Dynamics of Mycobacteriophage-Mycobacterial Host Interaction.

Mycobacterium sp. is exhibiting complex evolution of antimicrobial resistance (AMR) and can therefore be considered as a serious human pathogen. Many strategies were employed earlier to evade the pathogenesis but AMR became threatened. Molecular tools employing bacteriophage can be an alternative to effective treatment against Mycobacterium. Phage treatment using phage-encoded products, such as lysins, causes lysis of cells; particularly bacteria could be used instead of direct use of these bacteriophages. Modern technologies along with bacteriophage strategies such as in silico immunoinformatics approach, machine learning, and artificial intelligence have been described thoroughly to escape the pathogenesis. Therefore, understanding the molecular mechanisms could be a possible alternative to evade the pathogenesis.

[1]  B. Bowman QUANTITATIVE STUDIES ON SOME MYCOBACTERIAL PHAGE-HOST SYSTEMS , 1958, Journal of Bacteriology.

[2]  B. U. Bowman Properties of Mycobacteriophage DS6A I. Immunogenicity in Rabbits∗ , 1969, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

[3]  T. Tokunaga,et al.  Phage inactivation by an ethanol-ether extract of Mycobacterium smegmatis. , 1970, The American review of respiratory disease.

[4]  Proskurov Va Use of staphylococcal bacteriophage for therapeutic and preventive purposes , 1970 .

[5]  A. Lees,et al.  Toxicity form rifampicin plus isoniazid and rifampicin plus ethambutol therapy. , 1971, Tubercle.

[6]  T. Tokunaga,et al.  Nature of the Receptor Substance of Mycobacterium smegmatis for D4 Bacteriophage Adsorption , 1972, Journal of bacteriology.

[7]  W. D. Jones Differentiation of Known Strains of BCG from Isolates of Mycobacterium bovis and Mycobacterium tuberculosis by Using Mycobacteriophage 33D , 1975, Journal of clinical microbiology.

[8]  G. Orefici,et al.  A study on the receptor for a mycobacteriophage : phage phlei. , 1976, Biochimie.

[9]  J. Moniz-Pereira,et al.  Effects of antituberculosis and antileprosy drugs on mycobacteriophage D29 growth , 1980, Antimicrobial Agents and Chemotherapy.

[10]  T. Timme,et al.  Induction of bacteriophage from members of the Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium scrofulaceum serocomplex. , 1984, Journal of general microbiology.

[11]  M. Cisło,et al.  Bacteriophage treatment of suppurative skin infections. , 1987, Archivum immunologiae et therapiae experimentalis.

[12]  W. Jacobs,et al.  Site-specific integration of mycobacteriophage L5: integration-proficient vectors for Mycobacterium smegmatis, Mycobacterium tuberculosis, and bacille Calmette-Guérin. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[13]  R. Young,et al.  Bacteriophage lysis: mechanism and regulation , 1992, Microbiological reviews.

[14]  G. Sarkis,et al.  DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics , 1993, Molecular microbiology.

[15]  S. Sau,et al.  Isolation, characterization, and mapping of temperature-sensitive mutations in the genes essential for lysogenic and lytic growth of the mycobacteriophage L1. , 1993, Virology.

[16]  W. Jacobs,et al.  Superinfection immunity of mycobacteriophage L5: applications for genetic transformation of mycobacteria , 1993, Molecular microbiology.

[17]  K. Parker,et al.  Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. , 1994, Journal of immunology.

[18]  Perepanova Ts,et al.  The efficacy of bacteriophage preparations in treating inflammatory urologic diseases , 1995 .

[19]  M. Berry,et al.  Toxicity of antibiotics and antifungals on cultured human corneal cells: Effect of mixing, exposure and concentration , 1995, Eye.

[20]  B. Levin,et al.  Phage Therapy Revisited: The Population Biology of a Bacterial Infection and Its Treatment with Bacteriophage and Antibiotics , 1996, The American Naturalist.

[21]  G. Besra,et al.  Chemistry of the Lyxose-Containing Mycobacteriophage Receptors of Mycobacterium phlei/Mycobacterium smegmatis† , 1996 .

