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Song JY, Yun YH, Kim GD, Kim SH, Lee SJ, Kim JF. Genome Analysis of Erwinia amylovora Strains Responsible for a Fire Blight Outbreak in Korea. PLANT DISEASE 2021; 105:1143-1152. [PMID: 32931384 DOI: 10.1094/pdis-06-20-1329-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Erwinia amylovora is a plant-pathogenic bacterium that causes fire blight disease in Rosaceae plants. Since fire blight is highly contagious and results in serious losses once introduced, it is regulated as a quarantine disease. Recently, for the first time in East Asia, fire blight emerged in Korea with strains of E. amylovora being isolated from lesions of infected trees. Five of those strains were selected and subjected to whole-genome shotgun sequencing. Each strain had two circular replicons, a 3.8-Mb chromosome and a 28-kb plasmid. The genome sequences were compared with those of other E. amylovora strains isolated from different hosts or geographical regions. Genome synteny was analyzed and sequence variations including nucleotide substitutions, inversions, insertions, and deletions were detected. Analysis of the population genomic structure revealed that the five strains form a distinct structural group. Phylogenomic analysis was performed to infer the evolutionary relationships among E. amylovora strains, which indicated that the Korean isolates, all descended from a common ancestor, are closely related to a lineage of North American strains. These results provide useful information for understanding the genomic dynamics of E. amylovora strains including those in Korea, developing genetic markers for surveillance of the pathogen or diagnosis of the disease, and eventually developing measures to eradicate it.
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Affiliation(s)
- Ju Yeon Song
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yeo Hong Yun
- Department of Microbiology and Institute for Biodiversity, Dankook University, Dongnam-gu, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Gi-Don Kim
- Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea
| | - Seong Hwan Kim
- Department of Microbiology and Institute for Biodiversity, Dankook University, Dongnam-gu, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Seong-Jin Lee
- Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
- Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
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Roe C, Stegger M, Lilje B, Johannesen TB, Ng KL, Sieber RN, Driebe E, Engelthaler DM, Andersen PS. Genomic analyses of Staphylococcus aureus clonal complex 45 isolates does not distinguish nasal carriage from bacteraemia. Microb Genom 2020; 6:mgen000403. [PMID: 32667872 PMCID: PMC7641415 DOI: 10.1099/mgen.0.000403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/16/2020] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a colonizing opportunistic pathogen and a leading cause of bloodstream infection with high morbidity and mortality. S. aureus carriage frequency is reportedly between 20 and 40 % among healthy adults, with S. aureus colonization considered to be a risk factor for S. aureus bacteraemia. It is unknown whether a genetic component of the bacterium is associated with S. aureus bacteraemia in comparison to nasal carriage strains. Previous association studies primarily focusing on the clinical outcome of an S. aureus infection have produced conflicting results, often limited by study design challenged by sample collections and the clonal diversity of S. aureus. To date, no study has investigated whether genomic features separate nasal carriage isolates from S. aureus bacteraemia isolates within a single clonal lineage. Here we have investigated whether genomic features, including single-nucleotide polymorphisms (SNPs), genes, or kmers, distinguish S. aureus nasal carriage isolates from bacteraemia isolates that all belong to the same clonal lineage [clonal complex 45 (CC45)] using whole-genome sequencing (WGS) and a genome-wide association (GWA) approach. From CC45, 100 isolates (50 bacteraemia and 50 nasal carriage, geographically and temporally matched) from Denmark were whole-genome sequenced and subjected to GWA analyses involving gene copy number variation, SNPs, gene content, kmers and gene combinations, while correcting for lineage effects. No statistically significant association involving SNPs, specific genes, gene variants, gene copy number variation, or a combination of genes was identified that could distinguish bacteraemia isolates from nasal carriage isolates. The presented results suggest that all S. aureus nasal CC45 isolates carry the potential to cause invasive disease, as no core or accessory genome content or variations were statistically associated with invasiveness.
