1
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Gregg KA, Wang Y, Warfel J, Schoenfeld E, Jankowska E, Cipollo JF, Mayho M, Boinett C, Prasad D, Brickman TJ, Armstrong SK, Parkhill J, Da Silva Antunes R, Sette A, Papin JF, Wolf R, Merkel TJ. Antigen Discovery for Next-Generation Pertussis Vaccines Using Immunoproteomics and Transposon-Directed Insertion Sequencing. J Infect Dis 2023; 227:583-591. [PMID: 36575950 PMCID: PMC10169431 DOI: 10.1093/infdis/jiac502] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Despite high vaccination rates, the United States has experienced a resurgence in reported cases of pertussis after switching to the acellular pertussis vaccine, indicating a need for improved vaccines that enhance infection control. METHODS Bordetella pertussis antigens recognized by convalescent-baboon serum and nasopharyngeal wash were identified by immunoproteomics and their subcellular localization predicted. Genes essential or important for persistence in the baboon airway were identified by transposon-directed insertion-site sequencing (TraDIS) analysis. RESULTS In total, 314 B. pertussis antigens were identified by convalescent baboon serum and 748 by nasopharyngeal wash. Thirteen antigens were identified as immunogenic in baboons, essential for persistence in the airway by TraDIS, and membrane-localized: BP0840 (OmpP), Pal, OmpA2, BP1485, BamA, Pcp, MlaA, YfgL, BP2197, BP1569, MlaD, ComL, and BP0183. CONCLUSIONS The B. pertussis antigens identified as immunogenic, essential for persistence in the airway, and membrane-localized warrant further investigation for inclusion in vaccines designed to reduce or prevent carriage of bacteria in the airway of vaccinated individuals.
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Affiliation(s)
- Kelsey A Gregg
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yihui Wang
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jason Warfel
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Elizabeth Schoenfeld
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Ewa Jankowska
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - John F Cipollo
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | | | | | - Deepika Prasad
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Timothy J Brickman
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sandra K Armstrong
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | | | | | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA.,Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - James F Papin
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Roman Wolf
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Tod J Merkel
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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2
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Korlević P, McAlister E, Mayho M, Makunin A, Flicek P, Lawniczak MKN. A Minimally Morphologically Destructive Approach for DNA Retrieval and Whole-Genome Shotgun Sequencing of Pinned Historic Dipteran Vector Species. Genome Biol Evol 2021; 13:evab226. [PMID: 34599327 PMCID: PMC8536546 DOI: 10.1093/gbe/evab226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2021] [Indexed: 01/08/2023] Open
Abstract
Museum collections contain enormous quantities of insect specimens collected over the past century, covering a period of increased and varied insecticide usage. These historic collections are therefore incredibly valuable as genomic snapshots of organisms before, during, and after exposure to novel selective pressures. However, these samples come with their own challenges compared with present-day collections, as they are fragile and retrievable DNA is low yield and fragmented. In this article, we tested several DNA extraction procedures across pinned historic Diptera specimens from four disease vector genera: Anopheles, Aedes, Culex, and Glossina. We identify an approach that minimizes morphological damage while maximizing DNA retrieval for Illumina library preparation and sequencing that can accommodate the fragmented and low yield nature of historic DNA. We identify several key points in retrieving sufficient DNA while keeping morphological damage to a minimum: an initial rehydration step, a short incubation without agitation in a modified low salt Proteinase K buffer (referred to as "lysis buffer C" throughout), and critical point drying of samples post-extraction to prevent tissue collapse caused by air drying. The suggested method presented here provides a solid foundation for exploring the genomes and morphology of historic Diptera collections.
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Affiliation(s)
- Petra Korlević
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Erica McAlister
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Matthew Mayho
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alex Makunin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mara K N Lawniczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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3
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Abd El Ghany M, Barquist L, Clare S, Brandt C, Mayho M, Joffre´ E, Sjöling Å, Turner AK, Klena JD, Kingsley RA, Hill-Cawthorne GA, Dougan G, Pickard D. Functional analysis of colonization factor antigen I positive enterotoxigenic Escherichia coli identifies genes implicated in survival in water and host colonization. Microb Genom 2021; 7:000554. [PMID: 34110281 PMCID: PMC8461466 DOI: 10.1099/mgen.0.000554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) expressing the colonization pili CFA/I are common causes of diarrhoeal infections in humans. Here, we use a combination of transposon mutagenesis and transcriptomic analysis to identify genes and pathways that contribute to ETEC persistence in water environments and colonization of a mammalian host. ETEC persisting in water exhibit a distinct RNA expression profile from those growing in richer media. Multiple pathways were identified that contribute to water survival, including lipopolysaccharide biosynthesis and stress response regulons. The analysis also indicated that ETEC growing in vivo in mice encounter a bottleneck driving down the diversity of colonizing ETEC populations.
