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Pilling OA, Sundararaman SA, Brisson D, Beiting DP. Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment. PLoS Pathog 2024; 20:e1012418. [PMID: 39264872 PMCID: PMC11392400 DOI: 10.1371/journal.ppat.1012418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionized microbiology, but many microbes exist at low abundance in their natural environment and/or are difficult, if not impossible, to culture in the laboratory. This makes it challenging to use HTS to study the genomes of many important microbes and pathogens. In this review, we discuss the development and application of selective whole genome amplification (SWGA) to allow whole or partial genomes to be sequenced for low abundance microbes directly from complex biological samples. We highlight ways in which genomic data generated by SWGA have been used to elucidate the population dynamics of important human pathogens and monitor development of antimicrobial resistance and the emergence of potential outbreaks. We also describe the limitations of this method and propose some potential innovations that could be used to improve the quality of SWGA and lower the barriers to using this method across a wider range of infectious pathogens.
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Affiliation(s)
- Olivia A Pilling
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sesh A Sundararaman
- Department of Pediatrics, Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Pennsylvania, United States of America
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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2
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Islam Sajib MS, Brunker K, Oravcova K, Everest P, Murphy ME, Forde T. Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection. J Mol Diagn 2024; 26:741-753. [PMID: 38925458 DOI: 10.1016/j.jmoldx.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/05/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
Bloodstream infection is a major cause of morbidity and death worldwide. Timely and appropriate treatment can reduce mortality among critically ill patients. Current diagnostic methods are too slow to inform precise antibiotic choice, leading to the prescription of empirical antibiotics, which may fail to cover the resistance profile of the pathogen, risking poor patient outcomes. Additionally, overuse of broad-spectrum antibiotics may lead to more resistant organisms, putting further pressure on the dwindling pipeline of antibiotics, and risk transmission of these resistant organisms in the health care environment. Therefore, rapid diagnostics are urgently required to better inform antibiotic choice early in the course of treatment. Sequencing offers great promise in reducing time to microbiological diagnosis; however, the amount of host DNA compared with the pathogen in patient samples presents a significant obstacle. Various host-depletion and bacterial-enrichment strategies have been used in samples, such as saliva, urine, or tissue. However, these methods have yet to be collectively integrated and/or extensively explored for rapid bloodstream infection diagnosis. Although most of these workflows possess individual strengths, their lack of analytical/clinical sensitivity and/or comprehensiveness demands additional improvements or synergistic application. This review provides a distinctive classification system for various methods based on their working principles to guide future research, and discusses their strengths and limitations and explores potential avenues for improvement to assist the reader in workflow selection.
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Affiliation(s)
- Mohammad S Islam Sajib
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom.
| | - Kirstyn Brunker
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom; Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Katarina Oravcova
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Paul Everest
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Michael E Murphy
- Department of Microbiology, National Health Service Greater Glasgow and Clyde, Glasgow, United Kingdom; School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, United Kingdom
| | - Taya Forde
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
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3
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Guo Y, Yang Y, Xu M, Shi G, Zhou J, Zhang J, Li H. Trends and Developments in the Detection of Pathogens in Central Nervous System Infections: A Bibliometric Study. Front Cell Infect Microbiol 2022; 12:856845. [PMID: 35573778 PMCID: PMC9100591 DOI: 10.3389/fcimb.2022.856845] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/29/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction Rapid, sensitive, and specific laboratory assays are critical for the diagnosis and management of central nervous system (CNS) infections. The purpose of this study is to explore the intellectual landscape of research investigating methods for the detection of pathogens in patients with CNS infections and to identify the development trends and research frontier in this field. Methods A bibliometric study is conducted by analyzing literature retrieved from the Web of Science (WoS) Core Collection Database for the years 2000 to 2021. CiteSpace software is used for bibliometric analysis and network visualization, including co-citation analysis of references, co-occurrence analysis of keywords, and cooperation network analysis of authors, institutions, and countries/regions. Results A total of 2,282 publications are eventually screened, with an upward trend in the number of publications per year. The majority of papers are attributed to the disciplines of MICROBIOLOGY, INFECTIOUS DISEASES, IMMUNOLOGY, NEUROSCIENCES & NEUROLOGY, and VIROLOGY. The co-citation analysis of references shows that recent research has focused on the largest cluster “metagenomic next-generation sequencing”; the results of the analysis of the highest-cited publications and the citation burst of publications reveal that there is a strong interest stimulated in metagenomic next-generation sequencing. The co-occurrence analysis of keywords indicates that “infection”, “pathogen”, “diagnosis”, “gene”, “virus”, “polymerase chain reaction”, “cerebrospinal fluid”, “epidemiology”, and “metagenomic next-generation sequencing” are the main research priorities in the field of pathogen detection for CNS infections, and the keyword with the highest strength of burst is “metagenomic next-generation sequencing”. Collaborative network analysis reveals that the USA, the Centers for Disease Control and Prevention of USA, and XIN WANG and JENNIFER DIEN BARD are the most influential country, institution, and researchers, respectively. Conclusions Exploring more advanced laboratory assays to improve the diagnostic accuracy of pathogens is essential for CNS infection research. Metagenomic next-generation sequencing is emerging as a novel useful unbiased approach for diagnosing infectious diseases of the CNS.
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Affiliation(s)
- Yangyang Guo
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanlin Yang
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ming Xu
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guangzhi Shi
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jianxin Zhou
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jindong Zhang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- *Correspondence: Jindong Zhang, ; Hongliang Li,
| | - Hongliang Li
- Intensive Care Unit, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Jindong Zhang, ; Hongliang Li,
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Shi Y, Wang G, Lau HCH, Yu J. Metagenomic Sequencing for Microbial DNA in Human Samples: Emerging Technological Advances. Int J Mol Sci 2022; 23:ijms23042181. [PMID: 35216302 PMCID: PMC8877284 DOI: 10.3390/ijms23042181] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Whole genome metagenomic sequencing is a powerful platform enabling the simultaneous identification of all genes from entirely different kingdoms of organisms in a complex sample. This technology has revolutionised multiple areas from microbiome research to clinical diagnoses. However, one of the major challenges of a metagenomic study is the overwhelming non-microbial DNA present in most of the host-derived specimens, which can inundate the microbial signals and reduce the sensitivity of microorganism detection. Various host DNA depletion methods to facilitate metagenomic sequencing have been developed and have received considerable attention in this context. In this review, we present an overview of current host DNA depletion approaches along with explanations of their underlying principles, advantages and disadvantages. We also discuss their applications in laboratory microbiome research and clinical diagnoses and, finally, we envisage the direction of the further perfection of metagenomic sequencing in samples with overabundant host DNA.
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Affiliation(s)
| | | | | | - Jun Yu
- Correspondence: ; Tel.: +852-37636099; Fax:+852-21445330
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Jothikumar N, Cromeans T, Shivajothi J, Vinjé J, Murphy J. Development and evaluation of a ligation-free sequence-independent, single-primer amplification (LF-SISPA) assay for whole genome characterization of viruses. J Virol Methods 2022; 299:114346. [PMID: 34740706 PMCID: PMC11075090 DOI: 10.1016/j.jviromet.2021.114346] [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: 07/07/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 11/24/2022]
Abstract
Molecular identification and characterization of novel or re-emerging infectious pathogens is critical for disease surveillance and outbreak investigations. Next generation sequencing (NGS) using Sequence-Independent, Single-Primer Amplification (SISPA) is being used extensively in sequencing of viral genomes but it requires an expensive library preparation step. We developed a simple, low-cost method that enriches nucleic acids followed by a ligation-free (LF) 2-step Polymerase Chain Reaction (PCR) procedure for library preparation. A pan-chimeric universal primer (JS15N14) containing 15 nucleotides with a random tetradecamer (14N) attached to the 3'-end was designed. The complimentary primer (JS15) was used for nucleic acid enrichment in a first round PCR. A second PCR was designed to create Illumina sequencer-compatible sequencing-ready libraries for NGS. The new LF-SISPA protocol was tested using six RNA and DNA viral genomes (10.8-229.4 kilobases, kb) from an ATCC virome nucleic acid mix (ATCC® MSA-1008™) followed by analysis using One Codex, an online identification tool. In addition, a human stool sample known to be positive for norovirus GII was sequenced, and de novo assembly was performed using the Genome Detective Virus Tool allowing for near complete genome identification in less than 24 h. The LF-SISPA method does not require prior knowledge of target sequences and does not require an expensive enzymatic library preparation kit, thereby providing a simple, fast, low-cost alternative for the identification of unknown viral pathogens.
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Affiliation(s)
- Narayanan Jothikumar
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
| | - Theresa Cromeans
- CDC Foundation, USA Contracted to Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | | | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Jennifer Murphy
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA.
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Liu D, Zhou H, Xu T, Yang Q, Mo X, Shi D, Ai J, Zhang J, Tao Y, Wen D, Tong Y, Ren L, Zhang W, Xie S, Chen W, Xing W, Zhao J, Wu Y, Meng X, Ouyang C, Jiang Z, Liang Z, Tan H, Fang Y, Qin N, Guan Y, Gai W, Xu S, Wu W, Zhang W, Zhang C, Wang Y. Multicenter assessment of shotgun metagenomics for pathogen detection. EBioMedicine 2021; 74:103649. [PMID: 34814051 PMCID: PMC8608867 DOI: 10.1016/j.ebiom.2021.103649] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Shotgun metagenomics has been used clinically for diagnosing infectious diseases. However, most technical assessments have been limited to individual sets of reference standards, experimental workflows, and laboratories. METHODS A reference panel and performance metrics were designed and used to examine the performance of shotgun metagenomics at 17 laboratories in a coordinated collaborative study. We comprehensively assessed the reliability, key performance determinants, reproducibility, and quantitative potential. FINDINGS Assay performance varied significantly across sites and microbial classes, with a read depth of 20 millions as a generally cost-efficient assay setting. Results of mapped reads by shotgun metagenomics could indicate relative and intra-site (but not absolute or inter-site) microbial abundance. INTERPRETATION Assay performance was significantly impacted by the microbial type, the host context, and read depth, which emphasizes the importance of these factors when designing reference reagents and benchmarking studies. Across sites, workflows and platforms, false positive reporting and considerable site/library effects were common challenges to the assay's accuracy and quantifiability. Our study also suggested that laboratory-developed shotgun metagenomics tests for pathogen detection should aim to detect microbes at 500 CFU/mL (or copies/mL) in a clinically relevant host context (10^5 human cells/mL) within a 24h turn-around time, and with an efficient read depth of 20M. FUNDING This work was supported by National Science and Technology Major Project of China (2018ZX10102001).