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Affiliation(s)
- Chandler Roe
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- Northern Arizona University, Flagstaff, AZ, USA
| | - Marc Stegger
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Berit Lilje
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Kim Lee Ng
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N. Sieber
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Paal Skytt Andersen
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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Sethi S, Hao Y, Brown SM, Walker T, Yadav R, Zaman K, Aggarwal AN, Behera D. Elucidation of drug resistance mutations in Mycobacterium tuberculosis isolates from North India by whole-genome sequencing. J Glob Antimicrob Resist 2019; 20:11-15. [PMID: 31121336 DOI: 10.1016/j.jgar.2019.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 05/06/2019] [Accepted: 05/12/2019] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES Rapid diagnosis of drug-resistant tuberculosis (TB) is required for better patient management and treatment outcomes. Whole-genome sequencing (WGS) can be used to detect single nucleotide polymorphisms (SNPs) and deletions/insertions that are responsible for mostMycobacterium tuberculosis drug resistance. WGS is being performed at scale in high-income countries, but there are limited reports of its use in India. METHODS In this study, 33 clinicalM. tuberculosis isolates from the Mycobacterial Repository in Chandigarh underwent WGS. Phenotypic drug susceptibility testing was performed according to World Health Organization (WHO) recommendations. Four isolates were excluded from the analysis due to culture contamination or mislabelling during the study. RESULTS Among the remaining 29 isolates, 21 (72.4%) were multidrug-resistant TB (MDR-TB) and 1 (3.4%) was extensively-drug resistant TB (XDR-TB). The most common mutations observed for isoniazid, rifampicin, ofloxacin and kanamycin resistance werekatG(S315T), rpoB(S450L), gyrA(A90V) and rrs(A1401G), respectively. The isolates mainly belonged to lineages 2 and 3, with most MDR-TB among lineage 2 isolates. CONCLUSION WGS ofM. tuberculosis isolates allows the detection of drug resistance to all drugs in a single test and also provides insight into the evolution and drug-resistant TB.
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Affiliation(s)
- Sunil Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India.
| | - Yuhan Hao
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA; Applied Bioinformatics Laboratories, New York University School of Medicine, NY 10016, USA
| | - Stuart M Brown
- Applied Bioinformatics Laboratories, New York University School of Medicine, NY 10016, USA; Department of Cell Biology, New York University School of Medicine, NY 10016, USA
| | - Timothy Walker
- Department of Microbiology and Infectious Diseases, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rakesh Yadav
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Kamran Zaman
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Ashutosh Nath Aggarwal
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Digambar Behera
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
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Genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s. Genomics 2019; 112:528-544. [PMID: 30974149 DOI: 10.1016/j.ygeno.2019.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/22/2019] [Accepted: 04/05/2019] [Indexed: 02/02/2023]
Abstract
A total of 91 draft genome sequences were used to analyze isolates of Salmonella enterica serovar Enteritidis obtained from feral mice caught on poultry farms in Pennsylvania. One objective was to find mutations disrupting open reading frames (ORFs) and another was to determine if ORF-disruptive mutations were present in isolates obtained from other sources. A total of 83 mice were obtained between 1995-1998. Isolates separated into two genomic clades and 12 subgroups due to 742 mutations. Nineteen ORF-disruptive mutations were found, and in addition, bigA had exceptional heterogeneity requiring additional evaluation. The TRAMS algorithm detected only 6 ORF disruptions. The sefD mutation was the most frequently encountered mutation and it was prevalent in human, poultry, environmental and mouse isolates. These results confirm previous assessments of the mouse as a rich source of Salmonella enterica serovar Enteritidis that varies in genotype and phenotype.
