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Kulathunga DGRS, Fakher AA, Costa MDO. Actinobacillus suis isolated from diseased pigs are phylogenetically related but harbour different number of toxin gene copies in their genomes. Vet Rec Open 2022; 9:e45. [PMID: 36213600 PMCID: PMC9528957 DOI: 10.1002/vro2.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 08/06/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Objective The Gram-negative bacterium Actinobacillus suis is an agent of global importance to the swine industry and the cause of lethal respiratory or septicaemic disease in pigs of different ages. Between 2018 and 2019, seven commercial farms in western Canada experienced episodes of increased mortality due to A. suis infection in grower pigs. The goal of this work was to profile, with molecular methods, A. suis isolated from diseased pigs and to compare them to other isolates. Design This inferential observational study used nine western Canadian strains obtained from diseased lungs (n = 6), heart (n = 2) and brain (n = 1) and whole genome sequencing was performed. Comparative genomic analyses were performed to characterise the genetic variability, antimicrobial resistance and the virulence genes present. Results Compared to the reference strain (ATCC 33415), an increased number of RTX (repeats in the structural toxin) gene copies were identified in strains isolated from organs without a mucosal surface, thus theoretically harder to invade. Western Canadian strains did not harbour genes associated with resistance to antimicrobial agents used in swine production. Novel regions were also identified in the genomes of five of nine strains demonstrating recombination and emergence of novel strains. Conclusions The results obtained in this study were associated with the emergence of new lineages. An increased number of RTX toxin gene copies is suggested to be associated with increased virulence. This study will contribute to improve our understanding regarding A. suis and may help guide vaccine development and agent control measures.
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Affiliation(s)
| | - Alaa Abou Fakher
- Department of Population Health SciencesFaculty of Veterinary MedicineUtrecht UniversityYalelaan 7UtrechtThe Netherlands
| | - Matheus de Oliveira Costa
- Department of Large Animal Clinical SciencesWestern College of Veterinary MedicineUniversity of SaskatchewanSaskatoonSaskatchewanCanada
- Department of Population Health SciencesFaculty of Veterinary MedicineUtrecht UniversityYalelaan 7UtrechtThe Netherlands
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2
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Network topology analysis of essential genes interactome of Helicobacter pylori to explore novel therapeutic targets. Microb Pathog 2021; 158:105059. [PMID: 34157412 DOI: 10.1016/j.micpath.2021.105059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022]
Abstract
The Helicobacter pylori chronic colonization produces a wide range of gastric diseases in the gastric mucosa by abetting inflammation. Amidst coevolution and reorganization of its metabolism with humans, it has become difficult still imperative to understand and prevent its growth. This study focus to explore functional insights into identification of hub proteins/genes by aggregating the behavior of genes connected in a protein-protein interaction (PPI) network. We have constructed a PPI network of 123 essential genes along with 1213 interactions in H. pylori 26695. The degree and other centrality measures analysis assist in identifying the important hub nodes, which are top-ranked proteins. A total of nine proteins (recA, guaA, dnaK, rpsB, rplQ, rpmA, rpmC, rpmF, and rpsE) were obtained with high degree (k), betweenness centrality (BC) value. Gene ontology analysis reveals 8, 5 and 3 GO terms correspond to biological processes, cellular components and molecular function respectively. Gene complexes of hypothetical proteins (HPs) were related to aminoacyl-tRNA biosynthesis, biosynthesis of secondary metabolites, bacterial secretion system and protein export. The MCODE analysis revealed that protein from module M1, M3 and M6 include the proteins which have highest degree and BC values. It is noteworthy to mention that the bifunctional GMP synthase/glutamine amidotransferase protein (guaA), molecular chaperon (dnaK), recombinase A (recA) constitute as hub proteins. As a result, these genes are considered as network hub nodes that might be used as therapeutic targets. Our analysis affords a detailed understanding of the molecular process and pathways regulated by the essential genes in H. pylori 26695.
