Comparison of a Real-Time Multiplex PCR and Sequetyping Assay for Pneumococcal Serotyping

PloS One
Felix S DubeMark P Nicol

Abstract

Pneumococcal serotype identification is essential to monitor pneumococcal vaccine effectiveness and serotype replacement. Serotyping by conventional serological methods are costly, labour-intensive, and require significant technical expertise. We compared two different molecular methods to serotype pneumococci isolated from the nasopharynx of South African infants participating in a birth cohort study, the Drakenstein Child Health Study, in an area with high 13-valent pneumococcal conjugate vaccine (PCV13) coverage. A real-time multiplex PCR (rmPCR) assay detecting 21 different serotypes/-groups and a sequetyping assay, based on the sequence of the wzh gene within the pneumococcal capsular locus, were compared. Forty pneumococcal control isolates, with serotypes determined by the Quellung reaction, were tested. In addition, 135 pneumococcal isolates obtained from the nasopharynx of healthy children were tested by both serotyping assays and confirmed by Quellung testing. Discordant results were further investigated by whole genome sequencing of four isolates. Of the 40 control isolates tested, 25 had a serotype covered by the rmPCR assay. These were all correctly serotyped/-grouped. Sequetyping PCR failed in 7/40 (18%) isolates....Continue Reading

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Citations

Sep 2, 2016·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·G ErricoR Camilli
Jan 31, 2017·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Hamidreza HouriAbdollah Karimi
May 14, 2016·Journal of Clinical Microbiology·Suporn PholwatEric R Houpt
Jul 4, 2019·Journal of Medical Microbiology·Lucia Gonzales-SilesEdward R B Moore
Nov 23, 2019·Diagnostics·María Del Mar García-SuárezEnrique Santiago
Jul 14, 2017·Pneumonia·Geetha NagarajKadahalli Lingegowda Ravikumar

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Datasets Mentioned

BETA
CR931668
CR931648

Methods Mentioned

BETA
dot
ELISA
PCR
nucleic acid extraction
nucleic acid amplification
electrophoresis

Software Mentioned

Trimmomatic
BLAST
WebACT
SAMtools
DNA Baser Sequence Assembler
Sequetyper
BLASTN
Artemis Comparison Tool ( ACT )
RAST ( Rapid Annotation
FastQC

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