msaABCR operon is involved in persister cell formation in Staphylococcus aureus

BMC Microbiology - Tập 17 - Trang 1-21 - 2017
Gyan S. Sahukhal1, Shanti Pandey1, Mohamed O. Elasri1
1Department of Biological Sciences, The University of Southern Mississippi, Hattiesburg, USA

Tóm tắt

Persister cells comprise a phenotypic variant that shows extreme antibiotic tolerance resulting in treatment failures of bacterial infections. While this phenomenon has posed a great threat in public health, mechanisms underlying their formation in Staphylococcus aureus remain largely unknown. Increasing evidences of the presence of persister cells in recalcitrant infections underscores the great urgency to unravel the mechanism by which these cells develop. Previously, we characterized msaABCR operon that plays roles in regulation of virulence, biofilm development and antibiotic resistance. We also characterized the function of MsaB protein and showed that MsaB is a putative transcription factor that binds target DNA in response to nutrients availability. In this study, we compared the number of persister cell in wild type, msaABCR deletion mutant and the complemented strain in two backgrounds USA300 LAC and Mu50. Herein, we report that msaABCR deletion mutant forms significantly less number of persister cells relative to wild type after challenge with various antibiotics in planktonic and biofilm growth conditions. Complementation of the msaABCR operon restored wild type phenotype. Combined antibiotic therapy along with msaABCR deletion significantly improves the killing kinetics of stationary phase and biofilm S. aureus cells. Transcriptomics analysis showed that msaABCR regulates several metabolic genes, transcription factors, transporters and enzymes that may play role in persister cells formation, which we seek to define in the future. This study presented a new regulator, msaABCR operon, that is involved in the persister cells formation, which is a poorly understood in S. aureus. Indeed, we showed that msaABCR deletion significantly reduces the persister cells formation in all growth phases tested. Although, we have not yet defined the mechanism, we have shown that msaABCR regulates several metabolic, transporters, and extracellular proteases genes that have been previously linked with persister cells formation in other bacterial systems. Taken together, this study showed that inactivation of the msaABCR operon enhances the effectiveness of antibiotics for the treatment of S. aureus infections, especially in context of persister cells.

Tài liệu tham khảo

Chambers HF, Deleo FR. Waves of resistance: Staphylococcus Aureus in the antibiotic era. Nat Rev Microbiol. 2009;7(9):629–41. Lowy FD. Staphylococcus Aureus infections. N Engl J Med. 1998;339(8):520–32. Wertheim HF, Vos MC, Ott A, van Belkum A, Voss A, Kluytmans JA, van Keulen PH, Vandenbroucke-Grauls CM, Meester MH, Verbrugh HA. Risk and outcome of nosocomial Staphylococcus Aureus bacteraemia in nasal carriers versus non-carriers. Lancet. 2004;364(9435):703–5. Conlon BP. Staphylococcus Aureus chronic and relapsing infections: evidence of a role for persister cells: an investigation of persister cells, their formation and their role in S. Aureus disease. BioEssays. 2014;36(10):991–6. Conlon BP, Rowe SE, Lewis K. Persister cells in biofilm associated infections. Adv Exp Med Biol. 2015;831:1–9. Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, Lin F, Lin J, Carleton HA, Mongodin EF, et al. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus Aureus. Lancet. 2006;367(9512):731–9. Henry NK, Rouse MS, Whitesell AL, McConnell ME, Wilson WR. Treatment of methicillin-resistant Staphylococcus Aureus experimental osteomyelitis with ciprofloxacin or vancomycin alone or in combination with rifampin. Am J Med. 1987;82(4A):73–5. Monack DM, Mueller A, Falkow S. Persistent bacterial infections: the interface of the pathogen and the host immune system. Nat Rev Microbiol. 2004;2(9):747–65. Murdoch MB, Peterson LR. Antimicrobial penetration into polymorphonuclear leukocytes and alveolar macrophages. Semin Respir Infect. 1991;6(2):112–21. Conlon BP, Nakayasu ES, Fleck LE, LaFleur MD, Isabella VM, Coleman K, Leonard SN, Smith RD, Adkins JN, Lewis K. Activated ClpP kills persisters and eradicates a chronic biofilm infection. Nature. 