Informing shigellosis treatment and management in resource-poor settings through pathogen genomics

Lead Research Organisation: University of Liverpool
Department Name: Institute of Integrative Biology


Shigella are the leading bacterial cause of diarrhoeal disease in children under 5 years old in low- to middle-income nations and kill approximately 100,000 people per year. Despite this large disease burden, treatment and prevention options for shigellosis are limited, with no licenced vaccine available and increasing antimicrobial resistance in Shigella. High-resolution portraits of the evolution and epidemiology of Shigella can be achieved by sequencing and comparing entire genomes of collections of Shigella isolates (a process called Whole Genome Sequence Analysis, WGSA), which then allow us to design the most effective treatment and management options for shigellosis. For example, WGSA recently showed a specific subtype of Shigella circulating in the United Kingdom became epidemic after it acquired a new antimicrobial resistance type, so treatment recommendations were updated. Despite the increased insight afforded through WGSA however, no one has yet applied WGSA to a representative set of Shigella genomes from those populations most affected (i.e. children under 5 in low- to middle- income nations), which is necessary for informing treatment and prevention in this important demographic. In this project, we will use WGSA on 1349 systematically-collected Shigella isolates from children under 5 in seven countries across Asia and Africa (from the Global Enteric Multicentre Study) to create a relevant, contemporary overview of the epidemiology and evolution of Shigella to inform treatment and management of shigellosis.

By mapping the evolutionary relationships of the Shigella with each other, and with those from elsewhere, we will determine which subtypes of Shigella are responsible for causing most of the disease. Subtyping approaches such as these are crucial for worldwide epidemiological tracing of diarrhoeal pathogens, that do not respect international borders (Shigella is a common cause of 'traveller's diarrhoea' in high-income nations). We will also determine what antimicrobial resistances predominate in Shigella bacteria and evaluate whether global and regional treatment recommendations need to be updated. Crucially, we will explore whether current vaccines in development for Shigella are likely to work based on the diversity found in the pathogen across the seven countries, and by better characterising a phenomenon known as serotype switching in Shigella, where bacteria can change the way they look to the human immune system through simple genetic rearrangements. Finally, we will compare isolates from sick children and the few healthy children from whom Shigella was isolated to see if we can determine factors that contribute to development of disease in people. Collectively, this will create our most up-to-date overview of shigellosis in those populations most affected and will help direct future research and strategies for treatment and management of this important disease.

Technical Summary

Shigellosis is the leading bacterial cause of moderate-to-severe diarrhoea in children under five years old in low-to-middle income nations. Our understanding of the agents of shigellosis, bacteria of the genus Shigella, is currently being transformed through Whole Genome Sequence Analysis (WGSA) studies which informs shigellosis treatment and management through an enhanced understanding of pathogen epidemiology, evolution and biology. However, WGSA studies on Shigella to date focused on defining population structures or characterising emerging national or risk-group-associated sublineages. To inform on treatment and management of shigellosis in its most important demographic, WGSA must be applied to a relevant, representative, contemporary collection of shigellae from endemic areas.
The Global Enteric Multicentre Study systematically-collected 1349 Shigella isolates from children under five years old from across Asia and Africa and represents just the collection needed to develop of most advanced overview of shigellosis to date relevant for informing treatment and management of the disease.

This project will achieve the following objectives:

1. Identify those Shigella subtypes and antimicrobial resistance profiles responsible for causing the most disease in the key demographic for shigellosis. This is crucial for epidemiological tracing and evaluating treatment recommendations.

2. Inform on the likelihood and potential timeframe of vaccine escape for both serotype-based and protein-based vaccine candidates currently in development for Shigella. We will work with industry to ensure our predictions are integrated into future development and implementation strategies.

3. Test the hypothesis that genomic factors are involved in the manifestation of clinical shigellosis by comparing Shigella isolates from case and control patients. This may identify novel pathogenesis factors for future functional research and perhaps therapeutic targeting.

Planned Impact

This project will generate the most advanced and relevant overview of shigellosis and its antimicrobial resistance to date. As such, it will benefit stakeholders in various sectors, and will be delivered through continual engagement with these key groups over the course of the project, as well as a targeted stakeholders workshop to be held toward the completion of the project.