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Affiliation(s)
- Donglai Liu
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Haiwei Zhou
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Teng Xu
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province and College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xi Mo
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Dawei Shi
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Jingwen Ai
- Department of Infectious Diseases, Huashan Hospital affiliated to Fudan University, Shanghai 200040, China
| | - Jingjia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yue Tao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donghua Wen
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, PR China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology. Beijing 100029
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China
| | - Wen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing 102206, China
| | - Shumei Xie
- Vision Medicals Center for Infectious Diseases, Guangzhou, Guangdong 510000, China
| | - Weijun Chen
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen 518083, China
| | - Wanli Xing
- School of Medicine Tsinghua University, Beijing, China; CapitalBio Technology Co., Ltd., Yizhuang Biomedical Park Beijing, China
| | - Jinyin Zhao
- Dalian GenTalker Clinical Laboratory, Dalian 116635, China
| | - Yilan Wu
- Guangzhou Sagene Biotech Co., Ltd., Guangzhou, China
| | - Xianfa Meng
- Guangzhou Kingmed Diagnostics, Guangzhou, Guangdong 510330, China
| | - Chuan Ouyang
- Hangzhou MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Zhi Jiang
- Genskey Medical Technology, Co., Ltd., Beijing 102206, China
| | - Zhikun Liang
- Guangzhou Darui Biotechnology, Co., Ltd., Guangzhou 510663, China
| | - Haiqin Tan
- Hangzhou IngeniGen XunMinKang Biotechnology Co., Ltd., Hangzhou 311121, China
| | - Yuan Fang
- Dinfectome Inc, Shanghai 201321, China
| | - Nan Qin
- Realbio Genomics Institute, Shanghai 201114, China
| | | | - Wei Gai
- WillingMed Technology Beijing Co., Ltd., Beijing, China
| | - Sihong Xu
- National Institutes for Food and Drug Control, Beijing 100050, China.
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, PR China.
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital affiliated to Fudan University, Shanghai 200040, China.
| | - Chuntao Zhang
- National Institutes for Food and Drug Control, Beijing 100050, China.
| | - Youchun Wang
- National Institutes for Food and Drug Control, Beijing 100050, China.
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7
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Mthethwa NP, Amoah ID, Reddy P, Bux F, Kumari S. A review on application of next-generation sequencing methods for profiling of protozoan parasites in water: Current methodologies, challenges, and perspectives. J Microbiol Methods 2021; 187:106269. [PMID: 34129906 DOI: 10.1016/j.mimet.2021.106269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 01/23/2023]
Abstract
The advancement in metagenomic techniques has provided novel tools for profiling human parasites in environmental matrices, such as water and wastewater. However, application of metagenomic techniques for the profiling of protozoan parasites in environmental matrices is not commonly reported in the literature. The key factors leading to the less common use of metagenomics are the complexity and large eukaryotic genome, the prevalence of small parasite populations in environmental samples compared to bacteria, difficulties in extracting DNA from (oo)cysts, and limited reference databases for parasites. This calls for further research to develop optimized methods specifically looking at protozoan parasites in the environment. This study reviews the current workflow, methods and provide recommendations for the standardization of techniques. The article identifies and summarizes the key methods, advantages, and limitations associated with metagenomic analysis, like sample pre-processing, DNA extraction, sequencing approaches, and analysis methods. The study enhances the understanding and application of standardized protocols for profiling of protozoan parasite community from highly complexe samples and further creates a resourceful comparison among datasets without any biases.
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Affiliation(s)
- N P Mthethwa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa; Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - I D Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - P Reddy
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - F Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - S Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
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8
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Liu S, Huckaby AC, Brown AC, Moore CC, Burbulis I, McConnell MJ, Güler JL. Single-cell sequencing of the small and AT-skewed genome of malaria parasites. Genome Med 2021; 13:75. [PMID: 33947449 PMCID: PMC8094492 DOI: 10.1186/s13073-021-00889-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/17/2021] [Indexed: 12/23/2022] Open
Abstract
Single-cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. We present a single-cell sequencing pipeline for an intracellular parasite, Plasmodium falciparum, with a small genome of extreme base content. Through optimization of a quasi-linear amplification method, we target the parasite genome over contaminants and generate coverage levels allowing detection of minor genetic variants. This work, as well as efforts that build on these findings, will enable detection of parasite heterogeneity contributing to P. falciparum adaptation. Furthermore, this study provides a framework for optimizing single-cell amplification and variant analysis in challenging genomes.
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Affiliation(s)
- Shiwei Liu
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Adam C Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Audrey C Brown
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Ian Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
- Current address: Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Jennifer L Güler
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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9
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Teyssier NB, Chen A, Duarte EM, Sit R, Greenhouse B, Tessema SK. Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples. Malar J 2021; 20:116. [PMID: 33637093 PMCID: PMC7912882 DOI: 10.1186/s12936-021-03630-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 02/06/2021] [Indexed: 12/22/2022] Open
Abstract
Background Whole-genome sequencing (WGS) is becoming increasingly useful to study the biology, epidemiology, and ecology of malaria parasites. Despite ease of sampling, DNA extracted from dried blood spots (DBS) has a high ratio of human DNA compared to parasite DNA, which poses a challenge for downstream genetic analyses. The effects of multiple methods for DNA extraction, digestion of methylated DNA, and amplification were evaluated on the quality and fidelity of WGS data recovered from DBS. Methods Low parasite density mock DBS samples were created, extracted either with Tween-Chelex or QIAamp, treated with or without McrBC, and amplified with one of three different amplification techniques (two sWGA primer sets and one rWGA). Extraction conditions were evaluated on performance of sequencing depth, percentiles of coverage, and expected SNP concordance. Results At 100 parasites/μL, Chelex-Tween-McrBC samples had higher coverage (5 × depth = 93% genome) than QIAamp extracted samples (5 × depth = 76% genome). The two evaluated sWGA primer sets showed minor differences in overall genome coverage and SNP concordance, with a newly proposed combination of 20 primers showing a modest improvement in coverage over those previously published. Conclusions Overall, Tween-Chelex extracted samples that were treated with McrBC digestion and are amplified using 6A10AD sWGA conditions had minimal dropout rate, higher percentages of coverage at higher depth, and more accurate SNP concordance than QiaAMP extracted samples. These findings extend the results of previously reported methods, making whole genome sequencing accessible to a larger number of low density samples that are commonly encountered in cross-sectional surveys.
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Affiliation(s)
- Noam B Teyssier
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA
| | - Anna Chen
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA
| | - Elias M Duarte
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA
| | - Rene Sit
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Bryan Greenhouse
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Sofonias K Tessema
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA.
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10
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Schwabl P, Maiguashca Sánchez J, Costales JA, Ocaña-Mayorga S, Segovia M, Carrasco HJ, Hernández C, Ramírez JD, Lewis MD, Grijalva MJ, Llewellyn MS. Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity. PLoS Genet 2020; 16:e1009170. [PMID: 33326438 PMCID: PMC7743988 DOI: 10.1371/journal.pgen.1009170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/02/2020] [Indexed: 12/30/2022] Open
Abstract
Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective 'genome-wide locus sequence typing' (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research.
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Affiliation(s)
- Philipp Schwabl
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Jalil Maiguashca Sánchez
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jaime A. Costales
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Maikell Segovia
- Laboratorio de Biología Molecular de Protozoarios, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Hernán J. Carrasco
- Laboratorio de Biología Molecular de Protozoarios, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Carolina Hernández
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Michael D. Lewis
- London School of Hygiene & Tropical Medicine, Keppel Street, London, United Kingdom
| | - Mario J. Grijalva
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Infectious and Tropical Disease Institute, Biomedical Sciences Department, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States of America
| | - Martin S. Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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11
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López-Labrador FX, Brown JR, Fischer N, Harvala H, Van Boheemen S, Cinek O, Sayiner A, Madsen TV, Auvinen E, Kufner V, Huber M, Rodriguez C, Jonges M, Hönemann M, Susi P, Sousa H, Klapper PE, Pérez-Cataluňa A, Hernandez M, Molenkamp R, der Hoek LV, Schuurman R, Couto N, Leuzinger K, Simmonds P, Beer M, Höper D, Kamminga S, Feltkamp MCW, Rodríguez-Díaz J, Keyaerts E, Nielsen XC, Puchhammer-Stöckl E, Kroes ACM, Buesa J, Breuer J, Claas ECJ, de Vries JJC. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. J Clin Virol 2020; 134:104691. [PMID: 33278791 DOI: 10.1016/j.jcv.2020.104691] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.
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Affiliation(s)
- F Xavier López-Labrador
- Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain.
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Heli Harvala
- Microbiology Services, NHS Blood and Transplant, London, United Kingdom.
| | - Sander Van Boheemen
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Ondrej Cinek
- Department of Paediatrics and Medical Microbiology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic.
| | - Arzu Sayiner
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, Division of Medical Virology. Izmir, Turkey.
| | - Tina Vasehus Madsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | - Eeva Auvinen
- Department of Virology, Helsinki University Hospital Laboratory and University of Helsinki, Helsinki, Finland.
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Christophe Rodriguez
- Microbiology Department and NGS Platform, University Hospital Henri Mondor (APHP), Créteil, France.
| | - Marcel Jonges
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Mario Hönemann
- Institute of Virology, Leipzig University, Leipzig, Germany.
| | - Petri Susi
- Institute of Biomedicine, University of Turku, Finland.
| | - Hugo Sousa
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal; Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal; Molecular Oncology and Viral Pathology Group, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.
| | - Paul E Klapper
- Faculty of Biology, Medicine, and Health, Division of Infection, Immunity, and Respiratory Medicine, University of Manchester, Manchester, United Kingdom.
| | - Alba Pérez-Cataluňa
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Paterna, Valencia, Spain.
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnologico Agrario de Castilla y Leon, Valladolid, Spain.
| | - Richard Molenkamp
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Lia van der Hoek
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Rob Schuurman
- Department of Virology, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands; Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
| | - Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Sergio Kamminga
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Mariet C W Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jesús Rodríguez-Díaz
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Els Keyaerts
- Laboratorium Klinische en Epidemiologische Virologie (Rega Instituut), Leuven, Belgium.
| | - Xiaohui Chen Nielsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | | | - Aloys C M Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Javier Buesa
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Judy Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
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12
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Brown AC, Guler JL. From Circulation to Cultivation: Plasmodium In Vivo versus In Vitro. Trends Parasitol 2020; 36:914-926. [DOI: 10.1016/j.pt.2020.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022]
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13
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Yang J, Yuan B, Wu Y, Li M, Li J, Xu D, Gao ZH, Ma G, Zhou Y, Zuo Y, Wang J, Guo Y. The wide distribution and horizontal transfers of beta satellite DNA in eukaryotes. Genomics 2020; 112:5295-5304. [PMID: 33065245 DOI: 10.1016/j.ygeno.2020.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 09/08/2020] [Accepted: 10/10/2020] [Indexed: 01/12/2023]
Abstract
Beta satellite DNA (satDNA), also known as Sau3A sequences, are repetitive DNA sequences reported in human and primate genomes. It is previously thought that beta satDNAs originated in old world monkeys and bursted in great apes. In this study, we searched 7821 genome assemblies of 3767 eukaryotic species and found that beta satDNAs are widely distributed across eukaryotes. The four major branches of eukaryotes, animals, fungi, plants and Harosa/SAR, all have multiple clades containing beta satDNAs. These results were also confirmed by searching whole genome sequencing data (SRA) and PCR assay. Beta satDNA sequences were found in all the primate clades, as well as in Dermoptera and Scandentia, indicating that the beta satDNAs in primates might originate in the common ancestor of Primatomorpha or Euarchonta. In contrast, the widely patchy distribution of beta satDNAs across eukaryotes presents a typical scenario of multiple horizontal transfers.
