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MOLECULAR STUDY OF CLONAL CHARACTERISTICS OF STREPTOCOCCUS PNEUMONIAE STRAINS ISOLATED FROM PATIENTS WITH INVASIVE PNEUMOCOCCAL DISEASE IN THE CZECH REPUBLIC IN 2017 (ID 427)

Session Name
Basic Sciences - Conventional and Molecular Microbiology

INNOVATIVE DATA MANAGEMENT IN THE PNEUMOCOCCAL VACCINE SCHEDULES IN RURAL GAMBIA (ID 726)

Session Name
Vaccines - Pneumococcal Vaccines Development

Abstract

Background

Research data management for field studies in rural Africa poses unique challenges. Data management in the Pneumococcal Vaccine Schedules (PVS) trial in The Gambia uses the following innovative procedures to maintain data integrity and validity with large numbers of observations where there is no electricity or internet.

Methods

•Confirming residential status and identity of infants in the study area in a continuously updated live sampling frame of over 10,000 births per year.

•User prompts and decision rules for group allocation for over 10,000 births per year and correct vaccine administration according to village of residence for over 50,000 PCV doses per year.

•Weekly synchronisation of data to a central server (up to 400 trial enrolments, 2500 PCV doses and 800 clinical presentations per week monitoring residence of 300,000 population).

•Weekly update of a back-end relational database combining variables from five different applications.

•Linkage of demographic identity details to patients presenting to health facilities using family geneology and photographs.

•Remote data viewing for off-site external trial monitoring, query and resolution audit trail, as well as trial staff real-time viewing of data.

Results

Interactive experience of the data systems will be available at the conference.

Conclusions

Those systems are working properly for PVS data collection.

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DEVELOPMENT AND VALIDATION OF A MACHINE LEARNING PREDICTION MODEL FOR PNEUMONIA MORTALITY IN CHILDREN AGED UNDER FIVE YEARS IN RURAL GAMBIA (ID 126)

Session Name
Clinical Sciences - Diagnosis

Abstract

Background

Pneumonia accounts for many deaths in children aged under 5 years in developing countries. A reliable and generalizable tool to predict mortality and thus assess the severity of pneumonia would aid patient management.

Methods

We used a dataset of 11,012 children admitted with clinical pneumonia to develop a model to predict mortality. Using a High Performance Computing platform, we generated multiple models for all possible feature combinations, applying support vector machine, neural networks, random forests and logistic regression to 2/3 of the dataset with repeated cross-validation (5 repetitions, 10 folds). We chose the final model based on its performance and on the number of and measurement reliability of the included features to increase generalizability. In the validation stage, we applied the selected model to the held-out dataset to test its performance on unseen cases.

Results

Not only did the selected model have good sensitivity and specificity (both >80%) on the training set, but more importantly, it had promising performance when applied to the test set.

Conclusions

Our predictive model performed well not only in cross-validated data, but also in our test dataset, increasing our confidence in its generalizability.

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COVERAGE OF THE 20-VALENT CONJUGATE VACCINE AGAINST INVASIVE PNEUMOCOCCAL DISEASE BY AGE GROUP IN THE UNITED STATES, 2017 (ID 237)

Abstract

Background

The United States experienced a substantial reduction in the incidence of invasive pneumococcal disease (IPD) following the introduction of pneumococcal conjugate vaccines (PCVs), PCV7 in 2000 and PCV13 in 2010, yet, disease remains. Expanded valency PCVs, PCV15 and PCV20 that contain two and seven additional serotypes compared to PCV13, are in advanced development.

Methods

We used the CDC Active Bacterial Core surveillance (ABCs) data from 2017 to quantify the incidence and to assess PCV coverage of IPD. ABC is an active laboratory and population-based surveillance system in 10 geographically diverse sites in the United States. Analyses were limited to the serotypes covered by PCV13 (1,3,4,5,6A,6B, 7F,9V,14,18C,19A,19F,23F, plus 6C, which is highly-related to 6A), PCV15 (PCV13-types, 22F,33F), and PCV20 (PCV15-types, 8,10A,11A,12F, plus 15C, which is highly-related to 15B).

Results

In 2017, non-PCV13 and PCV13 serotypes accounted for 63.1-75.0% and 25.0-36.9% of IPD cases across different age groups. The additional two serotypes in PCV15 and the seven serotypes in PCV20 accounted for 8.3-17.0% and 23.8-37.1% of the remaining IPD cases, respectively (Table).