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Affiliation(s)
- Moataz Abd El Ghany
- The Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
- The Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Simon Clare
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Cordelia Brandt
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Mayho
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Enrique Joffre´
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - A. Keith Turner
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - John D. Klena
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Robert A. Kingsley
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Gordon Dougan
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Derek Pickard
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
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4
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Belcher T, MacArthur I, King JD, Langridge GC, Mayho M, Parkhill J, Preston A. Fundamental differences in physiology of Bordetella pertussis dependent on the two-component system Bvg revealed by gene essentiality studies. Microb Genom 2020; 6:mgen000496. [PMID: 33295860 PMCID: PMC8116675 DOI: 10.1099/mgen.0.000496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/30/2020] [Indexed: 11/18/2022] Open
Abstract
The identification of genes essential for a bacterium's growth reveals much about its basic physiology under different conditions. Bordetella pertussis, the causative agent of whooping cough, adopts both virulent and avirulent states through the activity of the two-component system, Bvg. The genes essential for B. pertussis growth in vitro were defined using transposon sequencing, for different Bvg-determined growth states. In addition, comparison of the insertion indices of each gene between Bvg phases identified those genes whose mutation exerted a significantly different fitness cost between phases. As expected, many of the genes identified as essential for growth in other bacteria were also essential for B. pertussis. However, the essentiality of some genes was dependent on Bvg. In particular, a number of key cell wall biosynthesis genes, including the entire mre/mrd locus, were essential for growth of the avirulent (Bvg minus) phase but not the virulent (Bvg plus) phase. In addition, cell wall biosynthesis was identified as a fundamental process that when disrupted produced greater fitness costs for the Bvg minus phase compared to the Bvg plus phase. Bvg minus phase growth was more susceptible than Bvg plus phase growth to the cell wall-disrupting antibiotic ampicillin, demonstrating the increased susceptibility of the Bvg minus phase to disruption of cell wall synthesis. This Bvg-dependent conditional essentiality was not due to Bvg-regulation of expression of cell wall biosynthesis genes; suggesting that this fundamental process differs between the Bvg phases in B. pertussis and is more susceptible to disruption in the Bvg minus phase. The ability of a bacterium to modify its cell wall synthesis is important when considering the action of antibiotics, particularly if developing novel drugs targeting cell wall synthesis.
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Affiliation(s)
- Thomas Belcher
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
- Present address: Institute Pasteur Lille, Lille, France
| | - Iain MacArthur
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Jerry D. King
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - Gemma C. Langridge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Present address: Quadram Institute, Norwich, UK
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Present address: Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew Preston
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
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5
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Karlinsey JE, Stepien TA, Mayho M, Singletary LA, Bingham-Ramos LK, Brehm MA, Greiner DL, Shultz LD, Gallagher LA, Bawn M, Kingsley RA, Libby SJ, Fang FC. Genome-wide Analysis of Salmonella enterica serovar Typhi in Humanized Mice Reveals Key Virulence Features. Cell Host Microbe 2019; 26:426-434.e6. [PMID: 31447308 DOI: 10.1016/j.chom.2019.08.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/03/2019] [Accepted: 07/31/2019] [Indexed: 11/29/2022]
Abstract
Salmonella enterica serovar Typhi causes typhoid fever only in humans. Murine infection with S. Typhimurium is used as a typhoid model, but its relevance to human typhoid is limited. Non-obese diabetic-scid IL2rγnull mice engrafted with human hematopoietic stem cells (hu-SRC-SCID) are susceptible to lethal S. Typhi infection. In this study, we use a high-density S. Typhi transposon library in hu-SRC-SCID mice to identify virulence loci using transposon-directed insertion site sequencing (TraDIS). Vi capsule, lipopolysaccharide (LPS), and aromatic amino acid biosynthesis were essential for virulence, along with the siderophore salmochelin. However, in contrast to the murine S. Typhimurium model, neither the PhoPQ two-component system nor the SPI-2 pathogenicity island was required for lethal S. Typhi infection, nor was the CdtB typhoid toxin. These observations highlight major differences in the pathogenesis of typhoid and non-typhoidal Salmonella infections and demonstrate the utility of humanized mice for understanding the pathogenesis of a human-specific pathogen.
