1
|
Dekaj E, Gjini E. Pneumococcus and the stress-gradient hypothesis: A trade-off links R 0 and susceptibility to co-colonization across countries. Theor Popul Biol 2024; 156:77-92. [PMID: 38331222 DOI: 10.1016/j.tpb.2024.02.001] [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: 05/30/2022] [Revised: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Modern molecular technologies have revolutionized our understanding of bacterial epidemiology, but reported data across studies and different geographic endemic settings remain under-integrated in common theoretical frameworks. Pneumococcus serotype co-colonization, caused by the polymorphic bacteria Streptococcus pneumoniae, has been increasingly investigated and reported in recent years. While the global genomic diversity and serotype distribution of S. pneumoniae have been well-characterized, there is limited information on how co-colonization patterns vary globally, critical for understanding the evolution and transmission dynamics of the bacteria. Gathering a rich dataset of cross-sectional pneumococcal colonization studies in the literature, we quantified patterns of transmission intensity and co-colonization prevalence variation in children populations across 17 geographic locations. Linking these data to an SIS model with cocolonization under the assumption of quasi-neutrality among multiple interacting strains, our analysis reveals strong patterns of negative co-variation between transmission intensity (R0) and susceptibility to co-colonization (k). In line with expectations from the stress-gradient-hypothesis in ecology (SGH), pneumococcus serotypes appear to compete more in co-colonization in high-transmission settings and compete less in low-transmission settings, a trade-off which ultimately leads to a conserved ratio of single to co-colonization μ=1/(R0-1)k. From the mathematical model's behavior, such conservation suggests preservation of 'stability-diversity-complexity' regimes in coexistence of similar co-colonizing strains. We find no major differences in serotype compositions across studies, pointing to adaptation of the same set of serotypes across variable environments as an explanation for their differential interaction in different transmission settings. Our work highlights that the understanding of transmission patterns of Streptococcus pneumoniae from global scale epidemiological data can benefit from simple analytical approaches that account for quasi-neutrality among strains, co-colonization, as well as variable environmental adaptation.
Collapse
Affiliation(s)
- Ermanda Dekaj
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Erida Gjini
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.
| |
Collapse
|
2
|
Wang MH, Onnela JP. Flexible Bayesian inference on partially observed epidemics. JOURNAL OF COMPLEX NETWORKS 2024; 12:cnae017. [PMID: 38533184 PMCID: PMC10962317 DOI: 10.1093/comnet/cnae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/02/2024] [Indexed: 03/28/2024]
Abstract
Individual-based models of contagious processes are useful for predicting epidemic trajectories and informing intervention strategies. In such models, the incorporation of contact network information can capture the non-randomness and heterogeneity of realistic contact dynamics. In this article, we consider Bayesian inference on the spreading parameters of an SIR contagion on a known, static network, where information regarding individual disease status is known only from a series of tests (positive or negative disease status). When the contagion model is complex or information such as infection and removal times is missing, the posterior distribution can be difficult to sample from. Previous work has considered the use of Approximate Bayesian Computation (ABC), which allows for simulation-based Bayesian inference on complex models. However, ABC methods usually require the user to select reasonable summary statistics. Here, we consider an inference scheme based on the Mixture Density Network compressed ABC, which minimizes the expected posterior entropy in order to learn informative summary statistics. This allows us to conduct Bayesian inference on the parameters of a partially observed contagious process while also circumventing the need for manual summary statistic selection. This methodology can be extended to incorporate additional simulation complexities, including behavioural change after positive tests or false test results.