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Lilje B, Rasmussen RV, Dahl A, Stegger M, Skov RL, Fowler VG, Ng KL, Kiil K, Larsen AR, Petersen A, Johansen HK, Schønheyder HC, Arpi M, Rosenvinge FS, Korup E, Høst U, Hassager C, Gill SUA, Hansen TF, Johannesen TB, Smit J, Søgaard P, Skytt Andersen P, Eske-Bruun N. Whole-genome sequencing of bloodstream Staphylococcus aureus isolates does not distinguish bacteraemia from endocarditis. Microb Genom 2019; 3. [PMID: 29208121 PMCID: PMC5729915 DOI: 10.1099/mgen.0.000138] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Most Staphylococcus aureus isolates can cause invasive disease given the right circumstances, but it is unknown if some isolates are more likely to cause severe infections than others. S. aureus bloodstream isolates from 120 patients with definite infective endocarditis and 121 with S. aureus bacteraemia without infective endocarditis underwent whole-genome sequencing. Genome-wide association analysis was performed using a variety of bioinformatics approaches including SNP analysis, accessory genome analysis and k-mer based analysis. Core and accessory genome analyses found no association with either of the two clinical groups. In this study, the genome sequences of S. aureus bloodstream isolates did not discriminate between bacteraemia and infective endocarditis. Based on our study and the current literature, it is not convincing that a specific S. aureus genotype is clearly associated to infective endocarditis in patients with S. aureus bacteraemia.
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Affiliation(s)
- Berit Lilje
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus Vedby Rasmussen
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Anders Dahl
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Marc Stegger
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert Leo Skov
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Vance G Fowler
- 3Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Kim Lee Ng
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kristoffer Kiil
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- 1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Helle Krogh Johansen
- 4Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Henrik Carl Schønheyder
- 5Department of Clinical Microbiology, Aalborg University Hospital, Clinical Institute, Aalborg University, Aalborg, Denmark
| | - Magnus Arpi
- 6Department of Clinical Microbiology, Copenhagen University Hospital, Herlev-Gentofte, Herlev, Denmark
| | | | - Eva Korup
- 8Department of Cardiology, Aalborg University Hospital, Aalborg, Denmark
| | - Ulla Høst
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Christian Hassager
- 9Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Thomas Fritz Hansen
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Thor Bech Johannesen
- 2Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Copenhagen, Denmark
| | - Jesper Smit
- 11Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Peter Søgaard
- 12Department of Cardiology, Clinical Institute, Aalborg University, Aalborg University Hospital, Aalborg, Denmark
| | - Paal Skytt Andersen
- 13Department of Animal and Veterinary Sciences, University of Copenhagen, Copenhagen, Denmark.,14Translational Genomics North, Flagstaff, USA.,1Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Niels Eske-Bruun
- 15Department of Cardiology, Copenhagen University Hospital, Herlev-Gentofte, Clinical Institute, Aalborg University, Copenhagen, Aalborg, Denmark
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Comparison of advanced whole genome sequence-based methods to distinguish strains of Salmonella enterica serovar Heidelberg involved in foodborne outbreaks in Québec. Food Microbiol 2018. [PMID: 29526232 DOI: 10.1016/j.fm.2018.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. This serovar ranks second and third among serovars that cause human infections in Québec and Canada, respectively, and has been associated with severe infections. Traditional typing methods such as PFGE do not display adequate discrimination required to resolve outbreak investigations due to the low level of genetic diversity of isolates belonging to this serovar. This study evaluates the ability of four whole genome sequence (WGS)-based typing methods to differentiate among 145 S. Heidelberg strains involved in four distinct outbreak events and sporadic cases of salmonellosis that occurred in Québec between 2007 and 2016. Isolates from all outbreaks were indistinguishable by PFGE. The core genome single nucleotide variant (SNV), core genome multilocus sequence typing (MLST) and whole genome MLST approaches were highly discriminatory and separated outbreak strains into four distinct phylogenetic clusters that were concordant with the epidemiological data. The clustered regularly interspaced short palindromic repeats (CRISPR) typing method was less discriminatory. However, CRISPR typing may be used as a secondary method to differentiate isolates of S. Heidelberg that are genetically similar but epidemiologically unrelated to outbreak events. WGS-based typing methods provide a highly discriminatory alternative to PFGE for the laboratory investigation of foodborne outbreaks.
