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Heller DM, Sivanathan V, Asai DJ, Hatfull GF. SEA-PHAGES and SEA-GENES: Advancing Virology and Science Education. Annu Rev Virol 2024. [PMID: 38684129 DOI: 10.1146/annurev-virology-113023-110757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Research opportunities for undergraduate students are strongly advantageous, but implementation at a large scale presents numerous challenges. The enormous diversity of the bacteriophage population and a supportive programmatic structure provide opportunities to engage early-career undergraduates in phage discovery, genomics, and genetics. The Science Education Alliance (SEA) is an inclusive Research-Education Community (iREC) providing centralized programmatic support for students and faculty without prior experience in virology at institutions from community colleges to research-active universities to participate in two course-based projects, SEA-PHAGES (SEA Phage Hunters Advancing Genomic and Evolutionary Science) and SEA-GENES (SEA Gene-function Exploration by a Network of Emerging Scientists). Since 2008, the SEA has supported more than 50,000 undergraduate researchers who have isolated more than 23,000 bacteriophages of which more than 4,500 are fully sequenced and annotated. Students have functionally characterized hundreds of phage genes, and the phage collection has fueled the therapeutic use of phages for treatment of Mycobacterium infections. Participation in the SEA promotes student persistence in science education, and its inclusivity promotes a more equitable scientific community.
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Affiliation(s)
- Danielle M Heller
- 1Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Viknesh Sivanathan
- 1Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - David J Asai
- 1Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Graham F Hatfull
- 2Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA;
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2
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Guerrero-Bustamante CA, Hatfull GF. Bacteriophage tRNA-dependent lysogeny: requirement of phage-encoded tRNA genes for establishment of lysogeny. mBio 2024; 15:e0326023. [PMID: 38236026 PMCID: PMC10865867 DOI: 10.1128/mbio.03260-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Bacteriophages are large and diverse components of the biosphere, and many phages are temperate. Upon infection, temperate phages can establish lysogeny in which a prophage is typically integrated into the bacterial chromosome. Here, we describe the phenomenon of tRNA-dependent lysogeny, a previously unrecognized behavior of some temperate phages. tRNA-dependent lysogeny is characterized by two unusual features. First, a phage-encoded tyrosine family integrase mediates site-specific recombination between a phage attP site and a bacterial attB site overlapping a host tRNA gene. However, attP and attB share only a short (~10 bp) common core such that a functional tRNA is not reconstructed upon integration. Second, the phage encodes a tRNA of the same isotype as the disrupted but essential host tRNA, complementing its loss, and consequently is required for the survival of lysogenic progeny. As expected, an integrase-defective phage mutant forms turbid plaques, and bacterial progeny are immune to superinfection, but they lack stability, and the prophage is rapidly lost. In contrast, a tRNA-defective phage mutant forms clear plaques and more closely resembles a repressor mutant, and lysogens are recovered only at very low frequency through the use of secondary attachment sites elsewhere in the host genome. Integration-proficient plasmids derived from these phages must also carry a cognate phage tRNA gene for efficient integration, and these may be useful tools for mycobacterial genetics. We show that tRNA-dependent lysogeny is used by phages within multiple different groups of related viruses and may be prevalent elsewhere in the broader phage community.IMPORTANCEBacteriophages are the most numerous biological entities in the biosphere, and a substantial proportion of phages are temperate, forming stable lysogens in which a prophage copy of the genome integrates into the bacterial chromosome. Many phages encode a variety of tRNA genes whose roles are poorly understood, although it has been proposed that they enhance translational efficiencies in lytic growth or that they counteract host defenses that degrade host tRNAs. Here, we show that phage-encoded tRNAs play key roles in the establishment of lysogeny of some temperate phages. They do so by compensating for the loss of tRNA function when phages integrate at an attB site overlapping a tRNA gene but fail to reconstruct the tRNA at the attachment junction. In this system of tRNA-dependent lysogeny, the phage-encoded tRNA is required for lysogeny, and deletion of the phage tRNA gives rise to a clear plaque phenotype and obligate lytic growth.
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Affiliation(s)
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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3
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Schmalstig AA, Wiggins A, Badillo D, Wetzel KS, Hatfull GF, Braunstein M. Bacteriophage infection and killing of intracellular Mycobacterium abscessus. mBio 2024; 15:e0292423. [PMID: 38059609 PMCID: PMC10790704 DOI: 10.1128/mbio.02924-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE As we rapidly approach a post-antibiotic era, bacteriophage (phage) therapy may offer a solution for treating drug-resistant bacteria. Mycobacterium abscessus is an emerging, multidrug-resistant pathogen that causes disease in people with cystic fibrosis, chronic obstructive pulmonary disease, and other underlying lung diseases. M. abscessus can survive inside host cells, a niche that can limit access to antibiotics. As current treatment options for M. abscessus infections often fail, there is an urgent need for alternative therapies. Phage therapy is being used to treat M. abscessus infections as an option of last resort. However, little is known about the ability of phages to kill bacteria in the host environment and specifically in an intracellular environment. Here, we demonstrate the ability of phages to enter mammalian cells and to infect and kill intracellular M. abscessus. These findings support the use of phages to treat intracellular bacterial pathogens.
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Affiliation(s)
- Alan A. Schmalstig
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Andrew Wiggins
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Debbie Badillo
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katherine S. Wetzel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Miriam Braunstein
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Abstract
IMPORTANCE Bacteriophage genomes are pervasively mosaic, presenting challenges to describing phage relatedness. Here, we describe PhamClust, a bioinformatic approach for phage genome comparisons that uses a new metric of proteomic equivalence quotient for comparative genomics. PhamClust reliably assorts genomes into groups or clusters of related phages and can subdivide clusters into subclusters. PhamClust is computationally efficient and can readily process thousands of phage genomes. It is also a useful analytic tool for exploring the different types of inter-genome relatedness characteristic of phages in different clusters.
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Affiliation(s)
- Christian H. Gauthier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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5
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Abad L, Gauthier CH, Florian I, Jacobs-Sera D, Hatfull GF. The heterogenous and diverse population of prophages in Mycobacterium genomes. mSystems 2023; 8:e0044623. [PMID: 37791767 PMCID: PMC10654092 DOI: 10.1128/msystems.00446-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/18/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Mycobacterium species include several human pathogens and mycobacteriophages show potential for therapeutic use to control Mycobacterium infections. However, phage infection profiles vary greatly among Mycobacterium abscessus clinical isolates and phage therapies must be personalized for individual patients. Mycobacterium phage susceptibility is likely determined primarily by accessory parts of bacterial genomes, and we have identified the prophage and phage-related genomic regions across sequenced Mycobacterium strains. The prophages are numerous and diverse, especially in M. abscessus genomes, and provide a potentially rich reservoir of new viruses that can be propagated lytically and used to expand the repertoire of therapeutically useful phages.
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Affiliation(s)
- Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christian H. Gauthier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Isabella Florian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Binsabaan SA, Freeman KG, Hatfull GF, VanDemark AP. The Cytotoxic Mycobacteriophage Protein Phaedrus gp82 Interacts with and Modulates the Activity of the Host ATPase, MoxR. J Mol Biol 2023; 435:168261. [PMID: 37678706 PMCID: PMC10593117 DOI: 10.1016/j.jmb.2023.168261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Approximately 70% of bacteriophage-encoded proteins are of unknown function. Elucidating these protein functions represents opportunities to discover new phage-host interactions and mechanisms by which the phages modulate host activities. Here, we describe a pipeline for prioritizing phage-encoded proteins for structural analysis and characterize the gp82 protein encoded by mycobacteriophage Phaedrus. Structural and solution studies of gp82 show it is a trimeric protein containing two domains. Co-precipitation studies with the host Mycobacterium smegmatis identified the ATPase MoxR as an interacting partner protein. Phaedrus gp82-MoxR interaction requires the presence of a loop sequence within gp82 that is highly exposed and disordered in the crystallographic structure. We show that Phaedrus gp82 overexpression in M. smegmatis retards the growth of M. smegmatis on solid medium, resulting in a small colony phenotype. Overexpression of gp82 containing a mutant disordered loop or the overexpression of MoxR both rescue this phenotype. Lastly, we show that recombinant gp82 reduces levels of MoxR-mediated ATPase activity in vitro that is required for its chaperone function, and that the disordered loop plays an important role in this phenotype. We conclude that Phaedrus gp82 binds to and reduces mycobacterial MoxR activity, leading to reduced function of host proteins that require MoxR chaperone activity for their normal activity.
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Affiliation(s)
- Saeed A Binsabaan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA
| | - Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh PA 15260, USA.
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Dedrick RM, Abad L, Storey N, Kaganovsky AM, Smith BE, Aull HA, Cristinziano M, Morkowska A, Murthy S, Loebinger MR, Hatfull GF, Satta G. The problem of Mycobacterium abscessus complex: multi-drug resistance, bacteriophage susceptibility and potential healthcare transmission. Clin Microbiol Infect 2023; 29:1335.e9-1335.e16. [PMID: 37364635 PMCID: PMC10583746 DOI: 10.1016/j.cmi.2023.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
OBJECTIVES Mycobacterium abscessus complex is responsible for 2.6-13.0% of all non-tuberculous mycobacterial pulmonary infections and these are notoriously difficult to treat due to the complex regimens required, drug resistance and adverse effects. Hence, bacteriophages have been considered in clinical practice as an additional treatment option. Here, we evaluated antibiotic and phage susceptibility profiles of M. abscessus clinical isolates. Whole-genome sequencing (WGS) revealed the phylogenetic relationships, dominant circulating clones (DCCs), the likelihood of patient-to-patient transmission and the presence of prophages. METHODS Antibiotic susceptibility testing was performed using CLSI breakpoints (n = 95), and plaque assays were used for phage susceptibility testing (subset of n = 88, 35 rough and 53 smooth morphology). WGS was completed using the Illumina platform and analysed using Snippy/snp-dists and Discovery and Extraction of Phages Tool (DEPhT). RESULTS Amikacin and Tigecycline were the most active drugs (with 2 strains resistant to amikacin, and one strain with Tigecycline MIC of 4 μg/mL). Most strains were resistant to all other drugs tested, with Linezolid and Imipenem showing the least resistance, at 38% (36/95) and 55% (52/95), respectively. Rough colony morphotype strains were more phage-susceptible than smooth strains (77%-27/35 versus 48%-25/53 in the plaque assays, but smooth strains are not killed efficiently by those phages in liquid infection assay). We have also identified 100 resident prophages, some of which were propagated lytically. DCC1 (20%-18/90) and DCC4 (22%-20/90) were observed to be the major clones and WGS identified 6 events of possible patient-to-patient transmission. DISCUSSION Many strains of M. abscessus complex are intrinsically resistant to available antibiotics and bacteriophages represent an alternative therapeutic option, but only for strains with rough morphology. Further studies are needed to elucidate the role of hospital-borne M. abscessus transmission.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nathaniel Storey
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ari M Kaganovsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bailey E Smith
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haley A Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Madison Cristinziano
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Saraswathi Murthy
- Royal Brompton and Harefield Hospitals, Guys and St Thomas's NHS Foundation Trust, London, UK
| | - Michael R Loebinger
- Royal Brompton and Harefield Hospitals, Guys and St Thomas's NHS Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College London, London, UK
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Giovanni Satta
- Centre for Clinical Microbiology, University College London, London, UK; Infection Division, University College London Hospitals NHS Foundation Trust, London, UK.