[22]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[23]  K. J. Fullner,et al.  Mycobacteriophage L5 infection of Mycobacterium bovis BCG: implications for phage genetics in the slow‐growing mycobacteria , 1997, Molecular microbiology.

[24]  R. Hendrix,et al.  Mycobacteriophage TM4: genome structure and gene expression. , 1998, Tubercle and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[25]  G. Hatfull,et al.  Mycobacteriophage D29 integrase-mediated recombination: specificity of mycobacteriophage integration. , 1998, Gene.

[26]  B. Barrell,et al.  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence , 1998, Nature.

[27]  E. Anes,et al.  The site-specific recombination locus of mycobacteriophage Ms6 determines DNA integration at the tRNAAlagene of Mycobacterium spp. , 1998 .

[28]  H. Rammensee,et al.  SYFPEITHI: database for MHC ligands and peptide motifs , 1999, Immunogenetics.

[29]  Marie-Paule Lefranc,et al.  IMGT, the international ImMunoGeneTics database , 1999, Nucleic Acids Res..

[30]  B. Weber-Dąbrowska,et al.  [Successful treatment with bacteriophage in purulent cerebrospinal meningitis in a newborn]. , 1999, Neurologia i neurochirurgia polska.

[31]  A high yielding mutant of mycobacteriophage L1 and its application as a diagnostic tool. , 2000, FEMS microbiology letters.

[32]  M. J. Waites,et al.  Industrial Microbiology: An Introduction , 2001 .

[33]  Gajendra P. S. Raghava,et al.  ProPred: prediction of HLA-DR binding sites , 2001, Bioinform..

[34]  S. Gillespie,et al.  Evolution of Drug Resistance in Mycobacterium tuberculosis: Clinical and Molecular Perspective , 2002, Antimicrobial Agents and Chemotherapy.

[35]  Raymond Schuch,et al.  A bacteriolytic agent that detects and kills Bacillus anthracis , 2002, Nature.

[36]  T. Hanai,et al.  Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules. , 2002, Journal of bioscience and bioengineering.

[37]  R. Young Bacteriophage holins: deadly diversity. , 2002, Journal of molecular microbiology and biotechnology.

[38]  Arne Elofsson,et al.  Prediction of MHC class I binding peptides, using SVMHC , 2002, BMC Bioinformatics.

[39]  D. Sosnowska,et al.  Killing of Mycobacterium avium and Mycobacterium tuberculosis by a mycobacteriophage delivered by a nonvirulent mycobacterium: a model for phage therapy of intracellular bacterial pathogens. , 2002, The Journal of infectious diseases.

[40]  E. Reinherz,et al.  Prediction of MHC class I binding peptides using profile motifs. , 2002, Human immunology.

[41]  W. Jacobs,et al.  Origins of Highly Mosaic Mycobacteriophage Genomes , 2003, Cell.

[42]  Fumio Arisaka,et al.  Bacteriophage T4 Genome , 2003, Microbiology and Molecular Biology Reviews.

[43]  R. Hendrix Bacteriophage genomics. , 2003, Current opinion in microbiology.

[44]  J. Bull,et al.  Population and evolutionary dynamics of phage therapy , 2004, Nature Reviews Microbiology.

[45]  J. Hammer,et al.  Discovery of promiscuous HLA-II-restricted T cell epitopes with TEPITOPE. , 2004, Methods.

[46]  J. Pelletier,et al.  Antimicrobial drug discovery through bacteriophage genomics , 2004, Nature Biotechnology.

[47]  Pingping Guan,et al.  EpiJen: a server for multistep T cell epitope prediction , 2006, BMC Bioinformatics.

[48]  Toshikazu Tani,et al.  Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases , 2005, Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy.

[49]  M. Loessner,et al.  Bacteriophage endolysins--current state of research and applications. , 2005, Current opinion in microbiology.

[50]  P. Dönnes,et al.  Integrated modeling of the major events in the MHC class I antigen processing pathway , 2005, Protein science : a publication of the Protein Society.

