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Cave R, Kalizang'oma A, Chaguza C, Mwalukomo TS, Kamng'ona A, Brown C, Msefula J, Bonomali F, Nyirenda R, Swarthout TD, Kwambana-Adams B, French N, Heyderman RS. Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi. Microb Genom 2024; 10. [PMID: 38896467 DOI: 10.1099/mgen.0.001264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
Since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Malawi in 2011, there has been persistent carriage of vaccine serotype (VT) Streptococcus pneumoniae, despite high vaccine coverage. To determine if there has been a genetic change within the VT capsule polysaccharide (cps) loci since the vaccine's introduction, we compared 1022 whole-genome-sequenced VT isolates from 1998 to 2019. We identified the clonal expansion of a multidrug-resistant, penicillin non-susceptible serotype 23F GPSC14-ST2059 lineage, a serotype 14 GPSC9-ST782 lineage and a novel serotype 14 sequence type GPSC9-ST18728 lineage. Serotype 23F GPSC14-ST2059 had an I253T mutation within the capsule oligosaccharide repeat unit polymerase Wzy protein, which is predicted in silico to alter the protein pocket cavity. Moreover, serotype 23F GPSC14-ST2059 had SNPs in the DNA binding sites for the cps transcriptional repressors CspR and SpxR. Serotype 14 GPSC9-ST782 harbours a non-truncated version of the large repetitive protein (Lrp), containing a Cna protein B-type domain which is also present in proteins associated with infection and colonisation. These emergent lineages also harboured genes associated with antibiotic resistance, and the promotion of colonisation and infection which were absent in other lineages of the same serotype. Together these data suggest that in addition to serotype replacement, modifications of the capsule locus associated with changes in virulence factor expression and antibiotic resistance may promote vaccine escape. In summary, the study highlights that the persistence of vaccine serotype carriage despite high vaccine coverage in Malawi may be partly caused by expansion of VT lineages post-PCV13 rollout.
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Affiliation(s)
- Rory Cave
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
| | - Akuzike Kalizang'oma
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Chrispin Chaguza
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
| | | | | | - Comfort Brown
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | | | | | | | - Todd D Swarthout
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Brenda Kwambana-Adams
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Neil French
- Clinical Infection, Microbiology and Immunology, Institute of Infection Veterinary & Ecological Science, University of Liverpool, Liverpool, UK
| | - Robert S Heyderman
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
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Warda K, Amari S, Boureddane M, Elkamouni Y, Arsalane L, Zouhair S, Bouskraoui M. Changes in pneumococcal serotypes distribution and penicillin resistance in healthy children five years after generalization of PCV10. Heliyon 2024; 10:e25741. [PMID: 38380016 PMCID: PMC10877248 DOI: 10.1016/j.heliyon.2024.e25741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/11/2024] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Objective Streptococcus pneumoniae (S. pneumoniae) nasopharyngeal carriage has significantly decreased after the generalization of pneumococcal vaccination worldwide. This study sought to investigate changes in S. pneumoniae carriage rates, serotype distribution and penicillin non-susceptibility following the generalization of 10-valent pneumococcal conjugate vaccine. Methods A prospective study was conducted in Marrakesh, Morocco, between 2017 and 2018, among healthy children attending vaccination centers. We collected nasopharyngeal swabs and questionnaire data for each child. Using univariate logistic regression, we analyzed the association between S. pneumoniae carriage and various risk factors. Comparisons of serotype diversity and penicillin resistance between 2017 and 2018 and the period before introduction of vaccination (2008-2009, n = 660) were performed using Simpson index and the chi-squared test, respectively. Results During 2017-2018, 515 children aged between 6 and 36 months participated. The S. pneumoniae carriage rate was 43.3%. Looking at the distribution serotypes, the rate of PCV10 serotypes rate was only 9.6%. Among non-vaccine serotypes, an increase in serotypes 6C/6D (22; 14%), 19B/19C (17; 10.8%), and 15B/15C (11; 7%) was observed. A particular increase in serotype diversity was also observed after the generalization of PCV10 (p < 0.001). S. pneumoniae non-susceptible to penicillin decreased, reaching a rate of 26.6% in 2017-2018. Conclusion The significant change in S. pneumoniae carriage, serotype distribution, and penicillin resistance highlights the effectiveness of the pneumococcal conjugate vaccine among children in Marrakesh, Morocco.