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8
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Wetzel KS, Illouz M, Abad L, Aull HG, Russell DA, Garlena RA, Cristinziano M, Malmsheimer S, Chalut C, Hatfull GF, Kremer L. Therapeutically useful mycobacteriophages BPs and Muddy require trehalose polyphleates. Nat Microbiol 2023; 8:1717-1731. [PMID: 37644325 PMCID: PMC10465359 DOI: 10.1038/s41564-023-01451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Mycobacteriophages show promise as therapeutic agents for non-tuberculous mycobacterium infections. However, little is known about phage recognition of Mycobacterium cell surfaces or mechanisms of phage resistance. We show here that trehalose polyphleates (TPPs)-high-molecular-weight, surface-exposed glycolipids found in some mycobacterial species-are required for infection of Mycobacterium abscessus and Mycobacterium smegmatis by clinically useful phages BPs and Muddy. TPP loss leads to defects in adsorption and infection and confers resistance. Transposon mutagenesis shows that TPP disruption is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss by mutation, and some M. abscessus clinical isolates are naturally phage-insensitive due to TPP synthesis gene mutations. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, and M. abscessus mutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.
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Affiliation(s)
- Katherine S Wetzel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Morgane Illouz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haley G Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Madison Cristinziano
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Silke Malmsheimer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France.
- INSERM, IRIM, Montpellier, France.
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9
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Freeman KG, Robotham AC, Parks OB, Abad L, Jacobs-Sera D, Lauer MJ, Podgorski JM, Zhang Y, Williams JV, White SJ, Kelly JF, Hatfull GF, Pope WH. Virion glycosylation influences mycobacteriophage immune recognition. Cell Host Microbe 2023; 31:1216-1231.e6. [PMID: 37329881 PMCID: PMC10527164 DOI: 10.1016/j.chom.2023.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/19/2023]
Abstract
Glycosylation of eukaryotic virus particles is common and influences their uptake, trafficking, and immune recognition. In contrast, glycosylation of bacteriophage particles has not been reported; phage virions typically do not enter the cytoplasm upon infection, and they do not generally inhabit eukaryotic systems. We show here that several genomically distinct phages of Mycobacteria are modified with glycans attached to the C terminus of capsid and tail tube protein subunits. These O-linked glycans influence antibody production and recognition, shielding viral particles from antibody binding and reducing production of neutralizing antibodies. Glycosylation is mediated by phage-encoded glycosyltransferases, and genomic analysis suggests that they are relatively common among mycobacteriophages. Putative glycosyltransferases are also encoded by some Gordonia and Streptomyces phages, but there is little evidence of glycosylation among the broader phage population. The immune response to glycosylated phage virions in mice suggests that glycosylation may be an advantageous property for phage therapy of Mycobacterium infections.
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Affiliation(s)
- Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Anna C Robotham
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - Olivia B Parks
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Pediatrics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michael J Lauer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jennifer M Podgorski
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
| | - Yu Zhang
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Pediatrics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - John V Williams
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Pediatrics and Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Simon J White
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
| | - John F Kelly
- Human Health Therapeutics, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Welkin H Pope
- Science Department, Chatham University, Pittsburgh, PA 15232, USA
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10
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Hurst-Hess K, Walz A, Yang Y, McGuirk H, Gonzalez-Juarrero M, Hatfull GF, Ghosh P, Ojha AK. Intrapulmonary Treatment with Mycobacteriophage LysB Rapidly Reduces Mycobacterium abscessus Burden. Antimicrob Agents Chemother 2023; 67:e0016223. [PMID: 37154689 PMCID: PMC10269076 DOI: 10.1128/aac.00162-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023] Open
Abstract
Intrinsic and acquired antibiotic resistance in Mycobacterium abscessus presents challenges in infection control, and new therapeutic strategies are needed. Bacteriophage therapy shows promise, but variabilities in M. abscessus phage susceptibility limits its broader utility. We show here that a mycobacteriophage-encoded lysin B (LysB) efficiently and rapidly kills both smooth- and rough-colony morphotype M. abscessus strains and reduces the pulmonary bacterial load in mice. LysB aerosolization presents a plausible treatment for pulmonary M. abscessus infections.
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Affiliation(s)
- Kelley Hurst-Hess
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Amanda Walz
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Yong Yang
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Helen McGuirk
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mercedes Gonzalez-Juarrero
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Pallavi Ghosh
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - Anil K. Ojha
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
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11
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Wetzel KS, Illouz M, Abad L, Aull HG, Russell DA, Garlena RA, Cristinziano M, Malmsheimer S, Chalut C, Hatfull GF, Kremer L. Mycobacterium trehalose polyphleates are required for infection by therapeutically useful mycobacteriophages BPs and Muddy. bioRxiv 2023:2023.03.14.532567. [PMID: 36993724 PMCID: PMC10055034 DOI: 10.1101/2023.03.14.532567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mycobacteriophages are good model systems for understanding their bacterial hosts and show promise as therapeutic agents for nontuberculous mycobacterium infections. However, little is known about phage recognition of Mycobacterium cell surfaces, or mechanisms of phage resistance. We show here that surface-exposed trehalose polyphleates (TPPs) are required for infection of Mycobacterium abscessus and Mycobacterium smegmatis by clinically useful phages BPs and Muddy, and that TPP loss leads to defects in adsorption, infection, and confers resistance. Transposon mutagenesis indicates that TPP loss is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss, and some M. abscessus clinical isolates are phage-insensitive due to TPP absence. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, and M. abscessus mutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.
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12
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Dulberger CL, Guerrero-Bustamante CA, Owen SV, Wilson S, Wuo MG, Garlena RA, Serpa LA, Russell DA, Zhu J, Braunecker BJ, Squyres GR, Baym M, Kiessling LL, Garner EC, Rubin EJ, Hatfull GF. Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection. Nat Microbiol 2023; 8:695-710. [PMID: 36823286 PMCID: PMC10066036 DOI: 10.1038/s41564-023-01333-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/23/2023] [Indexed: 02/25/2023]
Abstract
Mycobacteriophages are a diverse group of viruses infecting Mycobacterium with substantial therapeutic potential. However, as this potential becomes realized, the molecular details of phage infection and mechanisms of resistance remain ill-defined. Here we use live-cell fluorescence microscopy to visualize the spatiotemporal dynamics of mycobacteriophage infection in single cells and populations, showing that infection is dependent on the host nucleoid-associated Lsr2 protein. Mycobacteriophages preferentially adsorb at Mycobacterium smegmatis sites of new cell wall synthesis and following DNA injection, Lsr2 reorganizes away from host replication foci to establish zones of phage DNA replication (ZOPR). Cells lacking Lsr2 proceed through to cell lysis when infected but fail to generate consecutive phage bursts that trigger epidemic spread of phage particles to neighbouring cells. Many mycobacteriophages code for their own Lsr2-related proteins, and although their roles are unknown, they do not rescue the loss of host Lsr2.
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Affiliation(s)
- Charles L Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael G Wuo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lexi A Serpa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ben J Braunecker
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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13
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Dedrick RM, Smith BE, Cristinziano M, Freeman KG, Jacobs-Sera D, Belessis Y, Whitney Brown A, Cohen KA, Davidson RM, van Duin D, Gainey A, Garcia CB, Robert George CR, Haidar G, Ip W, Iredell J, Khatami A, Little JS, Malmivaara K, McMullan BJ, Michalik DE, Moscatelli A, Nick JA, Tupayachi Ortiz MG, Polenakovik HM, Robinson PD, Skurnik M, Solomon DA, Soothill J, Spencer H, Wark P, Worth A, Schooley RT, Benson CA, Hatfull GF. Phage Therapy of Mycobacterium Infections: Compassionate Use of Phages in 20 Patients With Drug-Resistant Mycobacterial Disease. Clin Infect Dis 2023; 76:103-112. [PMID: 35676823 PMCID: PMC9825826 DOI: 10.1093/cid/ciac453] [Citation(s) in RCA: 90] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Nontuberculous Mycobacterium infections, particularly Mycobacterium abscessus, are increasingly common among patients with cystic fibrosis and chronic bronchiectatic lung diseases. Treatment is challenging due to intrinsic antibiotic resistance. Bacteriophage therapy represents a potentially novel approach. Relatively few active lytic phages are available and there is great variation in phage susceptibilities among M. abscessus isolates, requiring personalized phage identification. METHODS Mycobacterium isolates from 200 culture-positive patients with symptomatic disease were screened for phage susceptibilities. One or more lytic phages were identified for 55 isolates. Phages were administered intravenously, by aerosolization, or both to 20 patients on a compassionate use basis and patients were monitored for adverse reactions, clinical and microbiologic responses, the emergence of phage resistance, and phage neutralization in serum, sputum, or bronchoalveolar lavage fluid. RESULTS No adverse reactions attributed to therapy were seen in any patient regardless of the pathogen, phages administered, or the route of delivery. Favorable clinical or microbiological responses were observed in 11 patients. Neutralizing antibodies were identified in serum after initiation of phage delivery intravenously in 8 patients, potentially contributing to lack of treatment response in 4 cases, but were not consistently associated with unfavorable responses in others. Eleven patients were treated with only a single phage, and no phage resistance was observed in any of these. CONCLUSIONS Phage treatment of Mycobacterium infections is challenging due to the limited repertoire of therapeutically useful phages, but favorable clinical outcomes in patients lacking any other treatment options support continued development of adjunctive phage therapy for some mycobacterial infections.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bailey E Smith
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Madison Cristinziano
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yvonne Belessis
- School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
- Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | | | - Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Andrew Gainey
- Department of Pharmacy, Division of Pediatric Infectious Diseases, Prisma Health Children's Hospital–Midlands, Columbia, South Carolina, USA
| | | | - C R Robert George
- New South Wales Health Pathology Microbiology, John Hunter Hospital, New Lambton, New South Wales, Australia
| | - Ghady Haidar
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Winnie Ip
- Department of Pediatric Immunology, Great Ormond Street Hospital, London, United Kingdom
| | - Jonathan Iredell
- Department of Immunology and Infectious Diseases, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Ameneh Khatami
- Department of Infectious Diseases and Microbiology, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Discipline of Child and Adolescent Health, University of Syndey, Sydney, New South Wales, Australia
| | - Jessica S Little
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Brendan J McMullan
- Department of Immunology and Infectious Diseases, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - David E Michalik
- Miller Children’s and Women’s Hospital, Division of Pediatric Infectious Diseases, Long Beach, California, USA
| | - Andrea Moscatelli
- Neonatal and Pediatric Intensive Care Unit, Instituto Giannina Gaslini, Genoa, Italy
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Maria G Tupayachi Ortiz
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Hari M Polenakovik
- Internal Medicine Department, Dayton Children’s Hospital, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Paul D Robinson
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Daniel A Solomon
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Helen Spencer
- Respiratory Medicine and Cardiothoracic Transplantation, Great Ormond Street Hospital, London, United Kingdom
| | - Peter Wark
- Immune Health Program, Hunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia
| | - Austen Worth
- Department of Pediatric Immunology, Great Ormond Street Hospital, London, United Kingdom
| | - Robert T Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, San Diego, California, USA
| | - Constance A Benson
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, San Diego, California, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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14
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Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell 2023; 186:17-31. [PMID: 36608652 PMCID: PMC9827498 DOI: 10.1016/j.cell.2022.11.017] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 01/07/2023]
Abstract
Increasing antimicrobial resistance rates have revitalized bacteriophage (phage) research, the natural predators of bacteria discovered over 100 years ago. In order to use phages therapeutically, they should (1) preferably be lytic, (2) kill the bacterial host efficiently, and (3) be fully characterized to exclude side effects. Developing therapeutic phages takes a coordinated effort of multiple stakeholders. Herein, we review the state of the art in phage therapy, covering biological mechanisms, clinical applications, remaining challenges, and future directions involving naturally occurring and genetically modified or synthetic phages.