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3
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Pasanen M, Waleron M, Schott T, Cleenwerck I, Misztak A, Waleron K, Pritchard L, Bakr R, Degefu Y, van der Wolf J, Vandamme P, Pirhonen M. Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence. Int J Syst Evol Microbiol 2020; 70:2440-2448. [PMID: 32100697 PMCID: PMC7395620 DOI: 10.1099/ijsem.0.004057] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 11/25/2022] Open
Abstract
Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.
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Affiliation(s)
- Miia Pasanen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Malgorzata Waleron
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | | | - Ilse Cleenwerck
- Ghent University, BCCM/LMG Bacteria Collection, Ghent, Belgium
| | - Agnieszka Misztak
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Medical University of Gdansk, Gdańsk, Poland
| | - Leighton Pritchard
- Information and Computational Sciences, The James Hutton Institute, Dundee, Scotland, UK
- Present address: Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Ramadan Bakr
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Present address: Department of Agricultural Botany, Faculty of Agriculture, Menoufia University, Shibin Elkom, Egypt
| | | | - Jan van der Wolf
- Wageningen University and Research, Bio-interactions and Plant Health, Wageningen, The Netherlands
| | - Peter Vandamme
- Ghent University, BCCM/LMG Bacteria Collection, Ghent, Belgium
| | - Minna Pirhonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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4
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Noureen M, Tada I, Kawashima T, Arita M. Rearrangement analysis of multiple bacterial genomes. BMC Bioinformatics 2019; 20:631. [PMID: 31881830 PMCID: PMC6933940 DOI: 10.1186/s12859-019-3293-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023] Open
Abstract
Background Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene order with sequence data can facilitate more robust phylogenetic reconstruction. Helicobacter pylori is a good model because of its unique evolution in niche environment. Results We have developed a method to identify genome rearrangements by comparing almost-conserved genes among closely related strains. Orthologous gene clusters, rather than the gene sequences, are used to align the gene order so that comparison of large number of genomes becomes easier. Comparison of 72 Helicobacter pylori strains revealed shared as well as strain-specific reversals, some of which were found in different geographical locations. Conclusion Degree of genome rearrangements increases with time. Therefore, gene orders can be used to study the evolutionary relationship among species and strains. Multiple genome comparison helps to identify the strain-specific as well as shared reversals. Identification of the time course of rearrangements can provide insights into evolutionary events.
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Affiliation(s)
- Mehwish Noureen
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Ipputa Tada
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Takeshi Kawashima
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Masanori Arita
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan. .,RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.
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5
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García-Zea JA, de la Herrán R, Robles Rodríguez F, Navajas-Pérez R, Ruiz Rejón C. Detection and variability analyses of CRISPR-like loci in the H. pylori genome. PeerJ 2019; 7:e6221. [PMID: 30648020 PMCID: PMC6330956 DOI: 10.7717/peerj.6221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR-like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure. We confirm the presence of a locus that was previously described in the VlpC gene in al lgenomes, and we characterize new CRISPR-like loci in other genomic locations. By studying the variability and gene location of these loci, the evolution and the possible roles of these sequences are discussed. Additionally, the usefulness of this type of sequences as a phylogenetic marker has been demonstrated, associating the different strains by geographical area.
