MITIGATING GRAM-NEGATIVE INFECTIONS

Theme lead: Professor Nicole Stoesser (University of Oxford)

Theme co-lead: Dr Katie Hopkins (UKHSA) 

We aim to understand and mitigate infections caused by an important group of Gram-negative bacteria, the Enterobacterales, which can cause many different types of infection and contribute substantially to the burden of healthcare-associated and antimicrobial-resistant infections in the UK and globally.

To optimise detection, prevention and management strategies for Enterobacterales-associated infections, we aim to address the following key health protection needs of the public, the UK Health Security Agency (UKHSA) and NHS in this area by:

• Identifying cost-effective, innovative, 'genomics-first' approaches to enhancing surveillance and infection prevention and control (IPC), including identifying mobile genetic element(MGE)-associated antimicrobial resistance (AMR) transmission.
• Developing the evidence-base to underpin interventions to mitigate the risk posed by healthcare-associated Gram-negative infections by characterising relevant reservoirs in hospital populations and healthcare environments.
• Identifying and evaluating accurate, cheap, rapid diagnostics for Gram-negative/AMR-associated infections, and contributing to an improved understanding of the relationship between bacterial genotype/phenotype and patient outcomes.
• Optimising strategies for the deployment of new vaccines developed for Gram-negatives/AMR.

Our main research focus is Escherichia coli/Klebsiella spp., but our research framework will inform approaches to mitigating other priority Gram-negative-associated infections, such as those caused by Pseudomonas aeruginosa and Acinetobacter baumannii.

We are adopting a highly collaborative approach to our research with investigators across UK regions, including centres in Birmingham, Brighton/Chichester, Bristol, Cambridge, Leeds, London, Manchester, Newcastle and Oxford. 

Genomics-supported surveillance to mitigate E. coli/ Klebsiella and carbapenemase-producing Enterobacterales (CPE) infections

To inform public health requirements for a cost-effective, innovative, 'genomics-first' approach to enhance surveillance and IPC, including identifying MGE -associated AMR transmission, we will leverage our national hospital network to test genomics-supported surveillance of E. coli/Klebsiella bloodstream infections (BSIs) and rectal CPE colonisation, integrated with electronic health records. We will characterise the national genomic epidemiology of E. coli/Klebsiella BSIs, and particularly factors associated with increased infections by region and socioeconomic group, and risks of plasmid-/other MGE-mediated AMR, to inform intervention. We will implement a genomics pipeline in UKHSA and support federated sequencing efforts at healthcare sites to strengthen local IPC and enable centralised data upload to facilitate UKHSA-led health protection interventions. Our research will inform the design of optimal and standardised sampling frames for the implementation of routine, integrated, genomics-based surveillance for these pathogens (e.g. how many isolates need to be sequenced, how they should be selected, whether rolling or responsive surveillance is required). We will define epidemiological signatures of plasmid (and other MGE)/gene-based “outbreaks”, where horizontal spread of important AMR genes and plasmids are highly likely. With participating sites and colleagues within UKHSA we will evaluate the acceptability and usefulness of genomics-based surveillance in network sites for e.g. IPC purposes, and the cost-effectiveness of this over mandatory surveillance. As a stretch objective we will explore AMR genes/MGE transmission amongst E. coli/Klebsiella spp./non-typhoidal Salmonella/Shigella spp. across One Health reservoirs. 

Evaluate rapid diagnostics for Enterobacterales infections/AMR

Accurate, cheap, rapid diagnostics for Gram-negative/AMR-associated infections, and an improved understanding of the relationship between bacterial resistance genotype/phenotype and patient outcomes are key health protection research priorities. We will scope out the rapid diagnostic testing landscape for key Enterobacterales pathogens causing invasive infection and major, clinically relevant, AMR phenotypes. We will expand on a national collection of reference isolates for testing to reflect the increasing biological variation underpinning phenotypic resistance. Given the growth in genomics approaches, we will develop in silico and real-life sequencing datasets that can be used to evaluate AMR gene reference databases and bioinformatic algorithms for AMR gene detection. Building on our successful Oxford-UKHSA partnership evaluating rapid SARS-CoV-2 tests by developing Target Product Profile-equivalents to define test use-case and standardise performance evaluations, we will collaborate with UKHSA diagnostic laboratories and other centres to design optimal, efficient evaluations of rapid Enterobacterales/AMR tests across specimen types, including for innovative tests developed by UKHSA-/academic-/industry partners. 

