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
| | - Amberley D Stephens
- 1Nottingham 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.,2Present Address: Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcette Drive, West Cambridge, Cambridge, CB3 0AS UK
| |
Collapse
|
12
|
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: 2.0] [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.
Collapse
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
| |
Collapse
|
13
|
Oleastro M, Rocha R, Vale FF. Population genetic structure of Helicobacter pylori strains from Portuguese-speaking countries. Helicobacter 2017; 22. [PMID: 28271597 DOI: 10.1111/hel.12382] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND The human gastric colonizer Helicobacter pylori is useful to track human migrations given the agreement between the bacterium phylogeographic distribution and human migrations. As Portugal was an African and Brazilian colonizer for over 400 years, we hypothesized that Portuguese isolates were likely genetically closer with those from countries colonized by Portuguese in the past. We aimed to characterize the population structure of several Portuguese-speaking countries, including Portugal, Brazil, Angola, and Cape Verde. MATERIALS AND METHODS We included strains isolated in Portugal from Portuguese and from former Portuguese colonies. These strains were typed by multilocus sequence typing (MLST) for seven housekeeping genes. We also retrieved from Multi Locus Sequence Typing Web site additional housekeeping gene sequences, namely from Angola and Brazil. RESULTS We provided evidence that strains from Portuguese belong to hpEurope and that the introgression of hpEurope in non-European countries that speak Portuguese is low, except for Brazil and Cape Verde, where hpEurope accounted for one quarter and one half of the population, respectively. We found genetic similarity for all strains from Portuguese-speaking countries that belong to hpEurope population. Moreover, these strains showed a predominance of ancestral Europe 2 (AE2) over ancestral Europe 1 (AE1), followed by ancestral Africa 1. CONCLUSIONS H. pylori is a useful marker even for relative recent human migration events and may become rapidly differentiated from founder populations. H. pylori from Portuguese-speaking countries assigned to hpEurope appears to be a hybrid population resulting from the admixture of AE1, AE2 and ancestral hpAfrica1.
Collapse
Affiliation(s)
- Mónica Oleastro
- Department of Infectious Diseases, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Raquel Rocha
- Department of Infectious Diseases, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
14
|
Abstract
The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of birds displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.
Collapse
Affiliation(s)
- Sarah M Hird
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
| |
Collapse
|
15
|
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: 41] [Impact Index Per Article: 5.9] [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.
Collapse
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
| |
Collapse
|
16
|
Impact of structural polymorphism for the Helicobacter pylori CagA oncoprotein on binding to polarity-regulating kinase PAR1b. Sci Rep 2016; 6:30031. [PMID: 27445265 PMCID: PMC4957108 DOI: 10.1038/srep30031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 06/28/2016] [Indexed: 12/28/2022] Open
Abstract
Chronic infection with cagA-positive Helicobacter pylori is the strongest risk factor for atrophic gastritis, peptic ulcers, and gastric cancer. CagA, the product of the cagA gene, is a bacterial oncoprotein, which, upon delivery into gastric epithelial cells, binds to and inhibits the polarity-regulating kinase, partitioning-defective 1b (PAR1b) [also known as microtubule affinity-regulating kinase 2 (MARK2)], via its CagA multimerization (CM) motif. The inhibition of PAR1b elicits junctional and polarity defects, rendering cells susceptible to oncogenesis. Notably, the polymorphism in the CM motif has been identified among geographic variants of CagA, differing in either the copy number or the sequence composition. In this study, through quantitative analysis of the complex formation between CagA and PAR1b, we found that several CagA species have acquired elevated PAR1b-binding activity via duplication of the CM motifs, while others have lost their PAR1b-binding activity. We also found that strength of CagA-PAR1b interaction was proportional to the degrees of stress fiber formation and tight junctional disruption by CagA in gastric epithelial cells. These results indicate that the CM polymorphism is a determinant for the magnitude of CagA-mediated deregulation of the cytoskeletal system and thereby possibly affects disease outcome of cagA-positive H. pylori infection, including gastric cancer.
Collapse
|
17
|
Boynton PJ, Stelkens R, Kowallik V, Greig D. Measuring microbial fitness in a field reciprocal transplant experiment. Mol Ecol Resour 2016; 17:370-380. [PMID: 27333260 DOI: 10.1111/1755-0998.12562] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/17/2016] [Accepted: 05/30/2016] [Indexed: 11/27/2022]
Abstract
Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to different habitats or locations. We designed a competitive fitness assay to detect adaptation of Saccharomyces paradoxus isolates to the habitat they were isolated from (oak or larch leaf litter). The assay accurately measures relative fitness by tracking genotype frequency changes in the field using digital droplet PCR (DDPCR). We expected locally adapted S. paradoxus strains to increase in frequency over time when growing on the leaf litter type from which they were isolated. The DDPCR assay successfully detected fitness differences among S. paradoxus strains, but did not find a tendency for strains to be adapted to the habitat they were isolated from. Instead, we found that the natural alleles of the hexose transport gene we used to distinguish S. paradoxus strains had significant effects on fitness. The origin of a strain also affected its fitness: strains isolated from oak litter were generally fitter than strains from larch litter. Our results suggest that dispersal limitation and genetic drift shape S. paradoxus populations in the forest more than local selection does, although further research is needed to confirm this. Tracking genotype frequency changes using DDPCR is a practical and accurate microbial fitness assay for natural environments.