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Affiliation(s)
- Steffanie A Strathdee
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert T Schooley
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA
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15
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Feiss M, Young R, Ramsey J, Adhya S, Georgopoulos C, Hendrix RW, Hatfull GF, Gilcrease EB, Casjens SR. Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology. Microbiol Mol Biol Rev 2022; 86:e0012421. [PMID: 36165780 PMCID: PMC9799177 DOI: 10.1128/mmbr.00124-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.
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Affiliation(s)
- Michael Feiss
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ryland Young
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Jolene Ramsey
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, The National Cancer Institute, Bethesda, Maryland, USA
| | - Costa Georgopoulos
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Roger W. Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Eddie B. Gilcrease
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Sherwood R. Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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16
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Gauthier CH, Cresawn SG, Hatfull GF. PhaMMseqs: a new pipeline for constructing phage gene phamilies using MMseqs2. G3 (Bethesda) 2022; 12:6717792. [PMID: 36161315 PMCID: PMC9635663 DOI: 10.1093/g3journal/jkac233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/30/2022] [Indexed: 06/09/2023]
Abstract
The diversity and mosaic architecture of phage genomes present challenges for whole-genome phylogenies and comparative genomics. There are no universally conserved core genes, ∼70% of phage genes are of unknown function, and phage genomes are replete with small (<500 bp) open reading frames. Assembling sequence-related genes into "phamilies" ("phams") based on amino acid sequence similarity simplifies comparative phage genomics and facilitates representations of phage genome mosaicism. With the rapid and substantial increase in the numbers of sequenced phage genomes, computationally efficient pham assembly is needed, together with strategies for including newly sequenced phage genomes. Here, we describe the Python package PhaMMseqs, which uses MMseqs2 for pham assembly, and we evaluate the key parameters for optimal pham assembly of sequence- and functionally related proteins. PhaMMseqs runs efficiently with only modest hardware requirements and integrates with the pdm_utils package for simple genome entry and export of datasets for evolutionary analyses and phage genome map construction.
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Affiliation(s)
- Christian H Gauthier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Steven G Cresawn
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Graham F Hatfull
- Corresponding author: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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17
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Hanauer DI, Graham MJ, Jacobs-Sera D, Garlena RA, Russell DA, Sivanathan V, Asai DJ, Hatfull GF. Broadening Access to STEM through the Community College: Investigating the Role of Course-Based Research Experiences (CREs). CBE Life Sci Educ 2022; 21:ar38. [PMID: 35670725 PMCID: PMC9508918 DOI: 10.1187/cbe.21-08-0203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Broadening access to science, technology, engineering, and mathematics (STEM) professions through the provision of early-career research experiences for a wide range of demographic groups is important for the diversification of the STEM workforce. The size and diversity of the community college system make it a prime educational site for achieving this aim. However, some evidence shows that women and Black, Latinx, and Native American student groups have been hindered in STEM at the community college level. One option for enhancing persistence in STEM is to incorporate the course-based research experiences (CREs) into the curriculum as a replacement for the prevalent traditional laboratory. This can be achieved through the integration of community colleges within extant, multi-institutional CREs such as the SEA-PHAGES program. Using a propensity score-matching technique, students in a CRE and traditional laboratory were compared on a range of psychosocial variables (project ownership, self-efficacy, science identity, scientific community values, and networking). Results revealed higher ratings for women and persons excluded because of their ethnicity or race (PEERs) in the SEA-PHAGES program on important predictors of persistence such as project ownership and science identity. This suggests that the usage of CREs at community colleges could have positive effects in addressing the gender gap for women and enhance inclusiveness for PEER students in STEM.
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Affiliation(s)
- David I. Hanauer
- Department of English, Indiana University of Pennsylvania, Indiana, PA 15705
| | - Mark J. Graham
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Viknesh Sivanathan
- Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - David J. Asai
- Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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18
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Nick JA, Dedrick RM, Gray AL, Vladar EK, Smith BE, Freeman KG, Malcolm KC, Epperson LE, Hasan NA, Hendrix J, Callahan K, Walton K, Vestal B, Wheeler E, Rysavy NM, Poch K, Caceres S, Lovell VK, Hisert KB, de Moura VC, Chatterjee D, De P, Weakly N, Martiniano SL, Lynch DA, Daley CL, Strong M, Jia F, Hatfull GF, Davidson RM. Host and pathogen response to bacteriophage engineered against Mycobacterium abscessus lung infection. Cell 2022; 185:1860-1874.e12. [PMID: 35568033 PMCID: PMC9840467 DOI: 10.1016/j.cell.2022.04.024] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/05/2022] [Accepted: 04/14/2022] [Indexed: 01/17/2023]
Abstract
Two mycobacteriophages were administered intravenously to a male with treatment-refractory Mycobacterium abscessus pulmonary infection and severe cystic fibrosis lung disease. The phages were engineered to enhance their capacity to lyse M. abscessus and were selected specifically as the most effective against the subject's bacterial isolate. In the setting of compassionate use, the evidence of phage-induced lysis was observed using molecular and metabolic assays combined with clinical assessments. M. abscessus isolates pre and post-phage treatment demonstrated genetic stability, with a general decline in diversity and no increased resistance to phage or antibiotics. The anti-phage neutralizing antibody titers to one phage increased with time but did not prevent clinical improvement throughout the course of treatment. The subject received lung transplantation on day 379, and systematic culturing of the explanted lung did not detect M. abscessus. This study describes the course and associated markers of a successful phage treatment of M. abscessus in advanced lung disease.
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Affiliation(s)
- Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alice L Gray
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Eszter K Vladar
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Bailey E Smith
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kenneth C Malcolm
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - L Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Jo Hendrix
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA; Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kimberly Callahan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Kendra Walton
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Brian Vestal
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Emily Wheeler
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Noel M Rysavy
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Katie Poch
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Silvia Caceres
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Valerie K Lovell
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Katherine B Hisert
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
| | - Prithwiraj De
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
| | - Natalia Weakly
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Stacey L Martiniano
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - David A Lynch
- Department of Radiology, National Jewish Health, Denver, CO 80206, USA
| | - Charles L Daley
- Department of Medicine, National Jewish Health, Denver, CO 80206, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Fan Jia
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Rebecca M Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO 80206, USA
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19
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Dedrick RM, Freeman KG, Nguyen JA, Bahadirli-Talbott A, Cardin ME, Cristinziano M, Smith BE, Jeong S, Ignatius EH, Ting Lin C, Cohen KA, Hatfull GF. Nebulized bacteriophage in a patient with refractory Mycobacterium abscessus lung disease. Open Forum Infect Dis 2022; 9:ofac194. [PMID: 35794944 PMCID: PMC9251665 DOI: 10.1093/ofid/ofac194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/07/2022] [Indexed: 11/30/2022] Open
Abstract
An elderly man with refractory Mycobacterium abscessus lung disease previously developed anti-phage neutralizing antibodies while receiving intravenous phage therapy. Subsequent phage nebulization resulted in transient weight gain, decreased C-reactive protein, and reduced Mycobacterium burden. Weak sputum neutralization may have limited the outcomes, but phage resistance was not a contributing factor.
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Affiliation(s)
| | | | - Jan A. Nguyen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Asli Bahadirli-Talbott
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mitchell E. Cardin
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Bailey E. Smith
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Soowan Jeong
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elisa H. Ignatius
- Division of Clinical Pharmacology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cheng Ting Lin
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Keira A. Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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20
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Hanauer DI, Graham MJ, Arnold RJ, Ayuk MA, Balish MF, Beyer AR, Butela KA, Byrum CA, Chia CP, Chung HM, Clase KL, Conant S, Coomans RJ, D’Elia T, Diaz J, Diaz A, Doty JA, Edgington NP, Edwards DC, Eivazova E, Emmons CB, Fast KM, Fisher EJ, Fleischacker CL, Frederick GD, Freise AC, Gainey MD, Gissendanner CR, Golebiewska UP, Guild NA, Hendrickson HL, Herren CD, Hopson-Fernandes MS, Hughes LE, Jacobs-Sera D, Johnson AA, Kirkpatrick BL, Klyczek KK, Koga AP, Kotturi H, LeBlanc-Straceski J, Lee-Soety JY, Leonard JE, Mastropaolo MD, Merkhofer EC, Michael SF, Mitchell JC, Mohan S, Monti DL, Noutsos C, Nsa IY, Peters NT, Plymale R, Pollenz RS, Porter ML, Rinehart CA, Rosas-Acosta G, Ross JF, Rubin MR, Scherer AE, Schroeder SC, Shaffer CD, Sprenkle AB, Sunnen CN, Swerdlow SJ, Tobiason D, Tolsma SS, Tsourkas PK, Ward RE, Ware VC, Warner MH, Washington JM, Westover KM, White SJ, Whitefleet-Smith JL, Williams DC, Wolyniak MJ, Zeilstra-Ryalls JH, Asai DJ, Hatfull GF, Sivanathan V. Instructional Models for Course-Based Research Experience (CRE) Teaching. CBE Life Sci Educ 2022; 21:ar8. [PMID: 34978921 PMCID: PMC9250372 DOI: 10.1187/cbe.21-03-0057] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
Abstract
The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.
