Diagn Microbiol Infect Dis. 2016 Mar 29. pii: S0732-8893(16)30072-4. doi: 10.1016/j.diagmicrobio.2016.03.018. [Epub ahead of print]

lytA-based identification methods can misidentify Streptococcus pneumoniae.

Simões AS1, Tavares DA1, Rolo D2, Ardanuy C2, Goossens H3, Henriques-Normark B4, Linares J2, de Lencastre H5, Sá-Leão R6.

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Abstract

During surveillance studies we detected, among over 1500 presumptive pneumococci, 11 isolates displaying conflicting or novel results when characterized by widely accepted phenotypic (optochin susceptibility and bile solubility) and genotypic (lytA-BsaAI-RFLP and MLST) identification methods. We aimed to determine the genetic basis for the unexpected results given by lytA-BsaAI-RFLP and investigate the accuracy of the WHO recommended lytA real-time PCR assay to classify these 11 isolates. Three novel lytA-BsaAI-RFLP signatures were found (one in pneumococcus and two in S. mitis). In addition, one pneumococcus displayed the atypical lytA-BsaAI-RFLP signature characteristic of non-pneumococci and two S. pseudopneumoniae displayed the typical lytA-BsaAI-RFLP pattern characteristic of pneumococci. lytA real-time PCR misidentified these three isolates. In conclusion, identification of pneumococci by lytA real-time PCR, and other lytA-based methodologies, may lead to false results. This is of particular relevance in the increasingly frequent colonization studies relying solely on culture-independent methods.

Copyright © 2016 Elsevier Inc. All rights reserved.

KEYWORDS:

Identification; Molecular methods; Real-time PCR; S. pneumoniae; S. pseudopneumoniae; lytA

PMID: 27107535 [PubMed - as supplied by publisher]