Risk Of Streptococcus Pneumoniae Transmission In Preschool Children Based On Genome-wide Epidemiology

ObejectivesThis study aimed to investigate the persistence carriage of Streptococcus pneumoniae in children’s nasal cavity and its influencing factors,so as to provide an important theoretical basis for the prevention and control of Streptococcus pneumoniae related diseases in children in community.The resistance and multidrug resistance of Streptococcus pneumoniae to various antibiotics were analyzed to provide an important theoretical basis for guiding the rational use of antibiotics in community children.The coverage of serotype-related vaccines of Streptococcus pneumoniae was analyzed to provide data support for the development of new candidate vaccines.The aggregation and homology of Streptococcus pneumoniae carriage in children was analyzed,so as to provide epidemiological and molecular biological evidence to reveal the risk of Streptococcus pneumoniae cross transmission among kindergarten children.MethodsA total of 1849 children from 6 kindergartens in Shunde district of Foshan city were selected by multi-stage stratified random sampling method using three consecutive surveillance studies combined with genome-wide epidemiology.Antimicrobial susceptibility test and whole genome sequencing analysis were performed on all the detected Streptococcus pneumoniae strains to obtain drug resistance phenotype,drug resistance genes,toxin genes,sterotypes and MLST typing.In the analysis of influencing factors of Streptococcus pneumoniae carriage(including at least one carriage and continuous carriage),c2 test or exact probability method was used for univariate analyses,and logistic regression models and random-effect logistic regression models were used for multivariate analyses.The dose-response relationship between different age groups and pneumonia vaccine coverage was analyzed using restricted cubic spline logistic regression models.The aggregation of Streptococcus pneumoniae carriage was analyzed using random-effect logistic regression models.Based on the SNPs of the core genome,the phylogenetic tree was constructed by the maximum parsimony method so as to explore the evolutionary relationship between strains.Homology between Streptococcus pneumoniae in children was explored through the SNPs of the core genome,so as to reveal the cross transmission risk and transmission route of Streptococcus pneumoniae among children.Results1.Strain carriage: In this study,a total of 1849 healthy kindergarten children were sampled for three consecutive times,with an age range of 1-7 years and an average age of 4.0±1.1 years.The cumulative carriage rate of Streptococcus pneumoniae in children was 46.8%(865/1849).The persistent carriage rate was 6.7%(106/1593).2.Analysis of influencing factors:(1)Analysis of influencing factors of children carrying Streptococcus pneumoniae at least once: The risk factors were rural areas(OR=1.52)and respiratory tract infection history in the last 3 months(OR=1.29),and the protective factors were allergic disease history in the last year(OR=0.76),hospitalization history of family members in the last year(OR=0.73)and Hib vaccination history(OR=0.64).(2)Analysis of influencing factors of persistent Streptococcus pneumoniae carriage: the risk of persistent Streptococcus pneumoniae carriage was lower in children aged ≥3 years than in children aged <3years(OR=0.45).The risk of persistent Streptococcus pneumoniae carriage was lower in large-class children than in small-class children(OR=0.18).3.Antimicrobial sensitivity analysis: A total of 1355 Streptococcus pneumoniae isolates were sensitive to linezolid and vancomycin,and the total resistance rates to azithromycin,erythromycin and clindamycin were all higher than 90.0%.The total resistance rate to cotrimoxazole was77.6%,and the total resistance rate to cefotaxime was 16.7%.The total resistance rates to chloramphenicol,levofloxacin and penicillin were less than 10%.The multidrug-resistant isolates accounted for 97.7%,and the main resistance pattern was resistant to erythromycin-azithromycintetracycline-clindamycin-cotrimoxazole.4.Serotyping: A total of 27 serotypes were detected,and 46 Streptococcus pneumoniae isolates were untypeable.The most common serotypes were 6B,19 F,15A,23 A,34 and 23 F.The overall coverage of PCV7,PCV10 and PCV13 was 45.0%、45.0% and 50.4%,respectively.The relationship between different age groups and the coverage rates of PCV7,PCV10 and PCV13 were nonlinear,and the shape of line segments was "S" shape.5.Molecular characteristics: The main ST types are ST902 and ST90,followed by ST271,ST9396,ST63 and ST320.The resistance genes of the strains were erm(B),followed by mef(A)and msr(D).The main tetracycline resistance gene was tet(M).Most strains carried adhesion genes(psa A,pav A,lyt A,lyt C,cbp D,pfb A),and ply gene of hemolysin,hys A gene of hyaluronidase,cps4 A and cps4 B of immune regulation,nan B of neuraminidase and other toxin gene pce.6.Aggregation and homology analysis: Aggregation analysis of Streptococcus pneumoniae in children showed statistically significant aggregation at the class level,and the intra-group correlation coefficient ICC was 12.5%.The homology rates of Streptococcus pneumoniae among children from different kindergartens were 82.3%~92.8%,with84.8%~94.0% for intra-class homology and 52.6%~85.8% for inter-class homology.Conclusions:1.The risk factors for children Streptococcus pneumoniae carriage were rural areas and respiratory tract infection history in the last 3 months,and the protective factors were allergic disease history in the last year,hospitalization history of family members in the last year and Hib vaccination history.The influencing factors of persistent Streptococcus pneumoniae carriage in children were age and grade.These findings provide important theoretical basis for the prevention and control of Streptococcus pneumoniae colonization and infection in children.2.Streptococcus pneumoniae isolates were sensitive to linezolid and vancomycin,and the total resistance rates to azithromycin,erythromycin and clindamycin were higher than 90.0%.The multidrug-resistant rate was97.7%.So it is necessary to strengthen the monitoring of the antibiotic resistance of Streptococcus pneumoniae in children,so as to guide the rational use of antibiotics in community children.3.The main serotypes of Streptococcus pneumoniae in children were6 B,19F,15 A,23A and 34.The total coverage rate of PCV7,PCV10 and PCV13 was 45.0%,45.0% and 50.4%,respectively.The relationship between different age groups and PCV coverage rate was non-linear,which provides data support for evaluating the vaccine coverage and guiding the research of new candidate vaccination.4.The Streptococcus pneumoniae carriage in children showed significant class aggregationa,and the genetic background of Streptococcus pneumoniae isolates have high homology in within and between classes,suggesting that the risk of cross transmission between children may be high and "direct contact between children" is the main transmission route of Streptococcus pneumoniae.The above findings provide a scientific basis for cutting off the route of disease transmission.