Plasmid NZ_CP013228.1

Sequence

Nucleotide Information

Accession NZ_CP013228.1
Description UNVERIFIED_ASMBLY: Staphylococcus aureus strain UTSW MRSA 55 plasmid UTSW55_2, complete sequence
Source refseq
Topology circular
Length 45868 bp
GC Content 0.30 %
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



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NZ_CP009425.1 See Comparison
NZ_CP013228.1 See Comparison
NZ_CP007177.1 See Comparison
NC_018963.1 See Comparison
NC_018961.1 See Comparison
NC_018959.1 See Comparison
NC_018957.1 See Comparison
NC_018956.1 See Comparison
NC_013298.1 See Comparison
NC_013294.1 See Comparison
NC_013289.1 See Comparison
CP030707.1 See Comparison
CP030633.1 See Comparison
CP030663.1 See Comparison
CP030511.1 See Comparison
CP030667.1 See Comparison
CP030513.1 See Comparison
CP030700.1 See Comparison
CP030660.1 See Comparison
CP030494.1 See Comparison
CP030444.1 See Comparison
CP030446.1 See Comparison
CP030672.1 See Comparison
NZ_CP014364.1 See Comparison
CP030427.1 See Comparison
CP030376.1 See Comparison
CP030409.1 See Comparison
CP030385.1 See Comparison
CP030414.1 See Comparison
CP030416.1 See Comparison
NZ_LR130519.1 See Comparison
NZ_CP031889.1 See Comparison
NZ_CP031891.1 See Comparison
NZ_CP040621.1 See Comparison
NZ_CP014370.1 See Comparison
NZ_CP014383.1 See Comparison
NZ_CP014367.1 See Comparison
NZ_CP014386.1 See Comparison
NZ_CP029665.1 See Comparison
NZ_CP029666.1 See Comparison
NZ_CP029677.1 See Comparison
NZ_CP016862.1 See Comparison
NZ_CP012118.2 See Comparison
NZ_CP152122.1 See Comparison
CP156704.1 See Comparison
CP097087.1 See Comparison
NZ_CP152411.1 See Comparison
CP151826.1 See Comparison
CP155821.1 See Comparison
CP152317.1 See Comparison
CP150837.1 See Comparison
CP152320.1 See Comparison
CP151890.1 See Comparison
NZ_CP151124.1 See Comparison
NZ_CP149457.1 See Comparison
CP154289.1 See Comparison
CP154283.1 See Comparison
CP150830.1 See Comparison
NZ_CP147970.1 See Comparison
NZ_CP002149.1 See Comparison
NZ_CP147695.1 See Comparison
NZ_CP147692.1 See Comparison
NZ_CP148077.1 See Comparison
NZ_CP148080.1 See Comparison
CP150114.1 See Comparison
CP150101.1 See Comparison
CP150112.1 See Comparison
CP049451.1 See Comparison
CP052027.1 See Comparison
CP052013.1 See Comparison
CP052011.1 See Comparison
CP051998.1 See Comparison
CP051977.1 See Comparison
CP051944.1 See Comparison
CP051911.1 See Comparison
CP051906.1 See Comparison
CP051900.1 See Comparison
CP050001.1 See Comparison
CP049585.1 See Comparison
CP049576.1 See Comparison
CP049559.1 See Comparison
CP049557.1 See Comparison
CP049507.1 See Comparison
CP049446.1 See Comparison
CP049492.1 See Comparison
CP049439.1 See Comparison
CP049433.1 See Comparison
CP049430.1 See Comparison
CP049426.1 See Comparison
CP049464.1 See Comparison
CP049415.1 See Comparison
CP049411.1 See Comparison
CP049407.1 See Comparison
CP049402.1 See Comparison
CP049398.1 See Comparison
CP049385.1 See Comparison
CP049382.1 See Comparison
CP049378.1 See Comparison
NZ_CP062325.1 See Comparison
NZ_CP113028.1 See Comparison
NZ_CP117205.1 See Comparison
NZ_CP103861.1 See Comparison
NZ_CP104021.1 See Comparison
NZ_CP062321.1 See Comparison
NZ_CP062367.1 See Comparison
CP083745.1 See Comparison
NZ_CP014414.1 See Comparison
NZ_CP081355.1 See Comparison
NZ_CP014437.1 See Comparison
NZ_CP014422.1 See Comparison
NZ_CP014443.1 See Comparison
NZ_CP014440.1 See Comparison
NZ_CP014428.1 See Comparison
NZ_CP014425.1 See Comparison
NZ_CP014411.1 See Comparison
NZ_CP014434.1 See Comparison
NZ_CP009425.1 See Comparison
NZ_CP014431.1 See Comparison
