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Schoville SD, Burke RL, Dong DY, Ginsberg HS, Maestas L, Paskewitz SM, Tsao JI. Genome resequencing reveals population divergence and local adaptation of blacklegged ticks in the United States. Mol Ecol 2024; 33:e17460. [PMID: 38963031 DOI: 10.1111/mec.17460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/12/2024] [Accepted: 04/15/2024] [Indexed: 07/05/2024]
Abstract
Tick vectors and tick-borne disease are increasingly impacting human populations globally. An important challenge is to understand tick movement patterns, as this information can be used to improve management and predictive modelling of tick population dynamics. Evolutionary analysis of genetic divergence, gene flow and local adaptation provides insight on movement patterns at large spatiotemporal scales. We develop low coverage, whole genome resequencing data for 92 blacklegged ticks, Ixodes scapularis, representing range-wide variation across the United States. Through analysis of population genomic data, we find that tick populations are structured geographically, with gradual isolation by distance separating three population clusters in the northern United States, southeastern United States and a unique cluster represented by a sample from Tennessee. Populations in the northern United States underwent population contractions during the last glacial period and diverged from southern populations at least 50 thousand years ago. Genome scans of selection provide strong evidence of local adaptation at genes responding to host defences, blood-feeding and environmental variation. In addition, we explore the potential of low coverage genome sequencing of whole-tick samples for documenting the diversity of microbial pathogens and recover important tick-borne pathogens such as Borrelia burgdorferi. The combination of isolation by distance and local adaptation in blacklegged ticks demonstrates that gene flow, including recent expansion, is limited to geographical scales of a few hundred kilometres.
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Affiliation(s)
- Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Russell L Burke
- Department of Biology, Hofstra University, Hempstead, New York, USA
| | - Dahn-Young Dong
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Howard S Ginsberg
- United States Geological Survey, Eastern Ecological Science Center, Woodward Hall - PSE, Field Station at the University of Rhode Island, Kingston, Rhode Island, USA
| | - Lauren Maestas
- Cattle Fever Tick Research Laboratory, USDA, Agricultural Research Service, Edinburg, Texas, USA
| | - Susan M Paskewitz
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jean I Tsao
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, USA
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2
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Weng YM, Kavanaugh DH, Schoville SD. Evidence for Admixture and Rapid Evolution During Glacial Climate Change in an Alpine Specialist. Mol Biol Evol 2024; 41:msae130. [PMID: 38935588 PMCID: PMC11247348 DOI: 10.1093/molbev/msae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/30/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet, despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success surviving in highly heterogeneous environments. Population genomic analyses demonstrating how alpine species have adapted to novel environments with limited genetic diversity remain rare, yet are important in understanding the potential for species to respond to contemporary climate change. In this study, we explored the evolutionary history of alpine ground beetles in the Nebria ingens complex, including the demographic and adaptive changes that followed the last glacier retreat. We first tested alternative models of evolutionary divergence in the species complex. Using millions of genome-wide SNP markers from hundreds of beetles, we found evidence that the N. ingens complex has been formed by past admixture of lineages responding to glacial cycles. Recolonization of alpine sites involved a distributional range shift to higher elevation, which was accompanied by a reduction in suitable habitat and the emergence of complex spatial genetic structure. We tested several possible genetic pathways involved in adaptation to heterogeneous local environments using genome scan and genotype-environment association approaches. From the identified genes, we found enriched functions associated with abiotic stress responses, with strong evidence for adaptation to hypoxia-related pathways. The results demonstrate that despite rapid demographic change, alpine beetles in the N. ingens complex underwent rapid physiological evolution.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
- Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan
| | - David H Kavanaugh
- California Academy of Sciences, Department of Entomology, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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3
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Vernon-Roberts A, Premaratne M, Wright R, Keenan JI, Day AS. Profile of Helicobacter pylori infections among children in the South Island of New Zealand (2010-2021). Helicobacter 2024; 29:e13037. [PMID: 37983850 DOI: 10.1111/hel.13037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/12/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Helicobacter pylori is a gram-negative gut bacterium most often acquired during childhood. International guidelines state that children with suspected H. pylori infection should be referred to a gastroenterologist for investigation via gastroscopy and biopsy. Eradication therapy should be prescribed for children with peptic ulcer disease or following a treatment risk/benefit discussion for those with an incidental gastroscopy finding. Guidelines state that for children a "test-and-treat" approach is not warranted, contrasting recommendations for adults. The aim of this study was to profile pediatric H. pylori infections in the South Island of New Zealand (NZ) to determine diagnostic and management strategies, and adherence to international guidelines. MATERIALS AND METHODS Retrospective data for positive H. pylori tests between 2010 and 2021 were retrieved from hospitals and regional testing laboratories throughout the South Island (NZ) for children ≤18 years. Outcome data were retrieved from tertiary care hospital records; sociodemographic, testing methods, eradication therapy, and symptoms. RESULTS Two-hundred and forty children were identified: 105 (44%) male, mean age 13.2 years (SD 4.3). Participants of Pasifika, Asian, and Middle Eastern/Latin American/African heritage were overrepresented compared to the NZ census data. Overall, 138 (58%) children were diagnosed via stool antigen tests, 78 (32%) serum, and only 24 (10%) adhered to international guidelines in being confirmed via gastroscopy. Only 59 (25%) had a record of eradication therapy, and 39/59 (66%) were retested to determine eradication success, with 32 (82%) negative tests and seven (18%) remaining positive. Of the 181 (75%) that had eradication status unknown, 66 (28%) had a retest result available with 48 (73%) testing negative and 18 (27%) positive, suggesting a substantial proportion had received eradication therapy without adhering to international guidelines. CONCLUSIONS International guidelines were not adhered to for most children in the study cohort. Implications of this include cost, unnecessary venipuncture, and unjustified antibiotic exposure.
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Affiliation(s)
| | - Malshi Premaratne
- Department of Paediatrics, University of Otago Christchurch, Christchurch, New Zealand
| | - Raewyn Wright
- Department of Paediatrics, University of Otago Christchurch, Christchurch, New Zealand
| | - Jacqueline I Keenan
- Department of Surgery, University of Otago Christchurch, Christchurch, New Zealand
| | - Andrew S Day
- Department of Paediatrics, University of Otago Christchurch, Christchurch, New Zealand
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Phuc BH, Tuan VP, Binh TT, Tung PH, Tri TD, Dung HDQ, Thuan NPM, Fauzia KA, Tshibangu-Kabamba E, Alfaray RI, Saruuljavkhlan B, Matsumoto T, Akada J, Yamaoka Y. Comparative genomics of two Vietnamese Helicobacter pylori strains, CHC155 from a non-cardia gastric cancer patient and VN1291 from a duodenal ulcer patient. Sci Rep 2023; 13:8869. [PMID: 37258611 DOI: 10.1038/s41598-023-35527-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Helicobacter pylori is involved in the etiology and severity of several gastroduodenal diseases; however, plasticity of the H. pylori genome makes complete genome assembly difficult. We report here the full genomes of H. pylori strains CHC155 and VN1291 isolated from a non-cardia gastric cancer patient and a duodenal ulcer patient, respectively, and their virulence demonstrated by in vitro infection. Whole-genome sequences were obtained by combining long- and short-reads with a hybrid-assembly approach. Both CHC155 and VN1291 genome possessed four kinds of genomic island: a cag pathogenicity island (cagPAI), two type 4 secretion system islands within an integrative and conjugative element (tfs ICE), and prophage. CHC155 and VN1291 carried East Asian-type cagA and vacA s1m1, and outer membrane protein genes, including two copies of oipA. Corresponded to genetic determinants of antibiotic resistance, chromosomal mutations were identified in CHC155 (rdxA, gyrA, and 23S rRNA) and VN1291 (rdxA, 23S rRNA, and pbp1A). In vitro infection of AGS cells by both strains induced the cell scattering phenotype, tyrosine phosphorylation of CagA, and promoted high levels of IL8 secretion, indicating fully intact phenotypes of the cagPAI. Virulence genes in CHC155 and VN1291 genomes are crucial for H. pylori pathogenesis and are risk factors in the development of gastric cancer and duodenal ulcer. Our in vitro studies indicate that the strains CHC155 and VN1291 carry the pathogenic potential.
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Grants
- 21K08010 Ministry of Education, Culture, Sports, Science and Technology, Japan
- 21K07898 Ministry of Education, Culture, Sports, Science and Technology, Japan
- 221S0002 Ministry of Education, Culture, Sports, Science and Technology, Japan
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Affiliation(s)
- Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Faculty of Applied Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Pham Huu Tung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Tran Dinh Tri
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Ho Dang Quy Dung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | | | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Evariste Tshibangu-Kabamba
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan.
- Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University, Yufu, Oita, Japan.
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, USA.
