In-depth resistome analysis by targeted metagenomics
Microbiome publish this investigation article
January 15th, 2018
BACKGROUND:
Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype. Here, we describe a novel strategy that combines targeted metagenomics using last generation in-solution capture platforms, with novel bioinformatics tools to establish a standardized framework that allows both quantitative and qualitative analyses of resistomes.
METHODS:
We developed ResCap, a targeted sequence capture platform based on SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals). Its performance was compared with metagenomic shotgun sequencing (MSS) for 17 fecal samples (9 humans, 8 swine). ResCap significantly improves MSS to detect "gene abundance" (from 2.0 to 83.2%) and "gene diversity" (26 versus 14.9 genes unequivocally detected per sample per million of reads; the number of reads unequivocally mapped increasing up to 300-fold by using ResCap), which were calculated using novel bioinformatic tools. ResCap also facilitated the analysis of novel genes potentially involved in the resistance to antibiotics, metals, biocides, or any combination thereof.
CONCLUSIONS:
ResCap, the first targeted sequence capture, specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes related to the selection and transfer of antimicrobial resistance (biocides, heavy metals, plasmids). The model opens the possibility to study other complex microbial systems in which minority populations play a relevant role
Lanza VF., Baquero F., Martinez JL., Ramos-Ruiz R., Gonzalez-Zorn B., Andremont A., Sanchez-Valenzuela A., Ehrlich SD., Kennedy S., Ruppe E., van Schaik W., Willems RJ., de la Cruz F. and Coque TM.
 | Servicio de Microbiología. Hospital Universitario Ramón y Cajal. Salud Madrid. Comunidad de Madrid. |
 | Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS). Universidad Complutense (UCM). Universidad Autónoma de Madrid (UAM). Universidad de Alcalá (UAH). Salud Madrid. Comunidad de Madrid. |
 | Unidad asociada de Resistencia a Antibióticos y Virulencia Bacteriana. Consejo Superior de Investigaciones Científicas (CSIC). |
 | Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP). Instituto de Salud Carlos III (ISCIII). |
| Centro Nacional de Biotecnología (CNB). Consejo Superior de Investigaciones Científicas (CSIC). |
 | Unidad de Genómica. Fundación Parque Científico de Madrid (FPCM). |
 | Servicio de Zoonosis de Transmisión Alimentaria y Resistencia a Antimicrobianos (ZTA). Centro de Vigilancia Sanitaria Veterinaria (VISAVET). Universidad Complutense (UCM). |
| Departamento de Sanidad Animal. Facultad de Veterinaria. Universidad Complutense (UCM). |
 | Hôpital Bichat-Claude Bernard. Université Paris Diderot. |
| MetaGénoPolis (MGP). | |
| Université Paris-Saclay. | |
| Center of Host Microbiome Interactions (CHMI). King´s College London (KCL). | |
 | Bioinformatics and Biostatistics HUB. Institut Pasteur. |
| C3BI and Biomics Pole. Institut Pasteur. |
| Centr d´innovation et reserche technologique (CITECH). Institut Pasteur. |
 | Medical Microbiology. Universitair Medisch Centrum Utrecht (UMC Utrecht). |
| Institute of Microbiology and Infection. University of Birmingham. | |
 | Biología Molecular. Instituto de Biomedicina y Biotecnología de Cantabria. Universidad de Cantabria (UC). |
| Hospital Universitario Ramón y Cajal. Salud Madrid. Comunidad de Madrid. |
| Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS). Universidad Complutense (UCM). Universidad Autónoma de Madrid (UAM). Universidad de Alcalá (UAH). Salud Madrid. Comunidad de Madrid. |
