Genomic surveillance of invasive Streptococcus pneumoniae strains in south Tunisia during 2012-2022

Abstract

Purpose. Invasive pneumococcal disease (IPD) remains a major global public health concern due to its high morbidity and mortality rates, particularly among children and the elderly. This study aimed to apply whole-genome sequencing (WGS) to characterize Streptococcus pneumoniae strains responsible for IPD in south Tunisia, including serotype distribution, clonal relationship and antimicrobial resistance (AMR) profiles.Methods. A total of 148 IPD S. pneumoniae isolates were collected from the microbiology laboratory at Habib Bourguiba University Hospital in Sfax, Tunisia, between 2012 and 2022. These isolates underwent WGS using Illumina technology. Bioinformatic analyses were performed to determine serotype distribution, sequence types (STs), Global Pneumococcal Sequence Clusters (GPSCs), phylogenetic relationships and AMR determinants.Results. Twenty-six different serotypes were identified, with the most prevalent being 14 (18%), 3 (13%), 19A (12%) and 19F (11%). The isolates showed high genomic diversity, as they belonged to 32 GPSCs and 59 STs. The most common GPSCs were GPSC-6, GPSC-10 and GPSC-44, associated with serotypes 14, 19A and 19F, respectively. The most frequent STs were ST2918, ST179 and ST3772. The most common resistance genes were ermB (53%) and tetM (55%), which were linked to resistance against erythromycin and tetracycline, respectively. There was a considerable concordance between WGS-based and phenotypic resistance profiles for most tested antibiotics, with few major and very major errors for most antibiotics. Temporal analysis showed a decline in serotypes 19F and 9V throughout the study period, which was associated with slight decreases in GPSC-6 and GPSC-44, while serotype 19A and GPSC-10 sharply increased.Conclusion. This study highlights the substantial genomic diversity, serotype distribution and high prevalence of AMR among IPD S. pneumoniae isolates in south Tunisia, underscoring the need for continued surveillance and effective vaccination strategies to combat this persistent public health threat.

Keywords: Streptococcus pneumoniae; Tunisia; genomic surveillance; global pneumococcal sequence cluster; invasive pneumococcal disease; whole-genome sequencing.

Fig. 1.. Distribution of S. pneumoniae serotypes according to their inclusion in PCVs in south Tunisia (2012–2022).

Fig. 2.. Upset plots of phenotypic resistance profiles based on non-meningitis breakpoints (a) and meningitis breakpoints (b).

Fig. 3.. Upset plots of resistance determinant carriage based on WGS.

Fig. 4.. Phylogenetic tree of the 148 south Tunisian S. pneumoniae responsible for invasive pneumococcal diseases between 2012 and 2022.

Fig. 5.. Distribution of phenotypic resistance and AMR determinants according to pneumococcal lineages.

Fig. 6.. Evolution of S. pneumoniae serotype and GPSC distribution from 2012 to 2022 in south Tunisia. Statistical significance is indicated in red, with the following thresholds: P-value between 0.1 and 0.05 (‘.’), P-value between 0.05 and 0.01 (‘*’), P-value between 0.01 and 0.001 (‘**’) and P-value below 0.001 (‘***’).

Fig. 7.. Changes in phenotypic AMR (a) and detection rates of AMR determinants (b) in S. pneumoniae in south Tunisia during 2012–2022. Statistical significance is indicated in red, with the following thresholds: P-value between 0.1 and 0.05 (‘.’), P-value between 0.05 and 0.01 (‘*’), P-value between 0.01 and 0.001 (‘**’) and P-value below 0.001 (‘***’).