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Mackenzie GA, Hossain I, Salaudeen R, Badji H, Manjang A, Usuf E, Bottomley C, Greenwood B, Hill PC. Impact of pneumococcal conjugate vaccination on pneumococcal nasopharyngeal carriage in the Gambia: Population-based cross-sectional surveys. Vaccine 2024; 42:2680-2686. [PMID: 38490820 PMCID: PMC11004668 DOI: 10.1016/j.vaccine.2024.02.066] [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] [Received: 06/01/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND The introduction of pneumococcal conjugate vaccines (PCV) has reduced carriage of vaccine-type (VT) pneumococci in many settings. We determined the impact of The Gambia's national PCV programme on carriage of VT pneumococci in the population. METHODS Seven-valent PCV (PCV7) was introduced in August 2009 without catch-up and with doses scheduled at 2, 3, 4 months of age; it was replaced by PCV13 in May 2011. We did cross-sectional carriage surveys in 2009, 2015, and 2017 in age-stratified, population-based samples. Nasopharyngeal specimens were collected and processed according to WHO guidelines. We calculated observed and adjusted prevalence ratios (PR) of VT carriage before and after PCV introduction. FINDINGS We enrolled 2988, 3162, and 2709 participants in 2009, 2015, and 2017 respectively. The baseline (2009) prevalence of VT pneumococcal carriage among children aged 0-4 years was 42.6 %, which declined to 14.9 % and 17.5 % in 2015 and 2017 respectively (adjPR 0.32 [95 % CI 0.27, 0.38] and 0.38 [0.31, 0.46] respectively). VT prevalence among children aged 5-14 years was 16.6 %, 15.1 %, and 15.8 % in the three surveys (2017 vs 2009, adjPR 0.70 [0.58, 0.83]). VT prevalence among 15-44 year-olds was 6.4 %, 5.7 %, and 7.1 % in the three surveys (2017 vs 2009, adjPR 0.59 [0.46, 0.75]), while in those aged ≥ 45 years it was 4.5 %, 6.5 %, and 4.5 % respectively. Non-VT carriage increased in all age-groups. Prevalent residual serotypes were 34 and 15B (age 0-4 years), 3 and 34 (age 5-14 years), and 3 and 16F (age ≥ 15 years). CONCLUSIONS Introduction of PCV was associated with reduced VT pneumococcal carriage in young, and older children, although with substantial residual prevalence. Persisting VT, and non-VT, carriage indicate significant, persistent transmission of pneumococci in the population.
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Affiliation(s)
- Grant A Mackenzie
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia; Murdoch Children's Research Institute, Parkville, 3052 Melbourne, Victoria, Australia; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK; Department of Paediatrics, University of Melbourne, Parkville, 3052 Melbourne, Victoria, Australia.
| | - Ilias Hossain
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Rasheed Salaudeen
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Henry Badji
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Ahmed Manjang
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, PO Box 273, Banjul, Gambia
| | - Christian Bottomley
- Tropical Epidemiology Group, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Brian Greenwood
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Philip C Hill
- Centre for International Health, University of Otago, McMillan Street, Dunedin 9010, New Zealand
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2
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Johnson CN, Wilde S, Tuomanen E, Rosch JW. Convergent impact of vaccination and antibiotic pressures on pneumococcal populations. Cell Chem Biol 2024; 31:195-206. [PMID: 38052216 PMCID: PMC10938186 DOI: 10.1016/j.chembiol.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/08/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
Streptococcus pneumoniae is a remarkably adaptable and successful human pathogen, playing dual roles of both asymptomatic carriage in the nasopharynx and invasive disease including pneumonia, bacteremia, and meningitis. Efficacious vaccines and effective antibiotic therapies are critical to mitigating morbidity and mortality. However, clinical interventions can be rapidly circumvented by the pneumococcus by its inherent proclivity for genetic exchange. This leads to an underappreciated interplay between vaccine and antibiotic pressures on pneumococcal populations. Circulating populations have undergone dramatic shifts due to the introduction of capsule-based vaccines of increasing valency imparting strong selective pressures. These alterations in population structure have concurrent consequences on the frequency of antibiotic resistance profiles in the population. This review will discuss the interactions of these two selective forces. Understanding and forecasting the drivers of antibiotic resistance and capsule switching are of critical importance for public health, particularly for such a genetically promiscuous pathogen as S. pneumoniae.
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Affiliation(s)
- Cydney N Johnson
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shyra Wilde
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elaine Tuomanen
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Jason W Rosch
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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3
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CALABRÒ GIOVANNAELISA, VITALE FRANCESCO, RIZZO CATERINA, PUGLIESE ANDREA, BOCCALINI SARA, BECHINI ANGELA, PANATTO DONATELLA, AMICIZIA DANIELA, DOMNICH ALEXANDER, AMODIO EMANUELE, COSTANTINO CLAUDIO, DI PIETRO MARIALUISA, SALVATI CRISTINA, D’AMBROSIO FLORIANA, ORSINI FRANCESCA, MAIDA ADA, DOMINICI ANNA, CLEMENTE DANIA, CECCI MARINA, PELLACCHIA ANDREA, DI SERAFINO FRANCESCA, BAKKER KEVIN, MALIK TUFAILMOHAMMAD, SHAROMI OLUWASEUN, BELLUZZO MIRIAM, LEONFORTE FRANCESCO, ZAGRA LUIGI, LA GATTA EMANUELE, PETRELLA LUIGI, BONANNI PAOLO, DE WAURE CHIARA. [The new 15-valent pneumococcal conjugate vaccine for the prevention of S. pneumoniae infections in pediatric age: a Health Technology Assessment]. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2023; 64:E1-E160. [PMID: 37655211 PMCID: PMC10468156 DOI: 10.15167/2421-4248/jpmh2023.64.1s1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Affiliation(s)
- GIOVANNA ELISA CALABRÒ
- Sezione di Igiene, Dipartimento Universitario di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
- VIHTALI (Value In Health Technology and Academy for Leadership & Innovation), Spin-off dell’Università Cattolica del Sacro Cuore, Roma, Italia
| | - FRANCESCO VITALE
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università degli Studi di Palermo
| | - CATERINA RIZZO
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università degli Studi di Pisa, Pisa, Italia
| | - ANDREA PUGLIESE
- Dipartimento di Matematica, Università di Trento, Trento, Italia
| | - SARA BOCCALINI
- Dipartimento di Scienze della Salute, Università degli di Studi di Firenze, Firenze, Italia
| | - ANGELA BECHINI
- Dipartimento di Scienze della Salute, Università degli di Studi di Firenze, Firenze, Italia
| | - DONATELLA PANATTO
- Dipartimento di Scienze della Salute, Università degli Studi di Genova, Genova, Italia
- Centro Interuniversitario di Ricerca sull’Influenza e le altre Infezioni Trasmissibili (CIRI-IT), Genova, Italia
| | - DANIELA AMICIZIA
- Dipartimento di Scienze della Salute, Università degli Studi di Genova, Genova, Italia
- Centro Interuniversitario di Ricerca sull’Influenza e le altre Infezioni Trasmissibili (CIRI-IT), Genova, Italia
| | | | - EMANUELE AMODIO
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università degli Studi di Palermo
| | - CLAUDIO COSTANTINO
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università degli Studi di Palermo
| | - MARIA LUISA DI PIETRO
- Sezione di Igiene, Dipartimento Universitario di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - CRISTINA SALVATI
- Dipartimento di Scienze della Salute, Università degli di Studi di Firenze, Firenze, Italia
| | - FLORIANA D’AMBROSIO
- Sezione di Igiene, Dipartimento Universitario di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - FRANCESCA ORSINI
- Alta Scuola di Economia e Management dei Sistemi Sanitari (ALTEMS), Università Cattolica del Sacro Cuore, Roma, Italia
| | - ADA MAIDA
- Sezione di Igiene, Dipartimento Universitario di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - ANNA DOMINICI
- Dipartimento di Medicina e Chirurgia, Università degli di Studi di Perugia, Italia
| | - DANIA CLEMENTE
- Dipartimento di Medicina e Chirurgia, Università degli di Studi di Perugia, Italia
| | - MARINA CECCI
- Dipartimento di Medicina e Chirurgia, Università degli di Studi di Perugia, Italia
| | - ANDREA PELLACCHIA
- Dipartimento di Medicina e Chirurgia, Università degli di Studi di Perugia, Italia
| | - FRANCESCA DI SERAFINO
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università degli Studi di Pisa, Pisa, Italia
| | - KEVIN BAKKER
- Health Economic and Decision Sciences (HEDS), Biostatistics & Research Decision Sciences (BARDS), Merck Research Laboratories, West Point, Pennsylvania
| | - TUFAIL MOHAMMAD MALIK
- Health Economic and Decision Sciences (HEDS), Biostatistics & Research Decision Sciences (BARDS), Merck Research Laboratories, West Point, Pennsylvania
| | - OLUWASEUN SHAROMI
