A 7-member SNP Assay on the iPlex MassARRAY Platform Provides a Rapid and Affordable Alternative to Typing Major African Staphylococcus aureus Types

Abstract

BackgroundData on the clonal distribution of Staphylococcus aureus in Africa is scanty, partly due to high costs and long turnaround times imposed by conventional genotyping methods such as spa and multilocus sequence typing (MLST) warranting the need for alternative typing approaches. This study applied and evaluated the accuracy, cost and time of using iPlex massARRAY genotyping method on Kenyan staphylococcal isolates.\n\nMethodsFifty four clinical S. aureus isolates from three counties were characterized using iPlex massARRAY, spa and MLST typing methods. Ten Single Nucleotide Polymorphisms (SNPs) from the S. aureus MLST database were assessed by iPlex massARRAY.\n\nResultsThe iPlex massARRAY assay grouped the isolates into 14 SNP genotypes with 9/10 SNPs interrogated showing high detection rates (average 89%). spa and MLST typing revealed 22 spa types and 21 STs that displayed unique regional distribution. spa type t355 (ST152) was the dominant type and t2029 and t037 (ST 241) were observed among MRSA strains. MassARRAY showed 83% and 82% accuracy against spa and MLST typing respectively in isolate classification. Moreover, massARRAY identified all MRSA strains and a novel spa type. MassARRAY had reduced turnaround time (<12 hrs) compared to spa (3 days) and MLST (20 days) typing. The iPlex massARRAY cost approximately 18 USD compared to spa (30 USD) and MLST (126 USD) typing based on consumable costs/isolate.\n\nConclusionUpon validation with a larger collection of isolates, iPlex massARRAY could provide a faster, more affordable and fairly accurate method of resolving African S.aureus isolates especially in large surveillance studies.