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Ouyang X, Li X, Song J, Wang H, Wang S, Fang R, Li Z, Song N. Mycobacteriophages in diagnosis and alternative treatment of mycobacterial infections. Front Microbiol 2023; 14:1277178. [PMID: 37840750 PMCID: PMC10568470 DOI: 10.3389/fmicb.2023.1277178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Antimicrobial resistance is an increasing threat to human populations. The emergence of multidrug-resistant "superbugs" in mycobacterial infections has further complicated the processes of curing patients, thereby resulting in high morbidity and mortality. Early diagnosis and alternative treatment are important for improving the success and cure rates associated with mycobacterial infections and the use of mycobacteriophages is a potentially good option. Since each bacteriophage has its own host range, mycobacteriophages have the capacity to detect specific mycobacterial isolates. The bacteriolysis properties of mycobacteriophages make them more attractive when it comes to treating infectious diseases. In fact, they have been clinically applied in Eastern Europe for several decades. Therefore, mycobacteriophages can also treat mycobacteria infections. This review explores the potential clinical applications of mycobacteriophages, including phage-based diagnosis and phage therapy in mycobacterial infections. Furthermore, this review summarizes the current difficulties in phage therapy, providing insights into new treatment strategies against drug-resistant mycobacteria.
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Affiliation(s)
- Xudong Ouyang
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Xiaotian Li
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Jinmiao Song
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Hui Wang
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Shuxian Wang
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Ren Fang
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Zhaoli Li
- SAFE Pharmaceutical Technology Co. Ltd., Beijing, China
| | - Ningning Song
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
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2
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Lv S, Wang Y, Jiang K, Guo X, Zhang J, Zhou F, Li Q, Jiang Y, Yang C, Teng T. Genetic Engineering and Biosynthesis Technology: Keys to Unlocking the Chains of Phage Therapy. Viruses 2023; 15:1736. [PMID: 37632078 PMCID: PMC10457950 DOI: 10.3390/v15081736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Phages possess the ability to selectively eliminate pathogenic bacteria by recognizing bacterial surface receptors. Since their discovery, phages have been recognized for their potent bactericidal properties, making them a promising alternative to antibiotics in the context of rising antibiotic resistance. However, the rapid emergence of phage-resistant strains (generally involving temperature phage) and the limited host range of most phage strains have hindered their antibacterial efficacy, impeding their full potential. In recent years, advancements in genetic engineering and biosynthesis technology have facilitated the precise engineering of phages, thereby unleashing their potential as a novel source of antibacterial agents. In this review, we present a comprehensive overview of the diverse strategies employed for phage genetic engineering, as well as discuss their benefits and drawbacks in terms of bactericidal effect.
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Affiliation(s)
- Sixuan Lv
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Yuhan Wang
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Kaixin Jiang
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Xinge Guo
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Jing Zhang
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Fang Zhou
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Qiming Li
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Yuan Jiang
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Changyong Yang
- School of Nursing and Health, Henan University, Kaifeng 475004, China
| | - Tieshan Teng
- School of Nursing and Health, Henan University, Kaifeng 475004, China
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
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3
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Lang J, Zhen J, Li G, Li B, Xie J. Characterization and genome analysis of G1 sub-cluster mycobacteriophage Lang. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 109:105417. [PMID: 36804468 DOI: 10.1016/j.meegid.2023.105417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Phage therapy is revitalized as an alternative to antibiotics therapy against antimicrobials resistant pathogens. Mycobacteriophages are genetically diverse viruses that can specifically infect Mycobacterium genus including Mycobacterium tuberculosis and Mycobacterium smegmatis. Here, we isolated and annotated the genome of a mycobacteriophage Lang, a temperate mycobacteriophage isolated from the soil of Hohhot, Inner Mongolia, China, by using Mycolicibacterium smegmatis mc2 155 as the host. It belongs to the Siphoviridae family of Caudovirales as determined by transmission electron microscopy. The morphological characteristics and certain biological properties of the phage were considered in detail. Phage Lang genomes is 41,487 bp in length with 66.85% GC content and encodes 60 putative open reading frames and belongs to the G1 sub-cluster. Genome annotation indicated that genes for structure proteins, assembly proteins, replications/transcription and lysis of the host are present in function clucters. The genome sequence of phage Lang is more than 95% similar to that of mycobacteriophage Grizzly and Sweets, differing in substitutions, insertions and deletions in Lang. One-step growth curve revealed that Lang has a latent period of 30 min and a outbreak period of 90 min. The short latent period and rapid outbreak mark the unique properties of phage Lang, which can be another potential source for combating M. tuberculosis.
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Affiliation(s)
- Junying Lang
- Tuberculosis Department of Hohhot Second Hospital, Inner Mongolia, 010020, China; Hohhot Tuberculosis Prevention and Control Institute, Inner Mongolia, 010020, China
| | - Junfeng Zhen
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Guimei Li
- Tuberculosis Department of Hohhot Second Hospital, Inner Mongolia, 010020, China
| | - Bin Li
- Intensive Care Medicine Department of Hohhot First Hospital, Inner Mongolia, 010020, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China.
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4
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Hosseiniporgham S, Sechi LA. A Review on Mycobacteriophages: From Classification to Applications. Pathogens 2022; 11:777. [PMID: 35890022 PMCID: PMC9317374 DOI: 10.3390/pathogens11070777] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/24/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Mycobacterial infections are a group of life-threatening conditions triggered by fast- or slow-growing mycobacteria. Some mycobacteria, such as Mycobacterium tuberculosis, promote the deaths of millions of lives throughout the world annually. The control of mycobacterial infections is influenced by the challenges faced in the diagnosis of these bacteria and the capability of these pathogens to develop resistance against common antibiotics. Detection of mycobacterial infections is always demanding due to the intracellular nature of these pathogens that, along with the lipid-enriched structure of the cell wall, complicates the access to the internal contents of mycobacterial cells. Moreover, recent studies depicted that more than 20% of M. tuberculosis (Mtb) infections are multi-drug resistant (MDR), and only 50% of positive MDR-Mtb cases are responsive to standard treatments. Similarly, the susceptibility of nontuberculosis mycobacteria (NTM) to first-line tuberculosis antibiotics has also declined in recent years. Exploiting mycobacteriophages as viruses that infect mycobacteria has significantly accelerated the diagnosis and treatment of mycobacterial infections. This is because mycobacteriophages, regardless of their cycle type (temperate/lytic), can tackle barriers in the mycobacterial cell wall and make the infected bacteria replicate phage DNA along with their DNA. Although the infectivity of the majority of discovered mycobacteriophages has been evaluated in non-pathogenic M. smegmatis, more research is still ongoing to find mycobacteriophages specific to pathogenic mycobacteria, such as phage DS6A, which has been shown to be able to infect members of the M. tuberculosis complex. Accordingly, this review aimed to introduce some potential mycobacteriophages in the research, specifically those that are infective to the three troublesome mycobacteria, M. tuberculosis, M. avium subsp. paratuberculosis (MAP), and M. abscessus, highlighting their theranostic applications in medicine.
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Affiliation(s)
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Microbiology and Virology, Azienda Ospedaliera Universitaria (AOU) Sassari, 07100 Sassari, Italy
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5
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Abstract
Mycobacteriophages-bacteriophages infecting Mycobacterium hosts-contribute substantially to our understanding of viral diversity and evolution, provide resources for advancing Mycobacterium genetics, are the basis of high-impact science education programs, and show considerable therapeutic potential. Over 10,000 individual mycobacteriophages have been isolated by high school and undergraduate students using the model organism Mycobacterium smegmatis mc2155 and 2,100 have been completely sequenced, giving a high-resolution view of the phages that infect a single common host strain. The phage genomes are revealed to be highly diverse and architecturally mosaic and are replete with genes of unknown function. Mycobacteriophages have provided many widely used tools for Mycobacterium genetics including integration-proficient vectors and recombineering systems, as well as systems for efficient delivery of reporter genes, transposons, and allelic exchange substrates. The genomic insights and engineering tools have facilitated exploration of phages for treatment of Mycobacterium infections, although their full therapeutic potential has yet to be realized.