- Health Economic and Decision Sciences (HEDS), Biostatistics & Research Decision Sciences (BARDS), Merck Research Laboratories, West Point, Pennsylvania
| | - MIRIAM BELLUZZO
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università degli Studi di Palermo
| | - FRANCESCO LEONFORTE
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università degli Studi di Palermo
| | - LUIGI ZAGRA
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro”, Università degli Studi di Palermo
| | - EMANUELE LA GATTA
- Sezione di Igiene, Dipartimento Universitario di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - LUIGI PETRELLA
- Sezione di Igiene, Dipartimento Universitario di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - PAOLO BONANNI
- Dipartimento di Scienze della Salute, Università degli di Studi di Firenze, Firenze, Italia
| | - CHIARA DE WAURE
- Dipartimento di Medicina e Chirurgia, Università degli di Studi di Perugia, Italia
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Devarakonda Y, Reddy MVNJ, Neethu RS, Chandran A, Syal K. Multi epitope vaccine candidate design against Streptococcus pneumonia. J Biomol Struct Dyn 2023; 41:12654-12667. [PMID: 36636838 DOI: 10.1080/07391102.2023.2167123] [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] [Received: 06/29/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023]
Abstract
Streptococcus pneumonia, the causative agent of sepsis, meningitis and pneumonia, is held responsible for causing invasive diseases predominantly in children along with adults from both developing and developed countries. The available vaccines coverage in the context of different serotypes is limited and emergence of non-vaccine serotypes could further emerge as a threat in future. Advanced immunoinformatics tools have been used for developing a multi epitope subunit vaccine. In the current study we have subjected these four surface antigenic proteins Ply, PsaA, PspA and PspK to construct vaccine designs. We have predicted different B-cell and T-cell epitopes by using NetCTL 1.2, IEDB (Immune Epitope Databases) and ABCpred. An adjuvant (griselimycin) has been added to the vaccine construct sequence in order to improve its immunogenicity. The vaccine construct has been evaluated for its antigenicity, allergenicity, toxicity and different physio-chemical properties. The bioinformatic tools have been used for prediction, refinement and validation of the 3 D structure. Further, the vaccine structure has been docked with a toll-like receptor (TLR-4) by ClusPro 2.0. In conclusion, the proposed multi-epitope vaccine designs could potentially activate both humoral and cellular immune responses and has a potential to be a vaccine candidate against S.pneumoniae, and requires experimental validation for ensuring immunogenicity and safety profile.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yogeshwar Devarakonda
- Department of Biological Sciences, Center for Genetics and Molecular Microbiology, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, India
| | - M V N Janaradhan Reddy
- Department of Biological Sciences, Center for Genetics and Molecular Microbiology, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, India
| | - R S Neethu
- Department of Biological Sciences, Center for Genetics and Molecular Microbiology, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, India
| | - Aneesh Chandran
- Department of Biotechnology and Microbiology, Kannur University, Kannur, India
| | - Kirtimaan Syal
- Department of Biological Sciences, Center for Genetics and Molecular Microbiology, Institute of Eminence, Birla Institute of Technology and Sciences-Pilani, Hyderabad, India
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5
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Modelling the effect of within-host dynamics on the diversity of a multi-strain pathogen. J Theor Biol 2022; 548:111185. [PMID: 35700769 DOI: 10.1016/j.jtbi.2022.111185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/10/2022] [Accepted: 06/01/2022] [Indexed: 11/23/2022]
Abstract
Multi-strain pathogens such as Group A Streptococcus, Streptococcus pneumoniae, and Staphylococcus aureus cause millions of infections each year with a substantial health burden. Control of multi-strain pathogens can be complicated by the high strain diversity often observed in endemic settings. It is not well understood how high strain diversity is maintained in populations, given that they compete with each other both directly (within an individual host) and indirectly (via host immunity). Previous modelling studies have investigated how indirect competition affects the prevalence and diversity of strains. However, these studies often make simplifying assumptions about the direct competition that occurs within hosts. Currently, little data is available to validate these assumptions, hence there is a need to clarify how sensitive model outputs are to these assumptions. In this study, we compare the dynamics of multi-strain pathogens under different assumptions about direct competition between strains using an agent-based model. We find that the assumptions made about direct competition can affect the epidemiological dynamics, particularly when there is no long-term immunity following infections and a low rate of importation of non-circulating strains. Our results suggest that while direct and indirect competition can each decrease strain diversity when they act in isolation, they may increase strain diversity when they act together. This finding highlights the importance of examining sensitivity to assumptions about strain competition. In particular, omitting consideration of direct competition can lead to inaccurate estimates of the likely effectiveness of control strategies as changes in strain diversity shift the level of direct strain competition.
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6
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Malik TM, Mohammed-Awel J, Gumel AB, Elbasha EH. Mathematical assessment of the impact of cohort vaccination on pneumococcal carriage and serotype replacement. JOURNAL OF BIOLOGICAL DYNAMICS 2021; 15:S214-S247. [PMID: 33594952 DOI: 10.1080/17513758.2021.1884760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Although pneumococcal vaccines are quite effective in reducing disease burden, factors such as imperfect vaccine efficacy and serotype replacement present an important challenge against realizing direct and herd protection benefits of the vaccines. In this study, a novel mathematical model is designed and used to describe the dynamics of two Streptococcus pneumoniae (SP) serotypes, in response to the introduction of a cohort vaccination program which targets one of the two serotypes. The model is fitted to a pediatric SP carriage prevalence data from Atlanta, GA. The model, which is rigorously analysed to investigate the existence and asymptotic stability properties of the associated equilibria (in addition to exploring conditions for competitive exclusion), is simulated to assess the impact of vaccination under different levels of serotype-specific competition and illustrate the phenomenon of serotype replacement. The calibrated model is used to forecast the carriage prevalence in the pediatric cohort over 30 years.
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Affiliation(s)
- Tufail M Malik
- Merck & Co. Inc., 2000 Galloping Hill Road, Kenilworth, NJ, USA
| | | | - Abba B Gumel
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
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7
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Kitano T, Aoki H. The incremental burden of invasive pneumococcal disease associated with a decline in childhood vaccination using a dynamic transmission model in Japan: A secondary impact of COVID-19. Comput Biol Med 2021; 133:104429. [PMID: 33930765 PMCID: PMC8065234 DOI: 10.1016/j.compbiomed.2021.104429] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/31/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has disrupted childhood vaccinations, including pneumococcal conjugate vaccine (PCV). Evaluating the possible impact on the invasive pneumococcal disease (IPD) incidence associated with a decline in childhood pneumococcal vaccination is important to advocate the PCV programs. Using a deterministic, dynamic transmission model, the differential incidence and burden of IPD in children younger than 5 years in Japan were estimated between the rapid vaccination recovery (January 2021) and the delayed vaccination recovery (April 2022) scenarios for the next 10 years. In our model, the IPD incidence was reduced from 11.9/100,000 in 2019 to 6.3/100,000 in 2020, caused by a reduced transmission rate due to the COVID-19 mitigation measures. Assuming a recovery in the transmission rate in 2022 April, the incidence of IPD was estimated to increase with maximal incidence of 12.1 and 13.1/100,000 children under 5 years in the rapid and the delayed vaccination recovery scenarios. The difference in the total IPD incidence between these two scenarios was primarily driven by vaccine serotypes IPD incidence. The difference of incidence was not observed between the two scenarios after 2025. The persistent decline in childhood pneumococcal vaccination rates due to the impact of COVID-19 might lead to an increased IPD incidence and an incremental disease burden.
