Genomic characterization of invasive disease-causing Streptococcus pneumoniae in Lebanon, 2003–2025
Rattachement africain : gb, lb, us. Niveau de preuve : code pays fourni par la source.
Le résumé fourni par la source
Background . Streptococcus pneumoniae is a major human pathogen responsible for invasive pneumococcal diseases (IPDs). We utilized whole-genome sequencing to assess the impact of pneumococcal conjugate vaccines (PCVs) on the pneumococcal population causing IPD in Lebanon. Methods. S. pneumoniae isolates collected between 2003 and 2025 ( n =273) were sequenced and included in the study, which was divided into three periods. Private-PCV7 (2003–2009) and Private-PCV13 (2010–2015) correspond to the periods when the PCV7 and PCV13 vaccines were available only in the private healthcare sector, respectively. EPI-PCV13 (2016–2025) represents the period following PCV13 incorporation into the Expanded Program on Immunization (EPI). The Global Pneumococcal Sequencing (GPS) genome analysis pipeline was used to infer serotypes, genetic lineages, pilus locus and antimicrobial resistance (AMR) for 19 antibiotics. Phylogeny was constructed based on SNPs across the pneumococcal genome. Results. A total of 58 GPS clusters (GPSCs) expressing 40 serotypes were identified. Overall, serotypes 3, 14 and 19F were the most prevalent serotypes, while GPSC6, GPSC12 and GPSC1 were the most predominant pneumococcal lineages. We detected a significant increase in non-vaccine types (NVTs) after PCV7 and PCV13 introduction. In contrast, PCV7 serotypes declined significantly over the three study periods. Collectively, PCV7 serotypes were associated with significantly higher mortality (31.1%) compared to NVT (15.9%). Moreover, IPD-associated mortality was significantly higher among older adult patients (33.3%) compared to children aged ≤5 years (12.1%). Non-susceptibility to penicillin was the most prevalent resistance (62.1%), and multidrug resistance (MDR; non-susceptibility to at least three antibiotics) was identified in 36.4% of the isolates. MDR was primarily driven by GPSC1, GPSC9, GPSC6 and GPSC10. A significant decline in MDR and AMR against seven antibiotics was observed in the EPI-PCV13 period compared to previous study periods. Conclusions. Genomic surveillance is robust for tracking current NVT and identifying lineages that may influence future IPD trends in Lebanon. Given the high mortality rate detected in older adult IPD patients, implementing a routine immunization programme in this population may be beneficial.
Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.
Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- Genomic characterization of invasive disease-causing Streptococcus pneumoniae in Lebanon, 2003–2025
- Date Crossref
- 13/03/2026
- Éditeur
- Microbiology Society
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
-
Wellcome Sanger Institute Parasites and Microbes Programme pays non établi dans la noticeOrganisation à but non lucratif
-
American University of Beirut Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens pays non établi dans la noticeUniversité ou école supérieure
-
University of Birmingham pays non établi dans la noticeUniversité ou école supérieure
-
Centers for Disease Control and Prevention pays non établi dans la noticeOrganisme public
-
Ministry of Public Health Epidemiological Surveillance Unit pays non établi dans la noticeOrganisme public
-
American University of Beirut Medical Center pays non établi dans la noticeÉtablissement de santé
-
Great Ormond Street Hospital pays non établi dans la noticeÉtablissement de santé
-
University College London The Great Ormond Street Institute of Child Health pays non établi dans la noticeUniversité ou école supérieure
-
University of Bath Department of Life Sciences pays non établi dans la noticeUniversité ou école supérieure
-
Faculty of Medicine Department of Experimental Pathology pays non établi dans la noticeUniversité ou école supérieure
-
College of Medicine and Health Institute of Microbiology and Infection pays non établi dans la noticeUniversité ou école supérieure
-
Division of Bacterial Diseases pays non établi dans la noticeInstitution
Parasites and Microbes Programme — Wellcome Sanger Institute, Center for Infectious Diseases Research (CIDR) and WHO Collaborating Center for Reference and Research on Bacterial Pathogens — American University of Beirut et University of Birmingham, avec 9 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.