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Targeted metagenomics for analysis of resistomes (RESCAP1.0)

AutorLanza, Val F. ; Baquero, Fernando; Gonzalez-Zorn, B.; Cruz, Fernando de la ; Coque, Teresa M.
Fecha de publicación2017
CitaciónFEMS 2017
Resumen[Backgrounds]: Antimicrobial resistance is considered a major Global Health challenge. The ensemble of antibiotic resistance genes in particular metagenomes constitutes a “resistome”. Methodological limitations of available high-throughput metagenomic technologies could have seriously influenced our perception about the size and diversity of different resistomes. [Objectives]: To develop a targeted capture platform (TCP) for improving the quantitative and qualitative analysis of resistomes (ensemble of genes encoding antibiotic resistance and their precursors in metagenomes). To evaluate the pool of antimicrobial resistance genes (heavy metals, biocides) and plasmid markers (relaxases), relevant for the selection and transmissibility of antimicrobial resistance genes. [Methods]: ResCap (a TCP based on NimbleGene-Roche technology), includes probes for 8,667 canonical genes (7,963 to antibiotics, 704 to metal & biocides), 76.000 genes homologous to the former ones (47,806 for antibiotics and 30,794 for biocide and metals) and 2,517 relaxase genes (plasmid markers). Comparison of ResCap with metagenomic shotgun sequencing (MSS) was performed using 17 fecal samples (9 humans, 8 swine). [Conclusions]: ResCap significantly improves MSS to detect “gene abundance” (from 2.0% to 83.2%) and “gene diversity” (26 versus 14.9 genes per sample per million of reads, 300 fold by using ResCap), which were calculated using novel bioinformatic tools. New approaches are also provided to compare disparate resistomes. ResCap, the first TCP to analyse resistomes, clearly enhance the sensitivity and specificity of available metagenomic methods, provides the possibility to analyse other genes related to antimicrobial resistance and opens the possibility to accurately study other complex microbial systems.
DescripciónResumen del trabajo presentado al 7th Congress of European Microbiologists, celebrado en Valencia (España) del 9 al 13 de julio de 2017.-- Lanza, Val F. et al.
URIhttp://hdl.handle.net/10261/164855
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