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Streptococcus pyogenes is a leading cause of human morbidity and mortality, especially in resource-limited settings. The development of a vaccine against S. pyogenes is a global health priority to reduce the burden of postinfection rheumatic heart disease. To support this, molecular characterization of circulating S. pyogenes isolates is needed. We performed whole-genome analyses of S. pyogenes isolates from skin and soft tissue infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where there is a high burden of such infections. To act as a comparator to these LIC isolates, skin infection isolates from Sheffield, United Kingdom (a high-income country [HIC]), were also sequenced. The LIC isolates from The Gambia were genetically more diverse (46

BackgroundImmunity toStreptococcus pyogenesin high burden settings is poorly understood. We exploredS. pyogenesnasopharyngeal colonization after intranasal live attenuated influenza vaccine (LAIV) among Gambian children aged 24-59 months, and resulting serological response to 7 antigens.MethodsA post-hoc analysis was performed in 320 children randomized to receive LAIV at baseline (LAIV group) or not (control).S. pyogenescolonization was determined by quantitative Polymerase Chain Reaction (qPCR) on nasopharyngeal swabs from baseline (D0), day 7 (D7) and day 21 (D21). Anti-streptococcal IgG was quantified, including a subset with paired serum pre/postS. pyogenesacquisition.ResultsThe point prevalence ofS. pyogenescolonization ranged from 7-13%. In children negative at D0,S. pyogeneswas detected at D7 or D21 in 18% of LAIV group and 11% of control group participants (p=0.12). The odds ratio (OR) for colonization over time was significantly increased in the LAIV group (D21 vs D0 OR 3.18, p=0.003) but not in the control group (OR 0.86, p=0.79). The highest IgG increases following asymptomatic colonization were seen for M1 and SpyCEP proteins.ConclusionsAsymptomaticS. pyogenescolonization appears modestly increased by LAIV, and may be immunologically significant. LAIV could be used to study influenza-S. pyogenesinteractions.

Streptococcus pyogenes is a leading cause of human morbidity and mortality, especially in resource limited settings. The World Health Organisation has recently made a vaccine for S. pyogenes a global health priority to reduce the burden of the post-infection rheumatic heart disease. For a vaccine to be active against all relevant strains in each region, molecular characterisation of circulating S. pyogenes isolates is needed. We performed extensive comparative whole genome analyses of S. pyogenes isolates from skin and soft tissue infections in The Gambia, West Africa, where there is a high burden of such infections. To act as a comparator to this low-income country (LIC) collection of isolates, we performed genome sequencing of isolates from skin infections in Sheffield, UK, as representative high-income country (HIC) isolates. LIC isolates from The Gambia were genetically more diverse (46 emm-types in 107 isolates) compared to HIC isolates from Sheffield (23 emm-types in 142 isolates), with only 7 overlapping emm-types and with diverse genetic backgrounds. Characterisation of other molecular markers indicated some shared features, including a high prevalence of the skin infection-associated emm-pattern D and the variable fibronectin-collagen-T antigen (FCT) types FCT-3 and FCT-4. A previously unidentified FCT (FCT-10) was identified in the LIC isolates, belonging to two different emm-types. A high proportion (79/107; 73.8%) of LIC isolates carried genes for tetracycline resistance, compared to 53/142 (37.3%) HIC isolates. There was also evidence of different circulating prophages, as very few prophage-associated DNases and lower numbers of superantigens were detected in LIC isolates. Our study provides much needed insight into the genetics of circulating isolates in a LIC (The Gambia), and how they differ from those circulating in HICs (Sheffield, UK). Common molecular features may act as bacterial drivers for specific infection types, regardless of the diverse genetic background.

Rationale: In children lacking adaptive immunity to influenza, upper respiratory tract innate immune responses may be important and explain variability in viral shedding and disease outcome. Objectives: We used live attenuated influenza vaccine (LAIV) as a surrogate challenge model in children to identify pre-infection mucosal transcriptomic signatures associated with subsequent viral shedding. We also determined whether asymptomatic respiratory viral infection impact these signatures. Methods: Children aged 24-59 months (n=82) were given one dose of trivalent LAIV during a prospective, observational, phase 4 study in The Gambia (NCT02972957). Nasopharyngeal swabs were used to determine gene expression and asymptomatic respiratory viral infection prior to challenge, and LAIV viral loads at day 2 and 7. Gene set enrichment analysis was used to identify transcriptomic signatures representing gene pathways and cell types at baseline associated with subsequent LAIV viral load. Main Results: In children seronegative for each influenza strain, upregulation of interferon signaling pathways prior to LAIV receipt was significantly associated with lower strain-specific viral loads at day 2 and 7. Asymptomatic respiratory viruses were detected in 42% of children. Several interferon-stimulated genes were differentially expressed in children with asymptomatic respiratory viral infection and negatively correlated with LAIV viral loads. Upregulation of genes enriched in macrophages, neutrophils and eosinophils was also associated with lower viral loads, and found more commonly in children with asymptomatic non-influenza viral infections. Conclusions: Variability in mucosal interferon gene expression prior to infection in children may impact the course of subsequent influenza infections. This variability may be due to frequent asymptomatic respiratory viral infections, demonstrating the potential importance of virus-virus interactions in the upper respiratory tract in determining the outcome of respiratory viral infections in children.