Collapse
Affiliation(s)
- Primrose J Boynton
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Rike Stelkens
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Vienna Kowallik
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Duncan Greig
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.,The Galton Laboratory, Department of Genetics, Evolution, and Environment, University College London, London, WC1E 6BT, UK
| |
Collapse
|
18
|
Torres K, Valderrama E, Sayegh M, Ramírez JL, Chiurillo MA. Study of the oipA genetic diversity and EPIYA motif patterns in cagA-positive Helicobacter pylori strains from Venezuelan patients with chronic gastritis. Microb Pathog 2014; 76:26-32. [PMID: 25223715 DOI: 10.1016/j.micpath.2014.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/20/2014] [Accepted: 09/11/2014] [Indexed: 12/16/2022]
Abstract
CagA and OipA are involved, among other virulence factors, in the ability of Helicobacter pylori to colonize the gastric mucosa and to modulate the host environment during the establishment of chronic infection. The number and type of EPIYA phosphorylation motifs and the presence and functional status of oipA have been involved in the induction of cellular transformations playing an important role in the development of H. pylori associated gastric diseases. This work determined the prevalence of the oipA virulence factor and EPIYA motif patterns in cagA-positive H. pylori gastric biopsies from chronic gastritis patients from the Central-Western region of Venezuela. DNA was extracted directly from gastric biopsies collected by upper endoscopy from 113 patients. The EPIYA motif genotyping and oipA gene functional status was determined by PCR and sequencing. Phylogenetic analysis with the 3' variable region of cagA sequences was performed. Only Western-type EPIYA variants were detected: ABC (68.14%), ABCC (29.20%) and ABCCC (2.66%). High prevalence of strains with the oipA gene (93.8%) and its functional status "ON" (83%) was observed. No significant association between EPIYA motif patterns or oipA functional status with the histological changes in the gastric mucosa was found. Our study demonstrated the absolute predominance of the Western-type cagA gene in a Venezuelan admixed population. This is the first report showing oipA status of H. pylori strains in Venezuela. Further studies with a larger number of samples and including other pathologies are necessary to continue evaluating the role of the H. pylori virulence factors in the prevalence of gastric diseases in our country.
Collapse
Affiliation(s)
- Keila Torres
- Laboratorio de Genética Molecular "Dr. Jorge Yunis-Turbay", Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado (UCLA), Barquisimeto, Venezuela.
| | - Elvis Valderrama
- Departamento de Anatomía Patológica, Hospital Antonio María Pineda-UCLA, Barquisimeto, Venezuela.
| | - Marjorie Sayegh
- Centro de Biotecnología, Instituto de Estudios Avanzados, Caracas, Venezuela.
| | - José Luis Ramírez
- Centro de Biotecnología, Instituto de Estudios Avanzados, Caracas, Venezuela.
| | - Miguel Angel Chiurillo
- Laboratorio de Genética Molecular "Dr. Jorge Yunis-Turbay", Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado (UCLA), Barquisimeto, Venezuela.
| |
Collapse
|
19
|
Kodaman N, Sobota RS, Mera R, Schneider BG, Williams SM. Disrupted human-pathogen co-evolution: a model for disease. Front Genet 2014; 5:290. [PMID: 25202324 PMCID: PMC4142859 DOI: 10.3389/fgene.2014.00290] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/05/2014] [Indexed: 02/06/2023] Open
Abstract
A major goal in infectious disease research is to identify the human and pathogenic genetic variants that explain differences in microbial pathogenesis. However, neither pathogenic strain nor human genetic variation in isolation has proven adequate to explain the heterogeneity of disease pathology. We suggest that disrupted co-evolution between a pathogen and its human host can explain variation in disease outcomes, and that genome-by-genome interactions should therefore be incorporated into genetic models of disease caused by infectious agents. Genetic epidemiological studies that fail to take both the pathogen and host into account can lead to false and misleading conclusions about disease etiology. We discuss our model in the context of three pathogens, Helicobacter pylori, Mycobacterium tuberculosis and human papillomavirus, and generalize the conditions under which it may be applicable.
Collapse
Affiliation(s)
- Nuri Kodaman
- Department of Genetics, Geisel School of Medicine, Dartmouth College Hanover, NH, USA ; Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical Center Nashville, TN, USA
| | - Rafal S Sobota
- Department of Genetics, Geisel School of Medicine, Dartmouth College Hanover, NH, USA ; Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical Center Nashville, TN, USA
| | - Robertino Mera
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center Nashville, TN, USA
| | - Barbara G Schneider
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center Nashville, TN, USA
| | - Scott M Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College Hanover, NH, USA
| |
Collapse
|
20
|
Shiota S, Suzuki R, Matsuo Y, Miftahussurur M, Tran TTH, Binh TT, Yamaoka Y. Helicobacter pylori from gastric cancer and duodenal ulcer show same phylogeographic origin in the Andean region in Colombia. PLoS One 2014; 9:e105392. [PMID: 25121764 PMCID: PMC4133377 DOI: 10.1371/journal.pone.0105392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/23/2014] [Indexed: 12/15/2022] Open
Abstract
Background A recent report has shown that the phylogenetic origin of Helicobacter pylori based on multi-locus sequence typing (MLST) was significantly associated with the severity of gastritis in Colombia. However, the potential relationship between phylogenetic origin and clinical outcomes was not examined in that study. If the phylogenetic origin rather than virulence factors were truly associated with clinical outcomes, identifying a population at high risk for gastric cancer in Colombia would be relatively straightforward. In this study, we examined the phylogenetic origins of strains from gastric cancer and duodenal ulcer patients living in Bogota, Colombia. Methods We included 35 gastric cancer patients and 31 duodenal ulcer patients, which are considered the variant outcomes. The genotypes of cagA and vacA were determined by polymerase chain reaction. The genealogy of these Colombian strains was analyzed by MLST. Bacterial population structure was analyzed using STRUCTURE software. Results H. pylori strains from gastric cancer and duodenal ulcer patients were scattered in the phylogenetic tree; thus, we did not detect any difference in phylogenetic distribution between gastric cancer and duodenal ulcer strains in the hpEurope group in Colombia. Sixty-six strains, with one exception, were classified as hpEurope irrespective of the cagA and vacA genotypes, and type of disease. STRUCTURE analysis revealed that Colombian hpEurope strains have a phylogenetic connection to Spanish strains. Conclusions Our study showed that a phylogeographic origin determined by MLST was insufficient for distinguishing between gastric cancer and duodenal ulcer risk among hpEurope strains in the Andean region in Colombia. Our analysis also suggests that hpEurope strains in Colombia were primarily introduced by Spanish immigrants.
Collapse
Affiliation(s)
- Seiji Shiota
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Yuichi Matsuo
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Muhammad Miftahussurur
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Trang Thu Huyen Tran
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Tran Thanh Binh
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
- Department of Medicine-Gastroenterology, Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
21
|
Molina-Castro SE, Herrera D, Malespín-Bendaña W, Ramírez V, Une C. The geographic origin of Helicobacter pylori isolated from Costa Rican patients. Gut Microbes 2014; 5:517-21. [PMID: 25137097 DOI: 10.4161/gmic.32148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Helicobacter pylori infects a significant proportion of the world population and it is associated with pathologies which include chronic atrophic gastritis, peptic ulcer, and gastric neoplasias such as gastric adenocarcinoma and MALT lymphoma. Costa Rica has a high prevalence of the infection and an elevated incidence of gastric cancer and its associated mortality. The global population structure for H. pylori has been established using a MLST scheme. The population structure of the strains of H. pylori circulating in Costa Rica is currently unknown. We characterized the geographical origin of 24 H. pylori isolates from Costa Rican patients. We identified 142 new alleles for the genes included in the scheme and in eight of the 24 isolates from Costa Rican patients, all seven alleles sequenced were described for the first time. Twenty-one isolates from Costa Rican patients group with hpEurope strains and the remaining three isolates grouped with hspWAfrica isolates (Bayesian posterior probability values above 0.70, P = 0.05, after 2 000 000 generations). The obtained result in the MLST analysis was not unexpected and reflects the genetic composition of the Costa Rican population.
