Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era.

Streptococcus pneumoniae is a major cause of pneumonia, meningitis and other invasive diseases resulting in high mortality and morbidity among children under the age of five. Inaccurate identification of S. pneumoniae masks the exact estimation of disease burden and could delay treatment options. This is the common problem most frequently faced in developing countries due to several reasons that include poor infrastructure, insensitive operational procedures and lack of expertise. Inconsistent methods for phenotypic detection often delay the early identification and confirmation of S. pneumoniae. For serotyping S. pneumoniae, Quellung method is the gold standard which can be performed only on viable isolates, needs expertise and is expensive. Therefore, the data available on disease burden and serotype prevalence is not truly estimated in most of the developing countries, in turn, the use of available pneumococcal vaccines have been restricted. This current review deliberates an overview on advantages and limitations of routinely used phenotypic tests for S. pneumoniae identification. Also discussed in this review are the roles and current challenges faced by various molecular identification and serogroup/serotype identification methods of S. pneumoniae, including PCR, real time PCR, sequence analysis of different specific genes of S. pneumoniae, PCR combined with RFLP, MALDI-TOF, MLST, MLSA and WGS.