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

Scientific reports publica este artículo de investigación

23 de agosto de 2022

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




Nunez-Garcia J., Abuoun M., Storey N., Brouwer MS., Delgado-Blas JF., Mo SS., Ellaby N., Veldman KT., Haenni M., Chatre P., Madec JY., Hammerl JA., Serna-Bernaldo C., Getino M., La Ragione R., Naas T., Telke AA., Glaser A., Sunde M., Gonzalez-Zorn B., Ellington MJ. y Anjum MF.




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

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



Participantes:

Animal and Plant Health AgencyAnimal and Plant Health Agency (APHA).

Wageningen Bioveterinary Research.

Universidad ComplutenseServicio de Zoonosis de Transmisión Alimentaria y Resistencia a Antimicrobianos (ZTA). Centro de Vigilancia Sanitaria Veterinaria (VISAVET). Universidad Complutense (UCM).

Norwegian Veterinary InstituteNorwegian Veterinary Institute.

Public Health EnglandPublic Health England (PHE).

Agence Nationale de Sécurité Sanitaire de l´alimentation, de l´environnement et du travailAgence Nationale de Sécurité Sanitaire de l´alimentation, de l´environnement et du travail (ANSES).

German Federal Institute for Risk Assessment.

University of SurreyUniversity of Surrey.

Institut PasteurInstitut Pasteur.

Assistance Publique-Hôpitaux de Paris.







Scientific reports
FACTOR YEAR Q
4.996 2021

NLMID: 101563288

PMID: 35999234

ISSN: 2045-2322



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


REVISTA: Sci Rep


NUMERACIÓN: 12(1):14372


AÑO: 2022


EDITORIAL: Nature Publishing Group


AUTORES: Nunez-Garcia J., Abuoun M., Storey N., Brouwer MS., Delgado-Blas JF., Mo SS., Ellaby N., Veldman KT., Haenni M., Chatre P., Madec JY., Hammerl JA., Serna-Bernaldo C., Getino M., La Ragione R., Naas T., Telke AA., Glaser A., Sunde M., Gonzalez-Zorn B., Ellington MJ. and Anjum MF.


PARTICIPANTES VISAVET


13th
Carlos Serna Bernaldo
20th
Bruno González Zorn

DOI: https://doi.org/10.1038/s41598-022-16760-9


CITA ESTA PUBLICACIÓN:

Nunez-Garcia J., Abuoun M., Storey N., Brouwer MS., Delgado-Blas JF., Mo SS., Ellaby N., Veldman KT., Haenni M., Chatre P., Madec JY., Hammerl JA., Serna-Bernaldo C., Getino M., La Ragione R., Naas T., Telke AA., Glaser A., Sunde M., Gonzalez-Zorn B., Ellington MJ. y Anjum MF. Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance. Scientific reports. 12(1):14372. 2022. (A). ISSN: 2045-2322. DOI: 10.1038/s41598-022-16760-9


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