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Affiliation(s)
- Taito Kitano
- Division of Infectious Diseases, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Ave, Toronto, ON, M5G 1X8, Canada.
| | - Hirosato Aoki
- Department of Neonatology, Kanagawa Children's Medical Center, 2-138-4 Mutsukawa, Minami-ku, Yokohama, Kanagawa, 232-8555, Japan
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8
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Lourenço J, Daon Y, Gori A, Obolski U. Pneumococcal Competition Modulates Antibiotic Resistance in the Pre-Vaccination Era: A Modelling Study. Vaccines (Basel) 2021; 9:265. [PMID: 33809706 PMCID: PMC8002235 DOI: 10.3390/vaccines9030265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 11/30/2022] Open
Abstract
The ongoing emergence of antibiotic resistant strains and high frequencies of antibiotic resistance of Streptococcus pneumoniae poses a major public health challenge. How and which ecological and evolutionary mechanisms maintain the coexistence of antibiotic resistant and susceptible strains remains largely an open question. We developed an individual-based, stochastic model expanding on a previous pneumococci modelling framework. We explore how between- and within-host mechanisms of competition can sustain observed levels of resistance to antibiotics in the pre-vaccination era. Our framework considers that within-host competition for co-colonization between resistant and susceptible strains can arise via pre-existing immunity (immunological competition) or intrinsic fitness differences due to resistance costs (ecological competition). We find that beyond stochasticity, population structure or movement, competition at the within-host level can explain observed resistance frequencies. We compare our simulation results to pneumococcal antibiotic resistance data in the European region using approximate Bayesian computation. Our results demonstrate that ecological competition for co-colonization can explain the variation in co-existence of resistant and susceptible pneumococci observed in the pre-vaccination era. Furthermore, we show that within-host pneumococcal competition can facilitate the maintenance of resistance in the pre-vaccination era. Accounting for these competition-related components of pneumococcal dynamics can improve our understanding of drivers for the emergence and maintenance of antibiotic resistance in pneumococci.
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Affiliation(s)
- José Lourenço
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Yair Daon
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel;
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK;
| | - Uri Obolski
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel;
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Madec S, Gjini E. Predicting N-Strain Coexistence from Co-colonization Interactions: Epidemiology Meets Ecology and the Replicator Equation. Bull Math Biol 2020; 82:142. [PMID: 33119836 PMCID: PMC7595998 DOI: 10.1007/s11538-020-00816-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023]
Abstract
Multi-type infection processes are ubiquitous in ecology, epidemiology and social systems, but remain hard to analyze and to understand on a fundamental level. Here, we study a multi-strain susceptible-infected-susceptible model with coinfection. A host already colonized by one strain can become more or less vulnerable to co-colonization by a second strain, as a result of facilitating or competitive interactions between the two. Fitness differences between N strains are mediated through \documentclass[12pt]{minimal}
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\begin{document}$$N^2$$\end{document}N2 altered susceptibilities to secondary infection that depend on colonizer-cocolonizer identities (\documentclass[12pt]{minimal}
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\begin{document}$$K_{ij}$$\end{document}Kij). By assuming strain similarity in such pairwise traits, we derive a model reduction for the endemic system using separation of timescales. This ‘quasi-neutrality’ in trait space sets a fast timescale where all strains interact neutrally, and a slow timescale where selective dynamics unfold. We find that these slow dynamics are governed by the replicator equation for N strains. Our framework allows to build the community dynamics bottom-up from only pairwise invasion fitnesses between members. We highlight that mean fitness of the multi-strain network, changes with their individual dynamics, acts equally upon each type, and is a key indicator of system resistance to invasion. By uncovering the link between N-strain epidemiological coexistence and the replicator equation, we show that the ecology of co-colonization relates to Fisher’s fundamental theorem and to Lotka-Volterra systems. Besides efficient computation and complexity reduction for any system size, these results open new perspectives into high-dimensional community ecology, detection of species interactions, and evolution of biodiversity.
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Affiliation(s)
- Sten Madec
- Institut Denis Poisson, University of Tours, Tours, France
| | - Erida Gjini
- Instituto Gulbenkian de Ciência, Oeiras, Portugal. .,Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.
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Løchen A, Anderson R. Dynamic transmission models and economic evaluations of pneumococcal conjugate vaccines: a quality appraisal and limitations. Clin Microbiol Infect 2020; 26:60-70. [DOI: 10.1016/j.cmi.2019.04.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/08/2019] [Accepted: 04/22/2019] [Indexed: 02/01/2023]
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Lourenço J, Obolski U, Swarthout TD, Gori A, Bar-Zeev N, Everett D, Kamng'ona AW, Mwalukomo TS, Mataya AA, Mwansambo C, Banda M, Gupta S, French N, Heyderman RS. Determinants of high residual post-PCV13 pneumococcal vaccine-type carriage in Blantyre, Malawi: a modelling study. BMC Med 2019; 17:219. [PMID: 31801542 PMCID: PMC6894346 DOI: 10.1186/s12916-019-1450-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/24/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND In November 2011, Malawi introduced the 13-valent pneumococcal conjugate vaccine (PCV13) into the routine infant schedule. Four to 7 years after introduction (2015-2018), rolling prospective nasopharyngeal carriage surveys were performed in the city of Blantyre. Carriage of Streptococcus pneumoniae vaccine serotypes (VT) remained higher than reported in high-income countries, and impact was asymmetric across age groups. METHODS A dynamic transmission model was fit to survey data using a Bayesian Markov-chain Monte Carlo approach, to obtain insights into the determinants of post-PCV13 age-specific VT carriage. RESULTS Accumulation of naturally acquired immunity with age and age-specific transmission potential were both key to reproducing the observed data. VT carriage reduction peaked sequentially over time, earlier in younger and later in older age groups. Estimated vaccine efficacy (protection against carriage) was 66.87% (95% CI 50.49-82.26%), similar to previous estimates. Ten-year projected vaccine impact (VT carriage reduction) among 0-9 years old was lower than observed in other settings, at 76.23% (CI 95% 68.02-81.96%), with sensitivity analyses demonstrating this to be mainly driven by a high local force of infection. CONCLUSIONS There are both vaccine-related and host-related determinants of post-PCV13 pneumococcal VT transmission in Blantyre with vaccine impact determined by an age-specific, local force of infection. These findings are likely to be generalisable to other Sub-Saharan African countries in which PCV impact on carriage (and therefore herd protection) has been lower than desired, and have implications for the interpretation of post-PCV carriage studies and future vaccination programs.
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Affiliation(s)
- J Lourenço
- Department of Zoology, University of Oxford, Oxford, UK.
| | - U Obolski
- School of Public Health, Tel Aviv University, Tel Aviv, Israel.,Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - T D Swarthout
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | - A Gori
- NIHR Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | - N Bar-Zeev
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - D Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,The Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - A W Kamng'ona
- Department of Biomedical Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
| | - T S Mwalukomo
- Department of Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - A A Mataya
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | - M Banda
- Ministry of Education, Blantyre, Malawi
| | - S Gupta
- Department of Zoology, University of Oxford, Oxford, UK
| | - N French
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Centre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - R S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,NIHR Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
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12
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Reid MC, Peebles K, Stansfield SE, Goodreau SM, Abernethy N, Gottlieb GS, Mittler JE, Herbeck JT. Models to predict the public health impact of vaccine resistance: A systematic review. Vaccine 2019; 37:4886-4895. [PMID: 31307874 DOI: 10.1016/j.vaccine.2019.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/12/2019] [Accepted: 07/02/2019] [Indexed: 12/19/2022]
Abstract
Pathogen evolution is a potential threat to the long-term benefits provided by public health vaccination campaigns. Mathematical modeling can be a powerful tool to examine the forces responsible for the development of vaccine resistance and to predict its public health implications. We conducted a systematic review of existing literature to understand the construction and application of vaccine resistance models. We identified 26 studies that modeled the public health impact of vaccine resistance for 12 different pathogens. Most models predicted that vaccines would reduce overall disease burden in spite of evolution of vaccine resistance. Relatively few pathogens and populations for which vaccine resistance may be problematic were covered in the reviewed studies, with low- and middle-income countries particularly under-represented. We discuss the key components of model design, as well as patterns of model predictions.
