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Lim FS, González-Cabrera J, Keilwagen J, Kleespies RG, Jehle JA, Wennmann JT. Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets. Sci Rep 2024; 14:8525. [PMID: 38609404 PMCID: PMC11014933 DOI: 10.1038/s41598-024-58768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Rapid and reliable detection of pathogens is crucial to complement the growing industry of mass-reared insects, in order to safeguard the insect colonies from outbreak of diseases, which may cause significant economic loss. Current diagnostic methods are mainly based on conventional PCR and microscopic examination, requiring prior knowledge of disease symptoms and are limited to identifying known pathogens. Here, we present a rapid nanopore-based metagenomics approach for detecting entomopathogens from the European house cricket (Acheta domesticus). In this study, the Acheta domesticus densovirus (AdDV) was detected from diseased individuals using solely Nanopore sequencing. Virus reads and genome assemblies were obtained within twenty-four hours after sequencing. Subsequently, due to the length of the Nanopore reads, it was possible to reconstruct significantly large parts or even the entire AdDV genome to conduct studies for genotype identification. Variant analysis indicated the presence of three AdDV genotypes within the same house cricket population, with association to the vital status of the diseased crickets. This contrast provided compelling evidence for the existence of non-lethal AdDV genotypes. These findings demonstrated nanopore-based metagenomics sequencing as a powerful addition to the diagnostic tool kit for routine pathogen surveillance and diagnosis in the insect rearing industry.
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Affiliation(s)
- Fang Shiang Lim
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Joel González-Cabrera
- Department of Genetics and Institute BIOTECMED, Universitat de València, Dr Moliner 50, 46100, Burjassot, Spain
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for the Safety of Biotechnological Processes in Plants, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221, Dossenheim, Germany.
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2
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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3
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Park DG, Ha ES, Kang B, Choi I, Kwak JE, Choi J, Park J, Lee W, Kim SH, Kim SH, Lee JH. Development and Evaluation of a Next-Generation Sequencing Panel for the Multiple Detection and Identification of Pathogens in Fermented Foods. J Microbiol Biotechnol 2023; 33:83-95. [PMID: 36457187 PMCID: PMC9895999 DOI: 10.4014/jmb.2211.11009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/03/2022]
Abstract
These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic Escherichia coli, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium, respectively. Evaluation of the primer sets using singleplex PCR, crosscheck PCR and multiplex PCR revealed high specificity and selectivity without interference of primers or genomic DNAs. Subsequent NGS panel analysis with six artificially contaminated food samples using those primer sets showed that all target genes were multi-detected in one reaction at 108-105 CFU of target strains. However, a few false-positive results were shown at 106-105 CFU. To validate this NGS panel analysis, three sets of qPCR analyses were independently performed with the same contaminated food samples, showing the similar specificity and selectivity for detection and identification. While this NGS panel still has some issues for detection and identification of specific foodborne pathogens, it has much more advantages, especially multiple detection and identification in one reaction, and it could be improved by further optimized NGS panel primer sets and even by application of a new real-time NGS sequencing technology. Therefore, this study suggests the efficiency and usability of NGS panel for rapid determination of origin strain in various foodborne outbreaks in one reaction.
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Affiliation(s)
- Dong-Geun Park
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Su Ha
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Byungcheol Kang
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Iseul Choi
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Jeong-Eun Kwak
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinho Choi
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Jeongwoong Park
- Research and Development Center, Sanigen Co., Ltd, Anyang 14059, Republic of Korea
| | - Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea,Corresponding author Phone: +82-2-880-4854 Fax: +82-2-873-5095 E-mail:
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4
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Ju Y, Pu M, Sun K, Song G, Geng J. Nanopore Electrochemistry for Pathogen Detection. Chem Asian J 2022; 17:e202200774. [PMID: 36069587 DOI: 10.1002/asia.202200774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Pathogen infections have seriously threatened human health, and there is an urgent demand for rapid and efficient pathogen identification to provide instructions in clinical diagnosis and therapeutic intervention. Recently, nanopore technology, a rapidly maturing technology which delivers ultrasensitive sensing and high throughput in real-time and at low cost, has achieved success in pathogen detection. Furthermore, the remarkable development of nanopore sequencing, for example, the MinION sequencer from Oxford Nanopore Technologies (ONT) as a competitive sequencing technology, has facilitated the rapid analysis of disease-related microbiomes at the whole-genome level and on a large scale. Here, we highlighted recent advances in nanopore approaches for pathogen detection at the single-molecule level. We also overviewed the applications of nanopore sequencing in pathogenic bacteria identification and diagnosis. In the end, we discussed the challenges and future developments of nanopore technology as promising tools for the management of infections, which may be helpful to aid understanding as well as decision-making.
