Detection of bacterial respiratory infections

Lead Research Organisation: University of Central Lancashire
Department Name: Sch of Pharmacy and Biomedical Sci

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Publications

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MacCalman TE (2019) Glycoconjugate vaccines: some observations on carrier and production methods. in Biotechnology & genetic engineering reviews

 
Description GRANT AIMS:
The main aim of this 6 month grant was to determine the feasibility of expressing key proteins in an active form to potentially/ultimately develop a device that can detect and distinguish bacterial respiratory infections. Many of these proteins are membrane proteins and technically challenging to work with; it was by no means certain that they may be successfully expressed. The aims of this grant therefore were to determine:

(i) whether selected membrane receptor proteins from the respiratory pathogenic bacteria Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis and group A streptococci can be successfully expressed in and purified from E. coli. Specific objectives were (a) to clone the genes encoding these proteins into suitable protein expression plasmids; (b) conduct expression trials using a range of E. coli expression hosts, growth conditions, inducer concentrations and incubation conditions; and (c) time permitting, to conduct larger scale growth expression trials to determine the yield of proteins that can be obtained;
(ii) Following these objectives, further approaches and funding would then be pursued to determine which of two approaches (CD spectroscopy using purified proteins, or a reporter-based detection) would be most suitable to develop the diagnostic methodology for development of a kit that can be used in GP surgeries and clinics for identifying and distinguishing bacterial respiratory infections (for example distinguishing these from viral infections which do not respond to antibiotics) and therefore providing a means for the judicious prescribing of precious antibiotics in an era in which guardianship of current antibiotics is paramountly important.
(iii) If expression of at least one protein is demonstrated above, to pursue further funding to prepare an independent market report to determine demand and scope of the envisaged commercialised diagnostic test kit.

DISCOVERIES & ACHIEVEMENTS
Aim & Objective (i): three proteins were successfully expressed. These three proteins occur in the main two causative agents of respiratory infections (Streptococcus pneumoniae and Haemophilus influenzae, together responsible for up to 75% of pneumonia cases); therefore a sufficient range of proteins were shown to be successfully produced to take the research further. Objectives (a)-(c) were fully accomplished for these three proteins: all three proteins have been optimised with regard to expression, verified as His-tagged proteins and successfully purified (to >90-98% purity) from large scale cultures, thus successfully meeting all these objectives of the grant.

Aim & Objective (ii) (preparation for further funding and deciding which of two approaches to go forward with) was achieved through a successful bid for an Innovation Grant from the University of Central Lancashire which took the project beyond the 6 months of this grant. Two of the purified receptors were investigated using a technique known as benchtop circular dichroism spectroscopy to determine if such an approach would be suitable for detection device development. These studies confirmed that benchtop CD would indeed be suitable. CD showed that that the expressed proteins were structurally intact after the harsh detergent treatments used to extract them, and that their natural environmental ligands bind to them in a distinct way which can be used or mimicked in the development of the diagnostic device (published - Azam, A.A. et al (2018) Eur. Biophys. J. 47: 723-737 and patent filed on 15/12/17: GB1721022.0).

(iii) Objective (iii) is being pursued at the University of Nottingham where I started working in January 2019. Here I am working on how to utilise knowledge of the interactions between pheromone and the above membrane proteins to design a device which mimics these interactions and changes in the membrane receptor. This will be pursued in a forthcoming Innovate UK (or similar) grant application.

In summary, this grant has shown that suitable membrane receptors can indeed be successfully expressed and purified and used in CD experiments to produce a measurable change in spectral characteristics in response to their cognate pheromone signals. These spectral changes can be used to detect the pheromones produced by bacteria that cause respiratory infections (published in Azam et al. (2018)). Therefore the results of the research are promising for the future development of a medical diagnostic test for the rapid detection of bacterial infection during respiratory illness and ultimately for guardianship of antibiotics usage.

