Three research tracks / consortium introduction

The research activities in PERFECTION consists of four project all building on the same principle of developing organoids and various types of biofilms to study host/microbe interactions.

Persistent lung infections

Professor Helle Krogh Johansen is the PI of the PERFECTION project. She has more than two decades of experience in studying lung infections in cystic fibrosis patients. In this project infection mechanisms will be studied by infecting lung-organoids or tissue cultures with Pseudomonas aeruginosa, a bacterium that causes problems for CF-patients. Using organoids as an infection model to envision what goes on in the patient lungs will shed light on what happens and how bacteria behave when they establish themselves in chronic patient lungs. Biomarkers identified in these experiments from bacteria as well as host cells, in early stages of infection can be used to predict when an infection will become chronic. This insight can in turn be translated into optimized treatment strategies.

Helle Krogh Johansen Professor, chief physician, DMSc

Contact: hkj@biosustain.dtu.dk

Research activities: Persistent lung infections

In order to ensure better treatment for people suffering from persistent bacterial infections, an extensive biobank has been established containing tissue and bacterial isolates from CF and COPD patients. Research on these samples has already generated a host of data and insights into specific geno- and phenotype adaptations of Pseudomonas aeruginosa to the airways. Combining genomic and phenotypical analysis and profiling with the organoid models should provide unique knowledge about how and why bacterial infections persist, and how we might deal with them in the future.

Apical-out organoids will be used to investigate how colonization potential and trajectories change over time by image analysis. Using P aeruginosa isolates will reveal if colonization is affected by adaptive geno- and phenotype changes. With dual-RNA sequencing it will be possible to look into how transcriptional profiles in the organoid epithelium and colonizing P aeruginosa changes over time and gene expression analysis will reveal the earliest steps of colonization, something never achieved before.
Comparison between different bacterial clone types will further reveal different colonization strategies and will enable identification of molecular biomarkers and targets that might explain the development from early bacterial colonization to persistence.

By co-culturing organoids with bacteria that are known to infect both CF and COPD airways it will be possible to look into competition between strains. Co-cultures in advanced organoid set-ups, in which antibiotic dosing mimics that of regimes seen in patients along with added macrophages and neutrophils will shed light on effects from antibiotics and immune response in the host-pathogen interactions.

Research group

Publication list

Selected publications 2018-2020

1) Bartell JA, Cameron DR, Mojsoska B, Haagensen JAJ, Pressler T, Sommer LM, Lewis K, Molin S, Johansen HK. Bacterial persisters in long-term infection: emergence and fitness in a complex host environment. PLoS Pathog. 2020 Dec 14;16(12):e1009112. doi: 10.1371/journal.ppat.1009112. eCollection 2020 Dec. PMID: 33315938

2) Bartell JA, Sommer LM, Marvig RL, Skov M, Pressler T, Molin S, Johansen HK. Omics-based tracking of Pseudomonas aeruginosa persistence in ‘eradicated’ CF patients. Eur Respir J. 2020 Oct 22:2000512. doi: 10.1183/13993003.00512-2020. Online ahead of print. PMID: 33093121

3) Gabrielaite M, Johansen HK, Molin S, Nielsen FC, Marvig RL. Gene loss and acquisition in lineages of P. aeruginosa evolving in cystic fibrosis patient airways. mBio 2020 Oct 27;11(5):e02359-20. doi: 10.1128/mBio.02359-20. (IF 6.50)

4) Rossi E, La Rosa R, Bartell JA, Marvig RL, Haagensen JAJ, Sommer LM, Molin S, Johansen HK. Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis. Nat Rev Microbiol. 2020 Nov 19. doi: 10.1038/s41579-020-00477-5. Online ahead of print. PMID: 33214718

5) Halfon Y, Jimenez-Fernandez A, La Rosa R, Espinosa R, Johansen HK, Matzov D, Eyal Z, Bashan A, Zimmerman E, Belousoff M, Molin S, Yonath A. Structure of Pseudomonas aeruginosa ribosomes from an aminoglycoside resistant clinical isolate. Proc Natl Acad Sci U S A. 2019 Oct 14. pii: 201909831. doi: 10.1073/pnas.1909831116.

6) Andersen SB, Ghoul M, Marvig RL, Lee ZB, Molin S, Johansen HK, Griffin AS. Privatisation rescues essential function following loss of cooperation. Elife. 2018 Dec 18;7. pii: e38594. doi: 10.7554/eLife.38594. PMID: 30558711

7) Bartell JA, Sommer LM, Haagensen JAJ, Loch A, Espinosa R, Molin S, Johansen HK. Evolutionary highways to persistent bacterial infection. Nat Commun. 2019 Feb 7;10(1):629. doi: 10.1038/s41467-019-08504-7. PMID: 30733448

8) Frimodt-Møller J, Rossi E, Haagensen JAJ, Falcone M, Molin S, Johansen HK. Mutations causing low level antibiotic resistance ensure bacterial survival in antibiotic-treated hosts. Sci Rep. 2018 Aug 21;8(1):12512. doi: 10.1038/s41598-018-30972-y. PMID: 30131514

