We aimed to assess the prevalence of nasopharyngeal pneumococcal carriage and to determine serotype distribution, antibiotic susceptibility patterns, and evolutionary dynamics of Streptococcus pneumoniae isolates in healthy under-five children. Nasopharyngeal swabs were collected from healthy children over three survey periods between 2020 and 2022. All pneumococcal isolates were serotyped and tested for antimicrobial susceptibility. A total of 309 S. pneumoniae isolates were collected, with an overall prevalence of nasopharyngeal pneumococcal carriage of 24.4% (CI95%: [22–26.8%]). These isolates were classified into 25 different serotypes. The most common serotypes were 14 (14.9%), 19F (12%), 6B (10.4%), and 23F (7.4%), which are covered by the PCV10 vaccine, as well as 19A (8.4%) and 6A (7.8%), which are covered by the PCV13 vaccine. A significant decrease in the proportion of serotype 19F (p = 0.001) and an increase in serotypes 19A (p = 0.034) and 6A (p = 0.029) were observed between the three survey periods. Multidrug resistance (MDR) was noted for 56.6% of the isolates. A significant association with antimicrobial resistance was observed for the most frequent serotypes, mainly serotype 19A. In conclusion, one-quarter of healthy under-five children in Tunisia carried S. pneumoniae in their nasopharynx. A dominance of vaccine serotypes significantly associated with antimicrobial resistance was recorded.

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.

Background/Objectives: Streptococcus pneumoniae is a leading respiratory pathogen responsible for significant morbidity and mortality, particularly among vulnerable populations. Understanding its antimicrobial resistance patterns and serotype distribution is crucial for guiding treatment and prevention strategies. This study aims to examine these trends in S. pneumoniae isolates from Tunisia over a two-decade period (2000–2019). Methods: A retrospective time series analysis was conducted on data (n = 4284) gathered from eight university hospital centers across Tunisia. Antimicrobial susceptibility testing was performed according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Pneumococcal serotypes were determined for a subset of samples from 2012 to 2019 (n = 903) using multiplex PCR and latex agglutination. Results: Penicillin G resistance decreased from 9–13.7% during 2000–2002 to 4.3% by 2019, while amoxicillin resistance increased until reaching 10% in 2019. Erythromycin resistance initially increased before stabilizing between 61.9% and 66.3% during 2014–2019, whereas tetracycline resistance declined from 2000 to 2008 and fluctuated around 40% during 2009–2019. Levofloxacin resistance did not exceed 1.2% throughout the study period. The most prevalent serotypes were 14, 19F, 19A, 23F, 3, 6B, 6A, and 9V. Among them, serotype 3 was the most susceptible overall. Serotypes 23F, 14, 9V, and 6B displayed the highest levels of multi-drug resistance. Conclusions: Penicillin G (high-dosage), cefotaxime, and levofloxacin are still effective against most S. pneumoniae strains in Tunisia, while erythromycin and tetracycline are not reliable options for treating pneumococcal infections. Alarming resistance rates among prevalent serotypes, except serotype 3, underscore the need for preventive measures, rational antibiotic use, and ongoing surveillance.