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Affiliation(s)
- Jiawen Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, China.
| | - Bin Yuan
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yu Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, China.
| | - Meiyu Li
- Key Laboratory of Tropical Disease Control, Sun Yat-Sen University; Ministry of Education Experimental Teaching Center, Zhongshan School of Medicine, Sun Yat-sen University, China.
| | - Jian Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Donglin Xu
- Guangzhou Academy of Agricultural Sciences, Guangzhou, China
| | - Zeng-Hong Gao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Guangwei Ma
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yiting Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Yachao Zuo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, China.
| | - Jin Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Yabin Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
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14
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The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples. Microorganisms 2020; 8:microorganisms8081252. [PMID: 32824654 PMCID: PMC7463849 DOI: 10.3390/microorganisms8081252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 11/21/2022] Open
Abstract
Cytosine C5 methylation is an important epigenetic control mechanism in a wide array of eukaryotic organisms and generally carried out by proteins of the C-5 DNA methyltransferase family (DNMTs). In several protozoans, the status of this mechanism remains elusive, such as in Leishmania, the causative agent of the disease leishmaniasis in humans and a wide array of vertebrate animals. In this work, we showed that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 subfamily, whose function is still unclear, and verified its expression at the RNA level. We created viable overexpressor and knock-out lines of this enzyme and characterized their genome-wide methylation patterns using whole-genome bisulfite sequencing, together with promastigote and amastigote control lines. Interestingly, despite the DNMT6 presence, we found that methylation levels were equal to or lower than 0.0003% at CpG sites, 0.0005% at CHG sites, and 0.0126% at CHH sites at the genomic scale. As none of the methylated sites were retained after manual verification, we conclude that there is no evidence for DNA methylation in this species. We demonstrated that this difference in DNA methylation between the parasite (no detectable DNA methylation) and the vertebrate host (DNA methylation) allowed enrichment of parasite vs. host DNA using methyl-CpG-binding domain columns, readily available in commercial kits. As such, we depleted methylated DNA from mixes of Leishmania promastigote and amastigote DNA with human DNA, resulting in average Leishmania:human enrichments from 62× up to 263×. These results open a promising avenue for unmethylated DNA enrichment as a pre-enrichment step before sequencing Leishmania clinical samples.
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15
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Manso CF, Bibby DF, Mohamed H, Brown DWG, Zuckerman M, Mbisa JL. Enhanced Detection of DNA Viruses in the Cerebrospinal Fluid of Encephalitis Patients Using Metagenomic Next-Generation Sequencing. Front Microbiol 2020; 11:1879. [PMID: 32903437 PMCID: PMC7435129 DOI: 10.3389/fmicb.2020.01879] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
The long and expanding list of viral pathogens associated with causing encephalitis confounds current diagnostic procedures, and in up to 50% of cases, the etiology remains undetermined. Sequence-agnostic metagenomic next-generation sequencing (mNGS) obviates the need to specify targets in advance and thus has great potential in encephalitis diagnostics. However, the low relative abundance of viral nucleic acids in clinical specimens poses a significant challenge. Our protocol employs two novel techniques to selectively remove human material at two stages, significantly increasing the representation of viral material. Our bioinformatic workflow using open source protein- and nucleotide sequence-matching software balances sensitivity and specificity in diagnosing and characterizing any DNA viruses present. A panel of 12 cerebrospinal fluid (CSFs) from encephalitis cases was retrospectively interrogated by mNGS, with concordant results in seven of nine samples with a definitive DNA virus diagnosis, and a different herpesvirus was identified in the other two. In two samples with an inconclusive diagnosis, DNA viruses were detected and in a virus-negative sample, no viruses were detected. This assay has the potential to detect DNA virus infections in cases of encephalitis of unknown etiology and to improve the current screening tests by identifying new and emerging agents.
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Affiliation(s)
- Carmen F Manso
- Virus Reference Department, Public Health England, London, United Kingdom
| | - David F Bibby
- Virus Reference Department, Public Health England, London, United Kingdom
| | - Hodan Mohamed
- Virus Reference Department, Public Health England, London, United Kingdom
| | - David W G Brown
- Virus Reference Department, Public Health England, London, United Kingdom.,Laboratorio de Virus Respiratorios e do Sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Mark Zuckerman
- South London Specialist Virology Centre, King's College Hospital NHS Foundation Trust, London, United Kingdom
| | - Jean L Mbisa
- Virus Reference Department, Public Health England, London, United Kingdom
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16
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Abstract
In this unit, we describe a set of protocols and recommendations for Illumina library preparation. We review best practices in template quantitation methods; template fragmentation methodologies; solid-phase reverse-immobilization cleanup, including buffer exchange and size selection; end repair, A-tailing, and adapter ligation; indexing strategies; considerations regarding whether to use polymerase chain reaction; final library quantification methodologies; and normalization and pooling strategies. These workflows are applicable to both high-throughput and low-throughput Illumina library preparation and should help reduce bias, increase cost effectiveness, and produce high library yields. This is an extensive update of the previous version of this unit. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Iraad F Bronner
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
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17
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Shah Z, Adams M, Moser KA, Shrestha B, Stucke EM, Laufer MK, Serre D, Silva JC, Takala-Harrison S. Optimization of parasite DNA enrichment approaches to generate whole genome sequencing data for Plasmodium falciparum from low parasitaemia samples. Malar J 2020; 19:135. [PMID: 32228559 PMCID: PMC7106660 DOI: 10.1186/s12936-020-03195-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 03/20/2020] [Indexed: 12/30/2022] Open
Abstract
Background Owing to the large amount of host DNA in clinical samples, generation of high-quality Plasmodium falciparum whole genome sequencing (WGS) data requires enrichment for parasite DNA. Enrichment is often achieved by leukocyte depletion of infected blood prior to storage. However, leukocyte depletion is difficult in low-resource settings and limits analysis to prospectively-collected samples. As a result, approaches such as selective whole genome amplification (sWGA) are being used to enrich for parasite DNA. However, sWGA has had limited success in generating reliable sequencing data from low parasitaemia samples. In this study, enzymatic digestion with MspJI prior to sWGA and whole genome sequencing was evaluated to determine whether this approach improved genome coverage compared to sWGA alone. The potential of sWGA to cause amplification bias in polyclonal infections was also examined. Methods DNA extracted from laboratory-created dried blood spots was treated with a modification-dependent restriction endonuclease, MspJI, and filtered via vacuum filtration. Samples were then selectively amplified using a previously reported sWGA protocol and subjected to WGS. Genome coverage statistics were compared between the optimized sWGA approach and the previously reported sWGA approach performed in parallel. Differential amplification by sWGA was assessed by comparing WGS data generated from lab-created mixtures of parasite isolates, from the same geographical region, generated with or without sWGA. Results MspJI digestion did not enrich for parasite DNA. Samples that underwent vacuum filtration (without MspJI digestion) prior to sWGA had the highest parasite DNA concentration and displayed greater genome coverage compared to MspJI + sWGA and sWGA alone, particularly for low parasitaemia samples. The optimized sWGA (filtration + sWGA) approach was successfully used to generate WGS data from 218 non-leukocyte depleted field samples from Malawi. Sequences from lab-created mixtures of parasites did not show evidence of differential amplification of parasite strains compared to directly sequenced samples. Conclusion This optimized sWGA approach is a reliable method to obtain WGS data from non-leukocyte depleted, low parasitaemia samples. The absence of amplification bias in data generated from mixtures of isolates from the same geographic region suggests that this approach can be appropriately used for molecular epidemiological studies.
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Affiliation(s)
- Zalak Shah
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew Adams
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kara A Moser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Biraj Shrestha
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emily M Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Miriam K Laufer
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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18
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Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
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19
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Domagalska MA, Dujardin JC. Next-Generation Molecular Surveillance of TriTryp Diseases. Trends Parasitol 2020; 36:356-367. [PMID: 32191850 DOI: 10.1016/j.pt.2020.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 12/20/2022]
Abstract
Elimination programs targeting TriTryp diseases (Leishmaniasis, Chagas' disease, human African trypanosomiasis) significantly reduced the number of cases. Continued surveillance is crucial to sustain this progress, but parasite molecular surveillance by genotyping is currently lacking. We explain here which epidemiological questions of public health and clinical relevance could be answered by means of molecular surveillance. Whole-genome sequencing (WGS) for molecular surveillance will be an important added value, where we advocate that preference should be given to direct sequencing of the parasite's genome in host tissues instead of analysis of cultivated isolates. The main challenges here, and recent technological advances, are discussed. We conclude with a series of recommendations for implementing whole-genome sequencing for molecular surveillance.
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Affiliation(s)
- Malgorzata Anna Domagalska
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerp, Belgium.
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerp, Belgium
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20
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Ji XC, Zhou LF, Li CY, Shi YJ, Wu ML, Zhang Y, Fei XF, Zhao G. Reduction of Human DNA Contamination in Clinical Cerebrospinal Fluid Specimens Improves the Sensitivity of Metagenomic Next-Generation Sequencing. J Mol Neurosci 2020; 70:659-666. [PMID: 32002752 DOI: 10.1007/s12031-019-01472-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 12/26/2019] [Indexed: 12/25/2022]
Abstract
Metagenomics next-generation sequencing (mNGS) is increasingly available for the detection of obscure infectious diseases of the central nervous system. However, human DNA contamination from elevated white cells, one of the characteristic cerebrospinal fluid (CSF) features in meningitis patients, greatly reduces the sensitivity of mNGS in the pathogen detection. Currently, effective approaches to selectively reduce host DNA contamination from clinical CSF samples are still lacking. In this study, a total of 20 meningitis patients were enrolled, including 10 definitively diagnosed tuberculous meningitis (TBM) and 10 definite cryptococcal meningitis (CM) cases. To evaluate the effect of reduced human DNA in the sensitivity of mNGS detection, three specimen-processing protocols were performed: (i) To remove human DNA, saponin, a nonionic surfactant, was used to selectively lyse white cells in CSF followed by DNase treatment prior to the extraction of DNA; (ii) to reduce host DNA, CSF was centrifuged to remove human cells, and the supernatant was collected for DNA extraction; and (iii) DNA extraction from the unprocessed specimens was set as the control. We found that saponin processing significantly elevated the NGS unique reads for Cryptococcus (P < 0.01) compared with the control but had no effects for Mycobacterium tuberculosis (P > 0.05). However, detection of centrifuged supernatants improved the NGS unique reads for both TBM and CM compared with controls (P < 0.01). Our results demonstrate that the use of mNGS of centrifuged supernatants from clinical CSF samples in patients with TBM and CM is a simple and effective method to improve the sensitivity of pathogen detection.