Although less related to the direct aims of the grant, another important outcome of the grant is the development of adapted Analytical Ultracentrifugation methods to investigate membrane protein-ligand interactions. Rather than being applied to the membrane receptors of direct relevance to this grant, it was applied to a related membrane receptor known as VanS and its weak interactions with antibiotic vancomycin. The work has resulted in many publications (listed in other Sections of this report) revealing new insights into the precious antibiotic itself and its interactions with the VanS receptor which activates vancomycin resistance amongst hospital-acquired enterococci and Staphylococcus aureus.
Exploitation Route Using Innovation funding from the University of Central Lancashire, the research was expanded for ultimate development of a diagnostic test for distinguishing bacterial from viral respiratory infections and for identifying which bacterial species may be responsible for any given bacterial respiratory infection (as described above). A patent on the methodology was filed by the University of Central Lancashire on 15/12/17: GB1721022.0. Several approaches are now being trialled for developing a device involving these purified bacterial proteins and/or knowledge gained from their interactions with key ligands from bacterial pathogens and funding is currently being sought to pursue those avenues .
Sectors Agriculture, Food and Drink,Electronics,Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description This 6 month grant resulted in the following outputs: (1) A research paper reporting the successful overexpression and purification and scaleup production of 2 intact membrane sensor kinases involved in sensing key ligand signals in the major bacterial species that cause bacterial respiratory infections (Azam et al., 2018). (2) The work resulted in the successful production of 2 technically-challenging intact membrane sensors which were also shown to be active, retain structural integrity and retain their ability to bind with their cognate ligand/signals resulting in promisingly large conformational changes detectable by benchtop CD spectroscopy. (3) The research overcame the problem of not knowing whether the key receptor proteins for respiratory pathogen detection could be successfully expressed and purified in active forms. This difficulty existed because many of the selected receptors are membrane proteins which are technically challenging to work with. With the demonstration here and subsequent funding that three of the most important membrane proteins can indeed be expressed, that two of these proteins are purified in an active form, and that CD spectroscopy experiments reveal that ligand binding can be clearly discerned in the CD spectral data, it has been established that the approach is suitable for further development of a medical device that provides a rapid means for detecting the presence of bacterial respiratory pathogens. (4) A patent GB1721022.0 (filed 15/12/17) for a means of developing a device which senses bacterial sources of respiratory infections, distinguishing them from viral agents of respiratory disease, and enabling distinction between viral and bacterial causative agents and thereby permitting judicious use of antibiotic therapies which in turn will reduce unnecessary build up of antimicrobial resistance. (5) A review addressing respiratory infection agents (MacCalman et al., 2020). (6) Further follow-up funding (University Innovation Funding). (7) Together with other previous BBSRC funding (but also with an important role played by the current grant), we developed/adapted Analytical Ultracentrifugation techniques to investigate these and other related membrane sensor kinases and their ligand interactions, resulting in 4 further research papers (Phillips-Jones et al., 2017a,b & Hughes et al. 2017 a,b), three of which were published in Scientific Reports and Biochim Biophys Acta Biomembranes, and 2 reviews (Hussain et al., 2016; Phillips-Jones & Harding 2018)/ These papers contributed knowledge of last line antibiotic vancomycin (ligand) and its weak interactions with membrane sensor VanS (and significant conformational changes in VanS identified upon vancomycin interactions).
First Year Of Impact 2016
Sector Electronics,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic

 
Description BBSRC Pathfinder
Amount £19,000 (GBP)
Funding ID BB/M013081/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2014 
End 04/2015
 
Description Diamond Light Source B23 Beamtime
Amount £2,400 (GBP)
Funding ID Proposal 13753 (successful application; beamtime granted by panel in 2015 - now awaiting beamtime to be organised by Dr Rohanah Hussain 
Organisation Diamond Light Source 
Sector Private
Country United Kingdom
Start  
 
