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.

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

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

	Animal and Plant Health Agency (APHA).
	Wageningen Bioveterinary Research.
	Servicio de Zoonosis de Transmisión Alimentaria y Resistencia a Antimicrobianos (ZTA). Centro de Vigilancia Sanitaria Veterinaria (VISAVET). Universidad Complutense (UCM).
	Norwegian Veterinary Institute.
	Public Health England (PHE).
	Agence Nationale de Sécurité Sanitaire de l´alimentation, de l´environnement et du travail (ANSES).
	German Federal Institute for Risk Assessment.
	University of Surrey.
	Institut Pasteur.
	Assistance Publique-Hôpitaux de Paris.