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5
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Cohen ZP, Schoville SD, Hawthorne DJ. The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say). Mol Ecol 2023; 32:1425-1440. [PMID: 36591939 DOI: 10.1111/mec.16838] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/30/2022] [Accepted: 12/15/2022] [Indexed: 01/03/2023]
Abstract
Structural variation has been associated with genetic diversity and adaptation. Despite these observations, it is not clear what their relative importance is for evolution, especially in rapidly adapting species. Here, we examine the significance of structural polymorphisms in pesticide resistance evolution of the agricultural super-pest, the Colorado potato beetle, Leptinotarsa decemlineata. By employing a parent offspring trio sequencing procedure, we develop highly contiguous reference genomes to characterize structural variation. These updated assemblies represent >100-fold improvement of contiguity and include derived pest and ancestral nonpest individuals. We identify >200,000 structural variations, which appear to be nonrandomly distributed across the genome as they co-occur with transposable elements and genes. Structural variations intersect with exons in a large proportion of gene annotations (~20%) that are associated with insecticide resistance (including cytochrome P450s), development, and transcription. To understand the role structural variations play in adaptation, we measure their allele frequencies among an additional 57 individuals using whole genome resequencing data, which represents pest and nonpest populations of North America. Incorporating multiple independent tests to detect the signature of natural selection using SNP data, we identify 14 genes that are probably under positive selection, include structural variations, and SNPs of elevated frequency within the pest lineages. Among these, three are associated with insecticide resistance based on previous research. One of these genes, CYP4g15, is coinduced during insecticide exposure with glycosyltransferase-13, which is a duplicated gene enclosed within a structural variant adjacent to the CYP4g15 genic region. These results demonstrate the significance of structural variations as a genomic feature to describe species history, genetic diversity, and adaptation.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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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.
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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.
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7
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Fu HW, Lai YC. The Role of Helicobacter pylori Neutrophil-Activating Protein in the Pathogenesis of H. pylori and Beyond: From a Virulence Factor to Therapeutic Targets and Therapeutic Agents. Int J Mol Sci 2022; 24:ijms24010091. [PMID: 36613542 PMCID: PMC9820732 DOI: 10.3390/ijms24010091] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori neutrophil-activating protein (HP-NAP), a major virulence factor of H. pylori, plays a role in bacterial protection and host inflammation. HP-NAP activates a variety of innate immune cells, including neutrophils, monocytes, and mast cells, to induce their pro-oxidant and pro-inflammatory activities. This protein also induces T-helper type 1 (Th1) immune response and cytotoxic T lymphocyte (CTL) activity, supporting that HP-NAP is able to promote gastric inflammation by activation of adaptive immune responses. Thus, HP-NAP is a potential therapeutic target for the treatment of H. pylori-induced gastric inflammation. The inflammatory responses triggered by HP-NAP are mediated by a PTX-sensitive G protein-coupled receptor and Toll-like receptor 2. Drugs designed to block the interactions between HP-NAP and its receptors could alleviate the inflammation in gastric mucosa caused by H. pylori infection. In addition, HP-NAP acts as a promising therapeutic agent for vaccine development, allergy treatment, and cancer immunotherapy. The high antigenicity of HP-NAP makes this protein a component of vaccines against H. pylori infection. Due to its immunomodulatory activity to stimulate the Th1-inducing ability of dendritic cells, enhance Th1 immune response and CTL activity, and suppress Th2-mediated allergic responses, HP-NAP could also act as an adjuvant in vaccines, a drug candidate against allergic diseases, and an immunotherapeutic agent for cancer. This review highlights the role of HP-NAP in the pathogenesis of H. pylori and the potential for this protein to be a therapeutic target in the treatment of H. pylori infection and therapeutic agents against H. pylori-associated diseases, allergies, and cancer.
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Affiliation(s)
- Hua-Wen Fu
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan
- Correspondence: ; Tel.: +886-3-574-2485
| | - Yu-Chang Lai
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
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8
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Thorpe HA, Tourrette E, Yahara K, Vale FF, Liu S, Oleastro M, Alarcon T, Perets TT, Latifi-Navid S, Yamaoka Y, Martinez-Gonzalez B, Karayiannis I, Karamitros T, Sgouras DN, Elamin W, Pascoe B, Sheppard SK, Ronkainen J, Aro P, Engstrand L, Agreus L, Suerbaum S, Thorell K, Falush D. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nat Commun 2022; 13:6842. [PMID: 36369175 PMCID: PMC9652371 DOI: 10.1038/s41467-022-34475-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck.
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Affiliation(s)
- Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Elise Tourrette
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Filipa F Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Siqi Liu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Teresa Alarcon
- Department of Microbiology, Hospital Universitario La Princesa, Instituto de Investigación Sanitaria Princesa, Madrid, Spain
| | - Tsachi-Tsadok Perets
- Gastroenterology Laboratory, Rabin Medical Center, Petah Tikva, Israel
- Department of Digital Medical Technologies, Holon Institute of Technology, Holon, Israel
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Department of Medicine-Gastroenterology, Baylor College of Medicine, Houston, TX, USA
| | | | - Ioannis Karayiannis
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | | | | | - Wael Elamin
- G42 Healthcare, Abu Dhabi, UAE
- Elrazi University, Khartoum, Sudan
| | - Ben Pascoe
- Department of Biology, University of Oxford, Oxford, UK
| | - Samuel K Sheppard
- Ineos Oxford Institute, Department of Biology, University of Oxford, Oxford, UK
| | - Jukka Ronkainen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Primary Health Care Center, Tornio, Finland
| | | | - Lars Engstrand
- Center for Translational Microbiome Research, Department for Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Lars Agreus
- Division of Family Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Suerbaum
- Department of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
- DZIF German Center for Infection Research, Hannover-Braunschweig and Munich Partner Sites, Munich, Germany
| | - Kaisa Thorell
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Daniel Falush
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
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9
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Balamurugan M, Banerjee R, Kasibhatla SM, Achalere A, Joshi R. Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches. Front Genet 2022; 13:800083. [PMID: 35495132 PMCID: PMC9043288 DOI: 10.3389/fgene.2022.800083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
A total of two lineages of Mycobacterium tuberculosis var. africanum (Maf), L5 and L6, which are members of the Mycobacterium tuberculosis complex (MTBC), are responsible for causing tuberculosis in West Africa. Regions of difference (RDs) are usually used for delineation of MTBC. With increased data availability, single nucleotide polymorphisms (SNPs) promise to provide better resolution. Publicly available 380 Maf samples were analyzed for identification of “core-cluster-specific-SNPs,” while additional 270 samples were used for validation. RD-based methods were used for lineage-assignment, wherein 31 samples remained unidentified. The genetic diversity of Maf was estimated based on genome-wide SNPs using phylogeny and population genomics approaches. Lineage-based clustering (L5 and L6) was observed in the whole genome phylogeny with distinct sub-clusters. Population stratification using both model-based and de novo approaches supported the same observations. L6 was further delineated into three sub-lineages (L6.1–L6.3), whereas L5 was grouped as L5.1 and L5.2 based on the occurrence of RD711. L5.1 and L5.2 were further divided into two (L5.1.1 and L5.1.2) and four (L5.2.1–L5.2.4) sub-clusters, respectively. Unassigned samples could be assigned to definite lineages/sub-lineages based on clustering observed in phylogeny along with high-confidence posterior membership scores obtained during population stratification. Based on the (sub)-clusters delineated, “core-cluster-specific-SNPs” were derived. Synonymous SNPs (137 in L5 and 128 in L6) were identified as biomarkers and used for validation. Few of the cluster-specific missense variants in L5 and L6 belong to the central carbohydrate metabolism pathway which include His6Tyr (Rv0946c), Glu255Ala (Rv1131), Ala309Gly (Rv2454c), Val425Ala and Ser112Ala (Rv1127c), Gly198Ala (Rv3293) and Ile137Val (Rv0363c), Thr421Ala (Rv0896), Arg442His (Rv1248c), Thr218Ile (Rv1122), and Ser381Leu (Rv1449c), hinting at the differential growth attenuation. Genes harboring multiple (sub)-lineage-specific “core-cluster” SNPs such as Lys117Asn, Val447Met, and Ala455Val (Rv0066c; icd2) present across L6, L6.1, and L5, respectively, hinting at the association of these SNPs with selective advantage or host-adaptation. Cluster-specific SNPs serve as additional markers along with RD-regions for Maf delineation. The identified SNPs have the potential to provide insights into the genotype–phenotype correlation and clues for endemicity of Maf in the African population.
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Angst P, Ebert D, Fields PD. Demographic history shapes genomic variation in an intracellular parasite with a wide geographic distribution. Mol Ecol 2022; 31:2528-2544. [DOI: 10.1111/mec.16419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Peter D. Fields
- Department of Environmental Sciences, Zoology University of Basel Vesalgasse 1 4051 Basel Switzerland
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11
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Kato I, Zhang J, Sun J. Bacterial-Viral Interactions in Human Orodigestive and Female Genital Tract Cancers: A Summary of Epidemiologic and Laboratory Evidence. Cancers (Basel) 2022; 14:425. [PMID: 35053587 PMCID: PMC8773491 DOI: 10.3390/cancers14020425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Infectious agents, including viruses, bacteria, fungi, and parasites, have been linked to pathogenesis of human cancers, whereas viruses and bacteria account for more than 99% of infection associated cancers. The human microbiome consists of not only bacteria, but also viruses and fungi. The microbiome co-residing in specific anatomic niches may modulate oncologic potentials of infectious agents in carcinogenesis. In this review, we focused on interactions between viruses and bacteria for cancers arising from the orodigestive tract and the female genital tract. We examined the interactions of these two different biological entities in the context of human carcinogenesis in the following three fashions: (1) direct interactions, (2) indirect interactions, and (3) no interaction between the two groups, but both acting on the same host carcinogenic pathways, yielding synergistic or additive effects in human cancers, e.g., head and neck cancer, liver cancer, colon cancer, gastric cancer, and cervical cancer. We discuss the progress in the current literature and summarize the mechanisms of host-viral-bacterial interactions in various human cancers. Our goal was to evaluate existing evidence and identify gaps in the knowledge for future directions in infection and cancer.
