Secvențierea metagenomică în diagnosticul rezistenței la antimicrobiene

Olga Burduniuc; Marina Lupu; Victoria Bucov; Livia Țapu; Maria Anton; Svetlana Colac

doi:10.52673/18570461.24.2-73.08

Authors

Olga Burduniuc Nicolae Testemițanu State University of Medicine and Pharmacy; National Agency for Public Health https://orcid.org/0000-0002-6944-0800
Marina Lupu National Agency for Public Health https://orcid.org/0009-0002-1161-633X
Victoria Bucov National Agency for Public Health https://orcid.org/0009-0005-1042-5947
Livia Tapu National Agency for Public Health; Nicolae Testemițanu State University of Medicine and Pharmacy https://orcid.org/0000-0002-4424-3501
Maria Anton National Agency for Public Health https://orcid.org/0000-0002-4804-7137
Svetlana Colac National Agency for Public Health https://orcid.org/0009-0006-4505-9948

DOI:

https://doi.org/10.52673/18570461.24.2-73.08

Keywords:

metagenomic sequencing, microbiome, antimicrobial resistance, human and non-human samples, riskfactors

Abstract

The purpose of the article is to analyze the literature on antimicrobial resistance and the metagenomic sequencing method. In total, 32 articles published in the years 2019–2024 and some previously published classic works were analyzed. Antimicrobial resistance (AMR) is one of the most serious threats to public health, animal health and environmental well-being globally, generating high costs. Metagenomic sequencing allows the detection of all genes in a sample, providing a complete picture of AMR. By sequencing it is possible to assess the location and transmissibility of the AMR genes. As surveillance networks and metagenomic sequencing, as one of the rapid diagnostic platforms, are implemented globally, it will be possible to detect and limit infectious outbreaks at a much earlier stage, thus saving lives and substantially reducing costs. In the near future, metagenomic sequencing will no longer be a luxury but a necessity as we engage in the ongoing fight against infectious diseases.

References

1. World Health Organisation (WHO). Antimicrobial resistance, [online] https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance(consultat: 19.02.2024).

2. United Nation. Department of Economic and Social Affairs Sustainable Development. Goal 3. Ensure healthy lives and promote well-being for all at all ages, [online] https://sdgs.un.org/goals/goal3 (consultat: 07.02.2024).

3. Murray, C.J., Ikuta, K.S., Sharara, F. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. In: The Lancet, February, 2022, vol. 399 (10325), 629-655.

4. Naylor, N.R., Atun, R., Zhu, N. et al. Estimating the burden of antimicrobial resistance: a systematic literature review. In: Antimicrob Resist Infect Control 7, 58 (2018), https://doi.org/10.1186/s13756-018-0336-y

5. Habboush, Y., Guzman, N. Antibiotic Resistance. 2023, Jun 20. In: StatPearls [Internet]. Treasure Island (FL).

6. Hutchings, M.I., Truman, A.W., Wilkinson, B. Antibiotics: past, present and future. In: Current Opinion Microbiology. 2019, Oct; 51: 72-80.

7. Machowska, A., & Lundborg, C. S. Drivers of irrational use of antibiotics in Europe. In: International Journal of Environmental Research and Public Health, 2019 (Vol. 16, Issue 1), https://doi.org/10.3390/ijerph16010027

8. Wall, S. Prevention of antibiotic resistance an epidemiological scoping review to identify research categories and knowledge gaps. In: Glob Health Action, 2019, Dec 13; 12(1):1756191.

9. Wallace, M.J., Fishbein, SRS, Dantas, G. Antimicrobial resistance in enteric bacteria: current state and next-generation solutions. In: Gut Microbes, 2020, Nov 9; 12(1):1799654.

10. Subramaniam, G., Girish M. Antibiotic Resistance – a cause for reemergence of infections. In: Indian J. Pediatr., 2020, Feb 5, 937-944.

11. Bucov, V., Burduniuc, O., Balan, G. et al. Rezistența la antimicrobiene. Caracteristica rezistenței la preparate antimicrobiene a bacteriilor gram-negative. În: Sănătate Publică, Economie și Management în Medicină, 2021, nr. 1(88), 50-56.

