Combatting the threat of carbapenem resistance in Gram-negative bacterial pathogens

Lead Research Organisation: Cardiff University
Department Name: School of Medicine

Abstract

Hospital-acquired infections (HAIs) are growing in importance as the numbers of susceptible individuals (e.g. elderly, transplant or cancer chemotherapy patients) increase in aging populations. HAIs caused by antibiotic-resistant bacteria are more difficult to treat and consequently more dangerous. While MRSA (methicillin-resistant Staphylococcus aureus) is the most notorious cause of HAIs, so-called Gram-negative bacteria, such as Escherichia coli, are also responsible for many thousands of HAIs each year. The most important antibiotics in the fight against HAIs caused by these organisms are the beta-lactam drugs, of which penicillin is the best known. Since Gram-negative bacteria have become resistant to most other antibiotics, drugs called carbapenems (the most powerful beta-lactams) are now the most important antibiotics used to treat these infections. Fortunately, until recently carbapenem resistance in Gram-negative bacteria has been relatively rare, and usually encountered in bacteria that cause fewer HAIs than E. coli and its relatives. However, this situation has now changed with the recent discovery that carbapenem-resistant strains of several Gram-negative bacteria (carrying a gene called NDM-1) are spreading rapidly worldwide. This is a significant concern because, while several new antibiotics are effective against MRSA, there are as yet no new drugs for antibiotic-resistant Gram-negative bacteria. Infections by carbapenem-resistant bacteria are consequently very hard to treat.
We aim to develop a new treatment for HAIs caused by carbapenem-resistant Gram-negative bacteria. Penicillin-resistant Gram-negative bacteria can be treated by combining penicillin with a drug that blocks the mechanism of resistance. However, it has not yet proved possible to block the activity of NDM-1 (or that of related genes). Our team, which combines chemists, biochemists and university and hospital microbiologists from the U.K. and Canada, will design, make and test molecules than block the function of carbapenem-resistance mechanisms like NDM-1 and that consequently will restore the ability of carbapenems to kill resistant Gram-negative bacteria. An antibiotic that is reliably active against these organisms will transform the outlook for many patients with HAIs. As part of this work we will also monitor the spread, particularly in hospitals, of bacteria that carry NDM-1 and similar genes, and identify the most important types to use in our testing programme. We will further develop new methods to test whether particular molecules are able to block the function of NDM-1. New methods and resources for testing how to block NDM-1 will also benefit efforts in the wider scientific community to overcome the threat of carbapenem-resistant HAIs.

Technical Summary

Hospital acquired (nosocomial) infections are a growing threat to global public health. Opportunist Gram-negative bacterial pathogens, both the Enterobacteriaceae and non-fermenters such as Pseudomonas aeruginosa or Acinetobacter baumannii, cause a wide variety of such conditions. Carbapenems are increasingly becoming first choice treatments for infections by these organisms, but resistant strains, in particular those carrying various metallo-beta-lactamases (MBLs) are now proliferating. Notably, the NDM-1 MBL is rapidly disseminating in the Enterobacteriaceae on a global scale. No new antibiotics with anti-Gram-negative activity are at or close to the clinic, and MBLs resist the activity of all available beta-lactamase inhibitors. We propose to develop new inhibitors of the most clinically important MBLs that are suitable for progress towards clinical trials as combinations with existing carbapenems. We will identify inhibitors by a combination of in structure-based discovery, use of focussed libraries and optimisation of existing molecules; and develop and use new assays with which to test inhibition of MBLs in vitro. We will test their ability to restore carbapenem activity against clinically relevant MBL-producing strains identified by a programme of resistance monitoring, and optimise identified hits by repeated rounds of synthesis and screening that are guided by structural and biophysical studies. We will demonstrate the suitability of MBL inhibitors for further development using in vitro pharmacokinetic/pharmacodynamic models and toxicity tests. An MBL inhibitor of clinical use will transform the outlook for patients with Gram-negative infections, and the tools that we develop will also aid the efforts of the wider community towards this goal.

Publications


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Brem J (2015) Structural Basis of Metallo-ß-Lactamase Inhibition by Captopril Stereoisomers. in Antimicrobial agents and chemotherapy
Cahill ST (2017) Cyclic Boronates Inhibit All Classes of ß-Lactamase. in Antimicrobial agents and chemotherapy
 
Description Advisor to WHO on global resistance and resistance mapping. Report released Jan 2014 (Walsh)
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in advisory committee
Impact Following this report the WHO has set up a Strategic and Technical Advisory Group (STAG) on antimicrobial resistance and is in the process of developing a Global Action Plan. See http://www.who.int/drugresistance/en/
URL http://www.who.int/drugresistance/documents/surveillancereport/en/
 
Description Author Go Science Foresight positioning paper on antimicrobial resistance (Walsh)
Geographic Reach National 
Policy Influence Type Participation in advisory committee
 