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Affiliation(s)
- Joyce E Karlinsey
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Taylor A Stepien
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | | | | | | | - Michael A Brehm
- Program in Molecular Medicine and the Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dale L Greiner
- Program in Molecular Medicine and the Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - Larry A Gallagher
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich, UK; Earlham Institute, Norwich, UK
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich, UK; School of Biological Science, University of East Anglia, Norwich, UK
| | - Stephen J Libby
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Ferric C Fang
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA.
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6
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Boinett CJ, Cain AK, Hawkey J, Do Hoang NT, Khanh NNT, Thanh DP, Dordel J, Campbell JI, Lan NPH, Mayho M, Langridge GC, Hadfield J, Chau NVV, Thwaites GE, Parkhill J, Thomson NR, Holt KE, Baker S. Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. Microb Genom 2019; 5. [PMID: 30720421 PMCID: PMC6421349 DOI: 10.1099/mgen.0.000246] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The increasing incidence and emergence of multi-drug resistant (MDR) Acinetobacter baumannii has become a major global health concern. Colistin is a historic antimicrobial that has become commonly used as a treatment for MDR A. baumannii infections. The increase in colistin usage has been mirrored by an increase in colistin resistance. We aimed to identify the mechanisms associated with colistin resistance in A. baumannii using multiple high-throughput-sequencing technologies, including transposon-directed insertion site sequencing (TraDIS), RNA sequencing (RNAseq) and whole-genome sequencing (WGS) to investigate the genotypic changes of colistin resistance in A. baumannii. Using TraDIS, we found that genes involved in drug efflux (adeIJK), and phospholipid (mlaC, mlaF and mlaD) and lipooligosaccharide synthesis (lpxC and lpsO) were required for survival in sub-inhibitory concentrations of colistin. Transcriptomic (RNAseq) analysis revealed that expression of genes encoding efflux proteins (adeI, adeC, emrB, mexB and macAB) was enhanced in in vitro generated colistin-resistant strains. WGS of these organisms identified disruptions in genes involved in lipid A (lpxC) and phospholipid synthesis (mlaA), and in the baeS/R two-component system (TCS). We additionally found that mutations in the pmrB TCS genes were the primary colistin-resistance-associated mechanisms in three Vietnamese clinical colistin-resistant A. baumannii strains. Our results outline the entire range of mechanisms employed in A. baumannii for resistance against colistin, including drug extrusion and the loss of lipid A moieties by gene disruption or modification.
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Affiliation(s)
- Christine J Boinett
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Amy K Cain
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,4Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Jane Hawkey
- 5Centre for Systems Genomics, University of Melbourne, Melbourne, Victoria, Australia.,6Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia.,7Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Nhu Tran Do Hoang
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhu Nguyen Thi Khanh
- 8School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Duy Pham Thanh
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Janina Dordel
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,9Department of Biology, Drexel University, Philadelphia 19104, PA, USA
| | - James I Campbell
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Nguyen Phu Huong Lan
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,10Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Matthew Mayho
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Gemma C Langridge
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,11Norwich Medical School, University of East Anglia, Norwich, UK
| | - James Hadfield
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | | | - Guy E Thwaites
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Julian Parkhill
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nicholas R Thomson
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,12Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Kathryn E Holt
- 5Centre for Systems Genomics, University of Melbourne, Melbourne, Victoria, Australia.,6Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen Baker
- 2Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,13Medicine, The University of Cambridge, Cambridge, UK.,3Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
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7
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Vohra P, Chaudhuri RR, Mayho M, Vrettou C, Chintoan-Uta C, Thomson NR, Hope JC, Hopkins J, Stevens MP. Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle. BMC Genomics 2019; 20:20. [PMID: 30621582 PMCID: PMC6325888 DOI: 10.1186/s12864-018-5319-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/27/2018] [Indexed: 01/05/2023] Open