Collapse
Affiliation(s)
| | - Dayana Herrera
- Instituto de Investigaciones en Salud; Universidad de Costa Rica; San José; Costa Rica
| | | | - Vanessa Ramírez
- Instituto de Investigaciones en Salud; Universidad de Costa Rica; San José; Costa Rica
| | - Clas Une
- Instituto de Investigaciones en Salud; Universidad de Costa Rica; San José; Costa Rica
| |
Collapse
|
22
|
Linz B, Vololonantenainab CRR, Seck A, Carod JF, Dia D, Garin B, Ramanampamonjy RM, Thiberge JM, Raymond J, Breurec S. Population genetic structure and isolation by distance of Helicobacter pylori in Senegal and Madagascar. PLoS One 2014; 9:e87355. [PMID: 24498084 PMCID: PMC3907543 DOI: 10.1371/journal.pone.0087355] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 12/19/2013] [Indexed: 01/05/2023] Open
Abstract
Helicobacter pylori has probably infected the human stomach since our origins and subsequently diversified in parallel with their human hosts. The genetic population history of H. pylori can therefore be used as a marker for human migration. We analysed seven housekeeping gene sequences of H. pylori strains isolated from 78 Senegalese and 24 Malagasy patients and compared them with the sequences of strains from other geographical locations. H. pylori from Senegal and Madagascar can be placed in the previously described HpAfrica1 genetic population, subpopulations hspWAfrica and hspSAfrica, respectively. These 2 subpopulations correspond to the distribution of Niger-Congo speakers in West and most of subequatorial Africa (due to Bantu migrations), respectively. H. pylori appears as a single population in Senegal, indicating a long common history between ethnicities as well as frequent local admixtures. The lack of differentiation between these isolates and an increasing genetic differentiation with geographical distance between sampling locations in Africa was evidence for genetic isolation by distance. The Austronesian expansion that started from Taiwan 5000 years ago dispersed one of the 10 subgroups of the Austronesian language family via insular Southeast Asia into the Pacific and Madagascar, and hspMaori is a marker for the entire Austronesian expansion. Strain competition and replacement of hspMaori by hpAfrica1 strains from Bantu migrants are the probable reasons for the presence of hspSAfrica strains in Malagasy of Southeast Asian descent. hpAfrica1 strains appear to be generalist strains that have the necessary genetic diversity to efficiently colonise a wide host spectrum.
Collapse
Affiliation(s)
- Bodo Linz
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | | | - Abdoulaye Seck
- Laboratoire de Biologie Médicale, Institut Pasteur, Dakar, Senegal
| | | | - Daouda Dia
- Centre Hospitalier Le Dantec, Département de Gastro-entérologie, Dakar, Senegal
| | - Benoit Garin
- Laboratoire de Biologie Médicale, Institut Pasteur, Dakar, Senegal
- Laboratoire de Bactériologie expérimentale, Institut Pasteur, Antananarivo, Madagascar
| | - Rado Manitrala Ramanampamonjy
- Centre Hospitalier Universitaire Joseph Ravoahangy Befelatanana, Département de Gastro-entérologie, Antananarivo, Madagascar
| | - Jean-Michel Thiberge
- Plate-forme Génotypage des Pathogènes et Santé Publique, Institut Pasteur, Paris, France
| | - Josette Raymond
- Unité Postulante Pathogenèse de Helicobacter, Institut Pasteur, Paris, France
| | - Sebastien Breurec
- Laboratoire de Biologie Médicale, Institut Pasteur, Dakar, Senegal
- Institut Pasteur, Laboratoire de Biologie médicale, Bangui, République Centrafricaine
- * E-mail:
| |
Collapse
|
23
|
Human and Helicobacter pylori coevolution shapes the risk of gastric disease. Proc Natl Acad Sci U S A 2014; 111:1455-60. [PMID: 24474772 DOI: 10.1073/pnas.1318093111] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Helicobacter pylori is the principal cause of gastric cancer, the second leading cause of cancer mortality worldwide. However, H. pylori prevalence generally does not predict cancer incidence. To determine whether coevolution between host and pathogen influences disease risk, we examined the association between the severity of gastric lesions and patterns of genomic variation in matched human and H. pylori samples. Patients were recruited from two geographically distinct Colombian populations with significantly different incidences of gastric cancer, but virtually identical prevalence of H. pylori infection. All H. pylori isolates contained the genetic signatures of multiple ancestries, with an ancestral African cluster predominating in a low-risk, coastal population and a European cluster in a high-risk, mountain population. The human ancestry of the biopsied individuals also varied with geography, with mostly African ancestry in the coastal region (58%), and mostly Amerindian ancestry in the mountain region (67%). The interaction between the host and pathogen ancestries completely accounted for the difference in the severity of gastric lesions in the two regions of Colombia. In particular, African H. pylori ancestry was relatively benign in humans of African ancestry but was deleterious in individuals with substantial Amerindian ancestry. Thus, coevolution likely modulated disease risk, and the disruption of coevolved human and H. pylori genomes can explain the high incidence of gastric disease in the mountain population.