Summary In children lacking influenza-specific adaptive immunity, upper respiratory tract innate immune responses may influence viral replication and disease outcome. We use trivalent live attenuated influenza vaccine (LAIV) as a surrogate challenge model in children aged 24–59 months to identify pre-infection mucosal transcriptomic signatures associated with subsequent viral shedding. Upregulation of interferon signaling pathways prior to LAIV is significantly associated with lower strain-specific viral loads (VLs) at days 2 and 7. Several interferon-stimulated genes are differentially expressed in children with pre-LAIV asymptomatic respiratory viral infections and negatively correlated with LAIV VLs. Upregulation of genes enriched in macrophages, neutrophils, and eosinophils is associated with lower VLs and found more commonly in children with asymptomatic viral infections. Variability in pre-infection mucosal interferon gene expression in children may impact the course of subsequent influenza infections. This variability may be due to frequent respiratory viral infections, demonstrating the potential importance of mucosal virus-virus interactions in children., Graphical abstract, Highlights • Upregulated mucosal interferon prior to vaccination leads to reduced LAIV shedding • Asymptomatic respiratory viral infections were seen in 42% of children • Other respiratory viral infections contribute to higher interferon gene expression, Costa-Martins et al. show that in children seronegative to influenza vaccine strains, upregulated nasopharyngeal interferon genes prior to LAIV receipt associates with reduced vaccine strain shedding. Asymptomatic respiratory viral infections are common and result in higher interferon gene expression, highlighting the importance of virus-virus interactions in the upper respiratory tract.

Directly measuring evidence of influenza infections is difficult, especially in low-surveillance settings such as sub-Saharan Africa. Using a Bayesian model, we estimated unobserved infection times and underlying antibody responses to influenza A/H3N2, using cross-sectional serum antibody responses to 4 strains in children aged 24–60 months. Among the 242 individuals, we estimated a variable seasonal attack rate and found that most children had ≥1 infection before 2 years of age. Our results are consistent with previously published high attack rates in children. The modeling approach highlights how cross-sectional serological data can be used to estimate epidemiological dynamics.

Background Scabies is a WHO neglected tropical disease common in children in low- and middle-income countries. Excoriation of scabies lesions can lead to secondary pyoderma infection, most commonly by Staphyloccocus aureus and Streptococcus pyogenes (group A streptococcus, GAS), with the latter linked to acute post-streptococcal glomerulonephritis (APSGN) and potentially rheumatic heart disease (RHD). There is a paucity of data on the prevalence of these skin infections and their bacterial aetiology from Africa. Methodology/Principal findings A cross-sectional study, conducted over a four-month period that included the dry and rainy season, was conducted to determine the prevalence of common skin infections in Sukuta, a peri-urban settlement in western Gambia, in children, Author summary Scabies is a WHO neglected tropical disease which is common in low- and middle-income countries with tropical climates, which can lead to serious compilations via secondary bacterial infection of skin lesions. Group A streptococcal skin infection is known to cause kidney disease, but may also contribute to rheumatic heart disease. Despite this, little is known about the prevalence of common paediatric skin infections in sub-Saharan Africa, or which bacteria most commonly cause skin infections. We conducted a cross-sectional study of skin infections in The Gambia into the prevalence of scabies, pyoderma and fungal infections in children