Abstract
Background Salmonella enterica subspecies enterica is an animal and zoonotic pathogen of global importance. Cattle are a significant reservoir of human non-typhoidal salmonellosis and can suffer enteric and systemic disease owing to the ability of Salmonella to survive within the bovine lymphatic system and intestines. Contamination of food can occur due to the incorporation of contaminated peripheral lymph nodes or by direct contamination of carcasses with gut contents. It is essential to understand the mechanisms used by Salmonella to enter and persist within the bovine lymphatic system and how they differ from those required for intestinal colonization to minimize zoonotic infections. Results Transposon-directed insertion site sequencing (TraDIS) was applied to pools of mutants recovered from mesenteric lymph nodes (MLNs) draining the distal ileum of calves after oral inoculation with a library of 8550 random S. Typhimurium mini-Tn5Km2 mutants in pools of 475 mutants per calf. A total of 8315 mutants representing 2852 different genes were detected in MLNs and their in vivo fitness was calculated. Using the same improved algorithm for analysis of transposon-flanking sequences, the identity and phenotype of mutants recovered from the distal ileal mucosa of the same calves was also defined, enabling comparison with previously published data and of mutant phenotypes across the tissues. Phenotypes observed for the majority of mutants were highly significantly correlated in the two tissues. However, 32 genes were identified in which transposon insertions consistently resulted in differential fitness in the ileal wall and MLNs, suggesting niche-specific roles for these genes in pathogenesis. Defined null mutations affecting ptsN and spvC were confirmed to result in tissue-specific phenotypes in calves, thus validating the TraDIS dataset. Conclusions This validation of the role of thousands of Salmonella genes and identification of genes with niche-specific roles in a key target species will inform the design of control strategies for bovine salmonellosis and zoonotic infections, for which efficacious and cross-protective vaccines are currently lacking. Electronic supplementary material The online version of this article (10.1186/s12864-018-5319-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Prerna Vohra
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.
| | - Roy R Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield, S10 2TN, Sheffield, UK
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Christina Vrettou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Cosmin Chintoan-Uta
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | | | - Jayne C Hope
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - John Hopkins
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Mark P Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
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8
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Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ, Mayho M, Goulding D, Charles IG, Filloux A, Parkhill J, Cain AK. A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa. Microb Genom 2018; 4. [PMID: 30383525 PMCID: PMC6321873 DOI: 10.1099/mgen.0.000229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is an extremely successful pathogen able to cause both acute and chronic infections in a range of hosts, utilizing a diverse arsenal of cell-associated and secreted virulence factors. A major cell-associated virulence factor, the Type IV pilus (T4P), is required for epithelial cell adherence and mediates a form of surface translocation termed twitching motility, which is necessary to establish a mature biofilm and actively expand these biofilms. P. aeruginosa twitching motility-mediated biofilm expansion is a coordinated, multicellular behaviour, allowing cells to rapidly colonize surfaces, including implanted medical devices. Although at least 44 proteins are known to be involved in the biogenesis, assembly and regulation of the T4P, with additional regulatory components and pathways implicated, it is unclear how these components and pathways interact to control these processes. In the current study, we used a global genomics-based random-mutagenesis technique, transposon directed insertion-site sequencing (TraDIS), coupled with a physical segregation approach, to identify all genes implicated in twitching motility-mediated biofilm expansion in P. aeruginosa. Our approach allowed identification of both known and novel genes, providing new insight into the complex molecular network that regulates this process in P. aeruginosa. Additionally, our data suggest that the flagellum-associated gene products have a differential effect on twitching motility, based on whether components are intra- or extracellular. Overall the success of our TraDIS approach supports the use of this global genomic technique for investigating virulence genes in bacterial pathogens.
