Direct sequencing technologies for bacterial sexually transmitted infections

Amy Jennison; Shivani Pasricha; Francesca Azzato

doi:10.1071/MA24033

RESEARCH ARTICLE (Open Access)

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Direct sequencing technologies for bacterial sexually transmitted infections

Amy Jennison ^A ^* , Shivani Pasricha ^B and Francesca Azzato ^B ^C

+ Author Affiliations

- Author Affiliations

^A Public and Environmental Health Reference Laboratories, Pathology Queensland, Queensland Health, Brisbane, Qld, Australia.

^B Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic., Australia.

^C Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection & Immunity, Melbourne, Vic., Australia.

Assoc. Prof. Amy Jennison is the chief scientist of the Public Health Microbiology laboratory of the Queensland Department of Health, which is Queensland’s reference laboratory responsible for the molecular surveillance of notifiable bacterial pathogens and characterisation of public health related outbreaks. Dr Jennison has led the laboratory in the application of whole-genome sequencing for pathogen surveillance and has a particular interest in genomic analysis for understanding environmental threats from emerging pathogens and addressing antimicrobial resistance (AMR) issues in bacterial pathogens including Neisseria gonorrhoeae.

Dr Shivani Pasricha is a microbiologist and laboratory head in the Department of Infectious Diseases of The University of Melbourne. Using molecular and genomic approaches, her research aims to improve the detection, prevention and surveillance of sexually transmitted infections (STIs). Her current research includes developing cutting-edge clustered regularly interspaced short palindromic repeats (CRISPR)-diagnostics for the point-of-care detection of STIs and AMR.

Francesca Azzato is the section head of the Bacteriology, Victorian Mycology and Parasitology reference laboratories at the Victorian Infectious Diseases Reference Laboratory. She has expertise in the design, evaluation and implementation of novel molecular diagnostic assays. Currently, she is completing a PhD focusing on STI genomics and is involved in numerous projects, which focus on evaluating the use of new molecular methods to improve the diagnosis of bacterial and parasitic pathogens from clinical samples.

^* Correspondence to: amy.jennison@health.qld.gov.au

Microbiology Australia 45(3) 112-116 https://doi.org/10.1071/MA24033

Submitted: 29 June 2024 Accepted: 22 July 2024 Published: 2 August 2024

© 2024 The Author(s) (or their employer(s)). Published by CSIRO Publishing on behalf of the ASM. This is an open access article distributed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC)

Abstract

There is an important role for direct sequencing of patient samples to complement traditional culture-based methods for bacterial sexually transmitted infections (STIs), effectively overcoming limitations posed by fastidious or unculturable pathogens such as Neisseria gonorrhoeae, Treponema pallidum, Mycoplasma genitalium and Chlamydia trachomatis. Metagenomic techniques can enable profiling of antimicrobial resistance (AMR), strain typing and microbiome analysis in the absence of a cultured isolate, contributing critical information to understanding epidemiological trends and guiding targeted therapies. Despite significant advancements, challenges persist, such as cost, bioinformatics complexity and ethical considerations. The paper discusses current applications, technological innovations, and future prospects for integrating metagenomics into routine bacterial STI surveillance, emphasising the need to identify cost and time-effective workflows and enhanced accessibility of genomic data. By addressing these challenges, direct sequencing promises to fill critical gaps in AMR monitoring and pathogen typing, offering new avenues for enhancing public health strategies in combating bacterial STIs worldwide.

Keywords: AMR, antimicrobial resistance, direct sequencing, disease surveillance, metagenomics, public health, sexually transmitted infections, STI.

Biographies

Assoc. Prof. Amy Jennison is the chief scientist of the Public Health Microbiology laboratory of the Queensland Department of Health, which is Queensland’s reference laboratory responsible for the molecular surveillance of notifiable bacterial pathogens and characterisation of public health related outbreaks. Dr Jennison has led the laboratory in the application of whole-genome sequencing for pathogen surveillance and has a particular interest in genomic analysis for understanding environmental threats from emerging pathogens and addressing antimicrobial resistance (AMR) issues in bacterial pathogens including Neisseria gonorrhoeae.

Dr Shivani Pasricha is a microbiologist and laboratory head in the Department of Infectious Diseases of The University of Melbourne. Using molecular and genomic approaches, her research aims to improve the detection, prevention and surveillance of sexually transmitted infections (STIs). Her current research includes developing cutting-edge clustered regularly interspaced short palindromic repeats (CRISPR)-diagnostics for the point-of-care detection of STIs and AMR.

