Mycobacterium trehalose polyphleates are required for infection by therapeutically useful mycobacteriophages BPs and Muddy

Mycobacteriophages are good model systems for understanding their bacterial hosts and show promise as therapeutic agents for nontuberculous mycobacterium infections. However, little is known about phage recognition of Mycobacterium cell surfaces, or mechanisms of phage resistance. We show here that surface-exposed trehalose polyphleates (TPPs) are required for infection of Mycobacterium abscessus and Mycobacterium smegmatis by clinically useful phages BPs and Muddy, and that TPP loss leads to defects in adsorption, infection, and confers resistance. Transposon mutagenesis indicates that TPP loss is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss, and some M. abscessus clinical isolates are phage-insensitive due to TPP absence. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, and M. abscessus mutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.

[1]  Charles L. Dulberger,et al.  Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection , 2023, Nature Microbiology.

[2]  G. Hatfull.  Phage Therapy for Nontuberculous Mycobacteria: Challenges and Opportunities , 2022, Pulmonary Therapy.

[3]  J. Nick,et al.  Nontuberculous Mycobacterial Infections in Cystic Fibrosis. , 2022, Clinics in chest medicine.

[4]  Steven G. Cresawn,et al.  PhaMMseqs: a new pipeline for constructing phage gene phamilies using MMseqs2 , 2022, G3.

[5]  G. Hatfull.  Mycobacteriophages: From Petri dish to patient , 2022, PLoS pathogens.

[6]  Charles L. Dulberger,et al.  Transposon mutagenesis in Mycobacterium abscessus identifies an essential penicillin-binding protein involved in septal peptidoglycan synthesis and antibiotic sensitivity , 2022, eLife.

[7]  T. Bernhardt,et al.  Phage resistance profiling identifies new genes required for biogenesis and modification of the corynebacterial cell envelope , 2022, bioRxiv.

[8]  C. Benson,et al.  Bacteriophage treatment of disseminated cutaneous Mycobacterium chelonae infection , 2022, Nature Communications.

[9]  Brian E. Vestal,et al.  Host and pathogen response to bacteriophage engineered against Mycobacterium abscessus lung infection , 2022, Cell.

[10]  L. Kremer,et al.  Mycobacteriophage–antibiotic therapy promotes enhanced clearance of drug-resistant Mycobacterium abscessus , 2021, Disease models & mechanisms.

[11]  R. Schooley,et al.  Phage Therapy for Antibiotic-Resistant Bacterial Infections. , 2021, Annual review of medicine.

[12]  Dalin Rifat,et al.  Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing , 2021, mBio.

[13]  G. Hatfull,et al.  Toward a Phage Cocktail for Tuberculosis: Susceptibility and Tuberculocidal Action of Mycobacteriophages against Diverse Mycobacterium tuberculosis Strains , 2021, mBio.

[14]  G. Hatfull,et al.  Mycobacterium abscessus Strain Morphotype Determines Phage Susceptibility, the Repertoire of Therapeutically Useful Phages, and Phage Resistance , 2021, mBio.

[15]  M. Palumbo,et al.  A Mycobacterial Systems Resource for the Research Community , 2021, mBio.

[16]  G. Besra,et al.  Synthesis and recycling of the mycobacterial cell envelope , 2021, Current opinion in microbiology.

[17]  P. Turner,et al.  High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria , 2020, Proceedings of the National Academy of Sciences.

[18]  O. Burlet-Schiltz,et al.  The final assembly of trehalose polyphleates takes place within the outer layer of the mycobacterial cell envelope , 2020, The Journal of Biological Chemistry.

[19]  Vivek K. Mutalik,et al.  High-throughput mapping of the phage resistance landscape in E. coli , 2020, bioRxiv.

[20]  R. Schooley,et al.  Engineered bacteriophages for treatment of a patient with a disseminated drug resistant Mycobacterium abscessus , 2019, Nature Medicine.

[21]  G. Hatfull,et al.  Mycobacteriophage ZoeJ: A broad host-range close relative of mycobacteriophage TM4. , 2019, Tuberculosis.

[22]  L. Kremer,et al.  Glycopeptidolipids, a Double-Edged Sword of the Mycobacterium abscessus Complex , 2018, Front. Microbiol..

[23]  G. Hatfull,et al.  Mycobacteriophage Fruitloop gp52 inactivates Wag31 (DivIVA) to prevent heterotypic superinfection , 2018, Molecular microbiology.

[24]  Kristin N. Parent,et al.  Genes affecting progression of bacteriophage P22 infection in Salmonella identified by transposon and single gene deletion screens , 2018, Molecular microbiology.

[25]  Marta Llorens-Fons,et al.  Trehalose Polyphleates, External Cell Wall Lipids in Mycobacterium abscessus, Are Associated with the Formation of Clumps with Cording Morphology, Which Have Been Associated with Virulence , 2017, Front. Microbiol..

[26]  K. Skolnik,et al.  Nontuberculous Mycobacteria in Cystic Fibrosis , 2016, Current Treatment Options in Infectious Diseases.

[27]  L. Kremer,et al.  Insights into the smooth‐to‐rough transitioning in Mycobacterium bolletii unravels a functional Tyr residue conserved in all mycobacterial MmpL family members , 2016, Molecular microbiology.

[28]  A. Lemassu,et al.  Trehalose Polyphleates Are Produced by a Glycolipid Biosynthetic Pathway Conserved across Phylogenetically Distant Mycobacteria. , 2016, Cell chemical biology.

[29]  John Vu,et al.  Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity , 2015, eLife.

[30]  C. Bertozzi,et al.  The rv1184c Locus Encodes Chp2, an Acyltransferase in Mycobacterium tuberculosis Polyacyltrehalose Lipid Biosynthesis , 2014, Journal of bacteriology.

[31]  E. Koonin,et al.  Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing , 2013, Biology Direct.

[32]  Kira S. Makarova,et al.  Comparative genomics of defense systems in archaea and bacteria , 2013, Nucleic acids research.

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

[34]  Michael S. Scherman,et al.  INHIBITION OF MYCOLIC ACID TRANSPORT ACROSS THE MYCOBACTERIUM TUBERCULOSIS PLASMA MEMBRANE , 2011, Nature chemical biology.

[35]  R. Wallace,,et al.  Susceptibility Testing of Mycobacteria, Nocardiae, and Other Aerobic Actinomycetes , 2011 .

[36]  Graham F. Hatfull,et al.  Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. , 2010, Journal of molecular biology.

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

[38]  R. Hendrix,et al.  Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements. , 2009, Microbiology.

[39]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[40]  Deborah Jacobs-Sera,et al.  Exploring the Mycobacteriophage Metaproteome: Phage Genomics as an Educational Platform , 2006, PLoS genetics.

[41]  Thomas Ludwig,et al.  RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees , 2005, Bioinform..

[42]  Thomas Ludwig,et al.  A fast program for maximum likelihood-based inference of large phylogenetic trees , 2004, SAC '04.

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

[44]  C. Nesbit,et al.  Transcriptional regulation of repressor synthesis in mycobacteriophage L5 , 1995, Molecular microbiology.