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Affiliation(s)
- Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States of America
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6
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Crane A, Versoza CJ, Hua T, Kapoor R, Lloyd L, Mehta R, Menolascino J, Morais A, Munig S, Patel Z, Sackett D, Schmit B, Sy M, Pfeifer SP. Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages. G3 (BETHESDA, MD.) 2021; 11:6353607. [PMID: 34849792 PMCID: PMC8527509 DOI: 10.1093/g3journal/jkab291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/09/2021] [Indexed: 01/21/2023]
Abstract
Bacteriophages infecting pathogenic hosts play an important role in medical research, not only as potential treatments for antibiotic-resistant infections but also offering novel insights into pathogen genetics and evolution. A prominent example is cluster K mycobacteriophages infecting Mycobacterium tuberculosis, a causative agent of tuberculosis in humans. However, as handling M. tuberculosis as well as other pathogens in a laboratory remains challenging, alternative nonpathogenic relatives, such as Mycobacterium smegmatis, are frequently used as surrogates to discover therapeutically relevant bacteriophages in a safer environment. Consequently, the individual host ranges of the majority of cluster K mycobacteriophages identified to date remain poorly understood. Here, we characterized the complete genome of Stinson, a temperate subcluster K1 mycobacteriophage with a siphoviral morphology. A series of comparative genomic analyses revealed strong similarities with other cluster K mycobacteriophages, including the conservation of an immunity repressor gene and a toxin/antitoxin gene pair. Patterns of codon usage bias across the cluster offered important insights into putative host ranges in nature, highlighting that although all cluster K mycobacteriophages are able to infect M. tuberculosis, they are less likely to have shared an evolutionary infection history with Mycobacterium leprae (underlying leprosy) compared to the rest of the genus’ host species. Moreover, subcluster K1 mycobacteriophages are able to integrate into the genomes of Mycobacterium abscessus and Mycobacterium marinum—two bacteria causing pulmonary and cutaneous infections which are often difficult to treat due to their drug resistance.
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Affiliation(s)
- Adele Crane
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Cyril J Versoza
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
| | - Tiana Hua
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Rohan Kapoor
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Lillian Lloyd
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Rithik Mehta
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | - Abraham Morais
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Saige Munig
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Zeel Patel
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Daniel Sackett
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Brandon Schmit
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Makena Sy
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
- Corresponding author: School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85281, USA.
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7
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Barr DA, Omollo C, Mason M, Koch A, Wilkinson RJ, Lalloo DG, Meintjes G, Mizrahi V, Warner DF, Davies G. Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria. Sci Rep 2021; 11:18661. [PMID: 34545154 PMCID: PMC8452731 DOI: 10.1038/s41598-021-98176-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/30/2021] [Indexed: 11/25/2022] Open
Abstract
Detection and accurate quantitation of viable Mycobacterium tuberculosis is fundamental to understanding mycobacterial pathogenicity, tuberculosis (TB) disease progression and outcomes; TB transmission; drug action, efficacy and drug resistance. Despite this importance, methods for determining numbers of viable bacilli are limited in accuracy and precision owing to inherent characteristics of mycobacterial cell biology—including the tendency to clump, and “differential” culturability—and technical challenges consequent on handling an infectious pathogen under biosafe conditions. We developed an absolute counting method for mycobacteria in liquid cultures using a bench-top flow cytometer, and the low-cost fluorescent dyes Calcein-AM (CA) and SYBR-gold (SG). During exponential growth CA + cell counts are highly correlated with CFU counts and can be used as a real-time alternative to simplify the accurate standardisation of inocula for experiments. In contrast to CFU counting, this method can detect and enumerate cell aggregates in samples, which we show are a potential source of variance and bias when using established methods. We show that CFUs comprise a sub-population of intact, metabolically active mycobacterial cells in liquid cultures, with CFU-proportion varying by growth conditions. A pharmacodynamic application of the flow cytometry method, exploring kinetics of fluorescent probe defined subpopulations compared to CFU is demonstrated. Flow cytometry derived Mycobacterium bovis bacillus Calmette-Guérin (BCG) time-kill curves differ for rifampicin and kanamycin versus isoniazid and ethambutol, as do the relative dynamics of discrete morphologically-distinct subpopulations of bacilli revealed by this high-throughput single-cell technique.
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Affiliation(s)
- David A Barr
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa. .,Institute of Infection and Global Health, University of Liverpool, Liverpool, L7 3EA, UK. .,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Charles Omollo
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mandy Mason
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Anastasia Koch
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa.,Department of Medicine, University of Cape Town, Cape Town, South Africa.,The Francis Crick Institute, London, NW11AT, UK.,Department of Medicine, Imperial College, London, W12 0NN, UK
| | - David G Lalloo
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Graeme Meintjes
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa.,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Valerie Mizrahi
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa.,SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Digby F Warner
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa.,SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine, Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Gerry Davies
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L7 3EA, UK
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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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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] [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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10
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Phage Amplification Assay for Detection of Mycobacterial Infection: A Review. Microorganisms 2021; 9:microorganisms9020237. [PMID: 33498792 PMCID: PMC7912421 DOI: 10.3390/microorganisms9020237] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/28/2022] Open
Abstract
An important prerequisite for the effective control, timely diagnosis, and successful treatment of mycobacterial infections in both humans and animals is a rapid, specific, and sensitive detection technique. Culture is still considered the gold standard in the detection of viable mycobacteria; however, mycobacteria are extremely fastidious and slow-growing microorganisms, and therefore cultivation requires a very long incubation period to obtain results. Polymerase Chain Reaction (PCR) methods are also frequently used in the diagnosis of mycobacterial infections, providing faster and more accurate results, but are unable to distinguish between a viable and non-viable microorganism, which results in an inability to determine the success of tuberculosis patient treatment or to differentiate between an active and passive infection of animals. One suitable technique that overcomes these shortcomings mentioned is the phage amplification assay (PA). PA specifically detects viable mycobacteria present in a sample within 48 h using a lytic bacteriophage isolated from the environment. Nowadays, an alternative approach to PA, a commercial kit called Actiphage™, is also employed, providing the result within 6–8 h. In this approach, the bacteriophage is used to lyse mycobacterial cells present in the sample, and the released DNA is subsequently detected by PCR. The objective of this review is to summarize information based on the PA used for detection of mycobacteria significant in both human and veterinary medicine from various kinds of matrices.
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11
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Allué-Guardia A, Saranathan R, Chan J, Torrelles JB. Mycobacteriophages as Potential Therapeutic Agents against Drug-Resistant Tuberculosis. Int J Mol Sci 2021; 22:ijms22020735. [PMID: 33450990 PMCID: PMC7828454 DOI: 10.3390/ijms22020735] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 01/21/2023] Open
Abstract
The current emergence of multi-, extensively-, extremely-, and total-drug resistant strains of Mycobacterium tuberculosis poses a major health, social, and economic threat, and stresses the need to develop new therapeutic strategies. The notion of phage therapy against bacteria has been around for more than a century and, although its implementation was abandoned after the introduction of drugs, it is now making a comeback and gaining renewed interest in Western medicine as an alternative to treat drug-resistant pathogens. Mycobacteriophages are genetically diverse viruses that specifically infect mycobacterial hosts, including members of the M. tuberculosis complex. This review describes general features of mycobacteriophages and their mechanisms of killing M. tuberculosis, as well as their advantages and limitations as therapeutic and prophylactic agents against drug-resistant M. tuberculosis strains. This review also discusses the role of human lung micro-environments in shaping the availability of mycobacteriophage receptors on the M. tuberculosis cell envelope surface, the risk of potential development of bacterial resistance to mycobacteriophages, and the interactions with the mammalian host immune system. Finally, it summarizes the knowledge gaps and defines key questions to be addressed regarding the clinical application of phage therapy for the treatment of drug-resistant tuberculosis.