Collapse
|
24
|
Maldonado-Contreras A, Mane SP, Zhang XS, Pericchi L, Alarcón T, Contreras M, Linz B, Blaser MJ, Domínguez-Bello MG. Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance. BMC Microbiol 2013; 13:211. [PMID: 24050390 PMCID: PMC3849833 DOI: 10.1186/1471-2180-13-211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 08/28/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Helicobacter pylori has diverged in parallel to its human host, leading to distinct phylogeographic populations. Recent evidence suggests that in the current human mixing in Latin America, European H. pylori (hpEurope) are increasingly dominant at the expense of Amerindian haplotypes (hspAmerind). This phenomenon might occur via DNA recombination, modulated by restriction-modification systems (RMS), in which differences in cognate recognition sites (CRS) and in active methylases will determine direction and frequency of gene flow. We hypothesized that genomes from hspAmerind strains that evolved from a small founder population have lost CRS for RMS and active methylases, promoting hpEurope's DNA invasion. We determined the observed and expected frequencies of CRS for RMS in DNA from 7 H. pylori whole genomes and 110 multilocus sequences. We also measured the number of active methylases by resistance to in vitro digestion by 16 restriction enzymes of genomic DNA from 9 hpEurope and 9 hspAmerind strains, and determined the direction of DNA uptake in co-culture experiments of hspAmerind and hpEurope strains. RESULTS Most of the CRS were underrepresented with consistency between whole genomes and multilocus sequences. Although neither the frequency of CRS nor the number of active methylases differ among the bacterial populations (average 8.6 ± 2.6), hspAmerind strains had a restriction profile distinct from that in hpEurope strains, with 15 recognition sites accounting for the differences. Amerindians strains also exhibited higher transformation rates than European strains, and were more susceptible to be subverted by larger DNA hpEurope-fragments than vice versa. CONCLUSIONS The geographical variation in the pattern of CRS provides evidence for ancestral differences in RMS representation and function, and the transformation findings support the hypothesis of Europeanization of the Amerindian strains in Latin America via DNA recombination.
Collapse
|
25
|
Chiurillo MA, Moran Y, Cañas M, Valderrama E, Granda N, Sayegh M, Ramírez JL. Genotyping of Helicobacter pylori virulence-associated genes shows high diversity of strains infecting patients in western Venezuela. Int J Infect Dis 2013; 17:e750-6. [PMID: 23611633 DOI: 10.1016/j.ijid.2013.03.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 02/09/2013] [Accepted: 03/01/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Helicobacter pylori is a major cause of chronic gastritis and an established risk factor for gastric adenocarcinoma. This bacterium also exhibits an extraordinarily high genetic diversity. METHODS The genetic diversity of H. pylori strains from Venezuelan patients with chronic gastritis was evaluated by PCR-typing of vacA, cagA, iceA, and babA2 virulence-associated genes using DNA extracted directly from biopsies. The nucleotide sequence and prevalence of size variants of iceA1, iceA2, and babA2 PCR products were introduced in this analysis. RESULTS The frequency of vacA s1 was associated (p<0.01) with moderate/severe grades of atrophic gastritis. The cagA, iceA1, iceA2, and babA2 genotypes were found in 70.6%, 66.4%, 33.6%, and 92.3% of strains, respectively. The frequency of iceA2 and its subtype iceA2_D were higher (p<0.015) in cases with moderate/severe granulocytic inflammation. The most prevalent combined genotypes were vacA s1m1/cagA/iceA1/babA2 (26.3%), vacA s2m2/iceA1/babA2 (19.5%), and vacA s1m1/cagA/iceA2/babA2 (18.8%). Sequence analysis of iceA1, iceA2, and babA2 PCR-amplified fragments allowed us to define allelic variants and to increase the number of genotypes detected (from 19 to 62). A phylogenetic tree made with iceA1 sequences showed that the H. pylori strains analyzed here were grouped with those of Western origin. CONCLUSIONS Our results show that patients from the western region of Venezuela have an elevated prevalence of infection with H. pylori strains carrying known virulence genotypes with high genetic diversity. This highlights the importance of identifying gene variants for an early detection of virulent genotypes.
Collapse
Affiliation(s)
- Miguel Angel Chiurillo
- Laboratorio de Genética Molecular Dr. Jorge Yunis-Turbay, Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado (UCLA), Barquisimeto, Venezuela.
| | | | | | | | | | | | | |
Collapse
|
26
|
Haghighi MA, Mobarez AM, Salmanian AH, Moazeni M, Zali MR, Sadeghi M, Amani J. In silico experiment with an-antigen-toll like receptor-5 agonist fusion construct for immunogenic application to Helicobacter pylori. INDIAN JOURNAL OF HUMAN GENETICS 2013; 19:43-53. [PMID: 23901192 PMCID: PMC3722629 DOI: 10.4103/0971-6866.112885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUNDS Helicobacter pylori colonize the gastric mucosa of half of the world's population. Although it is classified as a definitive type I carcinogen by World Health Organization, there is no effective vaccine against this bacterium. H. pylori evade the host immune response by avoiding toll-like detection, such as detection via toll-like receptor-5 (TLR-5). Thus, a chimeric construct consisting of selected epitopes from virulence factors that is incorporated into a TLR-5 ligand (Pseudomonas flagellin) could result in more potent innate and adaptive immune responses. MATERIALS AND METHODS Based on the histocompatibility antigens of BALB/c mice, in silico techniques were used to select several fragments from H. pylori virulence factors with a high density of B- and T-cell epitopes. RESULTS These segments consist of cytotoxin-associated geneA (residue 162-283), neutrophil activating protein (residue 30-135) and outer inflammatory protein A (residue 155-268). The secondary and tertiary structure of the chimeric constructs and other bioinformatics analyses such as stability, solubility, and antigenicity were performed. The chimeric construct containing antigenic segments of H. pylori proteins was fused with the D3 domain of Pseudomonas flagellin. This recombinant chimeric gene was optimized for expression in Escherichia coli. The in silico results showed that the conserved C- and N-terminal domains of flagellin and the antigenicity of selected fragments were retained. DISCUSSION In silico analysis showed that Pseudomonas flagellin is a suitable platform for incorporation of an antigenic construct from H. pylori. This strategy may be an effective tool for the control of H. pylori and other persistent infections.