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Affiliation(s)
| | - Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | | | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Carmelo Ruiz Rejón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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6
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Tambong JT. Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops. PLoS One 2017; 12:e0172295. [PMID: 28319117 PMCID: PMC5358740 DOI: 10.1371/journal.pone.0172295] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/02/2017] [Indexed: 11/18/2022] Open
Abstract
Subspecies of Clavibacter michiganensis are important phytobacterial pathogens causing devastating diseases in several agricultural crops. The genome organizations of these pathogens are poorly understood. Here, the complete genomes of 5 subspecies (C. michiganensis subsp. michiganensis, Cmi; C. michiganensis subsp. sepedonicus, Cms; C. michiganensis subsp. nebraskensis, Cmn; C. michiganensis subsp. insidiosus, Cmi and C. michiganensis subsp. capsici, Cmc) were analyzed. This study assessed the taxonomic position of the subspecies based on 16S rRNA and genome-based DNA homology and concludes that there is ample evidence to elevate some of the subspecies to species-level. Comparative genomics analysis indicated distinct genomic features evident on the DNA structural atlases and annotation features. Based on orthologous gene analysis, about 2300 CDSs are shared across all the subspecies; and Cms showed the highest number of subspecies-specific CDS, most of which are mobile elements suggesting that Cms could be more prone to translocation of foreign genes. Cms and Cmi had the highest number of pseudogenes, an indication of potential degenerating genomes. The stress response factors that may be involved in cold/heat shock, detoxification, oxidative stress, osmoregulation, and carbon utilization are outlined. For example, the wco-cluster encoding for extracellular polysaccharide II is highly conserved while the sucrose-6-phosphate hydrolase that catalyzes the hydrolysis of sucrose-6-phosphate yielding glucose-6-phosphate and fructose is highly divergent. A unique second form of the enzyme is only present in Cmn NCPPB 2581. Also, twenty-eight plasmid-borne CDSs in the other subspecies were found to have homologues in the chromosomal genome of Cmn which is known not to carry plasmids. These CDSs include pathogenesis-related factors such as Endocellulases E1 and Beta-glucosidase. The results presented here provide an insight of the functional organization of the genomes of five core C. michiganensis subspecies, enabling a better understanding of these phytobacteria.
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Affiliation(s)
- James T. Tambong
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- * E-mail:
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7
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Sim DW, Kim JH, Kim HY, Jang JH, Lee WC, Kim EH, Park PJ, Lee KH, Won HS. Structural identification of the lipopolysaccharide-binding capability of a cupin-family protein from Helicobacter pylori. FEBS Lett 2016; 590:2997-3004. [PMID: 27466800 DOI: 10.1002/1873-3468.12332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 07/19/2016] [Accepted: 07/19/2016] [Indexed: 01/26/2023]
Abstract
We solved the crystal structure of a functionally uncharacterized protein, HP0902, from Helicobacter pylori. Its structure demonstrated an all-β cupin fold that cannot bind metal ions due to the absence of a metal-binding histidine that is conserved in many metallo-cupins. In contrast, isothermal titration calorimetry and NMR titration demonstrated that HP0902 is able to bind bacterial endotoxin lipopolysaccharides (LPS) through its surface-exposed loops, where metal-binding sites are usually found in other metallo-cupins. This report constitutes the first identification of an LPS-interacting protein, both in the cupin family and in H. pylori. Furthermore, identification of the ability of HP0902 to bind LPS uncovers a putative role for this protein in H. pylori pathogenicity.
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Affiliation(s)
- Dae-Won Sim
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungbuk, Korea
| | - Ji-Hun Kim
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungbuk, Korea
| | - Hye-Yeon Kim
- Protein Structure Group, Korea Basic Science Institute, Chungbuk, Korea
| | - Jung-Hwa Jang
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungbuk, Korea
| | - Woo Cheol Lee
- Protein Structure Group, Korea Basic Science Institute, Chungbuk, Korea.,Division of Biotechnology, Korea University, Seoul, Korea
| | - Eun-Hee Kim
- Protein Structure Group, Korea Basic Science Institute, Chungbuk, Korea
| | - Pyo-Jam Park
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungbuk, Korea
| | - Kwang-Ho Lee
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungbuk, Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungbuk, Korea
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8
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Maixner F, Krause-Kyora B, Turaev D, Herbig A, Hoopmann MR, Hallows JL, Kusebauch U, Vigl EE, Malfertheiner P, Megraud F, O'Sullivan N, Cipollini G, Coia V, Samadelli M, Engstrand L, Linz B, Moritz RL, Grimm R, Krause J, Nebel A, Moodley Y, Rattei T, Zink A. The 5300-year-old Helicobacter pylori genome of the Iceman. Science 2016; 351:162-165. [PMID: 26744403 DOI: 10.1126/science.aad2545] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The "Iceman" H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.