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Affiliation(s)
- David I. Hanauer
- Department of English, Indiana University of Pennsylvania, Indiana, PA 15705
| | - Mark J. Graham
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511
| | - Rachel J. Arnold
- Salish Sea Research Center, Northwest Indian College, Bellingham, WA 98229
| | - Mary A. Ayuk
- Biology, Howard University, Washington, DC 20059
| | | | - Andrea R. Beyer
- Department of Biology, Virginia State University, Petersburg, VA 23806
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | - Catherine P. Chia
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Hui-Min Chung
- Biology, University of West Florida, Pensacola, FL 32514
| | - Kari L. Clase
- Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
| | - Stephanie Conant
- Department of Biology, University of Detroit Mercy, Detroit, MI 48221
| | - Roy J. Coomans
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411
| | - Tom D’Elia
- Department of Biology, Indian River State College, Fort Pierce, FL 34981
| | - Jason Diaz
- Integrated Science, Business, and Technology, La Salle University, Philadelphia, PA 19141
| | - Arturo Diaz
- Department of Biology, La Sierra University, Riverside, CA 92505
| | - Jean A. Doty
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938
| | | | - Dustin C. Edwards
- Biological Sciences, Tarleton State University, Stephenville, TX 76402
| | - Elvira Eivazova
- Biology Department, Columbia State Community College, Columbia, Tennessee 38401
| | | | - Kayla M. Fast
- Biological and Environmental Sciences, University of West Alabama, Livingston, AL 35470
| | - Emily J. Fisher
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | | | - Gregory D. Frederick
- Department of Biology and Kinesiology, LeTourneau University, Longview, TX 75602
| | - Amanda C. Freise
- Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90025
| | - Maria D. Gainey
- Chemistry and Physics, Western Carolina University, Cullowhee, NC 28723
| | | | | | - Nancy A. Guild
- Molecular Cellular and Developmental Biology (MCDB), University of Colorado, Boulder, CO 80309
| | - Heather L. Hendrickson
- School of Natural and Computational Science, Massey University, Auckland 0632, New Zealand
| | | | | | - Lee E. Hughes
- Biological Sciences, University of North Texas, Denton, TX 76203
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Allison A. Johnson
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284
| | | | - Karen K. Klyczek
- Biology Department, University of Wisconsin-River Falls, River Falls, WI 54022
| | - Ann P. Koga
- Department of Biology, College of Idaho, Caldwell, ID 83605
| | - Hari Kotturi
- Department of Biology, University of Central Oklahoma, Edmond, OK 73034
| | | | - Julia Y. Lee-Soety
- Department of Biology, Saint Joseph’s University, Philadelphia, PA 19131
| | | | - Matthew D. Mastropaolo
- Mathematics and Sciences, School of Arts and Sciences, Neumann University, Aston, PA 19014
| | | | - Scott F. Michael
- Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965
| | - Jon C. Mitchell
- Department of Science and Mathematics, Northern State University, Aberdeen, SD 57401
| | - Swarna Mohan
- College of Computer, Mathematical, and Natural Sciences, University of Maryland College Park, College Park, MD 20742
| | - Denise L. Monti
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35223
| | | | - Imade Y. Nsa
- Microbiology, University of Lagos, Lagos 101017, Nigeria
| | - Nick T. Peters
- Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
| | - Ruth Plymale
- Department of Biology, Ouachita Baptist University, Arkadelphia, AR 71998
| | - Richard S. Pollenz
- Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620
| | - Megan L. Porter
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI 96822
| | - Claire A. Rinehart
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101
| | - German Rosas-Acosta
- Department of Biological Sciences, University of Texas at El Paso (UTEP), El Paso, TX 79968
| | - Joseph F. Ross
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125
| | - Michael R. Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | | | | | | | - C. Nicole Sunnen
- Biological Sciences, University of the Sciences, Philadelphia, PA 19104
| | | | | | - Sara S. Tolsma
- Department of Biology, Northwestern College, Orange City, IA 51041
| | | | - Robert E. Ward
- Biology, Case Western Reserve University, Cleveland, OH 44106
| | - Vassie C. Ware
- Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Marcie H. Warner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | | | - Simon J. White
- Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | | | | | | | | | - David J. Asai
- Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Viknesh Sivanathan
- Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815
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21
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Diacon AH, Guerrero-Bustamante CA, Rosenkranz B, Rubio Pomar FJ, Vanker N, Hatfull GF. Mycobacteriophages to Treat Tuberculosis: Dream or Delusion? Respiration 2021; 101:1-15. [PMID: 34814151 DOI: 10.1159/000519870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/10/2021] [Indexed: 11/19/2022] Open
Abstract
Rates of antimicrobial resistance are increasing globally while the pipeline of new antibiotics is drying up, putting patients with disease caused by drug-resistant bacteria at increased risk of complications and death. The growing costs for diagnosis and management of drug resistance threaten tuberculosis control where the disease is endemic and resources limited. Bacteriophages are viruses that attack bacteria. Phage preparations served as anti-infective agents long before antibiotics were discovered. Though small in size, phages are the most abundant and diverse biological entity on earth. Phages have co-evolved with their hosts and possess all the tools needed to infect and kill bacteria, independent of drug resistance. Modern biotechnology has improved our understanding of the biology of phages and their possible uses. Phage preparations are available to treat meat, fruit, vegetables, and dairy products against parasites or to prevent contamination with human pathogens, such as Listeria monocytogenes, Escherichia coli, or Staphylococcus aureus. Such phage-treated products are considered fit for human consumption. A number of recent case reports describe in great detail the successful treatment of highly drug-resistant infections with individualized phage preparations. Formal clinical trials with standardized products are slowly emerging. With its highly conserved genome and relative paucity of natural phage defence mechanisms Mycobacterium tuberculosis appears to be a suitable target for phage treatment. A phage cocktail with diverse and strictly lytic phages that kill all lineages of M. tuberculosis, and can be propagated on Mycobacterium smegmatis, has been assembled and is available for the evaluation of optimal dosage and suitable routes of administration for tuberculosis in humans. Phage treatment can be expected to be safe and active on extracellular organisms, but phage penetration to intracellular and granulomatous environments as well as synergistic effects with antibiotics are important questions to address during further evaluation.
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Affiliation(s)
| | | | - Bernd Rosenkranz
- Division of Pharmacology, Stellenbosch University, Cape Town, South Africa.,Fundisa African Academy of Medicines Development, Cape Town, South Africa
| | | | | | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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22
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Shield CG, Swift BMC, McHugh TD, Dedrick RM, Hatfull GF, Satta G. Application of Bacteriophages for Mycobacterial Infections, from Diagnosis to Treatment. Microorganisms 2021; 9:2366. [PMID: 34835491 PMCID: PMC8617706 DOI: 10.3390/microorganisms9112366] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium tuberculosis and other non-tuberculous mycobacteria are responsible for a variety of different infections affecting millions of patients worldwide. Their diagnosis is often problematic and delayed until late in the course of disease, requiring a high index of suspicion and the combined efforts of clinical and laboratory colleagues. Molecular methods, such as PCR platforms, are available, but expensive, and with limited sensitivity in the case of paucibacillary disease. Treatment of mycobacterial infections is also challenging, typically requiring months of multiple and combined antibiotics, with associated side effects and toxicities. The presence of innate and acquired drug resistance further complicates the picture, with dramatic cases without effective treatment options. Bacteriophages (viruses that infect bacteria) have been used for decades in Eastern Europe for the treatment of common bacterial infections, but there is limited clinical experience of their use in mycobacterial infections. More recently, bacteriophages' clinical utility has been re-visited and their use has been successfully demonstrated both as diagnostic and treatment options. This review will focus specifically on how mycobacteriophages have been used recently in the diagnosis and treatment of different mycobacterial infections, as potential emerging technologies, and as an alternative treatment option.
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Affiliation(s)
- Christopher G. Shield
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield AL9 7TA, UK;
| | - Benjamin M. C. Swift
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield AL9 7TA, UK;
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, London NW3 2PF, UK; (T.D.M.); (G.S.)
| | - Rebekah M. Dedrick
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.M.D.); (G.F.H.)
| | - Graham F. Hatfull
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.M.D.); (G.F.H.)
| | - Giovanni Satta
- Centre for Clinical Microbiology, University College London, London NW3 2PF, UK; (T.D.M.); (G.S.)
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23
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Abstract
Innovations in science education are desperately needed to find ways to engage and interest students early in their undergraduate careers. Exposing students to authentic research experiences is highly beneficial, but finding ways to include all types of students and to do this at large scale is especially challenging. An attractive solution is the concept of an inclusive research education community (iREC) in which centralized research leadership and administration supports multiple institutions, including diverse groups of schools and universities, faculty and students. The Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) programme is an excellent example of an iREC, in which students explore viral diversity and evolution through discovery and genomic analysis of novel bacteriophages. The SEA-PHAGES programme has proven to be sustainable, to be implemented at large scale, and to enhance student persistence in science, as well as to produce substantial research advances. Discovering a new virus with the potential for new biological insights and clinical applications is inherently exciting. Who wouldn't want to discover a new virus?
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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24
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Johansen MD, Alcaraz M, Dedrick RM, Roquet-Banères F, Hamela C, Hatfull GF, Kremer L. Mycobacteriophage-antibiotic therapy promotes enhanced clearance of drug-resistant Mycobacterium abscessus. Dis Model Mech 2021; 14:272140. [PMID: 34530447 PMCID: PMC8461822 DOI: 10.1242/dmm.049159] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/26/2021] [Indexed: 12/16/2022] Open
Abstract
Infection by multidrug-resistant Mycobacterium abscessus is increasingly prevalent in cystic fibrosis (CF) patients, leaving clinicians with few therapeutic options. A compassionate study showed the clinical improvement of a CF patient with a disseminated M. abscessus (GD01) infection, following injection of a phage cocktail, including phage Muddy. Broadening the use of phage therapy in patients as a potential antibacterial alternative necessitates the development of biological models to improve the reliability and successful prediction of phage therapy in the clinic. Herein, we demonstrate that Muddy very efficiently lyses GD01 in vitro, an effect substantially increased with standard drugs. Remarkably, this cooperative activity was retained in an M. abscessus model of infection in CFTR-depleted zebrafish, associated with a striking increase in larval survival and reduction in pathological signs. The activity of Muddy was lost in macrophage-ablated larvae, suggesting that successful phage therapy relies on functional innate immunity. CFTR-depleted zebrafish represent a practical model to rapidly assess phage treatment efficacy against M. abscessus isolates, allowing the identification of drug combinations accompanying phage therapy and treatment prediction in patients. This article has an associated First Person interview with the first author of the paper. Summary: A zebrafish model of infection was developed to evaluate the in vivo cooperative activity of specific phages and antibiotics for the treatment of Mycobacterium abscessus infection.
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Affiliation(s)
- Matt D Johansen
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique UMR 9004, Université de Montpellier, Montpellier 34293, France
| | - Matthéo Alcaraz
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique UMR 9004, Université de Montpellier, Montpellier 34293, France
| | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Françoise Roquet-Banères
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique UMR 9004, Université de Montpellier, Montpellier 34293, France
| | - Claire Hamela
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique UMR 9004, Université de Montpellier, Montpellier 34293, France
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique UMR 9004, Université de Montpellier, Montpellier 34293, France.,INSERM, Institut de Recherche en Infectiologie de Montpellier, Montpellier 34293, France
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25
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Mavrich TN, Gauthier C, Abad L, Bowman CA, Cresawn SG, Hatfull GF. pdm_utils: a SEA-PHAGES MySQL phage database management toolkit. Bioinformatics 2021; 37:2464-2466. [PMID: 33226064 DOI: 10.1093/bioinformatics/btaa983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/27/2020] [Accepted: 11/10/2020] [Indexed: 01/21/2023] Open
Abstract
SUMMARY Bacteriophages (phages) are incredibly abundant and genetically diverse. The volume of phage genomics data is rapidly increasing, driven in part by the SEA-PHAGES program, which isolates, sequences and manually annotates hundreds of phage genomes each year. With an ever-expanding genomics dataset, there are many opportunities for generating new biological insights through comparative genomic and bioinformatic analyses. As a result, there is a growing need to be able to store, update, explore and analyze phage genomics data. The package pdm_utils provides a collection of tools for MySQL phage database management designed to meet specific needs in the SEA-PHAGES program and phage genomics generally. AVAILABILITY AND IMPLEMENTATION https://pypi.org/project/pdm-utils/.
