SNaPaer. A Practical Single Nucleotide Polymorphism Multiplex Assay for Genotyping of Pseudomonas aeruginosa

• Type: Article in International Scientific Journal
• Date: 2013

Authors

Nadia Eusebio (Author) Other; Tiago Pinheiro (Author) Other; Adelina A Amorim (Author) Other; Fernanda Gamboa (Author) Other; Lucilia Saraiva (Author) FFUP; Leonor Gusmao (Author) Other; Antonio Amorim (Author) FCUP; Ricardo Araujo (Author) Other

Journal

Title: PLoS ONE

Vol. 8 No. 1

Final page: e66083

ISSN: 1932-6203

Publisher: Public Library of Science

Indexing

ISI Web of Knowledge - 12 Citations

Scopus - 13 Citations

Other information

Authenticus ID: P-005-01K

DOI: 10.1371/journal.pone.0066083

Abstract (EN): Multilocus sequence typing (MLST) represents the gold standard genotyping method in studies concerning microbial population structure, being particularly helpful in the detection of clonal relatedness. However, its applicability on large-scale genotyping is limited due to the high cost and time spent on the task. The selection of the most informative nucleotide positions simplifies genomic characterization of bacteria. A simple and informative multiplex, SNaPaer assay, was developed and genotyping of Pseudomonas aeruginosa was obtained after a single reaction of multiplex PCR amplification and mini-sequencing. This cost-effective technique allowed the analysis of a Portuguese set of isolates (n = 111) collected from three distinct hospitals and the genotyping data could be obtained in less than six hours. Point mutations were shown to be the most frequent event responsible for diversification of the Portuguese population sample. The Portuguese isolates corroborated the epidemic hypothesis for P. aeruginosa population. SNaPaer genotyping assay provided a discriminatory power of 0.9993 for P. aeruginosa, by testing in silico several hundreds of MLST profiles available online. The newly proposed assay targets less than 0.01% of the total MLST length and guarantees reproducibility, unambiguous analysis and the possibility of comparing and transferring data between different laboratories. The plasticity of the method still supports the addition of extra molecular markers targeting specific purposes/populations. SNaPaer can be of great value to clinical laboratories by facilitating routine genotyping of P. aeruginosa.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 8