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MESH Headings
- Adult
- Aged
- Cerebrospinal Fluid/microbiology
- Cryptococcus/genetics
- Cryptococcus/pathogenicity
- Female
- Genome, Bacterial
- Genome, Human
- High-Throughput Nucleotide Sequencing/methods
- High-Throughput Nucleotide Sequencing/standards
- Humans
- Male
- Meningitis, Cryptococcal/cerebrospinal fluid
- Meningitis, Cryptococcal/diagnosis
- Meningitis, Cryptococcal/microbiology
- Metagenomics/methods
- Metagenomics/standards
- Middle Aged
- Molecular Diagnostic Techniques/methods
- Molecular Diagnostic Techniques/standards
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/pathogenicity
- Sensitivity and Specificity
- Sequence Analysis, DNA/methods
- Sequence Analysis, DNA/standards
- Tuberculosis, Meningeal/cerebrospinal fluid
- Tuberculosis, Meningeal/diagnosis
- Tuberculosis, Meningeal/microbiology
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Affiliation(s)
- Xin-Chao Ji
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Lin-Fu Zhou
- Department of Neurology, The 987 Hospital of PLA, Baoji, China
| | - Chao-Yang Li
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Ya-Jun Shi
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Meng-Li Wu
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Yun Zhang
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Xiao-Fei Fei
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Gang Zhao
- Department of Neurology, Xijing Hospital, Air Force Military Medical University, Xi'an, China.
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21
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Kim GS, Kim TS, Son JS, Lai VD, Park JE, Wang SJ, Jheong WH, Mo IP. The difference of detection rate of avian influenza virus in the wild bird surveillance using various methods. J Vet Sci 2020; 20:e56. [PMID: 31565899 PMCID: PMC6769331 DOI: 10.4142/jvs.2019.20.e56] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/17/2019] [Accepted: 08/28/2019] [Indexed: 11/20/2022] Open
Abstract
Korea is located within the East Asian-Australian flyway of wild migratory birds during the fall and winter seasons. Consequently, the likelihood of introduction of numerous subtypes and pathotypes of the Avian influenza (AI) virus to Korea has been thought to be very high. In the current study, we surveyed wild bird feces for the presence of AI virus that had been introduced to Korea between September 2017 and February 2018. To identify and characterize the AI virus, we employed commonly used methods, namely, virus isolation (VI) via egg inoculation, real-time reverse transcription-polymerase chain reaction (rRT-PCR), conventional RT-PCR (cRT-PCR) and a newly developed next generation sequencing (NGS) approach. In this study, 124 out of 11,145 fresh samples of wild migratory birds tested were rRT-PCR positive; only 52.0% of VI positive samples were determined as positive by rRT-PCR from fecal supernatant. Fifty AI virus specimens were isolated from fresh fecal samples and typed. The cRT-PCR subtyping results mostly coincided with the NGS results, although NGS detected the presence of 11 HA genes and four NA genes that were not detected by cRT-PCR. NGS analysis confirmed that 12% of the identified viruses were mixed-subtypes which were not detected by cRT-PCR. Prevention of the occurrence of AI virus requires a workflow for rapid and accurate virus detection and verification. However, conventional methods of detection have some limitations. Therefore, different methods should be combined for optimal surveillance, and further studies are needed in aspect of the introduction and application of new methods such as NGS.
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Affiliation(s)
- Gang San Kim
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Tae Sik Kim
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Joo Sung Son
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Van Dam Lai
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Jung Eun Park
- Environmental Health Research Division, National Institute of Environmental Research, Incheon 22689, Korea
| | - Seung Jun Wang
- Environmental Health Research Division, National Institute of Environmental Research, Incheon 22689, Korea
| | - Weon Hwa Jheong
- Environmental Health Research Division, National Institute of Environmental Research, Incheon 22689, Korea
| | - In Pil Mo
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea.
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22
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Ung L, Bispo PJM, Doan T, Van Gelder RN, Gilmore MS, Lietman T, Margolis TP, Zegans ME, Lee CS, Chodosh J. Clinical metagenomics for infectious corneal ulcers: Rags to riches? Ocul Surf 2020; 18:1-12. [PMID: 31669750 PMCID: PMC9837861 DOI: 10.1016/j.jtos.2019.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 01/17/2023]
Abstract
The emergence of clinical metagenomics as an unbiased, hypothesis-free approach to diagnostic testing is set to fundamentally alter the way infectious diseases are detected. Long envisioned as the solution to the limitations of culture-based conventional microbiology, next generation sequencing methods will soon mature, and our attention will inevitably turn to how they can be applied to areas of medicine which need it most urgently. In ophthalmology, the demand for this technology is particularly pressing for the care of infectious corneal ulcers, where current diagnostic tests may fail to identify a causative organism in over half of cases. However, the optimism found in the budding discourse surrounding clinical metagenomics belies the reality that clinicians and scientists will soon be inundated by oppressive volumes of sequencing data, much of which will be foreign and unfamiliar. Therefore, our success in translating clinical metagenomics is likely to hinge on how we make sense of these data, and understanding its implications for the interpretation and implementation of sequencing into routine clinical care. In this consortium-led review, we provide an outline of these data-related issues and how they may be used to inform technical workflows, with the hope that we may edge closer to realizing the potential of clinical metagenomics for this important unmet need.
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Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Paulo J M Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thuy Doan
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | | | - Michael S Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Thomas Lietman
- Francis I. Proctor Foundation, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Todd P Margolis
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in Saint Louis, Saint Louis, USA
| | - Michael E Zegans
- Department of Surgery (Ophthalmology), and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, USA
| | - Cecilia S Lee
- Department of Ophthalmology, University of Washington, Seattle, WA, USA.
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA; Infectious Disease Institute and Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
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23
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Domagalska MA, Imamura H, Sanders M, Van den Broeck F, Bhattarai NR, Vanaerschot M, Maes I, D’Haenens E, Rai K, Rijal S, Berriman M, Cotton JA, Dujardin JC. Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent. PLoS Negl Trop Dis 2019; 13:e0007900. [PMID: 31830038 PMCID: PMC6932831 DOI: 10.1371/journal.pntd.0007900] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/26/2019] [Accepted: 11/01/2019] [Indexed: 12/02/2022] Open
Abstract
Whole genome sequencing (WGS) is increasingly used for molecular diagnosis and epidemiology of infectious diseases. Current Leishmania genomic studies rely on DNA extracted from cultured parasites, which might introduce sampling and biological biases into the subsequent analyses. Up to now, direct analysis of Leishmania genome in clinical samples is hampered by high levels of human DNA and large variation in parasite load in clinical samples. Here, we present a method, based on target enrichment of Leishmania donovani DNA with Agilent SureSelect technology, that allows the analysis of Leishmania genomes directly in clinical samples. We validated our protocol with a set of artificially mixed samples, followed by the analysis of 63 clinical samples (bone marrow or spleen aspirates) from visceral leishmaniasis patients in Nepal. We were able to identify genotypes using a set of diagnostic SNPs in almost all of these samples (97%) and access comprehensive genome-wide information in most (83%). This allowed us to perform phylogenomic analysis, assess chromosome copy number and identify large copy number variants (CNVs). Pairwise comparisons between the parasite genomes in clinical samples and derived in vitro cultured promastigotes showed a lower aneuploidy in amastigotes as well as genomic differences, suggesting polyclonal infections in patients. Altogether our results underline the need for sequencing parasite genomes directly in the host samples Visceral leishmaniasis (VL) is caused by parasitic protozoa of the Leishmania donovani complex and is lethal in the absence of treatment. Whole Genome Sequencing (WGS) of L. donovani clinical isolates revealed hitherto cryptic population structure in the Indian Sub-Continent and provided insights into the epidemiology and potential mechanisms of drug resistance. However, several biases are likely introduced during the culture step. We report here the development of a method that allows determination of parasite genomes directly in clinical samples, and validate it on bone marrow and splenic aspirates of VL patients in Nepal. Our study sheds a new light on the biology of Leishmania in the human host: we found that intracellular parasites of the patients had very low levels of aneuploidy, in sharp contrast to the situation in cultivated isolates. Moreover, the observed differences in genomes between intracellular amastigotes of the patient and the derived cultured parasites suggests polyclonality of infections, with different clones dominating in clinical samples and in culture, likely due to fitness differences. We believe this method is most suitable for clinical studies and for molecular tracking in the context of elimination programs.
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Affiliation(s)
- Malgorzata A. Domagalska
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
- * E-mail: (MAD); (JAC); (JC-D)
| | - Hideo Imamura
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | | | | | | | - Manu Vanaerschot
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Ilse Maes
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Erika D’Haenens
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Keshav Rai
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | - Suman Rijal
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | | | - James A. Cotton
- Wellcome Sanger Institute, Hinxton, United Kingdom
- * E-mail: (MAD); (JAC); (JC-D)
| | - Jean-Claude Dujardin
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
- University of Antwerp, Department of Biomedical Sciences, Antwerp, Belgium
- * E-mail: (MAD); (JAC); (JC-D)
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24
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Pereira-Marques J, Hout A, Ferreira RM, Weber M, Pinto-Ribeiro I, van Doorn LJ, Knetsch CW, Figueiredo C. Impact of Host DNA and Sequencing Depth on the Taxonomic Resolution of Whole Metagenome Sequencing for Microbiome Analysis. Front Microbiol 2019; 10:1277. [PMID: 31244801 PMCID: PMC6581681 DOI: 10.3389/fmicb.2019.01277] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/22/2019] [Indexed: 01/25/2023] Open
Abstract
The amount of host DNA poses a major challenge to metagenome analysis. However, there is no guidance on the levels of host DNA, nor on the depth of sequencing needed to acquire meaningful information from whole metagenome sequencing (WMS). Here, we evaluated the impact of a wide range of amounts of host DNA and sequencing depths on microbiome taxonomic profiling using WMS. Synthetic samples with increasing levels of host DNA were created by spiking DNA of a mock bacterial community, with DNA from a mouse-derived cell line. Taxonomic analysis revealed that increasing proportions of host DNA led to decreased sensitivity in detecting very low and low abundant species. Reduction of sequencing depth had major impact on the sensitivity of WMS for profiling samples with 90% host DNA, increasing the number of undetected species. Finally, analysis of simulated datasets with fixed depth of 10 million reads confirmed that microbiome profiling becomes more inaccurate as the level of host DNA increases in a sample. In conclusion, samples with high amounts of host DNA coupled with reduced sequencing depths, decrease WMS coverage for characterization of the microbiome. This study highlights the importance of carefully considering these aspects in the design of WMS experiments to maximize microbiome analyses.