NC_010063.1 See Comparison
NZ_CP007177.1 See Comparison
NC_013298.1 See Comparison
NC_013294.1 See Comparison
NC_013289.1 See Comparison
NC_019150.1 See Comparison
NC_018974.1 See Comparison
NC_018963.1 See Comparison
NC_018961.1 See Comparison
NC_018959.1 See Comparison
NC_018957.1 See Comparison
NC_018956.1 See Comparison
CP030578.1 See Comparison
CP030694.1 See Comparison
CP030707.1 See Comparison
CP030633.1 See Comparison
CP030663.1 See Comparison
CP030560.1 See Comparison
CP030667.1 See Comparison
CP030563.1 See Comparison
CP030549.1 See Comparison
CP030587.1 See Comparison
CP030444.1 See Comparison
CP030700.1 See Comparison
CP030446.1 See Comparison
CP030427.1 See Comparison
CP030660.1 See Comparison
CP030672.1 See Comparison
CP030644.1 See Comparison
CP030625.1 See Comparison
CP030597.1 See Comparison
CP030629.1 See Comparison
CP030511.1 See Comparison
CP030376.1 See Comparison
CP030409.1 See Comparison
CP030385.1 See Comparison
CP030414.1 See Comparison
CP030513.1 See Comparison
CP030416.1 See Comparison
CP030494.1 See Comparison
NZ_LR130519.1 See Comparison
NZ_CP040621.1 See Comparison
NZ_CP031889.1 See Comparison
NZ_CP031891.1 See Comparison
NZ_CP012118.2 See Comparison
NZ_CP014364.1 See Comparison
NZ_CP014370.1 See Comparison
NZ_CP014383.1 See Comparison
NZ_CP014367.1 See Comparison
NZ_CP014386.1 See Comparison
NZ_CP029677.1 See Comparison
NZ_CP016862.1 See Comparison
NZ_CP029665.1 See Comparison
NZ_CP029666.1 See Comparison
CP156704.1 See Comparison
NZ_CP152122.1 See Comparison
NZ_CP152411.1 See Comparison
CP097087.1 See Comparison
CP155821.1 See Comparison
CP152317.1 See Comparison
CP154289.1 See Comparison
CP154283.1 See Comparison
CP150830.1 See Comparison
CP151826.1 See Comparison
CP152320.1 See Comparison
CP151890.1 See Comparison
CP150837.1 See Comparison
NZ_CP151124.1 See Comparison
NZ_CP147970.1 See Comparison
NZ_CP149457.1 See Comparison
NZ_CP147695.1 See Comparison
NZ_CP148077.1 See Comparison
NZ_CP148080.1 See Comparison
NZ_CP147692.1 See Comparison
NZ_CP002149.1 See Comparison
CP150114.1 See Comparison
CP150101.1 See Comparison
CP150112.1 See Comparison
CP052013.1 See Comparison
CP052011.1 See Comparison
CP052027.1 See Comparison
CP051998.1 See Comparison
CP051977.1 See Comparison
CP051911.1 See Comparison
CP051944.1 See Comparison
CP051906.1 See Comparison
CP050001.1 See Comparison
CP051900.1 See Comparison
CP049585.1 See Comparison
CP049507.1 See Comparison
CP049576.1 See Comparison
CP049559.1 See Comparison
CP049492.1 See Comparison
CP049557.1 See Comparison
CP049446.1 See Comparison
CP049415.1 See Comparison
CP049439.1 See Comparison
CP049433.1 See Comparison
CP049430.1 See Comparison
CP049464.1 See Comparison
CP049451.1 See Comparison
CP049411.1 See Comparison
CP049398.1 See Comparison
CP049426.1 See Comparison
CP049407.1 See Comparison
CP049385.1 See Comparison
CP049402.1 See Comparison
CP049382.1 See Comparison
NZ_CP117205.1 See Comparison
CP049378.1 See Comparison
NZ_CP113028.1 See Comparison


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



Antimicrobial Resistance

based on NCBIAMRFinder and CARD

NUCCORE ACC Analysis Software Name Reference Database Version Gene Symbol Gene Name Drug Class Antimicrobial Agent Gene Start Gene Stop Gene Length Strand Orientation Sequence Identity (%) Coverage (%)
NUCCORE ACC Analysis Software Name Reference Database Version Gene Symbol Gene Name Drug Class Antimicrobial Agent Gene Start Gene Stop Gene Length Strand Orientation Sequence Identity (%) Coverage (%)



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