1. Comparison of Whole Genome Sequencing and Repetitive Element PCR for Multidrug-Resistant Pseudomonas aeruginosa Strain Typing
- Author
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Sabeen Raza, Ruth Ann Luna, Alamelu Venkatachalam, James Versalovic, Jennifer K. Spinler, Tiana Scott, James J. Dunn, Jessica K. Runge, and Santosh Thapa
- Subjects
Whole genome sequencing ,education.field_of_study ,Whole Genome Sequencing ,Strain (biology) ,Population ,Computational biology ,Biology ,Polymerase Chain Reaction ,Genome ,Bacterial Typing Techniques ,Pathology and Forensic Medicine ,genomic DNA ,Phylogenomics ,Pseudomonas aeruginosa ,Humans ,Molecular Medicine ,Multilocus sequence typing ,Typing ,Child ,education ,Phylogeny ,Multilocus Sequence Typing ,Repetitive Sequences, Nucleic Acid - Abstract
Hospital-acquired infections pose significant costly global challenges to patient care. Rapid and sensitive methods to identify potential outbreaks are integral to infection control measures. Whole-genome sequencing (WGS)-based bacterial strain typing provides higher discriminatory power over standard nucleotide banding pattern-based methods such as repetitive sequence-based PCR (rep-PCR). However, integration of WGS into clinical epidemiology is limited by the lack of consensus in methodology and data analysis/interpretation. In this study, WGS was performed on genomic DNA extracted from 22 multidrug-resistant Pseudomonas aeruginosa (MDR-PA) isolates using next-generation sequencing. Resulting high-quality reads were analyzed for phylogenetic relatedness using a whole-genome multilocus sequence typing (wgMLST)-based software program and single-nucleotide variant phylogenomics (SNVPhyl). WGS-based results were compared with conventional MLST and archived rep-PCR results. Rep-PCR identified three independent clonal clusters of MDR-PA. Only one clonal cluster identified by rep-PCR, an endemic strain within the pediatric cystic fibrosis population at Texas Children's Hospital, was concordantly identified using wgMLST and SNVPhyl. Results were highly consistent between the three sequence-based analyses (conventional MLST, wgMLST, and SNVPhyl), and these results remained consistent with the addition of 74 MDR-PA genomes. These WGS-based methods provided greater resolution for strain discrimination than rep-PCR or standard MLST classification, and the ease of use of wgMLST software renders it clinically viable for analysis, interpretation, and reporting of WGS-based strain typing.
- Published
- 2022
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