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Affiliation(s)
- Molly C Reid
- Department of Epidemiology, 1959 NE Pacific Street, Magnuson Health Sciences Center, Room F-262, Seattle, WA 98195, United States; International Clinical Research Center, Department of Global Health, 908 Jefferson St., Seattle, WA 98104, United States.
| | - Kathryn Peebles
- Department of Epidemiology, 1959 NE Pacific Street, Magnuson Health Sciences Center, Room F-262, Seattle, WA 98195, United States; International Clinical Research Center, Department of Global Health, 908 Jefferson St., Seattle, WA 98104, United States.
| | - Sarah E Stansfield
- Department of Epidemiology, 1959 NE Pacific Street, Magnuson Health Sciences Center, Room F-262, Seattle, WA 98195, United States; Department of Anthropologym Denny Hall, University of Washington, Seattle, WA 98195, United States.
| | - Steven M Goodreau
- Department of Epidemiology, 1959 NE Pacific Street, Magnuson Health Sciences Center, Room F-262, Seattle, WA 98195, United States; Department of Anthropologym Denny Hall, University of Washington, Seattle, WA 98195, United States.
| | - Neil Abernethy
- Department of Biomedical Informatics and Medical Education, University of Washington, Box 358047, Seattle, WA 98195, United States; Department of Health Services, 1959 NE Pacific St, Magnuson Health Sciences Center, Room H-680, Seattle, WA 98195-7660, United States.
| | - Geoffrey S Gottlieb
- Division of Allergy and Infectious Diseases & Center for Emerging & Re-Emerging Infectious Diseases, Department of Medicine & Department of Global Health, 750 Republican St., Building E, Seattle, WA 98109, United States.
| | - John E Mittler
- Department of Microbiology, 750 Republican St., Building F, Seattle, WA 98109, United States.
| | - Joshua T Herbeck
- International Clinical Research Center, Department of Global Health, 908 Jefferson St., Seattle, WA 98104, United States.
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13
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Usuf E, Bottomley C, Bojang E, Cox I, Bojang A, Gladstone R, Kampmann B, Hill PC, Roca A. Persistence of Nasopharyngeal Pneumococcal Vaccine Serotypes and Increase of Nonvaccine Serotypes Among Vaccinated Infants and Their Mothers 5 Years After Introduction of Pneumococcal Conjugate Vaccine 13 in The Gambia. Clin Infect Dis 2019; 68:1512-1521. [PMID: 30165376 PMCID: PMC6481996 DOI: 10.1093/cid/ciy726] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/22/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The widespread use of pneumococcal conjugate vaccine (PCV) has brought about a dramatic decrease in pneumococci of vaccine serotypes (VTs) but nonvaccine serotypes (NVTs) have emerged. METHODS We conducted a cross-sectional survey (CSS) among infants who received 3 doses of 13-valent PCV (PCV13) and their mothers 5 years (CSS3) after PCV13 introduction. Nasopharyngeal swab samples were collected and cultured for isolation of Streptococcus pneumoniae. Whole-genome sequencing of the nontypeable strains was performed. Data were compared with those from 2 previous surveys conducted before PCV13 introduction (CSS1) and 1 year later (CSS2). RESULTS Among infants, VT carriage decreased from 33.3% (113/339) in CSS1 to 11.4% (40/351) in CSS3 (P = .001) while NVTs increased from 53.1% (180/339) in CSS1 to 74.4% (261/351) in CSS3 (P < .001). Among mothers, there was a significant decrease in VTs between CSS2 8.4% (29/347) and CSS3 5.6% (19/342) (P = .006). NVTs increased from 16.6% (55/331) in CSS1 to 32.2% (110/342) in CSS3 (P < .001). In CSS3, the most prevalent VTs were 7F in infants and 3 in mothers, and the most prevalent NVTs were serogroup 16 and nontypeables, respectively. Genomic analysis showed that VTs were more likely than NVTs to lose their ability to express the capsule. CONCLUSIONS Five years after PCV13 introduction, we show both direct (infants) and indirect effects (mothers) of the vaccine, while NVT replacement has occurred in both groups. Ongoing circulation of VTs warrants further study of their relevance in any consideration of a reduced dose schedule.
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Affiliation(s)
- Effua Usuf
- Medical Research Council Unit–The Gambia at the London School of Hygiene and Tropical Medicine, Fajara
| | - Christian Bottomley
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Ebrima Bojang
- Medical Research Council Unit–The Gambia at the London School of Hygiene and Tropical Medicine, Fajara
| | - Isatou Cox
- Medical Research Council Unit–The Gambia at the London School of Hygiene and Tropical Medicine, Fajara
| | - Abdoulie Bojang
- Medical Research Council Unit–The Gambia at the London School of Hygiene and Tropical Medicine, Fajara
| | - Rebecca Gladstone
- Sanger Institute, Wellcome Trust, Pathogen Genomics, Cambridge, United Kingdom
| | - Beate Kampmann
- Medical Research Council Unit–The Gambia at the London School of Hygiene and Tropical Medicine, Fajara
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Philip C Hill
- Centre for International Health, University of Otago, Otago, New Zealand
| | - Anna Roca
- Medical Research Council Unit–The Gambia at the London School of Hygiene and Tropical Medicine, Fajara
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14
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Croucher NJ, Løchen A, Bentley SD. Pneumococcal Vaccines: Host Interactions, Population Dynamics, and Design Principles. Annu Rev Microbiol 2018; 72:521-549. [DOI: 10.1146/annurev-micro-090817-062338] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Streptococcus pneumoniae (the pneumococcus) is a nasopharyngeal commensal and respiratory pathogen. Most isolates express a capsule, the species-wide diversity of which has been immunologically classified into ∼100 serotypes. Capsule polysaccharides have been combined into multivalent vaccines widely used in adults, but the T cell independence of the antibody response means they are not protective in infants. Polysaccharide conjugate vaccines (PCVs) trigger a T cell–dependent response through attaching a carrier protein to capsular polysaccharides. The immune response stimulated by PCVs in infants inhibits carriage of vaccine serotypes (VTs), resulting in population-wide herd immunity. These were replaced in carriage by non-VTs. Nevertheless, PCVs drove reductions in infant pneumococcal disease, due to the lower mean invasiveness of the postvaccination bacterial population; age-varying serotype invasiveness resulted in a smaller reduction in adult disease. Alternative vaccines being tested in trials are designed to provide species-wide protection through stimulating innate and cellular immune responses, alongside antibodies to conserved antigens.
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Affiliation(s)
- Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom
| | - Alessandra Løchen
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom
| | - Stephen D. Bentley
- Infection Genomics Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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15
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Dynamic transmission modelling to address infant pneumococcal conjugate vaccine schedule modifications in the UK. Epidemiol Infect 2018; 146:1797-1806. [PMID: 30012224 PMCID: PMC9506701 DOI: 10.1017/s095026881800198x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AbstractThe 13-valent pneumococcal conjugate vaccine (PCV) has been part of routine immunisation in a 2 + 1 schedule (two primary infant doses and one booster during the second year of life) in the UK since 2010. Recently, the UK's Joint Committee on Vaccination and Immunisation recommended changing to a 1 + 1 schedule while conceding that this will increase disease burden; however, uncertainty remains on how much pneumococcal burden – including invasive pneumococcal disease (IPD) and non-invasive disease – will increase. We built a dynamic transmission model to investigate this question. The model predicted that a 1 + 1 schedule would incur 8777–27 807 additional cases of disease and 241–743 more deaths over 5 years. Serotype 19A caused 55–71% of incremental IPD cases. Scenario analyses showed that booster dose adherence, effectiveness against carriage and waning in a 1 + 1 schedule had the most influence on resurgence of disease. Based on the model assumptions, switching to a 1 + 1 schedule will substantially increase disease burden. The results likely are conservative since they are based on relatively low vaccine-type pneumococcal transmission, a paradigm that has been called into question by data demonstrating an increase of IPD due to several vaccine serotypes during the last surveillance year available.
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16
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Masala GL, Lipsitch M, Bottomley C, Flasche S. Exploring the role of competition induced by non-vaccine serotypes for herd protection following pneumococcal vaccination. J R Soc Interface 2018; 14:rsif.2017.0620. [PMID: 29093131 PMCID: PMC5721164 DOI: 10.1098/rsif.2017.0620] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/11/2017] [Indexed: 02/02/2023] Open
Abstract
The competitive pressure from non-vaccine serotypes may have helped pneumococcal conjugate vaccines (PCVs) to limit vaccine-type (VT) serotype prevalence. We aimed to investigate if, consequently, the indirect protection of vaccines targeting most pneumococcal serotypes could fall short of the profound effects of current formulations. We compared three previously described pneumococcal models harmonized to simulate 20 serotypes with a combined pre-vaccination prevalence in children younger than 5-years-old of 40%. We simulated vaccines of increasing valency by adding serotypes in order of their competitiveness and explored their ability to reduce VT carriage by 95% within 10 years after introduction. All models predicted that additional valency will reduce indirect vaccine effects and hence the overall vaccine impact on carriage both in children and adults. Consequently, the minimal effective coverage (efficacy against carriage×vaccine coverage) needed to eliminate VT carriage increased with increasing valency. One model predicted this effect to be modest, while the other two predicted that high-valency vaccines may struggle to eliminate VT pneumococci unless vaccine efficacy against carriage can be substantially improved. Similar results were obtained when settings of higher transmission intensity and different PCV formulations were explored. Failure to eliminate carriage as a result of increased valency could lead to overall decreased impact of vaccination if the disease burden caused by the added serotypes is low. Hence, a comparison of vaccine formulations of varying valency, and pan-valent formulations in particular, should consider the invasiveness of targeted serotypes, as well as efficacy against carriage.
