Evidence map›Paper›PMID 31536818›Full record

ArticleClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases2020

Multistate population and whole genome sequence-based strain surveillance of invasive pneumococci recovered in the USA during 2017.

J Varghese, S Chochua, T Tran, H Walker, Z Li, P M Snippes Vagnone, R Lynfield, L McGee, Y Li, B J Metcalf and 2 more

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Article in Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
30citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

30 citing papers in PubMed, 1 synthesis or guideline pooled it.

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  4. Journal of preventive medicine and hygiene · 2026
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

J VargheseIHRC Incorporated, Contractor to Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA.
S ChochuaCenters for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA.
T TranIHRC Incorporated, Contractor to Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA.
H WalkerIHRC Incorporated, Contractor to Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA.
Z LiIHRC Incorporated, Contractor to Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA.
P M Snippes VagnoneMinnesota Department of Health, Infectious Disease Laboratory, St Paul, MN, USA.
R LynfieldMinnesota Department of Health, Epidemiology and Community Health, St Paul, MN, USA.
L McGeeCenters for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA.
Y LiCenters for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA.
B J MetcalfCenters for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA.
T PilishviliCenters for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA.
B BeallCenters for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA. Electronic address: bbeall@cdc.gov.

Funding

Intramural CDC HHS CC999999
6 · The paper itself

Abstract

objectivesWe aimed to provide population-based and whole-genome sequence (WGS) -based characterization of invasive pneumococcal disease isolates collected from multistate surveillance in the USA during 2017.

methodsWe obtained short-read WGS from 2881 isolates with associated bioinformatics pipeline strain feature predictions. For quality control, capsular serotypes and antimicrobial MICs were also obtained conventionally from 442 isolates. Annotated WGS were provided (inclusive of serotypes, MICs, multilocus sequence types, pilus type(s)) from 2723 isolates. For 158 isolates with suboptimal WGS, antimicrobial MICs were obtained conventionally.

resultsThere were 127 isolates from children <5 years of age and 2754 isolates from those ≥5 years old in 2017. One of 43 different serotypes was predicted for 2877 of the 2881 isolates. Serotypes in the 13-valent conjugate vaccine together with 6C (PCV13+6C) accounted for 816 (28.3%) isolates, with PCV13 serotype 3 being the most common serotype overall. Non-PCV13-6C- serotypes accounted for 2065 (71.7%) isolates, comprising 96 (75.6%) isolates from children < 5 years old and 1969 (61.4%) isolates from those aged ≥5 years. Of 36 different categories of recently emerged serotype-switch variants, three showed marked increases relative to 2015-2016 in that the number from 2017 surpassed the number from 2015-2016 combined. Two of these included antimicrobial-resistant serotype 11A and 35B serotype-switch variants of the ST156 clonal complex.

conclusionsPCV13+6C strains are still identified in 2017 but non-PCV13-type strains impose a considerable burden. This well-annotated year 2017 WGS/strain data set will prove useful for a broad variety of analyses and improved our understanding of invasive pneumococcal disease-causing strains in the post-PCV13 era.

Indexed as

Epidemiological MonitoringGenome, BacterialWhole Genome SequencingAnti-Bacterial AgentsBacterial Typing TechniquesChild, PreschoolDrug Resistance, BacterialGenotypeHumansInfantMicrobial Sensitivity TestsMultilocus Sequence TypingPneumococcal InfectionsPopulation HealthSerogroupStreptococcus pneumoniaeAnti-Bacterial AgentsCapsular serotypesClonal complexesInvasive pneumococcal disease incidenceResistance featuresSerotype switch variants

Identifiers

PMID31536818
PMCPMC12019393

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.