Description Chair, BBSRC Research Committee D (Schofield)
Geographic Reach National 
Policy Influence Type Participation in advisory committee
Impact The BBSRC invests in world-class bioscience research and training on behalf of the UK public. Research Committee D has a portfolio spanning "Molecules, cells and industrial biotechnology" and is responsible for dispensing, and assessing the impact of, public research funding in these areas as well as providing advice to policymakers.
URL http://www.bbsrc.ac.uk/organisation/structures/committees/committee-d.aspx
 
Description Department of Health guidelines on detecting carbapenemases (Walsh)
Geographic Reach National 
Policy Influence Type Participation in a national consultation
Impact Proposed UK guidelines for screening admitted patients for carbapenemase-positive bacteria. As of 2014 the UK has implemented a Standard for Microbiological Investigation (SMI) for detection of carbapenemase-producing organisms.
URL https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/344071/P_8i1.1.pdf
 
Description French Guidelines of screening patients for carbapenemases (Walsh)
Geographic Reach Asia 
Policy Influence Type Gave evidence to a government review
Impact France now regularly screening high-risk patients prior to admission in all French hospitals.
 
Description Member, International Scientific Advisory Board, CHARLI project
Geographic Reach Africa 
Policy Influence Type Membership of a guidance committee
Impact This multicenter investigation will allow a homogenous collection of data and fulfill the need of improving international knowledge on multi-resistant bacteria infections in young children from low-income countries.
URL http://www.charliproject.org/home.html
 
Description New Antibiotics Initiative -IMI (Walsh)
Geographic Reach Asia 
Policy Influence Type Membership of a guidance committee
Impact European scientific advisory board representative for the IMI to establish a clinical trial network throughout Europe to facilitate the rapid evaluation of new /novel antibiotics.
 
Description Scientific Advisory Board: EU Joint Programming Initiative on Antimicrobial Resistance (Walsh)
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guidance committee
Impact JPIAMR has developed a strategic research agenda (SRA) which is supported by the initiative's member states and other international players and has so far been realised in the first of a series of funding calls.
URL http://www.jpiamr.eu/organisation/scentific-advisory-board/
 
Description Screening of patients for carbapenemase positive bacteria in South Africa (Walsh)
Geographic Reach Africa 
Policy Influence Type Participation in a national consultation
 
Description Treatment of potable water in India (Walsh)
Geographic Reach Asia 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact Although not yet proven, distribution of chlorine tablets by the Indian government in response to the findings of our research in India has appeared to affect the number of patients presenting with D&V in the Delhi area.
 
Description World Health Assembly (Walsh)
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guidance committee
Impact Positioning paper presented at the World Health Assembly Congress in June 2012 to re-establish the importance of sewerage treatment in containing antibiotic resistance. A resolution on antimicrobial resistance was adopted at the 2014 World Health Assembly.
URL http://www.euro.who.int/en/about-us/governance/regional-committee-for-europe/news/news/2014/05/world...
 
Description Bridging the Gaps between the Engineering and Physical Sciences and Antimicrobial Resistance (Spencer, Co-I)
Amount £592,169 (GBP)
Funding ID EP/M027546/1  
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 09/2015 
End 08/2017
 
Description IMI European Lead Factory (Schofield)
Amount € 100,000 (EUR)
Organisation European Commission (EC) 
Sector Public
Country European Union (EU)
Start 01/2013 
End 02/2013
 
Description IMI New Drugs for Bad Bugs (Walsh)
Amount € 1,300,000 (EUR)
Funding ID ENABLE consortium 
Organisation European Commission (EC) 
Sector Public
Country European Union (EU)
Start 02/2014 
End 01/2020
 
Description Industrial Studentship (Fishwick)
Amount £137,500 (GBP)
Organisation Biota Pharmaceuticals 
Sector Private
Country United States of America
Start 10/2012 
End 09/2016
 
Description Research Project Grant RO1 (Spencer)
Amount $596,080 (USD)
Funding ID 1R01AI100560-01 
Organisation National Institutes of Health (NIH) 
Department National Institute of Allergy and Infectious Diseases (NIAID)
Sector Public
Country United States of America
Start 02/2012 
End 02/2017
 
Title Chromo- and fluorigenic assays for beta-lactamases 
Description Chromo- and fluorigenic beta-lactams were synthesised and used as assays for beta-lactamase inhibitor screening. 
Type Of Material Technology assay or reagent 
Year Produced 2012 
Provided To Others? Yes  
Impact These assays have been used in high-throughput screens carried out at the European Lead Factory to identify new metallo-beta-lactamase inhibitors 
 
