Genetic Determinants of Intrinsic Antibiotic Tolerance in Mycobacterium avium

The prolonged treatment required to eradicate Mycobacterium avium complex (MAC) infection is likely due to the presence of subpopulations of antibiotic-tolerant bacteria with reduced susceptibility to currently available drugs. However, little is known about the genes and pathways responsible for antibiotic tolerance in MAC. ABSTRACT The Mycobacterium avium complex (MAC) is one of the most prevalent causes of nontuberculous mycobacteria pulmonary infection in the United States, and yet it remains understudied. Current MAC treatment requires more than a year of intermittent to daily combination antibiotic therapy, depending on disease severity. In order to shorten and simplify curative regimens, it is important to identify the innate bacterial factors contributing to reduced antibiotic susceptibility, namely, antibiotic tolerance genes. In this study, we performed a genome-wide transposon screen to elucidate M. avium genes that play a role in the bacterium’s tolerance to first- and second-line antibiotics. We identified a total of 193 unique M. avium mutants with significantly altered susceptibility to at least one of the four clinically used antibiotics we tested, including two mutants (in DFS55_00905 and DFS55_12730) with panhypersusceptibility. The products of the antibiotic tolerance genes we have identified may represent novel targets for future drug development studies aimed at shortening the duration of therapy for MAC infections. IMPORTANCE The prolonged treatment required to eradicate Mycobacterium avium complex (MAC) infection is likely due to the presence of subpopulations of antibiotic-tolerant bacteria with reduced susceptibility to currently available drugs. However, little is known about the genes and pathways responsible for antibiotic tolerance in MAC. In this study, we performed a forward genetic screen to identify M. avium antibiotic tolerance genes, whose products may represent attractive targets for the development of novel adjunctive drugs capable of shortening the curative treatment for MAC infections.

[1]  P. Karakousis,et al.  Mechanisms of Antibiotic Tolerance in Mycobacterium avium Complex: Lessons From Related Mycobacteria , 2020, Frontiers in Microbiology.

[2]  J. Brożek,et al.  Treatment of Nontuberculous Mycobacterial Pulmonary Disease: An Official ATS/ERS/ESCMID/IDSA Clinical Practice Guideline. , 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[3]  K. Winthrop,et al.  Incidence and Prevalence of Nontuberculous Mycobacterial Lung Disease in a Large U.S. Managed Care Health Plan, 2008–2015 , 2019, Annals of the American Thoracic Society.

[4]  P. Jaiswal,et al.  Quantitative analysis of Mycobacterium avium subsp. hominissuis proteome in response to antibiotics and during exposure to different environmental conditions , 2019, Clinical Proteomics.

[5]  B. Conlon,et al.  Reactive oxygen species induce antibiotic tolerance during systemic Staphylococcus aureus infection , 2019, Nature Microbiology.

[6]  J. Adkins,et al.  Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells , 2019, mBio.

[7]  J. Bader,et al.  Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure , 2019, Scientific Reports.

[8]  C. Dorman.  DNA supercoiling and transcription in bacteria: a two-way street , 2019, BMC Molecular and Cell Biology.

[9]  Z. Ziora,et al.  Quinolone antibiotics , 2019, MedChemComm.

[10]  E. Chan,et al.  Mycobacterium avium Infection in a C3HeB/FeJ Mouse Model , 2019, Front. Microbiol..

[11]  Yashwant Kumar,et al.  Conditional Silencing by CRISPRi Reveals the Role of DNA Gyrase in Formation of Drug-Tolerant Persister Population in Mycobacterium tuberculosis , 2019, Front. Cell. Infect. Microbiol..

[12]  J. Bader,et al.  Inhibiting the stringent response blocks Mycobacterium tuberculosis entry into quiescence and reduces persistence , 2019, Science Advances.

[13]  Joel S. Bader,et al.  Genome analysis of Mycobacterium avium subspecies hominissuis strain 109 , 2018, Scientific Data.

[14]  N. Krogan,et al.  Mycobacterial Mutagenesis and Drug Resistance Are Controlled by Phosphorylation- and Cardiolipin-Mediated Inhibition of the RecA Coprotease. , 2018, Molecular cell.

[15]  D. Schnappinger,et al.  Metabolic principles of persistence and pathogenicity in Mycobacterium tuberculosis , 2018, Nature Reviews Microbiology.

[16]  M. Braunstein,et al.  The SecA2 pathway of Mycobacterium tuberculosis exports effectors that work in concert to arrest phagosome and autophagosome maturation , 2018, PLoS pathogens.