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Affiliation(s)
- G L Masala
- Centre for Mathematical Modelling and Infectious Diseases, Department of Infectious disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.,School of Computing, Electronics and Mathematics, University of Plymouth, Plymouth, UK
| | - M Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - C Bottomley
- Centre for Mathematical Modelling and Infectious Diseases, Department of Infectious disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - S Flasche
- Centre for Mathematical Modelling and Infectious Diseases, Department of Infectious disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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17
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Herbeck JT, Peebles K, Edlefsen PT, Rolland M, Murphy JT, Gottlieb GS, Abernethy N, Mullins JI, Mittler JE, Goodreau SM. HIV population-level adaptation can rapidly diminish the impact of a partially effective vaccine. Vaccine 2018; 36:514-520. [PMID: 29241646 PMCID: PMC6701864 DOI: 10.1016/j.vaccine.2017.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND Development of an HIV vaccine might be essential to ending the HIV/AIDS pandemic. However, vaccines can result in the emergence and spread of vaccine-resistant strains. Indeed, analyses of breakthrough infections in the HIV phase 3 vaccine trial RV144 identified HIV genotypes with differential rates of transmission in vaccine and placebo recipients. We hypothesized that, for HIV vaccination programs based on partially effective vaccines similar to RV144, HIV adaptation will rapidly diminish the expected vaccine impact. METHODS AND FINDINGS Using two HIV epidemic models, we simulated large-scale vaccination programs and, critically, included HIV strain diversity with respect to the vaccine response. We show here that rapid population-level viral adaptation can lead to decreased overall vaccine efficacy and substantially fewer infections averted by vaccination, when comparing scenarios with and without viral evolution (with outcomes depending on vaccination coverage, vaccine efficacy against the sensitive allele, and the initial resistant allele frequency). Translating this to the epidemic in South Africa, a scenario with 70% vaccination coverage may result in 250,000 infections (non-averted by vaccination) within 10 years of vaccine rollout that are due solely to HIV adaptation, all else being equal. CONCLUSIONS These findings suggest that approaches to HIV vaccine development, program implementation, and epidemic modeling may require attention to viral adaptation in response to vaccination.
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Affiliation(s)
- Joshua T Herbeck
- International Clinical Research Center, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Kathryn Peebles
- International Clinical Research Center, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Paul T Edlefsen
- Vaccine and Infectious Disease Division, FHCRC, Seattle, WA, USA
| | - Morgane Rolland
- US Military HIV Research Program, WRAIR, Silver Spring, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - James T Murphy
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Neil Abernethy
- Department of Biomedical Inf. and Medical Education, University of Washington, Seattle, WA, USA; Department of Health Services, University of Washington, Seattle, WA, USA
| | - James I Mullins
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Microbiology, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - John E Mittler
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Steven M Goodreau
- Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, USA; Department of Anthropology, University of Washington, Seattle, WA, USA
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18
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Maternal pneumococcal nasopharyngeal carriage and risk factors for neonatal carriage after the introduction of pneumococcal conjugate vaccines in The Gambia. Clin Microbiol Infect 2017; 24:389-395. [PMID: 28743545 DOI: 10.1016/j.cmi.2017.07.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/15/2017] [Accepted: 07/19/2017] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Pneumococcal nasopharyngeal carriage occurs early in life. However, the role of vertical transmission is not well understood. The aims of this study were to describe carriage among mothers and their newborns, and to assess for risk factors for neonatal carriage. METHODS In a nested retrospective cohort study, we analysed data from the control arm of a randomized controlled trial conducted in The Gambia 2 to 3 years after introduction of pneumococcal conjugate vaccine (PCV) 13. Nasopharyngeal swabs were collected from 374 women and their newborns on the day of delivery, then 3, 6, 14 and 28 days later. Pneumococci were isolated and serotyped using conventional microbiologic methods. RESULTS Carriage increased from 0.3% (1/373) at birth to 37.2% (139/374) at day 28 (p <0.001) among neonates and from 17.1% (64/374) to 24.3% (91/374) (p 0.015) among women. In both groups, PCV13 vaccine-type (VT) serotypes accounted for approximately one-third of the pneumococcal isolates, with serotype 19A being the most common VT. Maternal carriage (adjusted odds ratio (OR) = 2.82; 95% confidence interval (CI), 1.77-4.80), living with other children in the household (adjusted OR = 4.06; 95% CI, 1.90-8.86) and dry season (OR = 1.98; 95% CI, 1.15-3.43) were risk factors for neonatal carriage. Over half (62.6%) of the neonatal carriage was attributable to living with other children in the same household. CONCLUSIONS Three years after the introduction of PCV in The Gambia, newborns are still rapidly colonized with pneumococcus, including PCV13 VT. Current strategies for pneumococcal control in Africa do not protect this age group beyond the herd effect.
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19
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Ojal J, Flasche S, Hammitt LL, Akech D, Kiti MC, Kamau T, Adetifa I, Nurhonen M, Scott JAG, Auranen K. Sustained reduction in vaccine-type invasive pneumococcal disease despite waning effects of a catch-up campaign in Kilifi, Kenya: A mathematical model based on pre-vaccination data. Vaccine 2017; 35:4561-4568. [PMID: 28729018 PMCID: PMC5571446 DOI: 10.1016/j.vaccine.2017.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 01/22/2023]
Abstract
We predict a substantial decline in the carriage prevalence of vaccine serotypes. About a 56% reduction in invasive pneumococcal disease is also predicted. The decline is predicted to be sustainable ten years post-vaccination. The current vaccination schedule is unlikely to achieve elimination of vaccine serotypes.
Background In 2011, Kenya introduced the 10-valent pneumococcal conjugate vaccine together with a catch-up campaign for children aged <5 years in Kilifi County. In a post-vaccination surveillance study based in Kilifi, there was a substantial decline in invasive pneumococcal disease (IPD). However, given the continued circulation of the vaccine serotypes it is possible that vaccine-serotype disease may re-emerge once the effects of the catch-up campaign wear off. Methods We developed a compartmental, age-structured dynamic model of pneumococcal carriage and invasive disease for three serotype groups: the 10-valent vaccine serotypes and two groups of non-vaccine serotypes based on their susceptibility to mutual competition. The model was calibrated to age- and serotype-specific data on carriage and IPD in the pre-vaccination era and used to predict carriage prevalence and IPD up to ten years post-vaccination in Kilifi. The model was validated against the observed carriage prevalence after vaccine introduction. Results The model predicts a sustained reduction in vaccine-type pneumococcal carriage prevalence from 33% to 8% in infants and from 30% to 8% in 1–5 year olds over the 10-year period following vaccine introduction. The incidence of IPD is predicted to decline across all age groups resulting in an overall reduction of 56% in the population, corresponding to 10.4 cases per 100,000 per year. The vaccine-type IPD incidence is estimated to decline by 83% while non-vaccine-type IPD incidence is predicted to increase by 52%. The model's predictions of carriage prevalence agrees well with the observed data in the first five years post-vaccination. Conclusion We predict a sustained and substantial decline in IPD through PCV vaccination and that the current regimen is insufficient to fully eliminate vaccine-serotype circulation in the model. We show that the observed impact is likely to be sustained despite waning effects of the catch-up campaign.