Title Crystal structures of beta-lactamases, beta-lactamase:inhibitor complexes and penicillin-binding proteins 
Description Co-ordinates for crystal structures determined under this project. Accession nos.: 4KQO 4KQQ 4KQR (released entries) 4BP0 4BZ3 4CO9 4C1H 4C1G 4C1F 4C1E 4C1D 4C1C (unreleased entries; on hold awaiting publication) 
Type Of Material Model of mechanisms or symptoms - in vitro 
Provided To Others? No  
Impact Structures are guiding internal SAR within the team. 
URL http://www.rcsb.org/pdb
 
Title Monitoring conformational changes in metallo-ß-lactamases by 19F NMR spectroscopy 
Description Site-selective labeling of target enzymes with 1,1,1-trifluoro-3-bromo acetone (BFA) enables binding events and conformational changes upon ligand binding to be monitored using (19) F NMR spectroscopy. 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact The method has been used to study ligand binding by the NDM-1 (Angew Chem Int Ed Engl. 2014, 53:3129-33) and SPM-1 (Chem Sci. 2015, 6:956-963) metallo-beta-lactamases, establishing that different ligands may utilise different modes of biding to a common target. 
 
Description Carraige and infection rates with NDM-1 positive bacteria in Pakistan 
Organisation Dow University of Health Sciences, Pakistan
Department Dow Medical College
Country Pakistan, Islamic Republic of 
Sector Hospitals 
PI Contribution Initiated, established and funded field work in Karachi plus transport
Collaborator Contribution Training nurses, data collection, transporting specimens
Impact ECCMID 2013 abstract "Frequency of carriage of NDM-1 and CTX-M-15 among patients from hospitals in Karachi: preliminary data assessing risk factors for carriage and infection"
Start Year 2012
 
Description Carriage of carbapenem resistant bacteria in Johannesburg and Sowetto 
Organisation Chris Hani Baragwanath Hospital, Johannesburg
Department Medical Microbiology
Country South Africa, Republic of 
Sector Hospitals 
PI Contribution Initiated collaboration and will undertake molecular biology
Collaborator Contribution Collecting and sending of specimens
Impact None so far
Start Year 2012
 
Description Genomic sequencing of NDM-1 positive Acinetobacter spp. 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Charity/Non Profit 
PI Contribution Initiated and established exchange of strains, data and ideas
Collaborator Contribution Know how on sequencing etc
Impact ECCMID 2013 abstract. "A broad host range conjugative plasmid carrying blaNDM-1 in an Acinetobacter bereziniae isolate from India: Complete sequence and comparison with related genetic contexts"
Start Year 2012
 
Description Genomic sequencing of NDM-1 positive V. cholerae 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Charity/Non Profit 
PI Contribution Initiated and established the collaboration
Collaborator Contribution Initiated and established the collaboration
Impact ECCMID 2012. The genetic context of blaNDM-1 in Vibrio cholerae
Start Year 2012
 
Description Genomic sequencing of Russian ST235 with VIM-2 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Charity/Non Profit 
PI Contribution Initated and established partnership. Preparation of DNA
Collaborator Contribution Sequencing and annotation of sequences
Impact None thus far
Start Year 2012
 
Description MRC CIHR Team grant 
Organisation Canadian Institutes of Health Research (CIHR)
Country Canada 
Sector Public 
PI Contribution UK team provides expertise in Clinical Microbiology (Walsh; Toleman); Structural Biology and Biochemistry (Spencer); in silico Drug Discovery (Fishwick) and ChemicalBiology (Schofield)
Collaborator Contribution Canada team provides complementary expertise in Clinical Microbiology (Pillai); Structural Biology (Strynadka); Inorganic Biochemistry (Siemann); Synthetic and Medicinal Chemistry (Dmitrienko, Lubell, Liu)
Impact As this is a co-funded proposal all listed outputs result from the partnership described.
Start Year 2011
 
Description Whole genome sequencing and sequence analysis of 12 NDM-1 harbouring enteric bacteria (Walsh; Toleman) 
Organisation RDECOM (Research Development and Engineering Command US Army Chemical and Biological centre
Country United States of America 
Sector Public 
PI Contribution Timothy Walsh and Mark Toleman at Cardiff supplied strains to be sequenced. The US Army have performed all the sequencing. Sequence analysis, plasmid analysis and plasmid construction performed mostly by Dr Mark Toleman in Cardiff.
Collaborator Contribution All sequencing performed and ~10% of the sequence analysis.
Impact Oral Presentation at the Interscience Conference on Antimicrobial Agents and Chemotherapy. September 2012 in San Francisco.
Start Year 2011
 
Description ABC TV interview (Walsh) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact The presentation raised Australian public awareness of issues around antibiotic resistance in environmental and veterinary contexts.