Characterise genotypic impacts on AMR, bacterial growth and clinical outcome

Defining the relationships between bacterial genotype, bacterial phenotypic features that are likely relevant to infection (including fitness, virulence and resistance), and patient outcomes will support several public health missions, including diagnostics, surveillance of the most high-risk lineages associated with antimicrobial resistance and infection, the identification of novel AMR mechanisms, and targeted interventions focused on strains that are likely to cause the most severe/persistent disease. Current AMR catalogues (e.g. AMRFinderPlus/ResFinder) do not integrate genotypic markers of expression and/or define drug-level susceptibility, requiring development to guide clinical decision-making. Focusing on E. coli in the first instance, and expanding to Klebsiella spp., we will exploit large-scale genomic and detailed susceptibility/growth data to quantify genotype/phenotype associations for >30 antibiotics, including novel drugs not yet widely deployed, and use functional genomics to characterise novel resistance genotypes. We will also evaluate relationships between genotype, resistance, growth and clinical outcomes.

Wastewater-based approaches to surveillance and interventions to mitigate risk from healthcare environmental reservoirs

Wastewater and sink-traps may represent both an effective surveillance tool for hospital-level infection and emergence of high-risk AMR-associated Enterobacterales lineages, and a source of Enterobacterales healthcare-associated infection (HAI) in patients. By surveying longitudinal hospital wastewater and sink-trap sites, we will assess the use of wastewater as an effective approach to surveillance of these infections, starting with detailed study across multiple wards in a single UK hospital. Using simulated data we will investigate optimal methods for wastewater metagenomics to identify novel threats (including novel pathogens, high-risk lineages, and novel AMR genes). To evaluate the impact of cleaning interventions on the risk posed by sink/wastewater-related reservoirs to HAI and AMR, we will undertake a qualitative study of hospital cleaners, the IPC Team and the Estates Department at a single hospital. We will develop a novel, non-chemical approach to decontaminating sink drains, and test the efficacy of this intervention in an experimental sink lab setting, and if efficacious, consider it as part of an interventional study designed to evaluate sink cleaning interventions. Our interventional study will be designed as a crossover study across multiple wards, evaluating the impact of each cleaning method on sink basin Enterobacterales contamination. We will also evaluate simple and cheap methods to detect environmental contamination with high-risk bacteria and important selection pressures for AMR (such as antibiotic dipsticks) in sink-trap reservoirs. As part of exploratory analyses considering what constitutes a “healthier” hospital microbiome, we will evaluate phage and bacterial defence system profiles in hospital sink metagenomes to identify any microbial signatures associated with lower pathogen and AMR burdens. 

informing vaccine development and strategy for Enterobacterales infections/AMR

Vaccines are a major cornerstone in the prevention of infection and recognised as an important strategy to mitigate AMR by jointly preventing infections and limiting antimicrobial use. There is an urgent need for effective vaccines against major Enterobacterales pathogens, including for extraintestinal pathogenic E. coli (ExPEC) and Klebsiella. We will summarise the vaccine target landscape for these species using large-scale whole genome sequencing (WGS) and metagenomic datasets to define hypothetical vaccine coverage of infection-associated isolates and the diversity and vaccine coverage of strains found colonising the human gut. For relevant targets identified, we will also define clinical outcomes associated with these targets and anticipated vaccine coverage. We will model the impact of vaccination on ExPEC/Klebsiella infections and AMR with varying vaccine roll-out, efficacy, population replacement, importation (e.g. global/zoonotic) and horizontal transfer of important AMR genes (e.g. ESBLs, carbapenemases).