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Affiliation(s)
- Yuan Ju
- Sichuan University, Sichuan University Library, CHINA
| | - Mengjun Pu
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Ke Sun
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Guiqin Song
- North Sichuan Medical College [Search North Sichuan Medical College]: North Sichuan Medical University, Shool of Basic Medical Sciences and Forensic Medicine, CHINA
| | - Jia Geng
- Sichuan University, State Key Laboratory of Biotherapy, No 17 Section 3 of South Renmin Rd, 610040, Chengdu, CHINA
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Bhar A. The application of next generation sequencing technology in medical diagnostics: a perspective. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [PMCID: PMC9395867 DOI: 10.1007/s43538-022-00098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid isolation, characterization, and identification are prerequisites of any successful medical intervention to infectious disease treatment. This is a real challenge to the scientific as well as a medical community to find out a proper and robust method of pathogen detection. Classical cultural, as well as biochemical test-based identification, has its own limitations to their time-consuming and ineffectiveness for closely related pathovars. Molecular diagnostics became a popular alternative to classical techniques for the past couple of decades but it required some prior information to detect the pathogen successfully. Recently, with the advent of next-generation sequencing (NGS) technology identification, and characterization of almost all the pathogenic bacteria become possible without any information a priori. Metagenomic next generation sequencing is another specialized type of NGS that is profoundly utilized in medical biotechnology and diagnostics now a days. Therefore, the present review is focused on a brief introduction to NGS technology, its application in medical microbiology, and possible future aspects for the development of medical sciences.
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Affiliation(s)
- Anirban Bhar
- Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118 India
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Nehra M, Kumar V, Kumar R, Dilbaghi N, Kumar S. Current Scenario of Pathogen Detection Techniques in Agro-Food Sector. BIOSENSORS 2022; 12:bios12070489. [PMID: 35884292 PMCID: PMC9313409 DOI: 10.3390/bios12070489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 05/05/2023]
Abstract
Over the past-decade, agricultural products (such as vegetables and fruits) have been reported as the major vehicles for foodborne diseases, which are limiting food resources. The spread of infectious diseases due to foodborne pathogens poses a global threat to human health and the economy. The accurate and timely detection of infectious disease and of causative pathogens is crucial in the prevention and treatment of disease. Negligence in the detection of pathogenic substances can be catastrophic and lead to a pandemic. Despite the revolution in health diagnostics, much attention has been paid to the agro-food sector regarding the detection of food contaminants (such as pathogens). The conventional analytical techniques for pathogen detection are reliable and still in operation. However, laborious procedures and time-consuming detection via these approaches emphasize the need for simple, easy-to-use, and affordable detection techniques. The rapid detection of pathogens from food is essential to avoid the morbidity and mortality originating from the suboptimal nature of empiric pathogen treatment. This review critically discusses both the conventional and emerging bio-molecular approaches for pathogen detection in agro-food.
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Affiliation(s)
- Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Virendra Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Rajesh Kumar
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Correspondence:
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7
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Simões J, Yang Z, Dong T. An ultrasensitive fluorimetric sensor for pre-screening of water microbial contamination risk. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119805. [PMID: 33957453 DOI: 10.1016/j.saa.2021.119805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/21/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
In recent years, global efforts have been directed towards the development of water safety routines, consequently demanding cost-effective sensors capable of detecting outbreaks at early stages. This work reports the development and study of an original in-field tryptophan fluorimetric sensor as a potential indicator of real-time microbial contamination in water. The sensor excitation and emission wavelengths were selected with respect to the coliform bacteria tryptophan peak; 280 nm for excitation and 330 nm for emission. The in-lab tests with standard samples show a detection limit of 4.89 nM (≈0.1 μg/l) for L-tryptophan. The sensor exhibited good linearity over three orders of magnitude and considerable detection reproducibility, which was confirmed during calibration tests. Small-scale in situ tests showed that the sensor was better correlated with coliform bacteria than other online sensors such as turbidity. This suggests that the fluorimetric tryptophan sensor can be integrated into early warning systems that quickly assess changes in water microbial quality.
