LytA-based identification methods can misidentify Streptococcus pneumoniae

Alexandra S. Simões; Débora A. Tavares; Dora Rolo; Carmen Ardanuy; Herman Goossens; Birgitta Henriques-Normark; Josefina Linares; Hermínia de Lencastre; Raquel Sá-Leão

doi:10.1016/j.diagmicrobio.2016.03.018

LytA-based identification methods can misidentify Streptococcus pneumoniae

Alexandra S. Simões, Débora A. Tavares, Dora Rolo, Carmen Ardanuy, Herman Goossens, Birgitta Henriques-Normark, Josefina Linares, Hermínia de Lencastre, Raquel Sá-Leão

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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.

Original language	English
Pages (from-to)	141-148
Number of pages	8
Journal	Diagnostic Microbiology And Infectious Disease
Volume	85
Issue number	2
DOIs	https://doi.org/10.1016/j.diagmicrobio.2016.03.018
Publication status	Published - 1 Jun 2016

Keywords

Identification
LytA
Molecular methods
Real-time PCR
S. pneumoniae
S. pseudopneumoniae

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LytA-based identification methods can misidentify Streptococcus pneumoniaeAccepted author manuscript, 503 KBLicence: CC BY

Cite this

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title = "LytA-based identification methods can misidentify Streptococcus pneumoniae",

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, LytA, Molecular methods, Real-time PCR, S. pneumoniae, S. pseudopneumoniae",

author = "Sim{\~o}es, {Alexandra S.} and Tavares, {D{\'e}bora A.} and Dora Rolo and Carmen Ardanuy and Herman Goossens and Birgitta Henriques-Normark and Josefina Linares and {de Lencastre}, Herm{\'i}nia and Raquel S{\'a}-Le{\~a}o",

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AU - Simões, Alexandra S.

AU - Tavares, Débora A.

AU - Rolo, Dora

AU - Ardanuy, Carmen

AU - Goossens, Herman

AU - Henriques-Normark, Birgitta

AU - Linares, Josefina

AU - de Lencastre, Hermínia

AU - Sá-Leão, Raquel

PY - 2016/6/1

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N2 - 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.

AB - 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.

KW - Identification

KW - LytA

KW - Molecular methods

KW - Real-time PCR

KW - S. pneumoniae

KW - S. pseudopneumoniae

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LytA-based identification methods can misidentify Streptococcus pneumoniae

Abstract

Keywords

UN SDGs

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