2013;503(7476):365–70. Helaine S, Cheverton AM, Watson KG, Faure LM, Matthews SA, Holden DW. Internalization of salmonella by macrophages induces formation of nonreplicating persisters. Science. 2014;343(6167):204–8. Lafleur MD, Qi Q, Lewis K. Patients with long-term oral carriage harbor high-persister mutants of Candida Albicans. Antimicrob Agents Chemother. 2010;54(1):39–44. Lewis K. Persister cells. Annu Rev Microbiol. 2010;64:357–72. Mulcahy LR, Burns JL, Lory S, Lewis K. Emergence of Pseudomonas Aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis. J Bacteriol. 2010;192(23):6191–9. Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S, Vulic M, Lewis K, Brennan RG. HipBA-promoter structures reveal the basis of heritable multidrug tolerance. Nature. 2015;524(7563):59–64. Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S. Bacterial persistence as a phenotypic switch. Science. 2004;305(5690):1622–5. Gefen O, Balaban NQ. The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress. FEMS Microbiol Rev. 2009;33(4):704–17. Brauner A, Fridman O, Gefen O, Balaban NQ. Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nat Rev Microbiol. 2016;14(5):320–30. Conlon BP, Rowe SE, Gandt AB, Nuxoll AS, Donegan NP, Zalis EA, Clair G, Adkins JN, Cheung AL, Lewis K. Persister formation in Staphylococcus Aureus is associated with ATP depletion. Nat Microbiol. 2016;1:16051. Rowe SE, Conlon BP, Keren I, Lewis K. Persisters: methods for isolation and identifying contributing factors--a review. Methods Mol Biol. 2016;1333:17–28. Waters EM, Rowe SE, O'Gara JP, Conlon BP. Convergence of Staphylococcus Aureus Persister and biofilm research: can biofilms be defined as communities of adherent Persister cells? PLoS Pathog. 2016;12(12):e1006012. Bernier SP, Lebeaux D, DeFrancesco AS, Valomon A, Soubigou G, Coppee JY, Ghigo JM, Beloin C. Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin. PLoS Genet. 2013;9(1):e1003144. Boles BR, Singh PK. Endogenous oxidative stress produces diversity and adaptability in biofilm communities. Proc Natl Acad Sci U S A. 2008;105(34):12503–8. Fauvart M, De Groote VN, Michiels J. Role of persister cells in chronic infections: clinical relevance and perspectives on anti-persister therapies. J Med Microbiol. 2011;60(Pt 6):699–709. Moker N, Dean CR, Tao J. Pseudomonas Aeruginosa increases formation of multidrug-tolerant persister cells in response to quorum-sensing signaling molecules. J Bacteriol. 2010;192(7):1946–55. Nguyen D, Joshi-Datar A, Lepine F, Bauerle E, Olakanmi O, Beer K, McKay G, Siehnel R, Schafhauser J, Wang Y, et al. Active starvation responses mediate antibiotic tolerance in biofilms and nutrient-limited bacteria. Science. 2011;334(6058):982–6. Orman MA, Brynildsen MP. Dormancy is not necessary or sufficient for bacterial persistence. Antimicrob Agents Chemother. 2013;57(7):3230–9. Vega NM, Allison KR, Khalil AS, Collins JJ. Signaling-mediated bacterial persister formation. Nat Chem Biol. 2012;8(5):431–3. Walters MC, 3rd, Roe F, Bugnicourt A, Franklin MJ, Stewart PS: Contributions of antibiotic penetration, oxygen limitation, and low metabolic activity to tolerance of Pseudomonas Aeruginosa biofilms to ciprofloxacin and tobramycin. Antimicrob Agents Chemother 2003, 47(1):317–323. Wu Y, Vulic M, Keren I, Lewis K. Role of oxidative stress in persister tolerance. Antimicrob Agents Chemother. 2012;56(9):4922–6. Amato SM, Orman MA, Brynildsen MP. Metabolic control of persister formation in Escherichia Coli. Mol Cell. 2013;50(4):475–87. Dorr T, Vulic M, Lewis K. Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia Coli. PLoS Biol. 2010;8(2):e1000317. Fasani RA, Savageau MA. Molecular mechanisms of multiple toxin-antitoxin systems are coordinated to govern the persister phenotype. Proc Natl Acad Sci U S A. 2013;110(27):E2528–37. Harrison JJ, Wade WD, Akierman S, Vacchi-Suzzi C, Stremick CA, Turner RJ, Ceri H. The chromosomal toxin gene yafQ is a determinant of multidrug tolerance for Escherichia Coli growing in a biofilm. Antimicrob Agents Chemother. 2009;53(6):2253–8. Helaine S, Kugelberg E. Bacterial persisters: formation, eradication, and experimental systems. Trends Microbiol. 2014;22(7):417–24. Li Y, Zhang Y. PhoU is a persistence switch involved in persister formation and tolerance to multiple antibiotics and stresses in Escherichia Coli. Antimicrob Agents Chemother. 