1. Public health beneficiaries will benefit from both the findings of the project and its utility as a public resource.

a. The antimicrobial resistance findings will be used to update treatment recommendations at national and potentially international levels. This will be of great direct benefit to public health at the sampling locations, all of which are DAC listed ODA recipients.
b. The data and findings will be made publically available and are essential for epidemiological tracing worldwide. In resource-poor settings where the data is less likely to be used directly, the development of low-cost diagnostics for surveillance will be explored.

2. Vaccine developers (both industrial and academic) will benefit from the findings of the project which will predict the likely efficacy of vaccine candidates currently in the public domain and generate data relevant to guiding future vaccine program implementation. Engagement with vaccine developers may lead to further collaboration on private-domain and/or novel vaccine candidates.

3. Public beneficiaries who will benefit through:

a. Improvements to health care provisions as a knock-on effect from the impact on public health (see 1) and
b. Enhanced understanding through public engagement with the project and the role of science in promoting health.

4. Academic beneficiaries through:

a. Scientific outputs that are significant across numerous fields, as well as an exemplar approach for value-adding through interdisciplinary collaboration
b. Skills development and an enhanced collaborative network in multiple early career researchers.
Description Enterics for Global Health
Amount £146,000 (GBP)
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 02/2021 
End 02/2024
Title A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella 
Description Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation, and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation efficiencies for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Title Biobanked and genome sequenced S. flexneri 3a 
Description We whole genome sequenced and biobanked and important international strain of S. flexneri 3a. This is something that the research community need to continue work toward a vaccine and didn't exist for this important pathogen. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact None yet 
Title Escherichia albertii tree files 
Description These are two newick format tree files used in the Escherichia albertii publication. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Title GEMS Shigella dataset 
Description This is a curated epidemiologically representative whole genome sequencing dataset of > 1000 Shigella isolates from hard to reach regions in LMIC. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? No  
Impact This is the subject of a major publication being submitted this year which will then be released publicly. 
Title colicin_database 
Description A database of over 10,000 colicins from over 50 species of bacteria were collated from the ENA as well as including some isolates from previously published sources. A multi-FASTA file containing the collated colicin sequences was utilised to generate a custom database via the prepareref command of ARIBA v2.14.6 where prepareref removes erroneous data and runs cd-hit to cluster the sequences based on a user-defined similarity threshold (90% in our case). ARIBA was then run with the FASTQ files of all isolates and the colicin database to report which sequences were observed in each isolate. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Description Genome sequencing of GEMS and other Shigella from case-control studies at UMB 
Organisation University of Maryland
Country United States 
Sector Academic/University 
PI Contribution We have analysed sequence data from a collection of Shigella isolates isolated during a large case control study conducted (led by investigators at UMB) across seven nations in Africa and Asia.
Collaborator Contribution The partners grew and extracted DNA from archived isolates of approximately 1500 Shigella and provided metadata for analysis.
Impact * Poster presented at 2019 American Society for Tropical Medicine and Hygiene * Internal seminar given at the Centre for Vaccine Development, University of Maryland * Public engagement project at Victoria Gallery and Museum * PDRA demonstrating on the Computational Molecular Evolution EBI course
Start Year 2018
Description University of Washington collaboration extension to GEMS 
Organisation University of Washington
Country United States 
Sector Academic/University 
PI Contribution Continued analysis of datasets
Collaborator Contribution Provision of relevant metadata for analysis
Impact These collaborators have provided additional data to extend the analyses, and we now have seed work for a grant application
Start Year 2022
Description Meet the scientists: a superbug's life 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The PDRA on the project, Dr Rebecca Bengtsson, designed and delivered a 'Meet the scientists' event at the University of Liverpool's Victoria Gallery and Museum. A game called 'A Super Bug's Life' which aimed to engage and inform children and parents on how bacteria can pick up antimicrobial resistant (AMR) genes from the environment and become drug resistant. The game involved a giant chess mat with different coloured plastic balls dotted around the mat, representing different AMR genes. The player will have to move around the board in order to pick up as many different coloured balls as possible within a time limit, they must pick up at least three different colours to become a super bug. The step number of steps the player can move is determined by rolling a giant inflatable dice.
Year(s) Of Engagement Activity 2019