Evidence map›Paper›PMID 26275904›Full record

ArticleBMC genomics2015

Comparative genome analysis of Mycoplasma pneumoniae.

Li Xiao, Travis Ptacek, John D Osborne, Donna M Crabb, Warren L Simmons, Elliot J Lefkowitz, Ken B Waites, T Prescott Atkinson, Kevin Dybvig

Open access · goldAbstract read
In one paragraph

Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.

0numbers the graph read from it
0cells of the map it votes in
55citing papers in PubMed
5.3field-weighted citation impact, top 4% 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

55 citing papers in PubMed, 84 citations in OpenAlex.

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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

9 authors at 1 institution in 1 country.

Li XiaoDepartment of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. lixiao@uab.edu.
Travis PtacekDepartment of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. tptacek@uab.edu.
John D OsborneDepartment of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. ozborn@uab.edu.
Donna M CrabbDepartment of Pathology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. dmcrabb@uab.edu.
Warren L SimmonsDepartment of Genetics, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. wsimmons@uab.edu.
Elliot J LefkowitzDepartment of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. ElliotL@uab.edu.
Ken B WaitesDepartment of Pathology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. waiteskb@uab.edu.
T Prescott AtkinsonDepartment of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. PAtkinson@peds.uab.edu.
Kevin DybvigDepartment of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. dybvig@uab.edu.
University of Alabama at Birmingham · US

Funding

UAB Center for Clinical and Translational Science (CCTS)UL1TR001417 · NCATS · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI KIMBERLY, ROBERT P. · 2015 to 2018
$31.4M
UAB Center for Clinical and Translational Science (CCTS) UL1UL1TR000165 · NCATS · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI KIMBERLY, ROBERT P. · 2012 to 2013
$9.6M
Mechanisms of Mycoplasmal Disease PathogenesisR01AI063909 · NIAID · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI DYBVIG, KEVIN F · 2005 to 2014
$3.0M
NCATS NIH HHS UL1 TR000165NCATS NIH HHS UL1 TR001417NCATS NIH HHS UL1TR00165NIAID NIH HHS R01 AI063909NIAID NIH HHS R01AI63909
6 · The paper itself

Abstract

backgroundMycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40% of community-acquired pneumonias. It also causes a wide array of extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the organism have been generally restricted to specific genes or regions of the genome, because whole genome sequencing has been completed for only 4 strains. To better understand the physiology and pathogenicity of this important human pathogen, we performed comparative genomic analysis of 15 strains of M. pneumoniae that were isolated between the 1940s to 2009 from respiratory specimens and cerebrospinal fluid originating from the USA, China and England.

resultsIllumina MiSeq whole genome sequencing was performed on the 15 strains and all genome sequences were completed. Results from the comparative genomic analysis indicate that although about 1500 SNP and indel variants exist between type1 and type 2 strains, there is an overall high degree of sequence similarity among the strains (>99% identical to each other). Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed. The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.

conclusionsThese data indicate that despite conclusions drawn from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is extraordinarily stable over time and geographic distance across the globe with a striking lack of evidence of horizontal gene transfer.

Indexed as

ChinaComparative Genomic HybridizationEnglandEvolution, MolecularGenetic VariationGenome, BacterialHigh-Throughput Nucleotide SequencingHumansMycoplasma pneumoniaePhylogenySequence Analysis, DNASequence Homology, Nucleic AcidUnited States

Identifiers

PMID26275904
PMCPMC4537597
OpenAlexW2115084050

What OpenQuestion holds

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LicenceCC BY
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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.