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. 2022 Mar 17;8(3):000788. doi: 10.1099/mgen.0.000788

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© 2022 The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

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Fig. 1. — Experimental and bioinformatic workflow for gene cassette amplicon sequencing. (a) Components of integrons amplified by the two PCR assays. The primer set HS287/HS286 targets cassettes that lie between two attC sites. Potentially any gene cassette(s) can be amplified by this primer set. The primer set intI-R / HS286 targets diverse integron integrases (intI) and cassette recombination sites (attC). The resulting amplicons include ~800 bp of intI and at least the first cassette(s) of an array. (b) The bioinformatic steps and software (in parentheses) used to process and filter amplicon data. Methods are shown for both primer sets sequenced with either Oxford Nanopore (ONT) or Illumina technologies.