Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements.

ABSTRACT: The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic ele

SUBMITTER: Stedtfeld RD 

PROVIDER: S-EPMC7250373 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature