101
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Cain AK, Barquist L, Goodman AL, Paulsen IT, Parkhill J, van Opijnen T. A decade of advances in transposon-insertion sequencing. Nat Rev Genet 2020; 21:526-540. [PMID: 32533119 PMCID: PMC7291929 DOI: 10.1038/s41576-020-0244-x] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2020] [Indexed: 01/12/2023]
Abstract
It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications. In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.
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Affiliation(s)
- Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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102
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Zhu L, Olsen RJ, Beres SB, Saavedra MO, Kubiak SL, Cantu CC, Jenkins L, Waller AS, Sun Z, Palzkill T, Porter AR, DeLeo FR, Musser JM. Streptococcus pyogenes genes that promote pharyngitis in primates. JCI Insight 2020; 5:137686. [PMID: 32493846 DOI: 10.1172/jci.insight.137686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/30/2020] [Indexed: 02/02/2023] Open
Abstract
Streptococcus pyogenes (group A streptococcus; GAS) causes 600 million cases of pharyngitis annually worldwide. There is no licensed human GAS vaccine despite a century of research. Although the human oropharynx is the primary site of GAS infection, the pathogenic genes and molecular processes used to colonize, cause disease, and persist in the upper respiratory tract are poorly understood. Using dense transposon mutant libraries made with serotype M1 and M28 GAS strains and transposon-directed insertion sequencing, we performed genome-wide screens in the nonhuman primate (NHP) oropharynx. We identified many potentially novel GAS fitness genes, including a common set of 115 genes that contribute to fitness in both genetically distinct GAS strains during experimental NHP pharyngitis. Targeted deletion of 4 identified fitness genes/operons confirmed that our newly identified targets are critical for GAS virulence during experimental pharyngitis. Our screens discovered many surface-exposed or secreted proteins - substrates for vaccine research - that potentially contribute to GAS pharyngitis, including lipoprotein HitA. Pooled human immune globulin reacted with purified HitA, suggesting that humans produce antibodies against this lipoprotein. Our findings provide new information about GAS fitness in the upper respiratory tract that may assist in translational research, including developing novel vaccines.
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Affiliation(s)
- Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Stephen B Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Samantha L Kubiak
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Concepcion C Cantu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Leslie Jenkins
- Department of Comparative Medicine, Houston Methodist Research Institute, Houston, Texas, USA
| | - Andrew S Waller
- Animal Health Trust, Lanwades Park, Newmarket, United Kingdom
| | - Zhizeng Sun
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Adeline R Porter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, Montana, USA
| | - Frank R DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, Montana, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
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103
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Schinner S, Engelhardt F, Preusse M, Thöming JG, Tomasch J, Häussler S. Genetic determinants of Pseudomonas aeruginosa fitness during biofilm growth. Biofilm 2020; 2:100023. [PMID: 33447809 PMCID: PMC7798452 DOI: 10.1016/j.bioflm.2020.100023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas aeruginosa is an environmental bacterium and an opportunistic human pathogen. It is also a well-established model organism to study bacterial adaptation to stressful conditions, such as those encountered during an infection process in the human host. Advancing knowledge on P. aeruginosa adaptation to biofilm growth conditions is bound to reveal novel strategies and targets for the treatment of chronic biofilm-associated infections. Here, we generated transposon insertion libraries in three P. aeruginosa strain backgrounds and determined the relative frequency of each insertion following biofilm growth using transposon sequencing. We demonstrate that in general the SOS response, several tRNA modifying enzymes as well as adaptation to microaerophilic growth conditions play a key role in bacterial survival under biofilm growth conditions. On the other hand, presence of genes involved in motility and PQS signaling were less important during biofilm growth. Several mutants exhibiting transposon insertions in genes detected in our screen were validated for their biofilm growth capabilities and biofilm specific transcriptional responses using independently generated transposon mutants. Our results provide new insights into P. aeruginosa adaptation to biofilm growth conditions. The detection of previously unknown determinants of biofilm survival supports the use of transposon insertion sequencing as a global genomic technology for understanding the establishment of difficult to treat biofilm-associated infections.
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Affiliation(s)
- Silvia Schinner
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Florian Engelhardt
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Janne Gesine Thöming
- Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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104
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Charbonneau ARL, Taylor E, Mitchell CJ, Robinson C, Cain AK, Leigh JA, Maskell DJ, Waller AS. Identification of genes required for the fitness of Streptococcus equi subsp. equi in whole equine blood and hydrogen peroxide. Microb Genom 2020; 6:e000362. [PMID: 32228801 PMCID: PMC7276704 DOI: 10.1099/mgen.0.000362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/12/2020] [Indexed: 12/25/2022] Open
Abstract
The availability of next-generation sequencing techniques provides an unprecedented opportunity for the assignment of gene function. Streptococcus equi subspecies equi is the causative agent of strangles in horses, one of the most prevalent and important diseases of equids worldwide. However, the live attenuated vaccines that are utilized to control this disease cause adverse reactions in some animals. Here, we employ transposon-directed insertion-site sequencing (TraDIS) to identify genes that are required for the fitness of S. equi in whole equine blood or in the presence of H2O2 to model selective pressures exerted by the equine immune response during infection. We report the fitness values of 1503 and 1471 genes, representing 94.5 and 92.5 % of non-essential genes in S. equi, following incubation in whole blood and in the presence of H2O2, respectively. Of these genes, 36 and 15 were identified as being important to the fitness of S. equi in whole blood or H2O2, respectively, with 14 genes being important in both conditions. Allelic replacement mutants were generated to validate the fitness results. Our data identify genes that are important for S. equi to resist aspects of the immune response in vitro, which can be exploited for the development of safer live attenuated vaccines to prevent strangles.
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Affiliation(s)
- Amelia R. L. Charbonneau
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Emma Taylor
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | | | - Carl Robinson
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Amy K. Cain
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - James A. Leigh
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Duncan J. Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- University of Melbourne, Victoria, Australia
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105
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Genome-Wide Screens Identify Group A Streptococcus Surface Proteins Promoting Female Genital Tract Colonization and Virulence. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:862-873. [PMID: 32200972 DOI: 10.1016/j.ajpath.2019.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/04/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023]
Abstract
Group A streptococcus (GAS) is a major pathogen that impacts health and economic affairs worldwide. Although the oropharynx is the primary site of infection, GAS can colonize the female genital tract and cause severe diseases, such as puerperal sepsis, neonatal infections, and necrotizing myometritis. Our understanding of how GAS genes contribute to interaction with the primate female genital tract is limited by the lack of relevant animal models. Using two genome-wide transposon mutagenesis screens, we identified 69 GAS genes required for colonization of the primate vaginal mucosa in vivo and 96 genes required for infection of the uterine wall ex vivo. We discovered a common set of 39 genes important for GAS fitness in both environments. They include genes encoding transporters, surface proteins, transcriptional regulators, and metabolic pathways. Notably, the genes that encode the surface-exclusion protein (SpyAD) and the immunogenic secreted protein 2 (Isp2) were found to be crucial for GAS fitness in the female primate genital tract. Targeted gene deletion confirmed that isogenic mutant strains ΔspyAD and Δisp2 are significantly impaired in ability to colonize the primate genital tract and cause uterine wall pathologic findings. Our studies identified novel GAS genes that contribute to female reproductive tract interaction that warrant translational research investigation.
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106
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Fabian BK, Tetu SG, Paulsen IT. Application of Transposon Insertion Sequencing to Agricultural Science. FRONTIERS IN PLANT SCIENCE 2020; 11:291. [PMID: 32256512 PMCID: PMC7093568 DOI: 10.3389/fpls.2020.00291] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/26/2020] [Indexed: 06/11/2023]
Abstract
Many plant-associated bacteria have the ability to positively affect plant growth and there is growing interest in utilizing such bacteria in agricultural settings to reduce reliance on pesticides and fertilizers. However, our capacity to utilize microbes in this way is currently limited due to patchy understanding of bacterial-plant interactions at a molecular level. Traditional methods of studying molecular interactions have sought to characterize the function of one gene at a time, but the slow pace of this work means the functions of the vast majority of bacterial genes remain unknown or poorly understood. New approaches to improve and speed up investigations into the functions of bacterial genes in agricultural systems will facilitate efforts to optimize microbial communities and develop microbe-based products. Techniques enabling high-throughput gene functional analysis, such as transposon insertion sequencing analyses, have great potential to be widely applied to determine key aspects of plant-bacterial interactions. Transposon insertion sequencing combines saturation transposon mutagenesis and high-throughput sequencing to simultaneously investigate the function of all the non-essential genes in a bacterial genome. This technique can be used for both in vitro and in vivo studies to identify genes involved in microbe-plant interactions, stress tolerance and pathogen virulence. The information provided by such investigations will rapidly accelerate the rate of bacterial gene functional determination and provide insights into the genes and pathways that underlie biotic interactions, metabolism, and survival of agriculturally relevant bacteria. This knowledge could be used to select the most appropriate plant growth promoting bacteria for a specific set of conditions, formulating crop inoculants, or developing crop protection products. This review provides an overview of transposon insertion sequencing, outlines how this approach has been applied to study plant-associated bacteria, and proposes new applications of these techniques for the benefit of agriculture.
