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

This project will connect a large number of 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. A recent WHO report states that resistance to one of the most widely used antibiotic classes (fluoroquinolones [FQs]) is very widespread. In many parts of the world, FQs are now ineffective in more than half of patients. A single E. coli clone, ST131, is predominantly responsible for this global FQ-R and cephalosporin-R 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. We propose a combined European-Canadian consortium that will investigate the transmission dynamics of ST131. This study will explore the vertical and horizontal transmission of resistance and virulence genes and how they contributed to the transmission success of ST131 among humans, animals and different environments. The broad goal is to improve human health by better understanding managing infections due to multidrug resistant E. coli. The study will explore explanations for the high transmission rates and success of ST131. A famous quote from Stephen Hawking; "Intelligence is the ability to adapt to change". ST131 adapted 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.

Objective 1: Determine the role of MGEs, genomic adaptions and fitness in the transmission success of ST131 clade C. The central hypothesis of objective 1 is that genomic islands containing certain VFs, plasmids with blaCTX-M-15 and transposons (i.e. ISEcp1) have been acquired by clade C in a specific and sequential fashion resulting in enhanced fitness and colonization that gave the subclades C1 and C2 the ability to outcompete other antimicrobial resistant clones. Hence, Objective 1 will serve as a model to predict how successful multidrug resistant clones can rapidly expand among bacteria. It might provide essential information for predicting the next clonal wave of multidrug-resistant ExPEC. Objective 1 will use NGS, fitness, adherence and invasiveness studies to identify the contributions of accessory genomes, GIs, recombination events, MGEs (plasmids and transposons) towards the evolutionary success of clade C.

The UK team will undertake a longitudinal analysis of the changes and evolution of the core and accessory genomes using WGS data from collections accrued over 15 years, and data from international partners in this consortium. Key changes in the bacterial core genome and the plasmid sequences will be explored to understand host-plasmid adaptations. The UK team will investigate the effect of genetic shifts, fitness and the role of host-plasmid adaptations to the success of ST131 clade C via detailed growth analysis (via BioLog) and basic infection models Galleria mellonella, by measuring larval survival, the degree of host melanisation (oxidative stress) response and cellular damage (lactate dehydrogenase release). Co-inoculation of strains and re-isolation of bacteria from larvae will allow fitness cost to be assessed between isolates with differing resistance mechanisms or other specific genetic traits. The UK team will also compare the distributions of such changes in ST131 isolates recovered from non-human sources.

The WHO cite drug resistance as a major challenge to global health and an UK review on global antimicrobial resistance (AMR) have led to the UK Prime Minister to project halving the number of drug-resistant BSIs acquired by patients in hospitals by 2020, reducing the need for antibiotics (www.amr-review.org). There is an enormous global public health burden due to MDR E. coli ST131 clade C and effective interventions against it would make major impact towards this goal. Yet there is currently a lack of understanding by the medical community on what specific features of this clone created such a successful pathogen in a relatively short time period. It is unclear which features resulted in the global clinical dominance of ST131 clade C. A recent US study showed that clade C targets compromised hosts and cause persistent infections associated with prolonged adverse outcomes.

Molecular evidence suggested that certain virulence factors, AMR determinants, increased transmission and fitness might be important. Mobile genetic elements [MGE] such as plasmids and conjugative transposons likely played a role in the diversification (clonalization) and success of ST131; however the exact mechanisms by which these factors contributed to the global dominance of ST131 remain elusive. The roles of MGEs on replicative and transmission fitness, adherence and compensatory mutations assuring a balanced lifestyle for the new high-risk clone have yet to be studied in detail. Moreover, the transmission modes of ST131 in the community and long term care settings are unknown. Finally, the role of the colonization, exploitation, and multiplication of human-surrounding reservoirs (i.e. animals, food, and environment) in the transmission of ST131 is uncertain. The detailed characterization of clade C provides unique opportunities to clarify the processes leading to high-risk transmission of antimicrobial resistance and virulence in emerging MDR clones. This can be accomplished by examining on a global scale the transmission dynamics of ST131 clonal variants, plasmids, transposons, resistance, virulence genes and determine their contributions to the success of this successful clone.

This project will explore the roles of these factors in the success of ST131. The global spread of AMR was recently identified by the WHO as one of the three greatest threats to human health. The short term goals are to recreate the evolutionary history of the ST131 clade C and determine the roles of MGEs and compensatory mutations in the fitness and clinical dominance of one of the most important gram negative clones that had emerged in the 21st century. We will study the vertical and horizontal transmission and maintenance of MGEs and VFs among E. coli ST131. We will also investigate the conditions for transmission among humans, animals, environments, and particularly how effective transmission among these hosts-environments and the colonization of novel niches acts as a condition for diversification (clonalization) and acquiring AMR determinants in ST131. The emphasis of this project will be using NGS technology for studying transmission aspects of the most successful clone of the 2000's.

This project will serve as a model to predict what can possibly happen in the future with successful MDR clones expanding among bacteria. It might provide essential information for predicting the next clonal wave of multidrug-resistant ExPEC. Without a better mechanistic understanding of the unique adaptations of this important clade, the medical community is unlikely to stop its continuing spread or to anticipate the next clonal wave of MDR ExPEC. The broad goal of this project is to improve human health by better managing extra-intestinal infections due to MDR E. coli. Its short-term objective is to determine explanations for the epidemic success of clade C and to use this information for predicting the next clonal wave of multidrug-resistant ExPEC.