Growing a Cystic Fibrosis-Relevant Polymicrobial Biofilm to Probe Community Phenotypes

Published: April 19, 2024

doi:

¹Département de Biologie,Université de Sherbrooke

Summary

This protocol describes a cystic fibrosis (CF) lung-relevant four-species polymicrobial biofilm model that can be used to explore the impact of bacterial interspecies interactions.

Abstract

Most in vitro models lack the capacity to fully probe bacterial phenotypes emerging from the complex interactions observed in real-life environments. This is particularly true in the context of hard-to-treat, chronic, and polymicrobial biofilm-based infections detected in the airways of individuals living with cystic fibrosis (CF), a multiorgan genetic disease. While multiple microbiome studies have defined the microbial compositions detected in the airway of people with CF (pwCF), no in vitro models thus far have fully integrated critical CF-relevant lung features. Therefore, a significant knowledge gap exists in the capacity to investigate the mechanisms driving the pathogenesis of mixed species CF lung infections. Here, we describe a recently developed four-species microbial community model, including Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis, and Prevotella melaninogenica grown in CF-like conditions. Through the utilization of this system, clinically relevant phenotypes such as antimicrobial recalcitrance of several pathogens were observed and explored at the molecular level. The usefulness of this in vitro model resides in its standardized workflow that can facilitate the study of interspecies interactions in the context of chronic CF lung infections.

Introduction

Strategies aimed at eradicating disease-causing microbes such as the ones detected in the cystic fibrosis (CF) airway, a multiorgan genetic disease, often fail¹. That is, the presence of resilient biofilm-like microbial communities growing in the mucus-rich CF lung environment can cause chronic infections spanning multiple decades². Furthermore, although the utilization of front-line antimicrobials (Abx) and modulators has resulted in improved outcomes in people with CF (pwCF), the "one bug, one infection" clinical approach typically employed against canonical CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus has been ineffective in resolving hard-to-treat infections detected in the lungs of these individuals³^,⁴^,⁵^,⁶^,⁷.

Over the last two decades, multiple studies have changed our understanding of chronic CF lung disease⁸. That is, reports indicate that infections detected in the airways of pwCF are not solely caused by a single pathogen but are rather polymicrobial in nature⁸. Furthermore, although the pathogenesis of mixed species CF lung infections is still poorly understood, clinical evidence shows that pwCF that are co-infected with both S. aureus and P. aeruginosa in their airways have worsened lung function than individuals colonized by either of these two pathogens⁹.

Interspecies interactions among CF pathogens are hypothesized to be a reason why polymicrobial biofilm-based infections are not readily eradicated through the utilization of CF therapeutics, ultimately impacting patient outcomes³. Supporting this, in vitro studies have demonstrated that interactions between microbes such as P. aeruginosa, S. aureus, and others can impact clinically relevant phenotypes such as Abx responsiveness to front-line CF drugs, including vancomycin and tobramycin⁶^,¹⁰^,¹¹. Therefore, revisiting the current treatment strategies aimed at eradicating CF pathogens in the context of mixed-species infections remains to be achieved.

The gold standard in the management of microbial-based CF lung infections heavily relies on the utilization of antimicrobial susceptibility testing (AST) to guide clinical interventions¹². However, AST is typically done using bacterial monocultures grown in rich and well-mixed cultures, which is not reflective of the microbial growth conditions detected in the CF airway³^,¹³. Given the significant disconnect between patient outcomes and treatment success, clinical reports now advocate for the development of novel approaches integrating critical features of the CF lung¹²^,¹⁴.

Few studies have developed CF-relevant bacterial multispecies in vitro systems containing more than two pathogens¹⁵^,¹⁶. However, these models (1) do not entirely reflect the polymicrobial and biofilm-like nature of the CF lung and (2) do not use nutritional and environmental conditions approximating the ones detected in the CF airway¹⁵^,¹⁶. Through the mining of large CF-lung derived 16S rRNA gene data sets and computation, Jean-Pierre and colleagues recently developed an in vitro co-culture model integrating the above-mentioned features¹⁰. This system includes P. aeruginosa, S. aureus, Streptococcus spp. and Prevotella spp. grown in CF airway-like conditions and stable for up to 14 days. The authors also reported community-specific growth of Prevotella spp. and several changes in the Abx responsiveness of these CF pathogens through mechanisms that remain to be identified¹⁰. This tractable in vitro system also offered the possibility to delve into mechanistically focused questions related to Abx recalcitrance of a common variant of P. aeruginosa frequently detected in the airways of pwCF¹⁰. Therefore, the goal of this protocol is to provide the CF research community with a standardized experimental workflow to grow an in vitro biofilm that has the potential to be further expanded to tackle a number of CF-relevant questions.