9) Rossi E, Falcone M, Molin S, Johansen HK. High-resolution in situ transcriptomics of Pseudomonas aeruginosa unveils genotype independent patho-phenotypes in cystic fibrosis lungs. Nat Commun. 2018 Aug 27;9(1):3459. doi: 10.1038/s41467-018-05944-5. PMID: 30150613

10) La Rosa R, Johansen HK, Molin S. Convergent metabolic specialization through distinct evolutionary paths in Pseudomonas aeruginosa. MBio. 2018 Apr 10;9(2). pii: e00269-18. doi: 10.1128/mBio.00269-18. PMID: 29636437

Persistent gastric infections

Professor Manuel Amieva, a pediatric infectious disease specialist at Stanford University in California, will investigate how Helicobacter bacteria infect epithelial surfaces from the stomach, and how this leads to disease. A method for creating organoids that have the epithelial facing out will form the basis for easier infection with bacteria, and this method can be used as colonization and infection models for multiple pathogens. At the moments, this model is primarily used study how Helicobacter pylori, the stomach ulcer and cancer pathogen, colonizes the surface of the stomach and survives in that hostile environment.

Manuel Amieva, Professor, MD Ph.D.

Contact: amieva@stanford.edu

Research activities: Persistent gastric infections

Helicobacter pylori and stomach epithelium serves as a great platform to study bacteria, and one specific question makes H pylori especially interesting to understand because why does H. pylori become aggressive being otherwise non-harmful to its host, when harmful behavior will make its habitat hostile to the bacterium itself?

A breakthrough has produced organoids that have been turned inside out, meaning that the epithelial cell surface faces apical-out just like it would in the body. This makes for easier study of bacterial interaction with the organoid, although it shortens life span of the organoid. The model will be used to identify traits in H. pylori that allow it to adapt to surfaces in gastric organoids that resemble the antral gland epithelium.

The Perfection consortium will bring together the expertise in genomic and phenotypic profiling, on one part, together with expertise in manipulating organoids and doing advanced microscopy.

Bacterial colonization will be studied using high-resolution microscopy and transcriptomic profiling of the bacteria and the host, as well as making comparisons of transcriptional profiles between organoid colonizing bacteria and free-swimming bacteria cultured in mucus from differentiated gastric organoids.

In more detail, investigations will be made in bacterial virulence factors, establish isogenic mutants and fluorescent labeled bacteria and elucidate specific steps in the colonization process namely attachment, growth, competition between bacterial strains and antibiotic susceptibility within the bacterial population.

Research group

Publication list

1) Amieva, MR, Vogelmann R, Covacci A, Tompkins LS, Nelson WJ, Falkow, S. Disruption of the epithelial apical-junctional complex by Helicobacter pylori CagA. Science. 2003. May 30, 300:1430-34. PMID: 12775840

2) Tan S, Tompkins LS, Amieva MR. Helicobacter pylori usurps cell polarity to turn the cell surface into a replicative niche. PLoS Pathogens. 2009, May;5(5):e1000407. PMID: 19412339.

3) Sigal M, Rothenberg ME, Logan CY, Lee JY, Honaker RW, Cooper RL, Passarelli B, Camorlinga M, Bouley DM, Alvarez G, Nusse R, Torres J, Amieva MR. Helicobacter pylori Activates and Expands Lgr5(+) Stem Cells Through Direct Colonization of the Gastric Glands. Gastroenterology. 2015. Jun;148(7):1392-404.e21. PMID: 25725293

4) Huang JY, Sweeney EG, Sigal M, Zhang HC, Remington SJ, Cantrell MA, Kuo CJ, Guillemin K, Amieva MR. Chemodetection and Destruction of Host Urea Allows Helicobacter pylori to Locate the Epithelium. Cell Host & Microbe. 2015 Aug 12;18(2):147-56. PMID: 26269952.

5) Co JY, Margalef-Catala M, Li X, Mah AT, Kuo CJ, Monack DM, Amieva MR. Controlling epithelial polarity: a novel human enteroid model for host-pathogen interactions. Cell Reports 26, 2509–2520, February 26, 2019. pp. 2509-2520. PMID: 30811997.

6) Fung C, Tan S, Nakajima M, Skoog EC, Camarillo-Guerrero LF, Klein JA, Lawley TD, Solnick JV, Fukami T, and Amieva MR. High resolution mapping reveals that microniches in the gastric glands control Helicobacter pylori colonization of the stomach. PLoS Biology. 2019 May 2;17(5):e3000231.PMID: 31048876.

Chronic wounds

Thomas Bjarnsholt, a professor at the University of Copenhagen, has great experience concerning infection mechanisms involving biofilm formation. In this project chronic non-healing wounds will be studied. Chronic wounds are a major burden to the health care system. The project will focus on microbial community structure, bacterial diversity and much faceted physiology. A newly developed model, in which alginate beads mimics’ bacterial aggregates, together with meta-genomic and transcriptomic analysis of patient skin samples, promises to reveal new important insights in wound infection mechanisms.

