Accuracy of detection of Streptococcus pneumoniae in clinical laboratories by using phenotypic and molecular methods

Streptococcus pneumoniae, is one of the most important bacterial pathogens and a member of viridians streptococci group. Accurate identification and differentiation of this form of bacteria from other relative streptococci, is the base of epidemiological study of this type of organism. The aim of this study was to evaluate the accuracy of detection of Streptococcus pneumoniae in clinical laboratories in Tehran, by using phenotypic and genotypic methods. A total number of 110 isolates, identified as pneumococci by some clinical laboratories in Tehran, were collected between March 2010 to May 2012.After isolating the colonies, biochemical identification tests by optochin susceptibility (Mast) and bile solubility (direct method) methods were performed. After DNA extraction, PCR was performed to define lytA gene as a molecular identification for Streptococcus pneumonia. After re-identifying the isolates, fifty of them were determined as true pneumococci, and other remaining sixty isolates were identified as: three gram negative coccobacilli, seven non alpha hemolytic streptococci, and fifty Viridans streptococci. Most of misidentifications were related to respiratory and eye infecting streptococci. Unlike non pneumococcal isolates, all 50 pneumococcal isolates were positive for lytA gene. There was 55% error in detection of pneumococci in this study. The use of optochin susceptibility test as the sole detection tool and also lack of supplemental tests and proper quality controlling, are the main causes of failure in diagnosing pneumococci in Iran. Misidentifications may result in incorrect epidemiological data gathering, unnecessary treatment, and false increased antibiotic resistance reports for this organism. Regarding the high incidence of inaccuracies in defining this specific type of microorganism, we suggest the presence of a clinical microbiologist in the hospital laboratories to perform the right diagnostic tests and quality controlling would be essential.