Collapse
Affiliation(s)
- Maxwell H Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA
| | - Jukka-Pekka Onnela
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA
| |
Collapse
|
3
|
Järvenpää M, Corander J. On predictive inference for intractable models via approximate Bayesian computation. STATISTICS AND COMPUTING 2023; 33:42. [PMID: 36785730 PMCID: PMC9911513 DOI: 10.1007/s11222-022-10163-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/02/2022] [Indexed: 06/18/2023]
Abstract
UNLABELLED Approximate Bayesian computation (ABC) is commonly used for parameter estimation and model comparison for intractable simulator-based statistical models whose likelihood function cannot be evaluated. In this paper we instead investigate the feasibility of ABC as a generic approximate method for predictive inference, in particular, for computing the posterior predictive distribution of future observations or missing data of interest. We consider three complementary ABC approaches for this goal, each based on different assumptions regarding which predictive density of the intractable model can be sampled from. The case where only simulation from the joint density of the observed and future data given the model parameters can be used for inference is given particular attention and it is shown that the ideal summary statistic in this setting is minimal predictive sufficient instead of merely minimal sufficient (in the ordinary sense). An ABC prediction approach that takes advantage of a certain latent variable representation is also investigated. We additionally show how common ABC sampling algorithms can be used in the predictive settings considered. Our main results are first illustrated by using simple time-series models that facilitate analytical treatment, and later by using two common intractable dynamic models. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11222-022-10163-6.
Collapse
Affiliation(s)
- Marko Järvenpää
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), University of Helsinki, Helsinki, Finland
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| |
Collapse
|
4
|
Miellet WR, van Veldhuizen J, Litt D, Mariman R, Wijmenga-Monsuur AJ, Badoux P, Nieuwenhuijsen T, Thombre R, Mayet S, Eletu S, Sheppard C, van Houten MA, Rots NY, Miller E, Fry NK, Sanders EAM, Trzciński K. It Takes Two to Tango: Combining Conventional Culture With Molecular Diagnostics Enhances Accuracy of Streptococcus pneumoniae Detection and Pneumococcal Serogroup/Serotype Determination in Carriage. Front Microbiol 2022; 13:859736. [PMID: 35509314 PMCID: PMC9060910 DOI: 10.3389/fmicb.2022.859736] [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: 01/21/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background The specificity of molecular methods for the detection of Streptococcus pneumoniae carriage is under debate. We propose a procedure for carriage surveillance and vaccine impact studies that increases the accuracy of molecular detection of live pneumococci in polymicrobial respiratory samples. Methods Culture and qPCR methods were applied to detect pneumococcus and pneumococcal serotypes in 1,549 nasopharyngeal samples collected in the Netherlands (n = 972) and England (n = 577) from 946 toddlers and 603 adults, and in paired oropharyngeal samples collected exclusively from 319 Dutch adults. Samples with no live pneumococci isolated at primary diagnostic culture yet generating signal specific for pneumococcus in qPCRs were re-examined with a second, qPCR-guided culture. Optimal Cq cut-offs for positivity in qPCRs were determined via receiver operating characteristic (ROC) curve analysis using isolation of live pneumococci from the primary and qPCR-guided cultures as reference. Results Detection of pneumococcus and pneumococcal serotypes with qPCRs in cultured (culture-enriched) nasopharyngeal samples exhibited near-perfect agreement with conventional culture (Cohen’s kappa: 0.95). Molecular methods displayed increased sensitivity of detection for multiple serotype carriage, and implementation of qPCR-guided culturing significantly increased the proportion of nasopharyngeal and oropharyngeal samples from which live pneumococcus was recovered (p < 0.0001). For paired nasopharyngeal and oropharyngeal samples from adults none of the methods applied to a single sample type exhibited good agreement with results for primary and qPCR-guided nasopharyngeal and oropharyngeal cultures combined (Cohens kappa; 0.13–0.55). However, molecular detection of pneumococcus displayed increased sensitivity with culture-enriched oropharyngeal samples when compared with either nasopharyngeal or oropharyngeal primary cultures (p < 0.05). Conclusion The accuracy of pneumococcal carriage surveillance can be greatly improved by complementing conventional culture with qPCR and vice versa, by using results of conventional and qPCR-guided cultures to interpret qPCR data. The specificity of molecular methods for the detection of live pneumococci can be enhanced by incorporating statistical procedures based on ROC curve analysis. The procedure we propose for future carriage surveillance and vaccine impact studies improves detection of pneumococcal carriage in adults in particular and enhances the specificity of serotype carriage detection.