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Affiliation(s)
- Anna Allué-Guardia
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Correspondence: (A.A.-G.); (J.B.T.)
| | - Rajagopalan Saranathan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA; (R.S.); (J.C.)
| | - John Chan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA; (R.S.); (J.C.)
| | - Jordi B. Torrelles
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Correspondence: (A.A.-G.); (J.B.T.)
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12
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Gong Z, Lv X, Li C, Gu Y, Fan X, Sun Q, Tong Y, Zhao F, Xing S, Pei G, Li Q, Xie L, Xie J. Genomic and proteomic portrait of a novel mycobacteriophage SWU2 isolated from China. INFECTION GENETICS AND EVOLUTION 2020; 87:104665. [PMID: 33279716 DOI: 10.1016/j.meegid.2020.104665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/22/2020] [Accepted: 12/01/2020] [Indexed: 11/30/2022]
Abstract
Phage therapy, especially combination with antibiotics, was revitalized to control the antibiotics resistance. Mycobacteriophage, the phage of mycobacterium with the most notorious Mycobacterium tuberculosis (M. tuberculosis), was intensively explored. A novel mycobacteriophage SWU2 was isolated from a soil sample collected at Nanchang city, Jiangxi province, China, by using Mycolicibacterium smegmatis (M. smegmatis) mc2 155 as the host. Phage morphology and biology were characterized. Phage structure proteins were analyzed by LC-MS/MS. The putative functions of phage proteins and multi-genome comparison were performed with bioinformatics. The transmission electron microscopy result indicated that this phage belongs to Siphoviridae of Caudovirales. Plaques of SWU2 appeared clear but small. In a one-step growth test, we demonstrated that SWU2 had a latent period of 30 min and a logarithmic phase of 120 min. Among the 76 predicted Open Reading Frames (ORFs), 9 ORFs were identified as phage structure proteins of SWU2. The assembled phage genome size is 50,013 bp, with 62.7% of G + C content. SWU2 genome sequence shares 88% identity with Mycobacterium phages HINdeR and Timshel, differing in substitutions, insertions and deletions in SWU2. Phylogenetic tree revealed that SWU2 is grouped into A7 sub-cluster. There are several substitutions, insertions and deletions in SWU2 genome in comparison with close cousin phages HINdeR and Timshel. The new phage adds another dimension of abundance to the mycobacteriophages.
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Affiliation(s)
- Zhen Gong
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xi Lv
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Chunyan Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yinzhong Gu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xiangyu Fan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China; School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Qingyu Sun
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Feiyang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Shaozhen Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Guangqian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qiming Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China.
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13
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Abstract
The diversity of advanced genetic engineering techniques that have become available in recent years has enabled a more precise manipulation of genes and genomes. Among these, bacteriophage genomes stand out as an interesting target due to their dependence on a host for replication, which previously complicated their manipulation, and due as well to the many possible fields in which they can be used. In this review, we highlight recent applications for which genetically modified bacteriophages are being employed: as phage therapy in medicine, animal industries and agricultural settings; as a source of new antimicrobials; as biosensors for research, health and environmental purposes; and as genetic engineering tools themselves.
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Affiliation(s)
| | - Hiroki Ando
- Department of Microbiology, Graduate School of Medicine, Gifu University
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14
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Mageeney CM, Mohammed HT, Dies M, Anbari S, Cudkevich N, Chen Y, Buceta J, Ware VC. Mycobacterium Phage Butters-Encoded Proteins Contribute to Host Defense against Viral Attack. mSystems 2020; 5:e00534-20. [PMID: 33024050 PMCID: PMC7542560 DOI: 10.1128/msystems.00534-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/15/2020] [Indexed: 01/21/2023] Open
Abstract
A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems.IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.
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Affiliation(s)
- Catherine M Mageeney
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Hamidu T Mohammed
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Marta Dies
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Samira Anbari
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Netta Cudkevich
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Yanyan Chen
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Javier Buceta
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Vassie C Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
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15
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Reporter Phage-Based Detection of Bacterial Pathogens: Design Guidelines and Recent Developments. Viruses 2020; 12:v12090944. [PMID: 32858938 PMCID: PMC7552063 DOI: 10.3390/v12090944] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/10/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Fast and reliable detection of bacterial pathogens in clinical samples, contaminated food products, and water supplies can drastically improve clinical outcomes and reduce the socio-economic impact of disease. As natural predators of bacteria, bacteriophages (phages) have evolved to bind their hosts with unparalleled specificity and to rapidly deliver and replicate their viral genome. Not surprisingly, phages and phage-encoded proteins have been used to develop a vast repertoire of diagnostic assays, many of which outperform conventional culture-based and molecular detection methods. While intact phages or phage-encoded affinity proteins can be used to capture bacteria, most phage-inspired detection systems harness viral genome delivery and amplification: to this end, suitable phages are genetically reprogrammed to deliver heterologous reporter genes, whose activity is typically detected through enzymatic substrate conversion to indicate the presence of a viable host cell. Infection with such engineered reporter phages typically leads to a rapid burst of reporter protein production that enables highly sensitive detection. In this review, we highlight recent advances in infection-based detection methods, present guidelines for reporter phage construction, outline technical aspects of reporter phage engineering, and discuss some of the advantages and pitfalls of phage-based pathogen detection. Recent improvements in reporter phage construction and engineering further substantiate the potential of these highly evolved nanomachines as rapid and inexpensive detection systems to replace or complement traditional diagnostic approaches.
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16
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Rampacci E, Stefanetti V, Passamonti F, Henao-Tamayo M. Preclinical Models of Nontuberculous Mycobacteria Infection for Early Drug Discovery and Vaccine Research. Pathogens 2020; 9:E641. [PMID: 32781698 PMCID: PMC7459799 DOI: 10.3390/pathogens9080641] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) represent an increasingly prevalent etiology of soft tissue infections in animals and humans. NTM are widely distributed in the environment and while, for the most part, they behave as saprophytic organisms, in certain situations, they can be pathogenic, so much so that the incidence of NTM infections has surpassed that of Mycobacterium tuberculosis in developed countries. As a result, a growing body of the literature has focused attention on the critical role that drug susceptibility tests and infection models play in the design of appropriate therapeutic strategies against NTM diseases. This paper is an overview of the in vitro and in vivo models of NTM infection employed in the preclinical phase for early drug discovery and vaccine development. It summarizes alternative methods, not fully explored, for the characterization of anti-mycobacterial compounds.
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Affiliation(s)
- Elisa Rampacci
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy; (E.R.); (V.S.)
| | - Valentina Stefanetti
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy; (E.R.); (V.S.)
| | - Fabrizio Passamonti
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy; (E.R.); (V.S.)
| | - Marcela Henao-Tamayo
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA;
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17
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Reuter M, Kruger DH. Approaches to optimize therapeutic bacteriophage and bacteriophage-derived products to combat bacterial infections. Virus Genes 2020; 56:136-149. [PMID: 32036540 PMCID: PMC7223754 DOI: 10.1007/s11262-020-01735-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/18/2020] [Indexed: 12/14/2022]
Abstract
The emerging occurrence of antibiotic-resistant bacterial pathogens leads to a recollection of bacteriophage as antimicrobial therapeutics. This article presents a short overview of the clinical phage application including their use in military medicine and discusses the genotypic and phenotypic properties of a potential "ideal" therapeutic phage. We describe current efforts to engineer phage for their improved usability in pathogen treatment. In addition, phage can be applied for pathogen detection, selective drug delivery, vaccine development, or food and surface decontamination. Instead of viable phage, (engineered) phage-derived enzymes, such as polysaccharide depolymerases or peptidoglycan-degrading enzymes, are considered as promising therapeutic candidates. Finally, we briefly summarize the use of phage for the detection and treatment of "Category A priority pathogens".
