ArticleProceedings of the National Academy of Sciences of the United States of America2022
Systems biology approach to functionally assess the
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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.
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Who cites it
13 citing papers in PubMed.
- Multi-strain analysis ofmSystems · 2026Article
- Pangenome-GWAS analysis ofCanadian journal of microbiology · 2026Article
- Multi-strain Analysis ofbioRxiv : the preprint server for biology · 2025Article
- Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Phenotypic analysis of variousApplied and environmental microbiology · 2025Article
- Unique growth and morphology properties of Clade 5bioRxiv : the preprint server for biology · 2025Article
- Unique growth and morphology properties of Clade 5 Clostridioides difficile strains revealed by single-cell time-lapse microscopy.PLoS pathogens · 2025Article
- Influence of Sequencing Technology on Pangenome-Level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens.Open forum infectious diseases · 2025Article
- EmergingmSystems · 2025Article
- Phenotypic analysis of variousbioRxiv : the preprint server for biology · 2025Article
- Antibiotic resistance of enteropathogenic bacteria in a teaching hospital in North Khuzestan during a three-year period.Journal of family medicine and primary care · 2024Article
- A high-throughput structural system biology approach to increase structure representation of proteins fromMicrobiology resource announcements · 2023Article
- Computational Insight into Intraspecies Distinctions inInternational journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Combatting Clostridioides difficile infections, a dominant cause of hospital-associated infections with incidence and resulting deaths increasing worldwide, is complicated by the frequent emergence of new virulent strains. Here, we employ whole-genome sequencing, high-throughput phenotypic screenings, and genome-scale models of metabolism to evaluate the genetic diversity of 451 strains of C. difficile. Constructing the C. difficile pangenome based on this set revealed 9,924 distinct gene clusters, of which 2,899 (29%) are defined as core, 2,968 (30%) are defined as unique, and the remaining 4,057 (41%) are defined as accessory. We develop a strain typing method, sequence typing by accessory genome (STAG), that identifies 176 genetically distinct groups of strains and allows for explicit interrogation of accessory gene content. Thirty-five strains representative of the overall set were experimentally profiled on 95 different nutrient sources, revealing 26 distinct growth profiles and unique nutrient preferences; 451 strain-specific genome scale models of metabolism were constructed, allowing us to computationally probe phenotypic diversity in 28,864 unique conditions. The models create a mechanistic link between the observed phenotypes and strain-specific genetic differences and exhibit an ability to correctly predict growth in 76% of measured cases. The typing and model predictions are used to identify and contextualize discriminating genetic features and phenotypes that may contribute to the emergence of new problematic strains.
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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.