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Ono T, Cruz M, Jiménez Abreu JA, Nagashima H, Subsomwong P, Hosking C, Shiota S, Suzuki R, Yamaoka Y. Comparative study between Helicobacter pylori and host human genetics in the Dominican Republic. BMC Evol Biol 2019; 19:197. [PMID: 31675915 PMCID: PMC6823972 DOI: 10.1186/s12862-019-1526-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/15/2019] [Indexed: 01/06/2023] Open
Abstract
Background Helicobacter pylori, a bacterium that infects the human stomach, has high genetic diversity. Because its evolution is parallel to human, H. pylori is used as a tool to trace human migration. However, there are few studies about the relationship between phylogeography of H. pylori and its host human. Methods We examined both H. pylori DNA and the host mitochondrial DNA and Y-chromosome DNA obtained from a total 119 patients in the Dominican Republic, where human demography consists of various ancestries. DNA extracted from cultured H. pylori were analyzed by multi locus sequence typing. Mitochondrial DNA and Y-chromosome DNA were evaluated by haplogroup analyses. Results H. pylori strains were divided into 2 populations; 68 strains with African group (hpAfrica1) and 51 strains with European group (hpEurope). In Y-chromosomal haplogroup, European origin was dominant, whereas African origin was dominant both in H. pylori and in mtDNA haplogroup. These results supported the hypothesis that mother-to-child infection is predominant in H. pylori infection. The Amerindian type of mtDNA haplogroup was observed in 11.8% of the patients; however, Amerindian type (hspAmerind) of H. pylori was not observed. Although subpopulation type of most hpAfrica1 strains in Central America and South America were hybrid (hspWAfrica/hpEurope), most Dominican Republic hpAfrica1 strains were similar to those of African continent. Conclusions Genetic features of H. pylori, mtDNA, and Y haplogroups reflect the history of colonial migration and slave trade in the Dominican Republic. Discrepancy between H. pylori and the host human genotypes support the hypothesis that adaptability of hspAmerind H. pylori strains are weaker than hpEurope strains. H. pylori strains in the Dominican Republic seem to contain larger proportion of African ancestry compared to other American continent strains.
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Affiliation(s)
- Takaaki Ono
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan.,Criminal Investigation Laboratory, Oita Prefectural Police H.Q, Oita, Japan
| | - Modesto Cruz
- Institute of Microbiology and Parasitology, Faculty of Science, Autonomous University of Santo Domingo, Santo Domingo, Dominican Republic.,Department of Biomedical Research, National Institute of Medicine and Diagnostic Imaging, Santo Domingo, Dominican Republic
| | - José A Jiménez Abreu
- Dominican-Japanese Digestive Disease Center, Dr Luis E. Aybar Health and Hygiene City, Santo Domingo, Dominican Republic
| | - Hiroyuki Nagashima
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan.,Department of Gastroenterology, Hokkaido Cancer Center, Sapporo, Hokkaido, Japan
| | - Phawinee Subsomwong
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Celso Hosking
- Institute of Microbiology and Parasitology, Faculty of Science, Autonomous University of Santo Domingo, Santo Domingo, Dominican Republic
| | - Seiji Shiota
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan. .,Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, USA.
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González-Saldía RR, Pino-Maureira NL, Muñoz C, Soto L, Durán E, Barra MJ, Gutiérrez S, Díaz V, Saavedra A. Fecal pollution source tracking and thalassogenic diseases: The temporal-spatial concordance between maximum concentrations of human mitochondrial DNA in seawater and Hepatitis A outbreaks among a coastal population. Sci Total Environ 2019; 686:158-170. [PMID: 31176815 DOI: 10.1016/j.scitotenv.2019.05.415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/13/2019] [Accepted: 05/27/2019] [Indexed: 05/25/2023]
Abstract
Fecal pollution source tracking (FST) studies the origin of fecal contamination and promotes action to eliminate it to improve human health and environmental sustainability. This work presents the temporal and spatial relations of human mitochondrial DNA (HmtDNA), fecal coliforms (FC) and live microbial biomass (ATP) in seawater during a hepatitis A outbreak among a human coastal population. The study area is approximately 100 km along the coastline of the Biobío Region in the southeastern Pacific (Humboldt Current System, Chile). Total data from the swash zone from summer 2015 to autumn 2016 show there were significant positive log-log correlations between FC and HmtDNA (R = 0.32) and ATP (R = 0.31). These correlations were highest during the austral spring of 2015 (R = 0.53 and 0.58 respectively), when HmtDNA also correlated significantly with ATP (R = 0.86). Maximum average values of the parameters measured in this season showed a temporal-spatial concordance with the peak in the number of hepatitis A cases among the nearby coastal population. FC correlated significantly with HmtDNA (R = 0.98) in the water column of the coastal zone close to Concepción Bay during the austral summer of 2016 and in the swash zone of the bay (R = 0.68) throughout the study period. Hepatitis A virus (HAV) has also been detected in organisms and seawater in Concepción Bay, which is consistent with the high incidence of hepatitis A among the coastal population. The concordance between human fecal pollution in the study area and a seasonal hepatitis A outbreak strongly suggests that HmtDNA and its relation with FC and ATP in the coastal zone of marine environments can be used as a proxy to evaluate the risk of outbreaks of thalassogenic diseases.