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Affiliation(s)
- Monika Reuter
- Institute of Virology, Helmut-Ruska-Haus, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Detlev H. Kruger
- Institute of Virology, Helmut-Ruska-Haus, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
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18
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Abstract
Fluoromycobacteriophages are a new class of reporter phages that contain Laboratorio fluorescent reporter genes (gfp, ZsYellow, and mCherry) and provide a simple means of revealing the metabolic state of mycobacterial cells and therefore their response to antibiotics. Here we described a simple and rapid method for drug susceptibility testing (DST) of Mycobacterium spp using a fluorescence microscope, a flow cytometer, or a fluorimeter in a convenient multiwell format.
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19
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Fina Martin J, Palomino MM, Cutine AM, Modenutti CP, Fernández Do Porto DA, Allievi MC, Zanini SH, Mariño KV, Barquero AA, Ruzal SM. Exploring lectin-like activity of the S-layer protein of Lactobacillus acidophilus ATCC 4356. Appl Microbiol Biotechnol 2019; 103:4839-4857. [PMID: 31053916 DOI: 10.1007/s00253-019-09795-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 02/06/2023]
Abstract
The surface layer (S-layer) protein of Lactobacillus acidophilus is a crystalline array of self-assembling, proteinaceous subunits non-covalently bound to the outmost bacterial cell wall envelope and is involved in the adherence of bacteria to host cells. We have previously described that the S-layer protein of L. acidophilus possesses anti-viral and anti-bacterial properties. In this work, we extracted and purified S-layer proteins from L. acidophilus ATCC 4356 cells to study their interaction with cell wall components from prokaryotic (i.e., peptidoglycan and lipoteichoic acids) and eukaryotic origin (i.e., mucin and chitin), as well as with viruses, bacteria, yeast, and blood cells. Using chimeric S-layer fused to green fluorescent protein (GFP) from different parts of the protein, we analyzed their binding capacity. Our results show that the C-terminal part of the S-layer protein presents lectin-like activity, interacting with different glycoepitopes. We further demonstrate that lipoteichoic acid (LTA) serves as an anchor for the S-layer protein. Finally, a structure for the C-terminal part of S-layer and possible binding sites were predicted by a homology-based model.
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Affiliation(s)
- Joaquina Fina Martin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Maria Mercedes Palomino
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Anabella M Cutine
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Carlos P Modenutti
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario A Fernández Do Porto
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana C Allievi
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sofia H Zanini
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
| | - Karina V Mariño
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Andrea A Barquero
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sandra M Ruzal
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Pabellón II, 4 piso, Lab QB40, C1428EGA, CABA, Buenos Aires, Argentina.
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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20
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Wisuthiphaet N, Yang X, Young GM, Nitin N. Rapid detection of Escherichia coli in beverages using genetically engineered bacteriophage T7. AMB Express 2019; 9:55. [PMID: 31004244 PMCID: PMC6474890 DOI: 10.1186/s13568-019-0776-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 04/09/2019] [Indexed: 11/10/2022] Open
Abstract
Foodborne illness due to bacterial contamination is a significant issue impacting public health that demands new technology which is practical to implement by food industry. Detection of bacteria in food products and production facilities is a crucial strategy supporting food safety assessments. Bacteriophages were investigated as a tool for bacterial detection due to their ability to infect specific strain of host bacteria in order to improve sensitivity, specificity, and rapidity of bacterial detection. The results of this investigation reveal a novel method for rapid detection. The method employs a genetically engineered bacteriophage, phage T7-ALP, which expresses alkaline phosphatase. Upon infection of Escherichia coli, overexpression of alkaline phosphatase provides an opportunity for rapid sensitive detection of a signal indicative of bacterial presence in model beverage samples as low as 100 bacteria per gram. The method employs a fluorescent precipitated substrate, ELF-97, as a substrate for alkaline phosphatase activity coupled with fluorescence imaging and image analysis allowing single-cell imaging results in high detection sensitivity. The method is easily completed within less than 6 h enabling it to be deployed within most large industrial food processing facilities that have routine 8-h operational shifts.
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Affiliation(s)
| | - Xu Yang
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Glenn M Young
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Nitin Nitin
- Department of Food Science and Technology, University of California, Davis, CA, USA.
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, USA.
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21
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Abstract
Mycobacteriophages are viruses that infect mycobacterial hosts. A large number of mycobacteriophages have been isolated and genomically characterized, providing insights into viral diversity and evolution, as well as fueling development of tools for mycobacterial genetics. Mycobacteriophages have intimate relationships with their hosts and provide insights into the genetics and physiology of the mycobacteria and tools for potential clinical applications such as drug development, diagnosis, vaccines, and potentially therapy.
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22
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Abstract
Bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been adapted for building gene circuits to program biological systems. Phages also exhibit significant medical potential as antibacterial agents and bacterial diagnostics due to their extreme specificity for their host, and our growing ability to engineer them further enhances this potential. Phages have also been used as scaffolds for genetically programmable biomaterials that have highly tunable properties. Furthermore, phages are central to powerful directed evolution platforms, which are being leveraged to enhance existing biological functions and even produce new ones. In this review, we discuss recent examples of how phage research is influencing these next-generation biotechnologies.
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Affiliation(s)
- Sebastien Lemire
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Kevin M Yehl
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; .,Synthetic Biology Group, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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23
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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] [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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Chhotaray C, Tan Y, Mugweru J, Islam MM, Adnan Hameed HM, Wang S, Lu Z, Wang C, Li X, Tan S, Liu J, Zhang T. Advances in the development of molecular genetic tools for Mycobacterium tuberculosis. J Genet Genomics 2018; 45:S1673-8527(18)30114-0. [PMID: 29941353 DOI: 10.1016/j.jgg.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis, a clinically relevant Gram-positive bacterium of great clinical relevance, is a lethal pathogen owing to its complex physiological characteristics and development of drug resistance. Several molecular genetic tools have been developed in the past few decades to study this microorganism. These tools have been instrumental in understanding how M. tuberculosis became a successful pathogen. Advanced molecular genetic tools have played a significant role in exploring the complex pathways involved in M. tuberculosis pathogenesis. Here, we review various molecular genetic tools used in the study of M. tuberculosis. Further, we discuss the applications of clustered regularly interspaced short palindromic repeat interference (CRISPRi), a novel technology recently applied in M. tuberculosis research to study target gene functions. Finally, prospective outcomes of the applications of molecular techniques in the field of M. tuberculosis genetic research are also discussed.
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Affiliation(s)
- Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biological Sciences, University of Embu, P.O Box 6 -60100, Embu, Kenya
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China.
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Trousil J, Ulmann V, Hrubý M. Fluorescence & bioluminescence in the quest for imaging, probing & analysis of mycobacterial infections. Future Microbiol 2018; 13:933-951. [PMID: 29893148 DOI: 10.2217/fmb-2017-0296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacterioses represent a global health problem and rapid diagnostic improvements are urgently required. Mycobacteria-specific fluorescence and bioluminescence phenomena have been found to be useful for a wide range of mycobacteria-focused research. Here, we present a critical survey of the most promising techniques in this field and the potential of new methods under investigation. These approaches include acid-fast staining, intrinsic fluorescence of the coenzyme F420, fluorogenic substrates (e.g., β-lactamase-sensitive coumpounds) and recombination of mycobacteria or mycobacteriophages. Probably the most interesting and emerging host-inspecting approach is in vivo imaging. Detection of fluorescence in vivo, however, is complicated by light scattering, light absorption, and autofluorescence, caused by the tissues. Despite this, many of these systems show promise as the foundations for improved rapid analysis and imaging of mycobacterial infections, both in vitro and in vivo.
