Whole-genome sequencing (WGS) analysis of microorganisms is poised to transform public health microbiology. WGS is a ‘one-stop technology’, a ‘one technology takes all’, a universal technology applicable to all microorganisms. WGS is particularly useful surrounding activities related to surveillance, epidemiology and response to communicable disease threats including outbreaks. 

WGS has the potential to replace all current methodologies used in the clinical microbiology laboratory and WGS data can be interrogated to provide information on microbial identification (genus/species/serotype), antimicrobial susceptibility and presence of antimicrobial resistance genes (determinants), virulence potential and presence of virulence genes, etc. In particular, interrogation of WGS data and comparative genomics are extremely useful in investigations surrounding surveillance and epidemiology, where the genetic relatedness of microbial isolates can be investigated and evolutionary relationships can be inferred.

The Centre for Enteric Diseases (CED) has secured grant funding to perform WGS on ~5000 microbial isolates over the years 2020 to 2021. The focus of the sequencing will be on the family of Enterobacteriaceae. Importantly, sequencing data for isolates need to be complemented with good epidemiological (explanatory) data, as WGS data often needs to be interpreted within the epidemiological context. This sequencing project will mostly have a prospective focus, so that relevant and up-to-date epidemiological data can be collected, to facilitate a ‘real-time’ analysis. We aim to investigate how WGS analysis can support and augment the current methodologies used in laboratory investigations at the NICD. In addition, WGS analysis will strengthen surveillance activities at the NICD and in particular, outbreak response and investigation.

CED will partner with the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses to sequence pathogens which form part of routine GERMS-SA surveillance activities. CED will sequence all isolates of Salmonella species, Shigella species, Campylobacter species, Escherichia coli and Vibrio cholerae O1. CHARM will sequence selected isolates of carbapenemase-producing Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus and Candida auris.