'See and Sequence' - Genomic surveillance of antimicrobial resistant and high-risk pathogenic clones within the Philippines

Lead Research Organisation: The Wellcome Trust Sanger Institute
Department Name: Wellcome Trust Genome Campus

Abstract

The spectre of increasing antimicrobial resistance in pathogenic bacterial species looms larger each day. Currnetly existing surveillance networks need new tools to enable richer and more detailed understanding of where and when AMR is arising across a region. This will aid public health and lead to better patient care and prevention of spread. However, there are significant challenges facing public health microbiologists when tackling pathogenic microbial species which can be broadly summarised as:

1) Identification of high-risk lineages - ie dangerous sub-types in a population likely to cause disease.
2) Risk assessment following identification (eg., what antibiotics is the lineage resistant to, how likely to cause disease, how easy to transmit to others).
3) Infection control. - Using this information to inform strategies in treatment and the prevention of spread.

Whole Genome Sequencing (WGS) of bacterial species provides us with the means to look for genomic signatures of resistance and virulence (ie genes that if present, give us some indication as to what drugs could be used to treat the individual) but also provides us with ways of identifying transmission - for example by building 'family trees' indicating which genomes are more similar to others. Furthermore, due to the digital nature of the data, genome sequences and associated metadata can be stored and accessed via the internet opening up the possible for regioinal, national and international comparison.

We intend to utilise WGS within the National antimicrobial surveillance network in the Philippines to introduce this increase in resolution to a national network.
Firstly, we will install local sequencing capacity in the Reference Laboratory and, in conjunction with The Wellcome Trust Sanger Institute, the world leader in the use of WGS for public health, will provide training and capacity building for the use of WGS throughout the project.
Secondly, we will sequence a representative set of historical strains circulating over the preceding years in the Philippines to provide a 'reference database' with which to start active surveillance.
Finally, we will, utilising current microbiology to 'flag' isolates with unusual antibiotic resistance, start a process of prospective sequencing and comparison between contempory data and the reference database.

Crucially, this will also allow the comparsion of data from the Philippines with data from other parts of the world to aid, not only identification of potential transmissions to/from the Region but to act as part of a global surveillance of antimicrobial resistance. This project places the Philippines at the forefront of molecular epidemiology.

Technical Summary

The challenges facing public health microbiologists when tackling pathogenic microbial species can be broadly summarised as 1) identification of high-risk lineages, 2) their risk assessment (eg., antimicrobial resistance) and 3) infection control. Whole Genome Sequencing (WGS) of bacterial species provides signatures of resistance and virulence and, uniquely, allows the build up of a 'digital library' for ongoing population comparison, which can be utilised to identify markers for rapid diagnostics. We will facilitate the implementation of WGS within AMR surveillance and clinical diagnostics within the Philippines Antimicrobial resistance surveillance laboratory network (22 sentinel laboratories) and develop bioinformatics to enable local, national and international comparison of data for key indicator species (Salmonella, N. gonorrhoeae, Carbapenem resistant species and S.aureus).
The proposal consists of 4 major parts:
1) Establishment of sequencing capacity and expertise in Genomic analysis within the National Reference Laboratory.
2) Retrospective sequencing of susceptible and resistant isolates of key species (to be undertaken at The Sanger Institute).
3) Provision of data throughout the surveillance network using tools developed at Sanger and Imperial College (eg www.microreact.org/project/NJqiECX8 and www.wgsa.net )
4) Active Prospective sequencing within the Philippines - isolates with novel antibiograms determined by routine susceptibility testing via a 'save for sequencing' flag within the WHONET software.
5) Capacity building in genomics, bioinformatics and sequencing (through staff exchange and training between locations and).

Planned Impact

A key deliverable of this project is the enabling of a national reference laboratory to harness the power of whole genome sequencing for surveillance of antimicrobial resistance. The provision of a central surveillance system with WGS capacity will allow key stakeholders to identify and provide early warning of novel pathogen variants that may be particularly virulent or transmissible. Moreover, the data will also provide convincing evidence (eg through identification of resistance genes) concerning management options leading to patient benefit and drop in cost to local hospitals and national public health. Further, evidence may point to areas within the healthcare network where spread is more likely, allowing further cost-benefit analysis and change in practice.

The primary initial beneficiaries will be members of the National reference laboratory receiving training and then passing that training on locally within the area of WGS analysis within clinical microbiology. This will trickle down to local laboratories and allow greater utility of the data. Clearly, existing surveillance practices must be enhanced by such capacity building.