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Affiliation(s)
- Jiří Trousil
- Department of Supramolecular Polymer Systems, Institute of Macromolecular Chemistry of the Academy of Sciences of the Czech Republic, Heyrovského náměstí 2, 162 06 Prague 6, Czech Republic.,Department of Analytical Chemistry, Charles University, Faculty of Science, Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Vít Ulmann
- Laboratory for Mycobacterial Diagnostics and Tuberculosis, Regional Institute of Public Health in Ostrava, Partyzánské náměstí 7, 702 00 Ostrava, Czech Republic
| | - Martin Hrubý
- Department of Supramolecular Polymer Systems, Institute of Macromolecular Chemistry of the Academy of Sciences of the Czech Republic, Heyrovského náměstí 2, 162 06 Prague 6, Czech Republic
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Galizia J, Acosta MP, Urdániz E, Martí MA, Piuri M. Evaluation of nitroxyl donors' effect on mycobacteria. Tuberculosis (Edinb) 2018; 109:35-40. [DOI: 10.1016/j.tube.2018.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/26/2017] [Accepted: 01/30/2018] [Indexed: 10/18/2022]
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Wei TY, Cheng CM. Synthetic Biology-Based Point-of-Care Diagnostics for Infectious Disease. Cell Chem Biol 2017; 23:1056-1066. [PMID: 27662252 DOI: 10.1016/j.chembiol.2016.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/15/2016] [Accepted: 07/08/2016] [Indexed: 02/09/2023]
Abstract
Infectious diseases outpace all other causes of death in low-income countries, posing global health risks, laying stress on healthcare systems and societies, and taking an avoidable human toll. One solution to this crisis is early diagnosis of infectious disease, which represents a powerful way to optimize treatment, increase patient survival rate, and decrease healthcare costs. However, conventional early diagnosis methods take a long time to generate results, lack accuracy, and are known to seriously underperform with regard to fungal and viral infections. Synthetic biology offers a fast and highly accurate alternative to conventional infectious disease diagnosis. In this review, we outline obstacles to infectious disease diagnostics and discuss two emerging alternatives: synthetic viral diagnostic systems and biosensors. We argue that these synthetic biology-based approaches may overcome diagnostic obstacles in infectious disease and improve health outcomes.
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Affiliation(s)
- Ting-Yen Wei
- Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan.
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Southeast Asian Medicinal Plants as a Potential Source of Antituberculosis Agent. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:7185649. [PMID: 29081822 PMCID: PMC5610802 DOI: 10.1155/2017/7185649] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/23/2017] [Accepted: 05/18/2017] [Indexed: 01/19/2023]
Abstract
Despite all of the control strategies, tuberculosis (TB) is still a major cause of death globally and one-third of the world's population is infected with TB. The drugs used for TB treatment have drawbacks of causing adverse side effects and emergence of resistance strains. Plant-derived medicines have since been used in traditional medical system for the treatment of numerous ailments worldwide. There were nine major review publications on antimycobacteria from plants in the last 17 years. However, none is focused on Southeast Asian medicinal plants. Hence, this review is aimed at highlighting the medicinal plants of Southeast Asian origin evaluated for anti-TB. This review is based on literatures published in various electronic database. A total of 132 plants species representing 45 families and 107 genera were reviewed; 27 species representing 20.5% exhibited most significant in vitro anti-TB activity (crude extracts and/or bioactive compounds 0–<10 µg/ml). The findings may motivate various scientists to undertake the project that may result in the development of crude extract that will be consumed as complementary or alternative TB drug or as potential bioactive compounds for the development of novel anti-TB drug.
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Franche N, Vinay M, Ansaldi M. Substrate-independent luminescent phage-based biosensor to specifically detect enteric bacteria such as E. coli. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:42-51. [PMID: 26903133 DOI: 10.1007/s11356-016-6288-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/14/2016] [Indexed: 06/05/2023]
Abstract
Water quality is a major safety consideration in environments that are impacted by human activity. The key challenge of the COMBITOX project is to develop a unique instrument that can accommodate several biodetector systems (see the accompanying COMBITOX papers) able to detect different pollutants such as bacteria, toxins, and heavy metals. The output signal chosen by our consortium is based on luminescence detection. Our group recently developed phage-based biosensors using gfp as a reporter gene to detect enteric bacteria in complex environments such as sea water, and the main challenge we faced was to adapt our biodetector to a luminescent signal that could fit the COMBITOX project requirements. Another key point was to use a substrate-independent reporter system in order to avoid substrate addition in the detection prototype. This paper describes the development of a phage-based biodetector using a luminescent and substrate-independent output to detect some enteric bacteria, such as Escherichia coli, in water samples. We have successfully engineered various prototypes using the HK620 and HK97 bacteriophages that use different packaging systems, and both proved functional for the integration of the full luxCDABE operon controlled by two different bacterial promoters. We show that the luxCDABE operon controlled by the PrplU bacterial promoter is the most efficient in terms of signal emission. The emission of luminescence is specific and allows the detection of 104 bacteria per milliliter in 1.5 h post-infection with neither a concentration nor enrichment step.
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Affiliation(s)
- Nathalie Franche
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Manon Vinay
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
- Biocentric, Bandol, France
| | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France.
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Fluorescent Reporter DS6A Mycobacteriophages Reveal Unique Variations in Infectibility and Phage Production in Mycobacteria. J Bacteriol 2016; 198:3220-3232. [PMID: 27672191 DOI: 10.1128/jb.00592-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/13/2016] [Indexed: 12/22/2022] Open
Abstract
Mycobacteriophage DS6A is unique among the more than 8,000 isolated mycobacteriophages due to its ability to form plaques exclusively on mycobacteria belonging to the Mycobacterium tuberculosis complex (MTBC). Speculation surrounding this specificity has led to unsupported assertions in published studies and patents that nontuberculous mycobacteria (NTM) are wholly resistant to DS6A infection. In this study, we identified two independent nonessential regions in the DS6A genome and replaced them with an mVenus-expressing plasmid to generate fluorescent reporter phages Φ2GFP12 and Φ2GFP13. We show that even though DS6A is able to form plaques only on MTBC bacteria, infection of various NTM results in mVenus expression in transduced cells. The efficiency of DS6A in delivering DNA varied between NTM species. Additionally, we saw a striking difference in the efficiency of DNA delivery between the closely related members of the Mycobacterium abscessus complex, M. abscessus and Mycobacterium massiliense We also demonstrated that TM4 and DS6A, two phages that do not form plaques on M. massiliense, differ in their ability to deliver DNA, suggesting that there is a phage-specific restriction between mycobacterial species. Phylogenetic analysis reveals that the DS6A genome has a characteristically mosaic structure but provided few insights into the basis for the specificity for MTBC hosts. This study demonstrates that the inability of the MTBC-specific phage DS6A to form plaques on NTM is more complex than previously thought. Moreover, the DS6A-derived fluorophages provide important new tools for the study of mycobacterial biology. IMPORTANCE The coevolution of bacteria and their infecting phages involves a constant arms race for bacteria to prevent phage infection and phage to overcome these preventions. Although a diverse array of phage defense systems is well characterized in bacteria, very few phage restriction systems are known in mycobacteria. The DS6A mycobacteriophage is unique in the mycobacterial world in that it forms plaques only on members of the Mycobacterium tuberculosis complex. However, the novel DS6A reporter phages developed in this work demonstrate that DS6A can infect nontuberculous mycobacteria at various efficiencies. By comparing the abilities of DS6A and another phage, TM4, to infect and form plaques on various mycobacterial species, we can begin to discern new phage restriction systems employed within the genus.