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Affiliation(s)
- Joana Pereira-Marques
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto, Porto, Portugal
| | - Anne Hout
- DDL Diagnostic Laboratory, Rijswijk, Netherlands
| | - Rui M Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | | | - Ines Pinto-Ribeiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Departmento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | | | | | - Ceu Figueiredo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Departmento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
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25
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Videvall E. Genomic Advances in Avian Malaria Research. Trends Parasitol 2019; 35:254-266. [PMID: 30642725 DOI: 10.1016/j.pt.2018.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/24/2018] [Accepted: 12/25/2018] [Indexed: 12/14/2022]
Abstract
Haemosporidian parasites causing malaria-like diseases in birds are globally distributed and have been associated with reduced host fitness and mortality in susceptible bird species. This group of parasites has not only enabled a greater understanding of host specificity, virulence, and parasite dispersal, but has also been crucial in restructuring the evolutionary history of apicomplexans. Despite their importance, genomic resources of avian haemosporidians have proved difficult to obtain, and they have, as a result, been lagging behind the congeneric Plasmodium species infecting mammals. In this review, I discuss recent genomic advances in the field of avian malaria research, and outline outstanding questions that will become possible to investigate with the continued successful efforts to generate avian haemosporidian genomic data.
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Affiliation(s)
- Elin Videvall
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA.
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26
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Toscani Field J, Weinberg J, Bensch S, Matta NE, Valkiūnas G, Sehgal RNM. Delineation of the Genera Haemoproteus and Plasmodium Using RNA-Seq and Multi-gene Phylogenetics. J Mol Evol 2018; 86:646-654. [PMID: 30426144 DOI: 10.1007/s00239-018-9875-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 11/01/2018] [Indexed: 01/24/2023]
Abstract
Members of the order Haemosporida are protist parasites that infect mammals, reptiles and birds. This group includes the causal agents of malaria, Plasmodium parasites, the genera Leucocytozoon and Fallisia, as well as the species rich genus Haemoproteus with its two subgenera Haemoproteus and Parahaemoproteus. Some species of Haemoproteus cause severe disease in avian hosts, and these parasites display high levels of diversity worldwide. This diversity emphasizes the need for accurate evolutionary information. Most molecular studies of wildlife haemosporidians use a bar coding approach by sequencing a fragment of the mitochondrial cytochrome b gene. This method is efficient at differentiating parasite lineages but insufficient for accurate phylogenetic inferences in highly diverse taxa such as haemosporidians. Recent studies have utilized multiple mitochondrial genes (cyt b, cox1 and cox3), sometimes combined with a few apicoplast and nuclear genes. These studies have been highly successful with one notable exception: the evolutionary relationships of the genus Haemoproteus remain unresolved. Here we describe the transcriptome of Haemoproteus columbae and investigate its phylogenetic position recovered from a multi-gene dataset (600 genes). This genomic approach restricts the taxon sampling to 18 species of apicomplexan parasites. We employed Bayesian inference and maximum likelihood methods of phylogenetic analyses and found H. columbae and a representative from the subgenus Parahaemoproteus to be sister taxa. This result strengthens the hypothesis of genus Haemoproteus being monophyletic; however, resolving this question will require sequences of orthologs from, in particular, representatives of Leucocytozoon species.
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Affiliation(s)
- Jasper Toscani Field
- Department of Biology, San Francisco State University, 1700 Holloway Ave, San Francisco, CA, 94132, USA.
| | - Josh Weinberg
- Department of Biology, San Francisco State University, 1700 Holloway Ave, San Francisco, CA, 94132, USA
| | - Staffan Bensch
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Nubia E Matta
- Sede Bogotá, Facultad de Ciencias, Departamento de Biología, Grupo de Investigación Caracterización genética e inmunología, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, 111321, Colombia
| | | | - Ravinder N M Sehgal
- Department of Biology, San Francisco State University, 1700 Holloway Ave, San Francisco, CA, 94132, USA
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27
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Conrad TA, Lo CC, Koehler JW, Graham AS, Stefan CP, Hall AT, Douglas CE, Chain PS, Minogue TD. Diagnostic targETEd seQuencing adjudicaTion (DETEQT): Algorithms for Adjudicating Targeted Infectious Disease Next-Generation Sequencing Panels. J Mol Diagn 2018; 21:99-110. [PMID: 30268944 DOI: 10.1016/j.jmoldx.2018.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/23/2018] [Accepted: 08/14/2018] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing (NGS) for infectious disease diagnostics is a relatively new and underdeveloped concept. If this technology is to become a regulatory-grade clinical diagnostic, standardization in the form of locked-down assays and firmly established underlying processes is necessary. Targeted sequencing, specifically by amplification of genomic signatures, has the potential to bridge the gap between PCR- and NGS-based diagnostics; however, existing NGS assay panels lack validated analytical techniques to adjudicate high background and error-prone NGS data. Herein, we present the Diagnostic targETEd seQuencing adjudicaTion (DETEQT) software, consisting of an intuitive bioinformatics pipeline entailing a set of algorithms to translate raw sequencing data into positive, negative, and indeterminate diagnostic determinations. After basic read filtering and mapping, the software compares abundance and quality metrics against heuristic and fixed thresholds. A novel generalized quality function provides an amalgamated quality score for the match between sequence reads of an assay and panel targets, rather than considering each component factor independently. When evaluated against numerous assay samples and parameters (mock clinical, human, and nonhuman primate clinical data sets; diverse amplification strategies; downstream applications; and sequence platforms), DETEQT demonstrated improved rejection of false positives and accuracies >95%. Finally, DETEQT was implemented in the user-friendly Empowering the Development of Genomics Expertise (EDGE) bioinformatics platform, providing a complete, end-to-end solution that can be operated by nonexperts in a clinical laboratory setting.
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Affiliation(s)
- Turner A Conrad
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland
| | - Chien-Chi Lo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Jeffrey W Koehler
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland
| | - Amanda S Graham
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland
| | - Christopher P Stefan
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland
| | - Adrienne T Hall
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland
| | - Christina E Douglas
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland
| | - Patrick S Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Timothy D Minogue
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland.
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28
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Flaherty BR, Talundzic E, Barratt J, Kines KJ, Olsen C, Lane M, Sheth M, Bradbury RS. Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing. MICROBIOME 2018; 6:164. [PMID: 30223888 PMCID: PMC6142370 DOI: 10.1186/s40168-018-0540-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/29/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Targeted amplicon deep sequencing (TADS) of the 16S rRNA gene is commonly used to explore and characterize bacterial microbiomes. Meanwhile, attempts to apply TADS to the detection and characterization of entire parasitic communities have been hampered since conserved regions of many conserved parasite genes, such as the 18S rRNA gene, are also conserved in their eukaryotic hosts. As a result, targeted amplification of 18S rRNA from clinical samples using universal primers frequently results in competitive priming and preferential amplification of host DNA. Here, we describe a novel method that employs a single pair of universal primers to capture all blood-borne parasites while reducing host 18S rRNA template and enhancing the amplification of parasite 18S rRNA for TADS. This was achieved using restriction enzymes to digest the 18S rRNA gene at cut sites present only in the host sequence prior to PCR amplification. RESULTS This method was validated against 16 species of blood-borne helminths and protozoa. Enzyme digestion prior to PCR enrichment and Illumina amplicon deep sequencing led to a substantial reduction in human reads and a corresponding 5- to 10-fold increase in parasite reads relative to undigested samples. This method allowed for discrimination of all common parasitic agents found in human blood, even in cases of multi-parasite infection, and markedly reduced the limit of detection in digested versus undigested samples. CONCLUSIONS The results herein provide a novel methodology for the reduction of host DNA prior to TADS and establish the validity of a next-generation sequencing-based platform for universal parasite detection.
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Affiliation(s)
- Briana R Flaherty
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
- Oak Ridge Institute for Science and Education, 100 ORAU Way, Oak Ridge, TN, 37830, USA
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
- Oak Ridge Institute for Science and Education, 100 ORAU Way, Oak Ridge, TN, 37830, USA
| | - Kristine J Kines
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Christian Olsen
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA, 94025, USA
| | - Meredith Lane
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
- IHRC, Inc., 2 Ravinia Drive, Atlanta, GA, 30346, USA
| | - Mili Sheth
- Biotechnology Core Facility, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Richard S Bradbury
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.
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29
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Zhong D, Lo E, Wang X, Yewhalaw D, Zhou G, Atieli HE, Githeko A, Hemming-Schroeder E, Lee MC, Afrane Y, Yan G. Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa. Malar J 2018; 17:185. [PMID: 29720181 PMCID: PMC5932820 DOI: 10.1186/s12936-018-2337-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/26/2018] [Indexed: 11/18/2022] Open
Abstract
Background Parasite genetic diversity and multiplicity of infection (MOI) affect clinical outcomes, response to drug treatment and naturally-acquired or vaccine-induced immunity. Traditional methods often underestimate the frequency and diversity of multiclonal infections due to technical sensitivity and specificity. Next-generation sequencing techniques provide a novel opportunity to study complexity of parasite populations and molecular epidemiology. Methods Symptomatic and asymptomatic Plasmodium vivax samples were collected from health centres/hospitals and schools, respectively, from 2011 to 2015 in Ethiopia. Similarly, both symptomatic and asymptomatic Plasmodium falciparum samples were collected, respectively, from hospitals and schools in 2005 and 2015 in Kenya. Finger-pricked blood samples were collected and dried on filter paper. Long amplicon (> 400 bp) deep sequencing of merozoite surface protein 1 (msp1) gene was conducted to determine multiplicity and molecular epidemiology of P. vivax and P. falciparum infections. The results were compared with those based on short amplicon (117 bp) deep sequencing. Results A total of 139 P. vivax and 222 P. falciparum samples were pyro-sequenced for pvmsp1 and pfmsp1, yielding a total of 21 P. vivax and 99 P. falciparum predominant haplotypes. The average MOI for P. vivax and P. falciparum were 2.16 and 2.68, respectively, which were significantly higher than that of microsatellite markers and short amplicon (117 bp) deep sequencing. Multiclonal infections were detected in 62.2% of the samples for P. vivax and 74.8% of the samples for P. falciparum. Four out of the five subjects with recurrent P. vivax malaria were found to be a relapse 44–65 days after clearance of parasites. No difference was observed in MOI among P. vivax patients of different symptoms, ages and genders. Similar patterns were also observed in P. falciparum except for one study site in Kenyan lowland areas with significantly higher MOI. Conclusions The study used a novel method to evaluate Plasmodium MOI and molecular epidemiological patterns by long amplicon ultra-deep sequencing. The complexity of infections were similar among age groups, symptoms, genders, transmission settings (spatial heterogeneity), as well as over years (pre- vs. post-scale-up interventions). This study demonstrated that long amplicon deep sequencing is a useful tool to investigate multiplicity and molecular epidemiology of Plasmodium parasite infections. Electronic supplementary material The online version of this article (10.1186/s12936-018-2337-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daibin Zhong
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA.
| | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Xiaoming Wang
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia.,Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
| | - Guofa Zhou
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA
| | - Harrysone E Atieli
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Andrew Githeko
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Ming-Chieh Lee
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA
| | - Yaw Afrane
- Department of Medical Microbiology, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Guiyun Yan
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA.
