ArticleScientific reports2017
Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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.
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.
Who cites it
26 citing papers in PubMed.
- Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing.Microbial genomics · 2026Article
- Rapid and reproducible haplotyping of complete mitochondrial genomes using split k-mers.BMC genomics · 2026Article
- Lineage-Specific Associations between the Resistome and Mobilome across 10,500 Globally DistributedComputational and structural biotechnology journal · 2026Article
- Article
- Metagenomic Identification of Fusarium solani Strain as Cause of US Fungal Meningitis Outbreak Associated with Surgical Procedures in Mexico, 2023.Emerging infectious diseases · 2025Article
- Can whole genome sequencing resolve taxonomic ambiguities in fungi? The case study ofFrontiers in fungal biology · 2025Article
- Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure ofMicrobial genomics · 2024Article
- Molecular typing methods to characterizeVeterinary world · 2024Review
- Understanding the influence of the microbiome on childhood infections.Expert review of anti-infective therapy · 2024Review
- Strain-resolved metagenomic analysis of the gut as a reservoir for bloodstream infection pathogens among premature infants in Singapore.Gut pathogens · 2023Article
- TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria.Database : the journal of biological databases and curation · 2023Article
- Article
- Comparative Pan-Genomic Analysis Revealed an Improved Multi-Locus Sequence Typing Scheme forGenes · 2022Article
- Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group).BMC ecology and evolution · 2021Article
- Article
- Article
- Multilocus Sequence Typing of Non-JP2 Serotype bFrontiers in cellular and infection microbiology · 2021Article
- Article
- Genome Sequencing and Comparative Genomics of Indian Isolates ofFrontiers in microbiology · 2021Article
- Phylogeography of the marine pathogen, Vibrio vulnificus, revealed the ancestral scenarios of its evolution.MicrobiologyOpen · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although multilocus sequence typing (MLST) is highly discriminatory and useful for outbreak investigations and epidemiological surveillance, it has always been controversial whether clustering and phylogeny inferred from the MLST gene loci can represent the real phylogeny of bacterial strains. In this study, we compare the phylogenetic trees constructed using three approaches, (1) concatenated blocks of homologous sequence shared between the bacterial genomes, (2) genome single-nucleotide polymorphisms (SNP) profile and (3) concatenated nucleotide sequences of gene loci in the corresponding MLST schemes, for 10 bacterial species with >30 complete genome sequences available. Major differences in strain clustering at more than one position were observed between the phylogeny inferred using genome/SNP data and MLST for all 10 bacterial species. Shimodaira-Hasegawa test revealed significant difference between the topologies of the genome and MLST trees for nine of the 10 bacterial species, and significant difference between the topologies of the SNP and MLST trees were present for all 10 bacterial species. Matching Clusters and R-F Clusters metrics showed that the distances between the genome/SNP and MLST trees were larger than those between the SNP and genome trees. Phylogeny inferred from MLST failed to represent genome phylogeny with the same bacterial species.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.