Genomic Surveillance of Invasive Meningococcal Disease During a National MenW Outbreak in Australia, 2017–2018

Abstract

Background In Australia, invasive meningococcal disease (IMD) incidence rapidly increased between 2014 and 2017 due to rising serogroup W (MenW) and MenY infections. We aimed to better understand the genetic diversity of IMD during 2017-18 using whole-genome sequencing (WGS) data. Methods Whole-genome sequencing data from 440 Australian IMD isolates collected during 2017-18 and 1737 international MenW:CC11 isolates collected in Europe, Africa, Asia, North America, and South America between 1974 and 2020 were used in phylogenetic analyses; genetic relatedness was determined from single nucleotide polymorphisms. Results Australian isolates comprised 181 MenW (41%), 144 MenB (33%), 88 MenY (20%), 16 MenC (4%), 1 MenW/Y (0.2%), and 10 non-genogroupable (2%) isolates. Eighteen clonal complexes (CC) were identified; three (CC11, CC23, CC41/44) accounted for 78% of isolates (343/440). These CCs were associated with specific serogroups; CC11 (199) predominated among MenW (181) & MenC (15), CC23 (80) among MenY (78), and CC41/44 (64) among MenB (64). MenB isolates were highly diverse, MenY intermediately diverse, and MenW & MenC isolates demonstrated the least genetic diversity. Thirty serogroup and CC-specific genomic clusters were identified. International CC11 comparison revealed diversification of MenW in Australia. Conclusions WGS comprehensively characterised Australian IMD isolates, indexed their genetic variability, provided increased within-CC resolution, and further elucidated the evolution of CC11 in Australia.