Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Mutua de Terrassa (Terrassa)
Hospital Admission Unit ICU
Patient Sex M
Patient Age 69
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Escherichia coli
Carbapenamase type(s) OXA-48
MLST 10:adk(10), fumC(11), gyrB(4), icd(8), mdh(8), purA(8), recA(2)
EDTA Assay (if any) None
PCR Result (if any) None
Agent MIC CLSI EUCAST
Piper >256 R R
P/T 256 R R
CTX >128 R R
CAZ >128 R R
CAZ-AVI 1 S S
CEF >128 R R
AZT >128 R R
MEM 32 R R
IMI 64 R R
IMI-RELE 32 R R
ERT 128 R R
FOSFO <32 S S
GENTA 32 R R
TOBRA 128 R R
AMK 4 S S
CIP 32 R R
COLIS 0.25 WT S
AI2852_v1
AI2852_v1

Sample 102 was assembled with Unicycler_v0.4.6 into 8 scaffolds, 8 of which are closed circles. More details can be found in the table below. Raw data such as the assembly FASTA and annotation files can be downloaded from the "Raw Data" box. The assembly can be browsed by clicking on the "Browse" link for each scaffold.

Scaffold Sample ST Jbrowse Resistance Genes All Genes Scaffold length Circular Est. Copy Number Species GC content Mobility Replicon type Replicon type accession Relaxase type Relaxase type accession MPF type Mpf type accession OriT type OriT accession MASH nearest neighbor MASH neighbor distance MASH neighbor cluster
AI2852_v1_c1 102 10 Browse 58 4558 4869560 1.00
Escherichia coli
50.74 Mobilizable - - MOBP NC_011416_00039 - - - - CP010208 0.20360400 2912
AI2852_v1_c2 102 10 Browse 14 104 106879 2.31
Escherichia coli
50.24 Mobilizable IncFII, IncFIB, IncFIIA 000136__AP014877_00014, 000121__CP024805, 000095__NZ_CP014273_00094 MOBF NC_017627_00068 - - - - CP000836 0.01056880 973
AI2852_v1_c3 102 10 Browse 1 114 103714 3.57
Klebsiella pneumoniae
50.14 Conjugative IncI1 000145__HE610900_00001 MOBP NC_019097, NC_011416_00039 MPF_I NC_019097_00056, NC_022267_00057, NC_023290_00086, NC_015965_00072, NC_019097_00075, NC_022267_00069, NZ_CM001473_00069, NC_019097_00085, NC_011419_00085 MOBP JN253636 JF274993 0.00427048 476
AI2852_v1_c4 102 10 Browse 1 86 63589 3.37
Klebsiella pneumoniae
51.22 Conjugative IncL/M 000148__NC_021488_00028 MOBP NC_004464_00056 MPF_I NC_004464_00105, NC_005246_00057, NC_019063_00094, NC_019344_00078, NC_004464_00066, NC_004464_00068, NC_019154_00069, NC_005246_00069, NC_004464_00073 - - CP015075 0.00000000 681
AI2852_v1_c5 102 10 Browse 0 50 35225 4.25
Escherichia coli
41.58 Conjugative IncX4 000222__CP010880_00038 MOBP NC_013718_00057 MPF_T NC_013718_00041, NC_013718_00044, NC_013718_00045, NC_019128_00037 - - CP018950 0.00028831 585
AI2852_v1_c6 102 10 Browse 0 14 12602 12.84
Escherichia coli
45.52 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 - - - - MOBP CP008720 CP019003 0.00009552 219
AI2852_v1_c7 102 10 Browse 0 8 7098 16.45
Shigella sonnei
50.54 Mobilizable - - - - - - MOBQ DQ318958, NZ_CP009767 DQ916145 0.01306380 834
AI2852_v1_c8 102 10 Browse 0 3 4073 17.01
Escherichia coli, Salmonella enterica
51.46 Mobilizable rep_cluster_1785 001211__AP017616_00002 - - - - MOBQ NC_013327, NC_009791 CP018996 0.00055724 469