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Affiliation(s)
- Frank Maixner
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Schittenhelmstr. 12, 24105 Kiel, Germany
| | - Dmitrij Turaev
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Alexander Herbig
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstr. 23, 72072 Tübingen, Germany.,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA
| | - Janice L Hallows
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA
| | - Eduard Egarter Vigl
- Scuola Superiore Sanitaria Provinciale "Claudiana", Via Lorenz Böhler 13, 39100 Bolzano, Italy
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University, Leipziger Strasse 44, 39120 Magdeburg, Germany
| | - Francis Megraud
- Université de Bordeaux, Centre National de Référence des Helicobacters et Campylobacters and INSERM U853, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Niall O'Sullivan
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Giovanna Cipollini
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Valentina Coia
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Marco Samadelli
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 141 83 Stockholm, Sweden
| | - Bodo Linz
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA
| | - Rudolf Grimm
- Robert Mondavi Institute for Food Science, University of California, Davis, California 95616, USA
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstr. 23, 72072 Tübingen, Germany.,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Schittenhelmstr. 12, 24105 Kiel, Germany
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa.,Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Savoyenstr. 1a, 1160 Vienna, Austria
| | - Thomas Rattei
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Albert Zink
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
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9
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Search for novel candidate mutations for metronidazole resistance in Helicobacter pylori using next-generation sequencing. Antimicrob Agents Chemother 2015; 59:2343-8. [PMID: 25645832 DOI: 10.1128/aac.04852-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Metronidazole resistance is a key factor associated with Helicobacter pylori treatment failure. Although this resistance is mainly associated with mutations in the rdxA and frxA genes, the question of whether metronidazole resistance is caused by the inactivation of frxA alone is still debated. Furthermore, it is unclear whether there are other mutations involved in addition to the two genes that are associated with resistance. A metronidazole-resistant strain was cultured from the metronidazole-susceptible H. pylori strain 26695-1 by exposure to low concentrations of metronidazole. The genome sequences of both susceptible and resistant H. pylori strains were determined by Illumina next-generation sequencing, from which putative candidate resistance mutations were identified. Natural transformation was used to introduce PCR products containing candidate mutations into the susceptible parent strain 26695-1, and the metronidazole MIC was determined for each strain. Mutations in frxA (hp0642), rdxA (hp0954), and rpsU (hp0562) were confirmed by the Sanger method. The mutated sequence in rdxA was successfully transformed into strain 26695-1, and the transformants showed resistance to metronidazole. The transformants containing a single mutation in rdxA showed a low MIC (16 mg/liter), while those containing mutations in both rdxA and frxA showed a higher MIC (48 mg/liter). No transformants containing a single mutation in frxA or rpsU were obtained. Next-generation sequencing was used to identify mutations related to drug resistance. We confirmed that the mutations in rdxA are mainly associated with metronidazole resistance, and mutations in frxA are able to enhance H. pylori resistance only in the presence of rdxA mutations. Moreover, mutations in rpsU may play a role in metronidazole resistance.