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Affiliation(s)
- Belinda K. Fabian
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sasha G. Tetu
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T. Paulsen
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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107
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Sonnabend MS, Klein K, Beier S, Angelov A, Kluj R, Mayer C, Groß C, Hofmeister K, Beuttner A, Willmann M, Peter S, Oberhettinger P, Schmidt A, Autenrieth IB, Schütz M, Bohn E. Identification of Drug Resistance Determinants in a Clinical Isolate of Pseudomonas aeruginosa by High-Density Transposon Mutagenesis. Antimicrob Agents Chemother 2020; 64:e01771-19. [PMID: 31818817 PMCID: PMC7038268 DOI: 10.1128/aac.01771-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/25/2019] [Indexed: 01/02/2023] Open
Abstract
With the aim to identify potential new targets to restore antimicrobial susceptibility of multidrug-resistant (MDR) Pseudomonas aeruginosa isolates, we generated a high-density transposon (Tn) insertion mutant library in an MDR P. aeruginosa bloodstream isolate (isolate ID40). The depletion of Tn insertion mutants upon exposure to cefepime or meropenem was measured in order to determine the common resistome for these clinically important antipseudomonal β-lactam antibiotics. The approach was validated by clean deletions of genes involved in peptidoglycan synthesis/recycling, such as the genes for the lytic transglycosylase MltG, the murein (Mur) endopeptidase MepM1, the MurNAc/GlcNAc kinase AmgK, and the uncharacterized protein YgfB, all of which were identified in our screen as playing a decisive role in survival after treatment with cefepime or meropenem. We found that the antibiotic resistance of P. aeruginosa can be overcome by targeting usually nonessential genes that turn essential in the presence of therapeutic concentrations of antibiotics. For all validated genes, we demonstrated that their deletion leads to the reduction of ampC expression, resulting in a significant decrease in β-lactamase activity, and consequently, these mutants partly or completely lost resistance against cephalosporins, carbapenems, and acylaminopenicillins. In summary, the determined resistome may comprise promising targets for the development of drugs that may be used to restore sensitivity to existing antibiotics, specifically in MDR strains of P. aeruginosa.
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Affiliation(s)
- Michael S Sonnabend
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Kristina Klein
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Sina Beier
- Center for Bioinformatics (ZBIT), Universität Tübingen, Tübingen, Germany
| | - Angel Angelov
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Robert Kluj
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Department of Biology, Microbiology & Biotechnology, Universität Tübingen, Tübingen, Germany
| | - Christoph Mayer
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Department of Biology, Microbiology & Biotechnology, Universität Tübingen, Tübingen, Germany
| | - Caspar Groß
- Institut für Medizinische Genetik und Angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Kathrin Hofmeister
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Antonia Beuttner
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Matthias Willmann
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Silke Peter
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Philipp Oberhettinger
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Annika Schmidt
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Ingo B Autenrieth
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Monika Schütz
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Erwin Bohn
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
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108
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Yasir M, Turner AK, Bastkowski S, Baker D, Page AJ, Telatin A, Phan MD, Monahan L, Savva GM, Darling A, Webber MA, Charles IG. TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance. Genome Res 2020; 30:239-249. [PMID: 32051187 PMCID: PMC7050523 DOI: 10.1101/gr.254391.119] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 01/17/2020] [Indexed: 01/14/2023]
Abstract
Understanding the genetic basis for a phenotype is a central goal in biological research. Much has been learnt about bacterial genomes by creating large mutant libraries and looking for conditionally important genes. However, current genome-wide methods are largely unable to assay essential genes which are not amenable to disruption. To overcome this limitation, we developed a new version of "TraDIS" (transposon directed insertion-site sequencing) that we term "TraDIS-Xpress" that combines an inducible promoter into the transposon cassette. This allows controlled overexpression and repression of all genes owing to saturation of inserts adjacent to all open reading frames as well as conventional inactivation. We applied TraDIS-Xpress to identify responses to the biocide triclosan across a range of concentrations. Triclosan is endemic in modern life, but there is uncertainty about its mode of action with a concentration-dependent switch from bacteriostatic to bactericidal action unexplained. Our results show a concentration-dependent response to triclosan with different genes important in survival between static and cidal exposures. These genes include those previously reported to have a role in triclosan resistance as well as a new set of genes, including essential genes. Novel genes identified as being sensitive to triclosan exposure include those involved in barrier function, small molecule uptake, and integrity of transcription and translation. We anticipate the approach we show here, by allowing comparisons across multiple experimental conditions of TraDIS data, and including essential genes, will be a starting point for future work examining how different drug conditions impact bacterial survival mechanisms.
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Affiliation(s)
- Muhammad Yasir
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - A Keith Turner
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Sarah Bastkowski
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - David Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Queensland, Australia
| | - Leigh Monahan
- Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Aaron Darling
- Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
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109
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Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Baym M, Ibba M, Hinton JCD. The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid. PLoS Pathog 2019; 15:e1007948. [PMID: 31560731 PMCID: PMC6785131 DOI: 10.1371/journal.ppat.1007948] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 10/09/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
We have used a transposon insertion sequencing (TIS) approach to establish the fitness landscape of the African Salmonella enterica serovar Typhimurium ST313 strain D23580, to complement our previous comparative genomic and functional transcriptomic studies. We used a genome-wide transposon library with insertions every 10 nucleotides to identify genes required for survival and growth in vitro and during infection of murine macrophages. The analysis revealed genomic regions important for fitness under two in vitro growth conditions. Overall, 724 coding genes were required for optimal growth in LB medium, and 851 coding genes were required for growth in SPI-2-inducing minimal medium. These findings were consistent with the essentiality analyses of other S. Typhimurium ST19 and S. Typhi strains. The global mutagenesis approach also identified 60 sRNAs and 413 intergenic regions required for growth in at least one in vitro growth condition. By infecting murine macrophages with the transposon library, we identified 68 genes that were required for intra-macrophage replication but did not impact fitness in vitro. None of these genes were unique to S. Typhimurium D23580, consistent with a high conservation of gene function between S. Typhimurium ST313 and ST19 and suggesting that novel virulence factors are not involved in the interaction of strain D23580 with murine macrophages. We discovered that transposon insertions rarely occurred in many pBT1 plasmid-encoded genes (36), compared with genes carried by the pSLT-BT virulence plasmid and other bacterial plasmids. The key essential protein encoded by pBT1 is a cysteinyl-tRNA synthetase, and our enzymological analysis revealed that the plasmid-encoded CysRSpBT1 had a lower ability to charge tRNA than the chromosomally-encoded CysRSchr enzyme. The presence of aminoacyl-tRNA synthetases in plasmids from a range of Gram-negative and Gram-positive bacteria suggests that plasmid-encoded essential genes are more common than had been appreciated.
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Affiliation(s)
- Rocío Canals
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Roy R Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Rebecca E Steiner
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America.,Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Siân V Owen
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Natalia Quinones-Olvera
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Melita A Gordon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi, Central Africa
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America.,Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Jay C D Hinton
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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110
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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: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [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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111
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Ondari EM, Klemm EJ, Msefula CL, El Ghany MA, Heath JN, Pickard DJ, Barquist L, Dougan G, Kingsley RA, MacLennan CA. Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313. Wellcome Open Res 2019; 4:74. [PMID: 31231691 PMCID: PMC6560496 DOI: 10.12688/wellcomeopenres.15059.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2019] [Indexed: 11/20/2022] Open
Abstract
Background:
Salmonella Typhimurium ST313 exhibits signatures of adaptation to invasive human infection, including higher resistance to humoral immune responses than gastrointestinal isolates. Full resistance to antibody-mediated complement killing (serum resistance) among nontyphoidal
Salmonellae is uncommon, but selection of highly resistant strains could compromise vaccine-induced antibody immunity. Here, we address the hypothesis that serum resistance is due to a distinct genotype or transcriptome response in
S. Typhimurium ST313. Methods: Six
S. Typhimurium ST313 bloodstream isolates, three of which were antibody resistant, were studied. Genomic content (single nucleotide polymorphisms and larger chromosomal modifications) of the strains was determined by Illumina and PACBIO sequencing, and functionally characterized using RNA-seq, transposon directed insertion site sequencing (TraDIS), targeted gene deletion and transfer of selected point mutations in an attempt to identify features associated with serum resistance.
