High-throughput molecular typing of microbes using the Sequenom Massarray platform

David Whiley; Ella Trembizki; Melanie Syrmis; Jenny Nakos; Cheryl Bletchly; Michael Nissen; Graeme Nimmo; Theo P Sloots

doi:10.1071/MA13058

RESEARCH ARTICLE

High-throughput molecular typing of microbes using the Sequenom Massarray platform

David Whiley ^A ^B ^E , Ella Trembizki ^A ^B , Melanie Syrmis ^A ^B , Jenny Nakos ^C , Cheryl Bletchly ^C , Michael Nissen ^A ^B ^C , Graeme Nimmo ^C ^D and Theo P Sloots ^A ^B ^C

+ Author Affiliations

- Author Affiliations

^A Queensland Paediatric Infectious Diseases Laboratory, Royal Children’s Hospital, Brisbane, Qld 4029, Australia

^B Queensland Children’s Medical Research Institute, Royal Children’s Hospital, The University of Queensland, Brisbane, Qld 4029, Australia

^C Pathology Queensland Central Laboratory, Herston, Qld 4029, Australia

^D Griffith University School of Medicine, Southport, Qld 4215, Australia

^E Corresponding author. Tel: +61 7 3636 1623, Fax: +61 7 3636 1401, Email: d.whiley@uq.edu.au

Microbiology Australia 34(4) 175-177 https://doi.org/10.1071/MA13058
Published: 10 October 2013

Abstract

The advent of newer technologies, including next-generation sequencing (NGS) and matrix assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS), have continued to drive a considerable renaissance in microbial molecular typing methods. The Sequenom Massarray iPLEX single nucleotide polymorphism (SNP) typing platform (Figure 1) combines MALDI-TOF MS with single-base extension PCR for high-throughput multiplex SNP characterisation¹. While the method has primarily been used in the human genetics field, it is now beginning to find its way into the microbiology laboratory. In our hands, the platform has proved highly advantageous for large-scale microbial investigations, enabling multiple SNPs to be characterised for many hundreds of isolates in just over one working day, and at a fraction of the cost of conventional technologies.

References

[1] Leushner, J. and Chiu, N.H. (2000) Automated mass spectrometry: a revolutionary technology for clinical diagnostics. Mol. Diagn. 5, 341–348.
| 1:CAS:528:DC%2BD3MXls1Gmsg%3D%3D&md5=6521f99794bee79f37c173c722bfdf1bCAS | 11172498PubMed |

[2] Syrmis, M.W. et al. (2011) Comparison of a multiplexed MassARRAY system with real-time allele-specific PCR technology for genotyping of methicillin-resistant Staphylococcus aureus. Clin. Microbiol. Infect. 17, 1804–1810.
| Comparison of a multiplexed MassARRAY system with real-time allele-specific PCR technology for genotyping of methicillin-resistant Staphylococcus aureus.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XmtlWitA%3D%3D&md5=024a05fe039c597dd185b69e0d0b974dCAS | 21595795PubMed |

[3] Syrmis, M.W. et al. (2013) High-throughput single-nucleotide polymorphism-based typing of shared Pseudomonas aeruginosa strains in cystic fibrosis patients using the Sequenom iPLEX platform. J. Med. Microbiol. 62, 734–740.
| High-throughput single-nucleotide polymorphism-based typing of shared Pseudomonas aeruginosa strains in cystic fibrosis patients using the Sequenom iPLEX platform.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXpsFCmsbg%3D&md5=26932e5d91e17621905fd9b69954f7e3CAS | 23412772PubMed |

[4] Wieser, A. et al. (2012) MALDI-TOF MS in microbiological diagnostics – identification of microorganisms and beyond (mini review). Appl. Microbiol. Biotechnol. 93, 965–974.
| 1:CAS:528:DC%2BC38Xht1Wru7s%3D&md5=358e6b917b78f7bbab5ee18a0441897eCAS | 22198716PubMed |

[5] Dunne, W.M. et al. (2012) Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur. J. Clin. Microbiol. Infect. Dis. 31, 1719–1726.
| Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhtFCjsb%2FO&md5=ccfc8a23eafbb057e67a238524afcbbaCAS | 22678348PubMed |

[6] Boers, S.A. et al. (2012) High-throughput multilocus sequence typing: bringing molecular typing to the next level. PLoS ONE 7, e39630.
| High-throughput multilocus sequence typing: bringing molecular typing to the next level.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhtV2msbrE&md5=274bd60901c6ccd43c0bdfb709409f49CAS | 22815712PubMed |