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10
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Binh TT, Shiota S, Suzuki R, Matsuda M, Trang TTH, Kwon DH, Iwatani S, Yamaoka Y. Discovery of novel mutations for clarithromycin resistance in Helicobacter pylori by using next-generation sequencing. J Antimicrob Chemother 2014; 69:1796-803. [PMID: 24648504 DOI: 10.1093/jac/dku050] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Resistance to clarithromycin is the most important factor causing failure of Helicobacter pylori eradication. Although clarithromycin resistance is mainly associated with three point mutations in the 23S rRNA genes, it is unclear whether other mutations are associated with this resistance. METHODS Two types of clarithromycin-resistant strains (low- and high-resistance strains) were obtained from clarithromycin-susceptible H. pylori following exposure to low clarithromycin concentrations. The genome sequences were determined with a next-generation sequencer. Natural transformation was used to introduce the candidate mutations into strain 26695. Etest and an agar dilution method were used to determine the MICs. RESULTS High-resistance strains contained the mutation A2143G in the 23S rRNA genes, whereas low-resistance strains did not. There were seven candidate mutations in six genes outside of the 23S rRNA genes. The mutated sequences in hp1048 (infB), hp1314 (rpl22) and the 23S rRNA gene were successfully transformed into strain 26695 and the transformants showed an increased MIC of and low resistance to clarithromycin. The transformants containing a single mutation in infB or rpl22 (either a 9 bp insertion or a 3 bp deletion) or the 23S rRNA gene showed low MICs (0.5, 2.0, 4.0 and 32 mg/L, respectively) while the transformants containing double mutations (mutation in the 23S rRNA genes and mutation in infB or rpl22) showed higher MICs (>256 mg/L). CONCLUSIONS Next-generation sequencing can be a useful tool for screening mutations related to drug resistance. We discovered novel mutations related to clarithromycin resistance in H. pylori (infB and rpl22), which have synergic effects with 23S rRNA resulting in higher MICs.
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Affiliation(s)
- Tran Thanh Binh
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Seiji Shiota
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Miyuki Matsuda
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Tran Thi Huyen Trang
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Dong Hyeon Kwon
- Biology Department, Long Island University, Brooklyn, NY, USA
| | - Shun Iwatani
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan Department of Medicine-Gastroenterology, Baylor College of Medicine and Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan Department of Medicine-Gastroenterology, Baylor College of Medicine and Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
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11
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Mohd Jaafar F, Belhouchet M, Belaganahalli M, Tesh RB, Mertens PPC, Attoui H. Full-genome characterisation of Orungo, Lebombo and Changuinola viruses provides evidence for co-evolution of orbiviruses with their arthropod vectors. PLoS One 2014; 9:e86392. [PMID: 24475112 PMCID: PMC3901712 DOI: 10.1371/journal.pone.0086392] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 12/07/2013] [Indexed: 01/06/2023] Open
Abstract
The complete genomes of Orungo virus (ORUV), Lebombo virus (LEBV) and Changuinola virus (CGLV) were sequenced, confirming that they each encode 11 distinct proteins (VP1-VP7 and NS1-NS4). Phylogenetic analyses of cell-attachment protein 'outer-capsid protein 1' (OC1), show that orbiviruses fall into three large groups, identified as: VP2(OC1), in which OC1 is the 2nd largest protein, including the Culicoides transmitted orbiviruses; VP3(OC1), which includes the mosquito transmitted orbiviruses; and VP4(OC1) which includes the tick transmitted viruses. Differences in the size of OC1 between these groups, places the T2 'subcore-shell protein' as the third largest protein 'VP3(T2)' in the first of these groups, but the second largest protein 'VP3(T2)' in the other two groups. ORUV, LEBV and CGLV all group with the Culicoides-borne VP2(OC1)/VP3(T2) viruses. The G+C content of the ORUV, LEBV and CGLV genomes is also similar to that of the Culicoides-borne, rather than the mosquito-borne, or tick borne orbiviruses. These data suggest that ORUV and LEBV are Culicoides- rather than mosquito-borne. Multiple isolations of CGLV from sand flies suggest that they are its primary vector. OC1 of the insect-borne orbiviruses is approximately twice the size of the equivalent protein of the tick borne viruses. Together with internal sequence similarities, this suggests its origin by duplication (concatermerisation) of a smaller OC1 from an ancestral tick-borne orbivirus. Phylogenetic comparisons showing linear relationships between the dates of evolutionary-separation of their vector species, and genetic-distances between tick-, mosquito- or Culicoides-borne virus-groups, provide evidence for co-evolution of the orbiviruses with their arthropod vectors.