[51]  H. Brüssow,et al.  Phage therapy: the Escherichia coli experience. , 2005, Microbiology.

[52]  D. Court,et al.  A New Look at Bacteriophage λ Genetic Networks , 2006 .

[53]  J. Rybniker,et al.  Host range of 14 mycobacteriophages in Mycobacterium ulcerans and seven other mycobacteria including Mycobacterium tuberculosis--application for identification and susceptibility testing. , 2006, Journal of medical microbiology.

[54]  Ora Schueler-Furman,et al.  Learning MHC I - peptide binding , 2006, ISMB.

[55]  M. Piuri,et al.  A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells , 2006, Molecular microbiology.

[56]  L. Hall-Stoodley,et al.  Mycobacterium marinum biofilm formation reveals cording morphology. , 2006, FEMS microbiology letters.

[57]  P. Auvinen,et al.  Global Changes in Cellular Gene Expression during Bacteriophage PRD1 Infection , 2006, Journal of Virology.

[58]  Ji Wan,et al.  SVRMHC prediction server for MHC-binding peptides , 2006, BMC Bioinformatics.

[59]  O. Lund,et al.  NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence , 2007, PloS one.

[60]  Dottore Emiliano Fruciano,et al.  Phage as an antimicrobial agent: d'Herelle's heretical theories and their role in the decline of phage prophylaxis in the West. , 2007, The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale.

[61]  C. Suttle Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.

[62]  Shinn-Ying Ho,et al.  POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties , 2007, Bioinform..

[63]  Sonja Hess,et al.  Mycobacterium tuberculosis produces pili during human infection , 2007, Proceedings of the National Academy of Sciences.

[64]  Morten Nielsen,et al.  Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction , 2007, BMC Bioinformatics.

[65]  G. Borriello,et al.  Experimental Phage Therapy against Staphylococcus aureus in Mice , 2007, Antimicrobial Agents and Chemotherapy.

[66]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[67]  D. Bamford,et al.  Global Transcriptional Responses of Pseudomonas aeruginosa to Phage PRR1 Infection , 2007, Journal of Virology.

[68]  N. Ariel,et al.  Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses , 2008, BMC Medical Genomics.

[69]  Morten Nielsen,et al.  NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11 , 2008, Nucleic Acids Res..

[70]  S. Chhibber,et al.  Therapeutic potential of bacteriophage in treating Klebsiella pneumoniae B5055-mediated lobar pneumonia in mice. , 2008, Journal of medical microbiology.

[71]  Jean-Philippe Vert,et al.  Efficient peptide-MHC-I binding prediction for alleles with few known binders , 2008, Bioinform..

[72]  Graham F Hatfull,et al.  Bacteriophage genomics. , 2008, Current opinion in microbiology.

[73]  Vasant G Honavar,et al.  Predicting linear B‐cell epitopes using string kernels , 2008, Journal of molecular recognition : JMR.

[74]  Graham F Hatfull,et al.  Growth of Mycobacterium tuberculosis biofilms containing free mycolic acids and harbouring drug-tolerant bacteria , 2008, Molecular microbiology.

[75]  V. Fischetti,et al.  Bacteriophage lysins as effective antibacterials. , 2008, Current opinion in microbiology.

[76]  R. Donlan,et al.  Structural Analysis of Biofilm Formation by Rapidly and Slowly Growing Nontuberculous Mycobacteria , 2008, Applied and Environmental Microbiology.

[77]  Pierre Baldi,et al.  COBEpro: a novel system for predicting continuous B-cell epitopes. , 2009, Protein engineering, design & selection : PEDS.

[78]  G. Besra,et al.  Defects in glycopeptidolipid biosynthesis confer phage I3 resistance in Mycobacterium smegmatis. , 2009, Microbiology.

[79]  S. Zuber,et al.  T4 phages against Escherichia coli diarrhea: potential and problems. , 2009, Virology.

[80]  C. Rees,et al.  Bacteriophage applications: where are we now? , 2010, Letters in applied microbiology.

[81]  A. Coffey,et al.  Recombinant bacteriophage lysins as antibacterials , 2010, Bioengineered bugs.