Collapse
Affiliation(s)
- Willem R Miellet
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Janieke van Veldhuizen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - David Litt
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Rob Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Alienke J Wijmenga-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Paul Badoux
- Regional Laboratory of Public Health (Streeklab) Haarlem, Haarlem, Netherlands
| | - Tessa Nieuwenhuijsen
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
| | - Rebecca Thombre
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Sanaa Mayet
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Seyi Eletu
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | - Carmen Sheppard
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom
| | | | - Nynke Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Elizabeth Miller
- Immunisation and Countermeasures Division, Public Health England (PHE) - National Infection Service, London, United Kingdom
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU), Public Health England - National Infection Service, London, United Kingdom.,Immunisation and Countermeasures Division, Public Health England (PHE) - National Infection Service, London, United Kingdom
| | - Elisabeth A M Sanders
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht (UMCU), Utrecht, Netherlands
| |
Collapse
|
5
|
Abruzzo AR, Aggarwal SD, Sharp ME, Bee GCW, Weiser JN. Serotype-Dependent Effects on the Dynamics of Pneumococcal Colonization and Implications for Transmission. mBio 2022; 13:e0015822. [PMID: 35289642 PMCID: PMC9040870 DOI: 10.1128/mbio.00158-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 11/23/2022] Open
Abstract
Capsule-switch mutants were compared to analyze how serotype affects the success of Streptococcus pneumoniae (Spn) during colonization and transmission. Strains of multiple serotypes were tested in highly susceptible infant mice, both singly and in competitive assays. Our findings demonstrated a role of serotype, apart from genetic background, in competitive success of strains, but this depended on timing postinoculation. As is the case for natural carriage, there was a hierarchy of success among serotypes using capsule-switch strains. The long-term dominance of a serotype was established within the first 4 h after acquisition, suggesting an effect independent of Spn-induced host responses. The hierarchy of serotype dominance correlated with decreased clearance rather than increased growth in vivo. Competitive assays staggering the timing of challenge showed that the first strain to dominate the niche sustained its competitive advantage, potentially explaining how increased density from delayed early clearance could result in serotype-dependent success. Effector molecules of intrastrain competition (fratricide), regulated by the competence operon in a quorum-sensing mechanism, were required for early niche dominance. This suggested a winner-takes-all scenario in which serotype is a major factor in achieving early niche dominance, such that once a strain reaches a threshold density it is able to exclude competitors through fratricide. Serotype was also an important determinant of transmission dynamics, although transit to a recipient host depended on effects of serotype different from its contribution to the dominance of colonization in the donor host. IMPORTANCE Capsule is the major virulence factor and surface antigen of the opportunistic respiratory pathogen Streptococcus pneumoniae (Spn). Strains of Spn express at least 100 structurally and immunologically distinct types (serotypes) of capsule, but for unknown reasons only a few are common. The effect of serotypes during the commensal interactions of Spn and its host, colonization and transmission, was tested. This was carried out by comparing genetically modified strains differing only in serotype in infant mouse models. Results show that serotype is an important factor in a strain's success during colonization. This was attributed to the effect of serotype on early clearance of the organism in the host. Competitive factors expressed by Spn (in a mechanism referred to as fratricide) allow the strain gaining this initial advantage to then dominate the upper respiratory tract niche. Serotype also plays an important role in a strain's success during transmission from one host to another.