The efficacy and effectiveness of the pandemic H1N1 (pH1N1) component in live attenuated influenza vaccine (LAIV) is poor. The reasons for this paucity are unclear but could be due to impaired replicative fitness of pH1N1 A/California/07/2009-like (Cal09) strains. We assessed whether an updated pH1N1 strain in the Russian-backbone trivalent LAIV resulted in greater shedding and immunogenicity compared with LAIV with Cal09.We did an open-label, prospective, observational, phase 4 study in Sukuta, a periurban area in The Gambia. We enrolled children aged 24-59 months who were clinically well. Children received one dose of the WHO prequalified Russian-backbone trivalent LAIV containing either A/17/California/2009/38 (Cal09) or A/17/New York/15/5364 (NY15) based on their year of enrolment. Primary outcomes were the percentage of children with LAIV strain shedding at day 2 and day 7, haemagglutinin inhibition seroconversion, and an increase in influenza haemagglutinin-specific IgA and T-cell responses at day 21 after LAIV. This study is nested within a randomised controlled trial investigating LAIV-microbiome interactions (NCT02972957).Between Feb 8, 2017, and April 12, 2017, 118 children were enrolled and received one dose of the Cal09 LAIV from 2016-17. Between Jan 15, 2018, and March 28, 2018, a separate cohort of 135 children were enrolled and received one dose of the NY15 LAIV from 2017-18, of whom 126 children completed the study. Cal09 showed impaired pH1N1 nasopharyngeal shedding (16 of 118 children [14%, 95% CI 8·0-21·1] with shedding at day 2 after administration of LAIV) compared with H3N2 (54 of 118 [46%, 36·6-55·2]; p0·0001) and influenza B (95 of 118 [81%, 72·2-87·2]; p0·0001), along with suboptimal serum antibody (seroconversion in six of 118 [5%, 1·9-10·7]) and T-cell responses (CD4+ interferon γ-positive and/or CD4+ interleukin 2-positive responses in 45 of 111 [41%, 31·3-50·3]). After the switch to NY15, a significant increase in pH1N1 shedding was seen (80 of 126 children [63%, 95% CI 54·4-71·9]; p0·0001 compared with Cal09), along with improvements in seroconversion (24 of 126 [19%, 13·2-26·8]; p=0·011) and influenza-specific CD4+ T-cell responses (73 of 111 [66%, 60·0-75·6; p=0·00028]). The improvement in pH1N1 seroconversion with NY15 was even greater in children who were seronegative at baseline (24 of 64 children [38%, 95% CI 26·7-49·8] vs six of 79 children with Cal09 [8%, 2·8-15·8]; p0·0001). Persistent shedding to day 7 was independently associated with both seroconversion (odds ratio 12·69, 95% CI 4·1-43·6; p0·0001) and CD4+ T-cell responses (odds ratio 7·83, 95% CI 2·99-23·5; p0·0001) by multivariable logistic regression.The pH1N1 component switch that took place between 2016 and 2018 might have overcome the poor efficacy and effectiveness reported with previous LAIV formulations. LAIV effectiveness against pH1N1 should, therefore, improve in upcoming influenza seasons. Our data highlight the importance of assessing replicative fitness, in addition to antigenicity, when selecting annual LAIV components.The Wellcome Trust.

BackgroundPoor efficacy and effectiveness of the pandemic H1N1 (pH1N1) component in intranasal live attenuated influenza vaccine (LAIV) has been demonstrated in several studies. The reasons for this are unclear, but may be due to impaired replicative fitness of pH1N1 A/California/07/2009-like (Cal09) LAIV strains.MethodsIn an open-label, prospective, observational, phase 4 study, we evaluated the impact of updating the pH1N1 component in the Russian-backbone trivalent LAIV from Cal09 in 2016-17 (n=118) to an A/Michigan/45/2015-like strain (A/17/New York/15/5364, NY15) in 2017-18 (n=126), on shedding and immunogenicity in Gambian children aged 2-4 years old. The study was nested within a larger randomised controlled trial investigating LAIV-microbiome interactions (ClinicalTrials.govNCT02972957).FindingsCal09 showed impaired nasopharyngeal shedding compared to H3N2 and influenza B, along with sub-optimal serum antibody and T-cell responses. Following the switch to NY15, a significant increase in pH1N1 shedding was seen, along with improvements in seroconversion and influenza-specific CD4+ T-cell responses. Viral kineticsin vitromirrored these findings, with NY15 showing greater replicative ability than Cal09 in human nasal epithelial cells. Persistent shedding to day 7 was independently associated with both seroconversion and CD4+ T cell response in multivariable logistic regression.InterpretationOur results suggest that the pH1N1 component switch in LAIV may have overcome problems in prior formulations. LAIV effectiveness against pH1N1 should therefore improve in upcoming influenza seasons. Our data also highlight the importance of evaluating replicative fitness, in addition to antigenicity, when selecting annual LAIV components and design of potentially more effective vaccines.FundingThe Wellcome Trust.

Background Recent observational studies in the United States have reported reduced effectiveness of the Ann Arbor-backbone live attenuated influenza vaccine (LAIV), coinciding with emergence of 2009 pandemic H1N1 (pH1N1). A recent RCT in Senegal of the Russian-backbone LAIV also showed no efficacy, with pH1N1 the predominant vaccine-matched strain circulating during the study. The reasons for this reduced effectiveness and efficacy are unclear but may involve pre-existing immunity or pH1N1 virus-specific factors. We explore these underlying reasons through an LAIV immunogenicity study in Gambian children across 2 influenza seasons. Methods Gambian children aged 24–59 months (n = 118) were given 2016–17 northern hemisphere Russian-backbone trivalent LAIV. Vaccine shedding, haemagglutinin inhibition (HAI) titre, influenza-specific T-cell responses, and mucosal IgA were measured using RT-PCR, HAI assay, flow cytometry, and ELISA, respectively. The following year, a further 127 children were given 2017–2018 formulation LAIV, where the pH1N1 strain was updated. Results In 2016–2017, significantly less pH1N1 shedding (13.6% children) was seen compared with H3N2 (45.8%) and B/Victoria (80.5%). Similarly, poor pH1N1-specific HAI (5.1% seroconversion), mucosal IgA (18.6% responders) and T-cell responses ( Conclusion Our data suggest that poor pH1N1 A/California strain replication in vivo may explain recent suboptimal LAIV performance and suggest that an improvement can be expected with new pH1N1 strains included in current LAIV formulations. Disclosures All authors: No reported disclosures.