Collapse
Affiliation(s)
- Mohamad Ali Haghighi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ashraf Mohabati Mobarez
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Hatef Salmanian
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohamad Moazeni
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohamad Reza Zali
- Gastroenterology and Liver Disease Research center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Sadeghi
- Department of Biochemistry National Institute of Genetic Engineering and Biotechnology, Baqiyatallah Medical Science University, Tehran, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Baqiyatallah Medical Science University, Tehran, Iran
| |
Collapse
|
27
|
Dong QJ, Zhan SH, Wang LL, Xin YN, Jiang M, Xuan SY. Relatedness of Helicobacter pylori populations to gastric carcinogenesis. World J Gastroenterol 2012; 18:6571-6. [PMID: 23236231 PMCID: PMC3516211 DOI: 10.3748/wjg.v18.i45.6571] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/17/2012] [Accepted: 08/25/2012] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) is a Gram-negative bacterium that infects half of the human population. The infection is associated with chronic inflammation of the gastric mucosa and peptic ulcers. It is also a major risk factor for gastric cancer. Phylogenetic analysis of global strains reveals there are seven populations of H. pylori, including hpAfrica1, hpAfrica2, hpEastAsia, hpEurope, hpNEAfrica, hpAsia2 and hpSahul. These populations are consistent with their geographical origins, and possibly result from geographical separation of the bacterium leading to reduced bacterial recombination in some populations. For each population, H. pylori has evolved to possess genomic contents distinguishable from others. The hpEurope population is distinct in that it has the largest genome of 1.65 mbp on average, and the highest number of coding sequences. This confers its competitive advantage over other populations but at the cost of a lower infection rate. The large genomic size could be a cause of the frequent occurrence of the deletion of the cag pathogenicity island in H. pylori strains from hpEurope. The incidence of gastric cancer varies among different geographical regions. This can be attributed in part to different rates of infection of H. pylori. Recent studies found that different populations of H. pylori vary in their carcinogenic potential and contribute to the variation in incidence of gastric cancer among geographical regions. This could be related to the ancestral origin of H. pylori. Further studies are indicated to investigate the bacterial factors contributing to differential virulence and their influence on the clinical features in infected individuals.
Collapse
|
28
|
Moodley Y, Linz B, Bond RP, Nieuwoudt M, Soodyall H, Schlebusch CM, Bernhöft S, Hale J, Suerbaum S, Mugisha L, van der Merwe SW, Achtman M. Age of the association between Helicobacter pylori and man. PLoS Pathog 2012; 8:e1002693. [PMID: 22589724 PMCID: PMC3349757 DOI: 10.1371/journal.ppat.1002693] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 03/27/2012] [Indexed: 02/07/2023] Open
Abstract
When modern humans left Africa ca. 60,000 years ago (60 kya), they were already infected with Helicobacter pylori, and these bacteria have subsequently diversified in parallel with their human hosts. But how long were humans infected by H. pylori prior to the out-of-Africa event? Did this co-evolution predate the emergence of modern humans, spanning the species divide? To answer these questions, we investigated the diversity of H. pylori in Africa, where both humans and H. pylori originated. Three distinct H. pylori populations are native to Africa: hpNEAfrica in Afro-Asiatic and Nilo-Saharan speakers, hpAfrica1 in Niger-Congo speakers and hpAfrica2 in South Africa. Rather than representing a sustained co-evolution over millions of years, we find that the coalescent for all H. pylori plus its closest relative H. acinonychis dates to 88–116 kya. At that time the phylogeny split into two primary super-lineages, one of which is associated with the former hunter-gatherers in southern Africa known as the San. H. acinonychis, which infects large felines, resulted from a later host jump from the San, 43–56 kya. These dating estimates, together with striking phylogenetic and quantitative human-bacterial similarities show that H. pylori is approximately as old as are anatomically modern humans. They also suggest that H. pylori may have been acquired via a single host jump from an unknown, non-human host. We also find evidence for a second Out of Africa migration in the last 52,000 years, because hpEurope is a hybrid population between hpAsia2 and hpNEAfrica, the latter of which arose in northeast Africa 36–52 kya, after the Out of Africa migrations around 60 kya. We previously showed that the population history of H. pylori may be used as a marker for human migrations, including the demonstration that humans carried H. pylori out of Africa 60,000 years ago during their recent global expansions. But how long were humans infected by H. pylori prior to the out-of-Africa event? Here we showed that chimpanzees in Central-East Africa do not possess Helicobacter-like bacteria, as would have been expected for pathogen-host co-evolution over millions of years. Using H. pylori gene sequences isolated from San, a group of click-speaking hunter-gatherers, and numerous other sources, we calculated that humans have been infected with H. pylori for at least 88,000–116,000 years. Phylogenetic comparisons showed similar evolutionary histories for human and H. pylori lineages and suggest that this association stemmed from a single host jump. We showed that hpAfrica2, the most divergent H. pylori population, arose in the San and that their progenitors were the source of H. acinonychis which was acquired by large felines approximately 50,000 years ago. Furthermore, our data provided clear evidence for a recent second exodus Out of Africa in the last 52,000 years which was essential for the formation of the hybrid population that currently infects Europeans.
Collapse
Affiliation(s)
- Yoshan Moodley
- Max-Planck-Institut für Infektionsbiologie, Department of Molecular Biology, Berlin, Germany
- Konrad Lorenz Institute for Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Vienna, Austria
- * E-mail: (YM); (BL); (MA)
| | - Bodo Linz
- Max-Planck-Institut für Infektionsbiologie, Department of Molecular Biology, Berlin, Germany
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail: (YM); (BL); (MA)
| | - Robert P. Bond
- Hepatology and GI-Research Laboratory, Department of Immunology, University of Pretoria, Pretoria, South Africa
| | - Martin Nieuwoudt
- Hepatology and GI-Research Laboratory, Department of Immunology, University of Pretoria, Pretoria, South Africa
| | - Himla Soodyall
- Human Genomic Diversity and Disease Research Unit, Division of Human Genetics, School of Pathology, University of the Witwatersrand/National Health Laboratory Services, Johannesburg, South Africa
| | - Carina M. Schlebusch
- Human Genomic Diversity and Disease Research Unit, Division of Human Genetics, School of Pathology, University of the Witwatersrand/National Health Laboratory Services, Johannesburg, South Africa
| | - Steffi Bernhöft
- Max-Planck-Institut für Infektionsbiologie, Department of Molecular Biology, Berlin, Germany
| | - James Hale
- Environmental Research Institute and Department of Microbiology, University College Cork, Cork, Ireland
| | - Sebastian Suerbaum
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | | | - Schalk W. van der Merwe
- Hepatology and GI-Research Laboratory, Department of Immunology, University of Pretoria, Pretoria, South Africa
| | - Mark Achtman
- Max-Planck-Institut für Infektionsbiologie, Department of Molecular Biology, Berlin, Germany
- Environmental Research Institute and Department of Microbiology, University College Cork, Cork, Ireland
- * E-mail: (YM); (BL); (MA)
| |
Collapse
|
29
|
Correa P, Piazuelo MB. Evolutionary History of the Helicobacter pylori Genome: Implications for Gastric Carcinogenesis. Gut Liver 2012; 6:21-8. [PMID: 22375167 PMCID: PMC3286735 DOI: 10.5009/gnl.2012.6.1.21] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 12/26/2011] [Indexed: 01/06/2023] Open
Abstract
The genome of the bacterium Helicobacter pylori has evolved over the millennia since its migration out of Africa along with its human host approximately 60,000 years ago. Human migrations, after thousands of years of permanent settlement in those lands, resulted in seven prototypes of genetic populations of H. pylori with distinct geographical distributions. In all continents, present day isolates of H. pylori have molecular markers that reflect population migrations. The colonization of the Americas as well as the slave trade introduced European and African strains to the New World. The relationship between H. pylori genome and gastric cancer rates is linked to the presence of the cagA gene, but the knowledge on this subject is incomplete because other genes may be involved in certain populations. A new situation for Homo sapiens is the absence of H. pylori colonization in certain, mostly affluent, populations, apparently brought about by improved home sanitation and widespread use of antibiotics during the last decades. The disappearance of H. pylori from the human microbiota may be linked to emerging epidemics of esophageal adenocarcinoma, some allergic diseases such as asthma and some autoimmune disorders.