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Affiliation(s)
- Laura M Nolan
- 1MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Cynthia B Whitchurch
- 2The ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Lars Barquist
- 3Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany.,4Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Marilyn Katrib
- 2The ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Christine J Boinett
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,†Present address: Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Matthew Mayho
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - David Goulding
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian G Charles
- 6Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK
| | - Alain Filloux
- 1MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Julian Parkhill
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Amy K Cain
- 5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,‡Present address: Chemical and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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9
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Zhang M, Wang C, Otto TD, Oberstaller J, Liao X, Adapa SR, Udenze K, Bronner IF, Casandra D, Mayho M, Brown J, Li S, Swanson J, Rayner JC, Jiang RHY, Adams JH. Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science 2018; 360:360/6388/eaap7847. [PMID: 29724925 DOI: 10.1126/science.aap7847] [Citation(s) in RCA: 512] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022]
Abstract
Severe malaria is caused by the apicomplexan parasite Plasmodium falciparum. Despite decades of research, the distinct biology of these parasites has made it challenging to establish high-throughput genetic approaches to identify and prioritize therapeutic targets. Using transposon mutagenesis of P. falciparum in an approach that exploited its AT-rich genome, we generated more than 38,000 mutants, saturating the genome and defining mutability and fitness costs for over 87% of genes. Of 5399 genes, our study defined 2680 genes as essential for optimal growth of asexual blood stages in vitro. These essential genes are associated with drug resistance, represent leading vaccine candidates, and include approximately 1000 Plasmodium-conserved genes of unknown function. We validated this approach by testing proteasome pathways for individual mutants associated with artemisinin sensitivity.
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Affiliation(s)
- Min Zhang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Jenna Oberstaller
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Xiangyun Liao
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Kenneth Udenze
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Iraad F Bronner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Deborah Casandra
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Matthew Mayho
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Jacqueline Brown
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Suzanne Li
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Justin Swanson
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK.
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
| | - John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
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10
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Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, Holt KE, Parkhill J, Thomson NR. Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. Sci Rep 2018; 8:9868. [PMID: 29959380 PMCID: PMC6026146 DOI: 10.1038/s41598-018-28199-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 06/08/2018] [Indexed: 11/09/2022] Open
Abstract
Colistin remains one of the few antibiotics effective against multi-drug resistant (MDR) hospital pathogens, such as Klebsiella pneumoniae. Yet resistance to this last-line drug is rapidly increasing. Characterized mechanisms of colR in K. pneumoniae are largely due to chromosomal mutations in two-component regulators, although a plasmid-mediated colR mechanism has recently been uncovered. However, the effects of intrinsic colistin resistance are yet to be characterized on a whole-genome level. Here, we used a genomics-based approach to understand the mechanisms of adaptive colR acquisition in K. pneumoniae. In controlled directed-evolution experiments we observed two distinct paths to colistin resistance acquisition. Whole genome sequencing identified mutations in two colistin resistance genes: in the known colR regulator phoQ which became fixed in the population and resulted in a single amino acid change, and unstable minority variants in the recently described two-component sensor crrB. Through RNAseq and microscopy, we reveal the broad range of effects that colistin exposure has on the cell. This study is the first to use genomics to identify a population of minority variants with mutations in a colR gene in K. pneumoniae.
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Affiliation(s)
- Amy K Cain
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia.
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Würzburg, D-97080, Germany
| | - Janina Dordel
- Department of Biology, Drexel University, Philadelphia, 19104, PA, USA
| | - Maria Fookes
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - David Goulding
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ryan R Wick
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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11
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Friedrich MJ, Rad L, Bronner IF, Strong A, Wang W, Weber J, Mayho M, Ponstingl H, Engleitner T, Grove C, Pfaus A, Saur D, Cadiñanos J, Quail MA, Vassiliou GS, Liu P, Bradley A, Rad R. Genome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice. Nat Protoc 2017; 12:289-309. [PMID: 28079877 DOI: 10.1038/nprot.2016.164] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transposon-mediated forward genetics screening in mice has emerged as a powerful tool for cancer gene discovery. It pinpoints cancer drivers that are difficult to find with other approaches, thus complementing the sequencing-based census of human cancer genes. We describe here a large series of mouse lines for insertional mutagenesis that are compatible with two transposon systems, PiggyBac and Sleeping Beauty, and give guidance on the use of different engineered transposon variants for constitutive or tissue-specific cancer gene discovery screening. We also describe a method for semiquantitative transposon insertion site sequencing (QiSeq). The QiSeq library preparation protocol exploits acoustic DNA fragmentation to reduce bias inherent to widely used restriction-digestion-based approaches for ligation-mediated insertion site amplification. Extensive multiplexing in combination with next-generation sequencing allows affordable ultra-deep transposon insertion site recovery in high-throughput formats within 1 week. Finally, we describe principles of data analysis and interpretation for obtaining insights into cancer gene function and genetic tumor evolution.