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Affiliation(s)
- John Ojal
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine-Coast, Kilifi, Kenya; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Stefan Flasche
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Laura L Hammitt
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine-Coast, Kilifi, Kenya; Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Donald Akech
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine-Coast, Kilifi, Kenya
| | - Moses C Kiti
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine-Coast, Kilifi, Kenya
| | - Tatu Kamau
- Kenya Ministry of Health, Nairobi, Kenya
| | - Ifedayo Adetifa
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine-Coast, Kilifi, Kenya; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Markku Nurhonen
- Department of Public Health Solutions, National Institute for Health and Welfare (THL), Finland
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine-Coast, Kilifi, Kenya; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kari Auranen
- Department of Public Health Solutions, National Institute for Health and Welfare (THL), Finland; Department of Mathematics and Statistics, University of Turku, Finland
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20
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Brandileone MCDC, Zanella RC, Almeida SCG, Brandao AP, Ribeiro AF, Carvalhanas TRMP, Sato H, Andrade AL, Verani JR. Effect of 10-valent pneumococcal conjugate vaccine on nasopharyngeal carriage of Streptococcus pneumoniae and Haemophilus influenzae among children in São Paulo, Brazil. Vaccine 2016; 34:5604-5611. [PMID: 27692770 DOI: 10.1016/j.vaccine.2016.09.027] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 10/20/2022]
Abstract
In March 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) in the routine infant immunization program using a 4-dose schedule and catch-up for children <23months. We investigated PCV10 effect on nasopharyngeal carriage with vaccine-type Streptococcus pneumoniae (Spn) and non-typeable Haemophilus influenzae (NTHi) among children in São Paulo city. Cross-sectional surveys were conducted in 2010 (baseline) and 2013 (post-PCV10). Healthy PCV-naïve children aged 12-23months were recruited from primary health centers during immunization campaigns. Nasopharyngeal swabs were collected and tested for Hi; for Spn, all baseline and a stratified random sample of 400 post-PCV10 swabs were tested. We compared vaccine-type Spn and NTHi carriage prevalence pre-/post-PCV10, and used logistic regression to estimate PCV10 effectiveness (1-adjusted odds ratio×100%). Overall 501 children were included in the baseline and 1167 in the post-PCV10 survey (including 400 tested for Spn). Spn was detected in 40.3% of children at baseline and 48.8% post-PCV10; PCV10 serotypes were found in 19.8% and 1.8% respectively, representing a decline of 90.9% (p<0.0001). Carriage of vaccine-related serotypes increased (10.8-21.0%, p<0.0001), driven primarily by a rise in serotype 6C (1.8-11.2%, p<0.0001); carriage of serotypes 6A and 19A did not significantly change. PCV10 effectiveness (4 doses) against vaccine-type carriage was 97.3% (95% confidence interval 88.7-99.3). NTHi prevalence increased from 26.0% (130/501) to 43.6% (509/1167, p<0.0001); PCV10 vaccination seemed significantly associated with NTHi carriage, even after adjusting for other known risk factors. Carriage with PCV10 serotypes among toddlers declined dramatically following PCV10 introduction in São Paulo, Brazil. No protection of PCV10 against NTHi was observed. Our findings contribute to a growing body of evidence of PCV10 impact on vaccine-type carriage and highlight the importance of PCV10 as a tool to reduce the burden of pneumococcal disease in Brazil and globally.
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Affiliation(s)
- Maria-Cristina de C Brandileone
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo, Brazil.
| | - Rosemeire C Zanella
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo, Brazil.
| | - Samanta C G Almeida
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo, Brazil.
| | - Angela P Brandao
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo, Brazil; Oswaldo-Cruz Foundation, Rio de Janeiro, Brazil.
| | - Ana F Ribeiro
- Institute of Infectious Diseases Emilio Ribas, São Paulo, Brazil.
| | | | - Helena Sato
- Center of Epidemiologic Surveillance, Secretary of Health of the State of São Paulo, Brazil.
| | - Ana-Lúcia Andrade
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goias, Brazil.
| | - Jennifer R Verani
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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21
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Chalmers JD, Campling J, Dicker A, Woodhead M, Madhava H. A systematic review of the burden of vaccine preventable pneumococcal disease in UK adults. BMC Pulm Med 2016; 16:77. [PMID: 27169895 PMCID: PMC4864929 DOI: 10.1186/s12890-016-0242-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/01/2016] [Indexed: 11/15/2022] Open
Abstract
Background Invasive pneumococcal disease (IPD) and pneumococcal pneumonia are common and carry a significant morbidity and mortality. Current strategies to prevent pneumococcal disease are under review in the United Kingdom (UK). We conducted a systematic review to evaluate the burden of vaccine type adult pneumococcal disease specifically in the UK. Methods A systematic review conducted and reported according to MOOSE guidelines. Relevant studies from 1990 to 2015 were included. The primary outcome was the incidence of vaccine type pneumococcal disease, focussing on the pneumococcal polysaccharide vaccine (PPSV), the 13-valent conjugate vaccine (PCV13) and the 7-valent conjugate vaccine (PCV7). Results Data from surveillance in England and Wales from 2013/14 shows an incidence of 6.85 per 100,000 population across all adult age groups for IPD, and an incidence of 20.58 per 100,000 population in those aged >65 years. The corresponding incidences for PCV13 serotype IPD were 1.4 per 100,000 and 3.72 per 100,000. The most recent available data for community-acquired pneumonia (CAP) including non-invasive disease showed an incidence of 20.6 per 100,000 for adult pneumococcal CAP and 8.6 per 100,000 population for PCV13 serotype CAP. Both IPD and CAP data sources in the UK suggest an ongoing herd protection effect from childhood PCV13 vaccination causing a reduction in the proportion of cases caused by PCV13 serotypes in adults. Despite this, applying the incidence rates to UK population estimates suggests more than 4000 patients annually will be hospitalised with PCV13 serotype CAP and more than 900 will be affected by IPD, although with a trend for these numbers to decrease over time. There was limited recent data on serotype distribution in high risk groups such as those with chronic respiratory or cardiac disease and no data available for vaccine type (VT) CAP managed in the community where there is likely to be a considerable unmeasured burden. Conclusion The most recent available data suggests that VT pneumococcal disease continues to have a high burden in UK adults despite the impact of childhood PCV13 vaccination. IPD estimates represent only a fraction of the total burden of pneumococcal disease. Study registration PROSPERO CRD42015025043 Electronic supplementary material The online version of this article (doi:10.1186/s12890-016-0242-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Alison Dicker
- School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
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22
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Mitchell PK, Lipsitch M, Hanage WP. Carriage burden, multiple colonization and antibiotic pressure promote emergence of resistant vaccine escape pneumococci. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140342. [PMID: 25918447 PMCID: PMC4424439 DOI: 10.1098/rstb.2014.0342] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pneumococcal conjugate vaccines target the limited subset of the more than 90 known serotypes of Streptococcus pneumoniae responsible for the greatest burden of pneumococcal disease and antibiotic resistance. Following the introduction of these vaccines, serotypes not targeted were able to expand and resistance became more common within these types. Here we use a stochastic dynamic model of pediatric pneumococcal carriage to evaluate potential influences on the emergence of new resistant lineages following the introduction of a vaccine targeting more common resistant types. Antibiotic pressure was the strongest driver, with no emergence at low levels and universal emergence at high levels. At intermediate levels of antibiotic pressure, higher carriage burden and a greater degree of dual carriage promoted emergence. This may have implications for current plans to introduce childhood pneumococcal vaccination in several high-burden countries.
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Affiliation(s)
- Patrick K Mitchell
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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23
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Roca A, Bojang A, Bottomley C, Gladstone RA, Adetifa JU, Egere U, Burr S, Antonio M, Bentley S, Kampmann B. Effect on nasopharyngeal pneumococcal carriage of replacing PCV7 with PCV13 in the Expanded Programme of Immunization in The Gambia. Vaccine 2015; 33:7144-7151. [PMID: 26592141 PMCID: PMC5352730 DOI: 10.1016/j.vaccine.2015.11.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 01/06/2023]
Abstract
INTRODUCTION In 2011, two years after the introduction of 7-valent Pneumococcal conjugate vaccine (PCV7), the Gambian immunization programme replaced PVC7 with PCV13 (13-valent). Our objective was to assess the additional impact of PCV13 on prevalence of pneumococcal nasopharyngeal carriage. METHODS We recruited healthy Gambian infants who had received three PCV doses. Nasopharyngeal swabs were collected from infants and their mothers during two cross-sectional surveys (CSS) conducted in infants vaccinated with PCV7 (CSS1) and vaccinated with PCV13 (CSS2). Pneumococci were isolated and serotyped following standardized methods. Whole genome sequencing was performed on non-typable pneumococcus isolated in CSS1 and CSS2. RESULTS 339 and 350 infants and their mothers were recruited in CSS1 and CSS2, respectively. Overall prevalence of pneumococcal carriage was 85.4% in infants. Among infants, prevalence of vaccine type (VT) carriage was lower in CSS2 [9.4% versus 4.9% (p=0.025) for PCV7-VT; 33.3% versus 18.3% (p<0.001) for PCV13-VT and 23.9% versus 13.7% (p=0.001) for the 6 additional serotypes included in PCV13]. At CSS2, there was a decrease of serotypes 6A (from 15.3% to 5.7%, p<0.001) and 19F (from 5.6% to 1.7%, p=0.007), and an increase of non-typable pneumococci (0.3-6.0%, p<0.001), most of which (82.4%) were from typable serotype backgrounds that had lost the ability to express a capsule. Prevalence of overall and VT carriage in mothers was similar in CSS1 and CSS2. CONCLUSIONS Replacing PCV7 for PCV13 rapidly decreased prevalence of VT carriage among vaccinated Gambian infants. An indirect effect in mothers was not observed yet. Vaccine-driven selection pressure may have been responsible for the increase of non-typable isolates.
