Evidence map›Paper›PMID 29329757›Full record

ArticleDiagnostic microbiology and infectious disease2018

Challenges of Francisella classification exemplified by an atypical clinical isolate.

L M Matz, K Y Kamdar, M E Holder, G A Metcalf, G M Weissenberger, Q Meng, V Vee, Y Han, D M Muzny, R A Gibbs and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Diagnostic microbiology and infectious disease, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–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

1 citing paper in PubMed.

  1. Article
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

13 authors.

L M MatzAlkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA. Electronic address: lisa.matz@alumni.bcm.edu.
K Y KamdarDepartment of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA.
M E HolderAlkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
G A MetcalfHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
G M WeissenbergerHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Q MengHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
V VeeHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Y HanHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
D M MuznyHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
R A GibbsHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
C L JohnsonDepartment of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Department of Pathology, Texas Children's Hospital, Houston, TX, USA.
P A RevellDepartment of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Department of Pathology, Texas Children's Hospital, Houston, TX, USA.
J F PetrosinoAlkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.

Funding

The Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3M
WRCE Nonhuman Primate CoreU54AI057156 · NIAID · UNIVERSITY OF TEXAS MEDICAL BR GALVESTON · PI WALKER, DAVID H · 2003 to 2013
$102.6M
NHGRI NIH HHS U54 HG003273NIAID NIH HHS U54 AI057156
6 · The paper itself

Abstract

The accumulation of sequenced Francisella strains has made it increasingly apparent that the 16S rRNA gene alone is not enough to stratify the Francisella genus into precise and clinically useful classifications. Continued whole-genome sequencing of isolates will provide a larger base of knowledge for targeted approaches with broad applicability. Additionally, examination of genomic information on a case-by-case basis will help resolve outstanding questions regarding strain stratification. We report the complete genome sequence of a clinical isolate, designated here as F. novicida-like strain TCH2015, acquired from the lymph node of a 6-year-old male. Two features were atypical for F. novicida: exhibition of functional oxidase activity and additional gene content, including proposed virulence determinants. These differences, which could potentially impact virulence and clinical diagnosis, emphasize the need for more comprehensive methods to profile Francisella isolates. This study highlights the value of whole-genome sequencing, which will lead to a more robust database of environmental and clinical genomes and inform strategies to improve detection and classification of Francisella strains.

Indexed as

GenotypeChildDNA, BacterialFrancisellaGenes, BacterialGenetic VariationGenome, BacterialHumansLymph NodesMaleOxidoreductasesSequence Analysis, DNATularemiaVirulence FactorsWhole Genome SequencingDNA, BacterialOxidoreductasesVirulence FactorsClinical microbiologyComparative genomicsWhole genome sequencing

Identifiers

PMID29329757
PMCPMC5857240

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Registered trials

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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.