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Affiliation(s)
- Fauziah Mohd Jaafar
- Department of Vector-Borne Viral Diseases, The Pirbright Institute, Pirbright, United Kingdom
| | - Mourad Belhouchet
- Department of Vector-Borne Viral Diseases, The Pirbright Institute, Pirbright, United Kingdom
| | | | - Robert B. Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Peter P. C. Mertens
- Department of Vector-Borne Viral Diseases, The Pirbright Institute, Pirbright, United Kingdom
| | - Houssam Attoui
- Department of Vector-Borne Viral Diseases, The Pirbright Institute, Pirbright, United Kingdom
- * E-mail:
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Fu Y, Zepeda-Gurrola RC, Aguilar-Gutiérrez GR, Lara-Ramírez EE, De Luna-Santillana EJ, Rodríguez-Luna IC, Sánchez-Varela A, Carreño-López R, Moreno-Medina VR, Rodríguez-Pérez MA, López-Vidal Y, Guo X. The detection of inherent homologous recombination between repeat sequences in H. pylori 26695 by the PCR-based method. Curr Microbiol 2013; 68:211-9. [PMID: 24097137 DOI: 10.1007/s00284-013-0466-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/20/2013] [Indexed: 01/11/2023]
Abstract
Helicobacter pylori infects more than half of the world's population, making it the most widespread infection of bacteria. It has high genetic diversity and has been considered as one of the most variable bacterial species. In the present study, a PCR-based method was used to detect the presence and the relative frequency of homologous recombination between repeat sequences (>500 bp) in H. pylori 26695. All the recombinant structures have been confirmed by sequencing. The inversion generated between inverted repeats showed distinct features from the recombination for duplication or deletion between direct repeats. Meanwhile, we gave the mathematic reasoning of a general formula for the calculation of relative recombination frequency and indicated the conditions for its application. This formula could be extensively applied to detect the frequency of homologous recombination, site-specific recombination, and other types of predictable recombination. Our results should be helpful for better understanding the genome evolution and adaptation of bacteria.
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Affiliation(s)
- Yajuan Fu
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro S/N esq. Elías Piña, Col. Narciso Mendoza, Cd., 88710, Reynosa, Tamaulipas, Mexico
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13
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Helicobacter pylori relies primarily on the purine salvage pathway for purine nucleotide biosynthesis. J Bacteriol 2011; 194:839-54. [PMID: 22194455 DOI: 10.1128/jb.05757-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Helicobacter pylori is a chronic colonizer of the gastric epithelium and plays a major role in the development of gastritis, peptic ulcer disease, and gastric cancer. In its coevolution with humans, the streamlining of the H. pylori genome has resulted in a significant reduction in metabolic pathways, one being purine nucleotide biosynthesis. Bioinformatic analysis has revealed that H. pylori lacks the enzymatic machinery for de novo production of IMP, the first purine nucleotide formed during GTP and ATP biosynthesis. This suggests that H. pylori must rely heavily on salvage of purines from the environment. In this study, we deleted several genes putatively involved in purine salvage and processing. The growth and survival of these mutants were analyzed in both nutrient-rich and minimal media, and the results confirmed the presence of a robust purine salvage pathway in H. pylori. Of the two phosphoribosyltransferase genes found in the H. pylori genome, only gpt appears to be essential, and an Δapt mutant strain was still capable of growth on adenine, suggesting that adenine processing via Apt is not essential. Deletion of the putative nucleoside phosphorylase gene deoD resulted in an inability of H. pylori to grow on purine nucleosides or the purine base adenine. Our results suggest a purine requirement for growth of H. pylori in standard media, indicating that H. pylori possesses the ability to utilize purines and nucleosides from the environment in the absence of a de novo purine nucleotide biosynthesis pathway.
