Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa

Abstract

In the context of infection, Pseudomonas aeruginosa and Staphylococcus aureus are frequently co-isolated, particularly in cystic fibrosis (CF) patients. Within lungs, the two pathogens exhibit a range of competitive and coexisting interactions. In the present study, we explored the impact of S. aureus on the physiology of P. aeruginosa in the context of coexistence. Transcriptomic analyses showed that S. aureus significantly and specifically affects the expression of numerous genes involved in P. aeruginosa carbon and amino acid metabolism. In particular, 65% of the strains presented considerable overexpression of the genes involved in the acetoin catabolic (aco) pathway. We demonstrated that acetoin is (i) produced by clinical S. aureus strains, (ii) detected in sputa from CF patients and (iii) involved in P. aeruginosa’s aco system induction. Furthermore, acetoin is catabolized by P. aeruginosa, a metabolic process that improves the survival of both pathogens by providing a new carbon source for P. aeruginosa and avoiding the toxic accumulation of acetoin on S. aureus. Due to its beneficial effects on both bacteria, acetoin catabolism could testify to the establishment of trophic cooperation between S. aureus and P. aeruginosa in the CF lung environment, thus promoting their persistence.

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Fig. 1: Alteration of the P. aeruginosa transcriptome induced by co-culture with S. aureus.
Fig. 2: Fold changes of P. aeruginosa acoR, PA4148, liuA and zwf induced by culture conditions.
Fig. 3: Acetoin and glucose concentrations in S. aureus and P. aeruginosa cultures during coexisting interaction.
Fig. 4: Production and catabolism of acetoin by competitive and coexisting strains of S. aureus and P. aeruginosa.
Fig. 5: P. aeruginosa growth and acetoin concentration in minimal medium supplemented with acetoin.
Fig. 6: S. aureus and P. aeruginosa survival and acetoin concentration during long-term co-culture.

References

  1. 1.

    Sibley CD, Rabin H, Surette MG. Cystic fibrosis: a polymicrobial infectious disease. Future Microbiol. 2006;1:53–61.

    CAS  Article  Google Scholar 

  2. 2.

    Guss AM, Roeselers G, Newton ILG, Young CR, Klepac-Ceraj V, Lory S, et al. Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME J. 2011;5:20–29.

    Article  Google Scholar 

  3. 3.

    Peters BM, Jabra-Rizk MA, O’May GA, Costerton JW, Shirtliff ME. Polymicrobial interactions: impact on pathogenesis and human disease. Clin Microbiol Rev. 2012;25:193–213.

    Article  Google Scholar 

  4. 4.

    Murray JL, Connell JL, Stacy A, Turner KH, Whiteley M. Mechanisms of synergy in polymicrobial infections. J Microbiol Seoul Korea. 2014;52:188–99.

    Google Scholar 

  5. 5.

    Abisado RG, Benomar S, Klaus JR, Dandekar AA, Chandler JR. Bacterial quorum sensing and microbial community interactions. mBio. 2018;9:e02331–17.

  6. 6.

    Tashiro Y, Yawata Y, Toyofuku M, Uchiyama H, Nomura N. Interspecies interaction between Pseudomonas aeruginosa and other microorganisms. Microbes Environ. 2013;28:13–24.

    Article  Google Scholar 

  7. 7.

    Hotterbeekx A, Kumar-Singh S, Goossens H, Malhotra-Kumar S. In vivo and in vitro interactions between Pseudomonas aeruginosa and Staphylococcus spp. Front Cell Infect Microbiol. 2017;7:106.

  8. 8.

    Serra R, Grande R, Butrico L, Rossi A, Settimio UF, Caroleo B, et al. Chronic wound infections: the role of Pseudomonas aeruginosa and Staphylococcus aureus. Expert Rev Anti Infect Ther. 2015;13:605–13.

    CAS  Article  Google Scholar 

  9. 9.

    O’Brien TJ, Welch M. Recapitulation of polymicrobial communities associated with cystic fibrosis airway infections: a perspective. Future Microbiol. 2019;14:1437–50.

    Article  Google Scholar 

  10. 10.

    Baldan R, Cigana C, Testa F, Bianconi I, De Simone M, Pellin D, et al. Adaptation of Pseudomonas aeruginosa in cystic Fibrosis airways influences virulence of Staphylococcus aureus in vitro and murine models of co-infection. PLoS ONE. 2014;9:e89614.

    Article  Google Scholar 

  11. 11.

    Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR, D’Argenio DA, et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci USA. 2006;103:8487–92.

    CAS  Article  Google Scholar 

  12. 12.

    Hoffman LR, Kulasekara HD, Emerson J, Houston LS, Burns JL, Ramsey BW, et al. Pseudomonas aeruginosa lasR mutants are associated with cystic fibrosis lung disease progression. J Cyst Fibros J Eur Cyst Fibros Soc. 2009;8:66–70.

    CAS  Article  Google Scholar 

  13. 13.