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Conclusions

PCV20 could address a substantial remaining burden of IPD, covering an estimated 55.1-66.1% of cases across all age groups.

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COVERAGE OF NEXT GENERATION PNEUMOCOCCAL CONJUGATE VACCINES FOR INVASIVE PNEUMOCOCCAL DISEASE IN CHILDREN OF HIGH-INCOME COUNTRIES (ID 608)

Abstract

Background

The serotype distribution of invasive pneumococcal disease (IPD) informs the coverage of next generation pneumococcal conjugate vaccines (PCVs). This analysis describes IPD coverage by the current PCVs (PCV10/PCV13) and next generation, PCV15 and PCV20.

Methods

Serotype counts for children <5 years were obtained from national or regionally-representative IPD surveillance systems from high-income countries. Up to the three most recent years of data were included. Excluded countries reported <20 cases overall or only reported data prior to pediatric PCV introduction into the National Immunization Program (NIP). Coverage was calculated for PCV10 (1,4,5,6B,7F,9V,14,18C,19F,23F), PCV13 (PCV10-types, 3,6A,19A, plus 6C, which is highly-related to 6A), PCV15 (PCV13-types, 22F,33F), and PCV20 (PCV15-types, 8,10A,11A,12F,15B, plus 15C, which is highly-related to 15B) as the number of cases in PCVs divided by the total number of cases (excluding missing and non-typeable cases) reported for each country.

Results

Twenty-seven of 80 (34%) high-income countries met inclusion criteria, reporting >5,000 cases that were included in the analysis. Coverage by current and next generation PCVs varied by country and World Health Organization (WHO) region (Table).

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Conclusions

PCV20 offers substantial coverage above current PCVs and next generation PCV15 and could address the considerable remaining IPD burden among children in high-income countries globally.

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COVERAGE OF NEXT GENERATION PNEUMOCOCCAL CONJUGATE VACCINES FOR INVASIVE PNEUMOCOCCAL DISEASE IN OLDER ADULTS OF HIGH-INCOME COUNTRIES (ID 612)

Abstract

Background

Despite the indirect effects of routine pediatric pneumococcal conjugate vaccine (PCV) use, invasive pneumococcal disease (IPD) persists in older adults. This analysis describes IPD coverage of current PCVs (PCV10/PCV13) and next generation, PCV15 and PCV20.

Methods

Serotype counts for adults ≥60/≥65 years were obtained from national or regionally-representative IPD surveillance systems in high-income countries. Up to the three most recent years of data were included. Excluded countries reported <20 cases overall or only reported data prior to pediatric PCV introduction into the National Immunization Program (NIP). Coverage was calculated for PCV10 (1,4,5,6B,7F,9V,14,18C,19F,23F), PCV13 (PCV10-types,3,6A,19A, plus 6C, which is highly-related to 6A), PCV15 (PCV13-types, 22F,33F), and PCV20 (PCV13-types, 8,10A,11A,12F,15B, plus 15C, which is highly-related to 15B) as the number of cases in PCVs divided by total number of cases (excluding missing and non-typeable) reported for each country.

Results

Twenty-eight of 80 (35%) high-income countries met inclusion criteria, reporting >25,000 cases that were included in the analysis. Coverage by current and next generation PCVs varied by country and World Health Organization (WHO) region (Table).

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Conclusions

PCV20 offers substantial coverage above current PCVs and next generation PCV15 and could address the considerable remaining IPD burden among older adults in high-income countries globally.

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STREPTOCOCCUS PNEUMONIAE SEROTYPE DISTRIBUTION AND COVERAGE OF PNEUMOCOCCAL CONJUGATE VACCINES IN ADULTS HOSPITALIZED WITH COMMUNITY-ACQUIRED PNEUMONIA IN THE UNITED STATES (ID 879)

Abstract

Background

The study objective was to determine the prevalence of serotypes and coverage provided by currently licensed and next generation pneumococcal conjugate vaccines (PCVs) in adults hospitalized with community-acquired pneumonia (CAP) in the United States.

