The evolutionary emergence of multidrug resistant bacterial pathogens

Lead Research Organisation: University of Sheffield
Department Name: Animal and Plant Sciences

Abstract

Increasing antibiotic resistance in bacterial infections is a serious threat to modern medicine, so understanding why some bacteria become resistant to multiple antibiotics whereas others do not is an important challenge for microbiologists, doctors and vets. In pathogenic E. coli - the most common cause of blood and urine infections worldwide and recognised by the World Health Organisation as a top global health threat - antibiotic resistance is associated with gaining extra loops of DNA called plasmids that carry several different antibiotic resistance genes. Not all E. coli strains seem to be able to maintain such plasmids, which is probably because gaining plasmids is typically very costly because the genes the plasmids carry interfere with the workings of the bacterial cell. Our work has led us to hypothesise that this variation between strains of E. coli is due to differences in how the various strains regulate the expression of their genes allowing some to mitigate for the disruption caused to the cell by the plasmid.
In this project we will test this idea in the laboratory using evolution experiments and cutting-edge sequencing technology. We have gathered together a collection of plasmid-free E. coli strains whose close relatives do typically carry antibiotic resistance plasmids in nature. First, we will compare the costs of acquiring a plasmid and the level of antibiotic resistance provided in both types of strain. We predict that costs will be higher in strains that don't typically carry plasmids. Second, we will compare the disruption caused to the cell by acquiring a plasmid in both types of strain by measuring patterns of how they express their genes. We predict that disruption to the cell caused by gaining the plasmid will be greater in strains that don't typically carry plasmids, and that this will scale with the costs we measure of carrying the plasmid. Third, we will experimentally evolve bacteria carrying plasmids in the lab to observe in real time how natural selection compensates for the cost of acquiring a plasmid. We predict that evolved bacteria will gain new mutations in regulators that turn genes on or off, to mitigate the disruption to the cell caused by carrying a plasmid, and that this process will be faster and more efficient in strains that typically carry plasmids. Fourth, we will test how the mutations observed during experimental evolution affect the expression of genes in cells with and without plasmids, to understand the molecular mechanisms by which evolution allows bacteria to maintain plasmids.
This project will advance our fundamental understanding of how and why pathogenic strains of E. coli that are highly resistant to antibiotics evolve. In future this insight could help us to identify potential superbugs before they emerge, or suggest novel targets for drugs that force bacteria to lose their antibiotic resistance plasmids making them susceptible to conventional treatments.

Technical Summary

A major risk factor in the emergence of bacterial pathogens from commensal or environmental reservoir populations is the evolution of drug resistance, either pre- or post-emergence, which then makes treatment of the infection more challenging and increases the likelihood of invasive disease. This process is facilitated in bacteria by acquisition of multidrug resistance (MDR) plasmids carrying multiple resistance determinants. Understanding the evolutionary processes and mechanisms by which emerging pathogens acquire and maintain MDR plasmids is an important area of research in the fight against rising levels of antibiotic resistance. At present our understanding of this process is limited by a paucity of studies where the evolutionary hypotheses derived from observational data are interrogated with experimental tests. The large amount of observational population genomic data available for E. coli makes it an ideal model system in which to investigate the emergence of pathogenic MDR lineages that are the major cause of blood and urinary infections worldwide. This project combines experimental evolution, high-throughput genome sequencing, and transcriptomics to understand the evolutionary and molecular mechanisms by which pathogenic lineages of MDR E. coli emerge via horizontal gene transfer.

Planned Impact

Who will benefit and how?
This is fundamental blue-skies research but results from this programme of research, and its practical application in clinical and environmental management of antibiotic use, has the potential to deliver far-reaching benefits across a wide range of sectors, from individuals and organizations, to societal benefits from long-term potential gains in the overall lifespan of existing and new antibiotics. The mechanistic understanding of the evolution of antibiotic resistance gained from this project will enable informed clinical decisions of antibiotic use, potential biomarkers of high-risk emerging pathogenic strains, and improved advice to the veterinary and farming community on the use of antibiotics. Although banned now in the EU, use of antibiotics as growth promoters is still widespread elsewhere - up to 40% of antibiotics used are as livestock growth promoters. The beneficiaries of this project can be divided in to 2 groups:
1) General Public: AMR is high on the news agenda, with recent reports of colistin resistance bacteria in China widely reported in the UK and beyond. Despite this, in August 2015, a report from NICE (National Institute for Health and Care Excellence) claimed that 10 million doses of antibiotics are inappropriately prescribed in the UK each year. We envisage that one key strand of impact activities associated with our project will be directed towards improving public understanding of the impending societal crisis surrounding rising antimicrobial resistance. There exists widespread misunderstanding of antimicrobial resistance (AMR) among the general public as shown by recent Wellcome Trust research ("Exploring the consumer perspective on antimicrobial resistance" report). The report identifies 3 key challenges:

1. Public attitudes to antibiotics and treatment are a barrier to improving antibiotic stewardship.
2. Poor knowledge of how antibiotics work and what resistance means lead to misconceptions about the nature of the AMR problem.
3. "Doomsday" scenarios and the huge numbers surrounding the AMR crisis in the media make individuals feel powerless to effect change.