Protocol

The details of all the reagents and equipment are listed in the Table of Materials. 1. Preparing artificial sputum medium NOTE: Throughout this protocol, artificial sputum medium (ASM) is defined as the CF-relevant medium modified from SCFM2, previously published by Turner and colleagues17. Below is a description of the steps to prepare this medium. See Table of Materials to make stock solution…

Representative Results

As represented in Figure 2, several phenotypes were reported including (1) a reduction in the number of P. aeruginosa and S. aureus viable cell counts when grown a mixed planktonic communities compared to monoculture, (2) an increase in polymicrobial growth of S. sanguinis cells and, (3) mixed community growth of P. melaninogenica as previously reported by Jean-Pierre and colleagues10. Furthermore, as dep…

Discussion

The usefulness of this clinically informed in vitro co-culture system resides in its capacity to detect polymicrobial-specific bacterial functions. That is, through the utilization of this model we have reported microbial phenotypes ranging from community-specific growth of Prevotella spp. (Figure 2) to changes in susceptibility to front-line CF Abx of P. aeruginosa, S. aureus and S. sanguinis (Figure 3). Moreover, ev…

Divulgations

The authors have nothing to disclose.

Acknowledgements

We would like to acknowledge Dr. George A. O'Toole and Dr. Thomas H. Hampton for their significant role in the design and development of the in vitro polymicrobial community model. We thank Dr. Sophie Robitaille for her helpful comments on the manuscript. This work was supported by a Cystic Fibrosis Foundation grant JEAN21F0 to F.J-P. Figure 1 of the manuscript was created using BioRender.

Materials

1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)	Fisher Scientific	NC0387928	Prepare a 250 mg/mL stock in chloroform directly in the bottle. Keep at -20°C. Final concentration 200 μg/mL in 2x ASM base.
3-morpholinopropane-1-sulfonic acid (MOPS)	Sigma	M1254	Final concentration 200 mM in 2X ASM base.
96-pin replicator	Fisher Scientific	05-450-9	Disposable replicators can also be used. Cat #NC1567338.
96-well sterile standard plate with lid	Fisher Scientific	62406-081
Agar	Fisher Scientific	DF0145-17-0
AnaeroPack 2.5 L Rectangular Jar	Fisher Scientific	23-246-385
CaCl₂*2H₂O	Fisher Scientific	C79-500	Prepare a 1 M stock in water and filter sterilize with a 0.22 μm filter. Final concentration 3.5 mM in 2x ASM base.
Defribrinated sheep's blood			To prepare growth plates for Streptococcus and Prevotella.
Deoxyribonucleic acid from herring sperm	Sigma	D7290	Final concentration 1.2 mg/mL in 2x ASM base.
FeSO₄*7H₂O	Fisher Scientific	AA1449830	Prepare a 1 mg/mL stock (3.6 mM) in water and filter sterilize with a 0.22 μm filter. Keep wrapped in aluminum foil. Final concentration 0.0072 mM in 2x ASM base.
GasPaks	Fisher Scientific	B260678
Glucose	Fisher Scientific	D16-3	Prepare as a 20% stock (1.1 M) in water and sterilize by autoclave. Final concentration 6 mM in 2x ASM base.
Hemin	Sigma	51280	Dissolve 100 mg of hemin in 2 mL of 1 M NaOH and then bring up volume to 200 mL with water. Store in an amber bottle or a regular bottle wrapped with aluminum foil at 4 °C.
K₂SO₄	Fisher Scientific	P304-500	Prepare a 0.25 M stock in water and filter sterilize with a 0.22 μm filter. Final concentration 0.54 mM in 2x ASM base.
Kanamycin			Prepare a 50 mg/mL stock solution in water. Filter sterilize with a 0.22 μm filter and store at 4 °C.
KCl	Fisher Scientific	P217-500	Final concentration 30.0 mM in 2x ASM base.
KNO₃	Fisher Scientific	P263-500	Prepare a 1 M stock in water and filter sterilize with a 0.22 μm filter. Final concentration 0.70 mM in 2x ASM base.
L-cysteine hydrochloride	Fisher Scientific	AAA1038922
L-Lactic acid	Sigma	L1750	Prepare a 1 M stock in water and filter sterilize with a 0.22 μm filter. pH adjust to 7.0. Final concentration 18.6 mM in 2x ASM base.
L-Tryptophan	Sigma	T0254	Prepare a 0.1 M stock in 0.2 M NaOH and filter sterilize with a 0.22 μm filter. Keep refrigerated at 4 °C wrapped in aluminum foil. Final concentration 0.132 mM in 2x ASM base.
Mannitol Salt Agar	Fisher Scientific	B11407	Prepare using manufacturer's recommendations.
Menadione	Sigma	M5625	Prepare a 10 mg/mL stock solution dissolved in 96-100% ethanol. Conserve at 4 °C wrapped in aluminium foil. Vortex before use.
MgCl₂*6H₂O	Fisher Scientific	AA12288A9	Prepare a 1 M stock in water and filter sterilize with a 0.22 μm filter. Final concentration 1.21 mM in 2x ASM base.
Mucin from porcine stomach – Type II	Sigma	M2378	Prepare a 10 mg/mL (2x) stock in water; mix thoroughly before autoclaving. Keep at 4 °C.
Na₂HPO₄	Fisher Scientific	S375-500	Prepare a 0.2 M stock in water and filter sterilize with a 0.22 μm filter. Final concentration 2.5 mM in 2x ASM base.
N-acetylglucosamine	Sigma	A8625	Prepare a 0.25 M stock in water and filter sterilize with a 0.22 μm filter. Keep stock refrigerated at 4 °C. Final concentration 0.6 mM in 2x ASM base.
NaCl	Fisher Scientific	S271-500	Final concentration 103.7 mM in 2x ASM base.
NaH₂PO₄*H2O	Fisher Scientific	S369-500	Prepare a 0.2 M stock in water and filter sterilize with a 0.22 μm filter. Final concentration 2.6 mM in 2x ASM base.
NaOH	Fisher Scientific	S318-500	Prepare a 5 M stock solution. Use to adjust pH of 2x ASM base stock.
NH₄Cl	Fisher Scientific	A661-500	Final concentration 4.6 mM in 2x ASM base.
Oxolinic acid			Prepare a 10 mg/mL stock solution 0.5 M NaOH. Filter sterilize with a 0.22 μm filter and store at 4 °C.
Polymixin B			Prepare a 10 mg/mL stock solution in water. Filter sterilize with a 0.22 μm filter and store at 4 °C.
Pseudomonas Isolation Agar	Fisher Scientific	DF0927-17-1	Prepare using manufacturer's recommendations.
Todd Hewitt Broth	Fisher Scientific	DF0492-17-6	Prepare using manufacturer's recommendations.
Tryptic Soy Broth	Fisher Scientific	DF0370-17-3	Prepare using manufacturer's recommendations.
Vancomycin			Prepare a 50 mg/mL stock solution in water. Filter sterilize with a 0.22 μm filter and store at 4 °C.
Yeast Extract	Fisher Scientific	B11929
Yeast Synthetic Dropout without Tryptophan	Sigma	Y1876	Final concentration 8.0 mg/mL in 2x ASM base.