Collapse
Affiliation(s)
- Annie R. Abruzzo
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Surya D. Aggarwal
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Molly E. Sharp
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Gavyn Chern Wei Bee
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jeffrey N. Weiser
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| |
Collapse
|
6
|
Senghore M, Chaguza C, Bojang E, Tientcheu PE, Bancroft RE, Lo SW, Gladstone RA, McGee L, Worwui A, Foster-Nyarko E, Ceesay F, Okoi CB, Klugman KP, Breiman RF, Bentley SD, Adegbola R, Antonio M, Hanage WP, Kwambana-Adams BA. Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints. Microb Genom 2022; 8. [PMID: 35119356 PMCID: PMC8942022 DOI: 10.1099/mgen.0.000732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transmission dynamics of Streptococcus pneumoniae in sub-Saharan Africa are poorly understood due to a lack of adequate epidemiological and genomic data. Here we leverage a longitudinal cohort from 21 neighbouring villages in rural Africa to study how closely related strains of S. pneumoniae are shared among infants. We analysed 1074 pneumococcal genomes isolated from 102 infants from 21 villages. Strains were designated for unique serotype and sequence-type combinations, and we arbitrarily defined strain sharing where the pairwise genetic distance between strains could be accounted for by the mean within host intra-strain diversity. We used non-parametric statistical tests to assess the role of spatial distance and prolonged carriage on strain sharing using a logistic regression model. We recorded 458 carriage episodes including 318 (69.4 %) where the carried strain was shared with at least one other infant. The odds of strain sharing varied significantly across villages (χ2=47.5, df=21, P-value <0.001). Infants in close proximity to each other were more likely to be involved in strain sharing, but we also show a considerable amount of strain sharing across longer distances. Close geographic proximity (<5 km) between shared strains was associated with a significantly lower pairwise SNP distance compared to strains shared over longer distances (P-value <0.005). Sustained carriage of a shared strain among the infants was significantly more likely to occur if they resided in villages within a 5 km radius of each other (P-value <0.005, OR 3.7). Conversely, where both infants were transiently colonized by the shared strain, they were more likely to reside in villages separated by over 15 km (P-value <0.05, OR 1.5). PCV7 serotypes were rare (13.5 %) and were significantly less likely to be shared (P-value <0.001, OR −1.07). Strain sharing was more likely to occur over short geographical distances, especially where accompanied by sustained colonization. Our results show that strain sharing is a useful proxy for studying transmission dynamics in an under-sampled population with limited genomic data. This article contains data hosted by Microreact.
Collapse
Affiliation(s)
- Madikay Senghore
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia.,Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA
| | - Chrispin Chaguza
- Infection Genomics, Wellcome Sanger Institute, Hinxton, UK.,Darwin College, University of Cambridge, Silver Street, Cambridge, UK.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Ebrima Bojang
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Peggy-Estelle Tientcheu
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Rowan E Bancroft
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Stephanie W Lo
- Infection Genomics, Wellcome Sanger Institute, Hinxton, UK
| | | | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Archibald Worwui
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Ebenezer Foster-Nyarko
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Fatima Ceesay
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Catherine Bi Okoi
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia
| | - Keith P Klugman
- Rollins School Public Health, Emory University, Atlanta, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | | | - Richard Adegbola
- Immunisation and Global Health Consulting, RAMBICON, Lagos, Nigeria
| | - Martin Antonio
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA
| | - Brenda A Kwambana-Adams
- WHO Regional Reference Laboratory (RRL), West Africa Strategy and Partnership, Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Road, Fajara, The Gambia.,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| |
Collapse
|
7
|
Løchen A, Anderson RM. Dynamic transmission models and economic evaluations of pneumococcal conjugate vaccines: a quality appraisal and limitations. Clin Microbiol Infect 2021. [DOI: 10.1016/j.cmi.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJ. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. THE ISME JOURNAL 2021; 15:1523-1538. [PMID: 33408365 PMCID: PMC8115253 DOI: 10.1038/s41396-020-00867-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations' ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.
Collapse
Affiliation(s)
- Gabrielle L Harrow
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Caroline Colijn
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK.
| |
Collapse
|
9
|
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.
Collapse
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
| | | |
Collapse
|
10
|
Touloupou P, Finkenstädt B, Besser TE, French NP, Spencer SEF. Bayesian inference for multistrain epidemics with application to ESCHERICHIA COLI O157:H7 in feedlot cattle. Ann Appl Stat 2020. [DOI: 10.1214/20-aoas1366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
11
|
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]
|
12
|
Almutiry W, Deardon R. Incorporating Contact Network Uncertainty in Individual Level Models of Infectious Disease using Approximate Bayesian Computation. Int J Biostat 2019; 16:ijb-2017-0092. [PMID: 31812945 DOI: 10.1515/ijb-2017-0092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/19/2019] [Indexed: 11/15/2022]
Abstract
Infectious disease transmission between individuals in a heterogeneous population is often best modelled through a contact network. However, such contact network data are often unobserved. Such missing data can be accounted for in a Bayesian data augmented framework using Markov chain Monte Carlo (MCMC). Unfortunately, fitting models in such a framework can be highly computationally intensive. We investigate the fitting of network-based infectious disease models with completely unknown contact networks using approximate Bayesian computation population Monte Carlo (ABC-PMC) methods. This is done in the context of both simulated data, and data from the UK 2001 foot-and-mouth disease epidemic. We show that ABC-PMC is able to obtain reasonable approximations of the underlying infectious disease model with huge savings in computation time when compared to a full Bayesian MCMC analysis.
