Uppsala Antibiotic Center

PhD projects at Uppsala Antibiotic Center

Uppsala Antibiotic Center is funding 14 PhD projects starting 2017, all relating to antibiotics and the fight against antibiotic resistance. Three in Humanities and Social Sciences, four in Science and Technology and seven in Medicine and Pharmacy.

These 14 PhD projects have been selected among 43 projects of impressive quality, submitted to Uppsala Antibiotic Center from a wide variety of scientific fields. The project applications were reviewed and ranked by internationally renowned reviewers.

List of PhD Projects

Project descriptions

Improving the use of antibiotics in the management of acute childhood illness, a study from Ujjain, India

Antibiotic resistance is considered one of the greatest threats to global public health. All use of antibiotics promotes resistance and measures to improve use are urgently needed. A newly developed electronic algorithm for the management of acute childhood illness, ALMANACH, resulted in an 80% reduction in antibiotic prescription without compromising health outcome in Tanzania. The finding confirms the current understanding of that antibiotic prescription patterns is a result of the local practices rather than accurate diagnosis.

This project aims to study the effect of the ALMANACH to improve antibiotic use and management of acute illnesses in children aged 2-59 months in Ujjain, India. The project will be carried out at different levels of the health system. Furthermore, the project aims to study the facilitation strategy to support the implementation of the electronic algorithm for improved care of children.

C-reactive protein (CRP) may further improve the diagnosis of bacterial diseases which require antibiotic treatment and has the potential to be integrated into the clinical algorithm. CRP is currently not available in the public health care in India. The proposed project therefore aims to study the feasibility of integrating CRP into the ALMANACH algorithm.

The project finally targets the sustainability of the implemented interventions employing ethnography to explore the political, social, cultural and biological aspects of the context, innovations, facilitation and recipients one year post implementation. The transdisciplinary approach is fundamental for a holistic understanding, setting a precedent for how different perspectives can be brought together in studying interventions to address antibiotic resistance.

PI: Andreas Mårtensson, Anna Bergström

Antibiotic prescription in Swedish primary care consultations: a multidisciplinary conversation analytic study

Antimicrobial resistance poses a serious threat to global public health. Sweden has comparatively low rates of antibiotic use. This gives an incentive to explore factors that contribute to low usage including communication between medical professionals and patients. Another reason to examine medical consultations is to identify ways to further reduce antibiotic prescription within the Swedish health care sector. This multidisciplinary PhD project will investigate the social and linguistic patterns of antibiotic prescription in Swedish primary care. We will make video-recordings of Swedish primary care visits where the patient is seeking medical care for routine upper respiratory infection symptoms. Previous research has established that this is a context where inappropriate antibiotic prescription is a concern. Our corpus will include consultations with nurses as well as doctors and it will be the first of its kind. We will use conversation analytic methods to document how expectations for particular remedies (including antibiotics) are raised, how triage, problem presentation, physical examination, paraclinical testing and diagnoses are carried out and how treatment recommendations are negotiated. Our findings will be developed into teaching resources targeted towards pre- and post-qualification medical training and nursing programs. These resources will document real life situations where antibiotics are prescribed as well as the communicative strategies used by experienced doctors and nurses to avoid inappropriate antibiotic prescription. Our study will fill a gap in international research on how antibiotic treatment discussions are carried out in situ within the details of primary care consultations and the educational materials that we will develop will provide tools for engaging in responsible antimicrobial stewardship.

PI: Anna Lindström

How is cell-to-cell variation in growth rate related to antibiotic tolerance and resistance development?

The speed of bacterial cell growth is important for how the cell will respond to antibiotic treatment. Fast growing cells replicate their genome more often and are thus likely to acquire protective mutations. Slow growers on the other hand are less metabolically active and might not suffer so much from drugs that act to prevent e.g. protein synthesis or membrane production. For example, we know that some cells, so called persisters, might escape the antibiotic treatment by entering a dormant state. However, it is not known why and how these cells appear in the population, as the dormancy is not a result of a genetic change. In fact, the assumption that genetically similar cells grow at similar speed is a gross oversimplification.

