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

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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.