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Affiliation(s)
- Karima Warda
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
| | - Sara Amari
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
| | - Majda Boureddane
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
| | - Youssef Elkamouni
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
- Laboratory of Microbiology-Virology and Molecular Biology, Avicenna Military Hospital, Marrakesh, Morocco
| | - Lamiae Arsalane
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
- Laboratory of Microbiology-Virology and Molecular Biology, Avicenna Military Hospital, Marrakesh, Morocco
| | - Said Zouhair
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
- Laboratory of Microbiology-Virology and Molecular Biology, Avicenna Military Hospital, Marrakesh, Morocco
| | - Mohammed Bouskraoui
- Laboratory of Microbiology and Virology, Cadi Ayad University, Marrakesh, Morocco
- Department of Pediatrics, Mohamed VI University Hospital Center, Marrakesh, Morocco
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Dula D, Morton B, Chikaonda T, Chirwa AE, Nsomba E, Nkhoma V, Ngoliwa C, Sichone S, Galafa B, Tembo G, Chaponda M, Toto N, Kamng'ona R, Makhaza L, Muyaya A, Thole F, Kudowa E, Howard A, Kenny-Nyazika T, Ndaferankhande J, Mkandawire C, Chiwala G, Chimgoneko L, Banda NPK, Rylance J, Ferreira D, Jambo K, Henrion MYR, Gordon SB. Effect of 13-valent pneumococcal conjugate vaccine on experimental carriage of Streptococcus pneumoniae serotype 6B in Blantyre, Malawi: a randomised controlled trial and controlled human infection study. THE LANCET. MICROBE 2023; 4:e683-e691. [PMID: 37659418 PMCID: PMC10469263 DOI: 10.1016/s2666-5247(23)00178-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND The effect of childhood pneumococcal conjugate vaccine implementation in Malawi is threatened by absence of herd effect. There is persistent vaccine-type pneumococcal carriage in both vaccinated children and the wider community. We aimed to use a human infection study to measure 13-valent pneumococcal conjugate vaccine (PCV13) efficacy against pneumococcal carriage. METHODS We did a double-blind, parallel-arm, randomised controlled trial investigating the efficacy of PCV13 or placebo against experimental pneumococcal carriage of Streptococcus pneumoniae serotype 6B (strain BHN418) among healthy adults (aged 18-40 years) from Blantyre, Malawi. We randomly assigned participants (1:1) to receive PCV13 or placebo. PCV13 and placebo doses were prepared by an unmasked pharmacist to maintain research team and participant masking with identification only by a randomisation identification number and barcode. 4 weeks after receiving either PCV13 or placebo, participants were challenged with 20 000 colony forming units (CFUs) per naris, 80 000 CFUs per naris, or 160 000 CFUs per naris by intranasal inoculation. The primary endpoint was experimental pneumococcal carriage, established by culture of nasal wash at 2, 7, and 14 days. Vaccine efficacy was estimated per protocol by means of a log-binomial model adjusting for inoculation dose. The trial is registered with the Pan African Clinical Trials Registry, PACTR202008503507113, and is now closed. FINDINGS Recruitment commenced on April 27, 2021 and the final visit was completed on Sept 12, 2022. 204 participants completed the study protocol (98 PCV13, 106 placebo). There were lower carriage rates in the vaccine group at all three inoculation doses (0 of 21 vs two [11%] of 19 at 20 000 CFUs per naris; six [18%] of 33 vs 12 [29%] of 41 at 80 000 CFUs per naris, and four [9%] of 44 vs 16 [35%] of 46 at 160 000 CFUs per naris). The overall carriage rate was lower in the vaccine group compared with the placebo group (ten [10%] of 98 vs 30 [28%] of 106; Fisher's p value=0·0013) and the vaccine efficacy against carriage was estimated at 62·4% (95% CI 27·7-80·4). There were no severe adverse events related to vaccination or inoculation of pneumococci. INTERPRETATION This is, to our knowledge, the first human challenge study to test the efficacy of a pneumococcal vaccine against pneumococcal carriage in Africa, which can now be used to establish vaccine-induced correlates of protection and compare alternative strategies to prevent pneumococcal carriage. This powerful tool could lead to new means to enhance reduction in pneumococcal carriage after vaccination. FUNDING Wellcome Trust.
