Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance

Autor: Nunez-Garcia, J., AbuOun, M., Storey, N., Brouwer, M.S., Delgado-Blas, J.F., Mo, S.S., Ellaby, N., Veldman, K.T., Haenni, M., Châtre, P., Madec, J.Y., Hammerl, J.A., Serna, C., Getino, M., La Ragione, R., Naas, T., Telke, A.A., Glaser, P., Sunde, M., Gonzalez-Zorn, B., Ellington, M.J., Anjum, M.F.
Přispěvatelé: Animal and Plant Health Agency [Addlestone, UK] (APHA), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Norwegian Veterinary Institute [Oslo], Public Health England [London], Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), German Federal Institute for Risk Assessment [Berlin] (BfR), University of Surrey (UNIS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Écologie et Évolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Rok vydání: 2022
Předmět:
Zdroj: Scientific Reports
Scientific Reports, 2022, 12 (1), pp.14372. ⟨10.1038/s41598-022-16760-9⟩
Scientific Reports, 12(1)
Scientific Reports 12 (2022) 1
Scientific reports
ISSN: 2045-2322
DOI: 10.1038/s41598-022-16760-9⟩
Popis: Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance (AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype–phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.
Databáze: OpenAIRE
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