The Molecular Approaches and Challenges of Streptococcus pneumoniae Serotyping for Epidemiological Surveillance in the Vaccine Era

Technique	Target areas	Benefits	Drawbacks	References
Quellung	Pneumococcal capsular polysaccharides	Straightforward High sensitivity and specificity Rapid outcomes	Time, cost, and labor intensive Cannot detect multiple serotypes using one sample Inconvenient for larger samples Extensive skills are required	Henrichsen 1979 Sørenson 1993 Lalitha et al. 1999 Jauneikaite et al. 2015 Jin et al. 2016
Latex agglutination	Pneumococcal capsular polysaccharides	Straightforward Easy Rapid outcomes Appropriate for resource-poor conditions Needs the least expertise	Cost-intensive Questionable accuracy Culture-negative isolate might be missed	Slotved et al. 2004 Ortika et al. 2013 Porter et al. 2014 Swarthout et al. 2021
Multiplex PCR	Glycosyltransferase gene	Economical Rapid outcomes Versatile Accurate Sensitive	Several primers Several steps Limited serotypes supported Lack of internal control for specific serotypes Emerging NVTs remain unexploited	Lawrence et al. 2003 Carvalho et al. 2010 Jin et al. 2016 Zhou et al. 2021
Sequetyping	CpsB gene	Straightforward and economical Single PCR amplification Single-step PCR Needs one primer set	Restricted to single isolate detection Some isolates exhibit high homology of the cpsB gene across different serotypes Needs sequencing facilities or services	Leung et al. 2012 Jin et al. 2016 Nagaraj et al. 2017 Zhou et al. 2021
Real-time PCR	Pneumococcal capsular polysaccharides	High sensitivity Able to replicate DNA in low copy number Serotyping from culture-negative samples No sample manipulation is needed after the amplification	Need specialised equipment Costly PCR probes Emerging NVTs remain unexploited	Tarragó et al. 2008 Azzari et al. 2010 Pimenta et al. 2013 Pernica et al. 2014 Kralik et al. 2017
PCR-RFLP	cps genes	Straightforward Fast Cost-effective Versatile Reproducible	Needs targeted restriction enzymes Needs several restriction enzymes Cannot assess mutation type Time-intensive	Batt et al. 2005 Camargo et al. 2015 Dai and Long 2015 Garcia Suarez et al. 2019
Whole genome sequencing (WGS)	Pneumococcal capsular polysaccharides	High accuracy Greater resolution Comprehensive analysis Reduced turnaround time	Cost-intensive Needs an advanced bioinformatic tool Requires technical expertise and skill	Kapatai et al. 2016 Mauffrey et al. 2017 Epping et al. 2018 Knight et al. 2021 Sheppard et al. 2022

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The Molecular Approaches and Challenges of Streptococcus pneumoniae Serotyping for Epidemiological Surveillance in the Vaccine Era

Nurul Asyikin Abdul Rahman

Mohd Nasir Mohd Desa

Siti Norbaya Masri

Niazlin Mohd Taib

Nurshahira Sulaiman

Hazmin Hazman

James John

Article Category: MINIREVIEW

Published Online: Jun 14, 2023

Page range: 103 - 115

Received: Jan 27, 2023

Accepted: May 09, 2023

DOI: https://doi.org/10.33073/pjm-2023-023

Keywordsserotyping, PCR, sequetyping, PCR-RFLP, WGS

© 2023 Nurul Asyikin Abdul Rahman et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Serotyping methods with associated benefits and challenges_

Keywords
serotyping, PCR, sequetyping, PCR-RFLP, WGS