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Affiliation(s)
- Dingase Dula
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Ben Morton
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Critical Care Department, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK.
| | | | | | - Edna Nsomba
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | | | - Clara Ngoliwa
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi; Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Simon Sichone
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | | | - Godwin Tembo
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | | | - Neema Toto
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | | | - Lumbani Makhaza
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Alfred Muyaya
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Faith Thole
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | | | - Ashleigh Howard
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Tinashe Kenny-Nyazika
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | | | - Gift Chiwala
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | | | - Ndaziona P K Banda
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi; School of Medicine, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Jamie Rylance
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi
| | - Daniela Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Kondwani Jambo
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Marc Y R Henrion
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Stephen B Gordon
- Malawi Liverpool Wellcome Research Programme, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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Swarthout TD, Henrion MYR, Thindwa D, Meiring JE, Mbewe M, Kalizang'Oma A, Brown C, Msefula J, Moyo B, Mataya AA, Barnaba S, Pearce E, Gordon M, Goldblatt D, French N, Heyderman RS. Waning of antibody levels induced by a 13-valent pneumococcal conjugate vaccine, using a 3 + 0 schedule, within the first year of life among children younger than 5 years in Blantyre, Malawi: an observational, population-level, serosurveillance study. THE LANCET. INFECTIOUS DISEASES 2022; 22:1737-1747. [PMID: 36029796 PMCID: PMC10555849 DOI: 10.1016/s1473-3099(22)00438-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pneumococcal conjugate vaccines (PCVs) induce serotype-specific IgG antibodies, effectively reducing vaccine-serotype carriage and invasive pneumococcal disease (IPD). IgG production wanes approximately 1 month after vaccination in absence of serotype-specific exposure. With uncertainty surrrounding correlate of protection (CoP) estimates and with persistent vaccine-serotype carriage and vaccine-serotype IPD after PCV13 introduction, we aimed to profile population-level immunogenicity among children younger than 5 years in Blantyre, Malawi. METHODS For this serosurveillance study, we used a random subset of samples from a prospective population-based serosurvey in Blantyre, Malawi, done between Dec 16, 2016, and June 27, 2018. Sample selection was based on age category optimisation among children younger than 5 years, adequate sample volume, and available budget. We measured serotype-specific IgGs against the 13 vaccine serotypes (1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F) and two non-vaccine serotypes (12F and 33F), as well as IgGs against three pneumococcal proteins (PsaA, NanA, and Ply), using ELISA and a direct-binding electrochemiluminescence-based multiplex assay. We estimated population-level, serotype-specific immunogenicity profiles using a linear spline regression model. Analyses included samples stratified to 20 3-month age strata (eg, age <3 months to 57-59 months). FINDINGS We evaluated 638 plasma samples: 556 primary samples and 82 unique secondary samples (each linked to one primary sample). Immunogenicity profiles revealed a consistent pattern among vaccine serotypes except serotype 3: a vaccine-induced IgG peak followed by waning to a nadir and subsequent increase in titre. For serotype 3, we observed no apparent vaccine-induced increase. Heterogeneity in parameters included age range at post-vaccination nadir (from 11·2 months [19A] to 27·3 months [7F]). The age at peak IgG titre ranged from 2·69 months (5) to 6·64 months (14). Titres dropped below CoPs against IPD among nine vaccine serotypes (1, 3, 4, 5, 6B, 7F, 9V, 18C, and 23F) and below CoPs against carriage for ten vaccine serotypes (1, 4, 5, 6B, 7F, 9V, 14, 18C, 19F, and 23F). Increasing antibody concentrations among older children and seroincident events were consistent with ongoing vaccine-serotype exposure. INTERPRETATION A 3 + 0 PCV13 schedule with high uptake has not led to sustained population-level antibody immunity beyond the first year of life. Indeed, post-vaccine antibody concentrations dropped below putative CoPs for several vaccine serotypes, potentially contributing to persistent vaccine-serotype carriage and residual vaccine-serotype IPD in Malawi and other similar settings. Policy decisions should consider alternative vaccine strategies, including a booster dose, to achieve sustained vaccine-induced antibody titres, and thus control. FUNDING Bill & Melinda Gates Foundation, Wellcome UK, and National Institute for Health and Care Research.
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Affiliation(s)
- Todd D Swarthout
- National Institute for Health and Care Research Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK; Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi.
| | - Marc Y R Henrion
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Deus Thindwa
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi; Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - James E Meiring
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Maurice Mbewe
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Akuzike Kalizang'Oma
- National Institute for Health and Care Research Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK; Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Comfort Brown
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Jacquline Msefula
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi; Faculty of Medicine, University of Amsterdam, Amsterdam, Netherlands
| | - Brewster Moyo
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Andrew A Mataya
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Susanne Barnaba
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi; Chancellor College, University of Malawi, Blantyre, Malawi
| | - Emma Pearce
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Melita Gordon
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Neil French
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Robert S Heyderman
- National Institute for Health and Care Research Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
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