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Affiliation(s)
- Travis N Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Christian Gauthier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Charles A Bowman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven G Cresawn
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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26
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Abstract
Antibiotic resistance in bacterial pathogens presents a substantial threat to the control of infectious diseases. Development of new classes of antibiotics has slowed in recent years due to pressures of cost and market profitability, and there is a strong need for new antimicrobial therapies. The therapeutic use of bacteriophages has long been considered, with numerous anecdotal reports of success. Interest in phage therapy has been renewed by recent clinical successes in case studies with personalized phage cocktails, and several clinical trials are in progress. We discuss recent progress in the therapeutic use of phages and contemplate the key factors influencing the opportunities and challenges. With strong safety profiles, the main challenges of phage therapeutics involve strain variation among clinical isolates of many pathogens, battling phage resistance, and the potential limitations of host immune responses. However, the opportunities are considerable, with the potential to enhance current antibiotic efficacy, protect newly developed antibiotics, and provide a last resort in response to complete antibiotic failure. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA; ,
| | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA; ,
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA;
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27
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Abstract
Actinobacteriophages are viruses that infect bacterial hosts in the phylum Actinobacteria. More than 17,000 actinobacteriophages have been described and over 3,000 complete genome sequences reported, resulting from large-scale, high-impact, integrated research-education initiatives such as the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) program. Their genomic diversity is enormous; actinobacteriophages comprise many architecturally mosaic genomes with distinct DNA sequences. Their genome diversity is driven by the highly dynamic interactions between phages and their hosts, and prophages can confer a variety of systems that defend against attack by genetically distinct phages; phages can neutralize these defense systems by coding for counter-defense proteins. These phages not only provide insights into diverse and dynamic phage populations but also have provided numerous tools for mycobacterial genetics. A case study using a three-phage cocktail to treat a patient with a drug-resistant Mycobacterium abscessus suggests that phages may have considerable potential for the therapeutic treatment of mycobacterial infections.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA;
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28
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Dedrick RM, Freeman KG, Nguyen JA, Bahadirli-Talbott A, Smith BE, Wu AE, Ong AS, Lin CT, Ruppel LC, Parrish NM, Hatfull GF, Cohen KA. Potent antibody-mediated neutralization limits bacteriophage treatment of a pulmonary Mycobacterium abscessus infection. Nat Med 2021; 27:1357-1361. [PMID: 34239133 DOI: 10.1038/s41591-021-01403-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/21/2021] [Indexed: 12/31/2022]
Abstract
An 81-year-old immunocompetent patient with bronchiectasis and refractory Mycobacterium abscessus lung disease was treated for 6 months with a three-phage cocktail active against the strain. In this case study of phage to lower infectious burden, intravenous administration was safe and reduced the M. abscessus sputum load tenfold within one month. However, after two months, M. abscessus counts increased as the patient mounted a robust IgM- and IgG-mediated neutralizing antibody response to the phages, which was associated with limited therapeutic efficacy.
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Affiliation(s)
| | - Krista G Freeman
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jan A Nguyen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Asli Bahadirli-Talbott
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bailey E Smith
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew E Wu
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aaron S Ong
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cheng Ting Lin
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lisa C Ruppel
- Investigational Pharmacy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole M Parrish
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Graham F Hatfull
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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29
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Zaworski J, McClung C, Ruse C, Weigele PR, Hendrix RW, Ko CC, Edgar R, Hatfull GF, Casjens SR, Raleigh EA. Genome analysis of Salmonella enterica serovar Typhimurium bacteriophage L, indicator for StySA (StyLT2III) restriction-modification system action. G3 (Bethesda) 2021; 11:6044188. [PMID: 33561243 PMCID: PMC8022706 DOI: 10.1093/g3journal/jkaa037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
Bacteriophage L, a P22-like phage of Salmonella enterica sv Typhimurium LT2, was important for definition of mosaic organization of the lambdoid phage family and for characterization of restriction-modification systems of Salmonella. We report the complete genome sequences of bacteriophage L cI–40 13–am43 and L cII–101; the deduced sequence of wildtype L is 40,633 bp long with a 47.5% GC content. We compare this sequence with those of P22 and ST64T, and predict 72 Coding Sequences, 2 tRNA genes and 14 intergenic rho-independent transcription terminators. The overall genome organization of L agrees with earlier genetic and physical evidence; for example, no secondary immunity region (immI: ant, arc) or known genes for superinfection exclusion (sieA and sieB) are present. Proteomic analysis confirmed identification of virion proteins, along with low levels of assembly intermediates and host cell envelope proteins. The genome of L is 99.9% identical at the nucleotide level to that reported for phage ST64T, despite isolation on different continents ∼35 years apart. DNA modification by the epigenetic regulator Dam is generally incomplete. Dam modification is also selectively missing in one location, corresponding to the P22 phase-variation-sensitive promoter region of the serotype-converting gtrABC operon. The number of sites for SenLTIII (StySA) action may account for stronger restriction of L (13 sites) than of P22 (3 sites).
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Affiliation(s)
- Julie Zaworski
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Colleen McClung
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Cristian Ruse
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robert Edgar
- Bioengineering Department, University of Pittsburgh, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.,School of Biological Science, University of Utah, Salt Lake City, UT 84112, USA
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30
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Guerrero-Bustamante CA, Dedrick RM, Garlena RA, Russell DA, Hatfull GF. Toward a Phage Cocktail for Tuberculosis: Susceptibility and Tuberculocidal Action of Mycobacteriophages against Diverse Mycobacterium tuberculosis Strains. mBio 2021; 12:e00973-21. [PMID: 34016711 PMCID: PMC8263002 DOI: 10.1128/mbio.00973-21] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022] Open
Abstract
The global health burden of human tuberculosis (TB) and the widespread antibiotic resistance of its causative agent Mycobacterium tuberculosis warrant new strategies for TB control. The successful use of a bacteriophage cocktail to treat a Mycobacterium abscessus infection suggests that phages could play a role in tuberculosis therapy. To assemble a phage cocktail with optimal therapeutic potential for tuberculosis, we have explored mycobacteriophage diversity to identify phages that demonstrate tuberculocidal activity and determined the phage infection profiles for a diverse set of strains spanning the major lineages of human-adapted strains of the Mycobacterium tuberculosis complex. Using a combination of genome engineering and bacteriophage genetics, we have assembled a five-phage cocktail that minimizes the emergence of phage resistance and cross-resistance to multiple phages, and which efficiently kills the M. tuberculosis strains tested. Furthermore, these phages function without antagonizing antibiotic effectiveness, and infect both isoniazid-resistant and -sensitive strains.IMPORTANCE Tuberculosis kills 1.5 million people each year, and resistance to commonly used antibiotics contributes to treatment failures. The therapeutic potential of bacteriophages against Mycobacterium tuberculosis offers prospects for shortening antibiotic regimens, provides new tools for treating multiple drug-resistant (MDR)-TB and extensively drug-resistant (XDR)-TB infections, and protects newly developed antibiotics against rapidly emerging resistance to them. Identifying a suitable suite of phages active against diverse M. tuberculosis isolates circumvents many of the barriers to initiating clinical evaluation of phages as part of the arsenal of antituberculosis therapeutics.
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Affiliation(s)
| | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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31
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Pezo V, Jaziri F, Bourguignon PY, Louis D, Jacobs-Sera D, Rozenski J, Pochet S, Herdewijn P, Hatfull GF, Kaminski PA, Marliere P. Noncanonical DNA polymerization by aminoadenine-based siphoviruses. Science 2021; 372:520-524. [PMID: 33926956 DOI: 10.1126/science.abe6542] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/25/2021] [Indexed: 01/05/2023]
Abstract
Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous to the Klenow fragment of bacterial DNA polymerase I that includes 3'-exonuclease but lacks 5'-exonuclease, were found to preferentially select for aminoadenine instead of adenine in deoxynucleoside triphosphate incorporation templated by thymine. Polymerase genes occur in synteny with genes for a biosynthesis enzyme that produces aminoadenine deoxynucleotides in a wide array of Siphoviridae bacteriophages. Congruent phylogenetic clustering of the polymerases and biosynthesis enzymes suggests that aminoadenine has propagated in DNA alongside adenine since archaic stages of evolution.
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Affiliation(s)
- Valerie Pezo
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Faten Jaziri
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France
| | - Pierre-Yves Bourguignon
- Werkstatt fuer Potenzielle Genetik, Naunynstrasse 30, 10997 Berlin, Germany.,TESSSI, 81 Rue Réaumur, 75002 Paris, France
| | | | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260 USA
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Sylvie Pochet
- Organic Chemistry, CNRS UMR3523, Department of Chemistry and Biocatalysis, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260 USA
| | - Pierre-Alexandre Kaminski
- Biology of Gram-Positive Pathogens, CNRS URL3526, Department of Microbiology, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Philippe Marliere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France. .,TESSSI, 81 Rue Réaumur, 75002 Paris, France
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Wetzel KS, Guerrero-Bustamante CA, Dedrick RM, Ko CC, Freeman KG, Aull HG, Divens AM, Rock JM, Zack KM, Hatfull GF. CRISPY-BRED and CRISPY-BRIP: efficient bacteriophage engineering. Sci Rep 2021; 11:6796. [PMID: 33762639 PMCID: PMC7990910 DOI: 10.1038/s41598-021-86112-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/10/2021] [Indexed: 02/07/2023] Open
Abstract
Genome engineering of bacteriophages provides opportunities for precise genetic dissection and for numerous phage applications including therapy. However, few methods are available for facile construction of unmarked precise deletions, insertions, gene replacements and point mutations in bacteriophages for most bacterial hosts. Here we describe CRISPY-BRED and CRISPY-BRIP, methods for efficient and precise engineering of phages in Mycobacterium species, with applicability to phages of a variety of other hosts. This recombineering approach uses phage-derived recombination proteins and Streptococcus thermophilus CRISPR-Cas9.
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Affiliation(s)
- Katherine S Wetzel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | | | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Haley G Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ashley M Divens
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
- Department of Biomedical Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Jeremy M Rock
- Department of Host-Pathogen Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Kira M Zack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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Judd JA, Canestrari J, Clark R, Joseph A, Lapierre P, Lasek-Nesselquist E, Mir M, Palumbo M, Smith C, Stone M, Upadhyay A, Wirth SE, Dedrick RM, Meier CG, Russell DA, Dills A, Dove E, Kester J, Wolf ID, Zhu J, Rubin ER, Fortune S, Hatfull GF, Gray TA, Wade JT, Derbyshire KM. A Mycobacterial Systems Resource for the Research Community. mBio 2021; 12:e02401-20. [PMID: 33653882 PMCID: PMC8092266 DOI: 10.1128/mbio.02401-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as Escherichia coli and Bacillus subtilis To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism Mycobacterium smegmatis This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including Mycobacterium tuberculosis, in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many Mycobacterium species, including the less experimentally tractable pathogens M. abscessus, M. avium, M. kansasii, M. leprae, M. marinum, M. tuberculosis, and M. ulceransIMPORTANCE Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using Mycobacterium smegmatis as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community.
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Affiliation(s)
- J A Judd
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - J Canestrari
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - R Clark
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - A Joseph
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - P Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - E Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - M Mir
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - M Palumbo
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - C Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - M Stone
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - A Upadhyay
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - S E Wirth
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - R M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - C G Meier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - D A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - A Dills
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - E Dove
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - J Kester
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - I D Wolf
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - J Zhu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - E R Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - S Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - G F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - T A Gray
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - J T Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - K M Derbyshire
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
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Ko CC, Hatfull GF. Identification of mycobacteriophage toxic genes reveals new features of mycobacterial physiology and morphology. Sci Rep 2020; 10:14670. [PMID: 32887931 PMCID: PMC7474061 DOI: 10.1038/s41598-020-71588-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/07/2020] [Indexed: 01/01/2023] Open
Abstract
Double-stranded DNA tailed bacteriophages typically code for 50–200 genes, of which 15–35 are involved in virion structure and assembly, DNA packaging, lysis, and DNA metabolism. However, vast numbers of other phage genes are small, are not required for lytic growth, and are of unknown function. The 1,885 sequenced mycobacteriophages encompass over 200,000 genes in 7,300 distinct protein ‘phamilies’, 77% of which are of unknown function. Gene toxicity provides potential insights into function, and here we screened 193 unrelated genes encoded by 13 different mycobacteriophages for their ability to impair the growth of Mycobacterium smegmatis. We identified 45 (23%) mycobacteriophage genes that are toxic when expressed. The impacts on M. smegmatis growth range from mild to severe, but many cause irreversible loss of viability. Expression of most of the severely toxic genes confers altered cellular morphologies, including filamentation, polar bulging, curving, and, surprisingly, loss of viability of one daughter cell at division, suggesting specific impairments of mycobacterial growth. Co-immunoprecipitation and mass spectrometry show that toxicity is frequently associated with interaction with host proteins and alteration or inactivation of their function. Mycobacteriophages thus present a massive reservoir of genes for identifying mycobacterial essential functions, identifying potential drug targets and for exploring mycobacteriophage physiology.