To be able to understand how and to what extent growth-rate variations affect the development of antibiotic resistance we will perform large-scale measurements of individual cells growing in presence of different antibiotics. We will also dig deeper into the possible mechanisms by actively perturbing individual genes and monitor the effect on bacterial growth. This type of random screen in search for complex mechanisms would not be possible without much effort on methods development. By combining advanced optics, genetic engineering and sequencing with microfluidic growth chambers that are custom designed to culture thousands of individual cells separately, we have introduced a totally new approach to disentangle cellular pathways bottom-up.

This new technique has the potential to fundamentally change the way we do genetic research in the future since it makes it possible to identify the genetic reasons for complex phenotypes at the level of individual cells.

PI: Johan Elf

Antibiotic usage and reduction strategies in diverse populations of healthcare users and healthcare professionals

A qualitative exploration of the social meanings of antibiotics in diverse populations of healthcare professionals who are also patients to inform reduction strategies. Sources of information and advice used by antibiotic-users in Sweden are mapped, reviewed and written up. This mapping is used as the basis to devise a sampling strategy for narrative interviews with diverse individuals who are medically trained, with experience or education in Sweden and elsewhere and have experience of using antibiotics. These reflective and interrogative interviews will examine when values that are avowed in general are contravened by actual behaviour. Qualitative analysis of these moments will be used to devise strategies to inform a reduction of antibiotic usage strategy and validated through focus group discussions. While qualitative methodology is emergent, with each phase being determined by the results of the previous phase, it is anticipated that these strategies will be piloted in a limited number of case studies and subject to a qualitative evaluation.

PI: Hannah Bradby

Targeted eradication of bacterial pathogens

Antibiotic resistance is an increasing problem worldwide and infections that cannot be treated with the antibiotics we have available are already a reality. Therefore, new means of treating bacterial infections are of utmost importance at this point. However, quick fixes like one new antibiotic is only going to solve the problem at hand for a short while, i.e. until resistance develops against that drug.

On the other hand, the human body contains as many bacterial cells than human cells, mainly situated in the gastrointestinal tract. These bacterial organisms, known as the microbiota, are essential to our well-being and disruption of this normal flora makes us more susceptible to new infections. Also, antibiotic resistant bacteria can reside in this normal flora and contributes to the spread of antibiotic resistance globally. In addition, antibiotic resistant bacteria increase the personal risk of future infections by resistant bacteria.

Here we propose a completely new way of treating bacterial infections, one that specifically target bacterial pathogens, leaving the beneficial normal flora intact. To do this we will use our knowledge about a recently discovered bacterial growth inhibition system that inhibits the growth of other bacteria in a species-specific manner. This inhibition requires direct contact between the inhibiting and target cell and has been named contact-dependent growth inhibition or CDI. In addition to treatment, we will investigate if probiotic bacteria armed with these systems can be used to cure carriers of antibiotic resistant or pathogenic bacteria.

PI: Sanna Koskiniemi

Phenotypes and potential of horizontally transferred antibiotic-resistance genes

The project will develop a robust experimental system to address the phenotypic and evolutionary potential of foreign antibiotic resistance and other genes to overcome expression barriers that might limit their successful maintenance after horizontal genetic transfer (HGT) into naïve bacterial species. It will focus initially on gene families with known relevance for resistance in clinical pathogens, whose products interact with essential cellular components. Specific aims will include: measuring the resistance and fitness-cost phenotypes of foreign resistance genes when transferred into isogenic host bacterial strains; measuring the potential of foreign genes to evolve higher level resistance, and/or reduced fitness costs, in the new bacterial species: tracking the evolutionary trajectories of co-adaptation in the new bacterial host: measuring the impact of HGT resistance genes, before and after adaptive evolution, on in vivo fitness and virulence. Additional studies will focus on the resistance-fitness phenotypes and evolutionary trajectories after HGT of larger genetic regions (mobile genetic elements are the natural context of many resistance genes). This experimental system could be used to predict new and emerging resistance threats to currently used antibiotics, and provide a rational basis for deciding which novel antimicrobial compounds should be chosen for development into clinical candidates.

