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. 2021 Sep 17;12:596984. doi: 10.3389/fmicb.2021.596984

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Copyright © 2021 Guernier-Cambert, Chamings, Collier and Alexandersen.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Flowchart describing three culture-independent methods to identify the presence of antimicrobial resistance genes (ARGs) in fecal samples (n = 10). (A) Non-targeted sequencing of sheared DNA or “Shotgun Metagenomic Sequencing” (SMS) method; (B,C) targeted sequencing using two commercially available AmpliSeq^TM panels targeting ARGs. Sequences obtained with the SMS method were analyzed using two web-based tools (ResFinder and KmerResistance, https://cge.cbs.dtu.dk/services/), and a method based on the comparison of reads and contigs against the NCBI-curated “Bacterial Antimicrobial Resistance Reference Gene Database” (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047). *Targeted sequencing was tested on a subset of samples: 4 with the AMR Research panel, 8 with the Pan-Bacterial Research panel. **refers to Ion Torrent Suite plugins available from the Thermo Fisher Scientific Plugin store. ***Refers to the “One Codex” online platform (available at: https://app.onecodex.com/) used with the AMR Research panel. “ID”: percentage identity threshold; “minL”: minimum length: minimum percentage of coverage compared to reference length or minimum number of nucleotides (nt); “ref”: reference sequences used for comparison with reads and/or contigs.