12. Al Wutayd, O., Al Nafeesah, A., Adam, I., Babikir, I. The antibiotic susceptibility patterns of uropathogens isolated in Qassim, Saudi Arabia. In: J Infect Dev Ctries. 2018, Nov 30; 12(11):946-952.

13. National Foundation for Infectious Diseases. Antibiotic Resistance, [online] https://www.nfid.org/antibiotic-resistance/ (consultat: 07.03.2024).

14. Consiliul European/Consiliul Uniunii Europene. Cinci motive pentru a acorda importanță rezistenței la antimicrobiene (RAM), [online] https://www.consilium.europa.eu/ro/infographics/antimicrobial-resistance/ (consultat: 07.02.2024).

15. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Guidelines, [online] http://prisma-statement.org/documents/PRISMA_2020_checklist.pdf (consultat: 19.02.2024).

16. Rezistenta la antibiotice: ce este și cum poate fi prevenita, [online] https://www.catena.ro/rezistenta-la-antibiotice-ce-este-si-cum-poate-fi-prevenita (consultat: 07.03.2024).

17. Antimicrobial resistant bacteria – Better Health Channel, [online] https://www.betterhealth.vic.gov.au/health/conditionsandtreatments/antibiotic-resistant-bacteria (consultat: 07.03.2024).

18. Pérez-Cobas, A.E., Gomez-Valero, L., Buchrieser, C. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. In: Microb Genom. 2020, Aug; 6(8).

19. Handelsman, J., Rondon, M.R., Brady, S.F. et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. In: Chem Biol. 1998, Oct; 5(10), p. 86.

20. Chiu, CY, Miller, SA. Clinical metagenomics. In: Nat Rev Genet. 2019, Jun; 20(6):341-355.

21. Voelkerding, K.V., Dames, S.A., Durtschi, J.D. Next-generation sequencing: from basic research to diagnostics. In: Clin. Chem., 2009, 55:641-658.

22. Waskito, L.A., Rezkitha, Y.A.A., Vilaichone, R.K. et al. Antimicrobial Resistance Profile by Metagenomic and Metatranscriptomic Approach in Clinical Practice: Opportunity and Challenge. In: Antibiotics (Basel). 2022 May 13; 11(5):654.

23. Zhang, Y., Chen, J., Yi X et al. Evaluation of the metagenomic next-generation sequencing performance in pathogenic detection in patients with spinal infection. In: Cell Infect Microbiol. 2022, Oct 27; 12:967584.

24. Danko, D., Bezdan, D., Afshin, E.E. et all. International MetaSUB Consortium. A global metagenomic map of urban microbiomes and antimicrobial resistance. In: Cell., 2021, Jun 24; 184(13):3376-3393.e17.

25. Govender, K.N., Street, T.L., Sanderson, N.D., Eyre, D.W. Metagenomic Sequencing as a Pathogen-Agnostic Clinical Diagnostic Tool for Infectious Diseases: a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies. In: J. Clin. Microbiol. 2021, Aug 18; 59(9).

26. Boolchandani, M., D’Souza, A.W., Dantas, G. Sequencing-based methods and resources to study antimicrobial resistance. In: Nat Rev Genet. 2019 Jun; 20(6):356-370.

27. Duan, H., Li, X., Mei, A., et al. The diagnostic value of metagenomic next generation sequencing in infectious diseases. In: BMC Infect Dis. 2021 Jan 13; 21(1):62.

28. Chen, Y., Wang, J., Niu, T. Clinical and diagnostic values of metagenomic next-generation sequencing for infection in hematology patients: a systematic review and meta-analysis. In: BMC Infect Dis. 2024 Feb 7; 24(1):167.

29. Hilt, E.E., Ferrieri, P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel). 2022 Aug 31; 13(9):1566.

30. Ren, D., Ren, C., Yao, R. et al. The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with sepsis. BMC Infect Dis. 2021 Dec 16; 21(1):1257.

31. Sukumar, S., Martin, F.E., Hughes, T.E., Adler, C.J. Think before you prescribe: how dentistry contributes to antibiotic resistance. Aust Dent J. 2020 Mar; 65(1):21-29.

32. Vinicius, A. C. de Abreu, Perdigão, J., Almeida, S. Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview. In: Front Genet. 2021, Jan 18;11:575592.