Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction.
| Title: | Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction. |
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| Authors: | Senghore M; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.; Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA.; Tientcheu PE; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.; Worwui AK; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.; Jarju S; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.; Okoi C; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.; Suso SMS; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.; Foster-Nyarko E; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.; Ebruke C; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.; Sonko M; Hopital d'Enfants Albert Royer, BP 5297, Fann, Dakar, Senegal.; Kourna MH; Hospital National Niamey, BP 238, Niamey, Niger.; Agossou J; Department of Mother and Child, Faculty of Medicine, University of Parakou, Parakou, Benin.; Borgou Regional University Teaching Hospital, Parakou, Benin.; Tsolenyanu E; Laboratoire Microbiologie, Centre Hospitalier Universitaire de Tokoin Lomé, BP 57, Lomé, Togo.; Renner LA; Central Laboratory Services, Korle-Bu Teaching Hospital, P.O. Box 77, Accra, Ghana.; Ansong D; Komfo Anokye Teaching Hospital, P.O. Box 1934, Kumasi, Ghana.; Sanneh B; Edward Francis Small Teaching Hospital, Banjul, The Gambia.; Cisse CB; Laboratoire Central du CHU de Yopougon, Institut Pasteur de Cote d'Ivoire, Abidjan, Ivory Coast.; Boula A; Centre Mere et Enfant de la Fondation, Chantal Biya, Yaounde, Cameroon.; Miwanda B; Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of Congo.; Lo SW; Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.; Gladstone RA; Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.; Schwartz S; Centers for Disease Control and Prevention, Atlanta, GA, USA.; Hawkins P; Centers for Disease Control and Prevention, Atlanta, GA, USA.; Rollins School of Public Health, Emory University, Atlanta, GA, USA.; McGee L; Centers for Disease Control and Prevention, Atlanta, GA, USA.; Klugman KP; Rollins School of Public Health, Emory University, Atlanta, GA, USA.; Breiman RF; Rollins School of Public Health, Emory University, Atlanta, GA, USA.; Emory Global Health Institute, Atlanta, GA, USA.; Bentley SD; Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.; Mwenda JM; World Health Organization Regional Office for Africa, BP 6, Brazzaville, Republic of Congo.; Kwambana-Adams BA; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.; NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.; Antonio M; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia. |
| Source: | Microbial genomics [Microb Genom] 2021 Jul; Vol. 7 (7). |
| Publication Type: | Journal Article; Research Support, Non-U.S. Gov't |
| Language: | English |
| Journal Info: | Publisher: Microbiology Society Country of Publication: England NLM ID: 101671820 Publication Model: Print Cited Medium: Internet ISSN: 2057-5858 (Electronic) Linking ISSN: 20575858 NLM ISO Abbreviation: Microb Genom Subsets: MEDLINE |
| Imprint Name(s): | Publication: Oct. 2015- : [London] : Microbiology Society; Original Publication: [London] : Society for General Microbiology, [2015]- |
| MeSH Terms: | Drug Resistance, Multiple, Bacterial/*genetics ; Heptavalent Pneumococcal Conjugate Vaccine/*immunology ; Meningitis, Pneumococcal/*epidemiology ; Pneumococcal Vaccines/*immunology ; Streptococcus pneumoniae/*drug effects ; Streptococcus pneumoniae/*genetics; Africa, Western/epidemiology ; Antitubercular Agents/pharmacology ; Genome, Bacterial/genetics ; Meningitis, Pneumococcal/immunology ; Meningitis, Pneumococcal/prevention & control ; Streptococcus pneumoniae/immunology ; Streptococcus pneumoniae/isolation & purification ; Adolescent ; Child ; Child, Preschool ; Humans ; Infant ; Infant, Newborn ; Microbial Sensitivity Tests ; Whole Genome Sequencing |
| Abstract: | Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of Streptococcus pneumoniae which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 S. pneumoniae isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test P value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (n=6) in the post-PCV introduction period compared to 21.9 % (n=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (n=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (n=27). The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact. |
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| Grant Information: | 001 International WHO_ World Health Organization |
| Contributed Indexing: | Keywords: West and Central Africa; antibiotic resistance; genomic epidemiology; paediatric meningitis; pneumococcus |
| Substance Nomenclature: | 0 (13-valent pneumococcal vaccine); 0 (Antitubercular Agents); 0 (Heptavalent Pneumococcal Conjugate Vaccine); 0 (Pneumococcal Vaccines) |
| Entry Date(s): | Date Created: 20210730 Date Completed: 20220118 Latest Revision: 20250530 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC8477402 |
| DOI: | 10.1099/mgen.0.000506 |
| PMID: | 34328412 |
| Database: | MEDLINE |
Journal Article; Research Support, Non-U.S. Gov't