1
|
Farrall T, Brawner J, Dinsdale A, Kehoe M. A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics. Int J Mol Sci 2024; 25:8348. [PMID: 39125919 PMCID: PMC11312432 DOI: 10.3390/ijms25158348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/20/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024] Open
Abstract
Modern diagnostic techniques based on DNA sequence similarity are currently the gold standard for the detection of existing and emerging pathogens. Whilst individual assays are inexpensive to use, assay development is costly and carries risks of not being sensitive or specific enough to capture an increasingly diverse range of targets. Sequencing can provide the entire nucleic acid content of a sample and may be used to identify all pathogens present in the sample when the depth of coverage is sufficient. Targeted enrichment techniques have been used to increase sequence coverage and improve the sensitivity of detection within virus samples, specifically, to capture sequences for a range of different viruses or increase the number of reads from low-titre virus infections. Vertebrate viruses have been well characterised using in-solution hybridisation capture to target diverse virus families. The use of probes for genotyping and strain identification has been limited in plants, and uncertainty around sensitivity is an impediment to the development of a large-scale virus panel to use within regulatory settings and diagnostic pipelines. This review aims to compare significant studies that have used targeted enrichment of viruses to identify approaches to probe design and potential for use in plant virus detection and characterisation.
Collapse
Affiliation(s)
- Thomas Farrall
- Plant Innovation Centre, Australian Government, Department of Agriculture, Fisheries and Forestry (DAFF), Canberra, ACT 2601, Australia; (T.F.); (A.D.)
- Forest Research Institute, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Jeremy Brawner
- Forest Research Institute, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
| | - Adrian Dinsdale
- Plant Innovation Centre, Australian Government, Department of Agriculture, Fisheries and Forestry (DAFF), Canberra, ACT 2601, Australia; (T.F.); (A.D.)
| | - Monica Kehoe
- Diagnostic Laboratory Services, Biosecurity and Sustainability, Department of Primary Industries and Regional Development (DPIRD), Perth, WA 6151, Australia
| |
Collapse
|
2
|
Dual RNA sequencing of group B Streptococcus-infected human monocytes reveals new insights into host-pathogen interactions and bacterial evasion of phagocytosis. Sci Rep 2023; 13:2137. [PMID: 36747074 PMCID: PMC9902490 DOI: 10.1038/s41598-023-28117-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/13/2023] [Indexed: 02/08/2023] Open
Abstract
Streptococcus agalactiae, also known as Group B Streptococcus (GBS) is a frequent cause of infections, including bacteraemia and other acute diseases in adults and immunocompromised individuals. We developed a novel system to study GBS within human monocytes to define the co-transcriptome of intracellular GBS (iGBS) and host cells simultaneously using dual RNA-sequencing (RNA-seq) to better define how this pathogen responds to host cells. Using human U937 monocytes and genome-sequenced GBS reference strain 874,391 in antibiotic protection assays we validated a system for dual-RNA seq based on measures of GBS and monocyte viability to ensure that the bacterial and host cell co-transcriptome reflected mainly intracellular (iGBS) rather than extracellular GBS. Elucidation of the co-transcriptome revealed 1119 dysregulated transcripts in iGBS with most genes, including several that encode virulence factors (e.g., scpB, hvgA, ribD, pil2b) exhibiting activation by upregulated expression. Infection with iGBS resulted in significant remodelling of the monocyte transcriptome, with 7587 transcripts differentially expressed including 7040 up-regulated and 547 down-regulated. qPCR confirmed that the most strongly activated genes included sht, encoding Streptococcal Histidine Triad Protein. An isogenic GBS mutant strain deficient in sht revealed a significant effect of this gene on phagocytosis of GBS and survival of the bacteria during systemic infection in mice. Identification of a novel contribution of sht to GBS virulence shows the co-transcriptome responses elucidated in GBS-infected monocytes help to shape the host-pathogen interaction and establish a role for sht in the response of the bacteria to phagocytic uptake. This study provides comprehension of concurrent transcriptional responses that occur in GBS and human monocytes that shape the host-pathogen interaction.
Collapse
|
3
|
Noyes NR, Weinroth ME, Parker JK, Dean CJ, Lakin SM, Raymond RA, Rovira P, Doster E, Abdo Z, Martin JN, Jones KL, Ruiz J, Boucher CA, Belk KE, Morley PS. Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. MICROBIOME 2017; 5:142. [PMID: 29041965 PMCID: PMC5645900 DOI: 10.1186/s40168-017-0361-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/05/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. RESULTS The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. CONCLUSIONS These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.