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Affiliation(s)
- Ikuko Kato
- Department of Oncology and Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jilei Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Sun
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
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12
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Wilkinson DJ, Dickins B, Robinson K, Winter JA. Genomic diversity of Helicobacter pylori populations from different regions of the human stomach. Gut Microbes 2022; 14:2152306. [PMID: 36469575 PMCID: PMC9728471 DOI: 10.1080/19490976.2022.2152306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Individuals infected with Helicobacter pylori harbor unique and diverse populations of quasispecies, but diversity between and within different regions of the human stomach and the process of bacterial adaptation to each location are not yet well understood. We applied whole-genome deep sequencing to characterize the within- and between-stomach region genetic diversity of H. pylori populations from paired antrum and corpus biopsies of 15 patients, along with single biopsies from one region of an additional 3 patients, by scanning allelic diversity. We combined population deep sequencing with more conventional sequencing of multiple H. pylori single colony isolates from individual biopsies to generate a unique dataset. Single colony isolates were used to validate the scanning allelic diversity pipelines. We detected extensive population allelic diversity within the different regions of each patient's stomach. Diversity was most commonly found within non-coding, hypothetical, outer membrane, restriction modification system, virulence, lipopolysaccharide biosynthesis, efflux systems, and chemotaxis-associated genes. Antrum and corpus populations from the same patient grouped together phylogenetically, indicating that most patients were initially infected with a single strain, which then diversified. Single colonies from the antrum and corpus of the same patients grouped into distinct clades, suggesting mechanisms for within-location adaptation across multiple H. pylori isolates from different patients. The comparisons made available by combined sequencing and analysis of isolates and populations enabled comprehensive analysis of the genetic changes associated with H. pylori diversification and stomach region adaptation.
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Affiliation(s)
- Daniel James Wilkinson
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
- School of Science and Technology, Nottingham Trent University, UK
| | - Benjamin Dickins
- School of Science and Technology, Nottingham Trent University, UK
| | - Karen Robinson
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Jody Anne Winter
- School of Science and Technology, Nottingham Trent University, UK
- CONTACT Jody Anne Winter School of Science and Technology, Nottingham Trent University Clifton Campus, Clifton Lane, NottinghamNG118NS, UK
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13
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Tshibangu-Kabamba E, Phuc BH, Tuan VP, Fauzia KA, Kabongo-Tshibaka A, Kayiba NK, Rosas-Aguirre A, Devleesschauwer B, Cimuanga-Mukanya A, Ngoma Kisoko PDJ, Matsumoto T, Akada J, Disashi GT, Mumba Ngoyi D, Kido Y, Speybroeck N, Yamaoka Y. Assessment of the diagnostic accuracy and relevance of a novel ELISA system developed for seroepidemiologic surveys of Helicobacter pylori infection in African settings. PLoS Negl Trop Dis 2021; 15:e0009763. [PMID: 34499649 PMCID: PMC8455143 DOI: 10.1371/journal.pntd.0009763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 09/21/2021] [Accepted: 08/25/2021] [Indexed: 01/18/2023] Open
Abstract
Beside diagnostic uncertainties due to the lack of a perfect gold standard test for Helicobacter pylori infection, the diagnosis and the prevalence estimation for this infection encounter particular challenges in Africa including limited diagnostic tools and specific genetic background. We developed and evaluated the accuracy of an enzyme-linked immunosorbent assay (ELISA) system tailored for H. pylori genetics in Africa (HpAfr-ELISA). Strains belonging to main genetic populations infecting Africans were exploited as sources for whole-cell antigens to establish in-house the ELISA system. A phase II unmatched case-control study explored the diagnostic accuracy of the HpAfr-ELISA using a training set of samples collected from dyspeptic patients from Kinshasa, the Democratic Republic of Congo (DRC) who had been tested with invasive standard tests (i.e., histology, culture, and rapid urease test) in 2017. Then the assay was cross-validated through a community-based survey assessing the prevalence of H. pylori and associated factors in 425 adults from Mbujimayi, DRC in 2018. Bayesian inferences were used to deal with statistical uncertainties of estimates (true prevalence, sensitivity, and specificity) in the study population. At its optimal cut-off-value 20.2 U/mL, the assay achieved an estimated sensitivity of 97.6% (95% credible interval [95%CrI]: 89.2; 99.9%) and specificity of 90.5% (95%CrI: 78.6; 98.5). Consistent outcomes obtained at repeated tests attested the robustness of the assay (negative and positive agreements always > 70%). The true prevalence of H. pylori was estimated 53.8% [95%CrI: 42.8; 62.7%]. Increasing age (adjusted odds ratio [aOR] > 1.0 [95% confidence interval (CI): > 1.0; 1.1]; p<0.001), overcrowding households (aOR = 3.2 [95%CI: 2.0; 5.1]; p<0.001), and non-optimal hand hygiene (aOR = 4.5 [95%CI: 2.0; 11.4]; p = 0.001) were independently associated with the H. pylori-seropositivity. The novel ELISA system has demonstrated good diagnostic accuracy and potential usefulness for management and mitigation strategies for H. pylori infection in African settings.
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Affiliation(s)
- Evariste Tshibangu-Kabamba
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Department of Internal Medicine, Faculty of Medicine, University of Mbujimayi, Mbujimayi, DR Congo
- Research Center for Infectious Diseases Sciences & Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Department of Endoscopy, Cho Ray Hospital, Cho Ray, Vietnam
| | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | | | - Nadine Kalenda Kayiba
- Research Institute of Health and Society (IRSS), Université catholoique de Louvain, Brussels, Belgium
- Department of Public Health, Faculty of Medicine, University of Mbujimayi, Mbujimayi, DR Congo
| | - Angel Rosas-Aguirre
- Research Institute of Health and Society (IRSS), Université catholoique de Louvain, Brussels, Belgium
| | - Brecht Devleesschauwer
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Ghent University, Merelbeke, Belgium
| | - Alain Cimuanga-Mukanya
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Department of Internal Medicine, Faculty of Medicine, University of Mbujimayi, Mbujimayi, DR Congo
| | - Patrick de Jésus Ngoma Kisoko
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Kinshasa, Kinshasa, DR Congo
- Department of Gastroenterology and Hepatology, General Referential Hospital of Bukavu, Bukavu, DR Congo
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Ghislain Tumba Disashi
- Department of Internal Medicine, Faculty of Medicine, University of Mbujimayi, Mbujimayi, DR Congo
| | - Dieudonné Mumba Ngoyi
- Department of Parasitology, National Institute of Biomedical Research, Kinshasa, DR Congo
| | - Yasutoshi Kido
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Research Center for Infectious Diseases Sciences & Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Niko Speybroeck
- Research Institute of Health and Society (IRSS), Université catholoique de Louvain, Brussels, Belgium
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Department of Medicine, Gastroenterology section, Baylor College of Medicine, Houston, Texas, United States of America
- Global Oita Medical Advanced Research Center for Health, Oita University, Yufu, Japan
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14
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Jiang X, Xu Z, Zhang T, Li Y, Li W, Tan H. Whole-Genome-Based Helicobacter pylori Geographic Surveillance: A Visualized and Expandable Webtool. Front Microbiol 2021; 12:687259. [PMID: 34408729 PMCID: PMC8366602 DOI: 10.3389/fmicb.2021.687259] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/07/2021] [Indexed: 01/08/2023] Open
Abstract
Helicobacter pylori exhibit specific geographic distributions that are related to clinical outcomes. Despite the high infection rate of H. pylori throughout the world, the genetic epidemiology surveillance of H. pylori still needs to be improved. This study used the single nucleotide polymorphisms (SNPs) profiling approach based on whole genome sequencing (WGS) to facilitate genomic population analyses of H. pylori and encourage the dissemination of microbial genotyping strategies worldwide. A total number of 1,211 public H. pylori genomes were downloaded and used to construct the typing tool, named HpTT (H. pylori Typing Tool). Combined with the metadata, we developed two levels of genomic typing, including a continent-scale and a country scale that nested in the continent scale. Results showed that Asia was the largest isolate source in our dataset, while isolates from Europe and Oceania were comparatively more widespread. More specifically, Switzerland and Australia are the main sources of widespread isolates in their corresponding continents. To integrate all the typing information and enable researchers to compare their dataset against the existing global database easily and rapidly, a user-friendly website (https://db.cngb.org/HPTT/) was developed with both genomic typing tools and visualization tools. To further confirm the validity of the website, ten newly assembled genomes were downloaded and tested precisely located on the branch as we expected. In summary, the H. pylori typing tool (HpTT) is a novel genomic epidemiological tool that can achieve high-resolution analysis of genomic typing and visualizing simultaneously, providing insights into the genetic population structure, evolution analysis, and epidemiological surveillance of H. pylori.
