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Diagn Microbiol Infect Dis. 2016 Jun;85(2):141-8. doi: 10.1016/j.diagmicrobio.2016.03.018. Epub 2016 Mar 29.

lytA-based identification methods can misidentify Streptococcus pneumoniae.

Author information

1
Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
2
Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain.
3
Department of Medical Microbiology, University of Antwerp, Antwerp, Belgium; Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
4
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.
5
Laboratory of Molecular Genetics, ITQB, UNL, Oeiras, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA.
6
Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal. Electronic address: rsaleao@itqb.unl.pt.

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.

KEYWORDS:

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

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