Results: Sequence polymorphisms in genes from strains with atypical serum susceptibility when transferred from strains that were highly resistant or susceptible to a strain that exhibited intermediate susceptibility did not significantly alter serum killing phenotype. No large chromosomal modifications typified serum resistance or susceptibility. Genes required for resistance to serum identified by TraDIS and RNA-seq included those involved in exopolysaccharide synthesis, iron scavenging and metabolism. Most of the down-regulated genes were associated with membrane proteins. Resistant and susceptible strains had distinct transcriptional responses to serum, particularly related to genes responsible for polysaccharide biosynthesis. There was higher upregulation of
wca locus genes, involved in the biosynthesis of colanic acid exopolysaccharide, in susceptible strains and increased expression of
fepE, a regulator of very long-chain lipopolysaccharide in resistant strains. Conclusion: Clinical isolates of
S. Typhimurium ST313 exhibit distinct antibody susceptibility phenotypes that may be associated with changes in gene expression on exposure to serum.
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Affiliation(s)
- Edna M Ondari
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Novartis Vaccines Institute for Global Health, Siena, Italy.,Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Chisomo L Msefula
- Wellcome Trust Sanger Institute, Hinxton, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Institute, Blantyre, Malawi.,Department of Microbiology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Moataz Abd El Ghany
- Wellcome Trust Sanger Institute, Hinxton, UK.,The Westmead Institute for Medical Research and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead, Australia.,King Abdullah University of Science and Technology , Thuwal, Saudi Arabia
| | - Jennifer N Heath
- Institute of Immunology and Immuotherapy, University of Birmingham, Birmingham, UK
| | | | - Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, UK.,Helmholtz Institute for RNA-based Infection Research , Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Medicine, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, UK
| | | | - Calman A MacLennan
- Institute of Immunology and Immuotherapy, University of Birmingham, Birmingham, UK.,Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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112
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Atanaskovic I, Kleanthous C. Tools and Approaches for Dissecting Protein Bacteriocin Import in Gram-Negative Bacteria. Front Microbiol 2019; 10:646. [PMID: 31001227 PMCID: PMC6455109 DOI: 10.3389/fmicb.2019.00646] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022] Open
Abstract
Bacteriocins of Gram-negative bacteria are typically multi-domain proteins that target and kill bacteria of the same or closely related species. There is increasing interest in protein bacteriocin import; from a fundamental perspective to understand how folded proteins are imported into bacteria and from an applications perspective as species-specific antibiotics to combat multidrug resistant bacteria. In order to translocate across the cell envelope and cause cell death, protein bacteriocins hijack nutrient uptake pathways. Their import is energized by parasitizing intermembrane protein complexes coupled to the proton motive force, which delivers a toxic domain into the cell. A plethora of genetic, structural, biochemical, and biophysical methods have been applied to find cell envelope components involved in bacteriocin import since their discovery almost a century ago. Here, we review the various approaches that now exist for investigating how protein bacteriocins translocate into Gram-negative bacteria and highlight areas of research that will need methodological innovations to fully understand this process. We also highlight recent studies demonstrating how bacteriocins can be used to probe organization and architecture of the Gram-negative cell envelope itself.
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Affiliation(s)
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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113
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Global Analysis of Genes Essential for Francisella tularensis Schu S4 Growth In Vitro and for Fitness during Competitive Infection of Fischer 344 Rats. J Bacteriol 2019; 201:JB.00630-18. [PMID: 30642993 PMCID: PMC6416918 DOI: 10.1128/jb.00630-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/02/2019] [Indexed: 01/02/2023] Open
Abstract
The highly virulent intracellular pathogen Francisella tularensis is a Gram-negative bacterium that has a wide host range, including humans, and is the causative agent of tularemia. To identify new therapeutic drug targets and vaccine candidates and investigate the genetic basis of Francisella virulence in the Fischer 344 rat, we have constructed an F. tularensis Schu S4 transposon library. This library consists of more than 300,000 unique transposon mutants and represents a transposon insertion for every 6 bp of the genome. A transposon-directed insertion site sequencing (TraDIS) approach was used to identify 453 genes essential for growth in vitro Many of these essential genes were mapped to key metabolic pathways, including glycolysis/gluconeogenesis, peptidoglycan synthesis, fatty acid biosynthesis, and the tricarboxylic acid (TCA) cycle. Additionally, 163 genes were identified as required for fitness during colonization of the Fischer 344 rat spleen. This in vivo selection screen was validated through the generation of marked deletion mutants that were individually assessed within a competitive index study against the wild-type F. tularensis Schu S4 strain.IMPORTANCE The intracellular bacterial pathogen Francisella tularensis causes a disease in humans characterized by the rapid onset of nonspecific symptoms such as swollen lymph glands, fever, and headaches. F. tularensis is one of the most infectious bacteria known and following pulmonary exposure can have a mortality rate exceeding 50% if left untreated. The low infectious dose of this organism and concerns surrounding its potential as a biological weapon have heightened the need for effective and safe therapies. To expand the repertoire of targets for therapeutic development, we initiated a genome-wide analysis. This study has identified genes that are important for F. tularensis under in vitro and in vivo conditions, providing candidates that can be evaluated for vaccine or antibacterial development.
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114
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Sharp C, Boinett C, Cain A, Housden NG, Kumar S, Turner K, Parkhill J, Kleanthous C. O-Antigen-Dependent Colicin Insensitivity of Uropathogenic Escherichia coli. J Bacteriol 2019; 201:e00545-18. [PMID: 30510143 PMCID: PMC6351738 DOI: 10.1128/jb.00545-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
The outer membrane of Gram-negative bacteria presents a significant barrier for molecules entering the cell. Nevertheless, colicins, which are antimicrobial proteins secreted by Escherichia coli, can target other E. coli cells by binding to cell surface receptor proteins and activating their import, resulting in cell death. Previous studies have documented high rates of nonspecific resistance (insensitivity) of various E. coli strains toward colicins that is independent of colicin-specific immunity and is instead associated with lipopolysaccharide (LPS) in the outer membrane. This observation poses a contradiction: why do E. coli strains have colicin-expressing plasmids, which are energetically costly to retain, if cells around them are likely to be naturally insensitive to the colicin they produce? Here, using a combination of transposon sequencing and phenotypic microarrays, we show that colicin insensitivity of uropathogenic E. coli sequence type 131 (ST131) is dependent on the production of its O-antigen but that minor changes in growth conditions render the organism sensitive toward colicins. The reintroduction of O-antigen into E. coli K-12 demonstrated that it is the density of O-antigen that is the dominant factor governing colicin insensitivity. We also show, by microscopy of fluorescently labelled colicins, that growth conditions affect the degree of occlusion by O-antigen of outer membrane receptors but not the clustered organization of receptors. The result of our study demonstrate that environmental conditions play a critical role in sensitizing E. coli toward colicins and that O-antigen in LPS is central to this role.IMPORTANCEEscherichia coli infections can be a major health burden, especially with the organism becoming increasingly resistant to "last-resort" antibiotics such as carbapenems. Although colicins are potent narrow-spectrum antimicrobials with potential as future antibiotics, high levels of naturally occurring colicin insensitivity have been documented which could limit their efficacy. We identify O-antigen-dependent colicin insensitivity in a clinically relevant uropathogenic E. coli strain and show that this insensitivity can be circumvented by minor changes to growth conditions. The results of our study suggest that colicin insensitivity among E. coli organisms has been greatly overestimated, and as a consequence, colicins could in fact be effective species-specific antimicrobials targeting pathogenic E. coli such as uropathogenic E. coli (UPEC).
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Affiliation(s)
- Connor Sharp
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Amy Cain
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Macquarie University, Sydney, Australia
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sandip Kumar
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Keith Turner
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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115
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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: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [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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116
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Zhu L, Olsen RJ, Beres SB, Eraso JM, Saavedra MO, Kubiak SL, Cantu CC, Jenkins L, Charbonneau ARL, Waller AS, Musser JM. Gene fitness landscape of group A streptococcus during necrotizing myositis. J Clin Invest 2019; 129:887-901. [PMID: 30667377 PMCID: PMC6355216 DOI: 10.1172/jci124994] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022] Open
Abstract
Necrotizing fasciitis and myositis are devastating infections characterized by high mortality. Group A streptococcus (GAS) is a common cause of these infections, but the molecular pathogenesis is poorly understood. We report a genome-wide analysis using serotype M1 and M28 strains that identified GAS genes contributing to necrotizing myositis in nonhuman primates (NHP), a clinically relevant model. Using transposon-directed insertion-site sequencing (TraDIS), we identified 126 and 116 GAS genes required for infection by serotype M1 and M28 organisms, respectively. For both M1 and M28 strains, more than 25% of the GAS genes required for necrotizing myositis encode known or putative transporters. Thirteen GAS transporters contributed to both M1 and M28 strain fitness in NHP myositis, including putative importers for amino acids, carbohydrates, and vitamins and exporters for toxins, quorum-sensing peptides, and uncharacterized molecules. Targeted deletion of genes encoding 5 transporters confirmed that each isogenic mutant strain was significantly (P < 0.05) impaired in causing necrotizing myositis in NHPs. Quantitative reverse-transcriptase PCR (qRT-PCR) analysis showed that these 5 genes are expressed in infected NHP and human skeletal muscle. Certain substrate-binding lipoproteins of these transporters, such as Spy0271 and Spy1728, were previously documented to be surface exposed, suggesting that our findings have translational research implications.
