PROJECT INFORMATION
GOLD Project ID
Gp0733941  
Project Name
Escherichia coli p11B  
Other Names
  
Legacy GOLD ID
  
NCBI BioProject Name Investigate ESBL-positive Enterobacteriaceae that develop carbapenem resistance through non-carbapenemase-producing mechanisms in cancer patients with recurrent bacteremia. The objective of this study is to characterize clonal, serial isolates that develop carbapenem resistance via non-carbapenemase mechanisms. Our hypothesis is that a proportion of recurrent bacteremia cases due to persistent carriage of the same clonal, re-infecting strains have the ability to develop resistance to carbapenems independent of carbapenemase acquisition within our cancer population. We believe this is occurring through a mobile genetic element amplification mechanism with concomitant outer membrane porin disruption.
NCBI BioProject Accession PRJNA603908
NCBI Locus Tag
NYO14  
NCBI BioSample Accession SAMN13948685
Source Sample ID
PI Unknown
Added By JGI automated process on 2023-03-30
Last Modified By
Project Comments
  
Project Status
Complete and Published  
Project Relevance Medical
Sequencing Center University of Texas Houston Health Science Center
Collaborating Institute
  
Funding Agency
  
Project Description
Escherichia coli p11B genome sequencing  
Is JGI Project
No  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
JGI Data Utilization Status
  
JGI Award DOI
Genome Publications The Journal of antimicrobial chemotherapy: 76(2):385-395 IS26-mediated amplification of blaOXA-1 and blaCTX-M-15 with concurrent outer membrane porin disruption associated with de novo carbapenem resistance in a recurrent bacteraemia cohort.
PubMed: 33164081 DOI: 10.1093/jac/dkaa447
Other Publications
  
Ignored Publications
  
Unassigned Publications
  
SRA Experiment
 
SRA Experiment Id SRX7783030  (Link to NCBI )
Experiment Title ONT-seq of E. coli:p11B
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name MB2489
Library Layout SINGLE
Library Instrument GRID_ION
 
SRA Experiment Id SRX7784762  (Link to NCBI )
Experiment Title ILMN-seq of E. coli:p11B
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name MB2489
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2500
PROJECT COMPOSITION
Study Conjunction of Modular Beta-lactamase Encoding Gene Amplification with Porin Loss Drives Carbapenem Resistance in ESBL Positive Enterobacteriaceae from Patients with Recurrent Bacteremia
Organism Escherichia coli p11B
Analysis Projects Escherichia coli p11B
Number of Analysis Projects (AP) 1
Number of Derived Analyis Projects (DAP)
0  
SEQUENCING INFORMATION
Sequencing Status In progress
Sequencing Quality (MIGS-31) Level 6: Finished
Finishing Goal
Contamination Screening Input
  
DNA Amplification Method
  
Single Cell Lysis Protocol
  
Single Cell Lysis Approach
  
Sequencing Comments
  
DNA Amplification Kit
  
Sequencing Technology (MIGS-29) Oxford Nanopore GridION
Library Method (MIGS-28)
  
Library Layout
  
Library Screening Method
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
50.8  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0666262
Organism Name
Escherichia coli p11B  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
PROTEOBACTERIA-GAMMA  
Genus
Escherichia  
Genus Synonyms
  
Species
Escherichia coli  
Subspecies
  
Species Synonyms
  
Strain
p11B  
Strain Synonyms
  
Serovar/Cultivar
  
Culture Collection ID
  
Type Strain
  
Exemplar DOI
  
Exemplar Name
  
Taxon DOI
  
Biosafety Level
  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 562
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Pseudomonadota  
NCBI Class
Gammaproteobacteria  
NCBI Order
Enterobacterales  
NCBI Family
Enterobacteriaceae  
NCBI Genus
Escherichia  
NCBI Species
Escherichia coli  
ISOLATION CLASSIFICATION
Ecosystem
Host-associated  
Ecosystem Category
Mammals: Human  
Ecosystem Type
Circulatory system  
Ecosystem Subtype
Blood  
Specific Ecosystem
Unclassified  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
  
Cell Shape
  
Motility
  
Sporulation
  
Temperature Range
  
Salinity
  
pH
  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
  
Biotic Relationships
  
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats
  
Metabolisms
  
Phenotypes
  
Energy Sources
  

 

 

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