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Affiliation(s)
- Xiaosen Jiang
- BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Xu
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | | | - Yuan Li
- BGI-Shenzhen, Shenzhen, China
| | - Wei Li
- BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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15
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Ailloud F, Estibariz I, Suerbaum S. Evolved to vary: genome and epigenome variation in the human pathogen Helicobacter pylori. FEMS Microbiol Rev 2021; 45:5900976. [PMID: 32880636 DOI: 10.1093/femsre/fuaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/31/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is a Gram-negative, spiral shaped bacterium that selectively and chronically infects the gastric mucosa of humans. The clinical course of this infection can range from lifelong asymptomatic infection to severe disease, including peptic ulcers or gastric cancer. The high mutation rate and natural competence typical of this species are responsible for massive inter-strain genetic variation exceeding that observed in all other bacterial human pathogens. The adaptive value of such a plastic genome is thought to derive from a rapid exploration of the fitness landscape resulting in fast adaptation to the changing conditions of the gastric environment. Nevertheless, diversity is also lost through recurrent bottlenecks and H. pylori's lifestyle is thus a perpetual race to maintain an appropriate pool of standing genetic variation able to withstand selection events. Another aspect of H. pylori's diversity is a large and variable repertoire of restriction-modification systems. While not yet completely understood, methylome evolution could generate enough transcriptomic variation to provide another intricate layer of adaptive potential. This review provides an up to date synopsis of this rapidly emerging area of H. pylori research that has been enabled by the ever-increasing throughput of Omics technologies and a multitude of other technological advances.
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Affiliation(s)
- Florent Ailloud
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Iratxe Estibariz
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 München, Germany.,DZIF Deutsches Zentrum für Infektionsforschung, Partner Site Munich, Pettenkoferstr. 9a, 80336 München, Germany.,National Reference Center for Helicobacter pylori, Pettenkoferstr. 9a, 80336 München, Germany
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16
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Excofffier L, Marchi N, Marques DA, Matthey-Doret R, Gouy A, Sousa VC. fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics 2021; 37:4882-4885. [PMID: 34164653 PMCID: PMC8665742 DOI: 10.1093/bioinformatics/btab468] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 01/25/2023] Open
Abstract
Motivation fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework. Results Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes. Availability and implementation fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.
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Affiliation(s)
- Laurent Excofffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Nina Marchi
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Alexander Marques
- Life Science Division, Natural History Museum Basel, 4051 Basel, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG swiss Federal institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Remi Matthey-Doret
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Alexandre Gouy
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Gouy Data Consulting, 1026 Denges, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
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17
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Abstract
The peopling of Siberia and the Americas is intriguing for archaeologists, linguists, and human geneticists, but despite significant recent developments, many details remain controversial. Here, we provide insights based on genetic diversity within Helicobacter pylori, a bacterium that infects 50% of all humans. H. pylori strains were collected from across eastern Eurasia and the Americas. Sequence analyses indicated that Siberia contains both anciently diverged and recently admixed bacteria, supporting both human persistence over the last glacial maximum and more recent human recolonization. We inferred a single migration across the Bering land bridge, accompanied by a dramatic reduction in effective population size, followed by bidirectional Holocene gene flow between Asia and the Americas. The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.
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18
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Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host Microbe 2021; 29:1167-1176.e9. [PMID: 34111423 PMCID: PMC8288446 DOI: 10.1016/j.chom.2021.05.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/19/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023]
Abstract
Human gut bacterial strains can co-exist with their hosts for decades, but little is known about how these microbes persist and disperse, and evolve thereby. Here, we examined these processes in 5,278 adult and infant fecal metagenomes, longitudinally sampled in individuals and families. Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota. These “tenacious” bacteria show high levels of genetic adaptation to the human host but a high probability of loss upon antibiotic interventions. By contrast, heredipersistent bacteria, notably Firmicutes, often rely on dispersal strategies with weak phylogeographic patterns but strong family transmissions, likely related to sporulation. These analyses describe how different dispersal strategies can lead to the long-term persistence of human gut microbes with implications for gut flora modulations. Bacterial strains may persist within family members through transfer Bacteria adapt dispersal strategies: heredipersistent, spatiopersistent, and tenacious Dispersal strategies correlate with genetic bottlenecks and effective population size
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Affiliation(s)
- Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK; Digital Biology, Earlham Institute, NR4 7UZ Norwich, UK; European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.
| | - Toni I Gossmann
- Department of Animal Behaviour, Bielefeld University, Bielefeld DE-33501, Germany
| | - Clémence Frioux
- Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK; Inria, INRAE, CNRS, Univ. Bordeaux, 33405 Talence, France
| | - Ezgi Özkurt
- Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK; Digital Biology, Earlham Institute, NR4 7UZ Norwich, UK
| | - Pernille Neve Myers
- Clinical Microbiomics A/S, Copenhagen, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Pamela Ferretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Michael Kuhn
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 750 07 Uppsala, Sweden; Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia
| | | | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, Berlin, Germany; Yonsei Frontier Lab (YFL), Yonsei University, Seoul 03722, South Korea; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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19
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Suganuma M, Watanabe T, Sueoka E, Lim IK, Fujiki H. Role of TNF-α-Inducing Protein Secreted by Helicobacter pylori as a Tumor Promoter in Gastric Cancer and Emerging Preventive Strategies. Toxins (Basel) 2021; 13:181. [PMID: 33804551 PMCID: PMC7999756 DOI: 10.3390/toxins13030181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/20/2021] [Accepted: 02/21/2021] [Indexed: 12/24/2022] Open
Abstract
The tumor necrosis factor-α (TNF-α)-inducing protein (tipα) gene family, comprising Helicobacter pylori membrane protein 1 (hp-mp1) and tipα, has been identified as a tumor promoter, contributing to H. pylori carcinogenicity. Tipα is a unique H. pylori protein with no similarity to other pathogenicity factors, CagA, VacA, and urease. American H. pylori strains cause human gastric cancer, whereas African strains cause gastritis. The presence of Tipα in American and Euro-Asian strains suggests its involvement in human gastric cancer development. Tipα secreted from H. pylori stimulates gastric cancer development by inducing TNF-α, an endogenous tumor promoter, through its interaction with nucleolin, a Tipα receptor. This review covers the following topics: tumor-promoting activity of the Tipα family members HP-MP1 and Tipα, the mechanism underlying this activity of Tipα via binding to the cell-surface receptor, nucleolin, the crystal structure of rdel-Tipα and N-terminal truncated rTipα, inhibition of Tipα-associated gastric carcinogenesis by tumor suppressor B-cell translocation gene 2 (BTG2/TIS21), and new strategies to prevent and treat gastric cancer. Thus, Tipα contributes to the carcinogenicity of H. pylori by a mechanism that differs from those of CagA and VacA.
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Affiliation(s)
- Masami Suganuma
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Tatsuro Watanabe
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Nabeshima, Saga 849-8501, Japan;
| | - Eisaburo Sueoka
- Department of Clinical Laboratory Medicine, Faculty of Medicine, Saga University, Nabeshima, Saga 849-8501, Japan; (E.S.); (H.F.)
| | - In Kyoung Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon 16499, Gyeonggi-do, Korea;
| | - Hirota Fujiki
- Department of Clinical Laboratory Medicine, Faculty of Medicine, Saga University, Nabeshima, Saga 849-8501, Japan; (E.S.); (H.F.)
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20
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Momigliano P, Florin AB, Merilä J. Biases in Demographic Modeling Affect Our Understanding of Recent Divergence. Mol Biol Evol 2021; 38:2967-2985. [PMID: 33624816 PMCID: PMC8233503 DOI: 10.1093/molbev/msab047] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Testing among competing demographic models of divergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic divergence scenarios, failure to account for population size (Ne) changes in daughter and ancestral populations leads to strong biases in divergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots (Scophthalmus maximus) by testing 16 isolation with migration (IM) and 16 secondary contact (SC) scenarios, modeling changes in Ne as well as the effects of linked selection and barrier loci. Failure to account for changes in Ne resulted in selecting SC models with long periods of strict isolation and divergence times preceding the formation of the Baltic Sea. In contrast, models accounting for Ne changes suggest recent (<6 kya) divergence with constant gene flow. We further show how interpreting genomic landscapes of differentiation can help discerning among competing models. For example, in the turbot data, islands of differentiation show signatures of recent selective sweeps, rather than old divergence resisting secondary introgression. The results have broad implications for the study of population divergence by highlighting the potential effects of unmodeled changes in Ne on demographic inference. Tested models should aim at representing realistic divergence scenarios for the target taxa, and extreme caution should always be exercised when interpreting results of demographic modeling.
