Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simultaneous identification of 29 prevalent invasive pneumococcal serotypes or pairs of serotypes by hybridization-ligation PCR.

ABSTRACT: A hybridization-ligation PCR assay was developed for the simultaneous detection and identification of 21 pneumococcal serotypes and 8 pairs of serotypes in the same serogroup: 1, 2, 3, 4, 5, 6A, 6B, 6C-6D, 7F-7A, 8, 9A-9V, 9N-9L, 11A, 14, 15B-15C, 16F, 17F, 18B-18C, 19A, 19F, 20, 21, 22A-22F, 23A, 23B, 23F, 28A-28F, 35B and 38. This novel assay was validated with 185 serotyped pneumococcal invasive clinical isolates and 57 culture-negative pleural fluids previously typed by real-time PCR.

SUBMITTER: Ortega Domenech M

PROVIDER: S-EPMC3372161 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Simultaneous identification of 29 prevalent invasive pneumococcal serotypes or pairs of serotypes by hybridization-ligation PCR.

Ortega Doménech Montserrat M Tarragó Asensio David D

Journal of clinical microbiology 20120314 6

A hybridization-ligation PCR assay was developed for the simultaneous detection and identification of 21 pneumococcal serotypes and 8 pairs of serotypes in the same serogroup: 1, 2, 3, 4, 5, 6A, 6B, 6C-6D, 7F-7A, 8, 9A-9V, 9N-9L, 11A, 14, 15B-15C, 16F, 17F, 18B-18C, 19A, 19F, 20, 21, 22A-22F, 23A, 23B, 23F, 28A-28F, 35B and 38. This novel assay was validated with 185 serotyped pneumococcal invasive clinical isolates and 57 culture-negative pleural fluids previously typed by real-time PCR. ...[more]

PMID: 22422847

Similar Datasets

Pneumococcal serotypes and mortality following invasive pneumococcal disease: a population-based cohort study.

Project description:BACKGROUND: Pneumococcal disease is a leading cause of morbidity and mortality worldwide. The aim of this study was to investigate the association between specific pneumococcal serotypes and mortality from invasive pneumococcal disease (IPD). METHODS AND FINDINGS: In a nationwide population-based cohort study of IPD in Denmark during 1977-2007, 30-d mortality associated with pneumococcal serotypes was examined by multivariate logistic regression analysis after controlling for potential confounders. A total of 18,858 IPD patients were included. Overall 30-d mortality was 18%, and 3% in children younger than age 5 y. Age, male sex, meningitis, high comorbidity level, alcoholism, and early decade of diagnosis were significantly associated with mortality. Among individuals aged 5 y and older, serotypes 31, 11A, 35F, 17F, 3, 16F, 19F, 15B, and 10A were associated with highly increased mortality as compared with serotype 1 (all: adjusted odds ratio >or=3, p<0.001). In children younger than 5 y, associations between serotypes and mortality were different than in adults but statistical precision was limited because of low overall childhood-related mortality. CONCLUSIONS: Specific pneumococcal serotypes strongly and independently affect IPD associated mortality.

| S-EPMC2680036 | biostudies-other

Identification of Pneumococcal Serotypes by PCR-Restriction Fragment Length Polymorphism.

Project description:Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg-wzh-wzd-wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.

| S-EPMC6963424 | biostudies-literature

Single-Step Multiplex PCR Assay for Determining 92 Pneumococcal Serotypes.

Project description:For pneumococcal disease surveillance, simple and cost-effective methods capable of determining all serotypes are needed. Combining a single-tube multiplex PCR with fluorescently labeled primers followed by amplicon analysis using automated fluorescent capillary electrophoresis, each serotype of 92 reference isolates and 297 recently collected clinical isolates was successfully determined.

| S-EPMC4963499 | biostudies-literature

Molecular subtyping of prevalent M serotypes of Streptococcus pyogenes causing invasive disease.

Project description:Reproducible methodologies and a scheme for high-resolution genotyping of Streptococcus pyogenes were defined with respect to a study of six predominant M serotypes causing invasive group A streptococcal disease in the United Kingdom. Serotype reference strains were compared with nine clinical isolates of each serotype from patients with diseases such as pneumonia, puerperal sepsis, toxic shock-like-syndrome, cellulitis, or necrotizing fasciitis. Four enzymes were evaluated for their discriminatory power in 16S rRNA gene-specific ribotyping. Discriminatory power was greatest with EcoRI, which generated serotype-specific ribotypes, and with SacI, which could subdivide strains of the same M serotype. Twenty-five combined ribotypes were found among the 60 strains, and the indices of discriminatory power (D values) of this method varied from 0.51 within serotype M1 to 0.98 within strains of serotype M5. Macrorestriction with the rarely cutting endonuclease SmaI and pulsed-field gel electrophoresis gave D values varying from 0.37 within serotype M1 to the maximal 1.0 within serotype M5. Comparison of macrorestriction profiles revealed various degrees of genetic heterogeneity within M serotypes. Strains of M1, M3, M6, and M11 exhibited clonally related macrorestriction profiles, while those of R28 and M5 strains were consistent with polyphyletic origin.

| S-EPMC228593 | biostudies-other

Pneumococcal serotypes and serogroups causing invasive disease in Pakistan, 2005-2013.