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Affiliation(s)
- Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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Jacobs-Sera D, Abad LA, Alvey RM, Anders KR, Aull HG, Bhalla SS, Blumer LS, Bollivar DW, Bonilla JA, Butela KA, Coomans RJ, Cresawn SG, D'Elia T, Diaz A, Divens AM, Edgington NP, Frederick GD, Gainey MD, Garlena RA, Grant KW, Gurney SMR, Hendrickson HL, Hughes LE, Kenna MA, Klyczek KK, Kotturi H, Mavrich TN, McKinney AL, Merkhofer EC, Moberg Parker J, Molloy SD, Monti DL, Pape-Zambito DA, Pollenz RS, Pope WH, Reyna NS, Rinehart CA, Russell DA, Shaffer CD, Sivanathan V, Stoner TH, Stukey J, Sunnen CN, Tolsma SS, Tsourkas PK, Wallen JR, Ware VC, Warner MH, Washington JM, Westover KM, Whitefleet-Smith JL, Wiersma-Koch HI, Williams DC, Zack KM, Hatfull GF. Genomic diversity of bacteriophages infecting Microbacterium spp. PLoS One 2020; 15:e0234636. [PMID: 32555720 PMCID: PMC7302621 DOI: 10.1371/journal.pone.0234636] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/29/2020] [Indexed: 11/19/2022] Open
Abstract
The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.
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Affiliation(s)
- Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lawrence A. Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Richard M. Alvey
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - Kirk R. Anders
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Haley G. Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Suparna S. Bhalla
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Lawrence S. Blumer
- Department of Biology, Morehouse College, Atlanta, Georgia, United States of America
| | - David W. Bollivar
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - J. Alfred Bonilla
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Roy J. Coomans
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina, United States of America
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Tom D'Elia
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Arturo Diaz
- Department of Biology, La Sierra University, Riverside, California, United States of America
| | - Ashley M. Divens
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nicholas P. Edgington
- Department of Biology, Southern Connecticut State University, New Haven, Connecticut, United States of America
| | - Gregory D. Frederick
- Department of Biology and Kinesiology, LeTourneau University, Longview, Texas, United States of America
| | - Maria D. Gainey
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kenneth W. Grant
- Department of Pathology, Wake Forest Baptist Health, Winston-Salem, North Carolina, United States of America
| | - Susan M. R. Gurney
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | | | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Margaret A. Kenna
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Karen K. Klyczek
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Hari Kotturi
- Department of Biology, University of Central Oklahoma, Edmond, Oklahoma, United States of America
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Angela L. McKinney
- Department of Biology, Nebraska Wesleyan University, Lincoln, Nebraska, United States of America
| | - Evan C. Merkhofer
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Sally D. Molloy
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, United States of America
| | - Denise L. Monti
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Dana A. Pape-Zambito
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Richard S. Pollenz
- Department Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathan S. Reyna
- Department of Biology, Ouachita Baptist University, Arkadelphia, Arkansas, United States of America
| | - Claire A. Rinehart
- Department of Biology, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christopher D. Shaffer
- Department of Biology, University of Washington in St. Louis, St. Louis, Missouri, United States of America
| | - Viknesh Sivanathan
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Ty H. Stoner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joseph Stukey
- Biology Department, Hope College, Holland, Michigan, United States of America
| | - C. Nicole Sunnen
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Sara S. Tolsma
- Biology Department, Northwestern College, Orange City, Iowa, United States of America
| | - Philippos K. Tsourkas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, United States of America
| | - Jamie R. Wallen
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Vassie C. Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Marcie H. Warner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Kristi M. Westover
- Department of Biology, Winthrop University, Rock Hill, South Carolina, United States of America
| | - JoAnn L. Whitefleet-Smith
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Helen I. Wiersma-Koch
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Daniel C. Williams
- Department of Biology, Coastal Carolina University, Conway, South Carolina, United States of America
| | - Kira M. Zack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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36
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Hutinet G, Kot W, Cui L, Hillebrand R, Balamkundu S, Gnanakalai S, Neelakandan R, Carstens AB, Fa Lui C, Tremblay D, Jacobs-Sera D, Sassanfar M, Lee YJ, Weigele P, Moineau S, Hatfull GF, Dedon PC, Hansen LH, de Crécy-Lagard V. 7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat Commun 2019; 10:5442. [PMID: 31784519 PMCID: PMC6884629 DOI: 10.1038/s41467-019-13384-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, was recently detected in genomic DNA of Enterobacteria phage 9g and was proposed to protect phage DNA from a wide variety of restriction enzymes. In this study, we identify three additional 2'-deoxy-7-deazaguanine modifications, which are all intermediates of the same pathway, in viruses: 2'-deoxy-7-amido-7-deazaguanine (dADG), 2'-deoxy-7-cyano-7-deazaguanine (dPreQ0) and 2'-deoxy-7- aminomethyl-7-deazaguanine (dPreQ1). We identify 180 phages or archaeal viruses that encode at least one of the enzymes of this pathway with an overrepresentation (60%) of viruses potentially infecting pathogenic microbial hosts. Genetic studies with the Escherichia phage CAjan show that DpdA is essential to insert the 7-deazaguanine base in phage genomic DNA and that 2'-deoxy-7-deazaguanine modifications protect phage DNA from host restriction enzymes.
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Affiliation(s)
- Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Roman Hillebrand
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Nitto Denko Avecia, 125 Fortune Boulevard, Milford, MA, 01757, USA
| | - Seetharamsingh Balamkundu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Shanmugavel Gnanakalai
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Ramesh Neelakandan
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | | | - Chuan Fa Lui
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Denise Tremblay
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Mandana Sassanfar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Peter Weigele
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Sylvain Moineau
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Graham F Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
- University of Florida, Genetics Institute, Gainesville, Florida, 32610, USA.
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37
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Oliveira H, Sampaio M, Melo LDR, Dias O, Pope WH, Hatfull GF, Azeredo J. Staphylococci phages display vast genomic diversity and evolutionary relationships. BMC Genomics 2019; 20:357. [PMID: 31072320 PMCID: PMC6507118 DOI: 10.1186/s12864-019-5647-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/27/2019] [Indexed: 11/25/2022] Open
Abstract
Background Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator–prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are under-sampled and therefore present an untapped and uncharacterized source of genetic diversity, typically characterized by highly mosaic genomes and no universal genes. To better understand the diversity and relationships among phages infecting human pathogens, we have analysed the complete genome sequences of 205 phages of Staphylococcus sp. Results These are predicted to encode 20,579 proteins, which can be sorted into 2139 phamilies (phams) of related sequences; 745 of these are orphams and possess only a single gene. Based on shared gene content, these phages were grouped into four clusters (A, B, C and D), 27 subclusters (A1-A2, B1-B17, C1-C6 and D1-D2) and one singleton. However, the genomes have mosaic architectures and individual genes with common ancestors are positioned in distinct genomic contexts in different clusters. The staphylococcal Cluster B siphoviridae are predicted to be temperate, and the integration cassettes are often closely-linked to genes implicated in bacterial virulence determinants. There are four unusual endolysin organization strategies found in Staphylococcus phage genomes, with endolysins predicted to be encoded as single genes, two genes spliced, two genes adjacent and as a single gene with inter-lytic-domain secondary translational start site. Comparison of the endolysins reveals multi-domain modularity, with conservation of the SH3 cell wall binding domain. Conclusions This study provides a high-resolution view of staphylococcal viral genetic diversity, and insights into their gene flux patterns within and across different phage groups (cluster and subclusters) providing insights into their evolution. Electronic supplementary material The online version of this article (10.1186/s12864-019-5647-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hugo Oliveira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
| | - Marta Sampaio
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Oscar Dias
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Welkin H Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
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38
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Dedrick RM, Guerrero-Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, Gilmour KC, Soothill J, Jacobs-Sera D, Schooley RT, Hatfull GF, Spencer H. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat Med 2019; 25:730-733. [PMID: 31068712 PMCID: PMC6557439 DOI: 10.1038/s41591-019-0437-z] [Citation(s) in RCA: 720] [Impact Index Per Article: 144.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022]
Abstract
A 15-year-old patient with cystic fibrosis with a disseminated Mycobacterium abscessus infection was treated with a three-phage cocktail following bilateral lung transplantation. Effective lytic phage derivatives that efficiently kill the infectious M. abscessus strain were developed by genome engineering and forward genetics. Intravenous phage treatment was well tolerated and associated with objective clinical improvement, including sternal wound closure, improved liver function, and substantial resolution of infected skin nodules.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | | | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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Dedrick RM, Guerrero Bustamante CA, Garlena RA, Pinches RS, Cornely K, Hatfull GF. Mycobacteriophage ZoeJ: A broad host-range close relative of mycobacteriophage TM4. Tuberculosis (Edinb) 2019; 115:14-23. [PMID: 30948168 DOI: 10.1016/j.tube.2019.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 10/27/2022]
Abstract
A collection of over 1600 sequenced bacteriophages isolated on a single host strain, Mycobacterium smegmatis mc2155, can be grouped into over two dozen types that have little or no nucleotide sequence similarity to each other. One group, Cluster K, can be divided into several subclusters, and the well-characterized and much exploited phage TM4 lies in Subcluster K2. Many of the Cluster K phages have broad host ranges and infect both fast- and slow-growing mycobacterial strains. Here we describe phage ZoeJ, a new Subcluster K2 member, which infects a broad spectrum of mycobacterial hosts including M. smegmatis, Mycobacterium tuberculosis, and Mycobacterium avium. ZoeJ has extensive sequence similarity to TM4, and comparative analysis reveals the precise deletion conferring the lytic phenotype of TM4. The ZoeJ immunity repressor was identified as gene 45, which is prophage-expressed, is required for lysogeny, and is sufficient to confer superinfection immunity to ZoeJ. ZoeJ gp45 also confers immunity to Subcluster K2 phage Milly, and Subcluster K1 phages Adephagia and CrimD, but surprisingly not to TM4. RNAseq analysis reveals the temporal pattern of early and late gene expressions in ZoeJ lytic growth and suggests a role for the ESAS motifs for gene regulation.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - R Seth Pinches
- Department of Chemistry and Biochemistry, Providence College, Providence, RI 02918, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, RI 02918, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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40
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Abstract
We describe a recombineering-based method for the genetic manipulation of lytically replicating bacteriophages, focusing on mycobacteriophages. The approach utilizes recombineering-proficient strains of Mycobacterium smegmatis and employs a cotransformation strategy with purified phage genomic DNA and a mutagenic substrate, which selects for only those cells that are competent to take up DNA. The cotransformation method, combined with the high rates of recombination obtained in M. smegmatis recombineering strains, allows for the efficient and rapid generation of bacteriophage mutants.