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Affiliation(s)
- Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Ann-Britt Florin
- Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Division of Ecology and Biodiversity, Faculty of Science, The University of Hong Kong, Hong Kong SAR
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21
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Mwangi C, Njoroge S, Tshibangu-Kabamba E, Moloo Z, Rajula A, Devani S, Matsumoto T, Nyerere K, Kariuki S, Revathi G, Yamaoka Y. Whole Genome Sequencing Reveals Virulence Potentials of Helicobacter pylori Strain KE21 Isolated from a Kenyan Patient with Gastric Signet Ring Cell Carcinoma. Toxins (Basel) 2020; 12:E556. [PMID: 32872465 PMCID: PMC7551074 DOI: 10.3390/toxins12090556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori (H.pylori) infection is etiologically associated with severe diseases including gastric cancer; but its pathogenicity is deeply shaped by the exceptional genomic diversification and geographic variation of the species. The clinical relevance of strains colonizing Africa is still debated. This study aimed to explore genomic features and virulence potentials of H. pylori KE21, a typical African strain isolated from a native Kenyan patient diagnosed with a gastric cancer. A high-quality circular genome assembly of 1,648,327 bp (1590 genes) obtained as a hybrid of Illumina Miseq short reads and Oxford Nanopore MinION long reads, clustered within hpAfrica1 population. This genome revealed a virulome and a mobilome encoding more than hundred features potentiating a successful colonization, persistent infection, and enhanced disease pathogenesis. Furthermore, through an experimental infection of gastric epithelial cell lines, strain KE21 showed the ability to promote interleukin-8 production and to induce cellular alterations resulting from the injection of a functional CagA oncogene protein into the cells. This study shows that strain KE21 is potentially virulent and can trigger oncogenic pathways in gastric epithelial cells. Expended genomic and clinical explorations are required to evaluate the epidemiological importance of H. pylori infection and its putative complications in the study population.
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Affiliation(s)
- Catherine Mwangi
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (C.M.); (S.N.); (K.N.)
- Department of Medical Microbiology and Parasitology, Kenyatta University, Nairobi P.O. Box 43844-00100, Kenya
| | - Stephen Njoroge
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (C.M.); (S.N.); (K.N.)
- Department of Medical Microbiology, Technical University of Kenya, Nairobi P.O. Box 52428, Kenya
| | - Evariste Tshibangu-Kabamba
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (T.M.)
| | - Zahir Moloo
- Department of Pathology and Laboratory Medicine, Aga Khan Hospital University, Nairobi P.O. Box 37002-00100, Kenya; (Z.M.); (G.R.)
| | - Allan Rajula
- Gastroenterology section, Aga Khan Hospital University, Nairobi P.O. Box 37002-00100, Kenya; (A.R.); (S.D.)
| | - Smita Devani
- Gastroenterology section, Aga Khan Hospital University, Nairobi P.O. Box 37002-00100, Kenya; (A.R.); (S.D.)
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (T.M.)
| | - Kimang’a Nyerere
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (C.M.); (S.N.); (K.N.)
| | - Samuel Kariuki
- Kenya Medical Research Institute, Nairobi P.O. Box 20778-00202, Kenya;
| | - Gunturu Revathi
- Department of Pathology and Laboratory Medicine, Aga Khan Hospital University, Nairobi P.O. Box 37002-00100, Kenya; (Z.M.); (G.R.)
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (T.M.)
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22
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Jalili M, Mahmoodabadi KA, Sayehmiri K. Relationship between Helicobacter pylori and Periodontal Diseases: A Meta-Analysis Study and Systematic Review. Open Dent J 2020. [DOI: 10.2174/1874210602014010362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Objective:
The present study aimed at the evaluation of the association between H. pylori and periodontal diseases by systematic review and meta-analysis study.
Materials and Methods:
We searched databases, including PubMed, SID, Magiran, Google Scholar, and Iranmedex using the following keywords in English: H. pylori, tooth decay, oral infection, dental infection, gingival infection and periodontal diseases. Data was analyzed using a meta-analysis and random effect model. Heterogeneity of studies was assessed using the I2 index, and data was finally analyzed with STATA (Version 11.2).
Results:
Among 10 articles reviewed that included 56,334 samples, results showed that association between H. pylori and periodontal diseases was significant with OR (odds ratio) = 1.13 (95% CI: 1.04 to 1.24).
Conclusion:
The results reveal that H. pylori can be one of the main causes of periodontal diseases. Thus, a novel way should be employed for the complete management of H. pylori infections.
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23
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Lamichhane B, Wise MJ, Chua EG, Marshall BJ, Tay CY. A novel taxon selection method, aimed at minimizing recombination, clarifies the discovery of a new sub-population of Helicobacter pylori from Australia. Evol Appl 2020; 13:278-289. [PMID: 31993076 PMCID: PMC6976958 DOI: 10.1111/eva.12864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/21/2019] [Accepted: 08/26/2019] [Indexed: 12/16/2022] Open
Abstract
We present a novel method for taxon selection, the aim being to minimize problems arising from highly recombinant species such as Helicobacter pylori. Helicobacter pylori has accompanied modern-human migration out of Africa and is marked by a phylogeographic strain distribution, which has been exploited to add an extra layer of information about human migrations to that obtained from human sources. However, H. pylori's genome has high sequence heterogeneity combined with a very high rate of recombination, causing major allelic diversification across strains. On the other hand, recombination events that have become preserved in sub-populations are a useful source of phylogenetic information. This creates a potential problem in selecting representative strains for particular genetic or phylogeographic clusters and generally ameliorating the impact on analyses of extensive low-level recombination. To address this issue, we perform multiple population structure-based analyses on core genomes to select exemplar strains, called 'quintessents', which exhibit limited recombination. In essence, quintessent strains are representative of their specific phylogenetic clades and can be used to refine the current MLST concatenation-based population structure classification system. The use of quintessents reduces the noise due to local recombination events, while preserving recombination events that have become fixed in sub-populations. We illustrate the method with an analysis of core genome concatenations from 185 H. pylori strains, which reveals a recent speciation event resulting from the recombination of strains from phylogeographic clade hpSahul, carried by Aboriginal Australians, and hpEurope, carried by some of the people who arrived in Australia over the past 200 years. The signal is much clearer when based on quintessent strains, but absent from the analysis based on MLST concatenations.
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Affiliation(s)
- Binit Lamichhane
- Helicobacter pylori Research LaboratoryMarshall Centre for Infectious Disease Research and TrainingSchool of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Michael J. Wise
- Helicobacter pylori Research LaboratoryMarshall Centre for Infectious Disease Research and TrainingSchool of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
- Department of Computer Science and Software EngineeringUniversity of Western AustraliaPerthWAAustralia
| | - Eng Guan Chua
- Helicobacter pylori Research LaboratoryMarshall Centre for Infectious Disease Research and TrainingSchool of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Barry J. Marshall
- Helicobacter pylori Research LaboratoryMarshall Centre for Infectious Disease Research and TrainingSchool of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Chin Yen Tay
- Helicobacter pylori Research LaboratoryMarshall Centre for Infectious Disease Research and TrainingSchool of Biomedical SciencesUniversity of Western AustraliaPerthWAAustralia
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24
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Koropoulis A, Alachiotis N, Pavlidis P. Detecting Positive Selection in Populations Using Genetic Data. Methods Mol Biol 2020; 2090:87-123. [PMID: 31975165 DOI: 10.1007/978-1-0716-0199-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High-throughput genomic sequencing allows to disentangle the evolutionary forces acting in populations. Among evolutionary forces, positive selection has received a lot of attention because it is related to the adaptation of populations in their environments, both biotic and abiotic. Positive selection, also known as Darwinian selection, occurs when an allele is favored by natural selection. The frequency of the favored allele increases in the population and, due to genetic hitchhiking, neighboring linked variation diminishes, creating so-called selective sweeps. Such a process leaves traces in genomes that can be detected in a future time point. Detecting traces of positive selection in genomes is achieved by searching for signatures introduced by selective sweeps, such as regions of reduced variation, a specific shift of the site frequency spectrum, and particular linkage disequilibrium (LD) patterns in the region. A variety of approaches can be used for detecting selective sweeps, ranging from simple implementations that compute summary statistics to more advanced statistical approaches, e.g., Bayesian approaches, maximum-likelihood-based methods, and machine learning methods. In this chapter, we discuss selective sweep detection methodologies on the basis of their capacity to analyze whole genomes or just subgenomic regions, and on the specific polymorphism patterns they exploit as selective sweep signatures. We also summarize the results of comparisons among five open-source software releases (SweeD, SweepFinder, SweepFinder2, OmegaPlus, and RAiSD) regarding sensitivity, specificity, and execution times. Furthermore, we test and discuss machine learning methods and present a thorough performance analysis. In equilibrium neutral models or mild bottlenecks, most methods are able to detect selective sweeps accurately. Methods and tools that rely on linkage disequilibrium (LD) rather than single SNPs exhibit higher true positive rates than the site frequency spectrum (SFS)-based methods under the model of a single sweep or recurrent hitchhiking. However, their false positive rate is elevated when a misspecified demographic model is used to build the distribution of the statistic under the null hypothesis. Both LD and SFS-based approaches suffer from decreased accuracy on localizing the true target of selection in bottleneck scenarios. Furthermore, we present an extensive analysis of the effects of gene flow on selective sweep detection, a problem that has been understudied in selective sweep literature.
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Affiliation(s)
- Angelos Koropoulis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
- Computer Science Department, University of Crete, Crete, Heraklion, Greece
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece.
