ABSTRACT
Streptococcus pneumoniae identification and serotyping are vital for disease management, surveillance, vaccinedevelopment, and to monitor the emerging serovars. Despite the potential benefits of conventional typing methodbased on culture isolate, it lacks the ability to type directly from the clinical samples. To address the challenge,a novel microarray method was developed to identify and serotype S. pneumoniae in culture positive andculture negative serum specimens. The custom pneumococcal microarray chip was designed using sure designsoftware and evaluated with 90 reference strains, culture positive quantitative real time multiplex polymerasechain reaction (qmPCR) positive (n = 8) and culture negative qmPCR positive (n = 96) serum samples. Toselectively amplify S. pneumoniae DNA from serum, three different methods: (a) Capsular polysaccharidePCR, (b) Whole genome amplification, and (c) Microbial DNA enrichment were assessed. An in-housedeveloped excel-based software was used to quantify the signals from each serotype. With a combination ofMicrobial DNA enrichment, the custom pneumococcal microarray chip identified all the reference strains andserum samples serogroup/type information accurately. Of the 104 serum samples, 65 were uniquely identifiedand 39 were assigned with a combination of their homologous types. A 100% concordance was observed withthe results of qmPCR and PCRSeqTyping methods with an additional advantage of multiple serotype detection.Our results signify the ability of the microarray technology to identify and detect S. pneumoniae serogroup/typefrom culture-negative serum specimens. The test is of use even in patients with prior antibiotic treatment andcan be used in surveillance and vaccine impact studies.