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Affiliation(s)
| | - Lena Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Iraad F Bronner
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Wei Wang
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Julia Weber
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthew Mayho
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Hannes Ponstingl
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Thomas Engleitner
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Carolyn Grove
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Anja Pfaus
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dieter Saur
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Juan Cadiñanos
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK.,Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
| | - Michael A Quail
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - George S Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Roland Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
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12
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Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge GC, Quail MA, Keane JA, Parkhill J. The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. Bioinformatics 2016; 32:1109-11. [PMID: 26794317 PMCID: PMC4896371 DOI: 10.1093/bioinformatics/btw022] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/13/2016] [Indexed: 12/05/2022] Open
Abstract
Summary: Transposon insertion sequencing is a high-throughput technique for assaying large libraries of otherwise isogenic transposon mutants providing insight into gene essentiality, gene function and genetic interactions. We previously developed the Transposon Directed Insertion Sequencing (TraDIS) protocol for this purpose, which utilizes shearing of genomic DNA followed by specific PCR amplification of transposon-containing fragments and Illumina sequencing. Here we describe an optimized high-yield library preparation and sequencing protocol for TraDIS experiments and a novel software pipeline for analysis of the resulting data. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. This article can serve as a general reference for the application of the TraDIS methodology. Availability and implementation: The optimized sequencing protocol is included as supplementary information. The Bio-Tradis analysis pipeline is available under a GPL license at https://github.com/sanger-pathogens/Bio-Tradis Contact:parkhill@sanger.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and Institute for Molecular Infection Biology, University of Würzburg, Würzburg D-97080, Germany
| | - Matthew Mayho
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Carla Cummins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | | | - Andrew J Page
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Gemma C Langridge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
| | | | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK and
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13
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Rad R, Rad L, Wang W, Strong A, Ponstingl H, Bronner IF, Mayho M, Steiger K, Weber J, Hieber M, Veltkamp C, Eser S, Geumann U, Öllinger R, Zukowska M, Barenboim M, Maresch R, Cadiñanos J, Friedrich M, Varela I, Constantino-Casas F, Sarver A, Ten Hoeve J, Prosser H, Seidler B, Bauer J, Heikenwälder M, Metzakopian E, Krug A, Ehmer U, Schneider G, Knösel T, Rümmele P, Aust D, Grützmann R, Pilarsky C, Ning Z, Wessels L, Schmid RM, Quail MA, Vassiliou G, Esposito I, Liu P, Saur D, Bradley A. A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer. Nat Genet 2014; 47:47-56. [PMID: 25485836 DOI: 10.1038/ng.3164] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/12/2014] [Indexed: 01/02/2023]
Abstract
Here we describe a conditional piggyBac transposition system in mice and report the discovery of large sets of new cancer genes through a pancreatic insertional mutagenesis screen. We identify Foxp1 as an oncogenic transcription factor that drives pancreatic cancer invasion and spread in a mouse model and correlates with lymph node metastasis in human patients with pancreatic cancer. The propensity of piggyBac for open chromatin also enabled genome-wide screening for cancer-relevant noncoding DNA, which pinpointed a Cdkn2a cis-regulatory region. Histologically, we observed different tumor subentities and discovered associated genetic events, including Fign insertions in hepatoid pancreatic cancer. Our studies demonstrate the power of genetic screening to discover cancer drivers that are difficult to identify by other approaches to cancer genome analysis, such as downstream targets of commonly mutated human cancer genes. These piggyBac resources are universally applicable in any tissue context and provide unique experimental access to the genetic complexity of cancer.