[17]  Sameer S. Kadri,et al.  Geographic Distribution of Nontuberculous Mycobacterial Species Identified among Clinical Isolates in the United States, 2009‐2013 , 2017, Annals of the American Thoracic Society.

[18]  G. Palù,et al.  The Alternative Sigma Factors SigE and SigB Are Involved in Tolerance and Persistence to Antitubercular Drugs , 2017, Antimicrobial Agents and Chemotherapy.

[19]  Sudheer Kumar Singh,et al.  Down-regulation of malate synthase in Mycobacterium tuberculosis H37Ra leads to reduced stress tolerance, persistence and survival in macrophages. , 2017, Tuberculosis.

[20]  Jason H. Yang,et al.  Carbon Sources Tune Antibiotic Susceptibility in Pseudomonas aeruginosa via Tricarboxylic Acid Cycle Control. , 2017, Cell chemical biology.

[21]  Thomas R. Ioerger,et al.  TRANSIT - A Software Tool for Himar1 TnSeq Analysis , 2015, PLoS Comput. Biol..

[22]  R. Wallace,,et al.  Semiquantitative Culture Analysis during Therapy for Mycobacterium avium Complex Lung Disease. , 2015, American journal of respiratory and critical care medicine.

[23]  Matthew D. Zimmerman,et al.  The association between sterilizing activity and drug distribution into tuberculosis lesions , 2015, Nature Medicine.

[24]  R. Letourneau,et al.  Distribution of ethambutol in primate tissues and cells. , 2015, The American review of respiratory disease.

[25]  E. Wolinsky.  Nontuberculous mycobacteria and associated diseases. , 2015, The American review of respiratory disease.

[26]  K. Winthrop,et al.  Population-based Incidence of Pulmonary Nontuberculous Mycobacterial Disease in Oregon 2007 to 2012. , 2015, Annals of the American Thoracic Society.

[27]  J. Bader,et al.  Deficiency of the Novel Exopolyphosphatase Rv1026/PPX2 Leads to Metabolic Downshift and Altered Cell Wall Permeability in Mycobacterium tuberculosis , 2015, mBio.

[28]  J. Grosset,et al.  Characterization of Mouse Models of Mycobacterium avium Complex Infection and Evaluation of Drug Combinations , 2015, Antimicrobial Agents and Chemotherapy.

[29]  C. Nathan,et al.  Isocitrate lyase mediates broad antibiotic tolerance in Mycobacterium tuberculosis , 2014, Nature Communications.

[30]  P. Fey,et al.  A Dysfunctional Tricarboxylic Acid Cycle Enhances Fitness of Staphylococcus epidermidis During β-Lactam Stress , 2013, mBio.

[31]  Corbin D. Jones,et al.  Suppressor Analysis Reveals a Role for SecY in the SecA2-Dependent Protein Export Pathway of Mycobacteria , 2013, Journal of bacteriology.

[32]  D. Belchis,et al.  The Polyphosphate Kinase Gene ppk2 Is Required for Mycobacterium tuberculosis Inorganic Polyphosphate Regulation and Virulence , 2013, mBio.

[33]  F. Drobniewski,et al.  The geographic diversity of nontuberculous mycobacteria isolated from pulmonary samples: an NTM-NET collaborative study , 2013, European Respiratory Journal.

[34]  S. Crosson,et al.  Bacterial lifestyle shapes stringent response activation. , 2013, Trends in microbiology.

[35]  C. Daley,et al.  The pharmacokinetics and pharmacodynamics of pulmonary Mycobacterium avium complex disease treatment. , 2012, American journal of respiratory and critical care medicine.

[36]  K. Sauer,et al.  The MerR-Like Transcriptional Regulator BrlR Contributes to Pseudomonas aeruginosa Biofilm Tolerance , 2012, Journal of bacteriology.

[37]  L. Amaral,et al.  Contribution of efflux activity to isoniazid resistance in the Mycobacterium tuberculosis complex. , 2012, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[38]  B. Kreiswirth,et al.  Induction of Mycobacterial Resistance to Quinolone Class Antimicrobials , 2012, Antimicrobial Agents and Chemotherapy.

[39]  J. Mckinney,et al.  Malachite Green Interferes with Postantibiotic Recovery of Mycobacteria , 2012, Antimicrobial Agents and Chemotherapy.

[40]  M. Braunstein,et al.  The Mycobacterium tuberculosis SecA2 System Subverts Phagosome Maturation To Promote Growth in Macrophages , 2012, Infection and Immunity.

[41]  P. Karakousis,et al.  The Role of the Novel Exopolyphosphatase MT0516 in Mycobacterium tuberculosis Drug Tolerance and Persistence , 2011, PloS one.

