Coexistence with Pseudomonas aeruginosa alters Staphylococcus aureus transcriptome, antibiotic resistance and internalization into epithelial cells

Paul Briaud, Laura Camus, Sylvère Bastien, Anne Doléans-Jordheim, François Vandenesch, Karen Moreau

Posted on: 22 October 2019 , updated on: 24 October 2019

Preprint posted on 19 September 2019

Article now published in Scientific Reports at

Friends with benefits: Mutualism between Pseudomonas aeruginosa and Staphylococcus aureus in Cystic Fibrosis patients

Selected by Sharmada Swaminath

Categories: microbiology, pathology

Background: Cystic fibrosis (CF) is a life-threatening genetic disease caused by mutations in the cftr gene, which codes for cystic fibrosis transmembrane conductance regulator (CFTR) protein [1]. The disease is characterized by thick mucus, leading to progressive chronic lung disease [2]. The airway of CF patients is usually colonized by various microorganisms, predominantly Staphylococcus aureus and Pseudomonas aeruginosa [3]. S. aureus and P. aeruginosa infections have been identified to occur in the same lobe of CF lungs [4], indicating their interaction in vivo. Studies have shown that early clinical isolates of P. aeruginosa out-compete S. aureus by secreting anti-staphylococcal compounds [5]. In contrast, late clinical isolates of P. aeruginosa co-exist with S. aureus and are less aggressive [5]. The interaction of P. aeruginosa and S. aureus in a co-existing environment is not very well-studied. In this preprint, the authors have used a transcriptomic approach, to study gene expression changes in S. aureus in the presence of non-competitive P. aeruginosa.


Experimental strategy: S. aureus and P. aeruginosa were collected from co-infected patients and the interaction between the two pathogens was examined by a competitive assay on trypticase soy agar (TSA) plates. Transcriptomic analysis was performed for competitive and co-existing S. aureus in monocultures as well as in co-culture with competitive and co-existing P. aeruginosa. Gene expression was considered dysregulated when it was dysregulated for both the pairs of strains.


Key findings:

The S. aureus transcriptome is differentially dysregulated by competitive and co-existing P. aeruginosa

While in a competitive state, the S. aureus transcriptome showed an increase in dehydrogenase enzymes, indicating a switch from aerobic respiration to lactic acid fermentation, and some of the dysregulated dehydrogenases were associated with the oxidative stress response. In addition, an increase in t-RNAs and ribosomal RNA was also observed, probably because of low translation efficiency. Collectively, these dysregulations were in correlation with the competitive effect of P. aeruginosa on S. aureus.

However, under coexisting condition, the S. aureus transcriptome showed downregulation of genes in the glycolysis and pentose phosphate pathways, as well as the de novo nucleotide synthesis pathway. On the other hand, an upregulation in alternative nucleotide synthesis pathways was observed. The authors hypothesize that S. aureus produces energy and nucleotides from sources besides glucose, probably due to nutritional competition between S. aureus and P. aeruginosa. Additionally, an increased expression of efflux pumps such as tet38, norA and norC were observed, which are implicated in antibiotic resistance.


Direct interaction of P. aeruginosa induces over-expression of nor genes in S. aureus, increasing its antibiotic resistance and internalization into epithelial cells  

The change in gene expression of S. aureus in co-existence with P. aeruginosa could not be attributed to any specific signaling molecule secreted by P. aeruginosa. Therefore, this effect of P. aeruginosa on S. aureus occurred when present in proximity. The over-expression of nor genes could not be detected in the presence of Burkholderia cepacia and Stenotrophomonas maltophilia species, which also live in close association with P. aeruginosa in CF patients [3], showing that the effect was specific to the interaction with P. aeruginosa.

S. aureus, in the presence of P. aeruginosa, showed better survival to antibiotics such as tetracycline and ciprofloxacin. This could be attributed to the nor (norA, norC) and tet38 genes, which are associated with quinolone and tetracycline resistance, respectively. Tet38 has been known to be involved in pulmonary epithelial cell internalization [6]. The internalization of S. aureus into A549 cells in the presence of P. aeruginosa increased by 3-fold in comparison to S. aureus monoculture.


Interesting aspects of the study:  This study shows the benefit for S. aureus when present in the same niche as P. aeruginosa. Studies so far had only focused on how P. aeruginosa profited in the presence of S. aureus and not the other way around. Also, the knowledge of the ability of S. aureus to be internalized in the epithelial cells and resist antibiotics in the presence of P. aeruginosa can help in developing new treatments.


Future directions: Though the authors have demonstrated many changes in S. aureus in the presence of P. aeruginosa, one question that remains is how this influence is being brought about. Though authors have eliminated the possibility of a signaling molecule, the question of how the close-proximity of P. aeruginosa is influencing the change in S. aureus and what is the advantage that P. aeruginosa gains by these changes need to be addressed.



  1. Welsh, M. J., Smith A. E. Molecular mechanisms of CFTR chloride channel dysfunction in cystic fibrosis. Cell 73, 1251-4 (1993).


  1. Ehre, M. J. et al. Cystic Fibrosis: An inherited disease affecting mucin-producing organs. Int J Biochem Cell Biol 52, 136-45 (2014).


  1. Limoli, D. H., Hoffman, L. R. Help, hinder, hide and harm: what can we learn from the interactions between Pseudomonas aeruginosa and Staphylococcus aureus during respiratory infections? Thorax 74, 684-92 (2019).


  1. Hogan, D. A. et al. Analysis of lung microbiota in bronchoalveolar lavage, protected brush and sputum samples from subjects with mild-to-moderate cystic fibrosis lung disease. PLoS One 11, e0149998 (2016).


  1. Balden R. et al. Adaptation of Pseudomonas aeruginosa in cystic fibrosis airway influences virulence of Staphylococcus aureus in vitro and murine models of co-infection. PLos One 9, e89614 (2014).


  1. Truong-Bolduc, Q. C. et al. Role of the Tet38 efflux pump in Staphylococcus aureus internalization and survival in epithelial cells. Infect Immun 83, 4362–72 (2015).



I am very grateful to Mate Palfy for his helpful comments on this highlight.


Tags: antibiotic resistance, pseudomonas aeruginosa, staphylococcus aureus


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Author's response

Karen Moreau shared

Thank you for choosing to highlight our study and for this excellent summary. The article has just been accepted for publication in Scientific reports.

This project is quite innovative because, as you mentioned, only few scientists have been interested in bacterial interactions between Staphylococcus aureus and Pseudomonas aeruginosa when both bacteria coexist. The dogma that Pseudomonas inhibits and kills staphylococcus is highly implanted. However, we have been able to show that in more than 50% of  co-infections cases, bacteria coexist  in Cystic Fibbrosis patients.

In this first study we could show that S. aureus benefited greatly from this cooperation with Pseudomonas.

I hope that we will soon be able to present our results of the impact of this coexistence on Pseudomonas.

We also have ideas to define how pseudomonas manages to modify the S. aureus transcriptome by direct interaction. It is under study.

Best regards,

Karen Moreau

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