Academic Journal
A comparison of two informative SNP-based strategies for typing Pseudomonas aeruginosa isolates from patients with cystic fibrosis
| العنوان: | A comparison of two informative SNP-based strategies for typing Pseudomonas aeruginosa isolates from patients with cystic fibrosis |
|---|---|
| المؤلفون: | Syrmis, MW, Kidd, TJ, Moser, RJ, Ramsay, KA, Gibson, KM, Anuj, S, Bell, SC, Wainwright, CE, Grimwood, K, Nissen, M, Sloots, TP, Whiley, DM |
| بيانات النشر: | BioMed Central |
| سنة النشر: | 2014 |
| المجموعة: | Griffith University: Griffith Research Online |
| مصطلحات موضوعية: | Microbiology, Clinical sciences, Medical microbiology, Public health |
| الوصف: | Background Molecular typing is integral for identifying Pseudomonas aeruginosa strains that may be shared between patients with cystic fibrosis (CF). We conducted a side-by-side comparison of two P. aeruginosa genotyping methods utilising informative-single nucleotide polymorphism (SNP) methods; one targeting 10 P. aeruginosa SNPs and using real-time polymerase chain reaction technology (HRM10SNP) and the other targeting 20 SNPs and based on the Sequenom MassARRAY platform (iPLEX20SNP). Methods An in-silico analysis of the 20 SNPs used for the iPLEX20SNP method was initially conducted using sequence type (ST) data on the P. aeruginosa PubMLST website. A total of 506 clinical isolates collected from patients attending 11 CF centres throughout Australia were then tested by both the HRM10SNP and iPLEX20SNP assays. Type-ability and discriminatory power of the methods, as well as their ability to identify commonly shared P. aeruginosa strains, were compared. Results The in-silico analyses showed that the 1401 STs available on the PubMLST website could be divided into 927 different 20-SNP profiles (D-value?=?0.999), and that most STs of national or international importance in CF could be distinguished either individually or as belonging to closely related single- or double-locus variant groups. When applied to the 506 clinical isolates, the iPLEX20SNP provided better discrimination over the HRM10SNP method with 147 different 20-SNP and 92 different 10-SNP profiles observed, respectively. For detecting the three most commonly shared Australian P. aeruginosa strains AUST-01, AUST-02 and AUST-06, the two methods were in agreement for 80/81 (98.8%), 48/49 (97.8%) and 11/12 (91.7%) isolates, respectively. Conclusions The iPLEX20SNP is a superior new method for broader SNP-based MLST-style investigations of P. aeruginosa. However, because of convenience and availability, the HRM10SNP method remains better suited for clinical microbiology laboratories that only utilise real-time PCR technology and where the main interest is ... |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1471-2334 |
| Relation: | BMC Infectious Diseases; http://hdl.handle.net/10072/66925 |
| DOI: | 10.1186/1471-2334-14-307 |
| الاتاحة: | http://hdl.handle.net/10072/66925 https://doi.org/10.1186/1471-2334-14-307 |
| Rights: | http://creativecommons.org/licenses/by/2.0 ; © 2014 Syrmis et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. ; open access |
| رقم الانضمام: | edsbas.7FF5C16B |
| قاعدة البيانات: | BASE |
Full Text Finder كن أول من يترك تعليقا!