Evidence map›Paper›PMID 29996780›Full record

ArticleBMC infectious diseases2018

Coinfections identified from metagenomic analysis of cervical lymph nodes from tularemia patients.

D N Birdsell, Y Özsürekci, A Rawat, A E Aycan, C L Mitchell, J W Sahl, A Johansson, R E Colman, J M Schupp, M Ceyhan and 2 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC infectious diseases, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
1.1field-weighted citation impact, top 22% of its field
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

5 citing papers in PubMed, 17 citations in OpenAlex.

  1. Article
  2. Viral coinfections in COVID-19.Journal of medical virology · 2021
    Review
  3. Detection and Genotyping ofComputational and mathematical methods in medicine · 2021
    Article
  4. Review
  5. 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

12 authors at 5 institutions in 5 countries.

D N BirdsellPathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. Dawn.Birdsell@nau.edu.ORCID 0000-0003-0055-9552
Y ÖzsürekciDepartment of Pediatric Infectious Disease Unit in Ankara, Hacettepe University Faculty of Medicine, Ankara, Turkey.
A RawatTranslational Genomics Research Institute, Flagstaff, AZ, USA.
A E AycanDepartment of Pediatric Infectious Disease Unit in Ankara, Hacettepe University Faculty of Medicine, Ankara, Turkey.
C L MitchellPathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
J W SahlPathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
A JohanssonDepartment of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden.
R E ColmanTranslational Genomics Research Institute, Flagstaff, AZ, USA.
J M SchuppTranslational Genomics Research Institute, Flagstaff, AZ, USA.
M CeyhanDepartment of Pediatric Infectious Disease Unit in Ankara, Hacettepe University Faculty of Medicine, Ankara, Turkey.
P S KeimPathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
D M WagnerPathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Translational Genomics Research Institute · USHacettepe University · TRNorthern Arizona University · USUmeå University · SEUniversity of North Carolina at Chapel Hill · US

Funding

Department of Homeland Security Science and Technology Directorate NBCH2070001
6 · The paper itself

Abstract

backgroundUnderlying coinfections may complicate infectious disease states but commonly go unnoticed because an a priori clinical suspicion is usually required so they can be detected via targeted diagnostic tools. Shotgun metagenomics is a broad diagnostic tool that can be useful for identifying multiple microbes simultaneously especially if coupled with lymph node aspirates, a clinical matrix known to house disparate pathogens. The objective of this study was to analyze the utility of this unconventional diagnostic approach (shotgun metagenomics) using clinical samples from human tularemia cases as a test model. Tularemia, caused by the bacterium Francisella tularensis, is an emerging infectious disease in Turkey. This disease commonly manifests as swelling of the lymph nodes nearest to the entry of infection. Because swollen cervical nodes are observed from many different types of human infections we used these clinical sample types to analyze the utility of shotgun metagenomics.

methodsWe conducted an unbiased molecular survey using shotgun metagenomics sequencing of DNA extracts from fine-needle aspirates of neck lymph nodes from eight tularemia patients who displayed protracted symptoms. The resulting metagenomics data were searched for microbial sequences (bacterial and viral).

resultsF. tularensis sequences were detected in all samples. In addition, we detected DNA of other known pathogens in three patients. Both Hepatitis B virus (HBV) and Human Parvovirus B-19 were detected in one individual and Human Parvovirus B-19 alone was detected in two other individuals. Subsequent PCR coupled with Sanger sequencing verified the metagenomics results. The HBV status was independently confirmed via serological diagnostics, despite evading notice during the initial assessment.

conclusionOur data highlight that shotgun metagenomics of fine-needle lymph node aspirates is a promising clinical diagnostic strategy to identify coinfections. Given the feasibility of the diagnostic approach demonstrated here, further steps to promote integration of this type of diagnostic capability into mainstream clinical practice are warranted.

Indexed as

MetagenomicsCoinfectionDNA, BacterialFemaleFrancisella tularensisHumansLymph NodesMaleMiddle AgedNeckPolymerase Chain ReactionSequence Analysis, DNATularemiaDNA, BacterialCoinfectionsConcurrent infectionsFine-needle lymph node aspirateFrancisella tularensisMetagenomicsTularemia

Identifiers

PMID29996780
PMCPMC6042416
OpenAlexW2867728090

What OpenQuestion holds

Textmetadata
LicenceCC BY
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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.