The Emergence of Invasive Streptococcus pneumoniae Serotype 24F in Lebanon: Complete Genome Sequencing Reveals High Virulence and Antimicrobial Resistance Characteristics

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.

Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study

“… 7 Unlike GPSC10, GPSC6 was susceptible to penicillin and erythromycin. This observation coincided with the lower consumption of penicillin and macrolides (a class of antibiotic that includes erythromycin) in Denmark, as compared with other countries such as France, 2 , 3 Lebanon, 12 and Spain 14 , 15 where the increase in serotype 24F was mediated by the multidrug-resistant GPSC10 ( appendix 1 p 23 ) lineage. According to ResistanceMap , France, Lebanon, and Spain consumed 1·8–2·2 times more penicillin and 1·2–2·0 times more macrolides than Denmark in 2015.…”

“… 4 In France, a big increase in pneumococcal meningitis cases occurred 5 years after the roll out of PCV13, mainly driven by serotype 24F. 2 , 3 This serotype also mediated serotype replacement in multiple other countries, such as Argentina, 5 Canada, 6 Denmark, 7 Germany, 8 Israel, 9 Italy, 10 Japan, 11 Lebanon, 12 Norway, 13 Spain, 14 , 15 and the UK, 16 and was reported to be the predominant serotype causing invasive pneumococcal disease (IPD) in Portugal 17 after PCV13 introduction.…”

“…Pneumococcal lineages driving the increase in serotype 24F varied between countries. In Argentina, 5 Lebanon, 12 and Spain, 19 the increase was mainly driven by the Global Pneumococcal Sequence Cluster (GPSC) and clonal complex (CC) GPSC10 (CC230), in Denmark 7 by GPSC6 (CC156), and in Japan by GPSC106 (CC2572). 11 In the present study, we used whole-genome sequencing to investigate the pneumococcal lineages driving the increase in serotype 24F after PCV13 introduction in France, then placed this lineage in global context and elucidated its spatiotemporal transmission in France and across the world.…”

Molecular Characterization of Antimicrobial Resistance and Virulence Genes of Bacterial Pathogens from Bovine and Caprine Mastitis in Northern Lebanon

“…Pneumococcus is a commensal bacterium that normally colonizes the human nasopharyngeal cavity and is transmitted by droplets and aerosols either from infected patients or healthy carriers [45]. Although this species is rarely reported in mastitis, various epidemiological studies showed its high prevalence in the Lebanese community [46,47]. This allows us to speculate that there is a potential threat of contamination by handlers.…”

Emerging pneumococcal serotypes in Iraq: scope for improved vaccine development

“…The NVT 24F has been reported to be an emerging serotype among patients with IPD (mostly [87.5%] <6 years of age with unknown pneumococcal vaccination status) in Lebanon, with 4 cases noted in 2019. 95 The genome sequencing of this serotype, isolated from samples collected between 2013 and 2019, showed that it is highly virulent and antimicrobial resistant. 95 The prevalence of this NVT among IPD cases in children has also been reported in the European and Western Pacific regions.…”