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Affiliation(s)
- Roland Rad
- 1] Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany. [2] German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany. [3] The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Lena Rad
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Wei Wang
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Hannes Ponstingl
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Iraad F Bronner
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Matthew Mayho
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Katja Steiger
- Department of Pathology, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Julia Weber
- 1] Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany. [2] German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maren Hieber
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Christian Veltkamp
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Stefan Eser
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Ulf Geumann
- 1] Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany. [2] German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rupert Öllinger
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Magdalena Zukowska
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Maxim Barenboim
- 1] Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany. [2] German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roman Maresch
- 1] Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany. [2] German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
| | - Mathias Friedrich
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (UC-CSIC-SODERCAN), Santander, Spain
| | | | - Aaron Sarver
- Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jelle Ten Hoeve
- Bioinformatics and Statistics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Haydn Prosser
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Barbara Seidler
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Judith Bauer
- Institute of Virology, Technische Universität München, Munich, Germany
| | | | | | - Anne Krug
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Ursula Ehmer
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Thomas Knösel
- Institute of Pathology, Ludwig Maximilians Universität München, München, Germany
| | - Petra Rümmele
- Institute of Pathology, Universität Regensburg, Regensburg, Germany
| | - Daniela Aust
- Institute of Pathology, Technische Universität Dresden, Dresden, Germany
| | - Robert Grützmann
- Department of Surgery, Technische Universität Dresden, Dresden, Germany
| | | | - Zemin Ning
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Lodewyk Wessels
- Bioinformatics and Statistics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roland M Schmid
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany
| | - Michael A Quail
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - George Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Irene Esposito
- Institute of Pathology, Medizinische Universität Insbruck, Insbruck, Austria
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
| | - Dieter Saur
- 1] Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, München, Germany. [2] German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
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14
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Luan SL, Chaudhuri RR, Peters SE, Mayho M, Weinert LA, Crowther SA, Wang J, Langford PR, Rycroft A, Wren BW, Tucker AW, Maskell DJ. Generation of a Tn5 transposon library in Haemophilus parasuis and analysis by transposon-directed insertion-site sequencing (TraDIS). Vet Microbiol 2013; 166:558-66. [PMID: 23928120 DOI: 10.1016/j.vetmic.2013.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/11/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
Haemophilus parasuis is an important respiratory tract pathogen of swine and the etiological agent of Glässer's disease. The molecular pathogenesis of H. parasuis is not well studied, mainly due to the lack of efficient tools for genetic manipulation of this bacterium. In this study we describe a Tn5-based random mutagenesis method for use in H. parasuis. A novel chloramphenicol-resistant Tn5 transposome was electroporated into the virulent H. parasuis serovar 5 strain 29755. High transposition efficiency of Tn5, up to 10(4) transformants/μg of transposon DNA, was obtained by modification of the Tn5 DNA in the H. parasuis strain HS071 and establishment of optimal electrotransformation conditions, and a library of approximately 10,500 mutants was constructed. Analysis of the library using transposon-directed insertion-site sequencing (TraDIS) revealed that the insertion of Tn5 was evenly distributed throughout the genome. 10,001 individual mutants were identified, with 1561 genes being disrupted (69.4% of the genome). This newly-developed, efficient mutagenesis approach will be a powerful tool for genetic manipulation of H. parasuis in order to study its physiology and pathogenesis.
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Affiliation(s)
- Shi-Lu Luan
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
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15
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Quail MA, Gu Y, Swerdlow H, Mayho M. Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation. Electrophoresis 2012; 33:3521-8. [PMID: 23147856 DOI: 10.1002/elps.201200128] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 04/25/2012] [Accepted: 05/12/2012] [Indexed: 11/11/2022]
Abstract
Size selection can be a critical step in preparation of next-generation sequencing libraries. Traditional methods employing gel electrophoresis lack reproducibility, are labour intensive, do not scale well and employ hazardous interchelating dyes. In a high-throughput setting, solid-phase reversible immobilisation beads are commonly used for size-selection, but result in quite a broad fragment size range. We have evaluated and optimised the use of two semi-automated preparative DNA electrophoresis systems, the Caliper Labchip XT and the Sage Science Pippin Prep, for size selection of Illumina sequencing libraries.