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Dual-Reporter Mycobacteriophages (Φ2DRMs) Reveal Preexisting Mycobacterium tuberculosis Persistent Cells in Human Sputum. mBio 2016; 7:mBio.01023-16. [PMID: 27795387 PMCID: PMC5080378 DOI: 10.1128/mbio.01023-16] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Persisters are the minor subpopulation of bacterial cells that lack alleles conferring resistance to a specific bactericidal antibiotic but can survive otherwise lethal concentrations of that antibiotic. In infections with Mycobacterium tuberculosis, such persisters underlie the need for long-term antibiotic therapy and contribute to treatment failure in tuberculosis cases. Here, we demonstrate the value of dual-reporter mycobacteriophages (Φ2DRMs) for characterizing M. tuberculosis persisters. The addition of isoniazid (INH) to exponentially growing M. tuberculosis cells consistently resulted in a 2- to 3-log decrease in CFU within 4 days, and the remaining ≤1% of cells, which survived despite being INH sensitive, were INH-tolerant persisters with a distinct transcriptional profile. We fused the promoters of several genes upregulated in persisters to the red fluorescent protein tdTomato gene in Φ2GFP10, a mycobacteriophage constitutively expressing green fluorescent protein (GFP), thus generating Φ2DRMs. A population enriched in INH persisters exhibited strong red fluorescence, by microscopy and flow cytometry, using a Φ2DRM with tdTomato controlled from the dnaK promoter. Interestingly, we demonstrated that, prior to INH exposure, a population primed for persistence existed in M. tuberculosis cells from both cultures and human sputa and that this population was highly enriched following INH exposure. We conclude that Φ2DRMs provide a new tool to identify and quantitate M. tuberculosis persister cells. IMPORTANCE Tuberculosis (TB) is again the leading cause of death from a single infectious disease, having surpassed HIV. The recalcitrance of the TB pandemic is largely due to the ability of the pathogen Mycobacterium tuberculosis to enter a persistent state in which it is less susceptible to antibiotics and immune effectors, necessitating lengthy treatment. It has been difficult to study persister cells, as we have lacked tools to isolate these rare cells. In this article, we describe the development of dual-reporter mycobacteriophages that encode a green fluorescent marker of viability and in which the promoters of genes we have identified as induced in the persister state are fused to a gene encoding a red fluorescent protein. We show that these tools can identify heterogeneity in a cell population that correlates with propensity to survive antibiotic treatment and that the proportions of these subpopulations change in M. tuberculosis cells within human sputum during the course of treatment.
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Pires DP, Cleto S, Sillankorva S, Azeredo J, Lu TK. Genetically Engineered Phages: a Review of Advances over the Last Decade. Microbiol Mol Biol Rev 2016; 80:523-43. [PMID: 27250768 PMCID: PMC4981678 DOI: 10.1128/mmbr.00069-15] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Soon after their discovery in the early 20th century, bacteriophages were recognized to have great potential as antimicrobial agents, a potential that has yet to be fully realized. The nascent field of phage therapy was adversely affected by inadequately controlled trials and the discovery of antibiotics. Although the study of phages as anti-infective agents slowed, phages played an important role in the development of molecular biology. In recent years, the increase in multidrug-resistant bacteria has renewed interest in the use of phages as antimicrobial agents. With the wide array of possibilities offered by genetic engineering, these bacterial viruses are being modified to precisely control and detect bacteria and to serve as new sources of antibacterials. In applications that go beyond their antimicrobial activity, phages are also being developed as vehicles for drug delivery and vaccines, as well as for the assembly of new materials. This review highlights advances in techniques used to engineer phages for all of these purposes and discusses existing challenges and opportunities for future work.
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Affiliation(s)
- Diana P Pires
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Sara Cleto
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sanna Sillankorva
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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A Flow Cytometry Method for Rapidly Assessing Mycobacterium tuberculosis Responses to Antibiotics with Different Modes of Action. Antimicrob Agents Chemother 2016; 60:3869-83. [PMID: 26902767 PMCID: PMC4914659 DOI: 10.1128/aac.02712-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/13/2016] [Indexed: 12/22/2022] Open
Abstract
Current methods for assessing the drug susceptibility of Mycobacterium tuberculosis are lengthy and do not capture information about viable organisms that are not immediately culturable under standard laboratory conditions as a result of antibiotic exposure. We have developed a rapid dual-fluorescence flow cytometry method using markers for cell viability and death. We show that the fluorescent marker calcein violet with an acetoxy-methyl ester group (CV-AM) can differentiate between populations of M. tuberculosis growing at different rates, while Sytox green (SG) can differentiate between live and dead mycobacteria. M. tuberculosis was exposed to isoniazid or rifampin at different concentrations over time and either dual stained with CV-AM and SG and analyzed by flow cytometry or plated to determine the viability of the cells. Although similar trends in the loss of viability were observed when the results of flow cytometry and the plate counting methods were compared, there was a lack of correlation between these two approaches, as the flow cytometry analysis potentially captured information about cell populations that were unable to grow under standard conditions. The flow cytometry approach had an additional advantage in that it could provide insights into the mode of action of the drug: antibiotics targeting the cell wall gave a flow cytometry profile distinct from those inhibiting intracellular processes. This rapid drug susceptibility testing method could identify more effective antimycobacterials, provide information about their potential mode of action, and accelerate their progress to the clinic.
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Yu X, Gu Y, Jiang G, Ma Y, Zhao L, Sun Z, Jain P, O'Donnell M, Larsen M, Jacobs WR, Huang H. Evaluation of a High-Intensity Green Fluorescent Protein Fluorophage Method for Drug- Resistance Diagnosis in Tuberculosis for Isoniazid, Rifampin, and Streptomycin. Front Microbiol 2016; 7:922. [PMID: 27379052 PMCID: PMC4911409 DOI: 10.3389/fmicb.2016.00922] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 05/31/2016] [Indexed: 11/30/2022] Open
Abstract
A novel method for detecting drug resistance in Mycobacterium tuberculosis using mycobacteriophage Φ (2) GFP10 was evaluated with clinical isolates. The phage facilitates microscopic fluorescence detection due to the high expression of green fluorescence protein which also simplifies the operative protocol as well. A total of 128 clinical isolates were tested by the phage assay for isoniazid (INH), rifampin (RIF), and streptomycin (STR) resistance while conventional drug susceptibility test, by MGIT960, was used as reference. The sensitivities of Φ (2) GFP10 assay for INH, RIF, and STR resistance detection were 100, 98.2, and 89.3%, respectively while their specificities were 85.1, 98.6, and 95.8%, respectively. The agreement between phage and conventional assay for detecting INH, RIF, and STR resistance was 92.2, 98.4, and 93.0%, respectively. The Φ (2) GFP10-phage results could be available in 2 days for RIF and STR, while it takes 3 days for INH, with an estimated cost of less than $2 to test all the three antibiotics. The Φ (2) GFP10-phage method has the potential to be a valuable, rapid and economical screening method for detecting drug-resistant tuberculosis.
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Affiliation(s)
- Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical UniversityBeijing, China
| | - Yunting Gu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical UniversityBeijing, China
| | - Guanglu Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical UniversityBeijing, China
| | - Yifeng Ma
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical UniversityBeijing, China
| | - Liping Zhao
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical UniversityBeijing, China
| | - Zhaogang Sun
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical UniversityBeijing, China
| | - Paras Jain
- Department of Microbiology and Immunology, Albert Einstein College of MedicineBronx, NY, USA
| | - Max O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical CenterNew York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University Medical CenterNew York, NY, USA
| | - Michelle Larsen
- Department of Microbiology and Immunology, Albert Einstein College of MedicineBronx, NY, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of MedicineBronx, NY, USA
- Howard Hughes Medical InstituteChevy Chase, MD, USA
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Institute, Capital Medical UniversityBeijing, China
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35
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Urdániz E, Rondón L, Martí MA, Hatfull GF, Piuri M. Rapid Whole-Cell Assay of Antitubercular Drugs Using Second-Generation Fluoromycobacteriophages. Antimicrob Agents Chemother 2016; 60:3253-6. [PMID: 26976860 PMCID: PMC4862496 DOI: 10.1128/aac.03016-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Estefanía Urdániz
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Liliana Rondón
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Graham F Hatfull
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
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Abstract
Infectious diseases have plagued humankind throughout history and have posed serious public health problems. Yet vaccines have eradicated smallpox and antibiotics have drastically decreased the mortality rate of many infectious agents. These remarkable successes in the control of infections came from knowing the causative agents of the diseases, followed by serendipitous discoveries of attenuated viruses and antibiotics. The discovery of DNA as genetic material and the understanding of how this information translates into specific phenotypes have changed the paradigm for developing new vaccines, drugs, and diagnostic tests. Knowledge of the mechanisms of immunity and mechanisms of action of drugs has led to new vaccines and new antimicrobial agents. The key to the acquisition of the knowledge of these mechanisms has been identifying the elemental causes (i.e., genes and their products) that mediate immunity and drug resistance. The identification of these genes is made possible by being able to transfer the genes or mutated forms of the genes into causative agents or surrogate hosts. Such an approach was limited in Mycobacterium tuberculosis by the difficulty of transferring genes or alleles into M. tuberculosis or a suitable surrogate mycobacterial host. The construction of shuttle phasmids-chimeric molecules that replicate in Escherichia coli as plasmids and in mycobacteria as mycobacteriophages-was instrumental in developing gene transfer systems for M. tuberculosis. This review will discuss M. tuberculosis genetic systems and their impact on tuberculosis research.
