High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform

Trembizki, Ella, Smith, Helen, Lahra, Monica M., Chen, Marcus, Donovan, Basil, Fairley, Christopher K., Guy, Rebecca, Kaldor, John, Regan, David, Ward, James, Nissen, Michael D., Sloots, Theo P. and Whiley, David M. (2014) High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform. Journal of Antimicrobial Chemotherapy, 69 6: 1526-1532. doi:10.1093/jac/dkt544


Author Trembizki, Ella
Smith, Helen
Lahra, Monica M.
Chen, Marcus
Donovan, Basil
Fairley, Christopher K.
Guy, Rebecca
Kaldor, John
Regan, David
Ward, James
Nissen, Michael D.
Sloots, Theo P.
Whiley, David M.
Title High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform
Formatted title
High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform
Journal name Journal of Antimicrobial Chemotherapy   Check publisher's open access policy
ISSN 1460-2091
0305-7453
Publication date 2014-06-01
Sub-type Article (original research)
DOI 10.1093/jac/dkt544
Open Access Status Not Open Access
Volume 69
Issue 6
Start page 1526
End page 1532
Total pages 7
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Formatted abstract
Objectives Neisseria gonorrhoeae antimicrobial resistance (AMR) is a global problem heightened by emerging resistance to ceftriaxone. Appropriate molecular typing methods are important for understanding the emergence and spread of N. gonorrhoeae AMR. We report on the development, validation and testing of a Sequenom MassARRAY iPLEX method for multilocus sequence typing (MLST)-style genotyping of N. gonorrhoeae isolates.

Methods An iPLEX MassARRAY method (iPLEX14SNP) was developed targeting 14 informative gonococcal single nucleotide polymorphisms (SNPs) previously shown to predict MLST types. The method was initially validated using 24 N. gonorrhoeae control isolates and was then applied to 397 test isolates collected throughout Queensland, Australia in the first half of 2012.

Results The iPLEX14SNP method provided 100% accuracy for the control isolates, correctly identifying all 14 SNPs for all 24 isolates (336/336). For the 397 test isolates, the iPLEX14SNP assigned results for 5461 of the possible 5558 SNPs (SNP call rate 98.25%), with complete 14 SNP profiles obtained for 364 isolates. Based on the complete SNP profile data, there were 49 different sequence types identified in Queensland, with 11 of the 49 SNP profiles accounting for the majority (nā€Š=ā€Š280; 77%) of isolates. AMR was dominated by several geographically clustered sequence types. Using the iPLEX14SNP method, up to 384 isolates could be tested within 1 working day for less than Aus$10 per isolate.

Conclusions The iPLEX14SNP offers an accurate and high-throughput method for the MLST-style genotyping of N. gonorrhoeae and may prove particularly useful for large-scale studies investigating the emergence and spread of gonococcal AMR.
Keyword Gonorrhoea
Typing
SNP
Sequenom
Resistance
Q-Index Code C1
Q-Index Status Provisional Code

Document type: Journal Article
Sub-type: Article (original research)
Collections: UQ Centre for Clinical Research Publications
School of Medicine Publications
 
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Created: Wed, 18 Nov 2015, 00:58:36 EST by Ella Trembizki on behalf of UQ Centre for Clinical Research