Abstract
BackgroundInvasive pneumococcal disease (IPD) remains a global health problem. IPD incidence has significantly decreased by the use of pneumococcal conjugate vaccines (PCV). Nevertheless, non-PCV serotypes remain a matter of concern. Eight Streptococcus pneumoniae serotype 24F isolates, belonging to a non-PCV serotype, were detected through the Lebanese Inter-Hospital Pneumococcal Surveillance Program. The aim of the study is to characterize phenotypic and genomic features of the 24F isolates in Lebanon.MethodsWGS using long reads sequencing (PacBio) was performed to produce complete circular genomes and to determine clonality, antimicrobial resistance and virulence determinants.ResultsThe sequencing results yielded eight closed circular genomes. Three multilocus sequence typing (MLST) types were identified (ST11618, ST14184, ST15253). Both MLST and WGS analyses revealed that these isolates from Lebanon were genetically homogenous belonging to clonal complex CC230 and clustered closely with isolates originating from Canada, United States of America, United Kingdom and Iceland. Their penicillin binding protein profiles correlated with both β-lactam susceptibility patterns and MLST types. Moreover, the isolates harbored the macrolide and tetracycline resistance genes and showed a similar virulence gene profile. To our knowledge, this study represents the first report of complete phenotypic and genomic characterization of the emerging Streptococcus pneumoniae, serotype 24F, in the Middle East and North Africa region.
Highlights
Streptococcus pneumoniae is a major causative agent responsible for severe infections mainly among young children, elderly individuals and those with chronic illnesses and immunodeficiency disorders (Global Burden of Disease Study, 2018; Principi et al, 2018)
Our findings showed a significant time effect where there was a significant increase of the prevalence of serotype 24F observed over 3 different periods with a p-value < 0.001 and odds ratio (OR) = 8.837, 95% Confidence Interval (CI) = (2.894– 26.985)
Pneumococcal vaccination status information was lacking pneumococcal conjugate vaccine (PCV)-13 was introduced to the national immunization program in January 2016 to be given in three doses at 4, 6, and 12–15 months
Summary
Streptococcus pneumoniae is a major causative agent responsible for severe infections mainly among young children, elderly individuals and those with chronic illnesses and immunodeficiency disorders (Global Burden of Disease Study, 2018; Principi et al, 2018). Based on the capsular polysaccharide structure, almost 100 pneumococcal serotypes have been identified so far (Ganaie et al, 2020) These serotypes vary in terms of incidence, antibiotic resistance, and disease manifestation (Hausdorff et al, 2005) and only a limited number of them cause the majority of invasive pneumococcal disease (IPD) (Namkoong et al, 2016). The pneumococcal conjugate vaccine (PCV) that covers seven serotypes known as PCV7 (4, 6B, 9 V, 14, 18C, 19F, and 23F) was implemented as a routine vaccination in 2000 and was replaced by PCV10 with three additional serotypes (1, 5, and 7F) followed by PCV13 covering six additional serotypes from PCV7 (1, 5, 7F, 3, 6A, and 19A) Those vaccines are recommended for children under the age of 2 (Daniels et al, 2016; Isturiz et al, 2018). The aim of the study is to characterize phenotypic and genomic features of the 24F isolates in Lebanon
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