A novel LAMP-based assay for the identification of <i>Streptococcus pneumoniae</i> and <i>Streptococcus pseudopneumoniae</i> in clinical isolates

The Gram-positive bacteria <i>Streptococcus pneumoniae</i> is part of the <i>Streptococcus mitis</i> group (SMG) and causes life-threatening infections, such as pneumonia, sepsis, and meningitis. The closely related <i>Streptococcus pseudopneumoniae</i> has recently been shown to cause respiratory tract infections, as well as invasive infections, especially in patients with comorbidities. Due to the genetic and phenotypic similarities of species belonging to the SMG, the identification of <i>S. pneumoniae</i> and <i>S. pseudopneumoniae</i> is difficult and unreliable using phenotypic tests, as well as matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and 16S rRNA sequencing. In this study, a loop-mediated isothermal amplification (LAMP)-based assay was developed using molecular markers specific for <i>S. pneumoniae</i> (SPN0001) and <i>S. pseudopneumoniae</i> (SPPN_RS10375). The LAMP assay was evaluated using a collection of SMG clinical isolates, concluding that the method provides a correct, reliable, and fast identification of both <i>S. pneumoniae</i> and <i>S. pseudopneumoniae</i> clinical isolates.