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Wang X, Khushk I, Xiao Y, Gao Q, Bao J. Tolerance improvement of Corynebacterium glutamicum on lignocellulose derived inhibitors by adaptive evolution. Appl Microbiol Biotechnol 2017; 102:377-388. [DOI: 10.1007/s00253-017-8627-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/24/2017] [Accepted: 11/06/2017] [Indexed: 01/09/2023]
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Quibod IL, Perez-Quintero A, Booher NJ, Dossa GS, Grande G, Szurek B, Vera Cruz C, Bogdanove AJ, Oliva R. Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment. Sci Rep 2016; 6:34137. [PMID: 27667260 PMCID: PMC5035989 DOI: 10.1038/srep34137] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/07/2016] [Indexed: 01/01/2023] Open
Abstract
Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts. Here, we took advantage of an historical record to examine the adaptation pathway of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) in a semi-isolated environment represented in the Philippine archipelago. By comparing genomes of key Xoo groups we showed that modern populations derived from three Asian lineages. We also showed that diversification of virulence factors occurred within each lineage, most likely driven by host adaptation, and it was essential to shape contemporary pathogen races. This finding is particularly important because it expands our understanding of pathogen adaptation to modern agriculture.
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Affiliation(s)
- Ian Lorenzo Quibod
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Alvaro Perez-Quintero
- Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Gerbert S Dossa
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Genelou Grande
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Boris Szurek
- Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Casiana Vera Cruz
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Ricardo Oliva
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
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Abstract
The number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.
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Baez-Ortega A, Lorenzo-Diaz F, Hernandez M, Gonzalez-Vila CI, Roda-Garcia JL, Colebrook M, Flores C. IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data. Bioinformatics 2015; 31:2870-3. [PMID: 25953799 DOI: 10.1093/bioinformatics/btv283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/29/2015] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED We introduce IonGAP, a publicly available Web platform designed for the analysis of whole bacterial genomes using Ion Torrent sequence data. Besides assembly, it integrates a variety of comparative genomics, annotation and bacterial classification routines, based on the widely used FASTQ, BAM and SRA file formats. Benchmarking with different datasets evidenced that IonGAP is a fast, powerful and simple-to-use bioinformatics tool. By releasing this platform, we aim to translate low-cost bacterial genome analysis for microbiological prevention and control in healthcare, agroalimentary and pharmaceutical industry applications. AVAILABILITY AND IMPLEMENTATION IonGAP is hosted by the ITER's Teide-HPC supercomputer and is freely available on the Web for non-commercial use at http://iongap.hpc.iter.es. CONTACT mcolesan@ull.edu.es or cflores@ull.edu.es SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Adrian Baez-Ortega
- Information Technology Department, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Fabian Lorenzo-Diaz
- Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain, Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Mariano Hernandez
- Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Carlos Ignacio Gonzalez-Vila
- Information Technology Department, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Jose Luis Roda-Garcia
- Departamento de Ingeniería Informática y de Sistemas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain and
| | - Marcos Colebrook
- Departamento de Ingeniería Informática y de Sistemas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain and
| | - Carlos Flores
- Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain, Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain, CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Podicheti R, Mockaitis K. FEATnotator: A tool for integrated annotation of sequence features and variation, facilitating interpretation in genomics experiments. Methods 2015; 79-80:11-7. [PMID: 25934264 DOI: 10.1016/j.ymeth.2015.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/25/2015] [Accepted: 04/22/2015] [Indexed: 11/16/2022] Open
Abstract
As approaches are sought for more efficient and democratized uses of non-model and expanded model genomics references, ease of integration of genomic feature datasets is especially desirable in multidisciplinary research communities. Valuable conclusions are often missed or slowed when researchers refer experimental results to a single reference sequence that lacks integrated pan-genomic and multi-experiment data in accessible formats. Association of genomic positional information, such as results from an expansive variety of next-generation sequencing experiments, with annotated reference features such as genes or predicted protein binding sites, provides the context essential for conclusions and ongoing research. When the experimental system includes polymorphic genomic inputs, rapid calculation of gene structural and protein translational effects of sequence variation from the reference can be invaluable. Here we present FEATnotator, a lightweight, fast and easy to use open source software program that integrates and reports overlap and proximity in genomic information from any user-defined datasets including those from next generation sequencing applications. We illustrate use of the tool by summarizing whole genome sequence variation of a widely used natural isolate of Arabidopsis thaliana in the context of gene models of the reference accession. Previous discovery of a protein coding deletion influencing root development is replicated rapidly. Appropriate even in investigations of a single gene or genic regions such as QTL, comprehensive reports provided by FEATnotator better prepare researchers for interpretation of their experimental results. The tool is available for download at http://featnotator.sourceforge.net.