[82]  Oliver Kohlbacher,et al.  T-cell epitope prediction based on self-tolerance , 2011, BCB '11.

[83]  Timothy K Lu,et al.  The next generation of bacteriophage therapy. , 2011, Current opinion in microbiology.

[84]  Yongfei Hu,et al.  Whole-Genome Sequences of Four Mycobacterium bovis BCG Vaccine Strains , 2011, Journal of bacteriology.

[85]  Ted Cohen,et al.  Spontaneous Emergence of Multiple Drug Resistance in Tuberculosis before and during Therapy , 2011, PloS one.

[86]  R. P. Ross,et al.  Genetic Response to Bacteriophage Infection in Lactococcus lactis Reveals a Four-Strand Approach Involving Induction of Membrane Stress Proteins, d-Alanylation of the Cell Wall, Maintenance of Proton Motive Force, and Energy Conservation , 2011, Journal of Virology.

[87]  Cole Trapnell,et al.  Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.

[88]  Morten Nielsen,et al.  Prediction of epitopes using neural network based methods. , 2011, Journal of immunological methods.

[89]  N. Chanishvili Phage therapy--history from Twort and d'Herelle through Soviet experience to current approaches. , 2012, Advances in virus research.

[90]  Graham F Hatfull,et al.  The secret lives of mycobacteriophages. , 2012, Advances in virus research.

[91]  Hau-San Wong,et al.  TEPITOPEpan: Extending TEPITOPE for Peptide Binding Prediction Covering over 700 HLA-DR Molecules , 2012, PloS one.

[92]  Manoj Rajaure,et al.  The Spanin Complex Is Essential for Lambda Lysis , 2012, Journal of bacteriology.

[93]  H. Erlich,et al.  HLA DNA typing: past, present, and future. , 2012, Tissue antigens.

[94]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[95]  Charles A. Bowman,et al.  On the nature of mycobacteriophage diversity and host preference. , 2012, Virology.

[96]  A. Longatto-Filho,et al.  Phage Therapy Is Effective against Infection by Mycobacterium ulcerans in a Murine Footpad Model , 2013, PLoS neglected tropical diseases.

[97]  G. Hatfull Complete Genome Sequences of 63 Mycobacteriophages , 2013, Genome Announcements.

[98]  M. Larsen,et al.  Pili contribute to biofilm formation in vitro in Mycobacterium tuberculosis , 2013, Antonie van Leeuwenhoek.

[99]  Alimuddin Zumla,et al.  WHO's 2013 global report on tuberculosis: successes, threats, and opportunities , 2013, The Lancet.

[100]  J. Moniz-Pereira,et al.  Diversity in bacterial lysis systems: bacteriophages show the way. , 2013, FEMS microbiology reviews.

[101]  S. Soni,et al.  Aeromonas punctata derived depolymerase that disrupts the integrity of Klebsiella pneumoniae capsule: optimization of depolymerase production , 2014, Journal of basic microbiology.

[102]  G. Hatfull Mycobacteriophages: Windows into Tuberculosis , 2014, PLoS pathogens.

[103]  A. Górski,et al.  Facing Antibiotic Resistance: Staphylococcus aureus Phages as a Medical Tool , 2014, Viruses.

[104]  S. Chhibber,et al.  Bacteriophage-aided intracellular killing of engulfed methicillin-resistant Staphylococcus aureus (MRSA) by murine macrophages , 2014, Applied Microbiology and Biotechnology.

[105]  Deborah Hix,et al.  The immune epitope database (IEDB) 3.0 , 2014, Nucleic Acids Res..

[106]  S. Sillankorva,et al.  Phage Therapy: a Step Forward in the Treatment of Pseudomonas aeruginosa Infections , 2015, Journal of Virology.

[107]  S. Roy,et al.  Dynamics of Mycobacteriophage-Mycobacterial Host Interaction: Evidence for Secondary Mechanisms for Host Lethality , 2015, Applied and Environmental Microbiology.

[108]  S. Chhibber Evading Antibody Mediated Inactivation of Bacteriophages Using Delivery Systems , 2017 .