2007;51(6):2092–9. Ma C, Sim S, Shi W, Du L, Xing D, Zhang Y. Energy production genes sucB and ubiF are involved in persister survival and tolerance to multiple antibiotics and stresses in Escherichia Coli. FEMS Microbiol Lett. 2010;303(1):33–40. Yee R, Cui P, Shi W, Feng J, Zhang Y. Genetic screen reveals the role of purine metabolism in Staphylococcus Aureus persistence to rifampicin. Antibiotics (Basel). 2015;4(4):627–42. Batte JL, Samanta D, Elasri MO. MsaB activates capsule production at the transcription level in Staphylococcus Aureus. Microbiology. 2016;162(3):575–89. Sahukhal GS, Batte JL, Elasri MO. msaABCR operon positively regulates biofilm development by repressing proteases and autolysis in Staphylococcus Aureus. FEMS Microbiol Lett. 2015;362(4) Sahukhal GS, Elasri MO. Identification and characterization of an operon, msaABCR, that controls virulence and biofilm development in Staphylococcus Aureus. BMC Microbiol. 2014;14:154. Samanta D, Elasri MO. The msaABCR operon regulates resistance in vancomycin-intermediate Staphylococcus Aureus strains. Antimicrob Agents Chemother. 2014;58(11):6685–95. CLSI.: Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically; Approved Standard—Ninth Edition. CLSI document M07-A9 Wayne, PA: Clinical and Laboratory Standards Institute 2012. Drago L, De Vecchi E, Nicola L, Gismondo MR. Vitro evaluation of antibiotics' combinations for empirical therapy of suspected methicillin resistant Staphylococcus Aureus severe respiratory infections. BMC Infect Dis. 2007;7:111. Eliopoulos GM MR: Antimicrobial combinations. Antibiotics in laboratory medicine. Edited by: Lorian V. Baltimore, The Williams & Wilkins Co 1991:432–492. Odds FC. Synergy, antagonism, and what the chequerboard puts between them. J Antimicrob Chemother. 2003;52(1):1. Ceri H, Olson ME, Stremick C, Read RR, Morck D, Buret A. The Calgary biofilm device: new technology for rapid determination of antibiotic susceptibilities of bacterial biofilms. J Clin Microbiol. 1999;37(6):1771–6. Weiss EC, Spencer HJ, Daily SJ, Weiss BD, Smeltzer MS. Impact of sarA on antibiotic susceptibility of Staphylococcus Aureus in a catheter-associated in vitro model of biofilm formation. Antimicrob Agents Chemother. 2009;53(6):2475–82. Moormeier DE, Bose JL, Horswill AR, Bayles KW. Temporal and stochastic control of Staphylococcus Aureus biofilm development. MBio. 2014;5(5):e01341–14. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105–11. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protoc. 2012;7(3):562–78. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–5. Fruzangohar M, Ebrahimie E, Ogunniyi AD, Mahdi LK, Paton JC, Adelson DL, Comparative GO. A web application for comparative gene ontology and gene ontology-based gene selection in bacteria. PLoS One. 2013;8(3):e58759. Liu C, Bayer A, Cosgrove SE, Daum RS, Fridkin SK, Gorwitz RJ, Kaplan SL, Karchmer AW, Levine DP, Murray BE, et al. Clinical practice guidelines by the infectious diseases society of america for the treatment of methicillin-resistant Staphylococcus Aureus infections in adults and children: executive summary. Clin Infect Dis. 2011;52(3):285–92. Lefebvre M, Jacqueline C, Amador G, Le Mabecque V, Miegeville A, Potel G, Caillon J, Asseray N. Efficacy of daptomycin combined with rifampicin for the treatment of experimental meticillin-resistant Staphylococcus Aureus (MRSA) acute osteomyelitis. Int J Antimicrob Agents. 2010;36(6):542–4. Saleh-Mghir A, Lefort A, Petegnief Y, Dautrey S, Vallois JM, Le Guludec D, Carbon C, Fantin B. Activity and diffusion of LY333328 in experimental endocarditis due to vancomycin-resistant enterococcus faecalis. Antimicrob Agents Chemother. 1999;43(1):115–20. Seaton RA, Malizos KN, Viale P, Gargalianos-Kakolyris P, Santantonio T, Petrelli E, Pathan R, Heep M, Chaves RL. Daptomycin use in patients with osteomyelitis: a preliminary report from the EU-CORE(SM) database. J Antimicrob Chemother. 2013;68(7):1642–9. Steenbergen JN, Mohr JF, Thorne GM. Effects of daptomycin in combination with other antimicrobial agents: a review of in vitro and animal model studies. J Antimicrob Chemother. 2009;64(6):1130–8. Tuazon CU, Lin MY, Sheagren JN. Vitro activity of rifampin alone and in combination with nafcillin and vancomycin against pathogenic strains of Staphylococcus Aureus. Antimicrob Agents Chemother. 