Description Innovation Fund
Amount £28,000 (GBP)
Organisation University of Central Lancashire 
Sector Academic/University
Country United Kingdom
Start 03/2016 
End 03/2017
 
Description University of Central Lancashire Internship Scheme
Amount £2,000 (GBP)
Organisation University of Central Lancashire 
Sector Academic/University
Country United Kingdom
Start 06/2017 
End 09/2017
 
Title Analytical Ultracentrifugation applied to Membrane Proteins 
Description Application of analytical ultracentrifugation methods (sedimentation velocity and sedimentation equilibrium) to study intact membrane histidine kinases including their ligand interactions and oligomerisation state and molecular mass. 
Type Of Material Biological samples 
Year Produced 2017 
Provided To Others? Yes  
Impact Revisiting the use of AUC methods to investigate membrane protein interactions was initiated within this current grant. The resulting AUC experiments resulted in several publications (listed below) of the interactions between an antibiotic (vancomycin) and VanS which is a membrane sensor kinase involved in activating vancomycin resistance in important pathogens such as Enterococcus faecalis and Staphylococcus aureus. Whilst not directly related to the specific membrane sensors associated with this grant (which were successfully studied using benchtop CD), this spinoff use of Analytical Ultracentrifugation (an already established method for membrane proteins, but adapted and refined during this grant) led to important discoveries on the properties of the antibiotic itself, on the weak binding by vancomycin to VanS accompanied by significant conformational changes in the VanS receptor, and revealed the discovery that orally-administered vancomycin binds to GI tract mucins: Publications: Dinu, V., Lu, Y., Weston, N., Lithgo, R., Coupe, H., Channell, G., Torcello Gómez, A., Sabater, C., Mackie, A., Parmenter, C., Fisk, I., Phillips-Jones, M.K. & Harding, S.E. (2020). The antibiotic vancomycin induces complexation and aggregation of gastrointestinal and submaxillary mucins. Scientific Reports 10: 960. Phillips-Jones, M.K. & Harding, S.E. (2018) Antimicrobial Resistance (AMR) Nanomachines - mechanisms for fluoroquinolone and glycopeptide recognition, efflux and deactivation. Biophys. Revs. 10: 347-362. Phillips-Jones, M.K., Lithgo, R., Dinu, V., Gillis, R.B., Harding, J.E., Adams, G.G. & Harding, S.E. (2017) Full hydrodynamic reversibility of the weak dimerization of vancomycin and elucidation of its interaction with VanS monomers at clinical concentration. Sci. Rep 7: 12697 Hughes, C.S., Longo, E., Phillips-Jones, M.K. & Hussain, R. (2017) Quality control and biophysical characterisation data of VanSA. Data in Brief 14: 41-47. Hughes, C.S., Longo, E., Phillips-Jones, M.K.* & Hussain, R.* (2017) Characterisation of the selective binding of antibiotics vancomycin and teicoplanin by the VanS receptor regulating type A vancomycin resistance in the enterococci. Biochim. Biophys. Acta 1861: 1951-1959. (IF 5.08) Phillips-Jones, M.K., Channell, G., Kelsall, C.J., Hughes, C.S., Ashcroft, A.E., Patching, S.G., Dinu, V., Gillis, R.B., Adams, G.A. & Harding, S.E. (2017) Hydrodynamics of the VanA-type VanS histidine kinase: an extended solution conformation and first evidence for interactions with vancomycin. Sci. Rep. 7: 46180. 
 
