Regional Variation in Pneumococcal Carriage and Disease Parameters Across Africa, Asia and South America: A Systematic Review for Infectious Disease Modelling Open Access

Abstract

Background: Pneumococcal disease remains a leading cause of morbidity and mortality among children in low- and middle-income countries (LMICs), with an estimated 300,000 annual deaths among children younger than five years. Shigella contributes an additional 212,000 deaths, emphasizing the need for improved prevention strategies. As countries consider expanding pneumococcal conjugate vaccine (PCV) programs or introducing multi-pathogen combination vaccines, relevant natural history parameters are essential for evaluating potential impacts on transmission and disease burden. Methods: A systematic review of the Emory University Library, PubMed and PubMed Central databases was conducted to characterize regional variation in pneumococcal carriage, clearance, vaccine effectiveness, invasive pneumococcal disease (IPD) incidence, and serotype competition across Africa, Asia, and South America. Thirty studies met inclusion criteria. Where transmission parameters were not reported, transmission rate and force of infection were derived analytically from observed carriage prevalence and clearance duration under steady-state assumptions. Shigella parameters were sourced from an established diarrheal disease model. Results: Carriage prevalence varied widely, from 0.208 among Peruvian children to 0.802 in rural sub-Saharan Africa, with consistently higher carriage observed in rural and high-burden settings. Vaccine-type (VT) carriage declined following PCV introduction, whereas non-vaccine type (NVT) carriage increased across regions, demonstrating serotype replacement dynamics. Clearance duration differed by serotype group and geographic setting, ranging from 38.6 days for non-PCV13 types in South Africa to 62.0 days for PCV13 types in Asia. Vaccine effectiveness against carriage ranged from 24% in India to 97% following a four-dose schedule in Brazil, whereas effectiveness against IPD was consistently higher, ranging from 56% to 92%. IPD incidence varied substantially, from 24.29 per 100,000 person-years in Latin America to 253 per 100,000 among Gambian children aged 2–23 months. Competition coefficients demonstrated serotype-specific differences, ranging from 0.48 for serotype 19F to 2.10 for serotype 33B. Discussion: These findings provide a parameter framework for evaluating two vaccine strategies: expanding PCV programs through additional pneumococcal serotypes, or developing a pneumococcal–Shigella combination vaccine, a comparison that is the subject of ongoing modelling work. The regional variation documented here highlights the importance of context specific parameterization in LMIC settings.

Table of Contents

Background ................................................................................................................................. 1

Methods ....................................................................................................................................... 4

General Model Structure ............................................................................................................. 4

Carriage ........................................................................................................................................ 5

Competition/Replacement Rates .................................................................................................. 5

Force of Infection ......................................................................................................................... 6

Invasive Pneumococcal Disease (IPD) Rates ............................................................................... 6

VT and NVT Invasiveness ............................................................................................................ 6

VT and NVT Clearance ................................................................................................................ 7

Waning .......................................................................................................................................... 8

Derivation of Transmission Rate and Force of Infection .............................................................. 8

Results .......................................................................................................................................... 9

Search Results .............................................................................................................................. 9

Carriage Rates ............................................................................................................................. 10

Vaccine-Type and Non-Vaccine-Type Carriage .......................................................................... 11

VT and NVT Clearance Rates ..................................................................................................... 11

Vaccine Effectiveness Against Carriage ...................................................................................... 12

Vaccine Effectiveness Against Disease ....................................................................................... 13

Invasive Pneumococcal Disease Rates ........................................................................................ 13

Competition and Replacement Parameters .................................................................................. 14

Derived Parameters (Transmission Rate & Force of Infection) .................................................... 14

Global Parameters and PCV Waning .......................................................................................... 15

Discussion .................................................................................................................................... 24

Key Findings ............................................................................................................................... 24

Strengths ...................................................................................................................................... 25

Limitations ................................................................................................................................... 26

Supplement .................................................................................................................................. 29

References .................................................................................................................................... 39

About this Master's Thesis

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School	Rollins School of Public Health
Department	Epidemiology
Subfield / Discipline	Global Epidemiology - MPH & MSPH
Degree	M.P.H.
Submission	Master's Thesis
Language	English
Research Field	Health Sciences, Epidemiology Health Sciences, Public Health
Keyword	Low- and middle-income countries Nasopharyngeal carriage Pneumococcal conjugate vaccine Infectious disease modelling Pneumococcal transmission dynamics
Committee Chair / Thesis Advisor	Elizabeth Rogawski McQuade, Emory University

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