ANTIRESDEV - The effects of antibiotic administration on the emergence and persistence of antibiotic-resistant bacteria in humans and on the composition of the indigenous microbiotas at various body sites

EC contribution: : € 5,368,088
Duration: : 36 months
Starting date: : 01/11/2009
Funding scheme: : Focused research project
Keywords: : antibiotic resistance, genetic determinants, microarrays, fitness cost, ecology, resistome, pyrosequencing, indigenous microbiota, metagenomics
Contract/Grant agreement number :: : 241446
Project web-site: : http://www.ucl.ac.uk/antiresdev

Summary:

The objective of the HEALTH-2009-2.3.1-2 call is to study the impact of different antibiotics on the prevalence of resistant bacteria in the human host. In ANTIRESDEV this objective will be achieved as follows. We will use culture-based and culture-independent approaches to investigate the impact of four different types of antibiotics (with different modes of action, antimicrobial spectra and pharmacokinetic properties) on the emergence of antibiotic-resistant organisms and their persistence at several body sites. Disruption of the indigenous microbiota is recognized as an important factor in the persistence and transmission of antibiotic-resistant organisms, therefore we will also study the ecological impact of the antibiotics on the indigenous microbiotas of several body sites using culture-dependent and -independent techniques. We will then identify, using state-of-the-art microarrays, the genes responsible for resistance in the antibiotic-resistant organisms isolated. The genetic elements involved in resistance transfer by a number of these organisms will also be determined as knowledge of these elements is essential to fully understand the mechanisms underlying resistance transmission. We will use state-of-the-art 454 pyrosequencing to determine the full complement of resistance genes (the “resistome”) present in cultivable and not-yet-cultivated members of the oral and faecal microbiotas and the effect on these resistomes of antibiotic administration. Another important aspect of the dynamics and transmission of resistance is the fitness cost associated with resistance acquisition by an organism and we will investigate this in a number of clinically-important organisms. We will ensure that the results of this study are made available to appropriate governmental and healthcare agencies so that they can be used to help in the formulation of measures designed to reduce the spread of antibiotic resistance.

Figure 1. Colonies of methicillin-resistant Staphylococcus aureus

Figure 2. Colonies of Clostridium difficile

Figure 3. Segment of the sequence of a gene encoding antibiotic resistance

Figure 4. Graph showing the proportions of a group of 105 adults
who harbour various tetracycline resistance genes in their oral cavity

Figure 5. Schematic representative of three antibiotic resistance-encoding mobile
genetic elements (conjugative transposons). These elements demonstrate
the mosaic architecture of mobile genetic elements and shows that the elements
are capable of acquiring, exchanging or replacing genes throughout their length.

Problem:

Antibiotic resistance is recognised as being one of the major medical problems facing humankind and measures to prevent, or contain, the increase in antibiotic-resistant organisms requires knowledge of both the genesis of antibiotic resistance genes and their dissemination. The problem of antibiotic resistance affects almost every bacterial species for which treatment with antibiotics is available. Examples include organisms responsible for pneumonia, ear infections, and meningitis (e.g., Streptococcus pneumoniae), skin, bone, lung, and bloodstream infections (e.g., Staphylococcus aureus), urinary tract infections (e.g., Escherichia coli), foodborne infections (e.g., Salmonella), and infections transmitted in hospitals (e.g., enterococci and Klebsiella). Furthermore, in recent years, resistance to several antibiotic classes has developed in some species, resulting in the occurrence of multidrug-resistant bacterial strains, also known as 'superbugs'. Pan-resistant Pseudomonas aeruginosa and Acinetobacter strains have been described and vancomycin resistance has emerged in Staphylococcus aureus and enterococci. The occurrence of superbugs is associated with treatment failures, higher morbidity and mortality, and increased cost. Consequently, the therapeutic options for some infections are limited, especially in developing countries, where second- and third-line antibiotics are unavailable or unaffordable. In Europe, it has long been recognized that antibiotic resistance is a multifaceted threat to the health of the European population. Although this ongoing pandemic varies dramatically in different European countries (due, largely, to different patterns of antibiotic usage and infection control strategies), nevertheless all European countries are seeing a steady decrease in antibiotic effectiveness. This trend is likely to become more pronounced because of increasing antimicrobial use in emerging market communities, travel and migration.