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Affiliation(s)
- Michael A Quail
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
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16
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Wilkinson P, Waterfield NR, Crossman L, Corton C, Sanchez-Contreras M, Vlisidou I, Barron A, Bignell A, Clark L, Ormond D, Mayho M, Bason N, Smith F, Simmonds M, Churcher C, Harris D, Thompson NR, Quail M, Parkhill J, Ffrench-Constant RH. Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens. BMC Genomics 2009; 10:302. [PMID: 19583835 PMCID: PMC2717986 DOI: 10.1186/1471-2164-10-302] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 07/07/2009] [Indexed: 01/05/2023] Open
Abstract
Background The Gram-negative bacterium Photorhabdus asymbiotica (Pa) has been recovered from human infections in both North America and Australia. Recently, Pa has been shown to have a nematode vector that can also infect insects, like its sister species the insect pathogen P. luminescens (Pl). To understand the relationship between pathogenicity to insects and humans in Photorhabdus we have sequenced the complete genome of Pa strain ATCC43949 from North America. This strain (formerly referred to as Xenorhabdus luminescens strain 2) was isolated in 1977 from the blood of an 80 year old female patient with endocarditis, in Maryland, USA. Here we compare the complete genome of Pa ATCC43949 with that of the previously sequenced insect pathogen P. luminescens strain TT01 which was isolated from its entomopathogenic nematode vector collected from soil in Trinidad and Tobago. Results We found that the human pathogen Pa had a smaller genome (5,064,808 bp) than that of the insect pathogen Pl (5,688,987 bp) but that each pathogen carries approximately one megabase of DNA that is unique to each strain. The reduced size of the Pa genome is associated with a smaller diversity in insecticidal genes such as those encoding the Toxin complexes (Tc's), Makes caterpillars floppy (Mcf) toxins and the Photorhabdus Virulence Cassettes (PVCs). The Pa genome, however, also shows the addition of a plasmid related to pMT1 from Yersinia pestis and several novel pathogenicity islands including a novel Type Three Secretion System (TTSS) encoding island. Together these data suggest that Pa may show virulence against man via the acquisition of the pMT1-like plasmid and specific effectors, such as SopB, that promote its persistence inside human macrophages. Interestingly the loss of insecticidal genes in Pa is not reflected by a loss of pathogenicity towards insects. Conclusion Our results suggest that North American isolates of Pa have acquired virulence against man via the acquisition of a plasmid and specific virulence factors with similarity to those shown to play roles in pathogenicity against humans in other bacteria.
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Affiliation(s)
- Paul Wilkinson
- School of Biosciences, University of Exeter in Cornwall, Penryn TR10 9EZ, UK.
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Mayho M, Fenn K, Craddy P, Crosthwaite S, Matthews K. Post-transcriptional control of nuclear-encoded cytochrome oxidase subunits in Trypanosoma brucei: evidence for genome-wide conservation of life-cycle stage-specific regulatory elements. Nucleic Acids Res 2006; 34:5312-24. [PMID: 17012283 PMCID: PMC1636420 DOI: 10.1093/nar/gkl598] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Trypanosomes represent an excellent model for the post-transcriptional regulation of gene expression because their genome is organized into polycistronic transcription units. However, few signals governing developmental stage-specific expression have been identified, with there being no compelling evidence for widespread conservation of regulatory motifs. As a tool to search for common regulatory sequences we have used the nuclear-encoded components of the cytochrome oxidase (COX) complex of the trypanosome respiratory chain. Components of this complex represent a form of post-transcriptional operon because trypanosome mitochondrial activity is unusual in being developmentally programmed. By genome analysis we identified the genes for seven components of the COX complex. Each mRNA exhibits bloodstream stage-specific instability, which is not mediated by the RNA silencing pathway but which is alleviated by cycloheximide. Reporter assays have identified regulatory regions within the 3′-untranslated regions of three COX mRNAs operating principally at the translational level, but also via mRNA stability. Interrogation of the mapped regions via oligonucleotide frequency scoring provides evidence for genome-wide conservation of regulatory sequences among a large cohort of procyclic-enriched transcripts. Analysis of the co-regulated subunits of a stage-specific enzyme is therefore a novel approach to uncover cryptic regulatory sequences controlling gene expression at the post-transcriptional level.
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Affiliation(s)
- Matthew Mayho
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King's BuildingsWest Mains Road, Edinburgh EH9 3JT, UK
- Faculty of Life Sciences, The University of ManchesterMichael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Katelyn Fenn
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King's BuildingsWest Mains Road, Edinburgh EH9 3JT, UK
| | - Paul Craddy
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King's BuildingsWest Mains Road, Edinburgh EH9 3JT, UK
| | - Susan Crosthwaite
- Faculty of Life Sciences, The University of ManchesterMichael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Keith Matthews
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King's BuildingsWest Mains Road, Edinburgh EH9 3JT, UK
- To whom correspondence should be addressed. Tel: +44 131 651 3639; Fax: +44 131 651 3670;
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