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Affiliation(s)
- Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J. Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Stephen B. Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Jesus M. Eraso
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Samantha L. Kubiak
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Concepcion C. Cantu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Leslie Jenkins
- Department of Comparative Medicine, Houston Methodist Research Institute, Houston, Texas, USA
| | - Amelia R. L. Charbonneau
- Animal Health Trust, Newmarket, Suffolk, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
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117
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Hill HR. Fitness genes of group A streptococci in necrotizing fasciitis and myositis. J Clin Invest 2019; 129:516-517. [DOI: 10.1172/jci126482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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118
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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: 2.0] [Reference Citation Analysis] [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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119
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Canals R, Hammarlöf DL, Kröger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J, Monack DM, Kingsley RA, Brownridge P, Chaudhuri RR, Rowe WPM, Predeus AV, Hokamp K, Gordon MA, Hinton JCD. Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580. PLoS Biol 2019; 17:e3000059. [PMID: 30645593 PMCID: PMC6333337 DOI: 10.1371/journal.pbio.3000059] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Salmonella Typhimurium sequence type (ST) 313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV+, malarial, or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580 and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in 16 infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium, SalComD23580: http://bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl. We discovered that the ablation of melibiose utilization was caused by three independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolize this carbon source has been negatively selected during ST313 evolution. The data revealed a novel, to our knowledge, plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multicondition analyses to pinpoint key phenotypic differences between bacterial pathovariants.
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Affiliation(s)
- Rocío Canals
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Disa L. Hammarlöf
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Carsten Kröger
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Siân V. Owen
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Wai Yee Fong
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Lizeth Lacharme-Lora
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Xiaojun Zhu
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Nicolas Wenner
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sarah E. Carden
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jared Honeycutt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Denise M. Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Philip Brownridge
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Roy R. Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Will P. M. Rowe
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Alexander V. Predeus
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Melita A. Gordon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Malawi, Central Africa
| | - Jay C. D. Hinton
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Lorenz A, Preuße M, Bruchmann S, Pawar V, Grahl N, Pils MC, Nolan LM, Filloux A, Weiss S, Häussler S. Importance of flagella in acute and chronicPseudomonas aeruginosainfections. Environ Microbiol 2018; 21:883-897. [DOI: 10.1111/1462-2920.14468] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Anne Lorenz
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| | - Matthias Preuße
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| | - Sebastian Bruchmann
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
- Wellcome Sanger Institute Cambridge UK
| | - Vinay Pawar
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Immunology, Medical School Hannover Hannover Germany
| | - Nora Grahl
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| | - Marina C. Pils
- Mouse PathologyAnimal Experimental Unit, Helmholtz Centre for Infection Research Braunschweig Germany
| | - Laura M. Nolan
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life SciencesImperial College London London UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life SciencesImperial College London London UK
| | - Siegfried Weiss
- Institute of Immunology, Medical School Hannover Hannover Germany
| | - Susanne Häussler
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
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Dorman MJ, Feltwell T, Goulding DA, Parkhill J, Short FL. The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort. mBio 2018; 9:e01863-18. [PMID: 30459193 PMCID: PMC6247091 DOI: 10.1128/mbio.01863-18] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/08/2018] [Indexed: 01/04/2023] Open
Abstract
Klebsiella pneumoniae infections affect infants and the immunocompromised, and the recent emergence of hypervirulent and multidrug-resistant K. pneumoniae lineages is a critical health care concern. Hypervirulence in K. pneumoniae is mediated by several factors, including the overproduction of extracellular capsule. However, the full details of how K. pneumoniae capsule biosynthesis is achieved or regulated are not known. We have developed a robust and sensitive procedure to identify genes influencing capsule production, density-TraDISort, which combines density gradient centrifugation with transposon insertion sequencing. We have used this method to explore capsule regulation in two clinically relevant Klebsiella strains, K. pneumoniae NTUH-K2044 (capsule type K1) and K. pneumoniae ATCC 43816 (capsule type K2). We identified multiple genes required for full capsule production in K. pneumoniae, as well as putative suppressors of capsule in NTUH-K2044, and have validated the results of our screen with targeted knockout mutants. Further investigation of several of the K. pneumoniae capsule regulators identified-ArgR, MprA/KvrB, SlyA/KvrA, and the Sap ABC transporter-revealed effects on capsule amount and architecture, serum resistance, and virulence. We show that capsule production in K. pneumoniae is at the center of a complex regulatory network involving multiple global regulators and environmental cues and that the majority of capsule regulatory genes are located in the core genome. Overall, our findings expand our understanding of how capsule is regulated in this medically important pathogen and provide a technology that can be easily implemented to study capsule regulation in other bacterial species.IMPORTANCE Capsule production is essential for K. pneumoniae to cause infections, but its regulation and mechanism of synthesis are not fully understood in this organism. We have developed and applied a new method for genome-wide identification of capsule regulators. Using this method, many genes that positively or negatively affect capsule production in K. pneumoniae were identified, and we use these data to propose an integrated model for capsule regulation in this species. Several of the genes and biological processes identified have not previously been linked to capsule synthesis. We also show that the methods presented here can be applied to other species of capsulated bacteria, providing the opportunity to explore and compare capsule regulatory networks in other bacterial strains and species.
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Affiliation(s)
- Matthew J Dorman
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Theresa Feltwell
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David A Goulding
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Francesca L Short
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit. BMC Genomics 2018; 19:822. [PMID: 30442113 PMCID: PMC6238374 DOI: 10.1186/s12864-018-5197-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/23/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudomonas syringae is a widespread bacterial species complex that includes a number of significant plant pathogens. Amongst these, P. syringae pv. actinidiae (Psa) initiated a worldwide pandemic in 2008 on cultivars of Actinidia chinensis var. chinensis. To gain information about the expression of genes involved in pathogenicity we have carried out transcriptome analysis of Psa during the early stages of kiwifruit infection. RESULTS Gene expression in Psa was investigated during the first five days after infection of kiwifruit plantlets, using RNA-seq. Principal component and heatmap analyses showed distinct phases of gene expression during the time course of infection. The first phase was an immediate transient peak of induction around three hours post inoculation (HPI) that included genes that code for a Type VI Secretion System and nutrient acquisition (particularly phosphate). This was followed by a significant commitment, between 3 and 24 HPI, to the induction of genes encoding the Type III Secretion System (T3SS) and Type III Secreted Effectors (T3SE). Expression of these genes collectively accounted for 6.3% of the bacterial transcriptome at this stage. There was considerable variation in the expression levels of individual T3SEs but all followed the same temporal expression pattern, with the exception of hopAS1, which peaked later in expression at 48 HPI. As infection progressed over the time course of five days, there was an increase in the expression of genes with roles in sugar, amino acid and sulfur transport and the production of alginate and colanic acid. These are both polymers that are major constituents of extracellular polysaccharide substances (EPS) and are involved in biofilm production. Reverse transcription-quantitative PCR (RT-qPCR) on an independent infection time course experiment showed that the expression profile of selected bacterial genes at each infection phase correlated well with the RNA-seq data. CONCLUSIONS The results from this study indicate that there is a complex remodeling of the transcriptome during the early stages of infection, with at least three distinct phases of coordinated gene expression. These include genes induced during the immediate contact with the host, those involved in the initiation of infection, and finally those responsible for nutrient acquisition.