    Folkesson A, Jelsbak L, Yang L, Johansen HK, Ciofu O, Høiby N, et al. Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective. Nat Rev Microbiol. 2012;10:841–51.

    CAS  Article  Google Scholar 

  14. 14.

    Marvig RL, Sommer LM, Molin S, Johansen HK. Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis. Nat Genet. 2015;47:57–64.

    CAS  Article  Google Scholar 

  15. 15.

    Limoli DH, Whitfield GB, Kitao T, Ivey ML, Davis MR, Grahl N, et al. Pseudomonas aeruginosa alginate overproduction promotes coexistence with Staphylococcus aureus in a model of cystic fibrosis respiratory infection. mBio. 2017;8:e00186–17.

  16. 16.

    La Rosa R, Johansen HK, Molin S. Adapting to the airways: metabolic requirements of Pseudomonas aeruginosa during the infection of cystic fibrosis patients. Metabolites. 2019;9:234.

  17. 17.

    Michelsen CF, Christensen A-MJ, Bojer MS, Høiby N, Ingmer H, Jelsbak L. Staphylococcus aureus alters growth activity, autolysis, and antibiotic tolerance in a human host-adapted Pseudomonas aeruginosa lineage. J Bacteriol. 2014;196:3903–11.

    Article  Google Scholar 

  18. 18.

    Briaud P, Camus L, Bastien S, Doléans-Jordheim A, Vandenesch F, Moreau K. Coexistence with Pseudomonas aeruginosa alters Staphylococcus aureus transcriptome, antibiotic resistance and internalization into epithelial cells. Sci Rep. 2019;9:16564.

  19. 19.

    Briaud P, Bastien S, Camus L, Boyadijian M, Reix P, Mainguy C, et al. Impact of coexistence phenotype between Staphylococcus aureus and Pseudomonas aeruginosa isolates on clinical outcomes among cystic fibrosis patients. Front Cell Infect Microbiol. 2020;10:266.

  20. 20.

    Frydenlund Michelsen C, Hossein Khademi SM, Krogh Johansen H, Ingmer H, Dorrestein PC, Jelsbak L. Evolution of metabolic divergence in Pseudomonas aeruginosa during long-term infection facilitates a proto-cooperative interspecies interaction. ISME J. 2016;10:1323–36.

    CAS  Article  Google Scholar 

  21. 21.

    Carriel D, Simon Garcia P, Castelli F, Lamourette P, Fenaille F, Brochier-Armanet C, et al. A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA. Genome Biol Evol. 2018;10:3058–75.

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Rietsch A, Vallet-Gely I, Dove SL, Mekalanos JJ. ExsE, a secreted regulator of type III secretion genes in Pseudomonas aeruginosa. Proc Natl Acad Sci USA. 2005;102:8006–11.

    CAS  Article  Google Scholar 

  23. 23.

    Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinforma Oxf Engl. 2015;31:3691–3.

    CAS  Article  Google Scholar 

  24. 24.

    Nicholson WL. The Bacillus subtilis ydjL (bdhA) gene encodes acetoin reductase/2,3-butanediol dehydrogenase. Appl Environ Microbiol. 2008;74:6832–8.

    CAS  Article  Google Scholar 

  25. 25.

    Lessie TG, Phibbs PV. Alternative pathways of carbohydrate utilization in pseudomonads. Annu Rev Microbiol. 1984;38:359–88.

    CAS  Article  Google Scholar 

  26. 26.

    Chevalier S, Bouffartigues E, Bodilis J, Maillot O, Lesouhaitier O, Feuilloley MGJ, et al. Structure, function and regulation of Pseudomonas aeruginosa porins. FEMS Microbiol Rev. 2017;41:698–722.

    CAS  Article  Google Scholar 

  27. 27.

    Liu Q, Liu Y, Kang Z, Xiao D, Gao C, Xu P, et al. 2,3-Butanediol catabolism in Pseudomonas aeruginosa PAO1: 2,3-butanediol catabolism in Pseudomonas aeruginosa. Environ Microbiol. 2018;20:3927–40.

    Article  Google Scholar 

  28. 28.

    Xiao Z, Xu P. Acetoin metabolism in bacteria. Crit Rev Microbiol. 2007;33:127–40.

    CAS  Article  Google Scholar 

  29. 29.

    Gade N, Negi SS, Jindal A, Gaikwad U, Das P, Bhargava A. Dual lower respiratory tract infection by Burkholderia cepacia and Acinetobacter baumannii in a neonate: a case report. J Clin Diagn Res. 2016;10:DD01–DD03.

    PubMed  PubMed Central  Google Scholar 

  30. 30.

    Amoli RI, Nowroozi J, Sabokbar A, Rajabniya R. Isolation of Stenotrophomonas maltophilia from clinical samples: an investigation of patterns motility and production of melanin pigment. Asian Pac J Trop Biomed. 2017;7:826–30.

    Article  Google Scholar 

  31. 31.

