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Sundararaman B, Shapiro K, Packham A, Camp LE, Meyer RS, Shapiro B, Green RE. Whole genome enrichment approach for genomic surveillance of Toxoplasma gondii. Food Microbiol 2024; 118:104403. [PMID: 38049278 DOI: 10.1016/j.fm.2023.104403] [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] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/15/2023] [Indexed: 12/06/2023]
Abstract
Pathogenic bacteria, viruses, fungi, and protozoa can cause food and waterborne diseases. Surveillance methods must therefore screen for these pathogens at various stages of water distribution and of food from production to consumption. Detection using nucleic acid amplification methods offer rapid identification, but such methods have limited utility for characterizing populations, variant types or virulence traits of pathogens. Whole genome sequencing (WGS) can be used to determine this information. However, pathogens must be isolated and cultured to yield sufficient DNA for WGS, which is laborious or not feasible for certain stages of parasites like oocysts of Toxoplasma gondii. We previously developed the Circular Nucleic acid Enrichment Reagent (CNER) method to make whole genome enrichment (WGE) baits for difficult-to-grow bacterial pathogens. WGE using CNERs facilitates direct sequencing of pathogens from samples without the need to isolate and grow them. Here, we made WGE-CNERs for T. gondii to demonstrate the use of the CNER method to make baits to enrich the large genomes of water and foodborne protozoan pathogens. By sequencing, we detected as few as 50 parasites spiked in an oyster hemolymph matrix. We discuss the use of WGE-CNERs for genomic surveillance of food and waterborne pathogens.
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Affiliation(s)
| | - Karen Shapiro
- One Health Institute, UC Davis, USA; Department of Pathology, Microbiology, and Immunology, UC Davis, USA.
| | | | - Lauren E Camp
- Department of Pathology, Microbiology, and Immunology, UC Davis, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, UC Santa Cruz, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, UC Santa Cruz, USA; Howard Hughes Medical Institute, UC Santa Cruz, USA
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Epi-Gene: An R-Package for Easy Pan-Genome Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5585586. [PMID: 34595238 PMCID: PMC8478537 DOI: 10.1155/2021/5585586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/28/2021] [Indexed: 11/18/2022]
Abstract
The main aim of this study was to develop a set of functions that can analyze the genomic data with less time consumption and memory. Epi-gene is presented as a solution to large sequence file handling and computational time problems. It uses less time and less programming skills in order to work with a large number of genomes. In the current study, some features of the Epi-gene R-package were described and illustrated by using a dataset of the 14 Aeromonas hydrophila genomes. The joining, relabeling, and conversion functions were also included in this package to handle the FASTA formatted sequences. To calculate the subsets of core genes, accessory genes, and unique genes, various Epi-gene functions have been used. Heat maps and phylogenetic genome trees were also constructed. This whole procedure was completed in less than 30 minutes. This package can only work on Windows operating systems. Different functions from other packages such as dplyr and ggtree were also used that were available in R computing environment.
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Delinasios GJ, Fragkou PC, Gkirmpa AM, Tsangaris G, Hoffman RM, Anagnostopoulos AK. The Experience of Greece as a Model to Contain COVID-19 Infection Spread. In Vivo 2021; 35:1285-1294. [PMID: 33622932 DOI: 10.21873/invivo.12380] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) emerged in late 2019 and has caused a pandemic known as corona virus disease 2019 (COVID-19), responsible for the death of more than 2 million people worldwide. The outbreak of COVID-19 has posed an unprecedented threat on human lives and public safety. The aim of this review is to describe key aspects of the bio-pathology of the novel disease, and discuss aspects of its spread, as well as targeted protective strategies that can help shape the outcome of the present and future health crises. Greece is used as a model to inhibit SARS-COV-2 spread, since it is one of the countries with the lowest fatality rates among nations of the European Union (E.U.), following two consecutive waves of COVID-19 pandemic. Furthermore, niche research technological approaches and scientific recommendations that emerged during the COVID-19 era are discussed.