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Rousset F, Cui L, Siouve E, Becavin C, Depardieu F, Bikard D. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PLoS Genet 2018; 14:e1007749. [PMID: 30403660 PMCID: PMC6242692 DOI: 10.1371/journal.pgen.1007749] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/19/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
High-throughput genetic screens are powerful methods to identify genes linked to a given phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be conveniently used to silence genes of interest in a method also known as CRISPRi. Here, we report a genome-wide CRISPR-dCas9 screen using a starting pool of ~ 92,000 sgRNAs which target random positions in the chromosome of E. coli. To benchmark our method, we first investigate its utility to predict gene essentiality in the genome of E. coli during growth in rich medium. We could identify 79% of the genes previously reported as essential and demonstrate the non-essentiality of some genes annotated as essential. In addition, we took advantage of the intermediate repression levels obtained when targeting the template strand of genes to show that cells are very sensitive to the expression level of a limited set of essential genes. Our data can be visualized on CRISPRbrowser, a custom web interface available at crispr.pasteur.fr. We then apply the screen to discover E. coli genes required by phages λ, T4 and 186 to kill their host, highlighting the involvement of diverse host pathways in the infection process of the three tested phages. We also identify colanic acid capsule synthesis as a shared resistance mechanism to all three phages. Finally, using a plasmid packaging system and a transduction assay, we identify genes required for the formation of functional λ capsids, thus covering the entire phage cycle. This study demonstrates the usefulness and convenience of pooled genome-wide CRISPR-dCas9 screens in bacteria and paves the way for their broader use as a powerful tool in bacterial genomics. Over the past few years, CRISPR-Cas technologies have emerged as powerful tools to edit genomes and modulate gene expression. They have been applied to perform high-throughput genetic screens with the purpose to understand the function of genes in a systematic manner, but the application of these screens to bacteria have so far remained limited. Here, we present the use of a library of ~92,000 guide RNAs directing the dCas9 protein to silence one by one all the genes in the chromosome of E. coli. To benchmark our method, we first investigate the performance of the technique to identify essential genes, highlighting several non-essential genes also found to be essential by other methods. We then apply our method to detect bacterial genes required by three different bacteriophages to kill E. coli and for the production of functional progeny by phage λ. Our screens highlight previously known and new genetic interactions between phages and their host’s pathways and emphasize the importance of bacterial capsule in the resistance to multiple phages. Altogether, our results demonstrate the usefulness of genome-wide CRISPR-dCas9 screens in bacteria to uncover genes involved in various phenotypes.
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Affiliation(s)
- François Rousset
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lun Cui
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Elise Siouve
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Christophe Becavin
- Hub Bioinformatique et Biostatistique, Institut Pasteur - C3BI, USR 3756 IP CNRS, Paris, France
| | - Florence Depardieu
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- * E-mail:
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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: 1.0] [Reference Citation Analysis] [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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125
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Rapid, Parallel Identification of Catabolism Pathways of Lignin-Derived Aromatic Compounds in Novosphingobium aromaticivorans. Appl Environ Microbiol 2018; 84:AEM.01185-18. [PMID: 30217841 DOI: 10.1128/aem.01185-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/05/2018] [Indexed: 11/20/2022] Open
Abstract
Transposon mutagenesis is a powerful technique in microbial genetics for the identification of genes in uncharacterized pathways. Recently, the throughput of transposon mutagenesis techniques has been dramatically increased through the combination of DNA barcoding and high-throughput sequencing. Here, we show that when applied to catabolic pathways, barcoded transposon libraries can be used to distinguish redundant pathways, decompose complex pathways into substituent modules, discriminate between enzyme homologs, and rapidly identify previously hypothetical enzymes in an unbiased genome-scale search. We used this technique to identify two genes, desC and desD, which are involved in the degradation of the lignin-derived aromatic compound sinapic acid in the nonmodel bacterium Novosphingobium aromaticivorans We show that DesC is a methyl esterase acting on an intermediate formed during sinapic acid catabolism, providing the last enzyme in a proposed catabolic pathway. This approach will be particularly useful in the identification of complete pathways suitable for heterologous expression in metabolic engineering.IMPORTANCE The identification of the genes involved in specific biochemical transformations is a key step in predicting microbial function from nucleic acid sequences and in engineering microbes to endow them with new functions. We have shown that new techniques for transposon mutagenesis can dramatically simplify this process and enable the rapid identification of genes in uncharacterized pathways. These techniques provide the necessary scale to fully elucidate complex biological networks such as those used to degrade mixtures of lignin-derived aromatic compounds.
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Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ, Day M, Perry N, Gally DL, Parkhill J, Jenkins C, Cain AK. Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157. mBio 2018. [PMID: 30042196 DOI: 10.1128/mbio] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Experiments using bacteriophage (phage) to infect bacterial strains have helped define some basic genetic concepts in microbiology, but our understanding of the complexity of bacterium-phage interactions is still limited. As the global threat of antibiotic resistance continues to increase, phage therapy has reemerged as an attractive alternative or supplement to treating antibiotic-resistant bacterial infections. Further, the long-used method of phage typing to classify bacterial strains is being replaced by molecular genetic techniques. Thus, there is a growing need for a complete understanding of the precise molecular mechanisms underpinning phage-bacterium interactions to optimize phage therapy for the clinic as well as for retrospectively interpreting phage typing data on the molecular level. In this study, a genomics-based fitness assay (TraDIS) was used to identify all host genes involved in phage susceptibility and resistance for a T4 phage infecting Shiga-toxigenic Escherichia coli O157. The TraDIS results identified both established and previously unidentified genes involved in phage infection, and a subset were confirmed by site-directed mutagenesis and phenotypic testing of 14 T4 and 2 T7 phages. For the first time, the entire sap operon was implicated in phage susceptibility and, conversely, the stringent starvation protein A gene (sspA) was shown to provide phage resistance. Identifying genes involved in phage infection and replication should facilitate the selection of bespoke phage combinations to target specific bacterial pathogens.IMPORTANCE Antibiotic resistance has diminished treatment options for many common bacterial infections. Phage therapy is an alternative option that was once popularly used across Europe to kill bacteria within humans. Phage therapy acts by using highly specific viruses (called phages) that infect and lyse certain bacterial species to treat the infection. Whole-genome sequencing has allowed modernization of the investigations into phage-bacterium interactions. Here, using E. coli O157 and T4 bacteriophage as a model, we have exploited a genome-wide fitness assay to investigate all genes involved in defining phage resistance or susceptibility. This knowledge of the genetic determinants of phage resistance and susceptibility can be used to design bespoke phage combinations targeted to specific bacterial infections for successful infection eradication.
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Affiliation(s)
- Lauren A Cowley
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alison S Low
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Martin Day
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Neil Perry
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - David L Gally
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ, Day M, Perry N, Gally DL, Parkhill J, Jenkins C, Cain AK. Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157. mBio 2018; 9:e00705-18. [PMID: 30042196 PMCID: PMC6058288 DOI: 10.1128/mbio.00705-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/27/2018] [Indexed: 01/01/2023] Open
Abstract
Experiments using bacteriophage (phage) to infect bacterial strains have helped define some basic genetic concepts in microbiology, but our understanding of the complexity of bacterium-phage interactions is still limited. As the global threat of antibiotic resistance continues to increase, phage therapy has reemerged as an attractive alternative or supplement to treating antibiotic-resistant bacterial infections. Further, the long-used method of phage typing to classify bacterial strains is being replaced by molecular genetic techniques. Thus, there is a growing need for a complete understanding of the precise molecular mechanisms underpinning phage-bacterium interactions to optimize phage therapy for the clinic as well as for retrospectively interpreting phage typing data on the molecular level. In this study, a genomics-based fitness assay (TraDIS) was used to identify all host genes involved in phage susceptibility and resistance for a T4 phage infecting Shiga-toxigenic Escherichia coli O157. The TraDIS results identified both established and previously unidentified genes involved in phage infection, and a subset were confirmed by site-directed mutagenesis and phenotypic testing of 14 T4 and 2 T7 phages. For the first time, the entire sap operon was implicated in phage susceptibility and, conversely, the stringent starvation protein A gene (sspA) was shown to provide phage resistance. Identifying genes involved in phage infection and replication should facilitate the selection of bespoke phage combinations to target specific bacterial pathogens.IMPORTANCE Antibiotic resistance has diminished treatment options for many common bacterial infections. Phage therapy is an alternative option that was once popularly used across Europe to kill bacteria within humans. Phage therapy acts by using highly specific viruses (called phages) that infect and lyse certain bacterial species to treat the infection. Whole-genome sequencing has allowed modernization of the investigations into phage-bacterium interactions. Here, using E. coli O157 and T4 bacteriophage as a model, we have exploited a genome-wide fitness assay to investigate all genes involved in defining phage resistance or susceptibility. This knowledge of the genetic determinants of phage resistance and susceptibility can be used to design bespoke phage combinations targeted to specific bacterial infections for successful infection eradication.