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Affiliation(s)
- Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, 1001 E. Third Street, Bloomington, IN 47405, USA; School of Informatics and Computing, Indiana University, 919 E. Tenth Street, Bloomington, IN 47408, USA.
| | - Keithanne Mockaitis
- Pervasive Technology Institute, Indiana University, 2709 E. Tenth Street, Bloomington, IN 47408, USA; Department of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA.
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Sangal V, Jones AL, Goodfellow M, Sutcliffe IC, Hoskisson PA. Comparative genomic analyses reveal a lack of a substantial signature of host adaptation in Rhodococcus equi ('Prescottella equi'). Pathog Dis 2014; 71:352-6. [PMID: 24376240 DOI: 10.1111/2049-632x.12126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/04/2013] [Accepted: 12/18/2013] [Indexed: 01/09/2023] Open
Abstract
Rhodococcus equi ('Prescottella equi') is a pathogenic actinomycete primarily infecting horses but has emerged as an opportunistic human pathogen. We have sequenced the genome of the type strain of this species, R. equi strain C7(T) , and compared the genome with that of another foal isolate 103S and of a human isolate ATCC 33707. The R. equi strains are closely related to each other and yet distantly related to other rhodococci and Nocardia brasiliensis. The comparison of gene contents among R. equi strains revealed minor differences that could be associated with host adaptation from foals to humans, including the presence of a paa operon in the human isolate, which is potentially involved in pathogenesis.
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Affiliation(s)
- Vartul Sangal
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK; Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
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14
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Sangal V, Burkovski A, Hunt AC, Edwards B, Blom J, Hoskisson PA. A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2013; 21:54-7. [PMID: 24200588 DOI: 10.1016/j.meegid.2013.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/22/2013] [Accepted: 10/23/2013] [Indexed: 11/26/2022]
Abstract
The differentiation of clinically important Corynebacterium diphtheriae into specific biovars is complex and phylogenetically unclear. Comparative genomic analyses of 17 strains indicate that the division of C. diphtheriae into different biovars does not correlate with the variation in the gene content in the relevant metabolic categories that are potentially involved in the biovar discrimination. The biochemical separation is also not supported by phylogenetic analyses, suggesting molecular methods of typing C. diphtheriae strains should be adopted much more widely.
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Affiliation(s)
- Vartul Sangal
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Andreas Burkovski
- Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Alison C Hunt
- Department of Medical Microbiology, Aberdeen Royal Infirmary, Foresterhill, Aberdeen AB25 2ZN, UK
| | - Becky Edwards
- Microbiology Department, Royal Infirmary of Edinburgh, 51 Little France Cresent, Old Dalkeith Road, Edinburgh EH16 4SA, UK
| | - Jochen Blom
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK.
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