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

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.

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).

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.