Project description:While pneumococcal conjugate vaccines have been implemented in most countries worldwide, use in Asia has lagged in part because of a lack of data on the amount of disease that is vaccine preventable in the region. We describe pneumococcal serotypes elicited from 111 episodes of invasive pneumococcal disease (IPD) from 2005 to 2013 among children and adults in Pakistan. Seventy-three percent (n = 81) of 111 IPD episodes were cases of meningitis (n = 76 in children 0-15 years and n = 5 among adults). Serotypes were determined by target amplification of DNA extracted from pneumococcal isolates (n = 52) or CSF specimens (n = 59). Serogroup 18 was the most common serogroup causing meningitis in children <5 years, accounting for 21% of cases (n = 13). The 10-valent pneumococcal conjugate vaccine (PCV 10) or PCV10- related serotypes were found in 61% (n = 47) of childhood (age 0-15 years) meningitis episodes. PCV-13 increased this coverage to 63% (one additional serotype 19A; n = 48). Our data indicate that use of PCVs would prevent a large proportion of serious pneumococcal disease.

| S-EPMC4043782 | biostudies-literature

Prediction of serotypes causing invasive pneumococcal disease in unvaccinated and vaccinated populations.

Project description:Before the introduction of the heptavalent pneumococcal conjugate vaccine (Prevnar-7), the relative prevalence of serotypes of Streptococcus pneumoniae was fairly stable worldwide. We sought to develop a statistical tool to predict the relative frequency of different serotypes among disease isolates in the pre- and post-Prevnar-7 eras using the limited amount of data that is widely available.We initially used pre-Prevnar-7 carriage prevalence and estimates of invasiveness derived from case-fatality data as predictors for the relative abundance of serotypes causing invasive pneumococcal disease during the pre- and post-Prevnar-7 eras, using negative binomial regression. We fit the model to pre-Prevnar-7 invasive pneumococcal disease data from England and Wales and used these data to (1) evaluate the performance of the model using several datasets and (2) evaluate the utility of the country-specific carriage data. We then fit an alternative model that used polysaccharide structure, a correlate of prevalence that does not require country-specific information and could be useful in determining the postvaccine population structure, as a predictor.Predictions from the initial model fit data from several pediatric populations in the pre-Prevnar-7 era. After the introduction of Prevnar-7, the model still had a good negative predictive value, though substantial unexplained variation remained. The alternative model had a good negative predictive value but poor positive predictive value. Both models demonstrate that the pneumococcal population follows a somewhat predictable pattern even after vaccination.This approach provides a preliminary framework to evaluate the potential patterns and impact of serotypes causing invasive pneumococcal disease.

| S-EPMC3142570 | biostudies-literature

Effect of Childhood Pneumococcal Conjugate Vaccination on Invasive Disease Serotypes in Serbia.

Project description:In Serbia, PCV10 was introduced into the routine immunization for children under 2 in 2018 and replaced by PCV13 in 2022. We evaluated their impact on the distribution of invasive pneumococcal disease (IPD) serotypes across all age groups. Overall, 756 isolates were obtained from patients with IPD between 2010 and 2023 through laboratory surveillance. In the post-vaccination period, serotypes 14, 19F, 23F, and 6A significantly declined, while 3 and 19A considerably increased. This was especially evident in the ≤2 years group, making these serotypes the most prevalent among them. Serotype 3 dominated, representing 19.1% of all invasive isolates prior to 2018 and 33.1% thereafter. While serotype coverage of PCV10 has significantly decreased in the ≤2 years group (from 74.2% before 2018 to 29.5% after 2018), PCV13 coverage was 63.9% after 2018. In the post-PCV period, non-PCV13 serotypes, such as 9N, 10A, 15A, 15B, 15C, 22F, 6C, 6D, and 7C, increased across all isolates. Antibiotic non-susceptibility considerably decreased after 2018. MLST analysis showed shifts in sequence type prevalence, with pre-PCV lineages replaced and ongoing serotype 3 persistence, alongside potential capsule-switching events. These findings emphasize a noticeable shift in the distribution of serotypes and adaptability of pneumococcal populations, highlighting the importance of ongoing surveillance and the requirement for the urgent introduction of higher valent vaccines into the National Immunization Program.

| S-EPMC11359874 | biostudies-literature

Systematic evaluation of serotypes causing invasive pneumococcal disease among children under five: the pneumococcal global serotype project.