Francesca Azzato is the section head of the Bacteriology, Victorian Mycology and Parasitology reference laboratories at the Victorian Infectious Diseases Reference Laboratory. She has expertise in the design, evaluation and implementation of novel molecular diagnostic assays. Currently, she is completing a PhD focusing on STI genomics and is involved in numerous projects, which focus on evaluating the use of new molecular methods to improve the diagnosis of bacterial and parasitic pathogens from clinical samples.

References

1 Baker KS et al. (2023) Genomics for public health and international surveillance of antimicrobial resistance. Lancet Microbe 4(12), e1047-e1055.
| Crossref | Google Scholar | PubMed |

2 Morens DM, Fauci AS (2020) Emerging pandemic diseases: how we got to COVID-19. Cell 182(5), 1077-1092.
| Crossref | Google Scholar | PubMed |

3 Mitchell SL, Simner PJ (2019) Next-generation sequencing in clinical microbiology: are we there yet? Clin Lab Med 39(3), 405-418.
| Crossref | Google Scholar | PubMed |

4 Ward J et al. (2013) STI in remote communities: improved and enhanced primary health care (STRIVE) study protocol: a cluster randomised controlled trial comparing ‘usual practice’ STI care to enhanced care in remote primary health care services in Australia. BMC Infect Dis 13, 425.
| Crossref | Google Scholar | PubMed |

5 Caruso G et al. (2021) Current and future trends in the laboratory diagnosis of sexually transmitted infections. Int J Environ Res Public Health 18(3), 1038.
| Crossref | Google Scholar | PubMed |

6 Jennison AV et al. (2019) Genetic relatedness of ceftriaxone-resistant and high-level azithromycin resistant Neisseria gonorrhoeae cases, United Kingdom and Australia, February to April 2018. Euro Surveill 24(8), 1900118.
| Crossref | Google Scholar | PubMed |

7 Martin I et al. (2019) Multidrug-resistant and extensively drug-resistant Neisseria gonorrhoeae in Canada, 2012–2016. Can Commun Dis Rep 45(2–3), 45-53.
| Crossref | Google Scholar | PubMed |

8 Maubaret C et al. (2023) Two cases of extensively drug-resistant (XDR) Neisseria gonorrhoeae infection combining ceftriaxone-resistance and high-level azithromycin resistance, France, November 2022 and May 2023. Euro Surveill 28(37), 2300456.
| Crossref | Google Scholar | PubMed |

9 Ouk V et al. (2024) High prevalence of ceftriaxone-resistant and XDR Neisseria gonorrhoeae in several cities of Cambodia, 2022–23: WHO Enhanced Gonococcal Antimicrobial Surveillance Programme (EGASP). JAC Antimicrob Resist 6(2), dlae053.
| Crossref | Google Scholar | PubMed |

10 Pleininger S et al. (2022) Extensively drug-resistant (XDR) Neisseria gonorrhoeae causing possible gonorrhoea treatment failure with ceftriaxone plus azithromycin in Austria, April 2022. Euro Surveill 27(24), 2200455.
| Crossref | Google Scholar | PubMed |

11 Australasian Society for HIV, Viral Hepatitis and Sexual Health Medicine (2021) Australian STI management guidelines for use in primary care – standard asymptomatic check-up. https://sti.guidelines.org.au/standard-asymptomatic-checkup/

12 World Health Organization (2021) WHO Bacterial Priority Pathogens List, 2024: bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance. 17 May 2024, Report. WHO, Geneva, Switzerland. https://www.who.int/publications/i/item/9789240093461

13 Sánchez-Busó L et al. (2021) A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch. Genome Med 13(1), 61.
| Crossref | Google Scholar |

14 Graham RM et al. (2017) Epidemiological typing of Neisseria gonorrhoeae and detection of markers associated with antimicrobial resistance directly from urine samples using next generation sequencing. Sex Transm Infect 93(1), 65-67.
| Crossref | Google Scholar | PubMed |

15 Street TL et al. (2024) Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with nanopore sequencing. Microb Genom 10(3), 001208.
| Crossref | Google Scholar | PubMed |

16 Zhang C et al. (2021) Multiplex PCR and nanopore sequencing of genes associated with antimicrobial resistance in Neisseria gonorrhoeae directly from clinical samples. Clin Chem 67(4), 610-620.
| Crossref | Google Scholar | PubMed |

