A single cell, single molecule microscopy platform for antibiotics research

Lead Research Organisation: Newcastle University
Department Name: Biosciences Institute


The use of antibiotics to supress and treat bacterial infections is a cornerstone of modern medicine. However, bacteria are increasingly developing resistance towards multiple classes of antibiotics currently in clinical use. Some strains of life-threatening bacteria like tuberculosis are already resistant to all available antibiotics, making them effectively untreatable. The rapidly unfolding antibiotic resistance crisis has been declared a global health emergency by the World Health Organization, and research aiming to tackle antibiotic resistance a strategic priority both by UK Government and UKRI. To address this major threat to human health, we need to ramp up our efforts to screen and develop novel antibiotics that can be used against the multidrug resistant bacteria already in circulation, and also to develop approaches to re-sensitise them for already existing antibiotics. In the longer term, it is crucial to identify novel antibiotic targets and treatment strategies with an intrinsically reduced risk of resistance development.

In recent years, bacteria have been found to have a highly complex and dynamic cellular internal organisation. As a result, many of the central properties of antibiotics such as their ability to trigger cell rupture can only be understood in the cellular framework. Following the cellular consequences of a novel antibacterial compound via microscopy is thus an extremely powerful tool to understand how antibiotics work (mode of action). Bacteria also exhibit large cell-to-cell differences across a single population that allows individual bacteria to evade and resist antibiotics. Due to the single cell nature of these phenomena, microscopic techniques are essential for understanding how antibiotics interact with bacterial cells and populations.

The Newcastle University Centre for Bacterial Cell Biology (CBCB) is world leading in studying the structure and function of bacterial cells. However, our research focus is not limited to fundamental bacterial cellular biology. Through research on host-pathogen interactions, antibiotic mode of action, identification of novel antibiotic targets, and also through direct novel antibiotic screening projects, researchers at the CBCB are actively engaged in research that aims to translate the gained knowledge to novel antibiotic discoveries and therapies.

In the very core of the success of CBCB has been a suite of high performance microscopes dedicated and optimised for work with live bacteria, including pathogenic ones. However, microscopy is still a rapidly developing field with new instrumentation enabling approaches that were previously not feasible. We have identified three complementary, cutting-edge techniques that we foresee to become particularly important for antibiotics research: (i) image-based screening for novel antibiotics, (ii) single cell imaging combined with on-chip drug treatment to understand how antibiotics kill bacteria and how bacteria resist antibiotics, (iii) single molecule microscopy that allows antibiotic action to be monitored directly on the level of individual proteins and complexes.

We request funds for the purchase of a microscope system capable of all three techniques, which thus is both extremely powerful and provides excellent value for money. Advanced microscopy systems such as this one require a high level of expertise that often prevents effective adoption of these techniques by non-specialists. To deliver access to these techniques to a widest user base, Newcastle University is supporting this application with commitment to hire a PhD-level staff scientist dedicated to assisting users with experimental planning, image acquisition and image analysis, in addition to managing access and maintenance.

Technical Summary

Antibiotic resistance is an unfolding global health emergency which requires urgent action. Major bacterial machineries such as those responsible for cell morphogenesis, transcription, translation, and DNA replication exhibit a high level of spatial organisation that is crucial for their function. These complex cellular structures are among our best antibiotic targets. To understand how antibiotics work, it is essential to determine how antibiotics compromise the cellular organisation of their target molecules. The Centre for Bacterial Cell Biology at Newcastle University is at the forefront of this field and has world-class bacterial imaging capabilities, which are available for a wide user base of microbiologists in Newcastle, and to an international network of academic and industrial collaborators.

We request funds to purchase a commercial system capable of three powerful new capabilities with great promise in antibiotic research: (i) high content automated image based screening (ii) single cell imaging combined with antibiotic injections through microfluidic devices, and (iii) single molecule microscopy. These approaches allow automated screening for novel antimicrobial compounds, and in-depth mode of action analyses at the level of individual cells and proteins.

Addition of these new capabilities will help maintain the globally leading position of the CBCB in bacterial cell biology and imaging. Access to these techniques will be made available to the widest possible user base, supported by a Newcastle University funded expert staff scientist. The microscope will enable a wide range of projects including image-based screening for antimicrobial inhibitors of targets including RNA polymerase and teichoic acid synthesis, mode of action studies of bacterial cell division and growth inhibitors, and supporting fundamental microbiology of chromosome replication and cell wall synthesis.

Planned Impact

Antimicrobial resistance (AMR) is a major public health crisis causing 700,000 deaths globally each year and these numbers are predicted to rise to 10 million by 2050 unless urgent action is taken. Researchers at the Newcastle University Centre for Bacterial Cell Biology (CBCB) acknowledge our societal duty to maximise our research efforts towards measures counteracting the unfolding AMR crisis.

The requested instrument would strongly support ongoing translational efforts to discover and develop novel resistance-breaking antibiotics, with the long term goal of ultimately bringing new drugs to market which result in improved patient outcomes. Several groups within CBCB (Errington, Zenkin, Murray and Strahl) are actively engaged in novel antibiotics screening projects. These projects leverage close ties between CBCB and Demuris Ltd, a Newcastle University antibiotics screening & discovery spin-out company founded by co-I Errington. Demuris represent a proven route for developing new antibiotic compounds, evidenced by a recent Newcastle University/ Demuris joint patent for Rifamycin analogues with activity against multi-drug resistant tuberculosis, arising from research of co-Is Zenkin and Errington. Antibiotic-screening efforts are also carried out in collaboration with the Newcastle University High Throughput Screening Facility (HTSF), and the European Lead Factory. Screening efforts would be strongly accelerated and enhanced by the automated screening capabilities provided by the requested microscope system.

