An integrated approach to understand the emergence and spread of extensively resistant Gram-negative bacteria in China

Since the discovery of penicillin in 1928 more than 100 antimicrobial agents have been identified and used to treat bacterial infections. This led to the near-eradication of some infectious diseases such as tuberculosis in the developed world. This advance in scientific discovery comes with a caveat, as microbes have acquired the ability to resist the toxic effects of these antimicrobial agents.

The majority of bacteria that constitute antimicrobial threats are facultative, opportunistic pathogens which are found in great numbers in the environment and readily exchange genes with a variety of other microbes. Such elements include virulence factors, which allow them to infect animals and elude the host's immune system, and antimicrobial resistance genes that render them resistant to drugs. Over recent years, the biggest emerging antimicrobial resistance threat is represented by Gram-negative bacteria, which are increasingly breaching the last-resort drugs.

With the advent of genome sequencing, we have learned a lot about the genes which make bacteria pathogenic and the ones that allow them to become resistant to drugs. However, we currently do not have the required computational tools to identify the routes through which "mobile elements" move between lineages of bacteria, or even quantify the extent of these exchanges. This in turn greatly limits our ability to block such transfer of resistance elements.

We have assembled a multidisciplinary team to address three integrated issues. First, we will generate an extensive database of complete genomes of unprecedented quality for three major antimicrobial threats, Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. This will represent the first such high-quality microbial genomic database ever and will constitute a precious resource for the development of future diagnostic and prognostic tools.

In a second step we will develop new computational tools to reconstruct the acquisition and spread of resistance in lineages of these three species in China. These tools will be flexible enough to be applied to genetic sequence data of any microbe and will allow us to reconstruct emergence and sread of resistance in these three species.

Finally, we will perform functional validation in the lab to corroborate the findings from the bioinformatics and computational analyses. This work will also allow establishing the complex link between the genetic makeup of different lineages and their level of resistance to the three most important last-resort drugs carbapenem, tigecycline and colistin.

The significance of this study lies in the multipronged approach to describe and characterise antimicrobial resistance in the most threatening Gram-negative bacteria in China. This effort will culminate in the identification of the key genetic and environmental factors that facilitate the proliferation and transmission of multi drug resistant pathogens. Such information should in turn lead to essential information on how to optimise antimicrobial stewardship both to the benefit of the patients and to stem the spread of resistance in the future.

Combatting antimicrobial resistance is a global challenge. In China, this manifests in the rapidly rising rates of resistance in the major nosocomial pathogens such as E.coli, Klebsiella and Acinetobacter spp. Current epidemiological studies suggest that pan-drug resistant strains already exist and will thwart any currently available antibiotic. In this proposal, we outline strategies to undertake the generation of the first comprehensive genomic database of clinical isolates of the three major pathogens. This will facilitate our next approach which focusses on the development of novel computational tools to reconstruct the acquisition and spread of AMR elements throughout the different gram-negative pathogens. This data will be biologically validated using both Chinese clinical isolates and a K.pneumoniae model system to identify the genetic factors and drivers required for resistance development and plasmid acquisition and maintenance. Our multidisciplinary approach (computational to biological) will allow us to construct an integrated model for resistance acquisition to last-line agents and the proliferation of epidemic clonal lineages. This will represent the first such high-quality microbial genomic database ever and will constitute a precious resource for the development of future diagnostic and prognostic tools in China where the rapid detection and stratification of antibiotic therapy is paramount to meet the increasing demands on its healthcare system.

We anticipate that the research outcomes from this project will have impacts on academic researchers, governmental researchers, stakeholders, industry and the general public.

Academia

User-friendly software addressing untapped needs can have a tremendous impact on an entire field of research. Both Didelot and Balloux have a good past track record at developing software for the analysis of genomic data that is highly cited and used by many colleagues. We anticipate that the suite of programs that will be developed during this project will prove equally, if not more, popular.

We will assemble three genomic datasets of exceptional quality. This data will be of interest to many of our colleagues for re-analyses or integration in comparative genomic studies. The data should prove of particular interest as all the strains will be carefully phenotyped for AMR and sequenced using PacBio long-read technology, thus producing high quality assemblies, which are still a rarity in microbial genomics.

We hope that the interdisciplinary nature of our collaboration between experimental microbiologists, evolutionary microbiologists and computational biologists will cross-fertilise the different fields with new ideas. More specifically, we anticipate the collaboration to create durable scientific links between Chinese and UK Academia. The UK-strength is based on the development of the bioinformatics pipeline and lab-models to study the transmission and dissemination of resistance which provides the infrastructure to create further avenues for capacity building and research. Our collaboration will also help foster academic training and exchange programs.

Chinese government
Antibiotic resistance is a strategic research priority globally. This is particularly relevant in China where there are incentives to use antibiotics clinically. This is also compounded by unregulated antibiotic use in the veterinary context. The continued march of this will impact on the Chinese economy as has been predicted by the O'Neill review. As such, our proposal fits in with the UK ODA commitment to aid and foster economic and welfare development in China.
Professor Wang is ideally placed to inform and influence public health policy in China thanks to her extensive network and contacts. She has organized several continuous nationwide surveillance networks (CMSS, GPRS and CARES) since 2000 in China. She is Head of Subcommittee of Clinical Microbiology, Society of Microbiology and Immunology, Chinese Medical Association and Executive Committee member of Asian Network for Surveillance of Resistance Pathogens.

Industry

We foresee several strands of this research might be of interest to industry. Possible translational applications should be facilitated by the established links with industry of the UK investigators. Balloux, Didelot and Weinert are involved in a collaboration to unravel the dynamic of the accessory genome of Pseudomonas aeruginosa with BioMérieux, the World leader in clinical microbiology. Weinert has existing links with Zoetis, the largest global animal health company and the United States Department of Agriculture (USDA) and is a co-inventor of a PCR pathotype marker undergoing licencing. Finally, Schneiders has links with Pfizer, Tetraphase and Actelion Pharmaceuticals to explore the role of the intrinsic microbial response to antibiotic challenge and in the development of relevant lab mutants for drug screening

General public

The research and ensuing results should be of considerable interest to the general public. Antimicrobial resistance is increasingly recognised as one of the major challenges to public health, even if the potential impact on human health and food security is generally not fully appreciated. The investigators involved in the project have an excellent previous track record of press attention and will devote considerable time and energy on education and public outreach.