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Affiliation(s)
- Lauren A Cowley
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alison S Low
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Christine J Boinett
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Martin Day
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Neil Perry
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - David L Gally
- Division of Immunity and Infection, the Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Midlothian, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, Public Health England, London United Kingdom
| | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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Willcocks SJ, Stabler RA, Atkins HS, Oyston PF, Wren BW. High-throughput analysis of Yersinia pseudotuberculosis gene essentiality in optimised in vitro conditions, and implications for the speciation of Yersinia pestis. BMC Microbiol 2018; 18:46. [PMID: 29855259 PMCID: PMC5984423 DOI: 10.1186/s12866-018-1189-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/18/2018] [Indexed: 12/12/2022] Open
Abstract
Background Yersinia pseudotuberculosis is a zoonotic pathogen, causing mild gastrointestinal infection in humans. From this comparatively benign pathogenic species emerged the highly virulent plague bacillus, Yersinia pestis, which has experienced significant genetic divergence in a relatively short time span. Much of our knowledge of Yersinia spp. evolution stems from genomic comparison and gene expression studies. Here we apply transposon-directed insertion site sequencing (TraDIS) to describe the essential gene set of Y. pseudotuberculosis IP32953 in optimised in vitro growth conditions, and contrast these with the published essential genes of Y. pestis. Results The essential genes of an organism are the core genetic elements required for basic survival processes in a given growth condition, and are therefore attractive targets for antimicrobials. One such gene we identified is yptb3665, which encodes a peptide deformylase, and here we report for the first time, the sensitivity of Y. pseudotuberculosis to actinonin, a deformylase inhibitor. Comparison of the essential genes of Y. pseudotuberculosis with those of Y. pestis revealed the genes whose importance are shared by both species, as well as genes that were differentially required for growth. In particular, we find that the two species uniquely rely upon different iron acquisition and respiratory metabolic pathways under similar in vitro conditions. Conclusions The discovery of uniquely essential genes between the closely related Yersinia spp. represent some of the fundamental, species-defining points of divergence that arose during the evolution of Y. pestis from its ancestor. Furthermore, the shared essential genes represent ideal candidates for the development of novel antimicrobials against both species. Electronic supplementary material The online version of this article (10.1186/s12866-018-1189-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel J Willcocks
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Richard A Stabler
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Helen S Atkins
- Microbiology, CBR Division, DSTL Porton Down, Salisbury, SP4 0JQ, UK
| | - Petra F Oyston
- Microbiology, CBR Division, DSTL Porton Down, Salisbury, SP4 0JQ, UK
| | - Brendan W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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129
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Brockmeier SL, Loving CL, Nicholson TL, Wang J, Peters SE, Weinert L, Chaudhuri R, Seilly DJ, Langford PR, Rycroft A, Wren BW, Maskell DJ, Tucker AW. Use of Proteins Identified through a Functional Genomic Screen To Develop a Protein Subunit Vaccine That Provides Significant Protection against Virulent Streptococcus suis in Pigs. Infect Immun 2018; 86:e00559-17. [PMID: 29203546 PMCID: PMC5820948 DOI: 10.1128/iai.00559-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/28/2017] [Indexed: 11/20/2022] Open
Abstract
Streptococcus suis is a bacterium that is commonly carried in the respiratory tract and that is also one of the most important invasive pathogens of swine, commonly causing meningitis, arthritis, and septicemia. Due to the existence of many serotypes and a wide range of immune evasion capabilities, efficacious vaccines are not readily available. The selection of S. suis protein candidates for inclusion in a vaccine was accomplished by identifying fitness genes through a functional genomics screen and selecting conserved predicted surface-associated proteins. Five candidate proteins were selected for evaluation in a vaccine trial and administered both intranasally and intramuscularly with one of two different adjuvant formulations. Clinical protection was evaluated by subsequent intranasal challenge with virulent S. suis While subunit vaccination with the S. suis proteins induced IgG antibodies to each individual protein and a cellular immune response to the pool of proteins and provided substantial protection from challenge with virulent S. suis, the immune response elicited and the degree of protection were dependent on the parenteral adjuvant given. Subunit vaccination induced IgG reactive against different S. suis serotypes, indicating a potential for cross protection.
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Affiliation(s)
| | | | | | - Jinhong Wang
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah E Peters
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Roy Chaudhuri
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - David J Seilly
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Andrew Rycroft
- The Royal Veterinary College, Hawkshead Campus, Hatfield, Hertfordshire, United Kingdom
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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130
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Barquist L, Westermann AJ, Vogel J. Molecular phenotyping of infection-associated small non-coding RNAs. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0081. [PMID: 27672158 DOI: 10.1098/rstb.2016.0081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Infection is a complicated balance, with both pathogen and host struggling to tilt the result in their favour. Bacterial infection biology has relied on forward genetics for many of its advances, defining phenotype in terms of replication in model systems. However, many known virulence factors fail to produce robust phenotypes, particularly in the systems most amenable to genetic manipulation, such as cell-culture models. This has particularly been limiting for the study of the bacterial regulatory small RNAs (sRNAs) in infection. We argue that new sequencing-based technologies can work around this problem by providing a 'molecular phenotype', defined in terms of the specific transcriptional dysregulation in the infection system induced by gene deletion. We illustrate this using the example of our recent study of the PinT sRNA using dual RNA-seq, that is, simultaneous RNA sequencing of host and pathogen during infection. We additionally discuss how other high-throughput technologies, in particular genetic interaction mapping using transposon insertion sequencing, may be used to further dissect molecular phenotypes. We propose a strategy for how high-throughput technologies can be integrated in the study of non-coding regulators as well as bacterial virulence factors, enhancing our ability to rapidly generate hypotheses with regards to their function.This article is part of the themed issue 'The new bacteriology'.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Alexander J Westermann
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97070 Würzburg, Germany
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131
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Peng C, Lin Y, Luo H, Gao F. A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes. Front Microbiol 2017; 8:2331. [PMID: 29230204 PMCID: PMC5711816 DOI: 10.3389/fmicb.2017.02331] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022] Open
Abstract
Genes critical for the survival or reproduction of an organism in certain circumstances are classified as essential genes. Essential genes play a significant role in deciphering the survival mechanism of life. They may be greatly applied to pharmaceutics and synthetic biology. The continuous progress of experimental method for essential gene identification has accelerated the accumulation of gene essentiality data which facilitates the study of essential genes in silico. In this article, we present some available online resources related to gene essentiality, including bioinformatic software tools for transposon sequencing (Tn-seq) analysis, essential gene databases and online services to predict bacterial essential genes. We review several computational approaches that have been used to predict essential genes, and summarize the features used for gene essentiality prediction. In addition, we evaluate the available online bacterial essential gene prediction servers based on the experimentally validated essential gene sets of 30 bacteria from DEG. This article is intended to be a quick reference guide for the microbiologists interested in the essential genes.
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Affiliation(s)
- Chong Peng
- Department of Physics, School of Science, Tianjin University, Tianjin, China
| | - Yan Lin
- Department of Physics, School of Science, Tianjin University, Tianjin, China
| | - Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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132
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Novel Genes Required for the Fitness of Streptococcus pyogenes in Human Saliva. mSphere 2017; 2:mSphere00460-17. [PMID: 29104937 PMCID: PMC5663985 DOI: 10.1128/mspheredirect.00460-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 10/09/2017] [Indexed: 12/29/2022] Open
Abstract
Streptococcus pyogenes (group A streptococcus [GAS]) causes 600 million cases of pharyngitis each year. Despite this considerable disease burden, the molecular mechanisms used by GAS to infect, cause clinical pharyngitis, and persist in the human oropharynx are poorly understood. Saliva is ubiquitous in the human oropharynx and is the first material GAS encounters in the upper respiratory tract. Thus, a fuller understanding of how GAS survives and proliferates in saliva may provide valuable insights into the molecular mechanisms at work in the human oropharynx. We generated a highly saturated transposon insertion mutant library in serotype M1 strain MGAS2221, a strain genetically representative of a pandemic clone that arose in the 1980s and spread globally. The transposon mutant library was exposed to human saliva to screen for GAS genes required for wild-type fitness in this clinically relevant fluid. Using transposon-directed insertion site sequencing (TraDIS), we identified 92 genes required for GAS fitness in saliva. The more prevalent categories represented were genes involved in carbohydrate transport/metabolism, amino acid transport/metabolism, and inorganic ion transport/metabolism. Using six isogenic mutant strains, we confirmed that each of the mutants was significantly impaired for growth or persistence in human saliva ex vivo. Mutants with an inactivated Spy0644 (sptA) or Spy0646 (sptC) gene had especially severe persistence defects. This study is the first to use of TraDIS to study bacterial fitness in human saliva. The new information we obtained will be valuable for future translational maneuvers designed to prevent or treat human GAS infections. IMPORTANCE The human bacterial pathogen Streptococcus pyogenes (group A streptococcus [GAS]) causes more than 600 million cases of pharyngitis annually worldwide, 15 million of which occur in the United States. The human oropharynx is the primary anatomic site for GAS colonization and infection, and saliva is the first material encountered. Using a genome-wide transposon mutant screen, we identified 92 GAS genes required for wild-type fitness in human saliva. Many of the identified genes are involved in carbohydrate transport/metabolism, amino acid transport/metabolism, and inorganic ion transport/metabolism. The new information is potentially valuable for developing novel GAS therapeutics and vaccine research.