Collapse
Affiliation(s)
- Pelayo Correa
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| |
Collapse
|
30
|
Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori. INFECTION GENETICS AND EVOLUTION 2011; 12:203-13. [PMID: 22197766 DOI: 10.1016/j.meegid.2011.12.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/07/2011] [Accepted: 12/08/2011] [Indexed: 12/17/2022]
Abstract
Helicobacter pylori infection is linked to various gastroduodenal diseases; however, only approximately 20% of infected individuals develop severe diseases. Despite the high prevalence of H. pylori infection in Africa and South Asia, the incidence of gastric cancer in these areas is much lower than in other countries. Furthermore, the incidence of gastric cancer tends to decrease from north to south in East Asia. Such geographic differences in the pathology can be explained, at least in part, by the presence of different types of H. pylori virulence factors, especially cagA, vacA, and the right end of the cag pathogenicity island. The genotype of the virulence genes is also useful as a tool to track human migration utilizing the high genetic diversity and frequent recombination between different H. pylori strains. Multilocus sequence typing (MLST) analysis using seven housekeeping genes can also help to predict the history of human migrations. Population structure analysis based on MLST has revealed seven modern population types of H. pylori, which derived from six ancestral populations. Interestingly, the incidence of gastric cancer is closely related to the distribution of H. pylori populations. The different incidence of gastric cancer can be partly attributed to the different genotypes of H. pylori circulating in different geographic areas. Although approaches by MLST and virulence factors are effective, these methods focus on a small number of genes and may miss information conveyed by the rest of the genome. Genome-wide analyses using DNA microarray or whole-genome sequencing technology give a broad view on the genome of H. pylori. In particular, next-generation sequencers, which can read DNA sequences in less time and at lower costs than Sanger sequencing, enabled us to efficiently investigate not only the evolution of H. pylori, but also novel virulence factors and genomic changes related to drug resistance.
Collapse
|
31
|
Delgado-Rosado G, Dominguez-Bello MG, Massey SE. Positive selection on a bacterial oncoprotein associated with gastric cancer. Gut Pathog 2011; 3:18. [PMID: 22078307 PMCID: PMC3228766 DOI: 10.1186/1757-4749-3-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 11/11/2011] [Indexed: 01/01/2023] Open
Abstract
Background Helicobacter pylori is a vertically inherited gut commensal that is carcinogenic if it possesses the cag pathogenicity island (cag PaI); infection with H.pylori is the major risk factor for gastric cancer, the second leading cause of death from cancer worldwide (WHO). The cag PaI locus encodes the cagA gene, whose protein product is injected into stomach epithelial cells via a Type IV secretion system, also encoded by the cag PaI. Once there, the cagA protein binds to various cellular proteins, resulting in dysregulation of cell division and carcinogenesis. For this reason, cagA may be described as an oncoprotein. A clear understanding of the mechanism of action of cagA and its benefit to the bacteria is lacking.
Collapse
Affiliation(s)
- Gisela Delgado-Rosado
- Biology Department, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan, Puerto Rico, USA 00931.
| | | | | |
Collapse
|
32
|
Dominguez-Bello MG, Blaser MJ. The Human Microbiota as a Marker for Migrations of Individuals and Populations. ANNUAL REVIEW OF ANTHROPOLOGY 2011. [DOI: 10.1146/annurev-anthro-081309-145711] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Martin J. Blaser
- Departments of Medicine and Microbiology, New York University Langone Medical Center, New York, NY 10016;
| |
Collapse
|
33
|
de Sablet T, Piazuelo MB, Shaffer CL, Schneider BG, Asim M, Chaturvedi R, Bravo LE, Sicinschi LA, Delgado AG, Mera RM, Israel DA, Romero-Gallo J, Peek RM, Cover TL, Correa P, Wilson KT. Phylogeographic origin of Helicobacter pylori is a determinant of gastric cancer risk. Gut 2011; 60:1189-95. [PMID: 21357593 PMCID: PMC3133872 DOI: 10.1136/gut.2010.234468] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND AND AIMS Helicobacter pylori colonises the stomach in half of all humans, and is the principal cause of gastric cancer, the second leading cause of cancer death worldwide. While gastric cancer rates correlate with H pylori prevalence in some areas, there are regions where infection is nearly universal, but rates of gastric cancer are low. In the case of Colombia, there is a 25-fold increase in gastric cancer rate in the Andean mountain (high risk) region compared to the coastal (low risk) region, despite similarly high (∼90%) prevalence of H pylori in the two locations. Our aim was to investigate the ancestral origin of H pylori strains isolated from subjects in these high- and low-risk regions and to determine whether this is a predictive determinant of precancerous lesions. METHODS Multi-locus sequence typing was used to investigate phylogeographic origins of infecting H pylori strains isolated from subjects in the Pacific coast and Andes Mountains in the state of Nariño, Colombia. We analysed 64 subjects infected with cagA+ vacA s1m1 strains. Gastric biopsy slides from each individual were scored for histological lesions and evaluated for DNA damage by immunohistochemistry. RESULTS We show that strains from the high-risk region were all of European phylogeographic origin, whereas those from the low risk region were of either European (34%) or African origin (66%). European strain origin was strongly predictive of increased premalignant histological lesions and epithelial DNA damage, even in the low-risk region; African strain origin was associated with reduced severity of these parameters. CONCLUSION The phylogeographic origin of H pylori strains provides an explanation for geographic differences in cancer risk deriving from this infection.