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Affiliation(s)
- Anna Roca
- Medical Research Council Unit, Fajara, The Gambia; London School of Hygiene & Tropical Medicine, London, United Kingdom.
| | | | | | - Rebecca A Gladstone
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | | | - Sarah Burr
- Medical Research Council Unit, Fajara, The Gambia; London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Stephen Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Beate Kampmann
- Medical Research Council Unit, Fajara, The Gambia; Department of Paediatrics, Imperial College London, United Kingdom
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24
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Gjini E, Valente C, Sá-Leão R, Gomes MGM. How direct competition shapes coexistence and vaccine effects in multi-strain pathogen systems. J Theor Biol 2015; 388:50-60. [PMID: 26471070 DOI: 10.1016/j.jtbi.2015.09.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/02/2015] [Accepted: 09/22/2015] [Indexed: 11/25/2022]
Abstract
We describe an integrated modeling framework for understanding strain coexistence in polymorphic pathogen systems. Previous studies have debated the utility of neutral formulations and focused on cross-immunity between strains as a major stabilizing mechanism. Here we convey that direct competition for colonization mediates stable coexistence only when competitive abilities amongst pathogen clones satisfy certain pairwise asymmetries. We illustrate our ideas with nested SIS models of single and dual colonization, applied to polymorphic pneumococcal bacteria. By fitting the models to cross-sectional prevalence data from Portugal (before and after the introduction of a seven-valent pneumococcal conjugate vaccine), we are able to not only statistically compare neutral and non-neutral epidemiological formulations, but also estimate vaccine efficacy, transmission and competition parameters simultaneously. Our study highlights that the response of polymorphic pathogen populations to interventions holds crucial information about strain interactions, which can be extracted by suitable nested modeling.
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Affiliation(s)
- Erida Gjini
- Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal.
| | - Carina Valente
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - M Gabriela M Gomes
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade de Porto, Portugal; Instituto de Matemática e Estatística, Universidade de São Paulo, Brazil; Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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25
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Vaccination Drives Changes in Metabolic and Virulence Profiles of Streptococcus pneumoniae. PLoS Pathog 2015; 11:e1005034. [PMID: 26181911 PMCID: PMC4504489 DOI: 10.1371/journal.ppat.1005034] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/19/2015] [Indexed: 11/20/2022] Open
Abstract
The bacterial pathogen, Streptococcus pneumoniae (the pneumococcus), is a leading cause of life-threatening illness and death worldwide. Available conjugate vaccines target only a small subset (up to 13) of >90 known capsular serotypes of S. pneumoniae and, since their introduction, increases in non-vaccine serotypes have been recorded in several countries: a phenomenon termed Vaccine Induced Serotype Replacement (VISR). Here, using a combination of mathematical modelling and whole genome analysis, we show that targeting particular serotypes through vaccination can also cause their metabolic and virulence-associated components to transfer through recombination to non-vaccine serotypes: a phenomenon we term Vaccine-Induced Metabolic Shift (VIMS). Our results provide a novel explanation for changes observed in the population structure of the pneumococcus following vaccination, and have important implications for strain-targeted vaccination in a range of infectious disease systems.
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26
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Bojang A, Jafali J, Egere UE, Hill PC, Antonio M, Jeffries D, Greenwood BM, Roca A. Seasonality of Pneumococcal Nasopharyngeal Carriage in Rural Gambia Determined within the Context of a Cluster Randomized Pneumococcal Vaccine Trial. PLoS One 2015; 10:e0129649. [PMID: 26132206 PMCID: PMC4488590 DOI: 10.1371/journal.pone.0129649] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 05/08/2015] [Indexed: 11/18/2022] Open
Abstract
Background We conducted an ancillary study among individuals who had participated in a PCV-7 trial in rural Gambia, to determine the influence of season on the prevalence of pneumococcal carriage. Methods 636 individuals above 30 months of age were followed from 4 to 20 months after vaccination with PCV-7 or meningococcal-conjugate-vaccine. Nasopharyngeal swabs were collected periodically between November 2006 and June 2008. Overall, 4,495 NPS were collected. Results Prevalence of pneumococcal nasopharyngeal carriage in the study subjects (median age 11 years) was 55.0%; this prevalence decreased linearly with increasing age (p = 0.001). Prevalence of carriage was significantly higher during the dry than the rainy season for any pneumococcal carriage [57.6% versus 47.8% (p<0.001)], pneumococcal vaccine serotype carriage [10.3% versus 6.5% (p< 0.001)] and non-vaccine serotype carriage [49.7% versus 42.7% (p<0.001)]. Differences remained significant in the adjusted analysis. Conclusions In areas of Africa with marked variation in rainfall, seasonality of pneumococcal carriage needs to be considered when interpreting carriage data.
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Affiliation(s)
| | - James Jafali
- Medical Research Council Unit, Fajara, The Gambia
| | | | - Phillip C. Hill
- Medical Research Council Unit, Fajara, The Gambia
- Centre for International Health, School of Medicine, University of Otago, Dunedin, New Zealand
| | | | | | - Brian M. Greenwood
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Anna Roca
- Medical Research Council Unit, Fajara, The Gambia
- * E-mail:
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27
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The serotype distribution among healthy carriers before vaccination is essential for predicting the impact of pneumococcal conjugate vaccine on invasive disease. PLoS Comput Biol 2015; 11:e1004173. [PMID: 25879748 PMCID: PMC4400047 DOI: 10.1371/journal.pcbi.1004173] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/05/2015] [Indexed: 11/24/2022] Open
Abstract
Pneumococcal conjugate vaccines (PCVs) have substantially reduced morbidity and mortality of pneumococcal disease. The impact of the 7-valent PCV on all-serotype invasive pneumococcal disease (IPD) among children was reported to vary between high-income countries. We investigate the ability to predict this heterogeneity from pre-vaccination data. We propose a parsimonious model that predicts the impact of PCVs from the odds of vaccine serotype (VT) among carriers and IPD cases in the pre-PCV period, assuming that VT are eliminated in a mature PCV programme, that full serotype replacement occurs in carriage and that invasiveness of the NVT group is unchanged. We test model performance against the reported impact of PCV7 on childhood IPD in high-income countries from a recent meta-analysis. The odds of pre-PCV7 VT IPD, PCV schedule, PCV coverage and whether a catch up campaign was used for introduction was gathered from the same analysis. We conducted a literature review and meta-analysis to obtain the odds of pre-PCV7 VT carriage in the respective settings. The model predicted the reported impact on childhood IPD of mature PCV programmes; the ratio of predicted and observed incidence risk ratios was close to 1 in all settings. In the high income settings studied differences in schedule, coverage, and catch up campaigns were not associated with the observed heterogeneity in impact of PCV7 on childhood all-serotype IPD. The pre-PCV7 proportion of VT IPD alone also had limited predictive value. The pre-PCV7 proportion of VT carriage and IPD are the main determinants for the impact of PCV7 on childhood IPD and can be combined in a simple model to provide predictions of the vaccine preventable burden of IPD. Pneumococcal vaccines (PCVs) that protect children against 7, 10 and 13 of the most pathogenic pneumococcal serotypes have substantially reduced childhood morbidity and mortality. A recent analysis that evaluated the impact of the 7 valent PCV in multiple high income settings in North America, Europe and Oceania found that the magnitude of all-serotype invasive pneumococcal disease reduction varied greatly between settings (24%-83%). We explored potential sources for that variation, including differences in disease epidemiology before vaccination, vaccine coverage, vaccine schedules and the use of catch-up campaigns for introduction. We find that differences in reported disease impact among mature PCV programmes are likely to be unrelated to the differences in the vaccine programme but can be predicted from a simple model based on pre-vaccination epidemiology, in particular the proportion of vaccine serotypes detected among patients with invasive pneumococcal disease and the proportion of vaccine serotypes that are found in the nasopharynx of healthy individuals. This model presents a useful tool to estimate the potential impact of PCVs (as a relative rate reduction), highlights the essential role of pre-vaccination carriage in healthy individuals for disease impact of PCVs and can estimate the prevented burden of disease where disease surveillance is unavailable.