PI: Diarmaid Hughes

Systematic mapping of antibiotic usage patterns among sick children across low- and middle-income countries from 2000–2015 and its health system, policy and epidemiology drivers

There is a critical need to achieve balance between access to and excess use of antibiotic medicines in order to combat resistance, one of today’s top global health challenges. While high-income countries must limit excess antibiotic use, millions of people worldwide lack access to life-saving medicines. Yet, it is increasingly recognized that the access-excess divide in antibiotic consumption is more complicated than simply between rich and poor countries. There are also important geographic and socioeconomic differentials in antibiotic usage across low- and middle-income countries that need to be identified and addressed to reduce access disparities. Previous global antibiotic consumption assessments have primarily relied on pharmaceutical sales data that do not directly measure population usage or its variations across socioeconomic groups. Other recent analyses have been limited to select countries, specific disease conditions or certain patient groups. To fill this evidence gap, this project aims to analyze approximately 200 national population-based surveys comparably conducted across low- and middle-income countries in 2000–2015 to identify global trends, regional variations and socio-economic differentials. Subsequent studies will further analyze health system readiness to provide antibiotic prescriptions to sick children per clinical guidelines based on comprehensive national facility assessments conducted in about 15 countries since 2000. These large-scale analyses will be complemented by an in-depth study in Zanzibar (Tanzania) where recent policy or epidemiology changes could drive new antibiotic consumption patterns. Taken together, project findings will provide new and important large-scale evidence of changing antibiotic use patterns for sick children in low- and middle-income countries including key health system, policy or epidemiological drivers.

PI: Katarina Ekholm Selling

A comparative systems biology approach to understand phenotypic metronidazole resistance

Metronidazole (MTZ) or 5-nitroimidazole is a unique antibiotic since it has activity against both bacterial and parasitic organisms. It is on the WHO essential medicines list, meaning that it is of utmost importance for global health systems. Metronidazole has been widely used for over 40 years and up until now minimal resistance development has been present. However, recently a rapid increase in the number of MTZ resistant bacteria and protozoa has emerged and this is a large problem considering the few alternative drugs available. MTZ has been used for treatment of the vaginal protozoa Trichomonas vaginalis since 1957 and is also efficient against the intestinal protozoans Entamoeba histolytica and Giardia intestinalis. MTZ has later also emerged as the main treatment for infections caused by anaerobic and microaerophilic bacteria such as Helicobacter pylori and Clostridium difficile. Similar to MTZ- resistance in the important gastrointestinal pathogen G. intestinalis, can C. difficile and H. pylori be associated with phenotypical resistance involving many different factors. Currently, very little is known about the details around this, which has limited the possibility to diagnose this kind of resistance. In this project, we will use comparative systems biology to identify resistance mechanisms. We will develop resistant mutants in the lab and study them with genome sequencing, transcriptomics, proteomics and metabolomics. Since there are a vast numbers of factors affecting the MTZ resistance, different bioinformatic methods will be used to reveal combinations of interacting factors. This project will enable the creation of new diagnostic tools for detection of MTZ resistance and other means of phenotypic antibiotic resistance. The experimental pipeline described here can be used in future studies of antibiotic resistance towards other drugs and in the development of new drugs.

PI: Staffan Svärd

Understanding and improving antibiotic prescribing at a tertiary hospital

Antibiotic overuse and misuse is the main driver of emerging crisis of multidrug-resistant bacteria. It has been estimated that as much as 50% of antibiotic prescriptions are inappropriate. Antibiotic interventions to improve prescribing patterns have been successfully implemented in primary care in Sweden and other countries. However, much of the last-resort antibiotics are used in hospitals in which decisions on therapy for bacterial infections are more complex. In this project, we will explore the appropriateness of antibiotic prescribing at Uppsala University Hospital, incentives for prescribing and measures to prevent inappropriate use. Antibiotic interventions will be conducted at selected hospital departments using a multifaceted and cross-disciplinary approach including physician, nurses and clinical pharmacists. We believe that a drastic and sustainable behavioural change in prescribing patterns can be obtained that will enhance the accuracy of prescriptions, reduce the risks of side effects for the individual patients and prevent emergence and spread of multidrug-resistant bacteria. By using a systematic approach to show causative effects of the measures taken the project will provide important new knowledge to this field and can serve as a best practice example for others striving to improve hospital antibiotic prescribing.