Thomas Bjarnsholt, Professor, Ph.D., DMSc.

Contact: tbjarnsholt@sund.ku.dk

Research activities: Chronic wounds

Part of the Perfection project is to understand chronic wounds in much greater depth than we do today. The ambition is to map the wound-microenvironment and essentially build up a three-dimensional understanding of where the bacteria grow, how they grow and what sort of interactions occur with the surrounding tissue.

With samples from the skin of healthy humans, acute trauma and chronic wounds Thomas' group will delve into the microbial community structure, diversity and physiology of chronic wound infections. Examination of host/microbe interactions will be done through meta-genomic and transcriptomic analysis, as well as advanced 3D microscopy.

A model based on alginate beads will be used to recreate the bacterial aggregates observed in patient samples of chronic wounds. In such a model, it is possible to alter and modulate the immediate environment (nutrients, O₂) to study bacterial growth- and gene expression profiles.

Advanced micro-sensors, MAR-FISH isotope probing and MALDI-TOF spectrometry will be used to investigate and describe how the bacterial species exploit and generate particular chemical microenvironments in chronic wounds.

Being part of the Perfection project brings the power of comparison to the research as results from the skin can be compared with those from the experiments in the airways and the stomach, which would reveal any commonality to how chronic infections establish and their dynamics across organs and tissues.

In time this work can be expanded to encompass development of prediction analysis to make it possible to prediction how any given chronic wound would develop.

Research group

Publication list

1) Bay L, Barnes C, Fritz BG, Thorsen J, Restrup M, Rasmussen L, Sørensen J, Hesselvig A , Odgaard A and Bjarnsholt T, Universal Dermal Microbiome in Human Skin, Accepted at mBio 2019

2) Raskov H, Kragh KN, Bjarnsholt T, Alamili M, Gögenur I., Bacterial biofilm formation inside colonic crypts may accelerate colorectal carcinogenesis. Clin Transl Med. 2018 Sep 17;7(1):30.

3) Fritz B, Stavnsbjerg C, Markvart M, Damgaard PB, Nielsen SH, Bjørndal L, Qvortrup K, Bjarnsholt T., Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition. Pathog Dis. 2019 Feb 1;77(1).

4) Jakobsen TH, Eickhardt SR, Gheorghe AG, Stenqvist C, Sønderholm M, Stavnsberg C, Jensen PØ, Odgaard A, Whiteley M, Moser C, Hvolris J, Hougen HP, Bjarnsholt T., Implants induce a new niche for microbiomes., APMIS. 2018 Aug;126(8):685-692.

5) Cornforth DM, Dees JL, Ibberson CB, Huse HK, Mathiesen IH, Kirketerp-Møller K, Wolcott RD, Rumbaugh KP, Bjarnsholt T, Whiteley M.; Pseudomonas aeruginosa transcriptome during human infection.; Proc Natl Acad Sci U S A. 2018 May 29;115(22):E5125-E5134.

6) Bay L, Kragh KN, Eickhardt SR, Poulsen SS, Gjerdrum LMR, Ghathian K, Calum H, Ågren MS, Bjarnsholt T.; Bacterial Aggregates Establish at the Edges of Acute Epidermal Wounds.; Adv Wound Care (New Rochelle). 2018 Apr 1;7(4):105-113

7) Sønderholm M, Kragh KN, Koren K, Jakobsen TH, Darch SE, Alhede M, Jensen PØ, Whiteley M, Kühl M, Bjarnsholt T.; Pseudomonas aeruginosa Aggregate Formation in an Alginate Bead Model System Exhibits In Vivo-Like Characteristics.; Appl Environ Microbiol. 2017 Apr 17;83(9)

8) Qvist T, Eickhardt S, Kragh KN, Andersen CB, Iversen M, Høiby N, Bjarnsholt T; Chronic pulmonary disease with Mycobacterium abscessus complex is a biofilm infection; Eur Respir J. 2015 Dec;46(6):1823-6

9) Høiby N, Bjarnsholt T, Moser C, Bassi GL, Coenye T, Donelli G, Hall-Stoodley L, Holá V, Imbert C, Kirketerp-Møller K, Lebeaux D, Oliver A, Ullmann AJ, Williams C; ESCMID Study Group for Biofilms and Consulting External Expert Werner Zimmerli.; ESCMID guideline for the diagnosis and treatment of biofilm infections 2014.; Clin Microbiol Infect. 2015 May;21 Suppl 1:S1-25

10)Bjarnsholt T, Alhede M, Alhede M, Eickhardt-Sørensen SR, Moser C, Kühl M, Jensen PO, Høiby N.; The in vivo biofilm; Trends Microbiol. 2013 Sep;21(9):466-74

Last updated: 31. January 2022

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