Collapse
Affiliation(s)
- Noelle R Noyes
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maggie E Weinroth
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jennifer K Parker
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Chris J Dean
- Department of Computer Sciences, Colorado State University, Fort Collins, CO, USA
| | - Steven M Lakin
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Robert A Raymond
- Department of Computer Sciences, Colorado State University, Fort Collins, CO, USA
| | - Pablo Rovira
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Enrique Doster
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer N Martin
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, Section of Hematology Oncology and Bone Marrow Transplant, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jaime Ruiz
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Christina A Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Keith E Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Paul S Morley
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
4
|
Bent ZW, Poorey K, LaBauve AE, Hamblin R, Williams KP, Meagher RJ. A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing. PLoS One 2016; 11:e0168788. [PMID: 28002481 PMCID: PMC5176299 DOI: 10.1371/journal.pone.0168788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/06/2016] [Indexed: 02/04/2023] Open
Abstract
When analyzing pathogen transcriptomes during the infection of host cells, the signal-to-background (pathogen-to-host) ratio of nucleic acids (NA) in infected samples is very small. Despite the advancements in next-generation sequencing, the minute amount of pathogen NA makes standard RNA-seq library preps inadequate for effective gene-level analysis of the pathogen in cases with low bacterial loads. In order to provide a more complete picture of the pathogen transcriptome during an infection, we developed a novel pathogen enrichment technique, which can enrich for transcripts from any cultivable bacteria or virus, using common, readily available laboratory equipment and reagents. To evenly enrich for pathogen transcripts, we generate biotinylated pathogen-targeted capture probes in an enzymatic process using the entire genome of the pathogen as a template. The capture probes are hybridized to a strand-specific cDNA library generated from an RNA sample. The biotinylated probes are captured on a monomeric avidin resin in a miniature spin column, and enriched pathogen-specific cDNA is eluted following a series of washes. To test this method, we performed an in vitro time-course infection using Klebsiella pneumoniae to infect murine macrophage cells. K. pneumoniae transcript enrichment efficiency was evaluated using RNA-seq. Bacterial transcripts were enriched up to ~400-fold, and allowed the recovery of transcripts from ~2000–3600 genes not observed in untreated control samples. These additional transcripts revealed interesting aspects of K. pneumoniae biology including the expression of putative virulence factors and the expression of several genes responsible for antibiotic resistance even in the absence of drugs.
Collapse
Affiliation(s)
- Zachary W. Bent
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail: (ZWB); (RJM)
| | - Kunal Poorey
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Annette E. LaBauve
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Rachelle Hamblin
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Kelly P. Williams
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Robert J. Meagher
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail: (ZWB); (RJM)
| |
Collapse
|
5
|
Jones MR, Good JM. Targeted capture in evolutionary and ecological genomics. Mol Ecol 2016; 25:185-202. [PMID: 26137993 PMCID: PMC4823023 DOI: 10.1111/mec.13304] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 12/17/2022]
Abstract
The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome-partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole-genome sequencing in ecological and evolutionary genomic studies. High-throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome-partitioning approaches in the light of the increasing accessibility of whole-genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole-genome sequencing.
Collapse
Affiliation(s)
- Matthew R. Jones
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
| |
Collapse
|
6
|
Abstract
Insensitivity and technical complexity have impeded the implementation of high-throughput nucleic acid sequencing in differential diagnosis of viral infections in clinical laboratories. Here, we describe the development of a virome capture sequencing platform for vertebrate viruses (VirCapSeq-VERT) that increases the sensitivity of sequence-based virus detection and characterization. The system uses ~2 million probes that cover the genomes of members of the 207 viral taxa known to infect vertebrates, including humans. A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform and used for solution-based capture of viral nucleic acids present in complex samples containing variable proportions of viral and host nucleic acids. The use of VirCapSeq-VERT resulted in a 100- to 10,000-fold increase in viral reads from blood and tissue homogenates compared to conventional Illumina sequencing using established virus enrichment procedures, including filtration, nuclease treatments, and RiboZero rRNA subtraction. VirCapSeq-VERT had a limit of detection comparable to that of agent-specific real-time PCR in serum, blood, and tissue extracts. Furthermore, the method identified novel viruses whose genomes were approximately 40% different from the known virus genomes used for designing the probe library. The VirCapSeq-VERT platform is ideally suited for analyses of virome composition and dynamics. Importance VirCapSeq-VERT enables detection of viral sequences in complex sample backgrounds, including those found in clinical specimens, such as serum, blood, and tissue. The highly multiplexed nature of the system allows both the simultaneous identification and the comprehensive genetic characterization of all known vertebrate viruses, their genetic variants, and novel viruses. The operational simplicity and efficiency of the VirCapSeq-VERT platform may facilitate transition of high-throughput sequencing to clinical diagnostic as well as research applications. VirCapSeq-VERT enables detection of viral sequences in complex sample backgrounds, including those found in clinical specimens, such as serum, blood, and tissue. The highly multiplexed nature of the system allows both the simultaneous identification and the comprehensive genetic characterization of all known vertebrate viruses, their genetic variants, and novel viruses. The operational simplicity and efficiency of the VirCapSeq-VERT platform may facilitate transition of high-throughput sequencing to clinical diagnostic as well as research applications.