Collapse
Affiliation(s)
- Waleed Almutiry
- Department of Mathematics, College of Science and Arts, Qassim University,Ar Rass, Qassim, Saudi Arabia
| | - Rob Deardon
- Department of Mathematics and Statistics and Department of Production Animal Health, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
13
|
Affiliation(s)
- James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia.
| | - Claudia Trappetti
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia
| |
Collapse
|
14
|
Järvenpää M, Sater MRA, Lagoudas GK, Blainey PC, Miller LG, McKinnell JA, Huang SS, Grad YH, Marttinen P. A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation. PLoS Comput Biol 2019; 15:e1006534. [PMID: 31009452 PMCID: PMC6497309 DOI: 10.1371/journal.pcbi.1006534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 05/02/2019] [Accepted: 02/22/2019] [Indexed: 11/19/2022] Open
Abstract
Bacterial populations that colonize a host can play important roles in host health, including serving as a reservoir that transmits to other hosts and from which invasive strains emerge, thus emphasizing the importance of understanding rates of acquisition and clearance of colonizing populations. Studies of colonization dynamics have been based on assessment of whether serial samples represent a single population or distinct colonization events. With the use of whole genome sequencing to determine genetic distance between isolates, a common solution to estimate acquisition and clearance rates has been to assume a fixed genetic distance threshold below which isolates are considered to represent the same strain. However, this approach is often inadequate to account for the diversity of the underlying within-host evolving population, the time intervals between consecutive measurements, and the uncertainty in the estimated acquisition and clearance rates. Here, we present a fully Bayesian model that provides probabilities of whether two strains should be considered the same, allowing us to determine bacterial clearance and acquisition from genomes sampled over time. Our method explicitly models the within-host variation using population genetic simulation, and the inference is done using a combination of Approximate Bayesian Computation (ABC) and Markov Chain Monte Carlo (MCMC). We validate the method with multiple carefully conducted simulations and demonstrate its use in practice by analyzing a collection of methicillin resistant Staphylococcus aureus (MRSA) isolates from a large recently completed longitudinal clinical study. An R-code implementation of the method is freely available at: https://github.com/mjarvenpaa/bacterial-colonization-model.
Collapse
Affiliation(s)
- Marko Järvenpää
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Mohamad R. Abdul Sater
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Georgia K. Lagoudas
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul C. Blainey
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Loren G. Miller
- Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor–UCLA Medical Center, Torrance, CA, USA
| | - James A. McKinnell
- Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Diseases, LA Biomed Research Institute at Harbor–UCLA Medical Center, Torrance, CA, USA
| | - Susan S. Huang
- Division of Infectious Diseases and Health Policy Research Institute, University of California, Irvine School of Medicine, Irvine, CA, USA
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Pekka Marttinen
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland
| |
Collapse
|
15
|
Shen P, Lees JA, Bee GCW, Brown SP, Weiser JN. Pneumococcal quorum sensing drives an asymmetric owner-intruder competitive strategy during carriage via the competence regulon. Nat Microbiol 2018; 4:198-208. [PMID: 30546100 DOI: 10.1038/s41564-018-0314-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/30/2018] [Indexed: 11/09/2022]
Abstract
Competition among microorganisms is a key determinant of successful host colonization and persistence. For Streptococcus pneumoniae, lower than predicted rates of co-colonizing strains suggest a competitive advantage for resident bacteria over newcomers. In light of evolutionary theory, we hypothesized that S. pneumoniae use owner-intruder asymmetries to settle contests, leading to the disproportionate success of the initial resident 'owner', regardless of the genetic identity of the 'intruder'. We investigated the determinants of within-host competitive success utilizing S. pneumoniae colonization of the upper respiratory tract of infant mice. Within 6 h, colonization by the resident inhibited colonization by an isogenic challenger. The competitive advantage of the resident was dependent on quorum sensing via the competence (Com) regulon and downstream choline binding protein D (CbpD) and on the competence-induced bacteriocins A and B (CibAB) implicated in fratricide. CbpD and CibAB are highly conserved across pneumococcal lineages, indicating evolutionary advantages for asymmetric competitive strategies within the species. Mathematical modelling supported a significant role for quorum sensing via the Com regulon in competition, even for strains with different competitive advantages. Our study suggests that asymmetric owner-intruder competitive strategies do not require complex cognition and are used by a major human pathogen to determine 'ownership' of human hosts.
