Longitudinal genomic analysis of Neisseria gonorrhoeae transmission dynamics in Australia

Mona L Taouk; George Taiaroa; Sebastian Duchene; Soo Jen Low; Charlie K Higgs; Darren Y J Lee; Shivani Pasricha; Nasra Higgins; Danielle J Ingle; Benjamin P Howden; Marcus Y Chen; Christopher K Fairley; Eric P F Chow; Deborah A Williamson

doi:10.1038/s41467-024-52343-0

Longitudinal genomic analysis of Neisseria gonorrhoeae transmission dynamics in Australia

Mona L Taouk, George Taiaroa, Sebastian Duchene, Soo Jen Low, Charlie K Higgs, Darren Y J Lee, Shivani Pasricha, Nasra Higgins, Danielle J Ingle, Benjamin P Howden, Marcus Y Chen, Christopher K Fairley, Eric P F Chow, Deborah A Williamson^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

N. gonorrhoeae, which causes the sexually transmissible infection gonorrhoea, remains a significant public health threat globally, with challenges posed by increasing transmission and antimicrobial resistance (AMR). The COVID-19 pandemic introduced exceptional circumstances into communicable disease control, impacting the transmission of gonorrhoea and other infectious diseases. Through phylogenomic and phylodynamic analysis of 5881 N. gonorrhoeae genomes from Australia, we investigated N. gonorrhoeae transmission over five years, including a time period during the COVID-19 pandemic. Using a novel cgMLST-based genetic threshold, we demonstrate persistence of large N. gonorrhoeae genomic clusters over several years, with some persistent clusters associated with heterosexual transmission. We observed a decline in both N. gonorrhoeae transmission and genomic diversity during the COVID-19 pandemic, suggestive of an evolutionary bottleneck. The longitudinal, occult transmission of N. gonorrhoeae over many years further highlights the urgent need for improved diagnostic, treatment, and prevention strategies for gonorrhoea.

Original language	English
Article number	8076
Number of pages	12
Journal	Nature Communications
Volume	15
DOIs	https://doi.org/10.1038/s41467-024-52343-0
Publication status	Published - 14 Sept 2024

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

SARS-CoV-2 - genetics
Young adult
Female
Neisseria gonorrhoeae - genetics - drug effects
COVID-19 - transmission - epidemiology
Longitudinal studies
Australia - epidemiology
Genome, Bacterial
Adult
Phylogeny
Genomics
Male
Humans
Gonorrhea - transmission - epidemiology - microbiology

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Taouk, M. L., Taiaroa, G., Duchene, S., Low, S. J., Higgs, C. K., Lee, D. Y. J., Pasricha, S., Higgins, N., Ingle, D. J., Howden, B. P., Chen, M. Y., Fairley, C. K., Chow, E. P. F., & Williamson, D. A. (2024). Longitudinal genomic analysis of Neisseria gonorrhoeae transmission dynamics in Australia. Nature Communications, 15, Article 8076. https://doi.org/10.1038/s41467-024-52343-0

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title = "Longitudinal genomic analysis of Neisseria gonorrhoeae transmission dynamics in Australia",

abstract = "N. gonorrhoeae, which causes the sexually transmissible infection gonorrhoea, remains a significant public health threat globally, with challenges posed by increasing transmission and antimicrobial resistance (AMR). The COVID-19 pandemic introduced exceptional circumstances into communicable disease control, impacting the transmission of gonorrhoea and other infectious diseases. Through phylogenomic and phylodynamic analysis of 5881 N. gonorrhoeae genomes from Australia, we investigated N. gonorrhoeae transmission over five years, including a time period during the COVID-19 pandemic. Using a novel cgMLST-based genetic threshold, we demonstrate persistence of large N. gonorrhoeae genomic clusters over several years, with some persistent clusters associated with heterosexual transmission. We observed a decline in both N. gonorrhoeae transmission and genomic diversity during the COVID-19 pandemic, suggestive of an evolutionary bottleneck. The longitudinal, occult transmission of N. gonorrhoeae over many years further highlights the urgent need for improved diagnostic, treatment, and prevention strategies for gonorrhoea.",

keywords = "SARS-CoV-2 - genetics, Young adult, Female, Neisseria gonorrhoeae - genetics - drug effects, COVID-19 - transmission - epidemiology, Longitudinal studies, Australia - epidemiology, Genome, Bacterial, Adult, Phylogeny, Genomics, Male, Humans, Gonorrhea - transmission - epidemiology - microbiology",

author = "Taouk, \{Mona L\} and George Taiaroa and Sebastian Duchene and Low, \{Soo Jen\} and Higgs, \{Charlie K\} and Lee, \{Darren Y J\} and Shivani Pasricha and Nasra Higgins and Ingle, \{Danielle J\} and Howden, \{Benjamin P\} and Chen, \{Marcus Y\} and Fairley, \{Christopher K\} and Chow, \{Eric P F\} and Williamson, \{Deborah A\}",