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Affiliation(s)
- Laura J Marinelli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
- Laboratorio "Bacteriófagos y Aplicaciones Biotecnológicas", Departamento de Química Biológica, FCEyN, UBA, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires, Argentina
| | - Graham F Hatfull
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA, USA
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41
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Carstens AB, Djurhuus AM, Kot W, Jacobs-Sera D, Hatfull GF, Hansen LH. Unlocking the Potential of 46 New Bacteriophages for Biocontrol of Dickeya Solani. Viruses 2018; 10:E621. [PMID: 30423804 PMCID: PMC6267328 DOI: 10.3390/v10110621] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 01/12/2023] Open
Abstract
Modern agriculture is expected to face an increasing global demand for food while also needing to comply with higher sustainability standards. Therefore, control of crop pathogens requires new, green alternatives to current methods. Potatoes are susceptible to several bacterial diseases, with infections by soft rot Enterobacteriaceae (SRE) being a significant contributor to the major annual losses. As there are currently no efficient ways of combating SRE, we sought to develop an approach that could easily be incorporated into the potato production pipeline. To this end, 46 phages infecting the emerging potato pathogen Dickeya solani were isolated and thoroughly characterized. The 46 isolated phages were grouped into three different groups based on DNA similarity, representing two distinct clusters and a singleton. One cluster showed similarity to phages previously used to successfully treat soft rot in potatoes, whereas the remaining phages were novel and showed only very limited similarity to previously isolated phages. We selected six diverse phages in order to create the hereto most complex phage cocktail against SRE. The cocktail was applied in a proof-of-principle experiment to treat soft rot in potatoes under simulated storage conditions. We show that the phage cocktail was able to significantly reduce the incidence of soft rot as well as disease severity after 5 days of storage post-infection with Dickeya solani. This confirms results from previous studies that phages represent promising biocontrol agents against SRE infection in potato.
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Affiliation(s)
- Alexander B Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Amaru M Djurhuus
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
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42
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Rondón L, Urdániz E, Latini C, Payaslian F, Matteo M, Sosa EJ, Do Porto DF, Turjanski AG, Nemirovsky S, Hatfull GF, Poggi S, Piuri M. Fluoromycobacteriophages Can Detect Viable Mycobacterium tuberculosis and Determine Phenotypic Rifampicin Resistance in 3-5 Days From Sputum Collection. Front Microbiol 2018; 9:1471. [PMID: 30026735 PMCID: PMC6041418 DOI: 10.3389/fmicb.2018.01471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/12/2018] [Indexed: 11/24/2022] Open
Abstract
The World Health Organization (WHO) estimates that 40% of tuberculosis (TB) cases are not diagnosed and treated correctly. Even though there are several diagnostic tests available in the market, rapid, easy, inexpensive detection, and drug susceptibility testing (DST) of Mycobacterium tuberculosis is still of critical importance specially in low and middle-income countries with high incidence of the disease. In this work, we have developed a microscopy-based methodology using the reporter mycobacteriophage mCherrybombϕ for detection of Mycobacterium spp. and phenotypic determination of rifampicin resistance within just days from sputum sample collection. Fluoromycobacteriophage methodology is compatible with regularly used protocols in clinical laboratories for TB diagnosis and paraformaldehyde fixation after infection reduces biohazard risks with sample analysis by fluorescence microscopy. We have also set up conditions for discrimination between M. tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM) strains by addition of p-nitrobenzoic acid (PNB) during the assay. Using clinical isolates of pre-XDR and XDR-TB strains from this study, we tested mCherrybombΦ for extended DST and we compared the antibiotic resistance profile with those predicted by whole genome sequencing. Our results emphasize the utility of a phenotypic test for M. tuberculosis extended DST. The many attributes of mCherrybombΦ suggests this could be a useful component of clinical microbiological laboratories for TB diagnosis and since only viable cells are detected this could be a useful tool for monitoring patient response to treatment.
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Affiliation(s)
- Liliana Rondón
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales - Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Estefanía Urdániz
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales - Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Cecilia Latini
- Instituto de Tisioneumonología Raúl F. Vaccarezza, Hospital de Infecciosas Dr. F. J. Muñiz, Buenos Aires, Argentina
| | - Florencia Payaslian
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales - Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Mario Matteo
- Instituto de Tisioneumonología Raúl F. Vaccarezza, Hospital de Infecciosas Dr. F. J. Muñiz, Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Darío F Do Porto
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adrian G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales - Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Sergio Nemirovsky
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales - Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Graham F Hatfull
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA, United States
| | - Susana Poggi
- Instituto de Tisioneumonología Raúl F. Vaccarezza, Hospital de Infecciosas Dr. F. J. Muñiz, Buenos Aires, Argentina
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales - Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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Abstract
Roger W. Hendrix was at the forefront of bacteriophage biology for nearly 50 years and was central to our understanding of both viral capsid assembly and phage genomic diversity and evolution. Roger's warm and gentle demeanor belied a razor-sharp mind and warmed him to numerous highly productive collaborations that amplified his scientific impact. Roger was always completely open with scientific ideas while at the same time quietly agitating with a stream of new ways of thinking about problems and nudging our communities to search for innovative solutions: a gentle but highly effective provocateur.
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Affiliation(s)
- Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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44
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Ko CC, Hatfull GF. Mycobacteriophage Fruitloop gp52 inactivates Wag31 (DivIVA) to prevent heterotypic superinfection. Mol Microbiol 2018; 108:443-460. [PMID: 29488662 DOI: 10.1111/mmi.13946] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2018] [Indexed: 01/04/2023]
Abstract
Bacteriophages engage in complex dynamic interactions with their bacterial hosts and with each other. Bacteria have numerous mechanisms to resist phage infection, and phages must co-evolve by overcoming bacterial resistance or by choosing an alternative host. Phages also compete with each other, both during lysogeny by prophage-mediated defense against viral attack and by superinfection exclusion during lytic replication. Phages are enormously diverse genetically and are replete with small genes of unknown function, many of which are not required for lytic growth, but which may modulate these bacteria-phage and phage-phage dynamics. Using cellular toxicity of phage gene overexpression as an assay, we identified the 93-residue protein gp52 encoded by Cluster F mycobacteriophage Fruitloop. The toxicity of Fruitloop gp52 overexpression results from interaction with and inactivation of Wag31 (DivIVA), an essential Mycobacterium smegmatis protein organizing cell wall biosynthesis at the growing cellular poles. Fruitloop gene 52 is expressed early in lytic growth and is not required for normal Fruitloop lytic replication but interferes with Subcluster B2 phages such as Hedgerow and Rosebush. We conclude that Hedgerow and Rosebush are Wag31-dependent phages and that Fruitloop gp52 confers heterotypic superinfection exclusion by inactivating Wag31.
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Affiliation(s)
- Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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45
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Cheng L, Marinelli LJ, Grosset N, Fitz-Gibbon ST, Bowman CA, Dang BQ, Russell DA, Jacobs-Sera D, Shi B, Pellegrini M, Miller JF, Gautier M, Hatfull GF, Modlin RL. Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages. BMC Microbiol 2018; 18:19. [PMID: 29490612 PMCID: PMC5831693 DOI: 10.1186/s12866-018-1159-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 02/15/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND A remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which are highly homogeneous. Phages infecting the related species, which is also a member of the Propionibacteriaceae family, Propionibacterium freudenreichii, a bacterium used in production of Swiss-type cheeses, have also been described and are common contaminants of the cheese manufacturing process. However, little is known about their genetic composition and diversity. RESULTS We obtained seven independently isolated bacteriophages that infect P. freudenreichii from Swiss-type cheese samples, and determined their complete genome sequences. These data revealed that all seven phage isolates are of similar genomic length and GC% content, but their genomes are highly diverse, including genes encoding the capsid, tape measure, and tail proteins. In contrast to C. acnes phages, all P. freudenreichii phage genomes encode a putative integrase protein, suggesting they are capable of lysogenic growth. This is supported by the finding of related prophages in some P. freudenreichii strains. The seven phages could further be distinguished as belonging to two distinct genomic types, or 'clusters', based on nucleotide sequences, and host range analyses conducted on a collection of P. freudenreichii strains show a higher degree of host specificity than is observed for the C. acnes phages. CONCLUSIONS Overall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, as evidenced by their higher genetic diversity, potential for lysogenic growth, and more restricted host ranges. This suggests substantial differences in the evolution of these related species from the Propionibacteriaceae family and their phages, which is potentially related to their distinct environmental niches.
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Affiliation(s)
- Lucy Cheng
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Laura J. Marinelli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Noël Grosset
- Equipe Microbiologie de l’œuf et des Ovoproduits (MICOV), Agrocampus Ouest, INRA, (UMR1253) Science et Technologie du Lait et de l’Œuf, Rennes, France
| | - Sorel T. Fitz-Gibbon
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Charles A. Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Brian Q. Dang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Baochen Shi
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Jeff F. Miller
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Michel Gautier
- Equipe Microbiologie de l’œuf et des Ovoproduits (MICOV), Agrocampus Ouest, INRA, (UMR1253) Science et Technologie du Lait et de l’Œuf, Rennes, France
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Robert L. Modlin
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
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46
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Abstract
The Actinobacteriophage Database (PhagesDB) is a comprehensive, interactive, database-backed website that collects and shares information related to the discovery, characterization and genomics of viruses that infect Actinobacterial hosts. To date, more than 8000 bacteriophages-including over 1600 with sequenced genomes-have been entered into the database. PhagesDB plays a crucial role in organizing the discoveries of phage biologists around the world-including students in the SEA-PHAGES program-and has been cited in over 50 peer-reviewed articles. Availability and Implementation http://phagesdb.org/. Contact gfh@pitt.edu.
