1887

Microbial Genomics logo

Volume 9, Issue 8

Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards Open Access

This article is part of the Implementation of Genomics in Clinical and Public Health Microbiology collection

Abstract

Pathogen genomics has transitioned rapidly from the research setting into a powerful tool now routinely used in public health microbiology, for surveillance, outbreak investigations and disease control. As these investigations can have significant public health, treatment and legal impacts, we must ensure the accuracy of these results through validation of testing processes. For laboratories working in this space, it is important to approach this work with a quality and accreditation framework in mind, working towards implementation of quality systems and test validation that meet international regulatory standards. Here we outline the key international standards and processes that lead toward accreditation for pathogen genomics.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): international standards , laboratory accreditation and whole-genome sequencing
Funding
This study was supported by the:
  • Medical Research Future Fund (Award FSPGN000049)
    • Principle Award Recipient: BenjaminP Howden
  • National Health and Medical Research Council (Award GNT1149991)
    • Principle Award Recipient: BenjaminP Howden
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.001097
2023-08-17
2024-05-18
Loading full text...

Full text loading...

/deliver/fulltext/mgen/9/8/mgen001097.html?itemId=/content/journal/mgen/10.1099/mgen.0.001097&mimeType=html&fmt=ahah

References

  1. Cameron A, Bohrhunter JL, Taffner S, Malek A, Pecora ND et al. Clinical pathogen genomics. Clin Lab Med 2020; 40:447–458 [View Article] [PubMed]
     [Google Scholar]
  2. Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG et al. Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis. Clin Microbiol Rev 2018; 31:1015–1063 [View Article] [PubMed]
     [Google Scholar]
  3. Kwong JC, Mercoulia K, Tomita T, Easton M, Li HY et al. Prospective whole-genome sequencing enhances National surveillance of Listeria monocytogenes. J Clin Microbiol 2016; 54:333–342 [View Article] [PubMed]
     [Google Scholar]
  4. Kwong JC, Lane CR, Romanes F, Gonçalves da Silva A, Easton M et al. Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak. PeerJ 2018; 6:e4210 [View Article] [PubMed]
     [Google Scholar]
  5. Kwong JC, Stafford R, Strain E, Stinear TP, Seemann T et al. Sharing is caring: international sharing of data enhances genomic surveillance of Listeria monocytogenes. Clin Infect Dis 2016; 63:846–848 [View Article] [PubMed]
     [Google Scholar]
  6. European Food Safety Authority (EFSA) EFSA statement on the requirements for whole genome sequence analysis of microorganisms intentionally used in the food chain. EFSA J 2021; 19:e06506 [View Article] [PubMed]
     [Google Scholar]
  7. Stevens EL, Carleton HA, Beal J, Tillman GE, Lindsey RL et al. Use of whole genome sequencing by the federal interagency collaboration for genomics for food and feed safety in the United States. J Food Prot 2022; 85:755–772 [View Article] [PubMed]
     [Google Scholar]
  8. Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL. Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev 2015; 28:541–563 [View Article] [PubMed]
     [Google Scholar]
  9. Lane CR, Sherry NL, Porter AF, Duchene S, Horan K et al. Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study. Lancet Public Health 2021; 6:e547–e556 [View Article] [PubMed]
     [Google Scholar]
  10. Coate J. COVID-19 Hotel Quarantine Inquiry Final Report and Recommendations. 2018-2020. n.d
  11. Victorian Government Victorian guideline on carbapenemase-producing Enterobacteriaceae Version 2.1; 2017 https://www.health.vic.gov.au/infectious-diseases/victorian-guideline-on-cpe-for-health-services-version-21 accessed 24 July 2023
  12. Donnan EJ, Marais BJ, Coulter C, Waring J, Bastian I et al. The use of whole genome sequencing for tuberculosis public health activities in Australia: a joint statement of the National Tuberculosis Advisory Committee and Communicable Diseases Genomics Network. Commun Dis Intell 2023; 47: [View Article] [PubMed]
     [Google Scholar]
  13. Allard MW, Strain E, Melka D, Bunning K, Musser SM et al. Practical value of food pathogen traceability through building a whole-genome sequencing network and database. J Clin Microbiol 2016; 54:1975–1983 [View Article] [PubMed]
