Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria’s experience

Abstract

Whole-genome sequencing (WGS) is finding important applications in the surveillance of antimicrobial resistance (AMR), providing the most granular data and broadening the scope of niches and locations that can be surveilled. A common but often overlooked application of WGS is to replace or augment reference laboratory services for AMR surveillance. WGS has supplanted traditional strain subtyping in many comprehensive reference laboratories and is now the gold standard for rapidly ruling isolates into or out of suspected outbreak clusters. These and other properties give WGS the potential to serve in AMR reference functioning where a reference laboratory did not hitherto exist. In this perspective, we describe how we have employed a WGS approach, and an academic–public health system collaboration, to provide AMR reference laboratory services in Nigeria, as a model for leapfrogging to national AMR surveillance.

Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000SalmonellaTyphi genomes

“…Salmonellae were among the first pathogens to transition to routine sequencing by public health laboratories in high-income countries (Chattaway et al, 2019;Stevens et al, 2022), and these systems often capture Typhi isolated from travel-associated typhoid infections, providing an informal mechanism for sentinel genomic surveillance of pathogen populations in typhoid endemic countries (Ingle et al, 2019). More recently, WGS has been adopted for typhoid surveillance by national reference laboratories in endemic countries including the Philippines, Nigeria (Okeke et al, 2022) and South Africa (Lagrada et al, 2022), and PulseNet International is gradually transitioning to WGS (Davedow et al, 2022;Nadon et al, 2017). Following the first global genomic snapshot study, which included nearly 2000 genomes of Typhi isolated from numerous typhoid prevalence and incidence studies conducted across Asia and Africa (Wong et al, 2015), WGS has become the standard tool for characterising clinical isolates.…”

High genetic diversity andblaNDM-1prevalence amongAcinetobacter baumanniiin Nigerian hospitals

“…Very few patients are cultured at all and A. baumannii are particularly difficult to identify using conventional diagnostics 7,38,39 . The institution of genomic surveillance for AMR in Nigeria has been coupled with efforts to improve basic microbiology capacity, and it is expected that these measures will help plug the existing gaps in the diagnostics and surveillance of these pathogens of major public health importance 40 .…”

Microbial Musings – Autumn 2022

“…The theme of diagnosis is continued in an interesting article led by Iruke Okeke (@iruka_okeke), which describes the successful setting up and running of a whole-genome sequencing reference laboratory in Nigeria [21]. The drivers for this were World Health Organization (WHO)-led initiatives to create a global surveillance framework for monitoring antimicrobial resistance (AMR), which required the creation of a national reference laboratory (NRL) to coordinate outlying labs and provide additional testing methods, such as serotyping and phage typing.…”