Title Use of benchtop circular dichroism spectroscopy to investigate ligand binding and structural integrity 
Description Use of benchtop circular dichroism spectroscopy to investigate ligand binding and structural integrity 
Type Of Material Biological samples 
Year Produced 2018 
Provided To Others? Yes  
Impact This enables analysis of ligand binding to intact membrane receptors in a benchtop CD instrument, rather than having to use a synchrotron source for CD measurements (due to improved yields of intact membrane proteins in higher concentrations together with improvements in benchtop instruments that can now analyse smaller volumes). This outcome is published in Azam et al (2018) Eur. Biophys. J. 47: 723-737 (an outcome of the grant) 
URL https://link.springer.com/article/10.1007%2Fs00249-018-1325-z
 
Description Collaboration with National Centre for Macromolecular Hydrodynamics 
Organisation University of Nottingham
Department School of Biosciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of purified intact membrane sensor kinases
Collaborator Contribution Provision of analytical ultracentrifugation facilities and technical support for analysis of intact purified membrane proteins relating to this grant.
Impact (1) Hussain, R., Harding, S.E., Hughes, C.S., Ma, P., Patching, S.G., Edara, S., Siligardi, G., Henderson, P.J.F. & Phillips-Jones, M.K. (2016) Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions. Biochem. Soc. Trans. 44: 810-823; (2) Azam, A.A., Kinder, J.M., Rostron, K.A., Khan, G.N., Alase, A., Ma, P., Liu, Y., Ault, J.R., Ashcroft, A.E., Henderson, P.J.F., Chowdhry, B., Alexander, B.D., Harding, S.E. & Phillips-Jones, M.K. Production of membrane proteins for characterisation of their sensory and antimicrobial resistance functions. Eur. Biophys. J. 47: 723-737.
Start Year 2014
 
Description Collaboration with University of Leeds (CD spectroscopy) 
Organisation University of Leeds
Department Faculty of Biological Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Submission of joint publication: Aalishaa A. Azam, Jean M. Kinder, G. Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R. Ault, Peter J.F. Henderson, Babur Chowdhry, Bruce D. Alexander, Stephen E. Harding and Mary K. Phillips-Jones Production of membrane proteins for characterisation of their sensory and antimicrobial resistance functions. Eur. Biophys. J. 47: 723-737.(Nasir Khan and Sheena Radford FRS collaboration)
Collaborator Contribution Provision of CD spectroscopy facilities (funded by Wellcome Trust) and technical support.
Impact Aalishaa A. Azam, Jean M. Kinder, G. Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R. Ault, Peter J.F. Henderson, Babur Chowdhry, Bruce D. Alexander, Stephen E. Harding and Mary K. Phillips-Jones. Production of membrane proteins for characterisation of their sensory and antimicrobial resistance functions.Eur. Biophys. J. 47: 723-737.
Start Year 2017
 
Description Partnership with University of Greenwich 
Organisation University of Greenwich
Department Department of Pharmaceutical, Chemical & Environmental Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of purified protein receptors relating to this grant BB/M013081/1
Collaborator Contribution Circular dichroism facilities
Impact Submission of joint publication: Aalishaa A. Azam, Jean M. Kinder, G. Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R. Ault, Peter J.F. Henderson, Babur Chowdhry, Bruce D. Alexander, Stephen E. Harding and Mary K. Phillips-Jones Production of membrane proteins for characterisation of their sensory and antimicrobial resistance functions. Eur. Biophys. J. 47: 723-737.
Start Year 2017
 
Description University of Leeds (Fermenter facility and Membrane Protein Expression) 
Organisation University of Leeds
Department Faculty of Biological Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Submission of joint publication: Aalishaa A. Azam, Jean M. Kinder, G. Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R. Ault, Peter J.F. Henderson, Babur Chowdhry, Bruce D. Alexander, Stephen E. Harding and Mary K. Phillips-Jones Production of membrane proteins for characterisation of their sensory and antimicrobial resistance functions. Eur. Biophys. J. 47: 723-737.
Collaborator Contribution The Fermenter facilities (including the technical support required to run the facility and provided by Mr David Sharples in the laboratory of Prof Peter Henderson) provided us at regular intervals with 30 litre cultures of recombinant E. coli cells harbouring plasmid-borne membrane protein genes. These cell pellets were received from the facility and used in the production of purified membrane proteins for CD and other studies relating to the grant.
Impact Aalishaa A. Azam, Jean M. Kinder, G. Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R. Ault, Peter J.F. Henderson, Babur Chowdhry, Bruce D. Alexander, Stephen E. Harding and Mary K. Phillips-Jones. Production of membrane proteins for characterisation of their sensory and antimicrobial resistance functions. Eur. Biophys. J. 47: 723-737.
Start Year 2015
 