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Affiliation(s)
- João Simões
- Department of Microsystems-IMS, Faculty of Technology, Natural Sciences and Maritime Sciences, University of South-Eastern Norway-USN, P.O. Box 235, Kongsberg 3603, Norway
| | - Zhaochu Yang
- Chongqing Key Laboratory of Micro-Nano Systems and Intelligent Transduction, Collaborative Innovation Center on Micro-Nano Transduction and Intelligent Eco-Internet of Things, Chongqing Municipal Key Laboratory of Institutions of Higher Education on Micro-Nano Systems Technology and Smart Transducing, National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Tao Dong
- Department of Microsystems-IMS, Faculty of Technology, Natural Sciences and Maritime Sciences, University of South-Eastern Norway-USN, P.O. Box 235, Kongsberg 3603, Norway.
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8
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Maurya R, Kanakan A, Vasudevan JS, Chattopadhyay P, Pandey R. Infection outcome needs two to tango: human host and the pathogen. Brief Funct Genomics 2021; 21:90-102. [PMID: 34402498 PMCID: PMC8385967 DOI: 10.1093/bfgp/elab037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022] Open
Abstract
Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. These are modulated by contributions from the human genetic variants, transcriptional response (including noncoding RNA) and the pathogen’s genome architecture. Modern genomic tools and techniques have been crucial for the detection and genomic characterization of pathogens with respect to the emerging infectious diseases. Aided by next-generation sequencing (NGS), risk stratification of host population/s allows for the identification of susceptible subgroups and better disease management. Nevertheless, many challenges to a general understanding of host–pathogen interactions remain. In this review, we elucidate how a better understanding of the human host-pathogen interplay can substantially enhance, and in turn benefit from, current and future applications of multi-omics based approaches in infectious and rare diseases. This includes the RNA-level response, which modulates the disease severity and outcome. The need to understand the role of human genetic variants in disease severity and clinical outcome has been further highlighted during the Coronavirus disease 2019 (COVID-19) pandemic. This would enhance and contribute toward our future pandemic preparedness.
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Affiliation(s)
- Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Akshay Kanakan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
| | - Janani Srinivasa Vasudevan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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9
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Lin L, Zheng Q, Lin J, Yuk HG, Guo L. Immuno- and nucleic acid-based current technique for Salmonella detection in food. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-019-03423-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Li Y, Lee JS. Recent developments in affinity-based selection of aptamers for binding disease-related protein targets. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00842-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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11
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Kafkas Ş, Abdelhakim M, Hashish Y, Kulmanov M, Abdellatif M, Schofield PN, Hoehndorf R. PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. Sci Data 2019; 6:79. [PMID: 31160594 PMCID: PMC6546783 DOI: 10.1038/s41597-019-0090-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/07/2019] [Indexed: 12/11/2022] Open
Abstract
Understanding the relationship between the pathophysiology of infectious disease, the biology of the causative agent and the development of therapeutic and diagnostic approaches is dependent on the synthesis of a wide range of types of information. Provision of a comprehensive and integrated disease phenotype knowledgebase has the potential to provide novel and orthogonal sources of information for the understanding of infectious agent pathogenesis, and support for research on disease mechanisms. We have developed PathoPhenoDB, a database containing pathogen-to-phenotype associations. PathoPhenoDB relies on manual curation of pathogen-disease relations, on ontology-based text mining as well as manual curation to associate host disease phenotypes with infectious agents. Using Semantic Web technologies, PathoPhenoDB also links to knowledge about drug resistance mechanisms and drugs used in the treatment of infectious diseases. PathoPhenoDB is accessible at http://patho.phenomebrowser.net/ , and the data are freely available through a public SPARQL endpoint.