Collapse
Affiliation(s)
- Thibaut de Sablet
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University School of Medicine, MRBIV, Room 1030C, 2215 Garland Avenue, Nashville, TN 37232, USA.
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Carrie L. Shaffer
- Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, USA
| | - Barbara G. Schneider
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Mohammad Asim
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA,Veterans Affairs Tennessee Valley Healthcare System, Nashville, USA
| | - Rupesh Chaturvedi
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA,Veterans Affairs Tennessee Valley Healthcare System, Nashville, USA
| | - Luis E. Bravo
- Department of Pathology, Universidad del Valle School of Medicine, Cali, Colombia
| | - Liviu A. Sicinschi
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Alberto G. Delgado
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Robertino M. Mera
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Dawn A. Israel
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Judith Romero-Gallo
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Richard M. Peek
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA,Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, USA,Veterans Affairs Tennessee Valley Healthcare System, Nashville, USA
| | - Timothy L. Cover
- Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, USA,Veterans Affairs Tennessee Valley Healthcare System, Nashville, USA,Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, USA
| | - Pelayo Correa
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA,Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, USA,Veterans Affairs Tennessee Valley Healthcare System, Nashville, USA
| |
Collapse
|
34
|
Breurec S, Guillard B, Hem S, Brisse S, Dieye FB, Huerre M, Oung C, Raymond J, Tan TS, Thiberge JM, Vong S, Monchy D, Linz B. Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia. PLoS One 2011; 6:e22058. [PMID: 21818291 PMCID: PMC3139604 DOI: 10.1371/journal.pone.0022058] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 06/14/2011] [Indexed: 12/16/2022] Open
Abstract
The human population history in Southeast Asia was shaped by numerous migrations and population expansions. Their reconstruction based on archaeological, linguistic or human genetic data is often hampered by the limited number of informative polymorphisms in classical human genetic markers, such as the hypervariable regions of the mitochondrial DNA. Here, we analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various countries in Southeast Asia and we provide evidence that H. pylori accompanied at least three ancient human migrations into this area: i) a migration from India introducing hpEurope bacteria into Thailand, Cambodia and Malaysia; ii) a migration of the ancestors of Austro-Asiatic speaking people into Vietnam and Cambodia carrying hspEAsia bacteria; and iii) a migration of the ancestors of the Thai people from Southern China into Thailand carrying H. pylori of population hpAsia2. Moreover, the H. pylori sequences reflect iv) the migrations of Chinese to Thailand and Malaysia within the last 200 years spreading hspEasia strains, and v) migrations of Indians to Malaysia within the last 200 years distributing both hpAsia2 and hpEurope bacteria. The distribution of the bacterial populations seems to strongly influence the incidence of gastric cancer as countries with predominantly hspEAsia isolates exhibit a high incidence of gastric cancer while the incidence is low in countries with a high proportion of hpAsia2 or hpEurope strains. In the future, the host range expansion of hpEurope strains among Asian populations, combined with human motility, may have a significant impact on gastric cancer incidence in Asia.
Collapse
Affiliation(s)
- Sebastien Breurec
- Unité de Biologie Médicale et Environnementale, Institut Pasteur, Dakar, Senegal.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Correa P, Piazuelo MB. Helicobacter pylori Infection and Gastric Adenocarcinoma. US GASTROENTEROLOGY & HEPATOLOGY REVIEW 2011; 7:59-64. [PMID: 21857882 PMCID: PMC3158605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Gastric adenocarcinoma is the second leading cause of cancer-related mortality worldwide. Infection with Helicobacter pylori is the strongest recognized risk factor for gastric adenocarcinoma. This bacterial species colonizes the stomach of more than half of the world's population; however, only a very small proportion of infected subjects develop adenocarcinoma. H. pylori causes a chronic gastritis that may last decades, and a multistep precancerous process is recognized for the most frequent histologic type of gastric adenocarcinoma: the intestinal type. The severity and long-term outcome of this infection is modulated by an increasing list of bacterial, host, and environmental factors, which interplay in a complex manner. Identification of individuals at high risk for gastric cancer that may enter a surveillance program and intervention during the precancerous process is the most suitable strategy for decreasing mortality due to this malignancy.
Collapse
Affiliation(s)
- Pelayo Correa
- Anne Potter Wilson Professor of Medicine, Vanderbilt University School of Medicine, Nashville
| | - M Blanca Piazuelo
- Research Instructor, Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville
| |
Collapse
|
36
|
|
37
|
Abstract
The role of infectious agents and chronic inflammation in carcinogenesis is being increasingly recognized. It has been estimated that about 18% of cancers are directly linked to infections, particularly gastric adenocarcinoma (Helicobacter pylori), cervical carcinoma (human papilloma viruses), and hepatocarcinoma (hepatitis B and C viruses). Multiple clinical trials of COX-2 inhibitors and other antiinflammatory agents have shown a beneficial effect on the development of diverse tumors, such as those of the colon, stomach, prostate, and breast. However, their mechanism of action is not completely understood and may differ among the infectious agents and tumor types. Because gastric adenocarcinomas account for more than 90% of all gastric malignancies, this review focuses on adenocarcinomas.
Collapse
Affiliation(s)
- M Blanca Piazuelo
- Division of Gastroenterology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| | | | | |
Collapse
|
38
|
Kersulyte D, Kalia A, Gilman RH, Mendez M, Herrera P, Cabrera L, Velapatiño B, Balqui J, Paredes Puente de la Vega F, Rodriguez Ulloa CA, Cok J, Hooper CC, Dailide G, Tamma S, Berg DE. Helicobacter pylori from Peruvian amerindians: traces of human migrations in strains from remote Amazon, and genome sequence of an Amerind strain. PLoS One 2010; 5:e15076. [PMID: 21124785 PMCID: PMC2993954 DOI: 10.1371/journal.pone.0015076] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 10/15/2010] [Indexed: 02/06/2023] Open
Abstract
Background The gastric pathogen Helicobacter pylori is extraordinary in its genetic diversity, the differences between strains from well-separated human populations, and the range of diseases that infection promotes. Principal Findings Housekeeping gene sequences from H. pylori from residents of an Amerindian village in the Peruvian Amazon, Shimaa, were related to, but not intermingled with, those from Asia. This suggests descent of Shimaa strains from H. pylori that had infected the people who migrated from Asia into The Americas some 15,000+ years ago. In contrast, European type sequences predominated in strains from Amerindian Lima shantytown residents, but with some 12% Amerindian or East Asian-like admixture, which indicates displacement of ancestral purely Amerindian strains by those of hybrid or European ancestry. The genome of one Shimaa village strain, Shi470, was sequenced completely. Its SNP pattern was more Asian- than European-like genome-wide, indicating a purely Amerind ancestry. Among its unusual features were two cagA virulence genes, each distinct from those known from elsewhere; and a novel allele of gene hp0519, whose encoded protein is postulated to interact with host tissue. More generally, however, the Shi470 genome is similar in gene content and organization to those of strains from industrialized countries. Conclusions Our data indicate that Shimaa village H. pylori descend from Asian strains brought to The Americas many millennia ago; and that Amerind strains are less fit than, and were substantially displaced by, hybrid or European strains in less isolated communities. Genome comparisons of H. pylori from Amerindian and other communities should help elucidate evolutionary forces that have shaped pathogen populations in The Americas and worldwide.