An essential part of the antibiotic development process is elucidation of antibacterial mode of action. Several groups within CBCB (Errington, Zenkin, Murray, Strahl, and Wollmer) are directly involved in antibacterial mode of action studies. This includes development of novel assays and methodologies for rapid determination of the antibacterial mode of action using microscopic single cell approaches. The fast, single-cell imaging enabled by the requested microscope system, combined with the microfluidic device allowing quick drug-addition experiments would represent a substantial technical advancement for such studies.

Addressing the AMR crisis also requires identifying novel antibiotics targets and drug-combinations with intrinsically reduced risk of resistance development. This long-term goal requires substantial efforts in fundamental research underpinning antibiotic function, host-pathogen interactions, infection, and bacterial physiology in general. CBCB researchers are uniquely and demonstrably well positioned to contribute to this goal by generating new fundamental knowledge underpinning antibiotic function and AMR through excellence in basic research. The new capabilities provided by the requested microscopy system would help us to maintain the cutting-edge research equipment infrastructure that is essential for generating this medically and societally relevant underpinning research.

CBCB PIs actively engage in delivering research and innovation though industrial collaborations. The commercial exploitation of most CBCB antibiotics discovery projects is primarily developed in close partnership with Demuris Ltd, supporting both the UK and local North East economy. Generated fundamental microbiology knowledge is also being actively exploited in other areas such as biotechnology, demonstrated though active co-I collaborations with biotechnology companies such as Royal DSM and Ingenza Ltd.

Bacterial physiology and imaging are identified as vulnerable skills areas. CBCB provides comprehensive, world-class training in these crucial skills areas for many post-doctoral researchers, PhD students, MRes and undergraduate students. Through enabling access to cutting-edge technology, the requested instrument would strongly enhance our efforts to train highly-skilled research professionals.


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Ernits K (2023) The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems. in Proceedings of the National Academy of Sciences of the United States of America

Description The goal of the grant was to establish a high performance microscope for antibiotic research, to be made available to a large pool of world class bacteriologists at Newcastle University, and beyond through collaborations. We have now achieved this goal: the instrument has been installed, commissioned and was made available for use by Newcastle bacteriologists since late summer 2021. We have also recruited a PhD-level staff scientist to support the advanced microscopy research performed with this instrument.
Based on initial uptake, we anticipate substantial future outputs across bacteriology and antibiotics research, but these outputs will be realised in the near to medium term.
The instrument is being used to enable research in areas highly relevant to antibiotics research, including: research into the molecular target of last line of defence antibiotic daptomycin; mechanistic studies of the bacterial replication initiation machinery, which is a major antibiotic target, and studies into bacterial cell wall remodelling, again a major antibiotic target. Two BBSRC grants (including an sLOLA grant) were awarded based on preliminary data obtained with the microscope. These, and several further grant applications both successful and in preparation will make extensive use of this system.
Exploitation Route The principal objective of this grant was to make a high performance microscope for antibiotic research easily accessible to a wide range of world class bacteriologists. This has now been achieved, and we therefore expect that this instrument will act as a research tool that directly enable the scientific research of a large number of bacteriology researchers based at Newcastle University and collaborators with those researchers.
Sectors Agriculture, Food and Drink,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

Description Direct research related impacts of this grant are expected to emerge in the medium term. This grant is already supporting societal impact via public engagement work. The staff scientist associated with this grant through in-kind contribution from Newcastle University is extremely passionate about microscopy and biology outreach to local schools, and he has already performed substantial microscopy outreach activities inspired and informed by his work on high performance microscopy (see ResearchFish Engagement section for full details).
First Year Of Impact 2021
Sector Education
Impact Types Societal

Amount £388,118 (GBP)
Funding ID BB/X001512/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2022 
End 09/2025
Description Understanding an ancient universal membrane effector system
Amount £4,431,990 (GBP)
Funding ID BB/X003035/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2022 
End 08/2027
Description Cell Detectives microscopy-themed outreach group 
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 Outreach activities have been performed by George Merces, the microscopy staff scientist hired as in-kind insitutional support for the 19ALERT grant. George has been working as part of the Cell Detectives microscopy-themed outreach group at Newcastle University. These events have included participation at the STEM Family Fun Day (12th March 2022), hosted by the Hancock Museum, Newcastle. This day-long event brought microscopes to the museum for young science enthusiasts to explore the microscopic world, with children from ages 2-14 taking the opportunity to explore biological samples including bacterial slide preparations. We also incorporated a station on building a simple water-based microscope out of Lego and cling film, allowing children and parents to explore microscopy within their own homes. A supply of silicone lenses were created also, for attachment onto conventional smart phones, allowing parents explore microscopy throughout the day with their children. Contacts were made with several school teachers and other outreach organisers to facilitate these silicone lenses being distributed to them for future events. Additionally, school visits from the Cell Detectives have been carried out (with many more organised for future implementation), for scientists to come into schools and provide days of science and microscopy exploration for primary and middle school children across the North East of England.
Year(s) Of Engagement Activity 2021