Granger Sutton

Granger Sutton
J. Craig Venter Institute | JCVI · Informatics

PhD

About

236
Publications
87,415
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84,087
Citations
Citations since 2016
39 Research Items
22991 Citations
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201620172018201920202021202205001,0001,5002,0002,5003,000
201620172018201920202021202205001,0001,5002,0002,5003,000

Publications

Publications (236)
Article
Background: Wall teichoic acid (WTA) genes are essential for production of cell walls in gram-positive bacteria and necessary for survival and variability in the cassette has led to recent antibiotic resistance acquisition in pathogenic bacteria. Methods: Using a pan-genome approach, we examined the evolutionary history of WTA genes in Bacillus sub...
Article
Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassett...
Article
Full-text available
Efficient response to the pandemic through the mobilization of the larger scientific community is challenged by the limited reusability of the available primary genomic data. Here, the Genomic Standards Consortium board highlights the essential need for contextual genomic data FAIRness, for empowering key data-driven biological questions.
Conference Paper
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Background: Carbapenemase-producing Enterobacteriaceae (CPE) has been a compelling cause of hospital-acquired infections with a high mortality rate. The recent rise in CPE infections has left clinicians with limited antimicrobial treatment options. Bacterial genomic studies provide useful data on pathogenicity, transmission pathways and can be appl...
Conference Paper
Full-text available
Background: Resistance to colistin conferred by plasmid-mediated genes has been identified in bacterial strains isolated from food, animals, inpatients and asymptomatic human carriers worldwide. This wide spread of resistant strains has raised public health concerns, especially that zoonotic transmission might be occurring. Here, we provide informa...
Article
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Background: There are a large and growing number of non-tuberculous mycobacteria (NTM) species that have been isolated, identified, and described in the literature, yet there are many clinical isolates which are not assignable to known species even when the genome has been sequenced. Additionally, a recent manuscript has proposed the reclassificati...
Article
Previously, by targeting penicillin-binding protein 3, Pseudomonas-derived cephalosporinase (PDC), and MurA with ceftazidime-avibactam-fosfomycin, antimicrobial susceptibility was restored among multidrug-resistant (MDR) Pseudomonas aeruginosa. Herein, ceftazidime-avibactam-fosfomycin combination therapy against MDR P. aeruginosa clinical isolate C...
Article
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Background The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug resistance, as well as phylog...
Article
Full-text available
Background By targeting penicillin binding protein-3, the AmpC β-lactamase, and MurA, another enzyme involved in cell wall synthesis, with the ceftazidime–avibactam–fosfomycin combination, we previously overcame multidrug resistance (MDR) in vitro in an archived collection of Pseudomonas aeruginosa clinical isolates. Here, we further validate the c...
Article
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Background Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to locate and analyze these regi...
Article
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Motivation: The vast number of available sequenced bacterial genomes occasionally exceeds the facilities of comparative genomic methods or is dominated by a single outbreak strain, and thus a diverse and representative subset is required. Generation of the reduced subset currently requires a priori supervised clustering and sequence-only selection...
Article
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In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article. © 2018 Nature America, Inc., part of Springer Nature. All rights reserved.
Article
Full-text available
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled G...
Article
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The CP 96-1252 cultivar of sugarcane is a complex hybrid of commercial importance. DNA was extracted from lab-grown leaf tissue and sequenced. The raw Illumina DNA sequencing results provide 101 Gbp of genome sequence reads. The dataset is available from https://www.ncbi.nlm.nih.gov/bioproject/PRJNA345486/.
Article
Full-text available
LOCUST is a custom sequence locus typer tool for classifying microbial genomes. It provides a fully automated opportunity to customize the classification of genome-wide nucleotide variant data most relevant to biological research. Availability and implementation: Source code, demo data, and detailed documentation are freely available at http://so...
Article
Full-text available
Importance: Enterobacter spp., especially carbapenemase-producing Enterobacter spp., have emerged as a clinically significant cause of nosocomial infections. However, only limited information is available on the distribution of carbapenem resistance across this genus. Augmenting this problem is an erroneous identification of Enterobacter strains b...
Data
Phylogenetic structure, subspecies identification, and pangenome analysis of Enterobacter spp. Download
Data
Plasmid gene content can influence gene content tree topology. An unrooted neighbor-joining tree was constructed by Neighbor by using the PanOCT Jaccard pairwise distance matrix of orthologous gene clusters with (A) and without (B) plasmid genes. Coloring is by assigned E. cloacae complex groupings A to E (see key and Fig. 5). Nodes are labeled by...
Data
Details of 351 Enterobacter genomes from GenBank. Download
Data
Comparison of blaKPC-harboring plasmids from four PacBio sequenced strains. Light blue shading denotes shared regions of homology with 99% identities. Light gray shading denotes homologous regions acquired from another plasmid (pENT-c88). Open reading frames are represented by arrows colored on the basis of the predicted gene function (see key, top...
Data
Comparison of blaKPC-4-harboring plasmids from BK34998. Light blue shading denotes IncA/C plasmid backbone regions shared among three plasmids, pRA1, p34998-E, and p35734-C. Light gray shading denotes region of homology surrounding blaKPC-4 from IncN plasmid pBK31551. Open reading frames are represented by arrows colored on the basis of the predict...
Data
Phylogenetic SNP tree of Enterobacter genomes. A whole-genome core SNP tree was constructed for 447 Enterobacter sp. genomes by using kSNP (30) and RAxML (31) (see Materials and Methods). The dendrogram was generated with FigTree v 1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). This data set included genomes within the 379 E. cloacae complex (...