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Affiliation(s)
- Şenay Kafkas
- Computer, Electrical and Mathematical Sciences & Engineering with Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Marwa Abdelhakim
- Computer, Electrical and Mathematical Sciences & Engineering with Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Yasmeen Hashish
- Computer, Electrical and Mathematical Sciences & Engineering with Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Maxat Kulmanov
- Computer, Electrical and Mathematical Sciences & Engineering with Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Marwa Abdellatif
- Computer, Electrical and Mathematical Sciences & Engineering with Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Paul N Schofield
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, United Kingdom
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences & Engineering with Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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12
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Paskey AC, Frey KG, Schroth G, Gross S, Hamilton T, Bishop-Lilly KA. Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples. BMC Genomics 2019; 20:155. [PMID: 30808306 PMCID: PMC6390631 DOI: 10.1186/s12864-019-5543-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/18/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. RESULTS This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage. CONCLUSIONS Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA
- Leidos, Reston, VA 20190 USA
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
| | | | | | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
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Okuda KI, Yoshii Y, Yamada S, Chiba A, Hironaka I, Hori S, Yanaga K, Mizunoe Y. Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: a preliminary clinical study. Ann Clin Microbiol Antimicrob 2018; 17:44. [PMID: 30577829 PMCID: PMC6303997 DOI: 10.1186/s12941-018-0297-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/17/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Catheter-related infection (CRI) is one of the serious challenges in clinical practice. This preliminary clinical study aimed to examine whether next-generation sequencing (NGS) targeting 16S rDNA, which was PCR-amplified directly from the tip of a central venous catheter (CVC), can be used to identify causative pathogens in CRI, compared to the culture method. METHODS Hospitalized patients, from whom a CVC had just been removed, were prospectively enrolled and divided into the CRI-suspected and routine removal groups. DNA was extracted from the sonication fluid of CVC specimens derived from patients. For analysis of bacterial composition by NGS, the V3-V4 fragments of bacterial 16S rDNA were PCR-amplified, followed by index PCR and paired-end sequencing on an Illumina MiSeq device. Conventional culture methods were also performed in the CRI-suspected group. RESULTS Of CVCs collected from the 156 enrolled patients (114 men; mean age 65.6 years), a total of 14 specimens [nine out of 31 patients suspected with CRI and five out of 125 patients without infection symptoms (routine removal group)] were PCR-positive. In five patients with definite CRI, Staphylococcus was the most frequently detected genus by NGS (4/5 specimens), although no pathogens were detected by NGS in the one remaining specimen. The genera identified by NGS were consistent with those from conventional culture tests. There was high agreement between NGS and the culture method in the CRI-suspected group, with sensitivity and specificity values of 80.0% and 76.9%, respectively; meanwhile, the false-positive rate of NGS was as low as 4.0% in the routine removal group. Moreover, several genera, besides the genus identified by culture test, were detected in each patient with definite CRI and surgical site infection (SSI). Additionally, in one patient with SSI, Enterococcaceae were detected not only by NGS but also by abdominal abscess drainage culture. CONCLUSIONS NGS targeting 16S rDNA was able to analyze the bacterial composition of CVC specimens and detect causative pathogens in patients with CRI and was therefore suggested as a promising diagnostic tool for CRI.
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Affiliation(s)
- Ken-Ichi Okuda
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan. .,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan.
| | - Yutaka Yoshii
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan.,Division of Respiratory Diseases, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Satomi Yamada
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Akio Chiba
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan
| | - Ippei Hironaka
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.,Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Seiji Hori
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan.,Department of Infectious Disease and Control, The Jikei University School of Medicine, Tokyo, Japan
| | - Katsuhiko Yanaga
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan.,Department of Surgery, The Jikei University School of Medicine, Tokyo, Japan
| | - Yoshimitsu Mizunoe
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan
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14
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Rantsiou K, Kathariou S, Winkler A, Skandamis P, Saint-Cyr MJ, Rouzeau-Szynalski K, Amézquita A. Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment. Int J Food Microbiol 2017; 287:3-9. [PMID: 29246458 DOI: 10.1016/j.ijfoodmicro.2017.11.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/16/2017] [Accepted: 11/12/2017] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other -omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented.
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Affiliation(s)
- Kalliopi Rantsiou
- Department of Agriculture, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy.
| | - Sophia Kathariou
- North Carolina State University, Department of Food, Bioprocessing and Nutrition Sciences, Raleigh, NC, USA
| | - Annet Winkler
- Mondelez International, Kraft Foods R&D, Unterbiberger St. 15, D-81737 Munich, Germany
| | - Panos Skandamis
- Laboratory of Food Quality Control & Hygiene, Department of Food Science & Technology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | | | | | - Alejandro Amézquita
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
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