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133
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DeJesus MA, Nambi S, Smith CM, Baker RE, Sassetti CM, Ioerger TR. Statistical analysis of genetic interactions in Tn-Seq data. Nucleic Acids Res 2017; 45:e93. [PMID: 28334803 PMCID: PMC5499643 DOI: 10.1093/nar/gkx128] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/16/2017] [Indexed: 11/25/2022] Open
Abstract
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model. However, these have limitations which necessitate an improved approach. We present a hierarchical Bayesian method for identifying genetic interactions through quantifying the statistical significance of changes in enrichment. The analysis involves a four-way comparison of insertion counts across datasets to identify transposon mutants that differentially affect bacterial fitness depending on genetic background. Our approach was applied to Tn-Seq libraries made in isogenic strains of Mycobacterium tuberculosis lacking three different genes of unknown function previously shown to be necessary for optimal fitness during infection. By analyzing the libraries subjected to selection in mice, we were able to distinguish several distinct classes of genetic interactions for each target gene that shed light on their functions and roles during infection.
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Affiliation(s)
- Michael A DeJesus
- Department of Computer Science, Texas A&M University, College Station, TX 77843, USA
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue N., Worcester, MA 01655, USA
| | - Clare M Smith
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue N., Worcester, MA 01655, USA
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue N., Worcester, MA 01655, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue N., Worcester, MA 01655, USA
| | - Thomas R Ioerger
- Department of Computer Science, Texas A&M University, College Station, TX 77843, USA
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134
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Ruiz L, Bottacini F, Boinett CJ, Cain AK, O'Connell-Motherway M, Lawley TD, van Sinderen D. The essential genomic landscape of the commensal Bifidobacterium breve UCC2003. Sci Rep 2017; 7:5648. [PMID: 28717159 PMCID: PMC5514069 DOI: 10.1038/s41598-017-05795-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/02/2017] [Indexed: 01/15/2023] Open
Abstract
Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach. Statistical analysis of transposon insertion distribution revealed a set of 453 genes that are essential for or markedly contribute to growth of this strain under laboratory conditions. These essential genes encode functions involved in the so-called bifid-shunt, most enzymes related to nucleotide biosynthesis and a range of housekeeping functions. Comparison to the Bifidobacterium and B. breve core genomes highlights a high degree of conservation of essential genes at the species and genus level, while comparison to essential gene datasets from other gut bacteria identified essential genes that appear specific to bifidobacteria. This work establishes a useful molecular tool for scientific discovery of bifidobacteria and identifies targets for further studies aimed at characterizing essential functions not previously examined in bifidobacteria.
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Affiliation(s)
- Lorena Ruiz
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.,Department of Nutrition, Bromatology and Food Technology, Complutense University, Avda Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Francesca Bottacini
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mary O'Connell-Motherway
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.
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135
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Fyson N, King J, Belcher T, Preston A, Colijn C. A curated genome-scale metabolic model of Bordetella pertussis metabolism. PLoS Comput Biol 2017; 13:e1005639. [PMID: 28715411 PMCID: PMC5553986 DOI: 10.1371/journal.pcbi.1005639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 08/11/2017] [Accepted: 06/15/2017] [Indexed: 11/30/2022] Open
Abstract
The Gram-negative bacterium Bordetella pertussis is the causative agent of whooping cough, a serious respiratory infection causing hundreds of thousands of deaths annually worldwide. There are effective vaccines, but their production requires growing large quantities of B. pertussis. Unfortunately, B. pertussis has relatively slow growth in culture, with low biomass yields and variable growth characteristics. B. pertussis also requires a relatively expensive growth medium. We present a new, curated flux balance analysis-based model of B. pertussis metabolism. We enhance the model with an experimentally-determined biomass objective function, and we perform extensive manual curation. We test the model’s predictions with a genome-wide screen for essential genes using a transposon-directed insertional sequencing (TraDIS) approach. We test its predictions of growth for different carbon sources in the medium. The model predicts essentiality with an accuracy of 83% and correctly predicts improvements in growth under increased glutamate:fumarate ratios. We provide the model in SBML format, along with gene essentiality predictions. Metabolic flux models have been used to understand how organisms adapt their metabolism under different growth conditions, and are finding increasing application in synthetic biology and biotechnology. One barrier to progress in this field is the construction and curation of metabolic flux models for new organisms. Here we present a curated genome-scale metabolic flux model for Bordetella pertussis, the causative agent of whooping cough. Producing vaccines against whooping cough requires growing B. pertussis in large volumes. However, its growth is relatively slow, final yields of biomass are relatively low and growth characteristics can be variable. Understanding B. pertussis metabolism has applications to improving vaccine production, as well as in understanding the basic biology of this organism.
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Affiliation(s)
- Nick Fyson
- Department of Mathematics, Imperial College, London, UK
| | - Jerry King
- The Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Thomas Belcher
- The Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Andrew Preston
- The Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Caroline Colijn
- Department of Mathematics, Imperial College, London, UK
- * E-mail:
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136
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Charbonneau ARL, Forman OP, Cain AK, Newland G, Robinson C, Boursnell M, Parkhill J, Leigh JA, Maskell DJ, Waller AS. Defining the ABC of gene essentiality in streptococci. BMC Genomics 2017; 18:426. [PMID: 28569133 PMCID: PMC5452409 DOI: 10.1186/s12864-017-3794-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant libraries to specific conditions and subsequent sequencing can be exploited to uncover gene essentiality relevant to the condition. Here we present a barcoded transposon directed insertion-site sequencing (TraDIS) system to define an essential gene list for Streptococcus equi subsp. equi, the causative agent of strangles in horses, for the first time. The gene essentiality data for this group C Streptococcus was compared to that of group A and B streptococci. RESULTS Six barcoded variants of pGh9:ISS1 were designed and used to generate mutant libraries containing between 33,000-66,000 unique mutants. TraDIS was performed on DNA extracted from each library and data were analysed separately and as a combined master pool. Gene essentiality determined that 19.5% of the S. equi genome was essential. Gene essentialities were compared to those of group A and group B streptococci, identifying concordances of 90.2% and 89.4%, respectively and an overall concordance of 83.7% between the three species. CONCLUSIONS The use of barcoded pGh9:ISS1 to generate mutant libraries provides a highly useful tool for the assignment of gene function in S. equi and other streptococci. The shared essential gene set of group A, B and C streptococci provides further evidence of the close genetic relationships between these important pathogenic bacteria. Therefore, the ABC of gene essentiality reported here provides a solid foundation towards reporting the functional genome of streptococci.
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Affiliation(s)
- Amelia R L Charbonneau
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK. .,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | | | - Amy K Cain
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Graham Newland
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Carl Robinson
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Mike Boursnell
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - James A Leigh
- The School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, Nottingham, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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137
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Paulsen IT, Cain AK, Hassan KA. Physical enrichment of transposon mutants from saturation mutant libraries using the TraDISort approach. Mob Genet Elements 2017; 7:1-7. [PMID: 28580195 DOI: 10.1080/2159256x.2017.1313805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 03/27/2017] [Indexed: 12/21/2022] Open
Abstract
Transposon-insertion sequencing methods are finding their way into the molecular toolbox of many fields of microbiology. These methods can identify the genomic locations and density of transposon insertions in saturated transposon mutant libraries and can be used to make inferences on gene function. For example, where no insertions or very few insertions are identified within a gene in a mutant library grown under permissive conditions, the gene may be essential. Furthermore, where mutations are enriched or lost in a gene after passaging the library through a selective process, the gene is likely to be involved in phenotypes linked to the process. Typically, a fitness based selection such as a stress condition is used in these experiments and the processed sequencing data are used to identify genes required for fitness under the selection. Our research team recently expanded the utility of the transposon directed insertion sequencing (TraDIS) method by applying a physical separation of a transposon mutant library mediated by fluorescence activated cell sorting, rather than a fitness-based selection. This approach, which we have named "TraDISort" is significant because it allows the study of phenotypes that are not linked to cell survival. The TraDISort approach has a broad range of future applications, in drug development, metabolic engineering and in studies of basic bacterial cell physiology.
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Affiliation(s)
- Ian T Paulsen
- Department of Chemistry and Biomolecular Science, Macquarie University, North Ryde, NSW, Australia
| | - Amy K Cain
- Department of Chemistry and Biomolecular Science, Macquarie University, North Ryde, NSW, Australia.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Liverpool School Tropical Medicine, Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Karl A Hassan
- Department of Chemistry and Biomolecular Science, Macquarie University, North Ryde, NSW, Australia.,School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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138
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Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE 6013 Elements in Staphylococcus aureus. J Bacteriol 2017; 199:JB.00629-16. [PMID: 28138100 DOI: 10.1128/jb.00629-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/25/2017] [Indexed: 01/04/2023] Open
Abstract
ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013 Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013 A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.