Methods

Hospitalized adults aged ≥18 years with radiologically-confirmed (CXR+) CAP were enrolled from 10 U.S. cities between October 2013 and September 2016. S. pneumoniae isolates cultured from normally-sterile standard-of-care specimens were serotyped by Quellung. Urine was tested using BinaxNOW® and a serotype-specific urine antigen detection (UAD) assay that detects serotypes contained in PCV13 plus 6C (highly-related to 6A), PCV15 (PCV13 serotypes, 22F, and 33F), PCV20 (PCV15 serotypes, 8, 10A, 11A, 12F, and 15B plus 15C (highly-related to 15B)), and non-PCV serotypes 2, 9N, 17F, and 20. Coverage was calculated as the percent of CXR+CAP participants positive for a serotype in PCV13, PCV15, and PCV20.

Results

Of 15,572 enrolled participants, 12,055 with CXR+CAP were included in the analysis; 52.7% (n=6347) were ≥65 years. Coverage of CXR+CAP varied by PCV formulation (Table). About 1% of CXR+CAP was due to serotypes 2, 9N, 17F, and 20 combined.

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Conclusions

Compared to PCV13, PCV20 increased coverage of CXR+CAP due to PCV serotypes by 71% (18-64 years) and 64% (≥65 years).

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NASOPHARYNGEAL PNEUMOCOCCAL SEROTYPE DETECTION COMBINING LATEX AGGLUTINATION SWEEP SEROTYPING WITH QUELLUNG IN THE GAMBIA. (ID 714)

Abstract

Background

Detection of multiple pneumococcal serotypes in nasopharyngeal swabs (NPS) by latex agglutination, either by the WHO protocol or sweep serotyping may yield incomplete serum factor reactions. We investigated the impact of combining latex sweep serotyping with Quellung to improve the specificity of reactions while detecting multiple pneumococcal serotypes.

Methods

We randomly selected 103 STGG-NPS samples cultured and serotyped by latex agglutination of different morphological colonies (WHO protocol) in two cross-sectional carriage studies. We performed Quellung capsular serotyping on 1, 2 or 3 morphologically distinct pneumococcal colonies from the culture plates and then swept the same plates.

Results

Sweep serotyping was more likely to detect multiple serotypes (Table 1) than the WHO protocol (p=0.004). A common serotype was identified in 95/103 (92.2%) NPS samples by the WHO, latex sweep and Quellung. Quellung gave more conclusive antisera reactions (Table 2) than the WHO protocol (p=0.007). No significant difference in conclusiveness of antisera reaction between Quellung and latex sweep (p=0.119).real.png

Conclusions

Combining sweep serotyping and Quellung is a cost-effective way of detecting multiple pneumococcal serotype co-colonization and resolving issues related to antisera reactivity in latex agglutination. Inconclusive Quellung results occurred because we detected more serotypes by latex sweep than were selected according to different morphological colonies.

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VACCINE-PREVENTABLE CLINICAL VERSUS RADIOLOGICALLY- OR ETIOLOGICALLY-CONFIRMED DISEASE IN PNEUMOCOCCAL CONJUGATE VACCINE EFFICACY TRIALS: A SYSTEMATIC LITERATURE REVIEW AND RE-ANALYSIS (ID 762)

Abstract

Background

While regulatory endpoints for pneumococcal conjugate vaccines (PCVs) routinely include radiologically- or vaccine serotype (VST) confirmed disease, public health decision-making benefits from consideration of all disease prevented regardless of diagnostic or etiological confirmation.

Methods

We followed PRISMA guidelines to perform a systematic literature review for Phase III/IV efficacy trials of PCVs from 1997 through 2019. We estimated study-specific vaccine-preventable disease incidence (VPDI) (control group minus intervention group incidences) for all-cause disease versus radiologically- and/or etiologically-confirmed outcomes. VPDI ratios between the broadest clinical and most narrowly defined outcomes were calculated [PROSPERO registration, CRD42019145268].

Results

Ten studies met the criteria. In children < 5 years, VPDI ratios ranged from 0.6 to 3.7 for otitis media (clinical versus VST etiologically-confirmed); from 1.3 to 1.8 for pneumonia (clinical versus radiologically-confirmed); 3.1 and 19.0 for pneumonia (clinical versus bacterial or VST); and 3.8 in one study of invasive pneumococcal disease (non-laboratory to laboratory-confirmed). In adults, VPDI ratios ranged from 2.2 to 2.9 for pneumonia (clinical to pneumococcal or VST).

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Conclusions

Relying on only radiologically-confirmed or etiologically-confirmed outcomes substantially underestimated PCVs’ public health benefits. Broader clinical outcomes should be considered by vaccine technical committees when making decisions for pediatric and adult PCV use.

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