Within the project the genome sequence data generated, both the retrospective and prospective sequencing, is of potential benefit to global researchers interested in understanding pathogen evolution, the acquisition of new resistance and virulence determinants. The broad geographic area represented by the sentinal laboratories in the network, allied with the background database which will arise from the initial sequencing makes this a unique venture, not just within the region but globally. Further academic beneficiaries within the area of mathematical modelling, who rely on good empirical data (and increasingly sequence data) to tailor and inform models of pathogen spread / evolution will benefit from such networked information. This will become a key reciprocal relationship wherein information from models may well inform areas of focus for change within surveillance practices.

However, most importantly, the potential impact on standard infection control practices, the time taken to identify outbreaks, and ultimately to the benefit of patients and general population is immense.
 
Description We have detailed for the very first time the genomic population structure for a number of bacterial pathogens across the Phillipines. This was enabled through transfer of ownership of technology and interpretation for genomics
Exploitation Route Data will be reused by the academic and public health community - the nation of The phillipines will continue to ustilise the technology and data for understnding and increasing infection control.
Sectors Digital/Communication/Information Technologies (including Software)

 
Description The capacity built within the projectg has contributed to a baseline understanding of bacterial pathogens in the phillipines. These data continue to be used locally and internationally. The ARSP continue to lead the region on the use of WGS for surveillance of AMR and are considered pioneers within the region and more broadly at the World Healrh Organisation. The project has led to a WHO Technical note with a direct description of the project as an exemplar use case
First Year Of Impact 2000
 
Description Antimicrobial resistance policy
Geographic Reach Asia 
Policy Influence Type Influenced training of practitioners or researchers
Impact The work carried out using these funds both in the UK and in the Philippines has continued to inform our understanding of antimicrobial resistance (AMR), and has directly impacted on AMR policies in the Philippines.
 
Description Antimicrobial resistance policy
Geographic Reach Asia 
Policy Influence Type Influenced training of practitioners or researchers
Impact The work carried out using these funds both in the UK and in the Philippines has informed antimicrobial resistance and directly impacted on the standarised policy across all of the sentinel sites in the Philippines.
 
Description lead Consultant on WHO white paper for the use of Molecular Methods to enhance global surveillance of AMR
Geographic Reach Multiple continents/international 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
URL https://www.who.int/glass/resources/publications/molecular-methods-for-amr-diagnostics/en/
 
Description Fleming Fund Regional Grant
Amount £3,999,029 (GBP)
Organisation Fleming Fund 
Sector Charity/Non Profit
Start 10/2018 
End 05/2020
 
Description Global Health Research 2016 Units
Amount £6,863,372 (GBP)
Organisation National Institute for Health Research 
Sector Public
Country United Kingdom
Start 08/2017 
End 03/2021
 
Title Pathogenwatch 
Description Pathogenwatch (previously WGSA) is a global platform for genomic surveillance, which provides users with fast predictions of resistant genotypes and clustering; real-time analytics and genomic epidemiology. Pathogenwatch facilitates the rapid processing, clustering and exploration of whole genome assemblies and easily integrates with Epicollect. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Pathogenwatch is helping make the analysis of genomic data more accessible to users worldwide, and as an example has been taken up and used used routinely by our project partner in the Philippines. 
URL https://pathogen.watch/
 
Title WGSA 
Description Whole Genome Sequence Analysis (WGSA) is a platform for the processing and visualisation of microbial genome sequences in a phylogenetic and geographical context. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact WGSA is enabling understanding of genomics in the Philipines 
URL https://www.wgsa.net/
 
Description WHONET 
Organisation Brigham and Women's Hospital
Country United States 
Sector Hospitals 
PI Contribution Statistical analysis of antimicrobial resistance patterns across a network of labs using the WHONET software developed by collaborator
Collaborator Contribution Training and additional methods implemented within software
Impact Still in the development stages so no outcomes to report.
Start Year 2016
 
Title Microreact 
Description Microreact is a web application for the interactive visualisation of trees, geographic data, and temporal data. Together with Pathogenwatch, a platform for the analysis of genomic and epidemiology surveillance data, these tools are enabling collective interpretation and data sharing between project participants in the Philippines and collaborators in the UK. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Impact With the support of the See and Sequence award, we have been able to inform the development of platforms to facilitate the linking, visualization and real time processing of genomic surveillance data. The data submitted as a result of this award funding will benefit other users by increasing the pool of information. Microreact has since been endorsed by the US CDC, the European CDC and Public Health England for routine investigation of public health incidents. 
URL https://microreact.org/showcase
 