[42]  F. Lépine,et al.  Active Starvation Responses Mediate Antibiotic Tolerance in Biofilms and Nutrient-Limited Bacteria , 2011, Science.

[43]  M. Glickman,et al.  Mycobacteria exploit three genetically distinct DNA double‐strand break repair pathways , 2011, Molecular microbiology.

[44]  Mary Ann Blosky,et al.  Nontuberculous mycobacterial lung disease prevalence at four integrated health care delivery systems. , 2010, American journal of respiratory and critical care medicine.

[45]  Jianjun Li,et al.  High-level antibiotic resistance in Pseudomonas aeruginosa biofilm: the ndvB gene is involved in the production of highly glycerol-phosphorylated beta-(1->3)-glucans, which bind aminoglycosides. , 2010, Glycobiology.

[46]  Anuj Gupta,et al.  Microarray analysis of efflux pump genes in multidrug-resistant Mycobacterium tuberculosis during stress induced by common anti-tuberculous drugs. , 2010, Microbial drug resistance.

[47]  J. Wain,et al.  Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. , 2009, Genome research.

[48]  L. Amaral,et al.  The role of efflux pumps in macrolide resistance in Mycobacterium avium complex. , 2009, International journal of antimicrobial agents.

[49]  Georgia Giannoukos,et al.  Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung , 2009, Proceedings of the National Academy of Sciences.

[50]  A. Camilli,et al.  Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms , 2009, Nature Methods.

[51]  Rob Knight,et al.  Identifying genetic determinants needed to establish a human gut symbiont in its habitat. , 2009, Cell host & microbe.

[52]  D. Schnappinger,et al.  Acid-Susceptible Mutants of Mycobacterium tuberculosis Share Hypersusceptibility to Cell Wall and Oxidative Stress and to the Host Environment , 2008, Journal of bacteriology.

[53]  D. Griffith.  Therapy of nontuberculous mycobacterial disease , 2007, Current opinion in infectious diseases.

[54]  T. Primm,et al.  Mycobacterium avium enters a state of metabolic dormancy in response to starvation. , 2005, Tuberculosis.

[55]  W. Jacobs,et al.  Two Nonredundant SecA Homologues Function in Mycobacteria , 2001, Journal of bacteriology.

[56]  James C. Sacchettini,et al.  Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase , 2000, Nature.

[57]  L. Bermudez,et al.  Mycobacterium avium interaction with macrophages and intestinal epithelial cells. , 1999, Frontiers in bioscience : a journal and virtual library.

[58]  R. Moellering,et al.  Antimicrobial-drug resistance. , 1996, The New England journal of medicine.

[59]  F ChenStanley,et al.  An Empirical Study of Smoothing Techniques for Language Modeling , 1996, ACL.

[60]  L. Wayne,et al.  An in vitro model for sequential study of shiftdown of Mycobacterium tuberculosis through two stages of nonreplicating persistence , 1996, Infection and immunity.

[61]  T. Blaschke,et al.  Clinical pharmacokinetics of rifabutin. , 1996, Clinical pharmacokinetics.

[62]  D. Fish,et al.  Penetration of clarithromycin into lung tissues from patients undergoing lung resection , 1994, Antimicrobial Agents and Chemotherapy.

[63]  Y. Hayashi,et al.  Effect of Tween 80 on the Growth of Mycobacterium avium Complex , 1990, Microbiology and immunology.

[64]  B. Parker,et al.  Epidemiology of Infection by Nontuberculous Mycobacteria , 1987 .

[65]  L G Wayne,et al.  Glyoxylate metabolism and adaptation of Mycobacterium tuberculosis to survival under anaerobic conditions , 1982, Infection and immunity.

[66]  A. Tomasz,et al.  Multiple Antibiotic Resistance in a Bacterium with Suppressed Autolytic System , 1970, Nature.

[67]  A. R. Jonckheere,et al.  A DISTRIBUTION-FREE k-SAMPLE TEST AGAINST ORDERED ALTERNATIVES , 1954 .

[68]  S. Muro,et al.  Predictors of 5-year mortality in pulmonary Mycobacterium avium-intracellulare complex disease. , 2012, The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[69]  P. Karakousis.  Mechanisms of Action and Resistance of Antimycobacterial Agents , 2009 .

[70]  H. Leclerc.  [Mycobacterium avium complex]. , 1995, La Revue de medecine interne.

[71]  T. J. Terpstra,et al.  The asymptotic normality and consistency of kendall's test against trend, when ties are present in one ranking , 1952 .