PI: Thomas Grenholm Tängden

Model‐based design and analysis of clinical trials on drug therapies aimed to overcome antibiotic resistance

One of the big challenges in developing new antibiotic treatments active against multi-drug resistant bacteria is the difficulty to recruit a sufficient number of patients for clinical trials.  Luckily, patients with such infections are still relatively rare, but those who can be identified are often critically ill, resulting in high variability in the outcome between patients. Therefore many patients are needed to evaluate a treatment response using classical statistical methods. These large studies become very costly and therefore drug developers are hesitant to invest in the disease area, despite the urgent need for novel antibiotic therapies. An increasingly used approach to overcome antibiotic resistance is to combine several antibiotics. Two drugs can however be combined in multiple ways and all combinations cannot be studied clinically; e.g. different dose sizes, infusion durations and time intervals between the administrations. 

Antibiotics´ effect on bacteria can be studied in the lab, and such information could be more efficiently used to support the design and analysis of studies performed in patients. It is also possible to retrieve more information from trials already performed by using mathematical-statistical modeling approaches where multiple measurements can be analysed simultaneously. Information from one type of infection, e.g. lung infection, may also be borrowed from of another type of infection, e.g. blood stream infection. In addition, information can be shared between different species of bacteria, and between patient groups with different antibiotic exposure patterns (pharmacokinetics) to reduce the need for additional data. This project aims to define methods for design and analysis of clinical trials so that only a low number of patients with infections caused by multi-drug resistant bacteria are needed for evaluating efficacy of antibiotic treatments. 

PI: Lena Friberg

The innovation paradox: Highly needed university antibacterial research in a dwindling ‘antibiotic eco system’

Novel antibiotics; along with new diagnostics, worldwide access and stewardship use, is due to antimicrobial resistance needed more than ever. Hence, the ‘heart’ of antibacterial knowledge advances; university and institute research, is presented with some significant challenges. The paradox is that resistance not only have detrimental health effects, it is also threatening the knowledge development and innovativeness of antibiotic eco system. During the same time as the numbers and variety of resistant pathogens have increased dramatically, academic and institute research program on this topic seems to dwindle, in the wake of dramatic changes in the pharmaceutical business landscape.

The aim of this PhD project is to investigate the content and consequences of contextual changes affecting university/institute antibacterial research 1980-2010; in terms of a) research collaborations with pharmaceutical business counterparts, b) external university/institute funding and support, and c) internal university/institute funding and support. The position implies an interest in the relation between scientific research advances and the use of science in business and society, as well as in historicizing these processes from STS and network perspectives.

PI: Alexandra Waluszewski

Antibiotic treatment in humans; relevance for the gut flora and type 1 diabetes risk

Type 1 diabetes is a severe, potentially life-threating disease. The number of children that gets type 1 diabetes has doubled in the last 30 years in Sweden, most likely because of a increase in one or several as yet unidentified changes in the child’s environment or lifestyle. The “hygiene hypothesis” proposes that a decrease in exposure to bacteria and other microorganisms could affect the immune system to overreact to tissues or allergens. The gut normally hosts a large amount of normal bacteria. Earlier studies have shown that children with early form of type 1 diabetes have a different composition of bacteria compared to healthy children. The overarching aim of the proposed research program is to study the effect of antibiotics on the gut flora in early life, and on type 1 diabetes risk.

In the first part of the project, we will use DNA techniques to determine what bacteria are present in stool samples from 80 mothers and their babies during pregnancy (mothers only) and up to two years of age (6 time points in total). By linking the samples with national registers, we will get information on when and what antimicrobial medications were given the mothers and their children.  We will be able to determine the short- and long-term effects of antibiotics on the gut flora and increase our understanding in this field.

