identifying drivers for the emergence and transmission of key human pathogens and amr in vietnam and the philippines (amr-vp)

Southeast Asia (SEA) remains particularly vulnerable to new and emerging disease threats due to poor infection control, unregulated antibiotic use, inadequate water sanitation, high population density and rapid urbanization. Sequencing technologies have transformed our understanding of infectious diseases and pathogen evolution, including the transmission of antimicrobial resistance (AMR). The COVID-19 pandemic highlighted the importance of frontier science efforts to analyse microbe diversity and its potential impacts on human health including the value of genomics-based approaches in tracking and tracing not only the presence of the virus but also its movement, enabling identification of where (and often how) new strains emerged. This enables resources to be targeted to 'hotspots' of emergence and 'nodes' of spread. It is of paramount importance that the knowledge and experience built during the pandemic are now consolidated and built on for other microbes with epidemic potential across One Health (OH) dimensions, i.e. in the food chain - in particular, multi-drug resistant bacteria, such as Acinetobacter baumannii, Klebsiella pneumonia, Escherichia coli, Salmonella spp. and Helicobacter pylori that have been prioritised in Vietnam and Philippines due to their ability to rapidly spread within environmental and human-animal interface or develop resistance to multiple antibiotics. Translating OH research priorities into action for human health is essential for the creation of evidence-based policies and programs for the prevention and control of infectious diseases and other health threats, and thus is an important component of a robust national capacity to effectively prevent, control, and mitigate biological incidents. Following, one of the most pivotal technical domains within an OH framework is understanding the emergence and evolution of key pathogens and AMR and one of the most pivotal research priorities that need to be translated into action for human health is limitations on inference regarding directionality of transmission or risk pathways deduced from conventional data. AMR-VP project brings together SEA and UK researchers working on interdisciplinary AMR challenges to study the epidemic potential of key human gastrointestinal pathogens and the molecular mechanisms underlying AMR in urban environmental, animal, food and human interface across major metropolitan areas in SEA, focusing on Manila (Philippines) and Ho Chi Minh City (Vietnam). Our project will adopt a systems approach to trace the origins and drivers of AMR bacteria overlapping with health practices, genetics, applied sciences, and social contexts. As the project progresses, pathogen and AMR dynamics will be analysed, comparing data across different contexts such as food systems and human activities to achieve its overarching objectives to: [1] provide training and capacity build for SEA researchers in next-generation sequencing (NGS) and bioinformatics, addressing identified weaknesses whilst simultaneously demonstrating the value of an OH systems approach, crucial for identifying epidemic strains circulating between humans, animals, and the environment in SEA; [2] explore the emergence, evolution and transmission of AMR and key resistant pathogens (A. baumannii, K. pneumonia, E. coli, Salmonella spp. and H. pylori) in and between human, animal and the environmental microbiomes within OH context; [3] perform big data analysis and systems modelling to identify transmission routes of these pathogens; and [4] develop artificial intelligence (AI) algorithms, based on machine learning, to expedite the genomic and epidemiological metadata in predicting epidemics, outbreaks and AMR. This will counteract the emergence, transmission and spread of bacterial pathogens and AMR, enhance genomic surveillance, improve targeted interventions, and boost public health resilience.