Project description:Approximately 800,000 children die each year due to pneumococcal disease and >90% of these deaths occur in developing countries where few children have access to life-saving serotype-based vaccines. Understanding the serotype epidemiology of invasive pneumococcal disease (IPD) among children is necessary for vaccine development and introduction policies. The aim of this study was to systematically estimate the global and regional distributions of serotypes causing IPD in children <5 years of age. We systematically reviewed studies with IPD serotype data among children <5 years of age from the published literature and unpublished data provided by researchers. Studies conducted prior to pneumococcal conjugate vaccine (PCV) introduction, from 1980 to 2007, with ≥12 months of surveillance, and reporting ≥20 serotyped isolates were included. Serotype-specific proportions were pooled in a random effects meta-analysis and combined with PD incidence and mortality estimates to infer global and regional serotype-specific PD burden. Of 1,292, studies reviewed, 169 were included comprising 60,090 isolates from 70 countries. Globally and regionally, six to 11 serotypes accounted for ≥70% of IPD. Seven serotypes (1, 5, 6A, 6B, 14, 19F, 23F) were the most common globally; and based on year 2000 incidence and mortality estimates these seven serotypes accounted for >300,000 deaths in Africa and 200,000 deaths in Asia. Serotypes included in both the 10- and 13-valent PCVs accounted for 10 million cases and 600,000 deaths worldwide. A limited number of serotypes cause most IPD worldwide. The serotypes included in existing PCV formulations account for 49%-88% of deaths in Africa and Asia where PD morbidity and mortality are the highest, but few children have access to these life-saving vaccines. Please see later in the article for the Editors' Summary.

| S-EPMC2950132 | biostudies-literature

Serotypes With Low Invasive Potential Are Associated With an Impaired Antibody Response in Invasive Pneumococcal Disease.

Project description:Pneumococcal polysaccharide vaccines may elicit a hyporesponse under certain conditions. There is limited knowledge, however, on the type of specific antibody response in individuals with invasive pneumococcal disease (IPD). The aim of this study was to investigate the functional antibody response in patients with IPD caused by different serotypes. Pre-immune and convalescent sera from 40 patients (age 14-91 years) with IPD caused by serotypes with low (serotype 3, 19F, and 23F) and high (1, 4, 7F, and 14) invasive potential were investigated. For each patient, the homologous serotype-specific antibody concentration was determined. The functionality of induced antibodies post-IPD was evaluated in an opsonophagocytic assay (OPA). Undetectable or decreased pneumococcal killing in OPA following IPD, i.e., a nonfunctional antibody response, was observed in 24 of 40 patients (60%). Patients with nonfunctional antibody responses had lower serotype specific IgG antibody ratios post-IPD than patients with increased OPA titres. A nonfunctional antibody response was associated with low invasive serotypes (3, 19F, and 23F, p = 0.015). In conclusion, a nonfunctional antibody response may follow IPD, and was in our cohort associated to serotypes with low invasive potential. These findings need to be confirmed in a larger material.

| S-EPMC6249558 | biostudies-literature

Dominance of vaccine serotypes in pediatric invasive pneumococcal infections in Portugal (2012-2015).

Project description:We evaluated the impact of continued 13-valent pneumococcal conjugate vaccine (PCV13) use in the private market (uptake of 61%) in pediatric invasive pneumococcal disease (pIPD) in Portugal (2012-2015). The most frequently detected serotypes were: 3 (n?=?32, 13.8%), 14 (n?=?23, 9.9%), 1 (n?=?23, 9.9%), 7F (n?=?15, 6.4%), 19A (n?=?13, 5.6%), 6B and 15B/C (both n?=?12, 5.2%), and 24F, 10A and 12B (all with n?=?10, 4.3%). Taken together, non-PCV13 serotypes were responsible for 42.2% of pIPD with a known serotype. The use of PCR to detect and serotype pneumococci in both pleural and cerebrospinal fluid samples contributed to 18.1% (n?=?47) of all pIPD. Serotype 3 was mostly detected by PCR (n?=?21/32, 65.6%) and resulted from a relevant number of vaccine failures. The incidence of pIPD varied in the different age groups but without a clear trend. There were no obvious declines of the incidence of pIPD due to serotypes included in any of the PCVs, and PCV13 serotypes still accounted for the majority of pIPD (57.8%). Our study indicates that a higher vaccination uptake may be necessary to realize the full benefits of PCVs, even after 15 years of moderate use, and highlights the importance of using molecular methods in pIPD surveillance, since these can lead to substantially increased case ascertainment and identification of particular serotypes as causes of pIPD.

| S-EPMC6327022 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data