Pneumococcal exposure routes for infants, a nested cross-sectional survey in Nha Trang, Vietnam

Qian, George; Toizumi, Michiko; Clifford, Samuel; Le, Lien Thuy; Papastylianou, Tasos; Quilty, Billy J; Iwasaki, Chihiro; Kitamura, Noriko; Takegata, Mizuki; Nguyen, Tan; Nguyen, Hien Anh; Dang, Duc Anh; Hoek, Albert Jan van; Yoshida, Lay‐Myint

doi:10.1101/2021.07.04.21259950

Cited by 4 publications

(4 citation statements)

References 27 publications

(31 reference statements)

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“…The observed asymmetry is consistent with <1-year-old infants being more susceptible to infections from within the household, and with the high proximity between mother and child. The exposure risk posed by adults has been observed in previous studies 33,34 , with routine vaccination of older children not found to have a significant effect on vaccine type carriage rates in unvaccinated infants 35 . Taken together, this suggests a possible benefit to a vaccination campaign targeting mothers or other adults with high contact rates to young infants before herd immunity in the adult population is established.…”

Section: Articlementioning

confidence: 72%

Pneumococcal within-host diversity during colonization, transmission and treatment

et al. 2022

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Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within 468 infants and 145 of their mothers by deep sequencing whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples. We demonstrate that deep sequencing has unsurpassed sensitivity for detecting multiple colonization, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared with gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child’s life. Comprehensive treatment data demonstrated that infants were at an elevated risk of both the acquisition and persistent colonization of a multidrug-resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting that they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonization imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.

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Section: Articlementioning

confidence: 72%

Pneumococcal within-host diversity during colonization, transmission and treatment

et al. 2022

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“…This asymmetry is consistent with <1 year old infants being more susceptible to infections from within the household, and with the high proximity between mother and child. The exposure risk posed by adults has been observed in previous studies (43–45) with routine vaccination of older children found to not have a significant effect on vaccine type carriage rates in unvaccinated infants (46). Taken together this suggests there may be a benefit to a vaccination campaign targeting mothers or other adults with high contact rates to young infants before herd immunity in the adult population is established.…”

Section: Introductionmentioning

confidence: 75%

Pneumococcal within-host diversity during colonisation, transmission and treatment

Tonkin‐Hill

Ling

Chaguza

et al. 2022

Preprint

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Characterising the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition, and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within individual infants and their mothers by deep sequencing whole pneumococcal populations from longitudinal nasopharyngeal samples. We demonstrate deep sequencing has unsurpassed sensitivity for detecting multiple colonisation, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared to gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child's life. Comprehensive treatment data demonstrated infants were at an elevated risk of both the acquisition, and persistent colonisation, of a multidrug resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonisation imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.

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“…Most find a limited role of age and some short-lived protection from previous infection. However, other factors that can be context-specific, for example changing contact patterns as young children become more mobile and start attending daycare [43], may mask some of the age effects observed.…”

Section: Discussionmentioning

confidence: 99%

Determinants of RSV epidemiology following suppression through pandemic contact restrictions

Koltai

Krauer

Hodgson

et al. 2021

Preprint

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Introduction COVID-19 related non-pharmaceutical interventions (NPIs) led to a suppression of RSV circulation in winter 2020/21 throughout Europe and an off-season resurgence in Summer 2021 in several European countries. We explore how such temporary interruption may shape future RSV epidemiology and what factors drive the associated uncertainty. Methods We developed an age-structured dynamic transmission model to simulate pre-pandemic RSV infections and hospitalisations. We sampled parameters governing RSV seasonality, immunity acquisition and duration of post-infection immunity and retained those simulations that qualitatively fit the UK's pre-pandemic epidemiology. From Spring 2020 to Summer 2021 we assumed a 50% reduced contact frequency, returning to pre-pandemic levels from mid-May 2021. We simulated transmission forwards until 2023 and evaluated the impact of the sampled parameters on the projected trajectories of RSV hospitalisations. Results Following a lifting of contact restrictions in summer 2021 the model replicated an out-of-season resurgence of RSV. If unmitigated, paediatric RSV hospitalisation incidence in the 2021/22 season was projected to increase by 32% to 67% compared to pre-pandemic levels. The size of the increase depended most on whether infection risk was primarily determined by immunity acquired from previous exposure or general immune maturation. While infants were less affected, the increase in seasonal hospitalisation incidence exceeded 100% in 1-2 year old children and 275% in 2-5 year old children, respectively, in some simulations where immunity from previous exposure dominated. Consequently, the average age of a case increased by 1 to 5 months, most markedly if there was strong immunity acquisition from previous exposure. If immunity to infection was largely determined by age rather than previous exposure, the 2021/22 season started earlier and lasted longer but with a peak incidence lower or similar to pre-pandemic levels. For subsequent seasons, simulations suggested a quick return to pre-pandemic epidemiology, with some slight oscillating behaviour possible depending on the strength of post-exposure immunity. Conclusion COVID-19 mitigation measures stopped RSV circulation in the 2020/21 season and generated immunity debt that will likely lead to a temporary increase in RSV burden in the season following the lifting of restrictions, particularly in 1 to 5 year old children. A more accurate understanding of immunity drivers for RSV is needed to better predict the size of such an increase and plan a potential expansion of pharmaceutical and non-pharmaceutical mitigation measures.

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Pneumococcal exposure routes for infants, a nested cross-sectional survey in Nha Trang, Vietnam

Cited by 4 publications

References 27 publications

Pneumococcal within-host diversity during colonization, transmission and treatment

Pneumococcal within-host diversity during colonization, transmission and treatment

Pneumococcal within-host diversity during colonisation, transmission and treatment

Determinants of RSV epidemiology following suppression through pandemic contact restrictions

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