Aim:

ANTIRESDEV will use a multidisciplinary approach to study the impact of different antibiotics in selecting resistance among pathogenic and commensal members of the indigenous microbiota of humans. The main aims of the project are:

to identify and quantify those cultivable antibiotic-resistant bacteria that emerge during the administration of four different antibiotics to healthy volunteers
to investigate, using 454 pyrosequencing, the full complement of resistance determinants (the resistome) in the cultivable and not-yet-cultivable microbiota and the effect on this of antibiotic administration
to ascertain the dynamics of resistance development and the persistence of antibiotic-resistant strains
to compare the pattern of antibiotic resistance development induced by different classes of antibiotics
to investigate, using traditional culture techniques and 454 pyrosequencing, the ecological impact of antibiotic administration on the cultivable and not-yet-cultivable indigenous microbiota
to characterise, using state-of-the-art microarrays, the antibiotic resistance determinants in the isolates obtained from the clinical studies
to determine the mobility of the resistance genes detected in the isolates obtained from the clinical studies
to ascertain the biological cost of antibiotic resistance in a number of clinically-important organisms isolated during the clinical studies
to disseminate the project findings to the clinical and scientific communities and to the general public and to ensure access to the ANTIRESDEV databases to enable future studies by other groups
to use the ANTIRESDEV findings to inform health care decision makers of some of the factors influencing the emergence and persistence of antibiotic-resistant bacteria following the administration of particular antibiotics and thereby provide opportunities for them to implement appropriate policies concerning antibiotic use

Expected results: :

knowledge of the dynamics of resistance emergence at a variety of body sites during the administration of a range of antibiotics frequently used in Europe
knowledge of the dynamics of the persistence of antibiotic-resistant organisms in humans at various body sites
information concerning the effects of antibiotic administration on the composition of the cultivable microbiota of the oral cavity, anterior nares, three skin sites and the colon
information derived from the use of state-of-the-art 454 pyrosequencing on the composition of the entire (cultivable plus not-yet-cultivated) microbial communities inhabiting the oral cavity and colon and the effect of antibiotic administration on these communities
information on the antibiotic concentrations at three body sites during and following the administration of different classes of antibiotics
identification, using state-of-the-art microarrays, of the resistance determinants in those antibiotic-resistant isolates that emerge during the administration of different classes of antibiotics
information on the emergence and persistence of resistance determinants following the administration of several different classes of antibiotics
knowledge of the nature, and persistence, of resistance determinants present in the indigenous microbiotas of a number of body sites in individuals who have not recently been administered antibiotics
development of improved microarrays for the identification of resistance determinants in Gram-negative and Gram-positive bacteria
information on the entire complement of resistance determinants (the resistome) in the oral and faecal microbiotas and the effect of antibiotic administration on these
determination of the molecular mechanisms underlying the spread of mobile genetic elements
development of a microarray for the identification of mobile genetic elements
information of the impact of different SCCmec elements and other resistance determinants on the fitness of S. aureus
information concerning how different resistances or resistance combinations affect the growth rate and virulence characteristics of staphylococci
information on how changing antibiotic regimes affect the resistance profiles, pathogenesis and dissemination of S. aureus clonal lineages
information concerning how different resistances, or resistance combinations, affect the growth rate of enterococci and various Gram-negative species
information concerning how the acquisition of transferable resistance elements affects the ability of selected clinically-important organisms to colonise, and survive in, the gastrointestinal tract in vivo.

Potential applications:

Although antibiotic resistance is a global issue, the exact nature of the problem shows geographical variation. Hence, the particular problems facing Europe differ from those in other geographical regions. The results obtained during the ANTIRESDEV project will enable governments and healthcare providers to formulate strategies to combat the growing threat posed by antibiotic-resistant bacteria in Europe. The new microarrays developed during the project will be very useful in diagnostic laboratories to rapidly determine which antibiotics would be ineffective against a disease-causing organism in a particular individual. Additionally, they will be useful in surveillance studies of antibiotic resistance. The project results will enable a better understanding of the molecular mechanisms underlying the spread of mobile genetic elements and this will help in the development of means of preventing or reducing horizontal gene transfer and the dissemination of resistance.

Coordinator:

Michael Wilson
Division of Microbial Diseases,
UCL Eastman Dental Institute,
University College London,
256 Grays Inn Road,
London WC1X 8LD
UK
m.wilson@eastman.ucl.ac.uk

European Commission