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Affiliation(s)
| | - Paraskevi C Fragkou
- Fourth Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Athina M Gkirmpa
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - George Tsangaris
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Robert M Hoffman
- AntiCancer Inc., San Diego, CA, U.S.A.,Department of Surgery, University of San Diego, San Diego, CA, U.S.A
| | - Athanasios K Anagnostopoulos
- International Institute of Anticancer Research, Kapandriti, Greece; .,Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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Rabaan AA, Al-Ahmed SH, Sah R, Al-Tawfiq JA, Haque S, Harapan H, Arteaga-Livias K, Aldana DKB, Kumar P, Dhama K, Rodriguez-Morales AJ. Genomic Epidemiology and Recent Update on Nucleic Acid-Based Diagnostics for COVID-19. CURRENT TROPICAL MEDICINE REPORTS 2020; 7:113-119. [PMID: 32989413 PMCID: PMC7513458 DOI: 10.1007/s40475-020-00212-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2020] [Indexed: 01/22/2023]
Abstract
Purpose of the Review The SARS-CoV-2 genome has been sequenced and the data is made available in the public domain. Molecular epidemiological investigators have utilized this information to elucidate the origin, mode of transmission, and contact tracing of SARS-CoV-2. The present review aims to highlight the recent advancements in the molecular epidemiological studies along with updating recent advancements in the molecular (nucleic acid based) diagnostics for COVID-19, the disease caused by SARS-CoV-2. Recent Findings Epidemiological studies with the integration of molecular genetics principles and tools are now mainly focused on the elucidation of molecular pathology of COVID-19. Molecular epidemiological studies have discovered the mutability of SARS-CoV-2 which is of utmost importance for the development of therapeutics and vaccines for COVID-19. The whole world is now participating in the race for development of better and rapid diagnostics and therapeutics for COVID-19. Several molecular diagnostic techniques have been developed for accurate and precise diagnosis of COVID-19. Summary Novel genomic techniques have helped in the understanding of the disease pathology, origin, and spread of COVID-19. The whole genome sequence established in the initial days of the outbreak has enabled to identify the virus taxonomy. Several rapid, accurate, and sensitive diagnostic methods have been developed; those are based on the principle of detecting SARS-CoV-2 nucleic acids in clinical samples. Most of these molecular diagnostics are based on RT-PCR principle.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Ranjit Sah
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia.,Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia.,Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia
| | - Kovy Arteaga-Livias
- Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco, Peru.,Universidad Científica del Sur, Lima, Peru
| | - D Katterine Bonilla Aldana
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda Colombia.,Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda Colombia
| | - Pawan Kumar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122 India
| | - Alfonso J Rodriguez-Morales
- Universidad Científica del Sur, Lima, Peru.,Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda Colombia.,Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda Colombia.,Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda Colombia
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Hill AA, Crotta M, Wall B, Good L, O'Brien SJ, Guitian J. Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160721. [PMID: 28405360 PMCID: PMC5383817 DOI: 10.1098/rsos.160721] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/27/2017] [Indexed: 05/05/2023]
Abstract
Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining 'big' data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would probably more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype.