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25
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Hanafiah A, Lopes BS. Genetic diversity and virulence characteristics of Helicobacter pylori isolates in different human ethnic groups. INFECTION GENETICS AND EVOLUTION 2019; 78:104135. [PMID: 31837482 DOI: 10.1016/j.meegid.2019.104135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 12/03/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori is the most predominant bacterium in almost 50% of the world's population and colonization causes a persistent inflammatory response leading to chronic gastritis. It shows high genetic diversity and individuals generally harbour a distinct bacterial population. With the advancement of whole-genome sequencing technology, new H. pylori subpopulations have been identified that show admixture between various H. pylori strains. Genotypic variation of H. pylori may be related to the presence of virulence factors among strains and is associated with different outcomes of infection in different individuals. This review summarizes the genetic diversity in H. pylori strain populations and its virulence characteristics responsible for variable outcomes in different ethnic groups.
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Affiliation(s)
- Alfizah Hanafiah
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Bruno S Lopes
- Department of Medical Microbiology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, 0:025 Polwarth Building, Aberdeen AB25 2ZD, United Kingdom.
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26
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Wang J, Yao Y, Zhang Q, Li S, Tang L. Inflammatory responses induced by Helicobacter pylori on the carcinogenesis of gastric epithelial GES‑1 cells. Int J Oncol 2019; 54:2200-2210. [PMID: 31081048 DOI: 10.3892/ijo.2019.4775] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/01/2019] [Indexed: 11/06/2022] Open
Abstract
Helicobacter pylori (HP) is a pathogenic bacterium associated with chronic gastritis, gastric ulcer and gastric cancer. In the present study, the primary carcinogenesis process of normal gastric epithelial cells (GES‑1) infected with HP was investigated. It was determined that infected gastric mucosal epithelial GES‑1 cells secreted increased interleukin‑8 (IL‑8) and IL‑23, and exhibited enhanced expression of inducible nitric oxide synthase and cyclooxygenase‑2, inducing inflammatory reactions and resulting in apoptosis. The bacterial infection significantly increased the expression of carcinogenesis‑associated genes, including p16, c‑Myc, p53 and p21, as well as the expression of cell surface signaling molecules cluster of differentiation 44 (CD44) and CD54 in GES‑1 cells or tissues of patients with gastritis and gastric cancer in vitro or in vivo. Simultaneously, the migration and invasion abilities of normal gastric epithelial GES‑1 cells were increased following HP infection. These observations demonstrated that the inflammatory response of HP infection could cause normal gastric epithelial cells to undergo significant cancerous reactions, indicating that HP is a risk factor for gastric cancer.
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Affiliation(s)
- Jianjun Wang
- Department of Clinical Laboratory, Kunshan First People's Hospital, Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Yongliang Yao
- Department of Clinical Laboratory, Kunshan First People's Hospital, Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Qinghui Zhang
- Department of Clinical Laboratory, Kunshan First People's Hospital, Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Shasha Li
- Department of Clinical Laboratory, Kunshan First People's Hospital, Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Lijun Tang
- Molecular Biology Research Center, School of Life Science, Central South University, Changsha, Hunan 410078, P.R. China
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27
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Genetic diversity of Streptococcus mutans serotype c isolated from white spot and cavitated caries lesions from schoolchildren. Arch Oral Biol 2019; 100:33-41. [PMID: 30776704 DOI: 10.1016/j.archoralbio.2019.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/06/2019] [Accepted: 02/07/2019] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To determine the genetic diversity of Streptococcus mutans (S. mutans) serotype c isolated from white spot and cavitated caries lesions of schoolchildren. METHODS S. mutans isolates were obtained and identify by Polymerase Chain Reaction (PCR) from 28 schoolchildren. A total of 92 S. mutans isolates, identified as serotype c by PCR, were analyzed by pulsed field gel electrophoresis after digestion of genomic DNA with SmaI enzyme. 62 isolates were obtained from white spot and cavitated caries lesions of schoolchildren that presented both lesions simultaneously and 30 isolates were from saliva and biofilm samples of schoolchildren without dental caries. Cluster analyses were performed using the Dice coefficient of the BioNumerics software version 6.0. RESULTS It was possible to determine the serotype in 190 isolates out of 255 isolates identified as S. mutans. Serotype c was the most frequent (n = 139), followed by serotype f (n = 31) and serotype e (n = 20). After analyzing the dendograms of the 92 serotype c isolates, this study identified three strains present in both types of lesions, two strains specific to the type of lesion: one strain from the white spot lesion and one strain from the cavitated caries lesion, and five strains specific to children with caries versus four strains for children without caries. CONCLUSION S. mutans serotype c genetic variability is similar in terms of the number of strains present according to the caries status and type of lesion.
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28
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The Story of Helicobacter pylori: Depicting Human Migrations from the Phylogeography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1149:1-16. [PMID: 31016625 DOI: 10.1007/5584_2019_356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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.
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29
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The arms race between man and Mycobacterium tuberculosis: Time to regroup. INFECTION GENETICS AND EVOLUTION 2018; 66:361-375. [DOI: 10.1016/j.meegid.2017.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/12/2022]
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30
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Chattopadhyay S, Chi PB, Minin VN, Berg DE, Sokurenko EV. Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori. BMC Genomics 2018; 19:835. [PMID: 30463511 PMCID: PMC6249973 DOI: 10.1186/s12864-018-5231-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Helicobacter pylori is a human stomach pathogen, naturally-competent for DNA uptake, and prone to homologous recombination. Extensive homoplasy (i.e., phylogenetically-unlinked identical variations) observed in H. pylori genes is considered a hallmark of such recombination. However, H. pylori also exhibits a high mutation rate. The relative adaptive role of homologous recombination and mutation in species diversity is a highly-debated issue in biology. Recombination results in homoplasy. While convergent mutation can also account for homoplasy, its contribution is thought to be minor. We demonstrate here that, contrary to dogma, convergent mutation is a key contributor to Helicobacter pylori homoplasy, potentially driven by adaptive evolution of proteins. RESULTS Our present genome-wide analysis shows that homoplastic nonsynonymous (amino acid replacement) changes are not typically accompanied by homoplastic synonymous (silent) variations. Moreover, the majority of the codon positions with homoplastic nonsynonymous changes also contain different (i.e. non-homoplastic) nonsynonymous changes arising from mutation only. This indicates that, to a considerable extent, nonsynonymous homoplasy is due to convergent mutations. High mutation rate or limited availability of evolvable sites cannot explain this excessive convergence, as suggested by our simulation studies. Rather, the genes with convergent mutations are overrepresented in distinct functional categories, suggesting possible selective responses to conditions such as distinct micro-niches in single hosts, and to differences in host genotype, physiology, habitat and diet. CONCLUSIONS We propose that mutational convergence is a key player in H. pylori's adaptation and extraordinary persistence in human hosts. High frequency of mutational convergence could be due to saturation of evolvable sites capable of responding to selection pressures, while the number of mutable residues is far from saturation. We anticipate a similar scenario of mutational vs. recombinational genome dynamics or plasticity for other naturally competent microbes where strong positive selection could favor frequent convergent mutations in adaptive protein evolution.
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Affiliation(s)
| | - Peter B Chi
- Department of Mathematics and Statistics, Villanova University, Villanova, PA, USA
| | - Vladimir N Minin
- Department of Statistics, University of California, Irvine, California, USA
| | - Douglas E Berg
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Evgeni V Sokurenko
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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31
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Wang MS, Otecko NO, Wang S, Wu DD, Yang MM, Xu YL, Murphy RW, Peng MS, Zhang YP. An Evolutionary Genomic Perspective on the Breeding of Dwarf Chickens. Mol Biol Evol 2018; 34:3081-3088. [PMID: 28961939 DOI: 10.1093/molbev/msx227] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The evolutionary history for dwarfism in chickens remains an enigma. Herein, we explore the evolution of the Serama, the smallest breed of chicken. Leveraging comparative population genomics, analyses identify several genes that are potentially associated with the growth and development of bones and muscles. These genes, and in particular both POU1F1 and IGF1, are under strong positive selection. Three allopatric dwarf bantams (Serama, Yuanbao, and Daweishan) with different breeding-histories, form distinct clusters and exhibit unique population structures. Parallel genetic mechanisms underlay their variation in body size. These findings provide insights into the multiple and complex pathways, depending on genomic variation, that chicken can take in response to aviculture selection for dwarfism.
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Affiliation(s)
- Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Sheng Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yi-Long Xu
- Xiaodu Veterinary Station in Tongnan District, Chongqing, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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32
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Waskito LA, Miftahussurur M, Lusida MI, Syam AF, Suzuki R, Subsomwong P, Uchida T, Hamdan M, Nasronudin, Yamaoka Y. Distribution and clinical associations of integrating conjugative elements and cag pathogenicity islands of Helicobacter pylori in Indonesia. Sci Rep 2018; 8:6073. [PMID: 29666390 PMCID: PMC5904169 DOI: 10.1038/s41598-018-24406-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/26/2018] [Indexed: 12/11/2022] Open
Abstract
The clinical associations and correlations with other virulence factors such as cag pathogenicity island (PAI) of the Integrating Conjugative Elements Helicobacter pylori TFSS (ICEHptfs), a new type IV secretion system (TFSS) in H. pylori has not been described. Among 103 studied strains from Indonesia, almost all strains (99.0%) contained cag PAI with more than half (55.8%) were intact cag PAI. Patients infected with intact cag PAI strains showed significantly higher antral activity, inflammation and atrophy as well as corporal inflammation than those with non-intact cag PAI strains, confirming the virulence of cag PAI. Over half of strains (53.8%) contained ICEHptfs, predominantly consisted of ICEHptfs3-tfs4a (42.8%) and ICEHptfs3 (16.3%). Although patients infected with ICEHptfs-positive strains had lower H. pylori density, those with the complete ICEHptfs4b strains tended to have higher antral activity than the negative one. In combination, patients infected with combination of intact cag PAI-ICEHptfs-positive strains had more severe inflammation than those with non-intact cag PAI-ICEHptfs-negative, suggesting a possibility of a mutual correlation between these TFSS(s).