Title PANINI : 
Description In order to fully understand the genomic components of, in particular, bacterial pathogens, we must address variation in the core genome (components present in all isolates of a particular species) along with non-core or accessory genes. Traditionally, only core genome data are utilised to create phylogenies and such phylogenies are utilised to map relevant epidemiological and other characteristics to enhance understanding of the system under investigation. Clearly, for public health utility we require ways to rapidly interrogate both core and non-core. We introduced PANINI, to enable the rapid processing of core and non-core gene content and the delivery of results in an integrated fashion , along with core phylogenies, geographic and epidemiological data through the Microreact.org platform. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact We released the tool : http://panini.pathogen.watch and publication : https://www.ncbi.nlm.nih.gov/pubmed/30465642 altMetric here: https://www.altmetric.com/details/51566591 PANINI is in use for investigating the emergence of clonal risk in The Phillipines in particular relevance for this grant. However, take up has seen PANINI utilised for other studies including dissemination of e. coli in the UK and globally and is routinely used by the community of users of Microreact. 
URL http://panini.pathogen.watch
 
Description ARSP annual meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact PI and senior post doc on the project attended the Philippines department of health committee on Antimicrobial Resistance Surveillance Program (ARSP) annual meeting (held in the Philippines). Both gave presentations on project progress.
The main objective of the meeting was to improve the overall operations of the ARSP and to better align the project's activities with the department of health's prevention and control programs. The meeting was attended by ARSP committee members, senior medical technologists in microbiology and pathologists, chairs of the Infectious Control Committees of the program's sentinel sites.
The hospital infection control chairs were invited to the meeting to inform them of the possible impact of the project on their hospital antimicrobial resistance surveillance and infection control activities.
Year(s) Of Engagement Activity 2016
 
Description Attendance at Annual ARSP meeting, celebrating the 30th anniversary of the program 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Two members of the See and Sequence project team, and a further three members of the NIHR GHRU project team attended the 30th Anniversary Annual Meeting of the Antimicrobial Resistance Surveillance Reference Laboratory Programme to feed back on work funded by the grant and share experiences and knowledge. There were presentations from senior members of the ARSRL as well as David Aanensen, and representatives of other public health agencies.
Year(s) Of Engagement Activity 2018
URL http://ritm.gov.ph/arsp-celebrates-30th-anniversary/
 
Description Attendance at annual ARSP meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Two members of the group attended the annual meeting of the Antimicrobial Resistance Surveillance Reference Laboratory Programme to present work funded by the grant and share experiences and knowledge.
Year(s) Of Engagement Activity 2017
URL http://ritm.gov.ph/reference-laboratories/national-reference-laboratories/antimicrobial-resistance-s...
 
Description Bioinformatics training 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Two visiting workers from the Philippines laboratory (our partner in the See and Sequence project) returned for further bioinformatics training in December 2018, focused on the analysis of the prospective data generated at ARSRL using Microreact software developed as part of this project.
Year(s) Of Engagement Activity 2018
 
Description Bioinformatics training 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A full month of bioinformatics training was provided to two visiting workers from the Philippines laboratory (partner on the grant). The grant encourages training provision. During this time they learned about bacterial data analysis and the use of the software developed by the team. Their knowledge will be transferred to colleagues at their home institution and they will now be able to carry out their own data analysis on current and future data sets generated during this project. They have built good relations with members of our group and the wider scientific community.
Year(s) Of Engagement Activity 2017
 
Description Gates Foundation meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation on the project
Year(s) Of Engagement Activity 2016
 
Description Laboratory training 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Members of our collaborating group visted for 2 weeks of training in laboratory practices at our institution. They also attended meetings and discussions to add value to their visit. The knoweldge they gained would be taken back to their home institution and shared with other colleagues. We maintain open communications with them for any queries.
Year(s) Of Engagement Activity 2017
 
Description Participated in the advisory Board meeting of the Philippine Council for Health Research and Development (PCHRD) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Two members of the See and Sequence project team participated in a 1-day Advisory Board meeting for the Philippine Council for Health Research and Development (PCHRD), also attended by representatives of the Antimicrobial Resistance Surveillance Reference Laboratory (ARSL). We presented results of retrospective sequencing for Salmonella Typhi, non-typhoidal Salmonella, and N. gonorrhoeae. The ARSRL presented a quality comparison of sequencing conducted on-site (preliminary prospective sequencing), and the investigation of a previously-undetected outbreak. We received highly positive feedback from the rest of the Advisory Board, who commended the See and Sequence project on its implementation of sequencing at the ARSRL, and the detection of a previously undetected outbreak.
Year(s) Of Engagement Activity 2018
 
Description Training in public health applications of next generation sequencing 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Three medical doctors from our collaborating institution visited for 1 week to meet with colleagues on site, local and national public health representatives to discuss antimicrobial resistance and surveillance both in the UK and in their country.
Year(s) Of Engagement Activity 2017