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Affiliation(s)
| | - M. Crotta
- Royal Veterinary College, University of London, London, UK
| | - B. Wall
- Royal Veterinary College, University of London, London, UK
| | - L. Good
- Royal Veterinary College, University of London, London, UK
| | - S. J. O'Brien
- NIHR Health Protection Research Unit in Gastrointestinal Infections, UK
| | - J. Guitian
- Royal Veterinary College, University of London, London, UK
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Chiò A, Logroscino G, Traynor BJ, Collins J, Simeone JC, Goldstein LA, White LA. Global epidemiology of amyotrophic lateral sclerosis: a systematic review of the published literature. Neuroepidemiology 2013; 41:118-30. [PMID: 23860588 DOI: 10.1159/000351153] [Citation(s) in RCA: 526] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/03/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is relatively rare, yet the economic and social burden is substantial. Having accurate incidence and prevalence estimates would facilitate efficient allocation of healthcare resources. OBJECTIVE To provide a comprehensive and critical review of the epidemiological literature on ALS. METHODS MEDLINE and EMBASE (1995-2011) databases of population-based studies on ALS incidence and prevalence reporting quantitative data were analyzed. Data extracted included study location and time, design and data sources, case ascertainment methods and incidence and/or prevalence rates. Medians and interquartile ranges (IQRs) were calculated, and ALS case estimates were derived using 2010 population estimates. RESULTS In all, 37 articles met the inclusion criteria. In Europe, the median incidence rate (/100,000 population) was 2.08 (IQR 1.47-2.43), corresponding to an estimated 15,355 (10,852-17,938) cases. Median prevalence (/100,000 population) was 5.40 (IQR 4.06-7.89), or 39,863 (29,971-58,244) prevalent cases. CONCLUSIONS Disparity in rates among ALS incidence and prevalence studies may be due to differences in study design or true variations in population demographics such as age and geography, including environmental factors and genetic predisposition. Additional large-scale studies that use standardized case ascertainment methods are needed to more accurately assess the true global burden of ALS.
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Affiliation(s)
- A Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy.
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Abstract
Interaction between the genome and the environment has been widely discussed in the literature, but has the importance ascribed to understanding these interactions been overstated? In this opinion piece, we critically discuss gene-environment interactions and attempt to answer three key questions. First, is it likely that gene-environment interactions actually exist? Second, what is the realistic value of trying to unravel these interactions, both in terms of understanding disease pathogenesis and as a means of ameliorating disease? Finally, and most importantly, do the technologies and methodologies exist to facilitate an unbiased search for gene-environment interactions? Addressing these questions highlights key areas of feasibility that must be considered in this area of research.
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Singleton AB, Hardy J, Traynor BJ, Houlden H. Towards a complete resolution of the genetic architecture of disease. Trends Genet 2010; 26:438-42. [PMID: 20813421 DOI: 10.1016/j.tig.2010.07.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 01/19/2023]
Abstract
After years of linear gains in the genetic dissection of human disease we are now in a period of exponential discovery. This is particularly apparent for complex disease. Genome-wide association studies (GWAS) have provided myriad associations between common variability and disease, and have shown that common genetic variability is unlikely to explain the entire genetic predisposition to disease. Here we detail how one can expand on this success and systematically identify genetic risks that lead or predispose to disease using next-generation sequencing. Geneticists have had for many years a protocol to identify Mendelian disease. A similar set of tools is now available for the identification of rare moderate-risk loci and common low-risk variants. Whereas major challenges undoubtedly remain, particularly regarding data handling and the functional classification of variants, we suggest that these will be largely practical and not conceptual.
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Affiliation(s)
- Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
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Abstract
Gene-Environment Interaction: A Genetic-Epidemiological ApproachClassical epidemiology addresses the distribution and determinants of diseases in populations, and the factors associated with disease causation, with the aim of preventing disease. Both genetic and environmental factors may contribute to susceptibility, and it is still unclear how these factors interact in their influence on risk. Genetic epidemiology is the field which incorporates concepts and methods from different disciplines including epidemiology, genetics, biostatistics, clinical and molecular medicine, and their interaction is crucial to understanding the role of genetic and environmental factors in disease processes. The study of gene-environment interaction is central in the field of genetic epidemiology. Gene-environment interaction is defined as »a different effect of an environmental exposure on disease risk in persons with different genotypes,« or, alternatively, »a different effect of a genotype on disease risk in persons with different environmental exposures.« Five biologically plausible models are described for the relations between genotypes and environmental exposures, in terms of their effects on disease risk. Therefore, the study of gene-environment interaction is important for improving accuracy and precision in the assessment of both genetic and environmental factors, especially in disorders of less defined etiology. Genetic epidemiology is also applied at the various levels of disease prevention.
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