Collapse
|
7
|
Perez-Arriaga MO, Wilson S, Williams KP, Schoeniger J, Waymire RL, Powell AJ. Omics Metadata Management Software (OMMS). Bioinformation 2015; 11:165-72. [PMID: 26124554 PMCID: PMC4479048 DOI: 10.6026/97320630011165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 03/16/2015] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Next-generation sequencing projects have underappreciated information management tasks requiring detailed attention to specimen curation, nucleic acid sample preparation and sequence production methods required for downstream data processing, comparison, interpretation, sharing and reuse. The few existing metadata management tools for genome-based studies provide weak curatorial frameworks for experimentalists to store and manage idiosyncratic, project-specific information, typically offering no automation supporting unified naming and numbering conventions for sequencing production environments that routinely deal with hundreds, if not thousands of samples at a time. Moreover, existing tools are not readily interfaced with bioinformatics executables, (e.g., BLAST, Bowtie2, custom pipelines). Our application, the Omics Metadata Management Software (OMMS), answers both needs, empowering experimentalists to generate intuitive, consistent metadata, and perform analyses and information management tasks via an intuitive web-based interface. Several use cases with short-read sequence datasets are provided to validate installation and integrated function, and suggest possible methodological road maps for prospective users. Provided examples highlight possible OMMS workflows for metadata curation, multistep analyses, and results management and downloading. The OMMS can be implemented as a stand alone-package for individual laboratories, or can be configured for webbased deployment supporting geographically-dispersed projects. The OMMS was developed using an open-source software base, is flexible, extensible and easily installed and executed. The OMMS can be obtained at http://omms.sandia.gov. AVAILABILITY The OMMS can be obtained at http://omms.sandia.gov.
Collapse
Affiliation(s)
- Martha O Perez-Arriaga
- Department of Computer Science, Mail stop: MSC01 1130, 1 University of New Mexico, Albuquerque, NM 87131-0001
| | - Susan Wilson
- Center for Advanced Research Computing, University of New Mexico, Albuquerque, NM 87131
| | - Kelly P Williams
- Systems Biology, Sandia National Laboratories, Mail Stop 9291, Livermore, CA 94550
| | - Joseph Schoeniger
- Systems Biology, Sandia National Laboratories, Mail Stop 9291, Livermore, CA 94550
| | - Russel L Waymire
- Security Systems Analysis, Sandia National Laboratories, Mail Stop 0757, Albuquerque, NM 87123
| | - Amy Jo Powell
- Center for Advanced Research Computing, University of New Mexico, Albuquerque, NM 87131 ; Department of Biology, Mail stop: MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001 ; Computational Simulation Infrastructure, Sandia National Laboratories, Mail Stop 0845, Albuquerque, NM 87123
| |
Collapse
|
8
|
Ge F, Parker J, Chul Choi S, Layer M, Ross K, Jilly B, Chen J. Preferential Amplification of Pathogenic Sequences. Sci Rep 2015; 5:11047. [PMID: 26067233 PMCID: PMC4464073 DOI: 10.1038/srep11047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 05/14/2015] [Indexed: 02/07/2023] Open
Abstract
The application of next generation sequencing (NGS) technology in the diagnosis of human pathogens is hindered by the fact that pathogenic sequences, especially viral, are often scarce in human clinical specimens. This known disproportion leads to the requirement of subsequent deep sequencing and extensive bioinformatics analysis. Here we report a method we called “Preferential Amplification of Pathogenic Sequences (PATHseq)” that can be used to greatly enrich pathogenic sequences. Using a computer program, we developed 8-, 9-, and 10-mer oligonucleotides called “non-human primers” that do not match the most abundant human transcripts, but instead selectively match transcripts of human pathogens. Instead of using random primers in the construction of cDNA libraries, the PATHseq method recruits these short non-human primers, which in turn, preferentially amplifies non-human, presumably pathogenic sequences. Using this method, we were able to enrich pathogenic sequences up to 200-fold in the final sequencing library. This method does not require prior knowledge of the pathogen or assumption of the infection; therefore, it provides a fast and sequence-independent approach for detection and identification of human viruses and other pathogens. The PATHseq method, coupled with NGS technology, can be broadly used in identification of known human pathogens and discovery of new pathogens.
