Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

Abstract

The global spread of antimicrobial resistance (AMR) and lack of novel alternative treatments have been declared a global public health emergency by WHO. The greatest impact of AMR is experienced in resource-poor settings, because of lack of access to alternative antibiotics and because the prevalence of multidrug-resistant bacterial strains may be higher in low-income and middle-income countries (LMICs). Intelligent surveillance of AMR infections is key to informed policy decisions and public health interventions to counter AMR. Molecular surveillance using whole-genome sequencing (WGS) can be a valuable addition to phenotypic surveillance of AMR. WGS provides insights into the genetic basis of resistance mechanisms, as well as pathogen evolution and population dynamics at different spatial and temporal scales. Due to its high cost and complexity, WGS is currently mainly carried out in high-income countries. However, given its potential to inform national and international action plans against AMR, establishing WGS as a surveillance tool in LMICs will be important in order to produce a truly global picture. Here, we describe a roadmap for incorporating WGS into existing AMR surveillance frameworks, including WHO Global Antimicrobial Resistance Surveillance System, informed by our ongoing, practical experiences developing WGS surveillance systems in national reference laboratories in Colombia, India, Nigeria and the Philippines. Challenges and barriers to WGS in LMICs will be discussed together with a roadmap to possible solutions.

Keywords: epidemiology; other diagnostic or tool; public health.

Figure 1

Virtuous circle of improved local capacity for WGS for AMR surveillance, improved reference databases and scientific research. Expanded capacity for AMR surveillance locally in LMICs (and HICs), including systematic sampling of resistant isolates, quality control and collaborative networks will improve and extend reference databases of AMR organisms which will drive scientific research and lead to new science-driven engineering solutions that in turn can improve the use of WGS for AMR surveillance. Together these three interlocking systems can lead to improved public health policy and AMR control and technological innovation. AMR, antimicrobial resistance; HICs, high-income countries; LMICs, low-income and middle-income countries; WGS, whole-genome sequencing.

Figure 2

Workflow components required to implement WGS for AMR surveillance. AMR, antimicrobial resistance; AST, antimicrobial susceptibility testing; WGS, whole-genome sequencing.