Antibiotic Resistance in Wastewater: Transmission Risks for Employees and Residents around Waste Water Treatment Plants (AWARE-WWTP)

The rise of antibiotic resistant infections is an imminent global public health threat, and Antibiotic resistance is a major health care concern worldwide. Wastewater (sewage) is considered an important source of dissemination of antibiotic resistant bacteria and resistance genes (ARB/ ARGs) to the environment.

Completed project

AWARE investigated whether people working at wastewater treatment plants (WWTP) and people living in the vicinity of WWTP have an increased risk of carriage of ARB/ARGs through exposure to contaminated water or air. This was studied in Germany, the Netherlands and Romania.

The main conclusion was that WWTP workers and nearby-residents may be at greater risk of carriage of ABR than the general population in some (as was shown for Romania) but not in other countries (as was shown for Germany and the Netherlands). Also, the results suggest that elevated carriage in Romanian nearby residents were not likely to be directly caused by the WWTP. Further analyses will quantify exposure risks and shed light on the role of WWTP in selection of antibiotic resistance.

Project partners

  • Heike Schmitt, National Institute for Public Health and the Environment (RIVM), Netherlands (Coordinator)
  • Carmen Chifiriuc, University of Bucharest, Romania
  • Joakim Larsson, University of Gothenburg, Sweden
  • Katja Radon, Ludwig-Maximilians-Universität, Germany
  • Susan Pettersson, Water and Health, Australia
  • Kate Medlicott, World Health Organization (WHO), Switzerland
  • Peter Ulleryd, Västra Götaland och Regionala Strama Södra Älvsborgs Sjukhus, Sweden

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Selection and Transmission of Antimicrobial Resistance in Complex Systems (STARCS)

Antibiotic-resistant bacteria are not new, but in the last two to three decades antibiotic resistant bacteria have been constantly increasing and rapidly spreading. As a result, the emergence of antibiotic resistance is increasingly limiting treatment options for mild to moderate infections, which makes it of pivotal importance to control the emergence and spread of antibiotic resistant nacterial pathogens.

Completed project

In the STARCS project we study the pathways by which resistant bacteria, particularly enterococci resistant to vancomycin and enterobacteriales resistant to extended-spectrum beta-lactamases, can emerge in complex ecosystems, such as the human intestinal tract, in which they can acquire genetic material that encodes resistance to antibiotics.

To this aim, we have developed a number of tools that are used to characterise the reservoir of resistant bacteria and resistance genes in microbial ecosystems. In addition, we perform research into the transfer of resistant bacteria and resistance genes between animals and humans. As antibiotic resistance can spread via horizontal gene transfer of mobile genetic elemenst (MGE) in addition to the spread of antibiotic resistant strains, we have developed in the STARCS consortium novel tools to identify and reconstruct MGE’s based on whole genome sequence data and to characterize with great precision the MGE-bacteria interaction networks of the microbiota in the mammalian gut using an approach called metaHi-C.

Using all these tools studies comparing bacteria found in humans and farm animals in the Netherlands by analysing their DNA revealed that resistant bacteria found in humans were different from those found in farm animals. This shows that humans are rarely infected by antibiotic resistant bacteria that come directly from farm animals.

Furthermore, three primary studies conducted in a community setting and two in hospital settings, using samples collected from different sources: patients, live and slaughtered food animals, and environmental samples in the slaughterhouses, taken from developing (Vietnam) and developed countries (Italy, Germany) with different antibiotic use and antibiotic resistance backgrounds, revealed, again, limited contribution of food-animal sources, particularly chickens and pigs, to causing urinary tract infections by ESBL-resistant enterobacteriaceae (ESBL-E) in Hanoi, Vietnam.

In hospital settings, actively screening and decolonising patients carrying ESBL-E are promising infection control strategies. Using simple mathematical models, we were able to show that the environment that is shared between farm animals and humans might be an important pathway for the transmission of antibiotic resistant bacteria as it can act as a reservoir between the two populations. Because of this, measures such as curtailing antibiotics in farm animals have much less impact on human health.

Furthermore, our modelling showed that the effect of curtailing of antibiotic resistance in farm-animals on human foodborne diseases is two-fold. By curtailing antibiotics is farm animals the proportion of human foodborne illnesses that is caused by a resistant pathogen will be decreased, but the number of food-borne illness cases is likely to increase due to this measure. However, further modelling showed that this can be mitigated by maintaining good farm bio-security (farm-to-fork and livestock health) and reducing transmission from animals to humans.

