ArticleMicrobial genomics2018
Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission.
Article in Microbial genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled 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.
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
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark.The Lancet. Microbe · 2021Pooled it
- Complete genomes reveal a refined map of Mycobacterium tuberculosis genetic diversity across evolutionary scales.Nature communications · 2026Article
- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- Benchmarking within-sample minority variant detection with short-read sequencing inbioRxiv : the preprint server for biology · 2026Article
- Genetic Diversity and Molecular Epidemiology ofPathogens (Basel, Switzerland) · 2026Article
- Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex.Nature reviews. Microbiology · 2025Review
- Bayesian estimation of transmission networks for infectious diseases.Journal of mathematical biology · 2025Article
- Clinical and Mycobacterium tuberculosis strain characteristics of tuberculosis patients with diabetes mellitus in Changping District, Beijing, China.BMC infectious diseases · 2025Article
- A Genome-Focused Investigation Reveals the Emergence of aMicroorganisms · 2024Article
- Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.Nature communications · 2023Article
- Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study.Wellcome open research · 2023Article
- Whole Genome Sequencing Assessing Impact of Diabetes Mellitus on Tuberculosis Mutations and Type of Recurrence in India.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Article
- Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts.PLoS pathogens · 2021Article
- Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts.bioRxiv : the preprint server for biology · 2021Article
- Genomic variant-identification methods may alterMicrobial genomics · 2020Article
- Possible Transmission Mechanisms of Mixed Mycobacterium tuberculosis Infection in High HIV Prevalence Country, Botswana.Emerging infectious diseases · 2020Article
- Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability.BMC biology · 2020Article
- Previously undetected super-spreading ofeLife · 2020Article
- Article
- Article
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
Abstract
Whole genome sequencing in conjunction with traditional epidemiology has been used to reconstruct transmission networks of Mycobacterium tuberculosis during outbreaks. Given its low mutation rate, genetic diversity within M. tuberculosis outbreaks can be extremely limited - making it difficult to determine precisely who transmitted to whom. In addition to consensus SNPs (cSNPs), examining heterogeneous alleles (hSNPs) has been proposed to improve resolution. However, few studies have examined the potential biases in detecting these hSNPs. Here, we analysed genome sequence data from 25 specimens from British Columbia, Canada. Specimens were sequenced to a depth of 112-296×. We observed biases in read depth, base quality, strand distribution and read placement where possible hSNPs were initially identified, so we applied conservative filters to reduce false positives. Overall, there was phylogenetic concordance between the observed 2542 cSNP and 63 hSNP loci. Furthermore, we identified hSNPs shared exclusively by epidemiologically linked patients, supporting their use in transmission inferences. We conclude that hSNPs may add resolution to transmission networks, particularly where the overall genetic diversity is low.
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.