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30
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Böhme U, Otto TD, Cotton JA, Steinbiss S, Sanders M, Oyola SO, Nicot A, Gandon S, Patra KP, Herd C, Bushell E, Modrzynska KK, Billker O, Vinetz JM, Rivero A, Newbold CI, Berriman M. Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. Genome Res 2018; 28:547-560. [PMID: 29500236 PMCID: PMC5880244 DOI: 10.1101/gr.218123.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/28/2018] [Indexed: 01/08/2023]
Abstract
Avian malaria parasites are prevalent around the world and infect a wide diversity of bird species. Here, we report the sequencing and analysis of high-quality draft genome sequences for two avian malaria species, Plasmodium relictum and Plasmodium gallinaceum We identify 50 genes that are specific to avian malaria, located in an otherwise conserved core of the genome that shares gene synteny with all other sequenced malaria genomes. Phylogenetic analysis suggests that the avian malaria species form an outgroup to the mammalian Plasmodium species, and using amino acid divergence between species, we estimate the avian- and mammalian-infective lineages diverged in the order of 10 million years ago. Consistent with their phylogenetic position, we identify orthologs of genes that had previously appeared to be restricted to the clades of parasites containing Plasmodium falciparum and Plasmodium vivax, the species with the greatest impact on human health. From these orthologs, we explore differential diversifying selection across the genus and show that the avian lineage is remarkable in the extent to which invasion-related genes are evolving. The subtelomeres of the P. relictum and P. gallinaceum genomes contain several novel gene families, including an expanded surf multigene family. We also identify an expansion of reticulocyte binding protein homologs in P. relictum, and within these proteins, we detect distinct regions that are specific to nonhuman primate, humans, rodent, and avian hosts. For the first time in the Plasmodium lineage, we find evidence of transposable elements, including several hundred fragments of LTR-retrotransposons in both species and an apparently complete LTR-retrotransposon in the genome of P. gallinaceum.
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Affiliation(s)
- Ulrike Böhme
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Sascha Steinbiss
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Samuel O Oyola
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- International Livestock Research Institute, Nairobi 00100, Kenya
| | - Antoine Nicot
- CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, 34293 Montpellier Cedex 5, France
| | - Sylvain Gandon
- CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, 34293 Montpellier Cedex 5, France
| | - Kailash P Patra
- Department of Medicine, Division of Infectious Diseases, University of California San Diego, School of Medicine, La Jolla, California 92093, USA
| | - Colin Herd
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Ellen Bushell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Katarzyna K Modrzynska
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Joseph M Vinetz
- Department of Medicine, Division of Infectious Diseases, University of California San Diego, School of Medicine, La Jolla, California 92093, USA
| | - Ana Rivero
- MIVEGEC (CNRS UMR 5290), 34394 Montpellier Cedex 5, France
| | - Chris I Newbold
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
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Nag S, Kofoed PE, Ursing J, Lemvigh CK, Allesøe RL, Rodrigues A, Svendsen CA, Jensen JD, Alifrangis M, Lund O, Aarestrup FM. Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots. Malar J 2018; 17:91. [PMID: 29471822 PMCID: PMC5824530 DOI: 10.1186/s12936-018-2232-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/13/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Plasmodium falciparum malaria remains a major health burden and genomic research represents one of the necessary approaches for continued progress towards malaria control and elimination. Sample acquisition for this purpose is troublesome, with the majority of malaria-infected individuals living in rural areas, away from main infrastructure and the electrical grid. The aim of this study was to describe a low-tech procedure to sample P. falciparum specimens for direct whole genome sequencing (WGS), without use of electricity and cold-chain. METHODS Venous blood samples were collected from malaria patients in Bandim, Guinea-Bissau and leukocyte-depleted using Plasmodipur filters, the enriched parasite sample was spotted on Whatman paper and dried. The samples were stored at ambient temperatures and subsequently used for DNA-extraction. Ratios of parasite:human content of the extracted DNA was assessed by qPCR, and five samples with varying parasitaemia, were sequenced. Sequencing data were used to analyse the sample content, as well as sample coverage and depth as compared to the 3d7 reference genome. RESULTS qPCR revealed that 73% of the 199 samples were applicable for WGS, as defined by a minimum ratio of parasite:human DNA of 2:1. WGS revealed an even distribution of sequence data across the 3d7 reference genome, regardless of parasitaemia. The acquired read depths varied from 16 to 99×, and coverage varied from 87.5 to 98.9% of the 3d7 reference genome. SNP-analysis of six genes, for which amplicon sequencing has been performed previously, confirmed the reliability of the WGS-data. CONCLUSION This study describes a simple filter paper based protocol for sampling P. falciparum from malaria patients for subsequent direct WGS, enabling acquisition of samples in remote settings with no access to electricity.
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Affiliation(s)
- Sidsel Nag
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark. .,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.
| | - Poul-Erik Kofoed
- Department of Paediatrics, Kolding Hospital, Kolding, Denmark.,Bandim Health Project, Bissau, Guinea-Bissau
| | - Johan Ursing
- Bandim Health Project, Bissau, Guinea-Bissau.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Danderyds Hospital, Danderyd, Sweden
| | | | | | | | - Christina Aaby Svendsen
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jacob Dyring Jensen
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael Alifrangis
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Ole Lund
- DTU Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Frank M Aarestrup
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Doggett NA, Mukundan H, Lefkowitz EJ, Slezak TR, Chain PS, Morse S, Anderson K, Hodge DR, Pillai S. Culture-Independent Diagnostics for Health Security. Health Secur 2017; 14:122-42. [PMID: 27314653 DOI: 10.1089/hs.2015.0074] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The past decade has seen considerable development in the diagnostic application of nonculture methods, including nucleic acid amplification-based methods and mass spectrometry, for the diagnosis of infectious diseases. The implications of these new culture-independent diagnostic tests (CIDTs) include bypassing the need to culture organisms, thus potentially affecting public health surveillance systems, which continue to use isolates as the basis of their surveillance programs and to assess phenotypic resistance to antimicrobial agents. CIDTs may also affect the way public health practitioners detect and respond to a bioterrorism event. In response to a request from the Department of Homeland Security, Los Alamos National Laboratory and the Centers for Disease Control and Prevention cosponsored a workshop to review the impact of CIDTs on the rapid detection and identification of biothreat agents. Four panel discussions were held that covered nucleic acid amplification-based diagnostics, mass spectrometry, antibody-based diagnostics, and next-generation sequencing. Exploiting the extensive expertise available at this workshop, we identified the key features, benefits, and limitations of the various CIDT methods for providing rapid pathogen identification that are critical to the response and mitigation of a bioterrorism event. After the workshop we conducted a thorough review of the literature, investigating the current state of these 4 culture-independent diagnostic methods. This article combines information from the literature review and the insights obtained at the workshop.
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Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples. mBio 2017; 8:mBio.02257-16. [PMID: 28174312 PMCID: PMC5296604 DOI: 10.1128/mbio.02257-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Whole-genome sequencing (WGS) of microbial pathogens from clinical samples is a highly sensitive tool used to gain a deeper understanding of the biology, epidemiology, and drug resistance mechanisms of many infections. However, WGS of organisms which exhibit low densities in their hosts is challenging due to high levels of host genomic DNA (gDNA), which leads to very low coverage of the microbial genome. WGS of Plasmodium vivax, the most widely distributed form of malaria, is especially difficult because of low parasite densities and the lack of an ex vivo culture system. Current techniques used to enrich P. vivax DNA from clinical samples require significant resources or are not consistently effective. Here, we demonstrate that selective whole-genome amplification (SWGA) can enrich P. vivax gDNA from unprocessed human blood samples and dried blood spots for high-quality WGS, allowing genetic characterization of isolates that would otherwise have been prohibitively expensive or impossible to sequence. We achieved an average genome coverage of 24×, with up to 95% of the P. vivax core genome covered by ≥5 reads. The single-nucleotide polymorphism (SNP) characteristics and drug resistance mutations seen were consistent with those of other P. vivax sequences from a similar region in Peru, demonstrating that SWGA produces high-quality sequences for downstream analysis. SWGA is a robust tool that will enable efficient, cost-effective WGS of P. vivax isolates from clinical samples that can be applied to other neglected microbial pathogens. Malaria is a disease caused by Plasmodium parasites that caused 214 million symptomatic cases and 438,000 deaths in 2015. Plasmodium vivax is the most widely distributed species, causing the majority of malaria infections outside sub-Saharan Africa. Whole-genome sequencing (WGS) of Plasmodium parasites from clinical samples has revealed important insights into the epidemiology and mechanisms of drug resistance of malaria. However, WGS of P. vivax is challenging due to low parasite levels in humans and the lack of a routine system to culture the parasites. Selective whole-genome amplification (SWGA) preferentially amplifies the genomes of pathogens from mixtures of target and host gDNA. Here, we demonstrate that SWGA is a simple, robust method that can be used to enrich P. vivax genomic DNA (gDNA) from unprocessed human blood samples and dried blood spots for cost-effective, high-quality WGS.