Public engagement events designed to reach different age groups in schools and the wider community will raise awareness of the science underpinning the evolution of antibiotic resistance, and what we can all do to minimise the risk. We will leverage the high-profile of Antibiotic Action, based at UoB, to promote the events and key findings among the general public.

2) Government, Clinical, Agriculture and Veterinary Policymakers: AMR is also high on the policy agenda, with antibiotics of last resort increasingly at risk. Many reports across all these areas are highlighting AMR as a concern, yet there is a dearth of knowledge about the evolutionary mechanisms of AMR emergence particularly in pathogens affecting both humans and animals and where AMR arises through horizontal gene transfer. Our findings will be communicated to key stakeholders that can impact the use of antibiotics and their dissemination in clinical and agri-food environments, including: medical professionals, veterinarians, farmers and the agri-food industry.

Publications

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Brockhurst MA (2019) Assessing evolutionary risks of resistance for new antimicrobial therapies. in Nature ecology & evolution

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Brockhurst MA (2019) The Ecology and Evolution of Pangenomes. in Current biology : CB

Related Projects

Project Reference Relationship Related To Start End Award Value
BB/R006253/1 01/02/2018 31/05/2020 £356,381
BB/R006253/2 Transfer BB/R006253/1 01/06/2020 31/10/2021 £117,219
 
Description Bacteria can become resistant to antibiotics by acquiring copies of resistance genes from other cells, however these resistance mechanisms are frequently costly to express in the new cell. We show that evolution can rapidly produce bacteria that are highly resistant to antibiotics but no longer have to pay the cost. Published in ISME Journal. We have published a major review on the role of mobile genetic elements in the evolution of bacterial genomes. Published in Current Biology. We have published an opinion article on ways to improve assessments of the risk of resistance evolution to new antibiotics. Published in Nature Ecology and Evolution.
Exploitation Route These findings help to explain how multidrug resistance plasmids are maintained and spread in bacterial populations, which is relevant to understanding the spread of antibiotic resistance.
Sectors Healthcare

 
Description Team members have spoken at a range of public engagement events reaching around 800 people including school children and members of the general public, including raising awareness of drug resistant infections with high-risk groups. These talks have sparked questions from the audience and led to increased interest in the subject area.
First Year Of Impact 2018
Sector Education,Healthcare
Impact Types Societal

 
Description Cathedral Archer Project (Sheffield Cathedral) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Outreach to homeless people raising awareness of drug resistant sexually transmitted infections (STIs). Approx. 30 people given information about drug resistant STIs. Offering sexual health information and STI screening.
Year(s) Of Engagement Activity 2019
 
Description Discovery Night at University of Sheffield 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact 50 people visited our exhibit and talked to researchers about their projects, including antimicrobial resistance. Sparked questions and discussion.
Year(s) Of Engagement Activity 2019
 
Description Illuminate the Gardens - British Science Association 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Over 50 school children attended a talk by team members about microbial evolution, which sparked audience questions and increased interest in the subject
Year(s) Of Engagement Activity 2018
URL https://www.illuminatethegardens.co.uk/whats-on/
 
Description Interactive microbiome exhibit (Great Yorkshire Show) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact 630 people visited our interactive exhibit about the important role that microbiomes play in health (in general encompassing soils, plants and animals) as part of the Discovery Zone. This was aimed at secondary school children but attended by a wider range of ages including adults. The exhibit sparked questions and discussion.
Year(s) Of Engagement Activity 2019
 
Description Pint of Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact 30 members of the general public attended a Pint of Science talk by team members in a local pub about microbial evolution and horizontal gene transfer, which sparked questions and discussions afterwards
Year(s) Of Engagement Activity 2018
URL https://pintofscience.co.uk/event/natures-bad-guys
 
Description Pitstop+ (Sheffield) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Across multiple sessions approx. 60 adults given information on drug resistant sexually transmitted infections.
Year(s) Of Engagement Activity 2019
 
Description Soapbox Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact 20 people attended a talk by team members at Soapbox Science about our research into bacterial evolution and horizontal gene transfer, which sparked questions and interest from the audience
Year(s) Of Engagement Activity 2018
URL http://soapboxscience.org/soapbox-science-2018-sheffield/
 
Description Vaccines and AMR workshop (Sheffield Theatres Fun Palace) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Workshop for school children on how vaccines work and their role in reducing antimicrobial resistant infections. Resulted in questions and discussion. School children wrote a short play about the topic which was performed at the end of the workshop.
Year(s) Of Engagement Activity 2019