1978;13(5):759–61. Deresinski S. Vancomycin in combination with other antibiotics for the treatment of serious methicillin-resistant Staphylococcus Aureus infections. Clin Infect Dis. 2009;49(7):1072–9. Microbiology ASf. Instructions to authors. Antimicrob Agents Chemother. 2006;50:1–21. Allison KR, Brynildsen MP, Collins JJ. Heterogeneous bacterial persisters and engineering approaches to eliminate them. Curr Opin Microbiol. 2011;14(5):593–8. Lechner S, Lewis K, Bertram R. Staphylococcus Aureus persisters tolerant to bactericidal antibiotics. J Mol Microbiol Biotechnol. 2012;22(4):235–44. Johnson PJ, Levin BR. Pharmacodynamics, population dynamics, and the evolution of persistence in Staphylococcus Aureus. PLoS Genet. 2013;9(1):e1003123. Keren I, Kaldalu N, Spoering A, Wang Y, Lewis K. Persister cells and tolerance to antimicrobials. FEMS Microbiol Lett. 2004;230(1):13–8. Amato SM, Fazen CH, Henry TC, Mok WW, Orman MA, Sandvik EL, Volzing KG, Brynildsen MP. The role of metabolism in bacterial persistence. Front Microbiol. 2014;5:70. Kussell E, Kishony R, Balaban NQ, Leibler S. Bacterial persistence: a model of survival in changing environments. Genetics. 2005;169(4):1807–14. Surdova K, Gamba P, Claessen D, Siersma T, Jonker MJ, Errington J, Hamoen LW. The conserved DNA-binding protein WhiA is involved in cell division in Bacillus Subtilis. J Bacteriol. 2013;195(24):5450–60. Ibarra JA, Perez-Rueda E, Carroll RK, Shaw LN. Global analysis of transcriptional regulators in Staphylococcus Aureus. BMC Genomics. 2013;14:126. Cheung AL, Projan SJ. Cloning and sequencing of sarA of Staphylococcus Aureus, a gene required for the expression of agr. J Bacteriol. 1994;176(13):4168–72. Beenken KE, Blevins JS, Smeltzer MS. Mutation of sarA in Staphylococcus Aureus limits biofilm formation. Infect Immun. 2003;71(7):4206–11. Lei MG, Lee CY. RbsR activates capsule but represses the rbsUDK operon in Staphylococcus Aureus. J Bacteriol. 2015;197(23):3666–75. Jin S, Sonenshein AL. Transcriptional regulation of Bacillus Subtilis citrate synthase genes. J Bacteriol. 1994;176(15):4680–90. Kester JC, Fortune SM. Persisters and beyond: mechanisms of phenotypic drug resistance and drug tolerance in bacteria. Crit Rev Biochem Mol Biol. 2014;49(2):91–101. Raad I, Hanna H, Jiang Y, Dvorak T, Reitzel R, Chaiban G, Sherertz R, Hachem R. Comparative activities of daptomycin, linezolid, and tigecycline against catheter-related methicillin-resistant staphylococcus bacteremic isolates embedded in biofilm. Antimicrob Agents Chemother. 2007;51(5):1656–60. Wang W, Chen J, Chen G, Du X, Cui P, Wu J, Zhao J, Wu N, Zhang W, Li M, et al. Transposon mutagenesis identifies novel genes associated with Staphylococcus Aureus Persister formation. Front Microbiol. 2015;6:1437. Singh R, Ray P, Das A, Sharma M. Role of persisters and small-colony variants in antibiotic resistance of planktonic and biofilm-associated Staphylococcus Aureus: an in vitro study. J Med Microbiol. 2009;58(Pt 8):1067–73. Proctor RA, Kriegeskorte A, Kahl BC, Becker K, Loffler B, Peters G. Staphylococcus Aureus small Colony variants (SCVs): a road map for the metabolic pathways involved in persistent infections. Front Cell Infect Microbiol. 2014;4:99. Kahl BC. Small colony variants (SCVs) of Staphylococcus Aureus--a bacterial survival strategy. Infect Genet Evol. 2014;21:515–22. Correia FF, D'Onofrio A, Rejtar T, Li L, Karger BL, Makarova K, Koonin EV, Lewis K. Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia Coli. J Bacteriol. 2006;188(24):8360–7. Spoering AL, Vulic M, Lewis K. GlpD and PlsB participate in persister cell formation in Escherichia Coli. J Bacteriol. 2006;188(14):5136–44. Wood TK, Knabel SJ, Kwan BW. Bacterial persister cell formation and dormancy. Appl Environ Microbiol. 2013;79(23):7116–21. Ge X, Kitten T, Chen Z, Lee SP, Munro CL, Xu P. Identification of streptococcus sanguinis genes required for biofilm formation and examination of their role in endocarditis virulence. Infect Immun. 2008;76(6):2551–9. Kim JK, Jang HA, Won YJ, Kikuchi Y, Han SH, Kim CH, Nikoh N, Fukatsu T, Lee BL. Purine biosynthesis-deficient Burkholderia mutants are incapable of symbiotic accommodation in the stinkbug. ISME J. 2014;8(3):552–63.