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

Ella Trembizki, Helen Smith, Monica M. Lahra, Marcus Chen, Basil Donovan, Christopher K. Fairley, Rebecca Guy, John Kaldor, David Regan, James Ward, Michael D. Nissen, Theo P. Sloots, David M. Whiley

Research output: Contribution to journalArticle

34 Citations (Scopus)

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 (n = 280; 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.

LanguageEnglish
Pages1526-1532
Number of pages7
JournalJournal of Antimicrobial Chemotherapy
Volume69
Issue number6
DOIs
Publication statusPublished - 1 Jan 2014

Keywords

  • Gonorrhoea
  • Resistance
  • SNP
  • Sequenom
  • Typing

ASJC Scopus subject areas

  • Pharmacology
  • Microbiology (medical)
  • Pharmacology (medical)
  • Infectious Diseases

Cite this

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. / High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform. In: Journal of Antimicrobial Chemotherapy. 2014 ; Vol. 69, No. 6. pp. 1526-1532.
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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 (n = 280; 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.",
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Trembizki, E, Smith, H, Lahra, MM, Chen, M, Donovan, B, Fairley, CK, Guy, R, Kaldor, J, Regan, D, Ward, J, Nissen, MD, Sloots, TP & Whiley, DM 2014, 'High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform', Journal of Antimicrobial Chemotherapy, vol. 69, no. 6, pp. 1526-1532. https://doi.org/10.1093/jac/dkt544

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.; Whiley, David M.

In: Journal of Antimicrobial Chemotherapy, Vol. 69, No. 6, 01.01.2014, p. 1526-1532.

Research output: Contribution to journalArticle

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AU - Smith, Helen

AU - Lahra, Monica M.

AU - Chen, Marcus

AU - Donovan, Basil

AU - Fairley, Christopher K.

AU - Guy, Rebecca

AU - Kaldor, John

AU - Regan, David

AU - Ward, James

AU - Nissen, Michael D.

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AU - Whiley, David M.

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