Description University of Leeds (Mass spectrometry) 
Organisation University of Leeds
Department Faculty of Biological Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Financial contribution for mass spectrometry services (James Ault and Alison Ashcroft) resulting in a joint publication: Aalishaa A. Azam, Jean M. Kinder, G. Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R. Ault, Peter J.F. Henderson, Babur Chowdhry, Bruce D. Alexander, Stephen E. Harding and Mary K. Phillips-Jones Production of membrane proteins for characterisation of their sensory and antimicrobial resistance functions. Eur. Biophys. J. 47: 723-737.
Collaborator Contribution Provision of mass spectrometry data and joint publication: Aalishaa A. Azam, Jean M. Kinder, G. Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R. Ault, Peter J.F. Henderson, Babur Chowdhry, Bruce D. Alexander, Stephen E. Harding and Mary K. Phillips-Jones Production of membrane proteins for characterisation of their sensory and antimicrobial resistance functions. Eur. Biophys. J. 47: 723-737.
Impact Aalishaa A. Azam, Jean M. Kinder, G. Nasir Khan, Ade Alase, Pikyee Ma, Yang Liu, James R. Ault, Peter J.F. Henderson, Babur Chowdhry, Bruce D. Alexander, Stephen E. Harding and Mary K. Phillips-Jones Production of membrane proteins for characterisation of their sensory and antimicrobial resistance functions.Eur. Biophys. J. 47: 723-737.
Start Year 2015
 
Description University of Manchester (fermenter facility) 
Organisation University of Manchester
Department Manchester Interdisciplinary Biocentre
Country United Kingdom 
Sector Academic/University 
PI Contribution Financial transaction for the cultivation in 20 litre volumes of recombinant E. coli harbouring plasmids carrying membrane protein genes encoding ComD, BlpH and QseC
Collaborator Contribution Our partners at Manchester provided us with 20 litre culture pellets of recombinant E.coli expressing qseC, blpH and comD genes.
Impact None yet. The cell pellets supplied by Manchester have not yielded the overexpressed proteins, so we have returned to successfully producing the overexpressed proteins using our smaller scale cultures.
Start Year 2015
 
Title Detection of bacterial infection 
Description Use of knowledge gained from the grant funding to detect bacterial infections. The patent was funded by the University of Central Lancashire who subsequently withdrew the patent on 14/12/18. 
IP Reference GB1721022.0 
Protection Patent application published
Year Protection Granted 2017
Licensed No
Impact None aware of
 
