Multiplex gyrB PCR Assay for Identification of Acinetobacter baumannii Is Validated by Whole Genome Sequence-Based Assays

• Published in: Medical principles and practice Vol. 31; no. 5; pp. 493 - 496
• Main Authors: Albert, M. John, Al-Hashem, Ghayda, Rotimi, Vincent O.
• Format: Journal Article
• Language: English
• Published: Basel, Switzerland S. Karger AG 01.12.2022
• Subjects: Acinetobacter baumannii - genetics; Acinetobacter Infections - diagnosis; Adult; Anti-Bacterial Agents; Automation; Bacteria; Brief Report; DNA; Genetic testing; Genomes; Humans; Identification; Infections; Intensive care; Laboratories; Multiplex Polymerase Chain Reaction - methods; Patients; Taxonomy; Whole genome sequencing; Acinetobacter baumannii; Kraken 2 program; Average nucleotide identity; gyrB PCR; Whole-genome sequencing; DNA-DNA hybridization
• ISSN: 1011-7571; 1423-0151; 1423-0151
• DOI: 10.1159/000526402

Objective: A multiplex gyrB PCR assay has been used to diagnose Acinetobacter baumannii. 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 k-mer-based search of sequence reads using the Kraken 2 program and average nucleotide identity (ANI). The objective was to validate the gyrB PCR assay with WGS-based methods. Subjects and Methods: We cultured 270 sequential A. baumannii isolates from the rectal swabs of 32 adult patients. The identity of the isolates was determined by gyrB PCR. The sequences of 269 isolates were determined by Illumina sequencing and the taxonomy was inferred by the Kraken 2 program and ANI. Results: All the 269 isolates were confirmed as A. baumannii by Kraken 2 and ANI. Conclusion: The gyrB PCR assay is now validated for easy identification of A. baumannii in comparison with gold standard WGS-based assays.