Collapse
Affiliation(s)
- Fang Ge
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Jayme Parker
- 1] Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA [2] Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, USA
| | - Sang Chul Choi
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Mark Layer
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Katherine Ross
- Alaska State Public Health Laboratories, Anchorage, Alaska, USA
| | - Bernard Jilly
- Alaska State Public Health Laboratories, Anchorage, Alaska, USA
| | - Jack Chen
- 1] Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA [2] Alaska State Public Health Virology Laboratory, Fairbanks, Alaska, USA
| |
Collapse
|
9
|
Transcriptomic Analysis of Yersinia enterocolitica Biovar 1B Infecting Murine Macrophages Reveals New Mechanisms of Extracellular and Intracellular Survival. Infect Immun 2015; 83:2672-85. [PMID: 25895974 DOI: 10.1128/iai.02922-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/10/2015] [Indexed: 11/20/2022] Open
Abstract
Yersinia enterocolitica is typically considered an extracellular pathogen; however, during the course of an infection, a significant number of bacteria are stably maintained within host cell vacuoles. Little is known about this population and the role it plays during an infection. To address this question and to elucidate the spatially and temporally dynamic gene expression patterns of Y. enterocolitica biovar 1B through the course of an in vitro infection, transcriptome sequencing and differential gene expression analysis of bacteria infecting murine macrophage cells were performed under four distinct conditions. Bacteria were first grown in a nutrient-rich medium at 26 °C to establish a baseline of gene expression that is unrelated to infection. The transcriptomes of these bacteria were then compared to bacteria grown in a conditioned cell culture medium at 37 °C to identify genes that were differentially expressed in response to the increased temperature and medium but not in response to host cells. Infections were then performed, and the transcriptomes of bacteria found on the extracellular surface and intracellular compartments were analyzed individually. The upregulated genes revealed potential roles for a variety of systems in promoting intracellular virulence, including the Ysa type III secretion system, the Yts2 type II secretion system, and the Tad pilus. It was further determined that mutants of each of these systems had decreased virulence while infecting macrophages. Overall, these results reveal the complete set of genes expressed by Y. enterocolitica in response to infection and provide the groundwork for future virulence studies.
Collapse
|
10
|
Lu ZH, Archibald AL, Ait-Ali T. Beyond the whole genome consensus: unravelling of PRRSV phylogenomics using next generation sequencing technologies. Virus Res 2014; 194:167-74. [PMID: 25312450 PMCID: PMC4275598 DOI: 10.1016/j.virusres.2014.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/01/2014] [Accepted: 10/01/2014] [Indexed: 02/05/2023]
Abstract
NGS allows the whole genome sequencing of PRRSV without any prior knowledge. Low frequency variants within the co-evolving quasispecies can be detected. Both macro- and micro-evolutionary events can be followed using NGS.
The highly heterogeneous porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent responsible for an economically important pig disease with the characteristic symptoms of reproductive losses in breeding sows and respiratory illnesses in young piglets. The virus can be broadly divided into the European and North American-like genotype 1 and 2 respectively. In addition to this intra-strains variability, the impact of coexisting viral quasispecies on disease development has recently gained much attention; owing very much to the advent of the next-generation sequencing (NGS) technologies. Genomic data produced from the massive sequencing capacities of NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequencing methods which require knowledge of conserved regions, NGS allows de novo assembly of the full viral genomes. Evolutionary variations gained from different genotypic strains provide valuable insights into functionally important regions of the virus. Together with the advancement of sophisticated bioinformatics tools, ultra-deep NGS technologies make the detection of low frequency co-evolving quasispecies possible. This short review gives an overview, including a proposed workflow, on the use of NGS to explore the genetic diversity of PRRSV at both macro- and micro-evolutionary levels.
Collapse
Affiliation(s)
- Zen H Lu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG Midlothian, United Kingdom.
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG Midlothian, United Kingdom
| | - Tahar Ait-Ali
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG Midlothian, United Kingdom.
| |
Collapse
|
11
|
Killick KE, Magee DA, Park SDE, Taraktsoglou M, Browne JA, Conlon KM, Nalpas NC, Gormley E, Gordon SV, MacHugh DE, Hokamp K. Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis. Front Immunol 2014; 5:422. [PMID: 25324841 PMCID: PMC4181336 DOI: 10.3389/fimmu.2014.00422] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 08/19/2014] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium bovis is an intracellular pathogen that causes tuberculosis in cattle. Following infection, the pathogen resides and persists inside host macrophages by subverting host immune responses via a diverse range of mechanisms. Here, a high-density bovine microarray platform was used to examine the bovine monocyte-derived macrophage transcriptome response to M. bovis infection relative to infection with the attenuated vaccine strain, M. bovis Bacille Calmette-Guérin. Differentially expressed genes were identified (adjusted P-value ≤0.01) and interaction networks generated across an infection time course of 2, 6, and 24 h. The largest number of biological interactions was observed in the 24-h network, which exhibited scale-free network properties. The 24-h network featured a small number of key hub and bottleneck gene nodes, including IKBKE, MYC, NFKB1, and EGR1 that differentiated the macrophage response to virulent and attenuated M. bovis strains, possibly via the modulation of host cell death mechanisms. These hub and bottleneck genes represent possible targets for immuno-modulation of host macrophages by virulent mycobacterial species that enable their survival within a hostile environment.
Collapse
Affiliation(s)
- Kate E Killick
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland ; Systems Biology Ireland, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Stephen D E Park
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland ; IdentiGEN Ltd. , Dublin , Ireland
| | - Maria Taraktsoglou
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland ; Biological Agents Unit, Health and Safety Executive , Leeds , UK
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Kevin M Conlon
- UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland ; Science Foundation Ireland (SFI) , Dublin , Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Eamonn Gormley
- Tuberculosis Diagnostics and Immunology Research Centre, UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland ; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland ; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin , Ireland
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College , Dublin , Ireland
| |
Collapse
|
12
|
The impact of "omic" and imaging technologies on assessing the host immune response to biodefence agents. J Immunol Res 2014; 2014:237043. [PMID: 25333059 PMCID: PMC4182007 DOI: 10.1155/2014/237043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/23/2014] [Accepted: 08/05/2014] [Indexed: 01/08/2023] Open
Abstract
Understanding the interactions between host and pathogen is important for the development and assessment of medical countermeasures to infectious agents, including potential biodefence pathogens such as Bacillus anthracis, Ebola virus, and Francisella tularensis. This review focuses on technological advances which allow this interaction to be studied in much greater detail. Namely, the use of “omic” technologies (next generation sequencing, DNA, and protein microarrays) for dissecting the underlying host response to infection at the molecular level; optical imaging techniques (flow cytometry and fluorescence microscopy) for assessing cellular responses to infection; and biophotonic imaging for visualising the infectious disease process. All of these technologies hold great promise for important breakthroughs in the rational development of vaccines and therapeutics for biodefence agents.
Collapse
|
13
|
Bent ZW, Brazel DM, Tran-Gyamfi MB, Hamblin RY, VanderNoot VA, Branda SS. Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages. PLoS One 2013; 8:e77834. [PMID: 24155975 PMCID: PMC3796476 DOI: 10.1371/journal.pone.0077834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/09/2013] [Indexed: 12/17/2022] Open
Abstract
Francisella tularensis is a zoonotic intracellular pathogen that is capable of causing potentially fatal human infections. Like all successful bacterial pathogens, F. tularensis rapidly responds to changes in its environment during infection of host cells, and upon encountering different microenvironments within those cells. This ability to appropriately respond to the challenges of infection requires rapid and global shifts in gene expression patterns. In this study, we use a novel pathogen transcript enrichment strategy and whole transcriptome sequencing (RNA-Seq) to perform a detailed characterization of the rapid and global shifts in F. tularensis LVS gene expression during infection of murine macrophages. We performed differential gene expression analysis on all bacterial genes at two key stages of infection: phagosomal escape, and cytosolic replication. By comparing the F. tularensis transcriptome at these two stages of infection to that of the bacteria grown in culture, we were able to identify sets of genes that are differentially expressed over the course of infection. This analysis revealed the temporally dynamic expression of a number of known and putative transcriptional regulators and virulence factors, providing insight into their role during infection. In addition, we identified several F. tularensis genes that are significantly up-regulated during infection but had not been previously identified as virulence factors. These unknown genes may make attractive therapeutic or vaccine targets.
Collapse
Affiliation(s)
- Zachary W. Bent
- Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
| | - David M. Brazel
- Sandia National Laboratories, Livermore, California, United States of America
| | - Mary B. Tran-Gyamfi
- Sandia National Laboratories, Livermore, California, United States of America
| | - Rachelle Y. Hamblin
- Sandia National Laboratories, Livermore, California, United States of America
| | | | - Steven S. Branda
- Sandia National Laboratories, Livermore, California, United States of America
| |
Collapse
|