note = "Funding: MLT is supported by an Australian Government Research Training Programme Scholarship. DAW is supported by a National Health and Medical Research Council (NHMRC) Investigator Grant (GNT1174555) and a Medical Research Future Fund (MRFF) Grant (FSPGN000045). BPH is supported by NHMRC Investigator Grant (GNT1196103). CKF is supported by an NHMRC Investigator Grant (APP1172900). EPFC is supported by an NHMRC Investigator Grant (GNT1172873). SD is supported by the Australian Research Council (ARC) Grant (DE190100805) and an NHMRC Investigator Grant (GNT1157586) and by the Inception Programme Investissement d{\textquoteright} Avenir Grant (ANR-16-CONV-0005). DJI is supported by an NHMRC Investigator Grant (GNT1195210). This work was also supported by an ARC Industrial Transformation Research Hub Grant (IH190100021). MDU PHL is funded by the Victorian Government, Australia.",

year = "2024",

month = sep,

day = "14",

doi = "10.1038/s41467-024-52343-0",

language = "English",

volume = "15",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

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TY - JOUR

T1 - Longitudinal genomic analysis of Neisseria gonorrhoeae transmission dynamics in Australia

AU - Taouk, Mona L

AU - Taiaroa, George

AU - Duchene, Sebastian

AU - Low, Soo Jen

AU - Higgs, Charlie K

AU - Lee, Darren Y J

AU - Pasricha, Shivani

AU - Higgins, Nasra

AU - Ingle, Danielle J

AU - Howden, Benjamin P

AU - Chen, Marcus Y

AU - Fairley, Christopher K

AU - Chow, Eric P F

AU - Williamson, Deborah A

N1 - Funding: MLT is supported by an Australian Government Research Training Programme Scholarship. DAW is supported by a National Health and Medical Research Council (NHMRC) Investigator Grant (GNT1174555) and a Medical Research Future Fund (MRFF) Grant (FSPGN000045). BPH is supported by NHMRC Investigator Grant (GNT1196103). CKF is supported by an NHMRC Investigator Grant (APP1172900). EPFC is supported by an NHMRC Investigator Grant (GNT1172873). SD is supported by the Australian Research Council (ARC) Grant (DE190100805) and an NHMRC Investigator Grant (GNT1157586) and by the Inception Programme Investissement d’ Avenir Grant (ANR-16-CONV-0005). DJI is supported by an NHMRC Investigator Grant (GNT1195210). This work was also supported by an ARC Industrial Transformation Research Hub Grant (IH190100021). MDU PHL is funded by the Victorian Government, Australia.

PY - 2024/9/14

Y1 - 2024/9/14

N2 - N. gonorrhoeae, which causes the sexually transmissible infection gonorrhoea, remains a significant public health threat globally, with challenges posed by increasing transmission and antimicrobial resistance (AMR). The COVID-19 pandemic introduced exceptional circumstances into communicable disease control, impacting the transmission of gonorrhoea and other infectious diseases. Through phylogenomic and phylodynamic analysis of 5881 N. gonorrhoeae genomes from Australia, we investigated N. gonorrhoeae transmission over five years, including a time period during the COVID-19 pandemic. Using a novel cgMLST-based genetic threshold, we demonstrate persistence of large N. gonorrhoeae genomic clusters over several years, with some persistent clusters associated with heterosexual transmission. We observed a decline in both N. gonorrhoeae transmission and genomic diversity during the COVID-19 pandemic, suggestive of an evolutionary bottleneck. The longitudinal, occult transmission of N. gonorrhoeae over many years further highlights the urgent need for improved diagnostic, treatment, and prevention strategies for gonorrhoea.

AB - N. gonorrhoeae, which causes the sexually transmissible infection gonorrhoea, remains a significant public health threat globally, with challenges posed by increasing transmission and antimicrobial resistance (AMR). The COVID-19 pandemic introduced exceptional circumstances into communicable disease control, impacting the transmission of gonorrhoea and other infectious diseases. Through phylogenomic and phylodynamic analysis of 5881 N. gonorrhoeae genomes from Australia, we investigated N. gonorrhoeae transmission over five years, including a time period during the COVID-19 pandemic. Using a novel cgMLST-based genetic threshold, we demonstrate persistence of large N. gonorrhoeae genomic clusters over several years, with some persistent clusters associated with heterosexual transmission. We observed a decline in both N. gonorrhoeae transmission and genomic diversity during the COVID-19 pandemic, suggestive of an evolutionary bottleneck. The longitudinal, occult transmission of N. gonorrhoeae over many years further highlights the urgent need for improved diagnostic, treatment, and prevention strategies for gonorrhoea.

KW - SARS-CoV-2 - genetics

KW - Young adult

KW - Female

KW - Neisseria gonorrhoeae - genetics - drug effects

KW - COVID-19 - transmission - epidemiology

KW - Longitudinal studies

KW - Australia - epidemiology

KW - Genome, Bacterial

KW - Adult

KW - Phylogeny

KW - Genomics

KW - Male

KW - Humans

KW - Gonorrhea - transmission - epidemiology - microbiology

UR - https://www.scopus.com/pages/publications/85204167746

U2 - 10.1038/s41467-024-52343-0

DO - 10.1038/s41467-024-52343-0

M3 - Article

C2 - 39277590

SN - 2041-1723

VL - 15

JO - Nature Communications

JF - Nature Communications

M1 - 8076

ER -

Longitudinal genomic analysis of Neisseria gonorrhoeae transmission dynamics in Australia

Abstract

UN SDGs

Keywords

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