    Dryahina K, Sovová K, Nemec A, Španěl P. Differentiation of pulmonary bacterial pathogens in cystic fibrosis by volatile metabolites emitted by their in vitro cultures: Pseudomonas aeruginosa, Staphylococcus aureus, Stenotrophomonas maltophilia and the Burkholderia cepacia complex. J Breath Res. 2016;10:037102.

    Article  Google Scholar 

  32. 32.

    Tsang LH, Cassat JE, Shaw LN, Beenken KE, Smeltzer MS. Factors contributing to the biofilm-deficient phenotype of Staphylococcus aureus sarA mutants. PLoS ONE. 2008;3:e3361.

    Article  Google Scholar 

  33. 33.

    Chaudhari SS, Thomas VC, Sadykov MR, Bose JL, Ahn DJ, Zimmerman MC, et al. The LysR-type transcriptional regulator, CidR, regulates stationary phase cell death in Staphylococcus aureus: metabolic control of cell death in S. aureus. Mol Microbiol. 2016;101:942–53.

    CAS  Article  Google Scholar 

  34. 34.

    Thomas VC, Sadykov MR, Chaudhari SS, Jones J, Endres JL, Widhelm TJ, et al. A central role for carbon-overflow pathways in the modulation of bacterial cell death. PLoS Pathog. 2014;10:e1004205.

    Article  Google Scholar 

  35. 35.

    Miller CL, Van Laar TA, Chen T, Karna SLR, Chen P, You T, et al. Global transcriptome responses including small RNAs during mixed-species interactions with methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa. MicrobiologyOpen. 2017;6:e427.

  36. 36.

    Mashburn LM, Jett AM, Akins DR, Whiteley M. Staphylococcus aureus serves as an iron source for Pseudomonas aeruginosa during in vivo coculture. J Bacteriol. 2005;187:554–66.

    CAS  Article  Google Scholar 

  37. 37.

    Visca P, Imperi F. An essential transcriptional regulator: the case of Pseudomonas aeruginosa Fur. Future Microbiol. 2018;13:853–6.

    CAS  Article  Google Scholar 

  38. 38.

    Cornelis P, Matthijs S, Van Oeffelen L. Iron uptake regulation in Pseudomonas aeruginosa. Biometals Int J Role Met Ions Biol Biochem Med. 2009;22:15–22.

    CAS  Article  Google Scholar 

  39. 39.

    Ochsner UA, Wilderman PJ, Vasil AI, Vasil ML. GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes. Mol Microbiol. 2002;45:1277–87.

    CAS  Article  Google Scholar 

  40. 40.

    Tognon M, Köhler T, Luscher A, van Delden C. Transcriptional profiling of Pseudomonas aeruginosa and Staphylococcus aureus during in vitro co-culture. BMC Genomics. 2019;20:30.

    Article  Google Scholar 

  41. 41.

    Španěl P, Sovová K, Dryahina K, Doušová T, Dřevínek P, Smith D. Do linear logistic model analyses of volatile biomarkers in exhaled breath of cystic fibrosis patients reliably indicate Pseudomonas aeruginosa infection? J Breath Res. 2016;10:036013.

    Article  Google Scholar 

  42. 42.

    Baishya J, Wakeman CA. Selective pressures during chronic infection drive microbial competition and cooperation. NPJ Biofilms Microbiomes. 2019;5:16.

    Article  Google Scholar 

  43. 43.

    Hoffman LR, Richardson AR, Houston LS, Kulasekara HD, Martens-Habbena W, Klausen M, et al. Nutrient availability as a mechanism for selection of antibiotic tolerant Pseudomonas aeruginosa within the CF airway. PLoS Pathog. 2010;6:e1000712.

    Article  Google Scholar 

  44. 44.

    Hoffman LR, Déziel E, D’Argenio DA, Lépine F, Emerson J, McNamara S, et al. Selection for Staphylococcus aureus small-colony variants due to growth in the presence of Pseudomonas aeruginosa. Proc Natl Acad Sci USA. 2006;103:19890–5.

    CAS  Article  Google Scholar 

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Acknowledgements

This work was supported by the Fondation pour la Recherche Médicale, grant number ECO20170637499 to LC; the Finovi foundation to KM; the associations “Vaincre la mucoviscidose” and “Gregory Lemarchal” to KM. We thank Kenneth W Bayles from the University of Nebraska Medical Center (Omaha) for providing S. aureus UAMS-1 WT and mutant strains.

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Correspondence to Karen Moreau.

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All the strains used in this study were collected as part of the periodic monitoring of patients at the Hospices Civils de Lyon (HCL). This study was submitted to the Ethics Committee of the HCL and registered under CNIL No. 17-216. All the patients were informed of the study; however, as the study was non-interventional, no written informed consent was required under local regulations.

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Camus, L., Briaud, P., Bastien, S. et al. Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa. ISME J (2020). https://doi.org/10.1038/s41396-020-00741-9

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