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In-Depth Resistome Analysis by Targeted Metagenomics

Val F. Lanza, Fernando Baquero, José Luós Martónez, Ricardo Ramos-Ruóz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Dusko Ehrlich, Sean Kennedy, Etienne Ruppe, Willem van Schaik, Rob J. Willems, Fernando de la Cruz, Teresa M. Coque
doi: https://doi.org/10.1101/104224
Val F. Lanza
1Servicio de Microbiología, Hospital Universitario Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
2Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC)
3Network Research Centre in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
4Centro Nacional de BiotecnologÍa. CSIC. Darwin 3. 28049-Madrid. Spain
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Fernando Baquero
1Servicio de Microbiología, Hospital Universitario Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
2Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC)
3Network Research Centre in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
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José Luós Martónez
2Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC)
4Centro Nacional de BiotecnologÍa. CSIC. Darwin 3. 28049-Madrid. Spain
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Ricardo Ramos-Ruóz
5Genomics Unit, Science Park, Madrid.
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Bruno González-Zorn
6Facultad de Veterinaria Universidad Complutense de Madrid, Spain
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Antoine Andremont
7IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Bactériologie Laboratory, Hôpital Bichat, AP-HP, Paris, France.
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Antonio Sánchez-Valenzuela
1Servicio de Microbiología, Hospital Universitario Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
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Dusko Ehrlich
8MGP MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
9Centre of Host Microbiome Interactions, King’s College, London, United Kingdom
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Sean Kennedy
8MGP MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Etienne Ruppe
8MGP MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Willem van Schaik
10Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands.
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Rob J. Willems
10Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands.
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Fernando de la Cruz
11Departamento de Biología Molecular, 4Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-CSIC), Santander, Spain
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Teresa M. Coque
1Servicio de Microbiología, Hospital Universitario Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
2Joint Unit of Antibiotic Resistance and Bacterial Virulence associated with the Spanish National Research Council (CSIC)
3Network Research Centre in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
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ABSTRACT

We developed ResCap, a targeted sequence capture platform based on SeqCapEZ technology, to analyse resistomes and other genes related to antimicrobial resistance (heavy metals, biocides and plasmids). ResCap includes probes for 8,667 canonical resistance genes (7,963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), plus 2,517 relaxase genes (plasmid markers). Besides, it includes 78.600 genes homologous to the previous ones (47,806 for antibiotics and 30,794 for biocide or metals). ResCap enriched 279-fold the targeted sequences detected by metagenomic shotgun sequencing and improves their identification. Novel bioinformatic approaches allow quantifying “gene abundance” and “gene diversity”. ResCap, the first targeted sequence capture specifically developed to analyse resistomes, enhances the sensitivity and specificity of available metagenomic methods to analyse antibiotic resistance in complex populations, enables the analysis of other genes related to antimicrobial resistance and opens the possibility to accurately study other complex microbial systems.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 30, 2017.
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In-Depth Resistome Analysis by Targeted Metagenomics
Val F. Lanza, Fernando Baquero, José Luós Martónez, Ricardo Ramos-Ruóz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Dusko Ehrlich, Sean Kennedy, Etienne Ruppe, Willem van Schaik, Rob J. Willems, Fernando de la Cruz, Teresa M. Coque
bioRxiv 104224; doi: https://doi.org/10.1101/104224
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In-Depth Resistome Analysis by Targeted Metagenomics
Val F. Lanza, Fernando Baquero, José Luós Martónez, Ricardo Ramos-Ruóz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Dusko Ehrlich, Sean Kennedy, Etienne Ruppe, Willem van Schaik, Rob J. Willems, Fernando de la Cruz, Teresa M. Coque
bioRxiv 104224; doi: https://doi.org/10.1101/104224

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