ArticleMicrobial genomics2019
rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree.
Article in Microbial genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology.Nature communications · 2026Article
- Temporal genomic dynamics of sequence type 39Microbial genomics · 2026Article
- A 46-week outbreak of ertapenem-resistant, non-carbapenemase encodingEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2025Article
- Non-tuberculous mycobacteria isolates from patients with chronic pulmonary disease and no epidemiological relationship show sequence clusters through whole-genome sequencing.Frontiers in microbiology · 2025Article
- Article
- Massive and Lengthy Clonal Nosocomial Expansion of Mycobacterium abscessus subsp.Microbiology spectrum · 2023Article
- A retrospective and regional approach assessing the genomic diversity ofNAR genomics and bioinformatics · 2022Article
- Potential Cross-Transmission of Mycobacterium abscessus among Non-Cystic Fibrosis Patients at a Tertiary Hospital in Japan.Microbiology spectrum · 2022Article
- Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.Nature microbiology · 2021Article
- Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemicMicrobial genomics · 2020Article
- Cross-transmission Is Not the Source of New Mycobacterium abscessus Infections in a Multicenter Cohort of Cystic Fibrosis Patients.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2020Article
- Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages.Nature communications · 2019Article
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Authors and funding
7 authors.
Funding
Abstract
The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this software was demonstrated using both simulated outbreaks and real genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.
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