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Antibiotic dispensation rates among participants in community-driven health research projects in Arctic Canada. BMC Public Health 2019; 19:949. [PMID: 31307422 PMCID: PMC6631451 DOI: 10.1186/s12889-019-7193-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 06/18/2019] [Indexed: 02/08/2023] Open
Abstract
Background Community-driven projects that aim to address public concerns about health risks from H. pylori infection in Indigenous Arctic communities (estimated H. pylori prevalence = 64%) show frequent failure of treatment to eliminate the bacterium. Among project participants, treatment effectiveness is reduced by antibiotic resistance of infecting H. pylori strains, which in turn, is associated with frequent exposure to antibiotics used to treat other infections. This analysis compares antibiotic dispensation rates in Canadian Arctic communities to rates in urban and rural populations in Alberta, a southern Canadian province. Methods Project staff collected antibiotic exposure histories for 297 participants enrolled during 2007–2012 in Aklavik, Tuktoyaktuk, and Fort McPherson in the Northwest Territories, and Old Crow, Yukon. Medical chart reviews collected data on systemic antibiotic dispensations for the 5-year period before enrolment for each participant. Antibiotic dispensation data for urban Edmonton, Alberta (average population ~ 860,000) and rural northern Alberta (average population ~ 450,000) during 2010–2013 were obtained from the Alberta Government Interactive Health Data Application. Results Antibiotic dispensation rates, estimated as dispensations/person-years (95% confidence interval) were: in Arctic communities, 0.89 (0.84, 0.94); in Edmonton, 0.55 (0.55, 0.56); in rural northern Alberta, 0.63 (0.62, 0.63). Antibiotic dispensation rates were higher in women and older age groups in all regions. In all regions, the highest dispensation rates occurred for β-lactam and macrolide antibiotic classes. Conclusions These results show more frequent antibiotic dispensation in Arctic communities relative to an urban and rural southern Canadian population.
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Fagan-Garcia K, Geary J, Chang HJ, McAlpine L, Walker E, Colquhoun A, van Zanten SV, Girgis S, Archie B, Hanley B, Corriveau A, Morse J, Munday R, Goodman KJ. Burden of disease from Helicobacter pylori infection in western Canadian Arctic communities. BMC Public Health 2019; 19:730. [PMID: 31185961 PMCID: PMC6560895 DOI: 10.1186/s12889-019-7065-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 05/29/2019] [Indexed: 12/17/2022] Open
Abstract
Background Indigenous communities across the circumpolar north have elevated H. pylori (Hp) prevalence and stomach cancer incidence. We aimed to describe the Hp-associated disease burden among western Canadian Arctic participants in community-driven projects that address concerns about health risks from Hp infection. Methods During 2008–2013, participants underwent Hp screening by urea breath test and gastroscopy with gastric biopsies. We estimated Hp prevalence and prevalence by Hp status of endoscopic and histopathologic diagnoses. Results Among 878 participants with Hp status data, Hp prevalence was: 62% overall; 66% in 740 Indigenous participants; 22% in 77 non-Indigenous participants (61 participants did not disclose ethnicity); 45% at 0–14 years old, 69% at 15–34 years old, and 61% at 35–96 years old. Among 309 participants examined endoscopically, visible mucosal lesions were more frequent in the stomach than the duodenum: the gastric to duodenal ratio was 2 for inflammation, 8 for erosions, and 3 for ulcers. Pathological examination in 308 participants with gastric biopsies revealed normal gastric mucosa in 1 of 224 Hp-positive participants and 77% (65/84) of Hp-negative participants with sharp contrasts in the prevalence of abnormalities between Hp-positive and Hp-negative participants, respectively: moderate-severe active gastritis in 50 and 0%; moderate-severe chronic gastritis in 91 and 1%; atrophic gastritis in 43 and 0%; intestinal metaplasia in 17 and 5%. Conclusions The observed pattern of disease is consistent with increased risk of stomach cancer and reflects substantial inequity in the Hp-associated disease burden in western Arctic Canadian hamlets relative to most North American settings. This research adds to evidence that demonstrates the need for interventions aimed at reducing health risks from Hp infection in Indigenous Arctic communities.
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Affiliation(s)
- Katharine Fagan-Garcia
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada.
| | - Janis Geary
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Hsiu-Ju Chang
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Laura McAlpine
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Emily Walker
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada.,School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Amy Colquhoun
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | | | - Safwat Girgis
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Billy Archie
- Aklavik Health Committee, Aklavik, Northwest Territories, Canada
| | | | - Andre Corriveau
- Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - John Morse
- Stanton Territorial Hospital, Yellowknife, Northwest Territories, Canada
| | - Rachel Munday
- Susie Husky Health Centre, Aklavik, Northwest Territories, Canada
| | - Karen J Goodman
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada.,School of Public Health, University of Alberta, Edmonton, Alberta, Canada
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Abstract
BACKGROUND Standard graphical tools for whole genome comparison require a reference genome. However, any reference is also subject to annotation biases and rearrangements, and may not serve as the standard except for those of extensively studied model species. To fully exploit the rapidly accumulating sequence data from the recent sequencing technologies, genome comparison without any reference has been anticipated. RESULTS We introduce a circular genome visualizer to compare complete genomes of closely related species. This tool visualizes the position of orthologous gene clusters rather than actual sequences or their features, thereby achieving the comparative view without using a single reference genome. The essential information is the matrix of orthologous gene clusters whose positions (not sequences) are color-coded in circular graphics. As a demonstration, comparison of 14 Lactobacillus paracasei strains and one L. casei strain revealed not only large-scale rearrangements but also genomic islands that are strain-specific. Comparison of 73 Helicobacter pylori strains confirmed their genetic consistency and also revealed the three general patterns of large-scale genome inversions. CONCLUSIONS From the ample sequence information in the GenBank/ENA/DDBJ repository, we can reconstruct a genomic consensus for particular species. By visualizing multiple strains at a glance, we can identify conserved as well as strain-specific regions in multiply sequenced genomes. Positional consistency for orthologous genes provides information orthogonal to major sequence features such as the GC content or sequence similarity of marker genes. The positional comparison is therefore useful for identifying large-scale genome rearrangements or gene transfers.