In the second part of the project, we want to determine whether antibiotic treatment during pregnancy and the first year of life is associated with type 1 diabetes. Antibiotic treatment is common during pregnancy and in infants, but the impact on type 1 diabetes risk is not clear. Because type 1 diabetes is a rather rare event, large sample sizes are needed. By combining different national registers, we can include all children born in Sweden between 2005 and 2013 in a large study to assess the risk of type 1 diabetes in relation to antibiotic treatment. We will investigate different types of antibiotics and we will be able to adjust for differences in prescription of antibiotics in different groups of children.

These studies will yield important information on the impact of antibiotic on the diversity and function of the human microbial ecosystem and type 1 diabetes risk. New knowledge in this field could help in making well-informed decisions of antibiotic therapy in pregnant women and infants. More important - if our hypothesis holds true, it would open up new avenues for intervention studies aiming at enriching the infant's microbiome in order to decrease risk of type 1 diabetes.

PI: Tove Fall

The role of ProQ and type I toxin-antitoxin systems in persister phenotypes in Salmonella enterica and Escherichia coli

The rampant emergence of antibiotic, multidrug, resistance in bacterial pathogens is a well known and publicized phenomenon. Less emphasis has been on a related phenomenon which however may be of similar impact, that of bacterial persisters. Persisters arise as a subpopulation that despite of being genetically identical to the majority of the population enters a dormant or very slow-growing state. The persistent cells are unsusceptible to treatment since the action of most antibiotics requires metabolic activity in targeted cells. Hence, some infections become untreatable due to the re-emergence of the surviving cells after treatment; the resuscitated persisters recreate the original antibiotics-susceptible population since they are not mutants but rather phenotypic variants. In recent years, it has become clear that toxin-antitoxin (TA) systems are key, and maybe the dominant, players in causing persistence. TA systems consist of a toxin and an antitoxin and are classified based on the molecular nature of the antitoxin and the mode of toxin inhibition. Type I TA systems consist of an mRNA encoding a toxin, and an antitoxin in the form of an antisense RNA that inihibit translation of the toxin mRNA. Depite their prominent contribution to formation of persister cells, the biological functions of many enterobacterial Type 1 TA systems remain obscure. Furthermore, it is unclear which accessory factors are involved in these processes. A comprehensive characterization of Type 1 TA systems, including analysis of their expression, regulation and molecular and genetic interactions will be crucial for elucidating their role in bacterial physiology, including persister cell formation.

PI: Gerhart Wagner, Erik Holmqvist

Development of an antibiotic susceptibility test to enable the fastest possible correct treatment of life-threatening bacterial infections

Increasing antibiotic resistance, when bacteria develop mechanisms so that they can keep multiplying in the presence of antibiotics, is one of the most critical medical problems of our time. Economic cost in terms of lost production caused by antimicrobial resistance from present to 2050 may exceed 100 trillion USD, and death rates associated with antimicrobial resistance may increase from 700 000 to over 10 million per year during the same time period, should no action be taken. There will be no single solution capable of stopping the emergence of resistance. A multitude of separate efforts including improved diagnostics will be necessary to combat the development of antibiotic resistance. We will in this project further develop a very rapid and robust method called QuickMIC that can be used to determine the resistance profile of bacteria isolated from patients in the shortest possible time. It is very important for patients that have severe and life-threatening bacterial infections to get the right antibiotic as fast as possible. The method that we are developing can handle complex and unpure clinical samples isolated from patients. The sample is injected into a chip where the growth of bacteria in gradients of a panel of antibiotics is monitored using advanced microscopy and automated image analysis. Initial indications of antibiotic susceptibility or resistance is obtained within 20 minutes, and exact values of the concentrations of the tested antibiotics that are required to inhibit growth of bacteria is obtained within 1-2 hours. The QuickMIC method thus enables faster diagnostics and optimization of treatments, to save lives and limit misuse of antibiotics that otherwise contributes to the formation of resistant bacteria. The project is a close collaboration between the biotech company Gradientech AB, Uppsala University, the Uppsala University Hospital, and the EUCAST Development Laboratory in Växjö.

PI: Johan Kreuger