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47
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Dedrick RM, Mavrich TN, Ng WL, Hatfull GF. Expression and evolutionary patterns of mycobacteriophage D29 and its temperate close relatives. BMC Microbiol 2017; 17:225. [PMID: 29197343 PMCID: PMC5712189 DOI: 10.1186/s12866-017-1131-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/16/2017] [Indexed: 11/17/2022] Open
Abstract
Background Mycobacteriophages are viruses that infect Mycobacterium hosts. A large collection of phages known to infect the same bacterial host strain – Mycobacterium smegmatis mc2155 – exhibit substantial diversity and characteristically mosaic architectures. The well-studied lytic mycobacteriophage D29 appears to be a deletion derivative of a putative temperate parent, although its parent has yet to be identified. Results Here we describe three newly-isolated temperate phages – Kerberos, Pomar16 and StarStuff – that are related to D29, and are predicted to be very close relatives of its putative temperate parent, revealing the repressor and additional genes that are lost in D29. Transcriptional profiles show the patterns of both lysogenic and lytic gene expression and identify highly-expressed, abundant, stable, small non-coding transcripts made from the Pleft early lytic promoter, and which are toxic to M. smegmatis. Conclusions Comparative genomics of phages D29, Kerberos, Pomar16 and StarStuff provide insights into bacteriophage evolution, and comparative transcriptomics identifies the pattern of lysogenic and lytic expression with unusual features including highly expressed, small, non-coding RNAs. Electronic supplementary material The online version of this article (10.1186/s12866-017-1131-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Travis N Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Wei L Ng
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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48
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Klyczek KK, Bonilla JA, Jacobs-Sera D, Adair TL, Afram P, Allen KG, Archambault ML, Aziz RM, Bagnasco FG, Ball SL, Barrett NA, Benjamin RC, Blasi CJ, Borst K, Braun MA, Broomell H, Brown CB, Brynell ZS, Bue AB, Burke SO, Casazza W, Cautela JA, Chen K, Chimalakonda NS, Chudoff D, Connor JA, Cross TS, Curtis KN, Dahlke JA, Deaton BM, Degroote SJ, DeNigris DM, DeRuff KC, Dolan M, Dunbar D, Egan MS, Evans DR, Fahnestock AK, Farooq A, Finn G, Fratus CR, Gaffney BL, Garlena RA, Garrigan KE, Gibbon BC, Goedde MA, Guerrero Bustamante CA, Harrison M, Hartwell MC, Heckman EL, Huang J, Hughes LE, Hyduchak KM, Jacob AE, Kaku M, Karstens AW, Kenna MA, Khetarpal S, King RA, Kobokovich AL, Kolev H, Konde SA, Kriese E, Lamey ME, Lantz CN, Lapin JS, Lawson TO, Lee IY, Lee SM, Lee-Soety JY, Lehmann EM, London SC, Lopez AJ, Lynch KC, Mageeney CM, Martynyuk T, Mathew KJ, Mavrich TN, McDaniel CM, McDonald H, McManus CJ, Medrano JE, Mele FE, Menninger JE, Miller SN, Minick JE, Nabua CT, Napoli CK, Nkangabwa M, Oates EA, Ott CT, Pellerino SK, Pinamont WJ, Pirnie RT, Pizzorno MC, Plautz EJ, Pope WH, Pruett KM, Rickstrew G, Rimple PA, Rinehart CA, Robinson KM, Rose VA, Russell DA, Schick AM, Schlossman J, Schneider VM, Sells CA, Sieker JW, Silva MP, Silvi MM, Simon SE, Staples AK, Steed IL, Stowe EL, Stueven NA, Swartz PT, Sweet EA, Sweetman AT, Tender C, Terry K, Thomas C, Thomas DS, Thompson AR, Vanderveen L, Varma R, Vaught HL, Vo QD, Vonberg ZT, Ware VC, Warrad YM, Wathen KE, Weinstein JL, Wyper JF, Yankauskas JR, Zhang C, Hatfull GF. Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages. PLoS One 2017; 12:e0180517. [PMID: 28715480 PMCID: PMC5513430 DOI: 10.1371/journal.pone.0180517] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/17/2017] [Indexed: 11/19/2022] Open
Abstract
The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single Arthrobacter sp. strain. These phages include representatives of all three virion morphologies, and Jasmine is the first sequenced podovirus of an actinobacterial host. The phages also span considerable sequence diversity, and can be grouped into 10 clusters according to their nucleotide diversity, and two singletons each with no close relatives. However, the clusters/singletons appear to be genomically well separated from each other, and relatively few genes are shared between clusters. Genome size varies from among the smallest of siphoviral phages (15,319 bp) to over 70 kbp, and G+C contents range from 45-68%, compared to 63.4% for the host genome. Although temperate phages are common among other actinobacterial hosts, these Arthrobacter phages are primarily lytic, and only the singleton Galaxy is likely temperate.
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Affiliation(s)
- Karen K. Klyczek
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - J. Alfred Bonilla
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tamarah L. Adair
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Patricia Afram
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Katherine G. Allen
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Megan L. Archambault
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Rahat M. Aziz
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Filippa G. Bagnasco
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Sarah L. Ball
- Center for Life Sciences Education, The Ohio State University, Columbus, Ohio, United States of America
| | - Natalie A. Barrett
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Robert C. Benjamin
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Christopher J. Blasi
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Katherine Borst
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Mary A. Braun
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Haley Broomell
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Conner B. Brown
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Zachary S. Brynell
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Ashley B. Bue
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Sydney O. Burke
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - William Casazza
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Julia A. Cautela
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Kevin Chen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | | | - Dylan Chudoff
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Jade A. Connor
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Trevor S. Cross
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Kyra N. Curtis
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jessica A. Dahlke
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Bethany M. Deaton
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Sarah J. Degroote
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Danielle M. DeNigris
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Katherine C. DeRuff
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Milan Dolan
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - David Dunbar
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Marisa S. Egan
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Daniel R. Evans
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Abby K. Fahnestock
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Amal Farooq
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Garrett Finn
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | | | - Bobby L. Gaffney
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kelly E. Garrigan
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Bryan C. Gibbon
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Michael A. Goedde
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | | | - Melinda Harrison
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Megan C. Hartwell
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Emily L. Heckman
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Jennifer Huang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Kathryn M. Hyduchak
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Aswathi E. Jacob
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Machika Kaku
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Allen W. Karstens
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Margaret A. Kenna
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Susheel Khetarpal
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rodney A. King
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Amanda L. Kobokovich
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Hannah Kolev
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Sai A. Konde
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Elizabeth Kriese
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Morgan E. Lamey
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Carter N. Lantz
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jonathan S. Lapin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Temiloluwa O. Lawson
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - In Young Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Scott M. Lee
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Julia Y. Lee-Soety
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Emily M. Lehmann
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Shawn C. London
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - A. Javier Lopez
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kelly C. Lynch
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Catherine M. Mageeney
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Tetyana Martynyuk
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Kevin J. Mathew
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christopher M. McDaniel
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Hannah McDonald
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - C. Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jessica E. Medrano
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Francis E. Mele
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Jennifer E. Menninger
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Sierra N. Miller
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Josephine E. Minick
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Courtney T. Nabua
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Caroline K. Napoli
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Martha Nkangabwa
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Elizabeth A. Oates
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Cassandra T. Ott
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sarah K. Pellerino
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - William J. Pinamont
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Ross T. Pirnie
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Marie C. Pizzorno
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Emilee J. Plautz
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Katelyn M. Pruett
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Gabbi Rickstrew
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Patrick A. Rimple
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Claire A. Rinehart
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Kayla M. Robinson
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Victoria A. Rose
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amelia M. Schick
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Julia Schlossman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Victoria M. Schneider
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chloe A. Sells
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jeremy W. Sieker
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Morgan P. Silva
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Marissa M. Silvi
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Stephanie E. Simon
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Amanda K. Staples
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Isabelle L. Steed
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Emily L. Stowe
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Noah A. Stueven
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Porter T. Swartz
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Emma A. Sweet
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Abigail T. Sweetman
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Corrina Tender
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Katrina Terry
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Chrystal Thomas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Daniel S. Thomas
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Allison R. Thompson
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Lorianna Vanderveen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rohan Varma
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Hannah L. Vaught
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Quynh D. Vo
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Zachary T. Vonberg
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Vassie C. Ware
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Yasmene M. Warrad
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Kaitlyn E. Wathen
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Jonathan L. Weinstein
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Jacqueline F. Wyper
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jakob R. Yankauskas
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Christine Zhang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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49
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Carrigy NB, Chang RY, Leung SSY, Harrison M, Petrova Z, Pope WH, Hatfull GF, Britton WJ, Chan HK, Sauvageau D, Finlay WH, Vehring R. Anti-Tuberculosis Bacteriophage D29 Delivery with a Vibrating Mesh Nebulizer, Jet Nebulizer, and Soft Mist Inhaler. Pharm Res 2017. [PMID: 28646325 DOI: 10.1007/s11095-017-2213-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE To compare titer reduction and delivery rate of active anti-tuberculosis bacteriophage (phage) D29 with three inhalation devices. METHODS Phage D29 lysate was amplified to a titer of 11.8 ± 0.3 log10(pfu/mL) and diluted 1:100 in isotonic saline. Filters captured the aerosolized saline D29 preparation emitted from three types of inhalation devices: 1) vibrating mesh nebulizer; 2) jet nebulizer; 3) soft mist inhaler. Full-plate plaque assays, performed in triplicate at multiple dilution levels with the surrogate host Mycobacterium smegmatis, were used to quantify phage titer. RESULTS Respective titer reductions for the vibrating mesh nebulizer, jet nebulizer, and soft mist inhaler were 0.4 ± 0.1, 3.7 ± 0.1, and 0.6 ± 0.3 log10(pfu/mL). Active phage delivery rate was significantly greater (p < 0.01) for the vibrating mesh nebulizer (3.3x108 ± 0.8x108 pfu/min) than for the jet nebulizer (5.4x104 ± 1.3x104 pfu/min). The soft mist inhaler delivered 4.6x106 ± 2.0x106 pfu per 11.6 ± 1.6 μL ex-actuator dose. CONCLUSIONS Delivering active phage requires a prudent choice of inhalation device. The jet nebulizer was not a good choice for aerosolizing phage D29 under the tested conditions, due to substantial titer reduction likely occurring during droplet production. The vibrating mesh nebulizer is recommended for animal inhalation studies requiring large amounts of D29 aerosol, whereas the soft mist inhaler may be useful for self-administration of D29 aerosol.
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Affiliation(s)
- Nicholas B Carrigy
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Rachel Y Chang
- Advanced Drug Delivery Group, Faculty of Pharmacy, University of Sydney, Sydney, Australia
| | - Sharon S Y Leung
- Advanced Drug Delivery Group, Faculty of Pharmacy, University of Sydney, Sydney, Australia
| | - Melissa Harrison
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Zaritza Petrova
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Welkin H Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Warwick J Britton
- Centenary Institute of Cancer Medicine and Cell Biology, and Sydney Medical School, University of Sydney, Sydney, Australia
| | - Hak-Kim Chan
- Advanced Drug Delivery Group, Faculty of Pharmacy, University of Sydney, Sydney, Australia
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Warren H Finlay
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Reinhard Vehring
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada.
- Department of Mechanical Engineering, 10-203 Donadeo Innovation Centre for Engineering, University of Alberta, 9211 116th Street NW, Edmonton, AB, T6G 1H9, Canada.
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50
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Hanauer DI, Graham MJ, Hatfull GF. A Measure of College Student Persistence in the Sciences (PITS). CBE Life Sci Educ 2017; 15:ar54. [PMID: 27810869 PMCID: PMC5132351 DOI: 10.1187/cbe.15-09-0185] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 05/06/2023]
Abstract
Curricular changes that promote undergraduate persistence in science, technology, engineering, and mathematics (STEM) disciplines are likely associated with particular student psychological outcomes, and tools are needed that effectively assess these developments. Here, we describe the theoretical basis, psychometric properties, and predictive abilities of the Persistence in the Sciences (PITS) assessment survey designed to measure these in course-based research experiences (CREs). The survey is constructed from existing psychological assessment instruments, incorporating a six-factor structure consisting of project ownership (emotion and content), self-efficacy, science identity, scientific community values, and networking, and is supported by a partial confirmatory factor analysis. The survey has strong internal consistency (Cronbach's alpha: α = 0.96) and was validated using standard simple and multiple regression analyses. The regression analyses demonstrated that the factors of the PITS survey were significant predictors of the intent to become a research scientist and, as such, potentially valid for the measurement of persistence in the sciences. The PITS survey provides an effective method for measuring the psychological outcomes of undergraduate research experiences relevant to persistence in STEM and offers an approach to the development and validation of more sophisticated assessment tools that recognize the specificities of the type of educational opportunities embedded in a CRE.
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Affiliation(s)
- David I Hanauer
- Department of English, Indiana University of Pennsylvania, Indiana, PA 15705
| | - Mark J Graham
- Yale Center for Teaching and Learning, Yale University, New Haven, CT 06510
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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