Collapse
Affiliation(s)
- Dangeruta Kersulyte
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Awdhesh Kalia
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Robert H. Gilman
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Asociacion Benefica PRISMA, Lima, Peru
- Department of International Health, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Melissa Mendez
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Phabiola Herrera
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Billie Velapatiño
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jacqueline Balqui
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Jaime Cok
- Policlinico Peruano Japones, Lima, Peru
| | - Catherine C. Hooper
- Departemento de Microbiologia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Giedrius Dailide
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sravya Tamma
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Douglas E. Berg
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Departments of Genetics and Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|
39
|
Sterling EJ, Gómez A, Porzecanski AL. A systemic view of biodiversity and its conservation: Processes, interrelationships, and human culture. Bioessays 2010; 32:1090-8. [DOI: 10.1002/bies.201000049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
40
|
Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses. J Bacteriol 2010; 192:3078-92. [PMID: 20400544 DOI: 10.1128/jb.00063-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Helicobacter pylori is the dominant member of the gastric microbiota and has been associated with an increased risk of gastric cancer and peptic ulcers in adults. H. pylori populations have migrated and diverged with human populations, and health effects vary. Here, we describe the whole genome of the cag-positive strain V225d, cultured from a Venezuelan Piaroa Amerindian subject. To gain insight into the evolution and host adaptation of this bacterium, we undertook comparative H. pylori genomic analyses. A robust multiprotein phylogenetic tree reflects the major human migration out of Africa, across Europe, through Asia, and into the New World, placing Amerindian H. pylori as a particularly close sister group to East Asian H. pylori. In contrast, phylogenetic analysis of the host-interactive genes vacA and cagA shows substantial divergence of Amerindian from Old World forms and indicates new genotypes (e.g., VacA m3) involving these loci. Despite deletions in CagA EPIYA and CRPIA domains, V225d stimulates interleukin-8 secretion and the hummingbird phenotype in AGS cells. However, following a 33-week passage in the mouse stomach, these phenotypes were lost in isolate V225-RE, which had a 15-kb deletion in the cag pathogenicity island that truncated CagA and eliminated some of the type IV secretion system genes. Thus, the unusual V225d cag architecture was fully functional via conserved elements, but the natural deletion of 13 cag pathogenicity island genes and the truncation of CagA impaired the ability to induce inflammation.
Collapse
|
41
|
Queiroz DMDM, Cunha RPDA, Saraiva IEB, Rocha AMC. Helicobacter pylori virulence factors as tools to study human migrations. Toxicon 2010; 56:1193-7. [PMID: 20144640 DOI: 10.1016/j.toxicon.2010.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 01/25/2010] [Accepted: 01/28/2010] [Indexed: 01/19/2023]
Abstract
Helicobacter pylori is one of the most common infections worldwide. In most individuals it consists in a lifelong host-pathogen relationship without consequences, but in some subjects it is associated with peptic ulcer disease and gastric cancer. Polymorphism in genes that code bacterial virulence factors, cagA and vacA, are independently associated with the infection severe outcomes and are geographically diverse. In the last decade, accumulated knowledge allowed to characterize typical H. pylori strain patterns for all the major human populations; patterns that can be used to study the origin of specific human groups. Thus, the presence or absence of cagA, cagA EPIYA genotypes, and vacA subtypes can be used as tools to study not only the geographic origin of specific human populations, but also to identify markers of historical contact between different ethnicities. We report here a study including a set of native Amazon Amerindians that had supposedly been some, but little, contact with European Brazilian colonizer and/or African slaves. They harbor H. pylori strains in a mixed pattern with Asian and Iberian Peninsula characteristics. It is possible that this finding represents H. pylori recombination upon short contact between human groups. Alternatively, it could be due to a founder effect from a small cluster of Asian origin native Americans.
Collapse
Affiliation(s)
- Dulciene Maria de Magalhães Queiroz
- Laboratory of Research in Bacteriology, Faculdade de Medicina, Universidade Federal de Minas Gerais. Av. Alfredo Balena 190/216., 30130-100 Belo Horizonte, MG, Brazil.
| | | | | | | |
Collapse
|
42
|
Abstract
Helicobacter pylori strains from different geographic areas exhibit clear phylogeographical differentiation; therefore, the genotypes of H. pylori strains can serve as markers for the migration of human populations. Currently, the genotypes of two virulence factors of H. pylori, cagA and vacA, and multilocus sequence typing (MLST) are widely used markers for genomic diversity within H. pylori populations. There are two types of cagA: the East Asian type and the Western type. In addition, the right end of the cag pathogenicity island is divided into five subtypes and there are distinct mosaic structures at the signal region and the middle region of vacA. Using combinations of the cagA, cag right end junction, and vacA genotypes, five major groups (East Asia type, South/Central Asia type, Iberian/Africa type and Europe type) have been defined according to geographical associations. MLST has revealed seven modern population types and six ancestral population types of H. pylori, and is a useful tool for mapping human migration patterns. Serial studies of large numbers of H. pylori strains, including strains isolated from aboriginal populations, show that MLST analysis provides more detailed information on human migration than does the analysis of human genetics. H. pylori infection is rapidly declining as a result of improvements in personal hygiene and quality of life. The molecular epidemiology of H. pylori infection has much to tell us and should be studied before it disappears entirely.
Collapse
Affiliation(s)
- Y Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu-city, Oita, Japan.
| |
Collapse
|