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28
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Usuf E, Badji H, Bojang A, Jarju S, Ikumapayi UN, Antonio M, Mackenzie G, Bottomley C. Pneumococcal carriage in rural Gambia prior to the introduction of pneumococcal conjugate vaccine: a population-based survey. Trop Med Int Health 2015; 20:871-9. [PMID: 25778937 DOI: 10.1111/tmi.12505] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To evaluate pneumococcal colonisation before and after the introduction of pneumococcal conjugate vaccine (PCV) in eastern Gambia. METHODS Population-based cross-sectional survey of pneumococcal carriage between May and August 2009 before the introduction of PCV into the Expanded Program on Immunization. Nasopharyngeal swabs were collected from all household members, but in selected households, only children aged 6-10 years were swabbed. This age group participated in an earlier trial of a nine-valent PCV between 2000 and 2004. RESULTS The prevalence of nasopharyngeal pneumococcal carriage in 2933 individuals was 72.0% in underfives (N = 515), 41.6% in children aged 5-17 (N = 1508) and 13.0% in adults ≥18 (N = 910) years. The age-specific prevalence of serotypes included in PCV7, PCV10 and PCV13 was 24.7%, 26.6% and 46.8% among children <5 years of age; 8.5%, 9.2% and 17.7% among children 5-17 years; and 2.5%, 3.3% and 5.5% among adults ≥18 years. The most common serotypes were 6A (13.1%), 23F (7.6%), 3 (7.3%), 19F (7.1%) and 34 (4.6%). There was no difference in the overall carriage of pneumococci between vaccinated and unvaccinated children 8 years after the primary vaccination with three doses of PCV (48.3% vs. 41.1%). CONCLUSION Before the introduction of PCV, serotypes included in PCV13 accounted for about half the pneumococcal serotypes in nasopharyngeal carriage. Thus, the potential impact of PCV13 on pneumococcal disease in the Gambia is substantial.
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Affiliation(s)
- Effua Usuf
- Medical Research Council Unit, Fajara, The Gambia
| | - Henry Badji
- Medical Research Council Unit, Fajara, The Gambia
| | | | - Sheikh Jarju
- Medical Research Council Unit, Fajara, The Gambia
| | | | - Martin Antonio
- Medical Research Council Unit, Fajara, The Gambia.,Microbiology and Infection Unit, University of Warwick, Coventry, UK.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Grant Mackenzie
- Medical Research Council Unit, Fajara, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Murdoch Children's Research Institute, Melbourne, Vic., Australia
| | - Christian Bottomley
- Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
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29
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Five challenges in evolution and infectious diseases. Epidemics 2015; 10:40-4. [DOI: 10.1016/j.epidem.2014.12.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 12/09/2014] [Accepted: 12/10/2014] [Indexed: 01/09/2023] Open
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30
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Gritzfeld JF, Cremers AJH, Ferwerda G, Ferreira DM, Kadioglu A, Hermans PWM, Gordon SB. Density and duration of experimental human pneumococcal carriage. Clin Microbiol Infect 2014; 20:O1145-51. [PMID: 24995531 PMCID: PMC4313687 DOI: 10.1111/1469-0691.12752] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/01/2014] [Accepted: 07/01/2014] [Indexed: 02/03/2023]
Abstract
The density and duration of pneumococcal carriage are considered to affect the likelihood of transmission and invasive disease. Because of its importance in both spreading and causing disease, carriage has been suggested as an endpoint in future vaccine studies. Culture is the current gold standard for detection, but may not be sensitive enough to detect changes at low density. Healthy adult volunteers received an intranasal inoculation of Streptococcus pneumoniae serotype 6B. Pneumococcal density in nasal washes collected at six time-points post-inoculation was determined by culture and quantitative PCR (qPCR). Natural pneumococcal carriers detected at initial screening were followed in parallel. In 331 nasal washes from 79 volunteers, the sensitivity and specificity of pneumococcal detection by qPCR, as compared with culture, were 92.3% and 75.9%. The estimation of pneumococcal density by culture and qPCR was highly correlated (rs = 0.73, p <0.0001), although qPCR had a lower detection limit. Pneumococcal density fluctuated within a carriage episode, and occasionally fell below the detection limit of both methods. The duration of carriage episodes was underestimated when only one method was used. Similar fluctuations in density were observed in natural carriers. Pneumococcal carriage is a dynamic event. Culture and qPCR are complementary for surveying the density and duration of pneumococcal carriage episodes.
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Affiliation(s)
- J F Gritzfeld
- Respiratory Infection Group, Liverpool School of Tropical Medicine, Liverpool, UK
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31
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Optimal serotype compositions for Pneumococcal conjugate vaccination under serotype replacement. PLoS Comput Biol 2014; 10:e1003477. [PMID: 24550722 PMCID: PMC3923658 DOI: 10.1371/journal.pcbi.1003477] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 01/02/2014] [Indexed: 11/19/2022] Open
Abstract
Pneumococcal conjugate vaccination has proved highly effective in eliminating vaccine-type pneumococcal carriage and disease. However, the potential adverse effects of serotype replacement remain a major concern when implementing routine childhood pneumococcal conjugate vaccination programmes. Applying a concise predictive model, we present a ready-to-use quantitative tool to investigate the implications of serotype replacement on the net effectiveness of vaccination against invasive pneumococcal disease (IPD) and to guide in the selection of optimal vaccine serotype compositions. We utilise pre-vaccination data on pneumococcal carriage and IPD and assume partial or complete elimination of vaccine-type carriage, its replacement by non-vaccine-type carriage, and stable case-to-carrier ratios (probability of IPD per carriage episode). The model predicts that the post-vaccination IPD incidences in Finland for currently available vaccine serotype compositions can eventually decrease among the target age group of children <5 years of age by 75%. However, due to replacement through herd effects, the decrease among the older population is predicted to be much less (20–40%). We introduce a sequential algorithm for the search of optimal serotype compositions and assess the robustness of inferences to uncertainties in data and assumptions about carriage and IPD. The optimal serotype composition depends on the age group of interest and some serotypes may be highly beneficial vaccine types in one age category (e.g. 6B in children), while being disadvantageous in another. The net effectiveness will be improved only if the added serotype has a higher case-to-carrier ratio than the average case-to-carrier ratio of the current non-vaccine types and the degree of improvement in effectiveness depends on the carriage incidence of the serotype. The serotype compositions of currently available pneumococcal vaccines are not optimal and the effectiveness of vaccination in the population at large could be improved by including new serotypes in the vaccine (e.g. 22 and 9N). The bacterial pathogen Streptococcus pneumoniae (pneumococcus) is a major contributor to child mortality worldwide. Hence, effective pneumococcal vaccination programmes are globally among the most cost-effective public health interventions. Three different conjugate vaccine compositions, targeting 7, 10 or 13 pneumococcal serotypes, have been used in infant vaccination programmes. The use of these vaccines has both decreased the disease burden and changed the patterns of pneumococcal carriage in locations where they have been in use. However, due to serotype replacement, where the lost vaccine serotype carriage is replaced by carriage of the non-vaccine serotypes, the net effect of vaccination on the disease burden has generally been milder than expected. Here, we apply a concise model for serotype replacement and present a ready-to-use tool for the prediction of patterns in post-vaccination pneumococcal incidence of carriage and invasive disease. We introduce a sequential algorithm for the identification of the most optimal additional serotypes to current vaccine formulations and demonstrate how differences in the invasiveness across serotypes imply that the disease incidence may either decrease or increase after vaccination. The methods we outline have direct relevance in decision making while reviewing the performance of the current pneumococcal vaccination programmes.
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