We furthermore looked at how (international) food imports affect the efficacy of antibiotic curtailment in livestock. For this we used a simple mathematical model. This shows that imports from non-domestic sources can reduce the efficacy of local livestock antibiotic curtailment.

Project partners

  • Rob Willems, University Medical Center Utrecht, Netherlands (Coordinator)
  • Dik Mevius, Wageningen University & Research, Netherlands
  • Dan Andersson, Uppsala University, Sweden
  • Teresa M Coque, Ramón y Cajal University Hospital, Spain
  • Romain Koszul, Pasteur Institute, France
  • Mark Woolhouse, University of Edinburgh, United Kingdom
  • Surbhi Malhotra-Kumar, University of Antwerp, Belgium 

Project resources

Tools

  • mlplasmids: Consists of binary classifiers to predict contigs either as plasmid-derived or chromosome-derived.
  • gplas: A tool to bin plasmid-predicted contigs based on sequence composition, coverage and assembly graph information.
  • RFPlasmid: Predicting plasmid contigs from assemblies.
  • ResCap: Repository for software, raw data tables and data bases.
  • PATO: A R package designed to analyze pangenomes (set of genomes) intra or inter species.
  • MetaTOR: Metagenomic Tridimensional Organisation-based Reassembly – A set of scripts that streamlines the processing and binning of metagenomic metaHiC datasets.

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The rates and routes of transmission of multidrug resistant Klebsiella clones and genes into the clinic from environmental sources (SpARK)

The rise of antimicrobial resistance is a pressing public health crisis on a global scale, but the use of antibiotics in humans only represents a small part of the problem.

Completed project

Effective management strategies need to incorporate antibiotics in agriculture, as well as the release of these drugs, and resistant bacteria, into the environment. This project conforms to this “One-Health” framework by discovering how frequently antibiotic resistant bacteria move between humans, animals and different settings in the environment such as river water and soil.

The project focusses on a group of bacterial species called Klebsiella which are common in the environment and in animals, but also cause infections in humans and livestock that are resistant to antibiotics. One species in particular, Klebsiella pneumoniae, is a very common cause of resistant infections in hospitals and is recognised by the WHO as critically high priority. Northern Italy is a ‘hotspot’ for these infections, but it is not clear whether these bacteria are confined to hospitals, or are also present elsewhere.

To address this, we took 3500 Klebsiella strains from hospital patients, wild and domesticated animals and multiple environmental sources. Importantly, all the strains were taken from a single city, Pavia, in Lombardy. By sequencing the genomes of these bacteria, combined with mathematical modelling, we could tell which resistant genes were present, and how the strains were moving. We found that resistant genes are strains were uncommon outside of hospitals, and that the vast majority (around 75%) of Klebsiella in humans comes from other humans. However, we did find some risk of transmission from companion animals (dogs and cats) and water sources.

Project partners

  • Edward Feil, University of Bath, United Kingdom (Coordinator)
  • Piero Marone, Fondazione IRCCS Policlinico San Matteo, Italy
  • Sylvain Brisse, Pasteur Institute, France
  • Louise Matthews, University of Glasgow, United Kingdom
  • Jukka Corander, University of Oslo, Norway
  • David Aanensen, Big Data Institute, Oxford, United Kingdom
  • Alan McNally, University of Birmingham, United Kingdom

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Escherichia coli ST131: a model for high-risk transmission dynamics of antimicrobial resistance (ST131TS)

This project has connected many transnational academic resources to investigate the transmission success of the Escherichia coli ST131 clone. E. coli is the most common cause of urinary tract and bloodstream infections worldwide. Resistance to widely used antibiotics for the treating E. coli infections is common and widespread.

Completed project

A single E. coli clone, ST131, is mainly responsible for this global AMR pandemic causing millions of antibiotic-resistant infections annually. It remains unclear which features of ST131 had resulted in the biggest antimicrobial resistance succes of the 2000s.

The ST131TS project created a combined European-Canadian consortium that investigated the transmission dynamics of ST131. The study explored transmission of resistance and virulence genes and how they contributed to the success of ST131. The project also investigated transmission of ST131 among humans, animals and different environments.