     [Google Scholar]
  14. Hoang T, da Silva AG, Jennison AV, Williamson DA, Howden BP et al. AusTrakka: fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic. Nat Commun 2022; 13:865 [View Article] [PubMed]
     [Google Scholar]
  15. Matthews TC, Bristow FR, Griffiths EJ, Petkau A, Adam J et al. The Integrated Rapid Infectious Disease Analysis (IRIDA) platform. Bioinformatics 2018381830 [View Article]
     [Google Scholar]
  16. Llarena A, Ribeiro‐Gonçalves BF, Nuno Silva D, Halkilahti J, Machado MP et al. INNUENDO: a cross‐sectoral platform for the integration of genomics in the surveillance of food‐borne pathogens. EFS3 2018; 15:11 [View Article]
     [Google Scholar]
  17. Zima T. Accreditation of medical laboratories - system, process, benefits for labs. J Med Biochem 2017; 36:231–237 [View Article] [PubMed]
     [Google Scholar]
  18. National Association of Testing Authorities Australia (NATA); 2021 https://nata.com.au]
  19. Singapore Accreditation Council; 2022 https://www.sac-accreditation.gov.sg
  20. United Kingdom Accreditation Services (UKAS); 2022 https://www.ukas.com
  21. Centres for Disease Control and Prevention (CDC) Clinical Laboratory Improvement Amendments; 2022 https://www.cms.gov/regulations-and-guidance/legislation/clia
  22. European Accreditation Cooperation; 2022 https://european-accreditation.org
  23. International Accreditation New Zealand; 2022 https://www.ianz.govt.nz
  24. Therapeutic Goods Administration Regulatory requirements for in-house IVDs. In: Australian Government Department of Health, editor. Canberra; 2016 https://www.tga.gov.au/resources/resource/guidance/regulatory-requirements-house-ivds
  25. Kozyreva VK, Truong C-L, Greninger AL, Crandall J, Mukhopadhyay R et al. Validation and implementation of clinical laboratory improvements act-compliant whole-genome sequencing in the public health microbiology laboratory. J Clin Microbiol 2017; 55:2502–2520 [View Article] [PubMed]
     [Google Scholar]
  26. Van Walle I, Björkman JT, Cormican M, Dallman T, Mossong J et al. Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015. Euro Surveill 2018; 23: [View Article]
     [Google Scholar]
  27. Portmann A-C, Fournier C, Gimonet J, Ngom-Bru C, Barretto C et al. A validation approach of an end-to-end whole genome sequencing workflow for source tracking of Listeria monocytogenes and Salmonella enterica. Front Microbiol 2018; 9:446 [View Article] [PubMed]
     [Google Scholar]
  28. Price TK, Realegeno S, Mirasol R, Tsan A, Chandrasekaran S et al. Validation, implementation, and clinical utility of whole genome sequence-based bacterial identification in the clinical microbiology laboratory. J Mol Diagn 2021; 23:1468–1477 [View Article] [PubMed]
     [Google Scholar]
  29. Arnold C, Edwards K, Desai M, Platt S, Green J et al. Setup, validation, and quality control of a centralized whole-genome-sequencing laboratory: lessons learned. J Clin Microbiol 2018; 56:e00261-18 [View Article] [PubMed]
     [Google Scholar]
  30. Bogaerts B, Delcourt T, Soetaert K, Boarbi S, Ceyssens P-J et al. A bioinformatics whole-genome sequencing workflow for clinical Mycobacterium tuberculosis complex isolate analysis, validated using a reference collection extensively characterized with conventional methods and In Silico approaches. J Clin Microbiol 2021; 59:e00202-21 [View Article] [PubMed]
     [Google Scholar]
  31. Bogaerts B, Nouws S, Verhaegen B, Denayer S, Van Braekel J et al. Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods. Microb Genom 2021; 7:mgen000531 [View Article] [PubMed]
     [Google Scholar]
  32. Bogaerts B, Winand R, Fu Q, Van Braekel J, Ceyssens P-J et al. Validation of a bioinformatics workflow for routine analysis of whole-genome sequencing data and related challenges for pathogen typing in a European National Reference Center: Neisseria meningitidis as a proof-of-concept. Front Microbiol 2019; 10:362 [View Article] [PubMed]
     [Google Scholar]
  33. Timme RE, Strain E, Baugher JD, Davis S, Gonzalez-Escalona N et al. Phylogenomic pipeline validation for foodborne pathogen disease surveillance. J Clin Microbiol 2019; 57:e01816-18 [View Article] [PubMed]
     [Google Scholar]
  34. Papp M, Solymosi N. Review and comparison of antimicrobial resistance gene databases. Antibiotics 2022; 11:339 [View Article] [PubMed]
     [Google Scholar]