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139
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Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells. Sci Rep 2017; 7:44736. [PMID: 28303933 PMCID: PMC5356192 DOI: 10.1038/srep44736] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/13/2017] [Indexed: 01/02/2023] Open
Abstract
Forward genetic screens using retroviral (or transposon) gene-trap vectors in a haploid genome revolutionized the investigation of molecular networks in mammals. However, the sequencing data generated by Phenotypic interrogation followed by Tag sequencing (PhiT-seq) were not well characterized. The analysis of human and mouse haploid screens allowed us to describe PhiT-seq data and to define quality control steps. Moreover, we identified several blind spots in both haploid genomes where gene-trap vectors can hardly integrate. Integration of transcriptomic data improved the performance of candidate gene identification. Furthermore, we experimented with various statistical tests to account for biological replicates in PhiT-seq and investigated the effect of normalization methods and other parameters on the performance. Finally, we developed: VISITs, a dedicated pipeline for analyzing PhiT-seq data (https://sourceforge.net/projects/visits/).
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140
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Mesarich CH, Rees-George J, Gardner PP, Ghomi FA, Gerth ML, Andersen MT, Rikkerink EHA, Fineran PC, Templeton MD. Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae. PLoS One 2017; 12:e0172790. [PMID: 28249011 PMCID: PMC5332098 DOI: 10.1371/journal.pone.0172790] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/09/2017] [Indexed: 01/15/2023] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa), the causal agent of kiwifruit canker, is one of the most devastating plant diseases of recent times. We have generated two mini-Tn5-based random insertion libraries of Psa ICMP 18884. The first, a 'phenotype of interest' (POI) library, consists of 10,368 independent mutants gridded into 96-well plates. By replica plating onto selective media, the POI library was successfully screened for auxotrophic and motility mutants. Lipopolysaccharide (LPS) biosynthesis mutants with 'Fuzzy-Spreader'-like morphologies were also identified through a visual screen. The second, a 'mutant of interest' (MOI) library, comprises around 96,000 independent mutants, also stored in 96-well plates, with approximately 200 individuals per well. The MOI library was sequenced on the Illumina MiSeq platform using Transposon-Directed Insertion site Sequencing (TraDIS) to map insertion sites onto the Psa genome. A grid-based PCR method was developed to recover individual mutants, and using this strategy, the MOI library was successfully screened for a putative LPS mutant not identified in the visual screen. The Psa chromosome and plasmid had 24,031 and 1,236 independent insertion events respectively, giving insertion frequencies of 3.65 and 16.6 per kb respectively. These data suggest that the MOI library is near saturation, with the theoretical probability of finding an insert in any one chromosomal gene estimated to be 97.5%. However, only 47% of chromosomal genes had insertions. This surprisingly low rate cannot be solely explained by the lack of insertions in essential genes, which would be expected to be around 5%. Strikingly, many accessory genes, including most of those encoding type III effectors, lacked insertions. In contrast, 94% of genes on the Psa plasmid had insertions, including for example, the type III effector HopAU1. These results suggest that some chromosomal sites are rendered inaccessible to transposon insertion, either by DNA-binding proteins or by the architecture of the nucleoid.
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Affiliation(s)
- Carl H. Mesarich
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
- Laboratory of Molecular Plant Pathology, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, New Zealand
| | - Jonathan Rees-George
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Paul P. Gardner
- Bio-Protection Research Centre, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Fatemeh Ashari Ghomi
- Bio-Protection Research Centre, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Monica L. Gerth
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Mark T. Andersen
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Erik H. A. Rikkerink
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Peter C. Fineran
- Bio-Protection Research Centre, New Zealand
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Matthew D. Templeton
- Bioprotection Portfolio, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
- Bio-Protection Research Centre, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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141
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The secondary resistome of multidrug-resistant Klebsiella pneumoniae. Sci Rep 2017; 7:42483. [PMID: 28198411 PMCID: PMC5309761 DOI: 10.1038/srep42483] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 01/11/2017] [Indexed: 12/22/2022] Open
Abstract
Klebsiella pneumoniae causes severe lung and bloodstream infections that are difficult to treat due to multidrug resistance. We hypothesized that antimicrobial resistance can be reversed by targeting chromosomal non-essential genes that are not responsible for acquired resistance but essential for resistant bacteria under therapeutic concentrations of antimicrobials. Conditional essentiality of individual genes to antimicrobial resistance was evaluated in an epidemic multidrug-resistant clone of K. pneumoniae (ST258). We constructed a high-density transposon mutant library of >430,000 unique Tn5 insertions and measured mutant depletion upon exposure to three clinically relevant antimicrobials (colistin, imipenem or ciprofloxacin) by Transposon Directed Insertion-site Sequencing (TraDIS). Using this high-throughput approach, we defined three sets of chromosomal non-essential genes essential for growth during exposure to colistin (n = 35), imipenem (n = 1) or ciprofloxacin (n = 1) in addition to known resistance determinants, collectively termed the "secondary resistome". As proof of principle, we demonstrated that inactivation of a non-essential gene not previously found linked to colistin resistance (dedA) restored colistin susceptibility by reducing the minimum inhibitory concentration from 8 to 0.5 μg/ml, 4-fold below the susceptibility breakpoint (S ≤ 2 μg/ml). This finding suggests that the secondary resistome is a potential target for developing antimicrobial "helper" drugs that restore the efficacy of existing antimicrobials.
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142
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A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis. Sci Rep 2017; 7:41923. [PMID: 28165493 PMCID: PMC5292949 DOI: 10.1038/srep41923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/30/2016] [Indexed: 01/14/2023] Open
Abstract
Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable. We report here a parametric model which introduces a novel mutation feature together with a noise trimming approach to predict the biological significance of Tn5 mutations. We show improved performance of essential gene prediction in the bacterium Yersinia pestis, the causative agent of plague. This method would have broad applicability to other organisms and to the identification of genes which are essential for competitiveness or survival under a broad range of stresses.
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143
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Fluorescence-Based Flow Sorting in Parallel with Transposon Insertion Site Sequencing Identifies Multidrug Efflux Systems in Acinetobacter baumannii. mBio 2016; 7:mBio.01200-16. [PMID: 27601573 PMCID: PMC5013296 DOI: 10.1128/mbio.01200-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Multidrug efflux pumps provide clinically significant levels of drug resistance in a number of Gram-negative hospital-acquired pathogens. These pathogens frequently carry dozens of genes encoding putative multidrug efflux pumps. However, it can be difficult to determine how many of these pumps actually mediate antimicrobial efflux, and it can be even more challenging to identify the regulatory proteins that control expression of these pumps. In this study, we developed an innovative high-throughput screening method, combining transposon insertion sequencing and cell sorting methods (TraDISort), to identify the genes encoding major multidrug efflux pumps, regulators, and other factors that may affect the permeation of antimicrobials, using the nosocomial pathogen Acinetobacter baumannii. A dense library of more than 100,000 unique transposon insertion mutants was treated with ethidium bromide, a common substrate of multidrug efflux pumps that is differentially fluorescent inside and outside the bacterial cytoplasm. Populations of cells displaying aberrant accumulations of ethidium were physically enriched using fluorescence-activated cell sorting, and the genomic locations of transposon insertions within these strains were determined using transposon-directed insertion sequencing. The relative abundance of mutants in the input pool compared to the selected mutant pools indicated that the AdeABC, AdeIJK, and AmvA efflux pumps are the major ethidium efflux systems in A. baumannii. Furthermore, the method identified a new transcriptional regulator that controls expression of amvA. In addition to the identification of efflux pumps and their regulators, TraDISort identified genes that are likely to control cell division, cell morphology, or aggregation in A. baumannii. Transposon-directed insertion sequencing (TraDIS) and related technologies have emerged as powerful methods to identify genes required for bacterial survival or competitive fitness under various selective conditions. We applied fluorescence-activated cell sorting (FACS) to physically enrich for phenotypes of interest within a mutant population prior to TraDIS. To our knowledge, this is the first time that a physical selection method has been applied in parallel with TraDIS rather than a fitness-induced selection. The results demonstrate the feasibility of this combined approach to generate significant results and highlight the major multidrug efflux pumps encoded in an important pathogen. This FACS-based approach, TraDISort, could have a range of future applications, including the characterization of efflux pump inhibitors, the identification of regulatory factors controlling gene or protein expression using fluorescent reporters, and the identification of genes involved in cell replication, morphology, and aggregation.
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