The project has showed that ST131 is a public health concern in Canada and Europe and has provided information to better understand the spread and managing infections due to multidrug resistant E. coli. Only by understanding how antibiotic resistance evolves and spreads in bacterial populations, can we begin to overcome such resistance.

ST131 adapts rapidly to environmental changes; we need to know why and how. This project will serve as a model to predict what can possibly happen in the future with the continuing emergence of multidrug resistant clones among bacteria.

ST131TS project logo

Project partners

  • Johan Pitout,University of Calgary, Canada (Coordinator)
  • Neil Woodford, ARHI-UK, United Kingdom
  • Fernando Baquero, Ramón y Cajal Institute for Health Research (IRYCIS), Spain
  • Marie-Hélène Nicolas-Chanoine, Beaujon Hospital/ Paris VII University, France
  • Laurent Poirel, University of Fribourg, Switzerland
  • Alvaro Pascual, Fundación Púbica para la Gestión de la Investigación de Salud en Sevilla, Spain
  • Jean-Yves Madec, National Agency for Food, Environmental and Occupational Health & Safety (ANSES), France
  • Tarah Lynch, University of Calgary, Canada

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Predicting the Persistence of Resistance Across Environments (PREPARE)

Antimicrobial resistance poses a serious challenge to health care worldwide. One common approach to tackling resistance is to stop using a particular antimicrobial for a period of months or years, in the hope that resistance will decrease.

Completed project

However, such attempts to control resistance by stopping antimicrobial use have met with mixed success. Failures of a critical assumption underlying such strategies – that resistant strains suffer a disadvantage in the absence of drug (the “cost of resistance”) – may be responsible for difficulties in controlling resistance by cessation of drug use.

The PREPARE consortium was convened to develop an experimental and theoretical framework for understanding, and ultimately predicting, the conditions under which resistance will persist. Specifically, we set out to address the roles of host genetic background and environment in determining the costs of resistance. That is, we asked whether there are particular environments, or particular bacterial strains, in which we would expect to see resistance persist.

We found that there are indeed strains, environments, and combinations thereof, where resistance confers no cost. This suggests that resistance could persist in some real-world settings, even when antimicrobial usage has been stopped or paused. Unfortunately, we found that it is very difficult to predict which environments or strains might act as reservoirs for resistance. Novel mathematical models do show promise in increasing our ability to predict persistence. The ability to make such predictions will assist policy-makers in formulating strategies for controlling the spread of resistance.

Project partners

  • Alex Wong, Carleton University, Canada (Coordinator)
  • Claudia Bank, Instituto Gulbenkian de Ciência, Portugal
  • Thomas Bataillon, University of Aarhus, Denmark
  • Isabel Gordo, Instituto Gulbenkian de Ciência, Portugal
  • Rees Kassen, University of Ottawa, Canada

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The impact of Host restriction of Escherichia coli on Transmission dynamics and spread of antimicrobial Resistance (HECTOR)

Bacteria are increasingly resistant to antibiotics, threatening treatment of bacterial infections. Antibiotic resistance (ABR) is encoded in the DNA of the bacteria. ABR is spreading rapidly in human and animal populations because resistant bacteria are transmitted or because bacteria can transfer DNA encoding ABR to other bacteria which then also become resistant.

Completed project

Escherichia coli (E. coli) resistant to specific antibiotics are considered a high priority risk. Transfer of such E. coli between animals, such as livestock, and humans may contribute to the spread of ABR.

The HECTOR project set out to understand if certain E. coli are adapted to certain host species (human or animal) and how this adaptation is encoded by the DNA. Through genome comparison of 1198 E. coli strains, we found which E. coli strains are associated with human host, and which parts of their DNA aid in this adaptation.

We discovered that the DNA encodes metabolic activities allowing E. coli to potentially survive better in the human gut.
In addition, we studied survival and ABR transfer of E. coli adapted to different host species, in live pigs and calves, and in laboratory experiments imitating the chicken gut. We identified E. coli strains which are better able to survive in these models than other strains. However, our findings highlight the complexity of host adaptation, as we could not identify E. coli types surviving and growing well in either model. Furthermore, we observed that transfer of DNA encoding ABR is rare in such experimental conditions.

The research of HECTOR has advanced our understanding of why some bacteria are able to spread between animal and human populations, thus contributing to the spread of ABR, and why others cannot. This can be helpful for risk assessment.

