A comparison of two informative SNP-based strategies for typing Pseudomonas aeruginosa isolates from patients with cystic fibrosis

被引:16
作者
Syrmis, Melanie W. [1 ,2 ]
Kidd, Timothy J. [1 ,2 ]
Moser, Ralf J. [3 ]
Ramsay, Kay A. [1 ,2 ]
Gibson, Kristen M. [1 ]
Anuj, Snehal [1 ]
Bell, Scott C. [1 ,4 ]
Wainwright, Claire E. [1 ,5 ]
Grimwood, Keith [1 ,2 ]
Nissen, Michael [1 ,2 ,6 ]
Sloots, Theo P. [1 ,2 ,6 ]
Whiley, David M. [1 ,2 ]
机构
[1] Univ Queensland, Queensland Childrens Med Res Inst, Brisbane, Qld 4029, Australia
[2] Royal Childrens Hosp, Queensland Paediat Infect Dis Lab, Brisbane, Qld 4029, Australia
[3] Sequenom Inc, Sequenom Asia Pacific, Brisbane, Qld 4029, Australia
[4] Prince Charles Hosp, Dept Thorac Med, Brisbane, Qld 4032, Australia
[5] Royal Childrens Hosp, Queensland Childrens Resp Ctr, Brisbane, Qld 4029, Australia
[6] Pathol Queensland Cent Lab, Div Microbiol, Brisbane, Qld 4029, Australia
来源
BMC INFECTIOUS DISEASES | 2014年 / 14卷
基金
英国医学研究理事会;
关键词
Pseudomonas aeruginosa; Typing; Cystic fibrosis; MLST; SNP; BACTERIAL; IDENTIFICATION; STRAINS; ERA;
D O I
10.1186/1471-2334-14-307
中图分类号
R51 [传染病];
学科分类号
100401 ;
摘要
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 detection of the most highly-prevalent P. aeruginosa CF strains within Australian clinics.
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页数:8
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