Multiplex <b><i>gyrB</i></b> PCR Assay for Identification of <b><i>Acinetobacter baumannii</i></b> Is Validated by Whole Genome Sequence-Based Assays

Abstract

<b><i>Objective:</i></b> A multiplex <i>gyrB</i> PCR assay has been used to diagnose <i>Acinetobacter baumannii</i>. However, this assay has not been validated against the gold standard DNA-DNA hybridization assay, which is a laborious method. DNA-DNA hybridization assay is now replaced by whole genome sequence (WGS)-based methods. Two such methods are a <i>k</i>-mer-based search of sequence reads using the Kraken 2 program and average nucleotide identity (ANI). The objective was to validate the <i>gyrB</i> PCR assay with WGS-based methods. <b><i>Subjects and Methods:</i></b> We cultured 270 sequential <i>A. baumannii</i> isolates from the rectal swabs of 32 adult patients. The identity of the isolates was determined by <i>gyrB</i> PCR. The sequences of 269 isolates were determined by Illumina sequencing and the taxonomy was inferred by the Kraken 2 program and ANI. <b><i>Results:</i></b> All the 269 isolates were confirmed as <i>A. baumannii</i> by Kraken 2 and ANI. <b><i>Conclusion:</i></b> The <i>gyrB</i> PCR assay is now validated for easy identification of <i>A. baumannii</i> in comparison with gold standard WGS-based assays.