Project partners

  • Constance Schultsz, University of Amsterdam, Netherlands (Coordinator)
  • Christian Menge, Friedrich-Loeffler-Institut, Germany
  • Torsten Semmler, Robert Koch Institute, Germany
  • Roberto Marcello La Regione, University of Surrey, United Kingdom
  • Lucas Domínguez Rodríguez, Universidad Complutense de Madrid, Spain
  • Stefan Schwarz, Freie Universität Berlin, Germany
  • Ngo Thi Hoa, University of Oxford, United Kingdom

Project resources

Tools

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Training on antibiotic usage and resistance, Go Cong Tay District, Tien Giang, Vietnam.

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Prevention and Restriction of Antimicrobial Resistance in Pneumococci by Multi-Level Modelling (Restrict-Pneumo-AMR)

Microorganisms live in most parts of our body, including the inside of our nose. Most of the microbes are harmless and can even be beneficial to our health. However, some microbes can cause diseases – although they often go unnoticed, as our immune system can remove them before we show any symptoms.

Completed project

For example, the bacterium Streptococcus pneumoniae can cause diseases such as pneumonia and meningitis, but generally, it lives harmlessly in the nose, and is particularly common in children and the elderly. The longer the bacteria live in the nose before being killed by the immune system, the more likely they are to be transmitted to another person. The amount of time it takes for the immune system to clear the bacteria depends on various factors, such as the age of the person or the bacterium’s defense mechanism and its genetic material. A particularly important aspect is to what subtype, also known as serotype, a bacterium belongs to, which is characterized by differences in the structure of the sugar coating that surrounds the microbe. However, until now, it was not known how much each of these factors contributes.

This project provides new information for understanding the processes of evolution within the host and the mechanisms by which antibiotic treatment can influence the selection for antibiotic resistance.

Project partners

  • Stephen Bentley, The Wellcome Trust Sanger Institute, United Kingdom (Coordinator)
  • Nahuel Fittipaldi, Public Health Ontario Laboratories, Canada
  • James Kellner, University of Calgary, Canada
  • Bernd Schmeck, Philipps-University Marburg, Germany
  • Paul Turner, University of Oxford, United Kingdom
  • Tom van der Poll, Academic Medical Center University of Amsterdam, Netherlands
  • Nicolas Croucher, Imperial College London, United Kingdom

Project resources

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The Global Pneumococcal Sequencing (GPS) project: How can whole-genome sequencing be used to make vaccines more effective?

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Using collateral sensitivity to reverse the selection and transmission of antibiotic resistance (COLLATERALDAMAGE)

Urgent action is required to stem the apocalyptic spread of antimicrobial resistance (AMR). However, because the pace of novel drug development lags behind the evolution of novel AMR determinants, new strategies of containment are required.

Completed project

In this multinational proposal we develop a resistance-reversal strategy based on the concept of collateral sensitivity (CS). CS between a pair of antibiotics occurs when resistance to one antibiotic potentiates susceptibility to another. Thus, by exploiting CS relationships through sequential drug application, resistant strains can be specifically targeted which will reduce their frequencies in the community and arrest their transmission.

Our broad aim in this proposal is to realize the unique promise of CS-informed therapies. To do so, our work packages (WP) integrate theoretical biology, evolutionary and molecular microbiology, and in vivo modeling with a specific focus on arresting the transmission of resistant E. coli and S. pneumoniae.

The expected outcomes of the proposal are to provide pre-clinical recommendations for therapy to reduce the emergence and transmission of these two globally important bacterial pathogens and to provide a framework to develop CS-based strategies for other bacterial threats.

UiT, The Arctic University of Norway, coordinates the project and run two WPs in this JPI-EC-AMR project. One WP includes experimental work on E. coli where we test if general patterns of CS can be identified in clinical E. coli strains and how horizontal gene transfer affects these networks. The other WP aims to develop a modelling framework that furthers our understanding of sequential therapy within patients in the context of CS that is scalable to investigate transmission across patient populations.

Project partners

  • Pål Jarle Johnsen, The Arctic University of Norway, Norway (Coordinator)
  • Daniel Rozen, Leiden University, Netherlands
  • Pia Abel zur Wiesch, The Arctic University of Norway, Norway
  • Dan Andersson, Uppsala University, Sweden
  • Niels Frimodt-Møller, Rigshospitalet, Denmark

Project resources

Microbiology Research Group, The Arctic University of Norway, lead by project coordinator Pål Jarle Johnsen

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Partnership against Biofilm-associated Expression, Acquisition and Transmission of AMR (BEAT-AMR)

Reducing the risk of infection associated with medical devices and surfaces in the healthcare setting has huge public health significance.

Completed project

This risk is compounded by the emergence and persistence of multi-antibiotic resistant bacteria which is considered as one of the greatest global threats to human health. Such resistance threatens the treatment of even simple infections. However, very little is known about how bacteria develop resistance on medical surfaces within which sometimes antimicrobials have been incorporated. The key mysteries are how bacteria evolve and respond dynamically to antimicrobials on such surfaces.

We developed a publicly available, experimental workflow that allows to reproducibly grow biofilms and study their underlying resistance mechanisms. Our findings show that the combination of antimicrobials used within surfaces and antibiotics supplied systemically can have an important impact on selecting for resistance. Further, we identified new mechanisms that bacteria use to dynamically adapt to antibiotics when these bacteria grow on surfaces. One such mechanism is associated to the molecular machine that allows bacteria to swim (i.e. the flagellum). These novel antibiotic resistance mechanisms associated to surface growth and the combination effects of antimicrobial surfaces together with systemically applied antibiotics should be taken into consideration when evaluating new antimicrobial surfaces used in the healthcare setting and in medical devices.

Project partners

  • Frank Schreiber, BAM-Federal Institute for Materials Research and Testing, Germany (Coordinator)
  • Qun Zulian Ren, Empa. Materials Science  and Technology, Switzerland
  • Henny C van der Mei, University Medical Center  Groningen, Netherlands
  • Saul Faust, University Hospital Southampton, United Kingdom
  • Matthias Buhmann, Empa. Materials Science  and Technology, Switzerland
  • Henk J.  Busscher, University Medical Center  Groningen, Netherlands
  • Jeremy Webb, University of Southampton, United Kingdom

Project resources

BEAT-AMR project website

Publications

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Bridging the gap between exposure to AMR in the environment and impact to human health

Exposure to antibiotic resistant bacteria in the environment (water, soil, air) will impact human health involving complex interactions between bacteria and humans. Our network of experts, and advisors, will explore and summarize available tools and study protocols to systematically quantify environmental exposures to antibiotic resistant bacteria.

Completed project 

Guidance will be given to standardise surveillance protocols and exposure assessments in order to increase current quantitative knowledge across borders. Detection methods and modelling approaches will be outlined on how to link exposure data and epidemiological data to health impacts from antibiotic resistant bacteria. This involves quantitative exposure assessments from environmental emissions, as well as model development for carriage, excretion, colonization, horizontal gene transfer and dose-response. This will provide guidance to funding agencies and researchers on how to integrate exposure assessments and human health impact assessment into surveillance programs, funding schemes and research proposals/ projects.

Environmental transmission routes will be prioritised for future human health impact assessment studies. White papers to define a toolbox of existing approaches, best practices for study setups, and to identify research gaps will be produced by the two working groups responsible for developing guidelines and protocols for exposure assessments and human health impact assessment, respectively

Network partners

  • Ana Maria de Roda Husman, National Institute for Public Health and the Environment (RIVM), Netherlands (Coordinator)

This network includes 15 partners, please click on the following link to see complete network composition: Network composition Bridging the gap between exposure to AMR in the environment and impact to human health

Antimicrobial resistance threatens prevention and treatment of an increasing range of infections. Circulation of antibiotic resistant bacteria (ARB) in the environment (water, soil, air) may significantly contribute to human exposure. However, information on exposure to ARB from environmental sources is scarce, and little is known about the complex relationships between environmental exposure to ARB and its health impact.

With the working group set up in this project, available tools and study protocols to systematically study environmental exposures to ARB and to evaluate the associated health impact have been explored and summarized. Approaches on how to link exposure data and epidemiological data to health impacts from ARB have been described. These include quantitative exposure assessment from environmental emissions, as well as model development for carriage, excretion, colonization, horizontal gene transfer and dose-response, also including epidemiological studies. The results can serve as guidance to funding agencies and researchers on how to integrate EA and human health impact assessment (HHIA) into surveillance programs, funding schemes and research proposals/ projects.

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