Plasmid NZ_CP013227.1

Sequence

Nucleotide Information

Accession NZ_CP013227.1
Description Staphylococcus aureus strain UTSW MRSA 55 plasmid UTSW55_1, complete sequence
Source refseq
Topology circular
Length 22042 bp
GC Content 0.32 %
Created at NCBI March 9, 2016



Assembly

Genome Data Information

Accession GCF_001580515.1
Assembly Coverage 955


Biosample

Curated Collection Information

Accession 4254471

PLASMID INFORMATION

GEOGRAPHICAL INFORMATION
Original Query 32.775833N;96.79666700W
Original Query Type coordinates
Coordinates (Lat/Lon) 32.78/-96.80
Address Dallas City Hall, 1500, Marilla Street, Downtown PID, Dallas, Dallas County, Texas, 75201, United States

ECOSYSTEM
Original Query Homo sapiens,blood,USA: Dallas Texas
Classification blood,circulatory_system,host_associated,location
Host-associated Taxon
  • Homo sapiens (9606)
Host-associated Age 12 year plus 11 month
Host-associated Sex female

DISEASE
Original Query Osteomyelitis,Osteomyelitis of the right proximal femur and right pelvis; septic arthritis of the right hip (MRSA+); pyomyositis of the right hip and pelvis; abscess of the right pelvis (MRSA+); deep venous thrombosis of the right iliac vein; pneumonia; septic pulmonary emboli; and urinary tract infection,She underwent 5 surgical procedures, had 2 readmissions, with initial hospital length of stay of 51 days and total length of stay (including readmission days) of 69 days. Her calculated severity of illness score was 10,A medical records query determined that her Medicare Severity Diagnosis Related Groups (MS DRG) score was 5.3491; All Patient Refined Diagnosis Related Groups (APR-DRG) score was 5.8067; Severity of Illness (SOI) score was 4; and Risk of Mortality (ROM) score was 4. She developed complications of chondrolysis, acetabular protrusion, avascular necrosis, proximal femoral dissolution which was treated with a 2 stage total hip arthroplasty
DOID/SYMP
  • Urinary tract infection (DOID:0080784 )
  • An urinary system disease that is characterized by an infection in any part of the urinary system, including the kidneys, ureters, bladder or urethra.
  • Pulmonary embolism (DOID:9477 )
  • An artery disease characterized by a blockage of the main artery of the lung or one of its branches by a substance that has travelled from elsewhere in the body, e.g. a blood clot.
  • Necrosis (SYMP:0000132 )
  • Necrosis is a general symptom where death of a portion of tissue differentially affected by local injury (as loss of blood supply, corrosion, burning, or the local lesion of a disease).
  • Pneumonia (DOID:552 )
  • A lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing.
  • Disease (DOID:4 )
  • A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
  • Osteomyelitis (DOID:1019 )
  • A bone inflammation disease that has_material_basis_in infection located_in bone or located_in bone marrow.
    • Has_material_basis_in: ['infection located_in bone or located_in bone marrow']
  • Thrombosis (DOID:0060903 )
  • A vascular disease caused by the formation of a blood clot inside a blood vessel, obstructing the flow of blood through the circulatory system.
  • Septic arthritis (DOID:813 )
  • An arthritis that involves infection by a pathogen located_in joint.

Visualization


Plasmids from same Biosample



Similar Plasmids

based on Mash distance


Plasmid Visualization


NUCCORE ACC Source Element Name Display Sequence Favorite
NUCCORE ACC Source Element Name Display Sequence Favorite



Annotations

based on the NCBI Prokaryotic Genome Annotation Pipeline (PGAP)

NUCCORE ACC Gene Locus Tag Product Protein id Codon Start Translation Table GO process
NUCCORE ACC Gene Locus Tag Product Protein id Codon Start Translation Table GO process



Typing


based on MOB-Typer and Plasmid Multilocus Sequencing Typing (PMLST)
NUCCORE ACC Contigs md5 hash Replicon Type Relaxase Type MPF Type OriT Type Predicted Mobility Primary Cluster ID Secondary Cluster ID Observed Host Range Ncbi Rank Observed Host Range Ncbi Name Mash Nearest Neighbor Mash Neighbor Distance Mash Neighbor Identification Reported Host Range Lit Rank Reported Host Range Lit Name Replicon Type Accession Relaxase Type Accession MPF Type Accession OriT Type Accession Associated PMID(s)
NUCCORE ACC Contigs md5 hash Replicon Type Relaxase Type MPF Type OriT Type Predicted Mobility Primary Cluster ID Secondary Cluster ID Observed Host Range Ncbi Rank Observed Host Range Ncbi Name Mash Nearest Neighbor Mash Neighbor Distance Mash Neighbor Identification Reported Host Range Lit Rank Reported Host Range Lit Name Replicon Type Accession Relaxase Type Accession MPF Type Accession OriT Type Accession Associated PMID(s)




BLAST results of detected typing markers by MOB-type
NUCCORE ACC biomarker MOB-suite ID Element Start End Strand Identity Coverage Evalue Bitscore
NUCCORE ACC biomarker MOB-suite ID Element Start End Strand Identity Coverage Evalue Bitscore


Detected typing markers by plasmidfinder
NUCCORE ACC Typing Identity Coverage Start End Strand HSP length Template length Position in ref Positions in Contig Note Accession Hit id Organism L1 Organism L2
NUCCORE ACC Typing Identity Coverage Start End Strand HSP length Template length Position in ref Positions in Contig Note Accession Hit id Organism L1 Organism L2