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Affiliation(s)
- Langgeng Agung Waskito
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan.,Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Muhammad Miftahussurur
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan.,Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Gastroentero-Hepatology Division, Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Maria Inge Lusida
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Ari Fahrial Syam
- Division of Gastroenterology, Department of Internal Medicine, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Phawinee Subsomwong
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Tomohisa Uchida
- Department of Molecular Pathology, Oita University Faculty of Medicine, Yufu, Japan
| | - Muhammad Hamdan
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Faculty of Medicine, Universitas Muhammadiyah Surabaya, Surabaya, Indonesia
| | - Nasronudin
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan. .,Department of Medicine, Gastroenterology and Hepatology section, Baylor College of Medicine, Houston, Texas, USA.
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33
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Kabamba ET, Tuan VP, Yamaoka Y. Genetic populations and virulence factors of Helicobacter pylori. INFECTION GENETICS AND EVOLUTION 2018; 60:109-116. [PMID: 29471116 DOI: 10.1016/j.meegid.2018.02.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 12/16/2022]
Abstract
Helicobacter pylori is a bacterium that has infected more than half of the human population worldwide. This bacterium is closely associated with serious human diseases, such as gastric cancer, and identifying and understanding factors that predict bacterial virulence is a priority. In addition, this pathogen shows high genetic diversity and co-evolution with human hosts. H. pylori population genetics, therefore, has emerged as a tool to track human demographic history. As the number of genome sequences available is increasing, studies on the evolution and virulence of H. pylori are gaining momentum. This review article summarizes the most recent findings on H. pylori virulence factors and population genetics.
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Affiliation(s)
- Evariste Tshibangu Kabamba
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593, Japan; Department of Internal Medicine, University of Mbujimayi Faculty of Medicine, Mbujimayi, The Democratic Republic of Congo
| | - Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593, Japan; Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Viet Nam
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593, Japan; Department of Medicine-Gastroenterology, Baylor College of Medicine and Michael E. Debakey Veterans Affairs Medical Center, 2002 Holcombe Blvd., Houston, TX 77030, USA.
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Draft Genome Sequences of 42 Helicobacter pylori Isolates from Rural Regions of South India. GENOME ANNOUNCEMENTS 2018; 6:6/5/e01486-17. [PMID: 29437093 PMCID: PMC5794940 DOI: 10.1128/genomea.01486-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Helicobacter pylori is a successful human gastric pathogen that is associated with the development of gastric cancer. The draft genome sequences of 42 H. pylori clinical strains isolated from South Indian rural populations will provide further insights into the evolution and genetic makeup of Indian H. pylori strains.
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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.
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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
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36
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Bullock KK, Shaffer CL, Brooks AW, Secka O, Forsyth MH, McClain MS, Cover TL. Genetic signatures for Helicobacter pylori strains of West African origin. PLoS One 2017; 12:e0188804. [PMID: 29186206 PMCID: PMC5706691 DOI: 10.1371/journal.pone.0188804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 11/13/2017] [Indexed: 01/22/2023] Open
Abstract
Helicobacter pylori is a genetically diverse bacterial species that colonizes the stomach in about half of the human population. Most persons colonized by H. pylori remain asymptomatic, but the presence of this organism is a risk factor for gastric cancer. Multiple populations and subpopulations of H. pylori with distinct geographic distributions are recognized. Genetic differences among these populations might be a factor underlying geographic variation in gastric cancer incidence. Relatively little is known about the genomic features of African H. pylori strains compared to other populations of strains. In this study, we first analyzed the genomes of H. pylori strains from seven globally distributed populations or subpopulations and identified encoded proteins that exhibited the highest levels of sequence divergence. These included secreted proteins, an LPS glycosyltransferase, fucosyltransferases, proteins involved in molybdopterin biosynthesis, and Clp protease adaptor (ClpS). Among proteins encoded by the cag pathogenicity island, CagA and CagQ exhibited the highest levels of sequence diversity. We then identified proteins in strains of Western African origin (classified as hspWAfrica by MLST analysis) with sequences that were highly divergent compared to those in other populations of strains. These included ATP-dependent Clp protease, ClpS, and proteins of unknown function. Three of the divergent proteins sequences identified in West African strains were characterized by distinct insertions or deletions up to 8 amino acids in length. These polymorphisms in rapidly evolving proteins represent robust genetic signatures for H. pylori strains of West African origin.
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Affiliation(s)
- Kennady K. Bullock
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Carrie L. Shaffer
- Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Andrew W. Brooks
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Ousman Secka
- Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Mark H. Forsyth
- Department of Biology, The College of William and Mary, Williamsburg, Virginia, United States of America
| | - Mark S. McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Timothy L. Cover
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
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37
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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.
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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
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38
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Pavlidis P, Alachiotis N. A survey of methods and tools to detect recent and strong positive selection. ACTA ACUST UNITED AC 2017; 24:7. [PMID: 28405579 PMCID: PMC5385031 DOI: 10.1186/s40709-017-0064-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/29/2017] [Indexed: 01/25/2023]
Abstract
Positive selection occurs when an allele is favored by natural selection. The frequency of the favored allele increases in the population and due to genetic hitchhiking the neighboring linked variation diminishes, creating so-called selective sweeps. Detecting traces of positive selection in genomes is achieved by searching for signatures introduced by selective sweeps, such as regions of reduced variation, a specific shift of the site frequency spectrum, and particular LD patterns in the region. A variety of methods and tools can be used for detecting sweeps, ranging from simple implementations that compute summary statistics such as Tajima's D, to more advanced statistical approaches that use combinations of statistics, maximum likelihood, machine learning etc. In this survey, we present and discuss summary statistics and software tools, and classify them based on the selective sweep signature they detect, i.e., SFS-based vs. LD-based, as well as their capacity to analyze whole genomes or just subgenomic regions. Additionally, we summarize the results of comparisons among four open-source software releases (SweeD, SweepFinder, SweepFinder2, and OmegaPlus) regarding sensitivity, specificity, and execution times. In equilibrium neutral models or mild bottlenecks, both SFS- and LD-based methods are able to detect selective sweeps accurately. Methods and tools that rely on LD exhibit higher true positive rates than SFS-based ones under the model of a single sweep or recurrent hitchhiking. However, their false positive rate is elevated when a misspecified demographic model is used to represent the null hypothesis. When the correct (or similar to the correct) demographic model is used instead, the false positive rates are considerably reduced. The accuracy of detecting the true target of selection is decreased in bottleneck scenarios. In terms of execution time, LD-based methods are typically faster than SFS-based methods, due to the nature of required arithmetic.
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Affiliation(s)
- Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Crete, Greece
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Crete, Greece
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39
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Lipson M, Reich D. A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa. Mol Biol Evol 2017; 34:889-902. [PMID: 28074030 PMCID: PMC5400393 DOI: 10.1093/molbev/msw293] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogenetic tree with gene flow events for a wide diversity of non-Africans remains a difficult problem. Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. While our results still represent a simplified picture, they provide a useful summary of deep Eurasian population history that can serve as a null model for future studies and a baseline for further discoveries.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA
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40
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Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, Mendez A, Rizzato C, Bravo MM, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D. Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas. PLoS Genet 2017; 13:e1006546. [PMID: 28231283 PMCID: PMC5322909 DOI: 10.1371/journal.pgen.1006546] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/19/2016] [Indexed: 12/13/2022] Open
Abstract
For the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach-dwelling bacterium Helicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence of H. pylori isolated in North, Central and South America, we found evidence for admixture between H. pylori of European and African origin throughout the Americas, without substantial input from pre-Columbian (hspAmerind) bacteria. In the US, strains of African and European origin have remained genetically distinct, while in Colombia and Nicaragua, bottlenecks and rampant genetic exchange amongst isolates have led to the formation of national gene pools. We found three outer membrane proteins with atypical levels of Asian ancestry in American strains, as well as alleles that were nearly fixed specifically in South American isolates, suggesting a role for the ethnic makeup of hosts in the colonization of incoming strains. Our results show that new H. pylori subpopulations can rapidly arise, spread and adapt during times of demographic flux, and suggest that differences in transmission ecology between high and low prevalence areas may substantially affect the composition of bacterial populations. Helicobacter pylori is one of the best studied examples of an intimate association between bacteria and humans, due to its ability to colonize the stomach for decades and to transmit from generation to generation. A number of studies have sought to link diversity in H. pylori to human migrations but there are some discordant signals such as an “out of Africa” dispersal within the last few thousand years that has left a much stronger signal in bacterial genomes than in human ones. In order to understand how such discrepancies arise, we have investigated the evolution of H. pylori during the recent colonization of the Americas. We find that bacterial populations evolve quickly and can spread rapidly to people of different ethnicities. Distinct new bacterial subpopulations have formed in Colombia from a European source and in Nicaragua and the US from African sources. Genetic exchange between bacterial populations is rampant within Central and South America but is uncommon within North America, which may reflect differences in prevalence. Our results also suggest that adaptation of bacteria to particular human ethnic groups may be confined to a handful of genes involved in interaction with the immune system.
