Data challenge

Antimicrobial resistance (AMR) is a constantly evolving multiscale phenomenon representing a growing public health issue worldwide, particularly in low- and middle-income countries (LMIC). So far, clinical data are under-exploited, and there is a paucity of surveillance data in LMIC. Among all the gram-negative pathogens, members of Enterobacteriaceae are among the World Health Organization's priority pathogens with high resistant rates, causing serious infections worldwide. Currently, the AMR dynamics and patterns among the Enterobacteriaceae population from LMIC remain unclear. Moreover, the exact drug-resistant Enterobacteriaceae clones circulating in Africa and their mechanisms of resistance and spread remain to be ascertained. Interestingly, with the advances and availability of clinical and genomic data, it is currently possible to dig deep into certain pathogen-related factors contributing to and mediating AMR. Firstly, we aim to identify and demystify the temporal and spatial AMR dynamics and patterns among the Enterobacteriaceae population and subpopulation from LMIC over different sampling periods. Thereafter, and more interestingly, we aim to use available genomic data with the help of bioinformatics tools to unravel the prevalence of resistance genes, understand the exact AMR circulating clones in LMIC and also demystify the precise mechanisms of the spread of the clones in this region. We intend to use data from ATLAS databases, Venatorx-GEAR, and publicly available databases. Overall, our approach is necessary to track AMR trends properly, understand circulating bacterial clones of importance, identify potential outbreak clusters in certain regions, and prevent and control infections in LMIC. In addition, aside from understanding AMR dynamics in LMIC, integrating scalable genomics into routine surveillance programs is a critical task, an area we are highly passionate about. The result of this study is critical for new drug discovery and development strategies. It is also vital to inform public health practice.