17 Centers for Disease Control and Prevention (2022) Sexually transmitted infections surveillance, 2022. Last reviewed: 30 January 2024. CDC, US Department of Health & Human Services. https://www.cdc.gov/std/statistics/2022/default.htm

18 Taouk ML et al. (2022) Characterisation of Treponema pallidum lineages within the contemporary syphilis outbreak in Australia: a genomic epidemiological analysis. Lancet Microbe 3(6), e417-e426.
| Crossref | Google Scholar | PubMed |

19 Multijurisdictional Syphilis Outbreak Working Group (2019) Multijurisdictional Syphilis Outbreak (MJSO) Surveillance Report – consolidated reports May 2019 to January 2019. Australia Communicable Diseases Network of Australia, Australian Government Department of Health and Aged Care. https://www.health.gov.au/resources/publications/multijurisdictional-syphilis-outbreak-mjso-surveillance-report-consolidated-reports-may-2018-to-january-2019?language=en

20 World Health Organization (2023) The diagnostics landscape for sexually transmitted infections. WHO, Geneva, Switzerland. https://www.who.int/publications/i/item/9789240077126

21 Beale MA et al. (2021) Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis. Nat Microbiol 6(12), 1549-1560.
| Crossref | Google Scholar | PubMed |

22 Waites KB et al. (2023) Latest advances in laboratory detection of Mycoplasma genitalium. J Clin Microbiol 61(3), e0079021.
| Crossref | Google Scholar | PubMed |

23 Workowski KA et al. (2021) Sexually transmitted diseases treatment guidelines, 2021. MMWR Rercomm Rep 70(4), 1-187.
| Crossref | Google Scholar |

24 Trembizki E et al. (2017) High levels of macrolide-resistant Mycoplasma genitalium in Queensland, Australia. J Med Microbiol 66(10), 1451-1453.
| Crossref | Google Scholar | PubMed |

25 Fookes MC et al. (2017) Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure. BMC Genomics 18(1), 993.
| Crossref | Google Scholar | PubMed |

26 Chiribau CB et al. (2024) Detection of resistance to macrolides and fluoroquinolones in Mycoplasma genitalium by targeted next-generation sequencing. Microbiol Spectr 12(3), e0384523.
| Crossref | Google Scholar | PubMed |

27 Plummer EL et al. (2020) A custom amplicon sequencing approach to detect resistance associated mutations and sequence types in Mycoplasma genitalium. J Microbiol Methods 179, 106089.
| Crossref | Google Scholar | PubMed |

28 Ojoo S (2003) Clinical practice in sexually transmissible infections. Sexually Transmitted Infect 79(5), 429.
| Crossref | Google Scholar |

29 Andersson P et al. (2013) Sequences of multiple bacterial genomes and a Chlamydia trachomatis genotype from direct sequencing of DNA derived from a vaginal swab diagnostic specimen. Clin Microbiol Infect 19(9), E405-E408.
| Crossref | Google Scholar | PubMed |

30 Suchland RJ et al. (2017) Demonstration of persistent infections and genome stability by whole-genome sequencing of repeat-positive, same-serovar Chlamydia trachomatis collected from the female genital tract. J Infect Dis 215(11), 1657-1665.
| Crossref | Google Scholar | PubMed |

31 Di Pietro M et al. (2018) HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women. New Microbiol 41(1), 34-41.
| Google Scholar | PubMed |

32 Christiansen MT et al. (2014) Whole-genome enrichment and sequencing of Chlamydia trachomatis directly from clinical samples. BMC Infect Dis 14, 591.
| Crossref | Google Scholar | PubMed |

33 Chen W et al. (2024) Revealing the genetic diversity of Chinese Chlamydia trachomatis strains directly from clinical samples through selective whole-genome amplification. J Infect Dis jiae163.
| Crossref | Google Scholar | PubMed |

34 Bommana S et al. (2022) Metagenomic shotgun sequencing of endocervical, vaginal, and rectal samples among Fijian women with and without Chlamydia trachomatis reveals disparate microbial populations and function across anatomic sites: a pilot study. Microbiol Spectr 10(3), e0010522.
| Crossref | Google Scholar | PubMed |

35 Song J et al. (2024) Interpretation of vaginal metagenomic characteristics in different types of vaginitis. mSystems 9(3), e0137723.
| Crossref | Google Scholar | PubMed |