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Affiliation(s)
- R R González-Saldía
- Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Departamento de Oceanografía, Concepción 4070386, Chile; Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Doctorado en Ciencias con mención en Manejo de Recursos Acuáticos Renovables, Concepción 4070386, Chile; Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Centro de Investigación Oceanográfica COPAS Sur-Austral, Concepción 4070386, Chile; Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Ingeniería en Biotecnología Marina y Acuicultura, Concepción 4070386, Chile.
| | - N L Pino-Maureira
- Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Doctorado en Ciencias con mención en Manejo de Recursos Acuáticos Renovables, Concepción 4070386, Chile; Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Centro de Investigación Oceanográfica COPAS Sur-Austral, Concepción 4070386, Chile.
| | - Ch Muñoz
- Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Centro de Investigación Oceanográfica COPAS Sur-Austral, Concepción 4070386, Chile.
| | - L Soto
- Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Ingeniería en Biotecnología Marina y Acuicultura, Concepción 4070386, Chile.
| | - E Durán
- Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Ingeniería en Biotecnología Marina y Acuicultura, Concepción 4070386, Chile.
| | - M J Barra
- Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Centro de Investigación Oceanográfica COPAS Sur-Austral, Concepción 4070386, Chile.
| | - S Gutiérrez
- Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Centro de Investigación Oceanográfica COPAS Sur-Austral, Concepción 4070386, Chile.
| | - V Díaz
- Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Centro de Investigación Oceanográfica COPAS Sur-Austral, Concepción 4070386, Chile.
| | - A Saavedra
- Universidad de Concepción, Facultad de Ciencias Naturales y Oceanográficas, Centro de Investigación Oceanográfica COPAS Sur-Austral, Concepción 4070386, Chile.
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Tan L, Li L, Ashbolt N, Wang X, Cui Y, Zhu X, Xu Y, Yang Y, Mao D, Luo Y. Arctic antibiotic resistance gene contamination, a result of anthropogenic activities and natural origin. Sci Total Environ 2018; 621:1176-1184. [PMID: 29070451 DOI: 10.1016/j.scitotenv.2017.10.110] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 06/07/2023]
Abstract
The increasing global prevalence of antibiotic resistance genes (ARGs) in the environment is attributed to anthropogenic activities, particularly the misuse of antimicrobial drugs in human care and animal production. In the present study, we first examined Arctic/sub-Arctic (polar) sediments for the abundance and diversity of 30 ARGs against sulfonamide, tetracycline, aminoglycoside, quinolone, macrolide, and β-lactam antibiotics. Polar sediment ARGs were detected by qPCR at relatively low levels (10-9 to 10-5 copies/16S rRNA gene copies) compared to the reference sites, which were heavily impacted regions of China (the Haihe River, the Tianjin Water Park water and the Qilihai Wetland water, at 10-8 to 10-2 copies/16S rRNA gene copies). A human mitochondrial gene target, Hmt, was first used to aid in the identification of ARGs associated with anthropogenic activities, being relatively persistent, in high copy number and a human-specific molecular marker. Hmt was consistently present in easily quantifiable amounts in the polar sediment samples, indicating their relationship with human-impact, and it was also positively correlated with the relative abundance of ARGs and to the concentrations of modern-day antibiotics. Phylogenetic analyses of resistance sequences from both the Arctic marine sediments and a major database of human pathogens indicated that the ARGs in polar region were the result of a mix of human influence and natural origins. To our knowledge, this is the first study to show that ARGs in Arctic marine sediments appear to be a mixture of both natural origins and recent human influence. This study provides a significant reference regarding the global reach of antibiotic resistance, which is associated with anthropogenic activities.
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Affiliation(s)
- Lu Tan
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Linyun Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Nicholas Ashbolt
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China; School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Xiaolong Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Yuxiao Cui
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Xiao Zhu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Yan Xu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Yang Yang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, China.
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China.
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Kapoor V, Elk M, Toledo-Hernandez C, Santo Domingo JW. Analysis of human mitochondrial DNA sequences from fecally polluted environmental waters as a tool to study population diversity. AIMS Environ Sci 2017; 4:443-455. [PMID: 32802939 PMCID: PMC7425658 DOI: 10.3934/environsci.2017.3.443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mitochondrial signature sequences have frequently been used to study human population diversity around the world. Traditionally, this requires obtaining samples directly from individuals which is cumbersome, time consuming and limited to the number of individuals that participated in these types of surveys. Here, we used environmental DNA extracts to determine the presence and sequence variability of human mitochondrial sequences as a means to study the diversity of populations inhabiting in areas nearby a tropical watershed impacted with human fecal pollution. We used high-throughput sequencing (Illumina) and barcoding to obtain thousands of sequences from the mitochondrial hypervariable region 2 (HVR2) and determined the different haplotypes present in 10 different water samples. Sequence analyses indicated a total of 19 distinct variants with frequency greater than 5%. The HVR2 sequences were associated with haplogroups of West Eurasian (57.6%), Sub-Saharan African (23.9%), and American Indian (11%) ancestry. This was in relative accordance with population census data from the watershed sites. The results from this study demonstrates the potential value of mitochondrial sequence data retrieved from fecally impacted environmental waters to study the population diversity of local municipalities. This environmental DNA approach may also have other public health implications such as tracking background levels of human mitochondrial genes associated with diseases. It may be possible to expand this approach to other animal species inhabiting or using natural water systems.
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Affiliation(s)
- Vikram Kapoor
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Michael Elk
- Pegasus Technical Services, Inc., Cincinnati, OH 45268, USA
| | | | - Jorge W Santo Domingo
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
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