Naima ELMDAGHRI, Morocco

Pneumococcal infections remain a major cause of infections among children. In this study, a part of the Global Pneumococcal Sequencing (GPS) Project, we described the genomic structure of the pneumococcal population in Casablanca, Morocco, before and after vaccination introduction.

Methods

DNA of 47 invasive isolates from children < 5 years old (32 isolates from pre-vaccine period, 15 isolates from post-vaccine period) were whole genome sequenced. Sequences were assembled, annotated and pangenome characterized. Core genome based phylogenetic trees were constructed. Finally, PopPUNK was used to group our isolates in different GPS Clusters (GPSC).

Results

Pangenomic analysis revealed 1,396, 1,465 and 1,357 core genes for pre-vaccination period, post-vaccination period and the two periods combined, respectively; and 2,915, 2,405, 3,432 accessory genes for the same periods. Phylogenomic analysis showed two major clusters GPSC6 (serotype 14) and GPSC10 (Serotype 19A and non-vaccine serogroup 24). Both clusters are non-susceptible to penicillin. The two serogroup 24 isolates in GPSC10 were found in pre-vaccine (n=1) and post-vaccine periods (n=1), and both were resistant to erythromycin and tetracycline.

Conclusions

The pneumococcal population in Casablanca was highly diverse regardless of serotype and period isolation. Several minor homogeneous and/or heterogeneous clusters were found with two major clusters.

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GLOBAL GENOMIC EPIDEMIOLOGY OF PNEUMOCOCCAL SEROTYPE 2 ISOLATED DURING 1989 TO 2019 (ID 1084)

Session Name

Basic Sciences - Genomics and Transmission

Presenter

Roly Malaker, Bangladesh

Authors

Abstract

Abstract

Background

Serotype 2 was a major cause of pneumococcal pneumonia about 100 years ago and then disappeared. Recently, serotype 2 re-emerged in many countries, including Bangladesh and associated with meningitis. This study aims to understand genomic and epidemiological characteristics of newly emerged serotype 2 strains.

Methods

Whole-genome sequencing was performed on 146 isolates (invasive= 125, carriage= 8 and other= 5, unknown= 8) collected between 1989 and 2017. Data were analyzed for comparative genomics, antimicrobial resistance and molecular typing.

Results

Isolates were from 16 countries, mostly in Asia (n=93), Africa (n=23) and Oceania (n=26). Bangladesh (n=66) and Papua New Guinea (n=26) contributed 63% of the isolates. Among the known clinical conditions, 80% (91/113) were from meningitis. All isolates belonged to GPSC96 lineage and descended from two predominant sequence types: ST74 found in Asia and Africa, and ST1504 found in Papua New Guinea and Israel. Almost all isolates were sensitive to all antibiotics. No significant genetic differences were detected between invasive and carriage isolates.

Conclusions

Our findings don’t explain why the recent increase in serotype 2 occurred but exclude an outbreak or emergence of an antimicrobial-resistant strain as the cause. These isolates have unusually high propensity to be invasive, mostly causing meningitis.

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