SRA

Antimicrobial resistance (AMR) is a serious global threat to the achievements of modern medicine, with the World Health Organization identifying the possibility of a forthcoming "post-antibiotic era – in which common infections and minor injuries can kill – far from being an apocalyptic fantasy, is instead a very real possibility for the 21st Century" (WHO Antimicrobial Resistance Division, 2014). AMR accounts for an estimated 700,000 to 750,000 annual deaths worldwide (Dag Hammarskjöld Foundation, 2019; IAGC, 2019). The Review on Antimicrobial Resistance (O'Neill, 2016) estimated the global burden of AMR to be 10 million deaths by 2050, an estimate provided well before the uptick in AMR incidence seen during the COVID-19 pandemic (Lai et al., 2021). A combination of inappropriate antibiotic usage (both clinical and veterinary), poor antimicrobial stewardship and a lack of appropriate and timely antibiotics drives the spread of AMR bacteria, particularly via exchange of mobile genetic elements (MGE), the AMR mobilome. Resources for identifying and monitoring infectious disease outbreaks are finite, particularly in low- and middle-income countries (LMIC). Providing costly sequencing platforms and the highly controlled laboratory environments they require is not a universally viable option for epidemiological analyses. Although the COVID-19 pandemic has led to a favourable re-evaluation of the merit in active surveillance and genomic epidemiological analyses, the limited resources available to LMICs necessitates particular care when identifying which of these processes and infrastructure to implement and support. While the above practicalities are not necessarily mentioned, a salient number of publications during the last 12 months promote successful “in house” Oxford Nanopore sequencing in African LMICs.