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Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori. INFECTION GENETICS AND EVOLUTION 2011; 12:203-13. [PMID: 22197766 DOI: 10.1016/j.meegid.2011.12.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/07/2011] [Accepted: 12/08/2011] [Indexed: 12/17/2022]
Abstract
Helicobacter pylori infection is linked to various gastroduodenal diseases; however, only approximately 20% of infected individuals develop severe diseases. Despite the high prevalence of H. pylori infection in Africa and South Asia, the incidence of gastric cancer in these areas is much lower than in other countries. Furthermore, the incidence of gastric cancer tends to decrease from north to south in East Asia. Such geographic differences in the pathology can be explained, at least in part, by the presence of different types of H. pylori virulence factors, especially cagA, vacA, and the right end of the cag pathogenicity island. The genotype of the virulence genes is also useful as a tool to track human migration utilizing the high genetic diversity and frequent recombination between different H. pylori strains. Multilocus sequence typing (MLST) analysis using seven housekeeping genes can also help to predict the history of human migrations. Population structure analysis based on MLST has revealed seven modern population types of H. pylori, which derived from six ancestral populations. Interestingly, the incidence of gastric cancer is closely related to the distribution of H. pylori populations. The different incidence of gastric cancer can be partly attributed to the different genotypes of H. pylori circulating in different geographic areas. Although approaches by MLST and virulence factors are effective, these methods focus on a small number of genes and may miss information conveyed by the rest of the genome. Genome-wide analyses using DNA microarray or whole-genome sequencing technology give a broad view on the genome of H. pylori. In particular, next-generation sequencers, which can read DNA sequences in less time and at lower costs than Sanger sequencing, enabled us to efficiently investigate not only the evolution of H. pylori, but also novel virulence factors and genomic changes related to drug resistance.
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Schott T, Kondadi PK, Hänninen ML, Rossi M. Comparative genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans. BMC Genomics 2011; 12:534. [PMID: 22039924 PMCID: PMC3234257 DOI: 10.1186/1471-2164-12-534] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 10/31/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The canine Gram-negative Helicobacter bizzozeronii is one of seven species in Helicobacter heilmannii sensu lato that are detected in 0.17-2.3% of the gastric biopsies of human patients with gastric symptoms. At the present, H. bizzozeronii is the only non-pylori gastric Helicobacter sp. cultivated from human patients and is therefore a good alternative model of human gastric Helicobacter disease. We recently sequenced the genome of the H. bizzozeronii human strain CIII-1, isolated in 2008 from a 47-year old Finnish woman suffering from severe dyspeptic symptoms. In this study, we performed a detailed comparative genome analysis with H. pylori, providing new insights into non-pylori Helicobacter infections and the mechanisms of transmission between the primary animal host and humans. RESULTS H. bizzozeronii possesses all the genes necessary for its specialised life in the stomach. However, H. bizzozeronii differs from H. pylori by having a wider metabolic flexibility in terms of its energy sources and electron transport chain. Moreover, H. bizzozeronii harbours a higher number of methyl-accepting chemotaxis proteins, allowing it to respond to a wider spectrum of environmental signals. In this study, H. bizzozeronii has been shown to have high level of genome plasticity. We were able to identify a total of 43 contingency genes, 5 insertion sequences (ISs), 22 mini-IS elements, 1 genomic island and a putative prophage. Although H. bizzozeronii lacks homologues of some of the major H. pylori virulence genes, other candidate virulence factors are present. In particular, we identified a polysaccharide lyase (HBZC1_15820) as a potential new virulence factor of H. bizzozeronii. CONCLUSIONS The comparative genome analysis performed in this study increased the knowledge of the biology of gastric Helicobacter species. In particular, we propose the hypothesis that the high metabolic versatility and the ability to react to a range of environmental signals, factors which differentiate H. bizzozeronii as well as H. felis and H. suis from H. pylori, are the molecular basis of the of the zoonotic nature of H. heilmannii sensu lato infection in humans.
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Affiliation(s)
- Thomas Schott
- Department of Food Hygiene and Environmental Health (DFHEH), Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014 University of Helsinki, Finland
| | - Pradeep K Kondadi
- Department of Food Hygiene and Environmental Health (DFHEH), Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014 University of Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health (DFHEH), Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014 University of Helsinki, Finland
| | - Mirko Rossi
- Department of Food Hygiene and Environmental Health (DFHEH), Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014 University of Helsinki, Finland
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