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Oyola SO, Ariani CV, Hamilton WL, Kekre M, Amenga-Etego LN, Ghansah A, Rutledge GG, Redmond S, Manske M, Jyothi D, Jacob CG, Otto TD, Rockett K, Newbold CI, Berriman M, Kwiatkowski DP. Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malar J 2016; 15:597. [PMID: 27998271 PMCID: PMC5175302 DOI: 10.1186/s12936-016-1641-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/28/2016] [Indexed: 12/05/2022] Open
Abstract
Background Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB. Methods Parasite DNA with high (>95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8–12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparum DNA) and contaminating (human) genomes. Results Using sWGA method, clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB were sequenced. Greater than 18-fold enrichment of P. falciparum DNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5× coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls. Conclusion The sWGA methods described here provide a reliable and scalable way of generating P. falciparum genome sequence data from DBS samples. The current data indicate that it will be possible to get good quality sequence on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor in P. falciparum genome sequencing from field samples, and paves the way for large-scale epidemiological applications. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1641-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel O Oyola
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. .,International Livestock Research Institute, Box 30709, Nairobi, Kenya.
| | | | - William L Hamilton
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Addenbrooke's Hospital, University of Cambridge School of Clinical Medicine, Hills Rd, Cambridge, CB2 0SP, UK
| | - Mihir Kekre
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, P. O. Box LG 581, Legon, Accra, Ghana
| | | | - Seth Redmond
- Broad Institute, 415 Main St, Cambridge, MA, 02142, USA
| | - Magnus Manske
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Chris G Jacob
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kirk Rockett
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, OX3 7BN, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Chris I Newbold
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | | | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,MRC Centre for Genomics and Global Health, University of Oxford, Oxford, OX3 7BN, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
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Auburn S, Barry AE. Dissecting malaria biology and epidemiology using population genetics and genomics. Int J Parasitol 2016; 47:77-85. [PMID: 27825828 DOI: 10.1016/j.ijpara.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 10/20/2022]
Abstract
Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies. Microsatellite genotyping remains a popular approach for both Plasmodium falciparum and Plasmodium vivax. However, with the increasing availability of whole genome sequencing data enabling effective single nucleotide polymorphism-based panels tailored to a given study question and setting, this approach is gaining popularity. The availability of new reference genomes for Plasmodium malariae and Plasmodium ovale should see a surge in similar molecular studies on these currently neglected species. Genomic studies are revealing new insights into important adaptive mechanisms of the parasite including antimalarial drug resistance. The advent of new methodologies such as selective whole genome amplification for dealing with extensive human DNA in low density field isolates should see genome-wide approaches becoming routine for parasite surveillance once the economic costs outweigh the current cost benefits of targeted approaches.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Alyssa E Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia.
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36
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Yigit E, Feehery GR, Langhorst BW, Stewart FJ, Dimalanta ET, Pradhan S, Slatko B, Gardner AF, McFarland J, Sumner C, Davis TB. A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation. ACTA ACUST UNITED AC 2016; 115:7.26.1-7.26.14. [PMID: 27366894 DOI: 10.1002/cpmb.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
"Microbiome" is used to describe the communities of microorganisms and their genes in a particular environment, including communities in association with a eukaryotic host or part of a host. One challenge in microbiome analysis concerns the presence of host DNA in samples. Removal of host DNA before sequencing results in greater sequence depth of the intended microbiome target population. This unit describes a novel method of microbial DNA enrichment in which methylated host DNA such as human genomic DNA is selectively bound and separated from microbial DNA before next-generation sequencing (NGS) library construction. This microbiome enrichment technique yields a higher fraction of microbial sequencing reads and improved read quality resulting in a reduced cost of downstream data generation and analysis. © 2016 by John Wiley & Sons, Inc.
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37
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Vembar SS, Seetin M, Lambert C, Nattestad M, Schatz MC, Baybayan P, Scherf A, Smith ML. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Res 2016; 23:339-51. [PMID: 27345719 PMCID: PMC4991835 DOI: 10.1093/dnares/dsw022] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/10/2016] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging due to the skewed AT-richness [∼80.6% (A + T)] of its genome and the lack of technology to assemble highly polymorphic subtelomeric regions that contain clonally variant, multigene virulence families (Ex: var and rifin). To address this, we performed amplification-free, single molecule, real-time sequencing of P. falciparum genomic DNA and generated reads of average length 12 kb, with 50% of the reads between 15.5 and 50 kb in length. Next, using the Hierarchical Genome Assembly Process, we assembled the P. falciparum genome de novo and successfully compiled all 14 nuclear chromosomes telomere-to-telomere. We also accurately resolved centromeres [∼90–99% (A + T)] and subtelomeric regions and identified large insertions and duplications that add extra var and rifin genes to the genome, along with smaller structural variants such as homopolymer tract expansions. Overall, we show that amplification-free, long-read sequencing combined with de novo assembly overcomes major challenges inherent to studying the P. falciparum genome. Indeed, this technology may not only identify the polymorphic and repetitive subtelomeric sequences of parasite populations from endemic areas but may also evaluate structural variation linked to virulence, drug resistance and disease transmission.
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Affiliation(s)
- Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris 75015, France CNRS, ERL 9195, Paris 75015, France INSERM, Unit U1201, Paris 75015, France
| | | | | | | | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris 75015, France CNRS, ERL 9195, Paris 75015, France INSERM, Unit U1201, Paris 75015, France
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Beckers B, Op De Beeck M, Thijs S, Truyens S, Weyens N, Boerjan W, Vangronsveld J. Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies. Front Microbiol 2016; 7:650. [PMID: 27242686 PMCID: PMC4865482 DOI: 10.3389/fmicb.2016.00650] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/18/2016] [Indexed: 12/29/2022] Open
Abstract
Next-generation sequencing technologies have revolutionized the methods for studying microbial ecology by enabling high-resolution community profiling. However, the use of these technologies in unraveling the plant microbiome remains challenging. Many bacterial 16S rDNA primer pairs also exhibit high affinity for non-target DNA such as plastid (mostly chloroplast) DNA and mitochondrial DNA. Therefore, we experimentally tested a series of commonly used primers for the analysis of plant-associated bacterial communities using 454 pyrosequencing. We evaluated the performance of all selected primer pairs in the study of the bacterial microbiomes present in the rhizosphere soil, root, stem and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) based on (a) co-amplification of non-target DNA, (b) low amplification efficiency for pure chloroplast DNA (real-time PCR), (c) high retrieval of bacterial 16S rDNA, (d) high operational taxonomic unit (OTU) richness and Inverse Simpson diversity and (e) taxonomic assignment of reads. Results indicate that experimental evaluation of primers provide valuable information that could contribute in the selection of suitable primer pairs for 16S rDNA metabarcoding studies in plant-microbiota research. Furthermore, we show that primer pair 799F-1391R outperforms all other primer pairs in our study in the elimination of non-target DNA and retrieval of bacterial OTUs.
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Affiliation(s)
- Bram Beckers
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | | | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Sascha Truyens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
| | - Wout Boerjan
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB)Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGent, Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University Diepenbeek, Belgium
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Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria. Nat Commun 2016; 7:11078. [PMID: 27002652 PMCID: PMC4804174 DOI: 10.1038/ncomms11078] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/18/2016] [Indexed: 01/29/2023] Open
Abstract
African apes harbour at least six Plasmodium species of the subgenus Laverania, one of which gave rise to human Plasmodium falciparum. Here we use a selective amplification strategy to sequence the genome of chimpanzee parasites classified as Plasmodium reichenowi and Plasmodium gaboni based on the subgenomic fragments. Genome-wide analyses show that these parasites indeed represent distinct species, with no evidence of cross-species mating. Both P. reichenowi and P. gaboni are 10-fold more diverse than P. falciparum, indicating a very recent origin of the human parasite. We also find a remarkable Laverania-specific expansion of a multigene family involved in erythrocyte remodelling, and show that a short region on chromosome 4, which encodes two essential invasion genes, was horizontally transferred into a recent P. falciparum ancestor. Our results validate the selective amplification strategy for characterizing cryptic pathogen species, and reveal evolutionary events that likely predisposed the precursor of P. falciparum to colonize humans. African apes harbour six Plasmodium species, one of which gave rise to the human malaria parasite. Here, Sundaraman et al. use selective whole-genome amplification to determine genome sequences from two chimpanzee Plasmodium species, shedding light on the evolutionary origin of the human parasite.
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40
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Comparison of independent and dependent culture methods for the detection of transient bacteremia in diabetic subjects with chronic periodontitis. BIOMEDICA 2016; 36:156-61. [PMID: 27622449 DOI: 10.7705/biomedica.v36i1.2674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 07/17/2015] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Oral-derived bacteremia may occur after several dental procedures and routine daily activities. Some conditions of the oral cavity may favor episodes of bacteremia. This would be the case of patients with diabetes mellitus and periodontitis, who exhibit exacerbated gingival inflammation and may be more prone to developing oral-derived bacteremia. OBJECTIVE To compare the effectiveness of an independent culture method (quantitative real-time PCR- qCR) and the most commonly used method (BacT-ALERT 3D®) for the diagnosis of bacteremia. MATERIALS AND METHODS Blood samples were drawn from subjects with type 2 diabetes mellitus and chronic periodontitis before and after apple chewing. Samples were processed by an automated blood culture system (BacT-ALERT 3D®) monitored for 15 days with suitable subculture of positive cultures. In parallel, whole DNA from blood samples was purified using a commercial kit and screened by qPCR using a universal primer set of16S rDNA for bacteria detection. RESULTS Blood cultures taken before apple chewing were shown to be negative by the two diagnostic methods. After chewing, two samples (11%) showed bacterial growth by BacT-ALERT 3D® whereas qPCR did not detect the presence of bacteria in any sample. CONCLUSIONS qPCR did not show greater effectiveness than the BacT-ALERT 3D® in the detection of bacteremia of oral origin.
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Datta S, Budhauliya R, Das B, Chatterjee S, Vanlalhmuaka, Veer V. Next-generation sequencing in clinical virology: Discovery of new viruses. World J Virol 2015; 4:265-276. [PMID: 26279987 PMCID: PMC4534817 DOI: 10.5501/wjv.v4.i3.265] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/23/2015] [Accepted: 05/08/2015] [Indexed: 02/05/2023] Open
Abstract
Viruses are a cause of significant health problem worldwide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of next-generation sequencers (NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequence-independent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.
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42
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Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL. Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev 2015; 28:541-63. [PMID: 25876885 PMCID: PMC4399107 DOI: 10.1128/cmr.00075-13] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In addition to the ever-present concern of medical professionals about epidemics of infectious diseases, the relative ease of access and low cost of obtaining, producing, and disseminating pathogenic organisms or biological toxins mean that bioterrorism activity should also be considered when facing a disease outbreak. Utilization of whole-genome sequencing (WGS) in outbreak analysis facilitates the rapid and accurate identification of virulence factors of the pathogen and can be used to identify the path of disease transmission within a population and provide information on the probable source. Molecular tools such as WGS are being refined and advanced at a rapid pace to provide robust and higher-resolution methods for identifying, comparing, and classifying pathogenic organisms. If these methods of pathogen characterization are properly applied, they will enable an improved public health response whether a disease outbreak was initiated by natural events or by accidental or deliberate human activity. The current application of next-generation sequencing (NGS) technology to microbial WGS and microbial forensics is reviewed.