References

Cogen, J. D., Nichols, D. P., Goss, C. H., Somayaji, R. Drugs, drugs, drugs: Current treatment paradigms in cystic fibrosis airway infections. J Pediatric Infect Dis Soc. 11 (2), S32-S39 (2022).
O’Sullivan, B. P., Freedman, S. D. Cystic fibrosis. Lancet. 373 (9678), 1891-1904 (2009).
Jean-Pierre, F., Vyas, A., Hampton, T. H., Henson, M. A., O’Toole, G. A. One versus many: Polymicrobial communities and the cystic fibrosis airway. mBio. 12 (2), e00006-e00021 (2021).
Martin, C., et al. Longitudinal microbial and molecular dynamics in the cystic fibrosis lung after elexacaftor-tezacaftor-ivacaftor therapy. Respir Res. 24 (1), 317 (2023).
Sosinski, L. M., et al. A restructuring of microbiome niche space is associated with elexacaftor-tezacaftor-ivacaftor therapy in the cystic fibrosis lung. J Cystic Fibros. 21 (6), 996 (2022).
Orazi, G., O’Toole, G. A. 34;It takes a village": Mechanisms underlying antimicrobial recalcitrance of polymicrobial biofilms. J Bacteriol. 202 (1), e00530-e00619 (2019).
Nichols, D. P., et al. Clinical effectiveness of elexacaftor/tezacaftor/ivacaftor in people with cystic fibrosis: A clinical trial. Am J Respir Crit Care Med. 205 (5), 529-539 (2022).
Filkins, L. M., O’Toole, G. A. Cystic fibrosis lung infections: Polymicrobial, complex, and hard to treat. PLoS Pathog. 11 (12), e1005258 (2015).
Limoli, D. H., et al. Staphylococcus aureus and Pseudomonas aeruginosa co-infection is associated with cystic fibrosis-related diabetes and poor clinical outcomes. Eur J Clin Microbiol Infect Dis. 35 (6), 947-953 (2016).
Jean-Pierre, F., et al. Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system. Elife. 12 (12), e81604 (2023).
Toole Orazi, G., O’Toole, G. A. Pseudomonas aeruginosa alters Staphylococcus aureus sensitivity to vancomycin in a biofilm model of cystic fibrosis infection. mBio. 8 (4), e00873-e00917 (2017).
Lipuma, J. J. The sense and nonsense of antimicrobial susceptibility testing in cystic fibrosis. J Pediatric Infect Dis Soc. 11 (2), S46-S52 (2022).
Coenye, T. Biofilm antimicrobial susceptibility testing: Where are we and where could we be going. Clin Microbiol Rev. 36 (4), e0002423 (2023).
Waters, V. J., et al. Reconciling antimicrobial susceptibility testing and clinical response in antimicrobial treatment of chronic cystic fibrosis lung infections. Clin Infect Dis. 69 (10), 1812-1816 (2019).
Vandeplassche, E., et al. Antibiotic susceptibility of cystic fibrosis lung microbiome members in a multispecies biofilm. Biofilm. 2, 100031 (2020).
Varga, J. J., et al. Antibiotics drive expansion of rare pathogens in a chronic infection microbiome model. mSphere. 7 (5), e0031822 (2022).
Turner, K. H., Wessel, A. K., Palmer, G. C., Murray, J. L., Whiteley, M. Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum. Proc Natl Acad Sci U S A. 112 (13), 4110-4115 (2015).
Clay, M. E., et al. Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an anr-regulated oxygen-binding hemerythrin. Proc Natl Acad Sci U S A. 117 (6), 3167-3173 (2020).
Hoffman, L. R., et al. Pseudomonas aeruginosa lasR mutants are associated with cystic fibrosis lung disease progression. J Cyst Fibros. 8 (1), 66-70 (2009).
Heirali, A., et al. Sputum microbiota in adults with CF associates with response to inhaled tobramycin. Thorax. 75 (12), 1058-1064 (2020).
Nelson, M. T., et al. Maintenance tobramycin primarily affects untargeted bacteria in the cf sputum microbiome. Thorax. 75 (9), 780-790 (2020).
Kesthely, C. A., Rogers, R. R., El Hafi, B., Jean-Pierre, F., O’Toole, G. A. Transcriptional profiling and genetic analysis of a cystic fibrosis airway-relevant model shows asymmetric responses to growth in a polymicrobial community. Microbiol Spectr. 11 (5), e0220123 (2023).
Jean-Pierre, F., Henson, M. A., O’Toole, G. A. Metabolic modeling to interrogate microbial disease: A tale for experimentalists. Front Mol Biosci. 8, 634479 (2021).
Hendricks, M. R., et al. Respiratory syncytial virus infection enhances Pseudomonas aeruginosa biofilm growth through dysregulation of nutritional immunity. Proc Natl Acad Sci U S A. 113 (6), 1642-1647 (2016).
Hogan, D. A., Vik, A., Kolter, R. A Pseudomonas aeruginosa quorum-sensing molecule influences Candida albicans morphology. Mol Microbiol. 54 (5), 1212-1223 (2004).
Wu, Y., et al. Co-assembling living material as an in vitro lung epithelial infection model. Matter. 7 (1), 216-236 (2024).