Serotype Distribution of Streptococcus pneumoniae Isolates Causing Invasive and Non-Invasive Infections Using Whole-Genome Sequencing in Ethiopia

Abstract

Background

In Ethiopia, pneumococcal conjugate vaccine 10 (PCV10) was introduced in 2011 in the national vaccination program. This study was aimed to assess serotype distribution of invasive and non-invasive Streptococcus pneumoniae isolates using whole-genome sequencing.

Methods

A hospital-based prospective study was conducted from 2018 to 2019 at Addis Ababa and Amhara region referral hospitals, from all patients. Clinical Samples were collected and initially cultured onto 5% sheep blood agar at 37°C in a 5% CO₂ atmosphere. Sequencing was done using the Illumina NextSeq 500 and SeroBA was used to predict serotypes from whole-genome sequencing raw data.

Results

Of the 57 S. pneumoniae isolates, there were 32 circulating serotypes. The most common serotypes were 15A/B/C (n=5, 8.8%), 6A (n=4, 7.0%), 10A/F (n=4, 7.0%), 23A (n=4, 7.0%) and 7C (n=3, 5.3%). The serotype coverage of PCV10 and PCV13 were 12.3% and 26.3% respectively. The most common invasive serotypes were 15A/B/C (n=5, 8.8%) and 6A (n=4, 7.0%), and non-invasive serotypes were 23A (n=4, 7.0%) and 10A/F (n=3, 5.3%). The most prevalent serotype obtained from PCV10 eligible children was 3 (n=2, 3.5%). The prevalent serotype obtained from PCV10 non-eligible patients were type 23A (n=4, 7%) and type 6A (n=3, 5.2%). The most common serotypes among children ≤18 years old were 10A/F, 7C, 35A/B, 16F, 19A, 3 and 38. However, the proportions of some non-vaccine serotypes (11A/B and 15A/B/C) were higher in adult patients.

Conclusion

In this study a shift in the distribution of non-vaccinated S. pneumoniae serotypes increases in the population, and PCV10 serotype coverage was reduced as compared to PCV13. Therefore, it is important to continue monitoring serotype changes among all patients in addition to assessing the impact and effectiveness brought by vaccines and provides a foundation for prevention strategies and vaccine policies.

Keywords:

• Streptococcus pneumoniae
• serotypes
• whole-genome sequencing

Acknowledgments

The authors would like to thank the study participants. We are also very thankful for the institutional support grant by the University of Gondar. We are indebted to thank Microbiology laboratory staff of the hospitals and the University of Gondar for collecting and rechecking the isolates. We would like to thank the staff of the Norwegian Institute of Public Health Microbiology Laboratory (especially Prof. Dominique A Caugant) for their assistance in doing the whole genome sequencing and serotyping.

Data Sharing Statement

All data generated or analyzed during this study are included in this published article.

Ethics Approval and Consent to Participate

All procedures performed in this study were reviewed and approved by the ethical review board of the University of Gondar (No. O/V/P/RCS/05/377/2017) in accordance with the 1964 Helsinki declaration. Permission was obtained from each hospital laboratory for collecting the isolates. Written informed consent was obtained from all patients, and a parent or legal guardian of patients under the age of 18 years after explaining the purpose and objective of the study.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors declare that they have no competing interests for the publication of this paper.