  35. Raphenya AR, Robertson J, Jamin C, de Oliveira Martins L, Maguire F et al. Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing. Sci Data 2022; 9:341 [View Article] [PubMed]
     [Google Scholar]
  36. Eppinger M, Pearson T, Koenig SSK, Pearson O, Hicks N et al. Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic. mBio 2014; 5:e01721 [View Article] [PubMed]
     [Google Scholar]
  37. Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 2011; 477:462–465 [View Article] [PubMed]
     [Google Scholar]
  38. Oprea M, Njamkepo E, Cristea D, Zhukova A, Clark CG et al. The seventh pandemic of cholera in Europe revisited by microbial genomics. Nat Commun 2020; 11:5347 [View Article] [PubMed]
     [Google Scholar]
  39. Bartels SA, Fraulin G, Etienne S, Wisner SC, Lee S. Cholera in the Time of MINUSTAH: experiences of community members affected by Cholera in Haiti. Int J Environ Res Public Health 2022; 19:4974 [View Article] [PubMed]
     [Google Scholar]
  40. Sarno E, Pezzutto D, Rossi M, Liebana E, Rizzi V. A review of significant European foodborne outbreaks in the last decade. J Food Prot 2021; 84:2059–2070 [View Article] [PubMed]
     [Google Scholar]
  41. Wu F, Zhao S, Yu B, Chen Y-M, Wang W et al. A new coronavirus associated with human respiratory disease in China. Nature 2020; 580:265–269 [View Article] [PubMed]
     [Google Scholar]
  42. Lucey M, Macori G, Mullane N, Sutton-Fitzpatrick U, Gonzalez G et al. Whole-genome Sequencing to Track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) transmission in nosocomial outbreaks. Clin Infect Dis 2021; 72:e727–e735 [View Article] [PubMed]
     [Google Scholar]
  43. World Health Organization Origin of SARS-CoV-2 virus. Geneva; 2020 https://www.who.int/publications/i/item/origin-of-sars-cov-2
  44. Maxmen A. Divisive COVID ‘lab leak’ debate prompts dire warnings from researchers. Nature 2021; 594:15–16 [View Article]
     [Google Scholar]
  45. Robinson JO, Coombs GW, Speers DJ, Keehner T, Keil AD et al. Mycobacterium chimaera colonisation of heater-cooler units (HCU) in Western Australia, 2015: investigation of possible iatrogenic infection using whole genome sequencing. Euro Surveill 2016; 21:46 [View Article] [PubMed]
     [Google Scholar]
  46. Schreiber PW, Kohl TA, Kuster SP, Niemann S, Sax H. The global outbreak of Mycobacterium chimaera infections in cardiac surgery-A systematic review of whole-genome sequencing studies and joint analysis. Clin Microbiol Infect 2021; 27:1613–1620 [View Article] [PubMed]
     [Google Scholar]
  47. Barker TA, Dandekar U, Fraser N, Dawkin L, Sweeney P et al. Minimising the risk of Mycobacterium chimaera infection during cardiopulmonary bypass by the removal of heater-cooler units from the operating room. Perfusion 2018; 33:264–269 [View Article] [PubMed]
     [Google Scholar]
  48. Public Health Laboratory Network Australia PHLN Guidance and Survey regarding Mycobacterium chimaera & heater-cooler units. Canberra: Australian Government Department of Health; 2016 https://www.health.gov.au/resources/publications/phln-guidance-regarding-mycobacterium-chimaera-and-heater-cooler-units?language=en
  49. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011; 364:730–739 [View Article] [PubMed]
     [Google Scholar]
  50. Meumann EM, Krause VL, Baird R, Currie BJ. Using genomics to understand the epidemiology of infectious diseases in the Northern territory of Australia. Trop Med Infect Dis 2022; 7:181 [View Article] [PubMed]
     [Google Scholar]
  51. Walker TM, Miotto P, Köser CU, Fowler PW, Knaggs J et al. The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis. Lancet Microbe 2022; 3:e265–e273 [View Article] [PubMed]
     [Google Scholar]
  52. Stanley S, Liu Q, Fortune SM. Mycobacterium tuberculosis functional genetic diversity, altered drug sensitivity, and precision medicine. Front Cell Infect Microbiol 2022; 12:1007958 [View Article] [PubMed]
     [Google Scholar]
  53. Australian Institute of Health & Safety Victorian Department of Health charged over hotel quarantine program; 2021 https://www.aihs.org.au/news-and-publications/news/victorian-department-health-charged-over-hotel-quarantine-program
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.001097
Loading
Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards
M Gen 9, 001097 (2023); https://doi.org/10.1099/mgen.0.001097
/content/journal/mgen/10.1099/mgen.0.001097
/content/journal/mgen/10.1099/mgen.0.001097
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error