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Affiliation(s)
- Carol A Gilchrist
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen D Turner
- Department of Public Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Margaret F Riley
- Department of Public Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA School of Law, University of Virginia, Charlottesville, Virginia, USA Batten School of Leadership and Public Policy, University of Virginia, Charlottesville, Virginia, USA
| | - William A Petri
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA Department of Microbiology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA Department of Pathology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Erik L Hewlett
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA Department of Microbiology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
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43
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Abstract
We compared current viral respiratory diagnostic techniques with NGS. NGS is able to detect respiratory viruses in clinical diagnostic samples. With the current sample preparation method, NGS is less sensitive than RT-PCR. NGS provided additional sequence and typing information compared with RT-PCR.
Background Molecular assays are the gold standard methods used to diagnose viral respiratory pathogens. Pitfalls associated with this technique include limits to the number of targeted pathogens, the requirement for continuous monitoring to ensure sensitivity/specificity is maintained and the need to evolve to include emerging pathogens. Introducing target independent next generation sequencing (NGS) could resolve these issues and revolutionise respiratory viral diagnostics. Objectives To compare the sensitivity and specificity of target independent NGS against the current standard diagnostic test. Study design Diagnostic RT-PCR of clinical samples was carried out in parallel with target independent NGS. NGS sequences were analyzed to determine the proportion with viral origin and consensus sequences were used to establish viral genotypes and serotypes where applicable. Results 89 nasopharyngeal swabs were tested. A viral pathogen was detected in 43% of samples by NGS and 54% by RT-PCR. All NGS viral detections were confirmed by RT-PCR. Conclusions Target independent NGS can detect viral pathogens in clinical samples. Where viruses were detected by RT-PCR alone the Ct value was higher than those detected by both assays, suggesting an NGS detection cut-off – Ct = 32. The sensitivity and specificity of NGS compared with RT-PCR was 78% and 80% respectively. This is lower than current diagnostic assays but NGS provided full genome sequences in some cases, allowing determination of viral subtype and serotype. Sequencing technology is improving rapidly and it is likely that within a short period of time sequencing depth will increase in-turn improving test sensitivity.
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Carpi G, Walter KS, Bent SJ, Hoen AG, Diuk-Wasser M, Caccone A. Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi. BMC Genomics 2015; 16:434. [PMID: 26048573 PMCID: PMC4458057 DOI: 10.1186/s12864-015-1634-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 05/18/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Rapid and accurate retrieval of whole genome sequences of human pathogens from disease vectors or animal reservoirs will enable fine-resolution studies of pathogen epidemiological and evolutionary dynamics. However, next generation sequencing technologies have not yet been fully harnessed for the study of vector-borne and zoonotic pathogens, due to the difficulty of obtaining high-quality pathogen sequence data directly from field specimens with a high ratio of host to pathogen DNA. RESULTS We addressed this challenge by using custom probes for multiplexed hybrid capture to enrich for and sequence 30 Borrelia burgdorferi genomes from field samples of its arthropod vector. Hybrid capture enabled sequencing of nearly the complete genome (~99.5 %) of the Borrelia burgdorferi pathogen with 132-fold coverage, and identification of up to 12,291 single nucleotide polymorphisms per genome. CONCLUSIONS The proprosed culture-independent method enables efficient whole genome capture and sequencing of pathogens directly from arthropod vectors, thus making population genomic study of vector-borne and zoonotic infectious diseases economically feasible and scalable. Furthermore, given the similarities of invertebrate field specimens to other mixed DNA templates characterized by a high ratio of host to pathogen DNA, we discuss the potential applicabilty of hybrid capture for genomic study across diverse study systems.
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Affiliation(s)
- Giovanna Carpi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA.
| | - Katharine S Walter
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA.
| | - Stephen J Bent
- Robinson Research Institute, University of Adelaide, 5005, Adelaide, SA, Australia.
| | - Anne Gatewood Hoen
- The Geisel School of Medicine, Dartmouth College, 03755, Hanover, NH, USA.
| | - Maria Diuk-Wasser
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. .,Department of Ecology, Evolution and Environmental Biology, Columbia University, 10027, New York, NY, USA.
| | - Adalgisa Caccone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. .,Department of Ecology and Evolutionary Biology, Yale University, 06520, New Haven, CT, USA.
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Pinheiro MM, Ahmed MA, Millar SB, Sanderson T, Otto TD, Lu WC, Krishna S, Rayner JC, Cox-Singh J. Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. PLoS One 2015; 10:e0121303. [PMID: 25830531 PMCID: PMC4382175 DOI: 10.1371/journal.pone.0121303] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/30/2015] [Indexed: 11/21/2022] Open
Abstract
Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology.
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Affiliation(s)
- Miguel M. Pinheiro
- School of Medicine, University of St Andrews, Medical and Biological Sciences Building, North Haugh, St Andrews, United Kingdom
| | - Md Atique Ahmed
- Malaria Research Centre, University Malaysia Sarawak, Kuching, Sarawak, Malaysia
| | - Scott B. Millar
- School of Medicine, University of St Andrews, Medical and Biological Sciences Building, North Haugh, St Andrews, United Kingdom
| | - Theo Sanderson
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Thomas D. Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Woon Chan Lu
- Sarikei Hospital, Sarikei, Sarawak, 96100, Malaysia
| | - Sanjeev Krishna
- Division of Clinical Sciences, St. George’s, University of London, London, United Kingdom
| | - Julian C. Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Janet Cox-Singh
- School of Medicine, University of St Andrews, Medical and Biological Sciences Building, North Haugh, St Andrews, United Kingdom
- * E-mail:
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Podgorny OV, Polina NF, Babenko VV, Karpova IY, Kostryukova ES, Govorun VM, Lazarev VN. Isolation of single Chlamydia-infected cells using laser microdissection. J Microbiol Methods 2015; 109:123-8. [DOI: 10.1016/j.mimet.2014.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 12/12/2014] [Accepted: 12/23/2014] [Indexed: 11/15/2022]
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Audebert C, Hot D, Lemoine Y, Caboche S. [High-throughput sequencing: towards a genome-based diagnosis in infectious diseases]. Med Sci (Paris) 2014; 30:1144-51. [PMID: 25537045 DOI: 10.1051/medsci/20143012018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
During a pathogen outbreak, the emergency resides in the identification and characterization of the infectious agent. In addition to the traditional phenotypic methods which are still widely used, the molecular biology is nowadays a common approach of clinical microbiology labs and the pathogen can be identified by comparing its molecular fingerprint to a data-bank. High-throughput sequencing should allow overcoming this single identification to exploit the whole information encoded in the pathogen genome. This evolution, supported by an increasing number of proof-of-concept studies, should result in moving from detection through fingerprints to the use of the pathogen whole genome; this forensic profile should allow the adaptation of the treatment to the pathogen specificities. From concept to routine use, many parameters need to be considered to promote high-throughput sequencing as a powerful tool to help physicians and clinicians in microbiological investigations.
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Affiliation(s)
- Christophe Audebert
- Gènes Diffusion, Douai, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France
| | - David Hot
- U1019, UMR8204, Université de Lille, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France
| | - Yves Lemoine
- FRE3642, Université de Lille, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France
| | - Ségolène Caboche
- FRE3642, Université de Lille, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France
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Oyola SO, Manske M, Campino S, Claessens A, Hamilton WL, Kekre M, Drury E, Mead D, Gu Y, Miles A, MacInnis B, Newbold C, Berriman M, Kwiatkowski DP. Optimized whole-genome amplification strategy for extremely AT-biased template. DNA Res 2014; 21:661-71. [PMID: 25240466 PMCID: PMC4263299 DOI: 10.1093/dnares/dsu028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Pathogen genome sequencing directly from clinical samples is quickly gaining importance in genetic and medical research studies. However, low DNA yield from blood-borne pathogens is often a limiting factor. The problem worsens in extremely base-biased genomes such as the AT-rich Plasmodium falciparum. We present a strategy for whole-genome amplification (WGA) of low-yield samples from P. falciparum prior to short-read sequencing. We have developed WGA conditions that incorporate tetramethylammonium chloride for improved amplification and coverage of AT-rich regions of the genome. We show that this method reduces amplification bias and chimera formation. Our data show that this method is suitable for as low as 10 pg input DNA, and offers the possibility of sequencing the parasite genome from small blood samples.
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Affiliation(s)
| | | | | | | | | | - Mihir Kekre
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Daniel Mead
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Yong Gu
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Alistair Miles
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Bronwyn MacInnis
- Wellcome Trust Sanger Institute, Hinxton, UK MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK
| | - Chris Newbold
- Wellcome Trust Sanger Institute, Hinxton, UK Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, UK MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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Tappe D, Alquezar-Planas DE. Medical and molecular perspectives into a forgotten epidemic: encephalitis lethargica, viruses, and high-throughput sequencing. J Clin Virol 2014; 61:189-95. [PMID: 25129855 DOI: 10.1016/j.jcv.2014.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 01/06/2023]
Abstract
The emergence of encephalitis lethargica (EL), an acute-onset polioencephalitis of unknown etiology as an epidemic in the years 1917-1925 is still unexplainable today. Questioned by the first descriptor of EL himself, Constantin von Economo, there has been much debate shrouding a possible role of the "Spanish" H1N1 influenza A pandemic virus in the development of EL. Previous molecular studies employing conventional PCR for the detection of influenza A virus RNA in archived human brain samples from patients who died of acute EL were negative. However, the clinical and laboratory characteristics of EL and its epidemiology are consistent with an infectious disease, and recently a possible enterovirus cause was investigated. With the rapid development of high-throughput sequencing, new information about a possible viral etiology can be obtained if sufficient specimens for analysis were still available today. Here, we discuss the implications of these technologies for the investigation of a possible infectious cause of EL from archived material, as well as a prospectus for future work for acquiring viral nucleic acids from these sources.
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Affiliation(s)
- Dennis Tappe
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark.
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Abstract
SUMMARY Malaria remains one of the most significant global public health burdens, with nearly half of the world's population at risk of infection. Malaria is not however a monolithic disease - it can be caused by multiple different parasite species of the Plasmodium genus, each of which can induce different symptoms and pathology, and which pose quite different challenges for control. Furthermore, malaria is in no way restricted to humans. There are Plasmodium species that have adapted to infect most warm-blooded vertebrate species, and the genus as a whole is both highly successful and highly diverse. How, where and when human malaria parasites originated from within this diversity has long been a subject of fascination and sometimes also controversy. The past decade has seen the publication of a number of important discoveries about malaria parasite origins, all based on the application of molecular diagnostic tools to new sources of samples. This review summarizes some of those recent discoveries and discusses their implication for our current understanding of the origin and evolution of the Plasmodium genus. The nature of these discoveries and the manner in which they are made are then used to lay out a series of opportunities and challenges for the next wave of parasite hunters.
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