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Abstract
Tuberculosis (TB), caused byMycobacterium tuberculosis(M.tb.), is one of the most prevalent and serious infectious diseases worldwide with an estimated annual global mortality of 1.4 million in 2010.
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Affiliation(s)
- Saurabh K. Srivastava
- Plant Research International
- Wageningen UR
- 6708 PB Wageningen
- The Netherlands
- Laboratory of Organic Chemistry
| | - Cees J. M. van Rijn
- Laboratory of Organic Chemistry
- Wageningen UR
- 6703 HB Wageningen
- The Netherlands
| | - Maarten A. Jongsma
- Plant Research International
- Wageningen UR
- 6708 PB Wageningen
- The Netherlands
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38
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Vinay M, Franche N, Grégori G, Fantino JR, Pouillot F, Ansaldi M. Phage-Based Fluorescent Biosensor Prototypes to Specifically Detect Enteric Bacteria Such as E. coli and Salmonella enterica Typhimurium. PLoS One 2015; 10:e0131466. [PMID: 26186207 PMCID: PMC4506075 DOI: 10.1371/journal.pone.0131466] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 06/02/2015] [Indexed: 12/30/2022] Open
Abstract
Water safety is a major concern for public health and for natural environment preservation. We propose to use bacteriophages to develop biosensor tools able to detect human and animal pathogens present in water. For this purpose, we take advantage of the highly discriminating properties of the bacteriophages, which specifically infect their bacterial hosts. The challenge is to use a fluorescent reporter protein that will be synthesized, and thus detected, only once the specific recognition step between a genetically modified temperate bacteriophage and its bacterial host has occurred. To ensure the accuracy and the execution speed of our system, we developed a test that does not require bacterial growth, since a simple 1-hour infection step is required. To ensure a high sensitivity of our tool and in order to detect up to a single bacterium, fluorescence is measured using a portable flow cytometer, also allowing on-site detection. In this study, we have constructed and characterized several "phagosensor" prototypes using the HK620 bacteriophage and its host Escherichia coli TD2158 and we successfully adapted this method to Salmonella detection. We show that the method is fast, robust and sensitive, allowing the detection of as few as 10 bacteria per ml with no concentration nor enrichment step. Moreover, the test is functional in sea water and allows the detection of alive bacteria. Further development will aim to develop phagosensors adapted on demand to the detection of any human or animal pathogen that may be present in water.
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Affiliation(s)
- Manon Vinay
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Nathalie Franche
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Gérald Grégori
- Aix-Marseille Université, Université Sud Toulon Var, IRD, CNRS, Mediterranean Institute of Oceanology UM110, Marseille, France
| | - Jean-Raphaël Fantino
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | | | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
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39
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van der Merwe RG, van Helden PD, Warren RM, Sampson SL, Gey van Pittius NC. Phage-based detection of bacterial pathogens. Analyst 2015; 139:2617-26. [PMID: 24658771 DOI: 10.1039/c4an00208c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial pathogens cause significant morbidity and mortality annually to both humans and animals. With the rampant spread of drug resistance and the diminishing effectiveness of current antibiotics, there is a pressing need for effective diagnostics for detection of bacterial pathogens and their drug resistances. Bacteriophages offer several unique opportunities for bacterial detection. This review highlights the means by which bacteriophages have been utilized to achieve and facilitate specific bacterial detection.
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Affiliation(s)
- R G van der Merwe
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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40
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Petrova ZO, Broussard GW, Hatfull GF. Mycobacteriophage-repressor-mediated immunity as a selectable genetic marker: Adephagia and BPs repressor selection. MICROBIOLOGY-SGM 2015; 161:1539-1551. [PMID: 26066798 DOI: 10.1099/mic.0.000120] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycobacteriophages provide an abundance of systems for use in mycobacterial genetics, including manipulation of Mycobacterium tuberculosis. Because of the dearth of antibiotic resistance cassettes and biosafety concerns in constructing recombinant virulent M. tuberculosis strains, we developed the use of mycobacteriophage-encoded repressor genes that can be selected in the presence of lytic versions of their cognate phages. The phage Adephagia repressor gene (43) was identified through its ability to confer immunity to Adephagia superinfection, together with the mapping of mutations in gene 43 that confer a clear-phage phenotype. Plasmid transformants containing either Adephagia 43 or the previously identified BPs repressor 33 can be readily selected following electroporation using engineered lytic derivatives of Adephagia and BPs, respectively. Selection is as efficient as antibiotic selection, can be used with either single-copy integration vectors or with extrachromosomal vectors, and works similarly in both Mycobacterium smegmatis and M. tuberculosis.
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Affiliation(s)
- Zaritza O Petrova
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gregory W Broussard
- 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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41
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Tawil N, Sacher E, Mandeville R, Meunier M. Bacteriophages: biosensing tools for multi-drug resistant pathogens. Analyst 2015; 139:1224-36. [PMID: 24434867 DOI: 10.1039/c3an01989f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pathogen detection is of utmost importance in many sectors, such as in the food industry, environmental quality control, clinical diagnostics, bio-defence and counter-terrorism. Failure to appropriately, and specifically, detect pathogenic bacteria can lead to serious consequences, and may ultimately be lethal. Public safety, new legislation, recent outbreaks in food contamination, and the ever-increasing prevalence of multidrug-resistant infections have fostered a worldwide research effort targeting novel biosensing strategies. This review concerns phage-based analytical and biosensing methods targeted towards theranostic applications. We discuss and review phage-based assays, notably phage amplification, reporter phage, phage lysis, and bioluminescence assays for the detection of bacterial species, as well as phage-based biosensors, including optical (comprising SPR sensors and fiber optic assays), electrochemical (comprising amperometric, potentiometric, and impedimetric sensors), acoustic wave and magnetoelastic sensors.
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Affiliation(s)
- N Tawil
- Regroupement Québécois de Matériaux de Pointe, Department of Engineering Physics, École Polytechnique de Montréal, Case Postale 6079, succursale Centre-ville, Montréal, Québec H3C 3A7, Canada.
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42
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Fu X, Ding M, Zhang N, Li J. Mycobacteriophages: an important tool for the diagnosis of Mycobacterium tuberculosis (review). Mol Med Rep 2015; 12:13-9. [PMID: 25760591 DOI: 10.3892/mmr.2015.3440] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 02/13/2015] [Indexed: 11/06/2022] Open
Abstract
The prevention and control of tuberculosis (TB) on a global scale has become increasingly important with the emergence of multidrug‑resistant TB. Mycobacterium tuberculosis phages have been identified as an important investigative tool. Phage genomes exhibit a significant level of diversity and mosaic genome architecture, however, they are simple structures, which are amenable to genetic manipulation. Based on these characteristics, the phages may be used to construct a shuttle plasmid, which is an indispensable tool in the investigation of TB. Furthermore, they may be used for rapid diagnosis and assessing drug susceptibility of TB, including phage amplified assessment and reporter phage technology. With an improved understanding of mycobacteriophages, further clarification of the pathogenesis of TB, and of the implications for its diagnosis and therapy, may be elucidated.