The item sparked public debate on social media and was picked up by other media outlets both in Australia (eg http://www.foodmag.com.au/news/antibiotic-resistant-superbugs-could-spread-throug) and the US (http://www.krwa.net/newsDB/MainAnnounce2.asp?key=782)
Year(s) Of Engagement Activity 2013
URL http://www.abc.net.au/7.30/content/2013/s3810324.htm
 
Description BBC Horizon (Walsh) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact BBC Horizon (October 2012) covered our collaborations with the Civil hospital in Karachi and how we are trying determine the global levels of carbapenem resistant bacteria.

Broadening public awareness of global issues on extreme antibiotic resistance.
Year(s) Of Engagement Activity 2012
URL http://www.bbc.co.uk/programmes/b01ms5c6
 
Description Back from the Dead Exhibition, History of Science Museum, Oxford (http://www.mhs.ox.ac.uk/backfromthedead/) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Professor Schofield was scientific advisor to the "Back from the Dead" exhibition at the Oxford Museum of the History of Science charting the development of penicillin as a clinically useful drug.
Year(s) Of Engagement Activity 2016
URL http://www.mhs.ox.ac.uk/backfromthedead/
 
Description Collaborating with developing Countries (Walsh) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Health professionals
Results and Impact 2000 people listened to the talk given at the 2012 IDSA, San Diego. 18/10/2012
http://www.idweek.org/

Undefined
Year(s) Of Engagement Activity 2012
 
Description ITV tonight (Walsh) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact This special report (October 24th 2013) featured Prof. Walsh sampling river water in India as part of an investigation into the distribution and prevalance of the NDM-1 carbapenemase.

.Broadening public awareness of global issues on extreme antibiotic resistance.
Year(s) Of Engagement Activity 2013
URL http://www.itv.com/news/2013-10-24/tonight-when-the-drugs-dont-work/
 
Description Interview for Daily Telegraph online feature (Walsh) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Interview formed part of a extensive online article on antimicrobial resistance

The item has been extensively shared on social media- Twitter, Facebook etc.
Year(s) Of Engagement Activity 2013
URL http://s.telegraph.co.uk/graphics/projects/antibiotic-resistance/index.html
 
Description Keynote speaker at the 2012 13th APCCMI Congress, Beijing (Walsh) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Health professionals
Results and Impact Invited key note speaker on the risk factors for emergence and dissemination of carbapenem resistant bacteria.
http://www.apccmi2012.org/index.html

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Year(s) Of Engagement Activity 2012
 
Description Lecture, St. Olave's School (Spencer) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Extensive formal and informal Q&A afterwards with audience members

Subsequent invitation to another schools event organised by the Royal Society of Chemistry
Year(s) Of Engagement Activity 2014
URL http://www.saintolaves.net/uploads/ckeditor/attachments/273/The_Olavian_Lecture_Series_II.pdf
 
Description Pint of Science: Oxford Oxygen Stories - from penicillin to hypoxia sensing (Schofield) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Talk for general public as part of the 2013 Pint of Science Festival sparked questions and discussion afterwards.
Year(s) Of Engagement Activity 2013
URL http://www.oxfordscibar.com/podcast.html
 
Description Royal Society of Chemistry panel meeting: Beating the Superbugs: avoiding an antibiotic apocalypse (Schofield; November 2013) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach National
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Royal Society of Chemistry meeting: "Beating the Superbugs: avoiding an antibiotic apocalypse"
18 November 2013
The Chemistry Centre, Burlington House, Piccadilly, London W1J 0BA

Event is yet to take place.
Year(s) Of Engagement Activity 2013
URL http://www.rsc.org/conferencesandevents/rscevents/chemistry-centre/antibiotic-apocalypse.asp
 
Description School visit (Bodmin College; Spencer) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact I talked to c. 120 yr 10 and yr 11 students as a part of a half day ChemNet event organised by the Royal Society of Chemistry. This generated questions and discussion with positive feedback from students and staff, and reported increased interest in the subject area.
Year(s) Of Engagement Activity 2015
URL http://www.rsc.org/events/detail/17252/look-what-chemistry-has-done-for-me
 
Description Symposium talk: "Do beta-lactams have a future?" (Spencer) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Dr. Spencer was an invited speaker at a symposium organised to mark the award of an ACS Citation for Chemical Breakthrough to the University of Oxford in recognition of their work on the development of penicillin.
Year(s) Of Engagement Activity 2016
 
Description Symposium talk: "Do beta-lactams have a future?" (Walsh) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Professor Walsh was an invited speaker at this symposium organised to mark the award of an ACS Citation for Chemical Breakthrough to Oxford University on recognition of their role in the development of penicillin
Year(s) Of Engagement Activity 2016
 
Description Visit to Southville Primary School as part of Literacy Week (Bristol; Spencer) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Talk generated extensive questioning on all aspects from science from a class of 7 year olds

Teacher reported continuing high levels of interest in science from that year group.
Year(s) Of Engagement Activity 2014