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Wang M, Goh YX, Tai C, Wang H, Deng Z, Ou HY. VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens. Nucleic Acids Res 2022; 50:W768-W773. [PMID: 35524563 PMCID: PMC9252795 DOI: 10.1093/nar/gkac321] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/10/2022] [Accepted: 04/21/2022] [Indexed: 01/10/2023] Open
Abstract
VRprofile2 is an updated pipeline that rapidly identifies diverse mobile genetic elements in bacterial genome sequences. Compared with the previous version, three major improvements were made. First, the user-friendly visualization could aid users in investigating the antibiotic resistance gene cassettes in conjunction with various mobile elements in the multiple resistance region with mosaic structure. VRprofile2 could compare the predicted mobile elements to the collected known mobile elements with similar architecture. A new mobilome indicator was proposed to give an overall estimation of the mobilome size in individual bacterial genomes. Second, the relationship between antibiotic resistance genes, mobile elements, and host strains would be efficiently examined with the aid of predicted strain's sequence typing, the incompatibility group and the transferability of plasmids. Finally, the updated back-end database, MobilomeDB2, now collected nearly a thousand active mobile elements retrieved from literature or based on prediction. The pre-computed results of the antibiotic resistance gene-carrying mobile elements of >5500 ESKAPEE genomes were also provided. We expect that VRprofile2 will provide better support for researchers interested in bacterial mobile elements and the dissemination of antibiotic resistance. VRprofile2 is freely available to all users without any login requirement at https://tool2-mml.sjtu.edu.cn/VRprofile.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ying-Xian Goh
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hui Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
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Ou HY, He X, Harrison EM, Kulasekara BR, Thani AB, Kadioglu A, Lory S, Hinton JCD, Barer MR, Deng Z, Rajakumar K. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res 2007; 35:W97-W104. [PMID: 17537813 PMCID: PMC1933208 DOI: 10.1093/nar/gkm380] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or 'mobile genome' (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate 'inferred contigs' produced by merging adjacent genes classified as 'present'. Collectively these 'fragments' represent a hypothetical 'microarray-visualized genome (MVG)'. ArrayOme permits recognition of discordances between physical genome and MVG sizes, thereby enabling identification of strains rich in microarray-elusive novel genes. Individual tRNAcc tools facilitate automated identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites and other integration hotspots in closely related sequenced genomes. Accessory tools facilitate design of hotspot-flanking primers for in silico and/or wet-science-based interrogation of cognate loci in unsequenced strains and analysis of islands for features suggestive of foreign origins; island-specific and genome-contextual features are tabulated and represented in schematic and graphical forms. To date we have used MobilomeFINDER to analyse several Enterobacteriaceae, Pseudomonas aeruginosa and Streptococcus suis genomes. MobilomeFINDER enables high-throughput island identification and characterization through increased exploitation of emerging sequence data and PCR-based profiling of unsequenced test strains; subsequent targeted yeast recombination-based capture permits full-length sequencing and detailed functional studies of novel genomic islands.
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Affiliation(s)
- Hong-Yu Ou
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Xinyi He
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Ewan M. Harrison
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Bridget R. Kulasekara
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Ali Bin Thani
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Aras Kadioglu
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Stephen Lory
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Jay C. D. Hinton
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Michael R. Barer
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Zixin Deng
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Kumar Rajakumar
- Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
- *To whom correspondence should be addressed. +44 116 2231498+44 116 2525030 Correspondence may also be addressed to Zixin Deng. +86 21 62933404+86 21 62932418
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Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biol 2007; 8:R10. [PMID: 17224063 PMCID: PMC1839125 DOI: 10.1186/gb-2007-8-1-r10] [Citation(s) in RCA: 229] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 10/31/2006] [Accepted: 01/15/2007] [Indexed: 11/23/2022] Open
Abstract
A novel computational approach shows a link between genome size and habitat from analysis of environmental metagenomic DNA reads. We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses) from short sequencing reads of environmental genomics (or metagenomics) projects. We observe considerable EGS differences between environments and link this with ecologic complexity as well as species composition (for instance, the presence of eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 megabases (Mb) whereas that of the bacteria therein is only 4.7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects.
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Affiliation(s)
- Jeroen Raes
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
- Molecular Biophysics & Biochemistry Department, Yale University, Whitney Avenue, New Haven, Connecticut, USA
| | - Martin J Lercher
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Christian von Mering
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
- Institute of Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Peer Bork
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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Smart CHM, Scott FW, Wright EA, Walshaw MJ, Hart CA, Pitt TL, Winstanley C. Development of a diagnostic test for the Midlands 1 cystic fibrosis epidemic strain of Pseudomonas aeruginosa. J Med Microbiol 2006; 55:1085-1091. [PMID: 16849729 DOI: 10.1099/jmm.0.46604-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a previous study of isolates from cystic fibrosis (CF) patients in England and Wales, the Midlands 1 strain of Pseudomonas aeruginosa was identified as the second most common clone, representing 10% of isolates and found in nearly one-third of all CF centres [Scott, F. W. & Pitt, T. L. (2004). J Med Microbiol 53, 609-615]. Using suppression subtractive hybridization, 54 sequences were identified as present in a Midlands 1 strain but were absent from strain PAO1. The distribution of 14 of these sequences amongst representatives of Midlands 1, other CF epidemic strains and unrelated P. aeruginosa CF isolates was determined using PCR assays. Using these data, a PCR-based test was developed that was specific for the Midlands 1 clone, which was confirmed using dot-blot hybridization. By applying the test to CF isolates from a CF centre in Liverpool, a Midlands 1 clone was identified. The identity was confirmed using typing by PFGE. The PCR test should facilitate a greater understanding of the distribution of the Midlands 1 strain in the UK and elsewhere.
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Affiliation(s)
- Catherine H M Smart
- Division of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - Fiona W Scott
- Laboratory of HealthCare Associated Infection, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Elli A Wright
- Division of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - Martin J Walshaw
- Regional Adult Cystic Fibrosis Unit, Cardiothoracic Centre, Liverpool L14 3PE, UK
| | - C Anthony Hart
- Division of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - Tyrone L Pitt
- Laboratory of HealthCare Associated Infection, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Craig Winstanley
- Division of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
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