Data
Resistance genes and incompatibility groups of plasmids from six PacBio sequenced Enterobacter strains.
Data
Comprehensive table with details about the 97 clinical isolates and six type strains sequenced in this study. Download
Article
Full-text available
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by i...
Article
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Enterobacter aerogenes Hormaeche and Edwards 1960 (Approved Lists 1980) and Klebsiella mobilis Bascomb et al. 1971 (Approved Lists 1980) were placed on the Approved Lists of Bacterial Names and were based on the same nomenclatural type, ATCC 13048. Consequently they are to be treated as homotypic synonyms. However, the names of homotypic synonyms a...
Article
Full-text available
Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-tr...
Article
Full-text available
Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-tr...
Data
Supplementary Figures 1-25, Supplementary Tables 1-38, Supplementary Note 1, Supplementary Methods and Supplementary References
Article
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Background: In an effort to identify the best practice for finding genes in prokaryotic genomes and propose it as a standard for automated annotation pipelines, 1,004,576 peptides were collected from various publicly available resources, and were used as a basis to evaluate various gene-calling methods. The peptides came from 45 bacterial replicon...
Article
Full-text available
Background Infections by pan-drug resistant Acinetobacter baumannii plague military and civilian healthcare systems. Previous A. baumannii pan-genomic studies used modest sample sizes of low diversity and comparisons to a single reference genome, limiting our understanding of gene order and content. A consensus representation of multiple genomes wi...
Chapter
Major technological developments in the field of microbial ecology are redefining the science, moving the focus of research away from studies of individual isolates and species that are studied under carefully controlled conditions in the laboratory, towards the study of entire communities of organisms in their natural environments. Ever more effic...
Article
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Leptospirosis is a globally important, neglected zoonotic infection caused by spirochetes of the genus Leptospira. Since genetic transformation remains technically limited for pathogenic Leptospira, a systems biology pathogenomic approach was used to infer leptospiral virulence genes by whole genome comparison of culture-attenuated Leptospira inter...
Data
Pie charts showing relative sequence similarity of uncharacterized proteins in COMBREX to experimentally characterized (green) proteins. (A) Blue proteins. (B) Black proteins. Within each pie, proteins are divided into those that exhibit “strong” similarity, “weak” similarity, or “no” similarity to characterized proteins. Strong similarity requires...
Data
Flowchart of GSDB construction. Source information includes external databases such as UniProtKB and other databases (“Source DBs”), and genes nominated by users via the COMBREX website. All entries originating outside of UniProtKB must be assigned a unique UniProtKB accession number before entry into the process. All candidates with a UniProtKB ac...
Data
Domain composition of proteins in COMBREX. All COMBREX proteins were clustered into groups based on identical domain composition. Along the x-axis, groups are separated based on the number of annotated Pfam domains per protein (as defined by Pfam). (A) Histogram, where the green portion of each bar indicates the number of proteins that have identic...
Data
Format of functional descriptions in COMBREX. (DOC)
Data
More detailed description of the following topics: selected COMBREX-funded experimental results; functional inference from existing experimental information; use of structured vocabulary; and prioritization of genes for experimental characterization. Materials and Methods, including the following topics: the COMBREX website; functional status of ge...
Data
Summary of proteins examined by COMBREX-funded projects. (XLSX)
Data
Association of structural data with uncharacterized proteins. (DOC)
Data
Function predictions submitted to COMBREX by external groups. (DOC)
Data
Number of clusters as a function of cluster size. Clusters are broken down into three types based on the functional status of their component proteins: clusters containing ≥1 experimentally characterized (green) gene are represented by the green line; clusters containing no experimentally characterized proteins but ≥1 protein with a predicted funct...
Data
Free-text strings analyzed by GOCat. (DOC)
Article
Full-text available
Experimental data exists for only a vanishingly small fraction of sequenced microbial genes. This community page discusses the progress made by the COMBREX project to address this important issue using both computational and experimental resources.
Article
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We report the genome sequences of four isolates of a human gut symbiont, Bifidobacterium longum. Strains 44B and 35B were isolated from two 1-year-old infants, while 1-6B and 2-2B were isolated from the same children 5 years later. The sequences permit investigations of factors enabling long-term colonization of bifidobacteria.
Article
Full-text available
Pan-genome ortholog clustering tool (PanOCT) is a tool for pan-genomic analysis of closely related prokaryotic species or strains. PanOCT uses conserved gene neighborhood information to separate recently diverged paralogs into orthologous clusters where homology-only clustering methods cannot. The results from PanOCT and three commonly used graph-b...
Article
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A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quali...
Article
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Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of...
Article
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The 5th International Biocuration Conference brought together over 300 scientists to exchange on their work, as well as discuss issues relevant to the International Society for Biocuration’s (ISB) mission. Recurring themes this year included the creation and promotion of gold standards, the need for more ontologies, and more formal interactions wit...
Article
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CharProtDB (http://www.jcvi.org/charprotdb/) is a curated database of biochemically characterized proteins. It provides a source of direct rather than transitive assignments of function, designed to support automated annotation pipelines. The initial data set in CharProtDB was collected through manual literature curation over the years by analysts...
Article
Full-text available
This document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent fo...