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Affiliation(s)
- Kaisa Thorell
- Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Koji Yahara
- Dept. of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Elvire Berthenet
- Medical Microbiology and Infectious Disease group, Swansea University, Swansea, Wales, United Kingdom
| | - Daniel J. Lawson
- Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Jane Mikhail
- Medical Microbiology and Infectious Disease group, Swansea University, Swansea, Wales, United Kingdom
| | - Ikuko Kato
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, United States of America
| | - Alfonso Mendez
- Instituto Politecnico Nacional, ENCB, Mexico City, Mexico
| | - Cosmeri Rizzato
- Dipartimento di Ricerca Traslazionale e Nuove Tecnologie in Medicina e Chirurgia, Universitá di Pisa, Pisa, Italy
| | - María Mercedes Bravo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogota, Colombia
| | - Rumiko Suzuki
- Dept. of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Yoshio Yamaoka
- Dept. of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico City, Mexico
| | - Samuel K. Sheppard
- Milner Center for Evolution, Dept. of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Daniel Falush
- Milner Center for Evolution, Dept. of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- * E-mail:
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41
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From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity. Microbiol Spectr 2017; 5. [PMID: 28155809 DOI: 10.1128/microbiolspec.emf-0009-2016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As the "human microbiome era" continues, there is an increasing awareness of our resident microbiota and its indispensable role in our fitness as holobionts. However, the host-microbe relationship is not so clearly defined for some human symbionts. Here we discuss examples of "accidental pathogens," meaning previously nonpathogenic and/or environmental microbes thought to have inadvertently experienced an evolutionary shift toward pathogenicity. For instance, symbionts such as Helicobacter pylori and JC polyomavirus have been shown to have accompanied humans since prehistoric times and are still abundant in extant populations as part of the microbiome. And yet, the relationship between a subgroup of these microbes and their human hosts seems to have changed with time, and they have recently gained notoriety as gastrointestinal and neuropathogens, respectively. On the other hand, environmental microbes such as Legionella spp. have recently experienced a shift in host range and are now a major problem in industrialized countries as a result of artificial ecosystems. Other variables involved in this accidental phenomenon could be the apparent change or reduction in the diversity of human-associated microbiota because of modern medicine and lifestyles. All of this could result in an increased prevalence of accidental pathogens in the form of emerging pathogens.
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42
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Kraemer SA, Boynton PJ. Evidence for microbial local adaptation in nature. Mol Ecol 2017; 26:1860-1876. [DOI: 10.1111/mec.13958] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Susanne A. Kraemer
- Ashworth Laboratories; University of Edinburgh; King's Buildings EH9 3FL Edinburgh UK
| | - Primrose J. Boynton
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Str. 2 24306 Plön Germany
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43
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Collins C, Didelot X. Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes. Methods Mol Biol 2017; 1535:109-137. [PMID: 27914076 DOI: 10.1007/978-1-4939-6673-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches.
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Affiliation(s)
- Caitlin Collins
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
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44
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Mégraud F, Lehours P, Vale F. The history of Helicobacter pylori : from phylogeography to paleomicrobiology. Clin Microbiol Infect 2016; 22:922-927. [DOI: 10.1016/j.cmi.2016.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/14/2016] [Accepted: 07/09/2016] [Indexed: 02/07/2023]
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45
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Goli YD, Moniri R. Efficacy of probiotics as an adjuvant agent in eradication of Helicobacter pylori infection and associated side effects. Benef Microbes 2016; 7:519-27. [DOI: 10.3920/bm2015.0130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The intestinal tract is a host to various types of bacteria that are essential to health. Interactions between intestinal bacteria, i.e. the normal microbiota of the host’s intestine, have been a subject of intensive research, as they may influence disease cycles. Recent studies of selected probiotic species and their therapeutic benefits have suggested a potential efficacy in treatment of several gastrointestinal illnesses, including Helicobacter pylori infection. The increasing evidence from these clinical studies supports the promising role of probiotics in improving the treatment of H. pylori by increasing eradication rates as well as decreasing the adverse effects of current medication therapy. However, many unsolved questions remain which require high quality trials on specific probiotic strains in the future. The main part of this review will focus on the effects of supplementary probiotic products during standard triple H. pylori therapy.
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Affiliation(s)
- Y. Dasteh Goli
- Department of Biological Sciences, Neurobiology and Physiology, University of Maryland, College Park, MD 20742, USA
| | - R. Moniri
- Department of Microbiology and Immunology, Anatomical Sciences Research Center, Kashan University of Medical Sciences, 87154 Kashan, Iran
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46
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Abstract
The development of high-throughput whole genome sequencing (WGS) technologies is changing the face of microbiology, facilitating the comparison of large numbers of genomes from different lineages of a same organism. Our aim was to review the main advances on Helicobacter pylori "omics" and to understand how this is improving our knowledge of the biology, diversity and pathogenesis of H. pylori. Since the first H. pylori isolate was sequenced in 1997, 510 genomes have been deposited in the NCBI archive, providing a basis for improved understanding of the epidemiology and evolution of this important pathogen. This review focuses on works published between April 2015 and March 2016. Helicobacter "omics" is already making an impact and is a growing research field. Ultimately these advances will be translated into a routine clinical laboratory setting in order to improve public health.
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Affiliation(s)
- Elvire Berthenet
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Sam Sheppard
- Departments of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Instituto de Medicina Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal
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47
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Abstract
This review of recent publications related to the epidemiology of Helicobacter pylori highlights the origin of the infection, its changing prevalence, transmission, and outcome. A number of studies have addressed the ancestor roots of the bacteria, and the first genomewide analysis of bacterial strains suggests that its coexistence with humans is more ancient than previously thought. As opposed to the generally declining prevalence of H. pylori (including China and Japan), in Sweden, the prevalence of atrophic gastritis in the young population has risen. The prevalence of the infection remains high in the indigenous populations of the Arctic regions, and reinfection rates are high. A high prevalence is permanently found in the Siberian regions of Russia as well. Several studies, some of which used multiplex serology, addressed prevalence of and risks associated with various H. pylori serotypes, thereby enabling more precise risk assessment. Transmission of H. pylori was discussed, specifically fecal-oral transmission and the use of well-water and other unpurified water. Finally, the long-term course of H. pylori infection was considered, with an estimated 89% of noncardia gastric cancer cases being attributable to the infection.
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Affiliation(s)
- Mārcis Leja
- Faculty of Medicine, University of Latvia, Riga, Latvia.,Riga East University Hospital, Riga, Latvia.,Digestive Diseases Centre GASTRO, Riga, Latvia
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
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48
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Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S, Matelska D, Dunin-Horkawicz S, Bujnicki JM, Uchiyama I, Kobayashi I. Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori. DNA Res 2016; 23:135-43. [PMID: 26961370 PMCID: PMC4833421 DOI: 10.1093/dnares/dsw003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 01/23/2016] [Indexed: 01/04/2023] Open
Abstract
Selection has been a central issue in biology in eukaryotes as well as prokaryotes. Inference of selection in recombining bacterial species, compared with clonal ones, has been a challenge. It is not known how codons under diversifying selection are distributed along the chromosome or among functional categories or how frequently such codons are subject to mutual homologous recombination. Here, we explored these questions by analysing genes present in >90% among 29 genomes of Helicobacter pylori, one of the bacterial species with the highest mutation and recombination rates. By a method for recombining sequences, we identified codons under diversifying selection (dN/dS> 1), which were widely distributed and accounted for ∼0.2% of all the codons of the genome. The codons were enriched in genes of host interaction/cell surface and genome maintenance (DNA replication,recombination, repair, and restriction modification system). The encoded amino acid residues were sometimes found adjacent to critical catalytic/binding residues in protein structures.Furthermore, by estimating the intensity of homologous recombination at a single nucleotide level, we found that these codons appear to be more frequently subject to recombination.We expect that the present study provides a new approach to population genomics of selection in recombining prokaryotes.
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Affiliation(s)
- Koji Yahara
- Biostatistics Center, Kurume University, Kurume, Fukuoka 830-0011, Japan
- Institute of Life Science, College of Medicine, Swansea University, Swansea SA2 8PP, UK
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo108-8639, Japan
| | - Yoshikazu Furuta
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo108-8639, Japan
| | - Shinpei Morimoto
- Division of Biostatistics, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Chie Kikutake
- Division of Biostatistics, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Sho Komukai
- Division of Biostatistics, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Dorota Matelska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trodena 4, 02-109 Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trodena 4, 02-109 Warsaw, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trodena 4, 02-109 Warsaw, Poland
- Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo108-8639, Japan
- Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Renzette N, Kowalik TF, Jensen JD. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity. Mol Ecol 2015. [PMID: 26211679 DOI: 10.1111/mec.13331] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.
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Affiliation(s)
- Nicholas Renzette
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA.,Immunology and Microbiology Program, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Jeffrey D Jensen
- Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
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