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Affiliation(s)
- Xiaoyan Fu
- Department of Medical Sciences, Jinhua College of Profession and Technology, Jinhua, Zhejiang 321007, P.R. China
| | - Mingxing Ding
- Department of Medical Sciences, Jinhua College of Profession and Technology, Jinhua, Zhejiang 321007, P.R. China
| | - Ning Zhang
- Department of Medical Sciences, Jinhua College of Profession and Technology, Jinhua, Zhejiang 321007, P.R. China
| | - Jicheng Li
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, P.R. China
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43
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Fan X, Yan J, Xie L, Zeng L, Young RF, Xie J. Genomic and proteomic features of mycobacteriophage SWU1 isolated from China soil. Gene 2015; 561:45-53. [PMID: 25701596 DOI: 10.1016/j.gene.2015.02.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 01/24/2015] [Accepted: 02/02/2015] [Indexed: 12/20/2022]
Abstract
Mycobacteriophage SWU1 is a newly isolated phage from soil sample collected in Sichuan province, China using Mycobacterium smegmatis mc(2)155 as host. Plaque, phage morphology and one-step growth curve were characterized. The complete genomic sequence of phage SWU1 was determined by shotgun sequencing. The ends of SWU1 were determined. Structural proteins of SWU1 were analyzed by NanoLC-ESI-MS/MS. Seven ORFs were identified as structural protein encoded by SWU1 genome. The genetic basis underlying the SWU1 plaque was explored using comparative genomics. Prophages homologous to SWU1 were identified in two pathogens, Segniliparus rugosus ATCC BAA-974 and Mycobacterium rhodesiae JS60. Genus Segniliparus is a member of the order Corynebacteriales. To our knowledge, this is the first report of Mycobacterium prophages in different genera.
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Affiliation(s)
- Xiangyu Fan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China; School of Biological Science and Technology, University of Jinan, Shandong 250022, China.
| | - Jianlong Yan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Lanying Zeng
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
| | - Ryland F Young
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China.
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44
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Teng T, Yu J, Yang H, Wei H. Isolation and complete genome sequence of a novel virulent mycobacteriophage, CASbig. Virol Sin 2015; 30:76-9. [PMID: 25646930 DOI: 10.1007/s12250-014-3545-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Tieshan Teng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
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45
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Marinelli LJ, Hatfull GF, Piuri M. Recombineering: A powerful tool for modification of bacteriophage genomes. BACTERIOPHAGE 2014; 2:5-14. [PMID: 22666652 PMCID: PMC3357384 DOI: 10.4161/bact.18778] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recombineering, a recently developed technique for efficient genetic manipulation of bacteria, is facilitated by phage-derived recombination proteins and has the advantage of using DNA substrates with short regions of homology. This system was first developed in E. coli but has since been adapted for use in other bacteria. It is now widely used in a number of different systems for a variety of purposes, and the construction of chromosomal gene knockouts, deletions, insertions, point mutations, as well as in vivo cloning, mutagenesis of bacterial artificial chromosomes and phasmids, and the construction of genomic libraries has been reported. However, these methods also can be effectively applied to the genetic modification of bacteriophage genomes, in both their prophage and lytically growing states. The ever-growing collection of fully sequenced bacteriophages raises more questions than they answer, including the unknown functions of vast numbers of genes with no known homologs and of unknown function. Recombineering of phage genomes is central to addressing these questions, enabling the simple construction of mutants, determination of gene essentiality, and elucidation of gene function. In turn, advances in our understanding of phage genomics should present similar recombineering tools for dissecting a multitude of other genetically naïve bacterial systems.
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46
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Palomino JC, Vandamme P, Martin A. Classical and new assays for detecting drug resistance in tuberculosis. Biomark Med 2014; 8:1105-14. [DOI: 10.2217/bmm.14.73] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tuberculosis is a public health concern worldwide. Particularly worrying is the emergence of severe forms of drug resistance, such as extensively drug resistant and totally drug resistant tuberculosis, with few treatment options for the afflicted patients. To avoid further spread of drug resistance, its early detection is extremely important. Conventional phenotypic procedures to detect drug resistance depended on the in vitro slow growth of the bacteria. More recent molecular approaches such as reverse-hybridization assays and real-time PCR tests have been introduced. Newer options proposed include, faster culture-based methods and whole-genome sequencing and nanotechnology. Not yet available is a real point-of-care test, applied directly in clinical samples and reliable enough for guiding a treatment option.
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Affiliation(s)
- Juan Carlos Palomino
- Laboratory of Microbiology, Department of Biochemistry & Microbiology, Ghent University, KL Ledeganckstraat 35, 9000 Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry & Microbiology, Ghent University, KL Ledeganckstraat 35, 9000 Gent, Belgium
| | - Anandi Martin
- Laboratory of Microbiology, Department of Biochemistry & Microbiology, Ghent University, KL Ledeganckstraat 35, 9000 Gent, Belgium
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Exposing the secrets of two well-known Lactobacillus casei phages, J-1 and PL-1, by genomic and structural analysis. Appl Environ Microbiol 2014; 80:7107-21. [PMID: 25217012 DOI: 10.1128/aem.02771-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage J-1 was isolated in 1965 from an abnormal fermentation of Yakult using Lactobacillus casei strain Shirota, and a related phage, PL-1, was subsequently recovered from a strain resistant to J-1. Complete genome sequencing shows that J-1 and PL-1 are almost identical, but PL-1 has a deletion of 1.9 kbp relative to J-1, resulting in the loss of four predicted gene products involved in immunity regulation. The structural proteins were identified by mass spectrometry analysis. Similarly to phage A2, two capsid proteins are generated by a translational frameshift and undergo proteolytic processing. The structure of gene product 16 (gp16), a putative tail protein, was modeled based on the crystal structure of baseplate distal tail proteins (Dit) that form the baseplate hub in other Siphoviridae. However, two regions of the C terminus of gp16 could not be modeled using this template. The first region accounts for the differences between J-1 and PL-1 gp16 and showed sequence similarity to carbohydrate-binding modules (CBMs). J-1 and PL-1 GFP-gp16 fusions bind specifically to Lactobacillus casei/paracasei cells, and the addition of l-rhamnose inhibits binding. J-1 gp16 exhibited a higher affinity than PL-1 gp16 for cell walls of L. casei ATCC 27139 in phage adsorption inhibition assays, in agreement with differential adsorption kinetics observed for both phages in this strain. The data presented here provide insights into how Lactobacillus phages interact with their hosts at the first steps of infection.
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Abstract
ABSTRACT
Mycobacteriophages have provided numerous essential tools for mycobacterial genetics, including delivery systems for transposons, reporter genes, and allelic exchange substrates, and components for plasmid vectors and mutagenesis. Their genetically diverse genomes also reveal insights into the broader nature of the phage population and the evolutionary mechanisms that give rise to it. The substantial advances in our understanding of the biology of mycobacteriophages including a large collection of completely sequenced genomes indicates a rich potential for further contributions in tuberculosis genetics and beyond.
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50
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Hatfull GF. Molecular Genetics of Mycobacteriophages. Microbiol Spectr 2014; 2:1-36. [PMID: 25328854 PMCID: PMC4199240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
Mycobacteriophages have provided numerous essential tools for mycobacterial genetics, including delivery systems for transposons, reporter genes, and allelic exchange substrates, and components for plasmid vectors and mutagenesis. Their genetically diverse genomes also reveal insights into the broader nature of the phage population and the evolutionary mechanisms that give rise to it. The substantial advances in our understanding of the biology of mycobacteriophages including a large collection of completely sequenced genomes indicates a rich potential for further contributions in tuberculosis genetics and beyond.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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