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

Emily Sotheran; Courtney R Lane; Kristy Horan; Kerrie Stevens; Christine Guglielmino; Susan Bradbury; Karina Kennedy; Louise Cooley; Belinda McEwan; Charlene M Kahler; Shakeel Mowlaboccus; David J Speers; Robert Baird; Kevin Freeman; Lex Leong; Morgyn Warner; Deborah A Williamson; Jodie McVernon; Monica Lahra; Amy V Jennison; Benjamin P Howden; Patiyan Andersson

doi:10.1093/ofid/ofae249

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

Open Forum Infect Dis. 2024 May 2;11(6):ofae249. doi: 10.1093/ofid/ofae249. eCollection 2024 Jun.

Authors

Emily Sotheran^{1

2}, Courtney R Lane^{1

2}, Kristy Horan^{1

2}, Kerrie Stevens¹, Christine Guglielmino³, Susan Bradbury⁴, Karina Kennedy⁴, Louise Cooley⁵, Belinda McEwan⁵, Charlene M Kahler⁶, Shakeel Mowlaboccus⁶, David J Speers⁷, Robert Baird⁸, Kevin Freeman⁸, Lex Leong⁹, Morgyn Warner⁹, Deborah A Williamson^{10

11}, Jodie McVernon^{10

11}, Monica Lahra¹², Amy V Jennison³, Benjamin P Howden^{1

2

13}, Patiyan Andersson^{1

2}

Affiliations

¹ Microbiological Diagnostic Unit Public Health Laboratory at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.
² Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.
³ Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Australia.
⁴ Department of Clinical Microbiology and Infectious Diseases, Canberra Health Services, Australian National University Medical School, Canberra, Australia.
⁵ Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, Australia.
⁶ Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Australia.
⁷ PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia.
⁸ Royal Darwin Hospital Pathology, Darwin, Australia.
⁹ SA Pathology, Adelaide, Australia.
¹⁰ Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
¹¹ Department of Infectious Diseases at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.
¹² New South Wales Health Pathology, Microbiology Randwick, The Prince of Wales Hospital, Sydney, Australia.
¹³ Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia.

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 and 2018 using whole genome sequencing data.

Methods: Whole genome sequencing data from 440 Australian IMD isolates collected during 2017 and 2018 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 were as follows: 181 MenW (41%), 144 MenB (33%), 88 MenY (20%), 16 MenC (4%), 1 MenW/Y (0.2%), and 10 nongenogroupable (2%). Eighteen clonal complexes (CCs) were identified, and 3 (CC11, CC23, CC41/44) accounted for 78% of isolates (343/440). These CCs were associated with specific serogroups: CC11 (n = 199) predominated among MenW (n = 181) and MenC (n = 15), CC23 (n = 80) among MenY (n = 78), and CC41/44 (n = 64) among MenB (n = 64). MenB isolates were highly diverse, MenY were intermediately diverse, and MenW and 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: Whole genome sequencing comprehensively characterized Australian IMD isolates, indexed their genetic variability, provided increased within-CC resolution, and elucidated the evolution of CC11 in Australia.

Keywords: Neisseria meningitidis; genomic epidemiology; meningococcal disease; pathogen genomics; public health.