Collapse
Affiliation(s)
- Pamela Shen
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gavyn Chern Wei Bee
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jeffrey N Weiser
- Department of Microbiology, New York University School of Medicine, New York, NY, USA.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Geographic variation in pneumococcal vaccine efficacy estimated from dynamic modeling of epidemiological data post-PCV7. Sci Rep 2017; 7:3049. [PMID: 28607461 PMCID: PMC5468270 DOI: 10.1038/s41598-017-02955-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 04/28/2017] [Indexed: 11/09/2022] Open
Abstract
Although mean efficacy of multivalent pneumococcus vaccines has been intensively studied, variance in vaccine efficacy (VE) has been overlooked. Different net individual protection across settings can be driven by environmental conditions, local serotype and clonal composition, as well as by socio-demographic and genetic host factors. Understanding efficacy variation has implications for population-level effectiveness and other eco-evolutionary feedbacks. Here I show that realized VE can vary across epidemiological settings, by applying a multi-site-one-model approach to data post-vaccination. I analyse serotype prevalence dynamics following PCV7, in asymptomatic carriage in children attending day care in Portugal, Norway, France, Greece, Hungary and Hong-Kong. Model fitting to each dataset provides site-specific estimates for vaccine efficacy against acquisition, and pneumococcal transmission parameters. According to this model, variable serotype replacement across sites can be explained through variable PCV7 efficacy, ranging from 40% in Norway to 10% in Hong-Kong. While the details of how this effect is achieved remain to be determined, here I report three factors negatively associated with the VE readout, including initial prevalence of serotype 19F, daily mean temperature, and the Gini index. The study warrants more attention on local modulators of vaccine performance and calls for predictive frameworks within and across populations.
Collapse
|
18
|
Ramiadantsoa T, Sirén J, Hanski I. Phylogenetic Comparative Method for Geographical Radiation. ANN ZOOL FENN 2017. [DOI: 10.5735/086.054.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Tanjona Ramiadantsoa
- Metapopulation Research Centre, Department of Biosciences, P.O. Box 65, FI-00014 University of Helsinki, Finland
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Cir Saint Paul, MN 55108-6097, USA
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Dr, Madison, WI 53706, USA
| | - Jukka Sirén
- Metapopulation Research Centre, Department of Biosciences, P.O. Box 65, FI-00014 University of Helsinki, Finland
| | - Ilkka Hanski
- Metapopulation Research Centre, Department of Biosciences, P.O. Box 65, FI-00014 University of Helsinki, Finland
| |
Collapse
|
19
|
Gutmann MU, Dutta R, Kaski S, Corander J. Likelihood-free inference via classification. STATISTICS AND COMPUTING 2017; 28:411-425. [PMID: 31997856 PMCID: PMC6956883 DOI: 10.1007/s11222-017-9738-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 02/28/2017] [Indexed: 06/10/2023]
Abstract
Increasingly complex generative models are being used across disciplines as they allow for realistic characterization of data, but a common difficulty with them is the prohibitively large computational cost to evaluate the likelihood function and thus to perform likelihood-based statistical inference. A likelihood-free inference framework has emerged where the parameters are identified by finding values that yield simulated data resembling the observed data. While widely applicable, a major difficulty in this framework is how to measure the discrepancy between the simulated and observed data. Transforming the original problem into a problem of classifying the data into simulated versus observed, we find that classification accuracy can be used to assess the discrepancy. The complete arsenal of classification methods becomes thereby available for inference of intractable generative models. We validate our approach using theory and simulations for both point estimation and Bayesian inference, and demonstrate its use on real data by inferring an individual-based epidemiological model for bacterial infections in child care centers.