Title Diagnostic test for detecting bacterial infections 
Description Diagnostic test for detecting bacterial infections. With funding from a follow-up Innovation Grant from the University of Central Lancashire (2015-16) together with this current grant, it was established that there is a feasibility for developing a sensor based on the interactions between the membrane sensor kinases from respiratory pathogens and the pheromones that we desire to detect. The work has been on hold since a move to University of Nottingham but there are plans to continue development via an Innovate UK grant. 
Type Diagnostic Tool - Non-Imaging
Current Stage Of Development Refinement. Non-clinical
Year Development Stage Completed 2017
Development Status On hold
Impact Revisiting the use of AUC methods to investigate the membrane protein-ligand interactions under study in this grant resulted in wider studies to apply this method to other important medical applications, resulted in several publications (listed below) of the interactions between an antibiotic (vancomycin) and VanS which is a membrane sensor kinase involved in activating vancomycin resistance in important pathogens such as Enterococcus faecalis and Staphylococcus aureus. Whilst not directly related to the specific membrane sensors associated with this grant (which were successfully studied using benchtop CD), this spinoff use of Analytical Ultracentrifugation (an already established method for membrane proteins, but adapted and refined during this grant) led to important discoveries on the properties of the antibiotic itself, on the weak binding by vancomycin to VanS accompanied by significant conformational changes in the VanS receptor, and revealed the discovery that orally-administered vancomycin binds to GI tract mucins: Publications: Dinu, V., Lu, Y., Weston, N., Lithgo, R., Coupe, H., Channell, G., Torcello Gómez, A., Sabater, C., Mackie, A., Parmenter, C., Fisk, I., Phillips-Jones, M.K. & Harding, S.E. (2020). The antibiotic vancomycin induces complexation and aggregation of gastrointestinal and submaxillary mucins. Scientific Reports 10: 960. Phillips-Jones, M.K. & Harding, S.E. (2018) Antimicrobial Resistance (AMR) Nanomachines - mechanisms for fluoroquinolone and glycopeptide recognition, efflux and deactivation. Biophys. Revs. 10: 347-362. Phillips-Jones, M.K., Lithgo, R., Dinu, V., Gillis, R.B., Harding, J.E., Adams, G.G. & Harding, S.E. (2017) Full hydrodynamic reversibility of the weak dimerization of vancomycin and elucidation of its interaction with VanS monomers at clinical concentration. Sci. Rep 7: 12697 Hughes, C.S., Longo, E., Phillips-Jones, M.K. & Hussain, R. (2017) Quality control and biophysical characterisation data of VanSA. Data in Brief 14: 41-47. Hughes, C.S., Longo, E., Phillips-Jones, M.K.* & Hussain, R.* (2017) Characterisation of the selective binding of antibiotics vancomycin and teicoplanin by the VanS receptor regulating type A vancomycin resistance in the enterococci. Biochim. Biophys. Acta 1861: 1951-1959. (IF 5.08) Phillips-Jones, M.K., Channell, G., Kelsall, C.J., Hughes, C.S., Ashcroft, A.E., Patching, S.G., Dinu, V., Gillis, R.B., Adams, G.A. & Harding, S.E. (2017) Hydrodynamics of the VanA-type VanS histidine kinase: an extended solution conformation and first evidence for interactions with vancomycin. Sci. Rep. 7: 46180. 
 
Description Kaleidoscope Event - Best of Innovation at the University of Central Lancashire 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Policymakers/politicians
Results and Impact The Kaleidoscope Event showcases the 'Best of UCLan' innovations and was held at the University of Central Lancashire on 17th November 2016. I presented a demonstration of techniques associated with membrane proteins and their application to the study of antimicrobial resistances. The audience comprised local politicians and decision makers, local business and industry as well as representatives from Schools and the NHS in the northwest region.
Year(s) Of Engagement Activity 2016
 
Description University News Bulletin 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Undergraduate students
Results and Impact To disseminate information on our latest research findings regarding antimicrobial resistances (AMR) in a second article in 2017 in Scientific Reports, to highlight the need for better diagnostics and to contribute to Antibiotic Guardian committments to spread the AMR message to the public, a news feature was produced in the UCLan News following an arrangement through The University's publicity office. The article (published on 22nd May 2017) was entitled: 'New research findings offer new hope in the fight to rescue antibiotic of last resort.
Year(s) Of Engagement Activity 2017
URL https://www.uclan.ac.uk/news/research-hope-antibiotic-last-resort.php
 
Description University News Bulletin 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Undergraduate students
Results and Impact To disseminate information on our latest research findings regarding antimicrobial resistances (AMR) in Scientific Reports, to highlight the need for better diagnostics and to contribute to Antibiotic Guardian committments to spread the AMR message to the public, an article was published following an interview arranged through The University's publicity office. The article (published on 11th April 2017) was entitled: 'Breakthrough research could rescue antibiotic of last resort'.
Year(s) Of Engagement Activity 2017
URL http://www.uclan.ac.uk/news/antibiotic-research.php