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Affiliation(s)
- Ipputa Tada
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540 Japan
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan
| | - Masanori Arita
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540 Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
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Muñoz-Ramírez ZY, Mendez-Tenorio A, Kato I, Bravo MM, Rizzato C, Thorell K, Torres R, Aviles-Jimenez F, Camorlinga M, Canzian F, Torres J. Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway. Front Cell Infect Microbiol 2017; 7:50. [PMID: 28293542 PMCID: PMC5328995 DOI: 10.3389/fcimb.2017.00050] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/10/2017] [Indexed: 12/21/2022] Open
Abstract
Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk.
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Affiliation(s)
- Zilia Y Muñoz-Ramírez
- Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional Ciudad de México, Mexico
| | - Alfonso Mendez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional Ciudad de México, Mexico
| | - Ikuko Kato
- Department of Oncology and of Pathology, Wayne State University School of Medicine Detroit, MI, USA
| | - Maria M Bravo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerologia Bogota, Colombia
| | - Cosmeri Rizzato
- Dipartmento di Ricerca Traslazionale e Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa Pisa, Italy
| | - Kaisa Thorell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Stockholm, Sweden
| | - Roberto Torres
- Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional Ciudad de México, Mexico
| | | | - Margarita Camorlinga
- Unidad de Investigacion en Enfermedades Infecciosas, IMSS Ciudad de México, Mexico
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Javier Torres
- Unidad de Investigacion en Enfermedades Infecciosas, IMSS Ciudad de México, Mexico
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Zawilak-Pawlik A, Zakrzewska-Czerwińska J. Recent Advances in Helicobacter pylori Replication: Possible Implications in Adaptation to a Pathogenic Lifestyle and Perspectives for Drug Design. Curr Top Microbiol Immunol 2017; 400:73-103. [PMID: 28124150 DOI: 10.1007/978-3-319-50520-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA replication is an important step in the life cycle of every cell that ensures the continuous flow of genetic information from one generation to the next. In all organisms, chromosome replication must be coordinated with overall cell growth. Helicobacter pylori growth strongly depends on its interaction with the host, particularly with the gastric epithelium. Moreover, H. pylori actively searches for an optimal microniche within a stomach, and it has been shown that not every microniche equally supports growth of this bacterium. We postulate that besides nutrients, H. pylori senses different, unknown signals, which presumably also affect chromosome replication to maintain H. pylori propagation at optimal ratio allowing H. pylori to establish a chronic, lifelong infection. Thus, H. pylori chromosome replication and particularly the regulation of this process might be considered important for bacterial pathogenesis. Here, we summarize our current knowledge of chromosome and plasmid replication in H. pylori and discuss the mechanisms responsible for regulating this key cellular process. The results of extensive studies conducted thus far allow us to propose common and unique traits in H. pylori chromosome replication. Interestingly, the repertoire of proteins involved in replication in H. pylori is significantly different to that in E. coli, strongly suggesting that novel factors are engaged in H. pylori chromosome replication and could represent attractive drug targets.
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Affiliation(s)
- Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Ul. Weigla 12, 53-114, Wrocław, Poland.
| | - Jolanta Zakrzewska-Czerwińska
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Ul. Weigla 12, 53-114, Wrocław, Poland
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Ul. Joliot-Curie 14A, 50-383, Wrocław, Poland
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van Vliet AHM. Use of pan-genome analysis for the identification of lineage-specific genes of Helicobacter pylori. FEMS Microbiol Lett 2016; 364:fnw296. [PMID: 28011701 DOI: 10.1093/femsle/fnw296] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/08/2016] [Accepted: 12/22/2016] [Indexed: 12/23/2022] Open
Abstract
The human bacterial pathogen Helicobacter pylori has a highly variable genome, with significant allelic and sequence diversity between isolates and even within well-characterised strains, hampering comparative genomics of H. pylori In this study, pan-genome analysis has been used to identify lineage-specific genes of H. pylori A total of 346 H. pylori genomes spanning the hpAfrica1, hpAfrica2, hpAsia2, hpEurope, hspAmerind and hspEAsia multilocus sequence typing (MLST) lineages were searched for genes specifically overrepresented or underrepresented in MLST lineages or associated with the cag pathogenicity island. The only genes overrepresented in cag-positive genomes were the cag pathogenicity island genes themselves. In contrast, a total of 125 genes were either overrepresented or underrepresented in one or more MLST lineages. Of these 125 genes, alcohol/aldehyde-reducing enzymes linked with acid resistance and production of toxic aldehydes were found to be overrepresented in African lineages. Conversely, the FecA2 ferric citrate receptor was missing from hspAmerind genomes, but present in all other lineages. This work shows the applicability of pan-genome analysis for identification of lineage-specific genes of H. pylori, facilitating further investigation to allow linkage of differential distribution of genes with disease outcome or virulence of H. pylori.
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Affiliation(s)
- Arnoud H M van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7AD, UK
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