Collapse
Affiliation(s)
| | - Ritabrata Dutta
- InterDisciplinary Institute of Data Science, Universitá della Svizzera italiana, Lugano, Switzerland
| | - Samuel Kaski
- Helsinki Institute for Information Technology, Department of Computer Science, Aalto University, Espoo, Finland
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Helsinki Institute for Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| |
Collapse
|
20
|
Pokharel G, Deardon R. Gaussian process emulators for spatial individual-level models of infectious disease. CAN J STAT 2016. [DOI: 10.1002/cjs.11304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Gyanendra Pokharel
- Department of Mathematics and Statistics, Faculty of Science; University of Calgary; Alberta Canada
- Department of Mathematics and Statistics, College of Physical and Engineering Science; University of Guelph; Ontario Canada
| | - Rob Deardon
- Department of Mathematics and Statistics, Faculty of Science; University of Calgary; Alberta Canada
- Department of Production Animal Health, Faculty of Veterinary Medicine; University of Calgary; Alberta Canada
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Numminen E, Chewapreecha C, Sirén J, Turner C, Turner P, Bentley SD, Corander J. Two-phase importance sampling for inference about transmission trees. Proc Biol Sci 2015; 281:20141324. [PMID: 25253455 PMCID: PMC4211445 DOI: 10.1098/rspb.2014.1324] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There has been growing interest in the statistics community to develop methods for inferring transmission pathways of infectious pathogens from molecular sequence data. For many datasets, the computational challenge lies in the huge dimension of the missing data. Here, we introduce an importance sampling scheme in which the transmission trees and phylogenies of pathogens are both sampled from reasonable importance distributions, alleviating the inference. Using this approach, arbitrary models of transmission could be considered, contrary to many earlier proposed methods. We illustrate the scheme by analysing transmissions of Streptococcus pneumoniae from household to household within a refugee camp, using data in which only a fraction of hosts is observed, but which is still rich enough to unravel the within-household transmission dynamics and pairs of households between whom transmission is plausible. We observe that while probability of direct transmission is low even for the most prominent cases of transmission, still those pairs of households are geographically much closer to each other than expected under random proximity.
Collapse
Affiliation(s)
- Elina Numminen
- Department of Mathematics and Statistics, University of Helsinki, PO Box 68, 00014 Helsinki, Finland
| | - Claire Chewapreecha
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Jukka Sirén
- Department of Biosciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sod, Thailand Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sod, Thailand Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen D Bentley
- Department of Biosciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, PO Box 68, 00014 Helsinki, Finland
| |
Collapse
|
23
|
Numminen E, Chewapreecha C, Turner C, Goldblatt D, Nosten F, Bentley SD, Turner P, Corander J. Climate induces seasonality in pneumococcal transmission. Sci Rep 2015; 5:11344. [PMID: 26067932 PMCID: PMC4464306 DOI: 10.1038/srep11344] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/21/2015] [Indexed: 01/31/2023] Open
Abstract
Streptococcus pneumoniae is a significant human pathogen and a leading cause of infant mortality in developing countries. Considerable global variation in the pneumococcal carriage prevalence has been observed and the ecological factors contributing to it are not yet fully understood. We use data from a cohort of infants in Asia to study the effects of climatic conditions on both acquisition and clearance rates of the bacterium, finding significantly higher transmissibility during the cooler and drier months. Conversely, the length of a colonization period is unaffected by the season. Independent carriage data from studies conducted on the African and North American continents suggest similar effects of the climate on the prevalence of this bacterium, which further validates the obtained results. Further studies could be important to replicate the findings and explain the mechanistic role of cooler and dry air in the physiological response to nasopharyngeal acquisition of the pneumococcus.
Collapse
Affiliation(s)
- Elina Numminen
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Claire Chewapreecha
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Claudia Turner
- 1] Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Goldblatt
- Immunobiology Unit, Institute of Child Health, University College London, UK
| | - Francois Nosten
- 1] Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen D Bentley
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Paul Turner
- 1] Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand [2] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| |
Collapse
|