Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario La Princesa (Madrid)
Hospital Admission Unit Primary care
Patient Sex F
Patient Age 96
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Escherichia coli
Carbapenamase type(s) Negative
MLST 10:adk(10), fumC(11), gyrB(4), icd(8), mdh(8), purA(8), recA(2)
EDTA Assay (if any) It could have an OXA-48
PCR Result (if any) OXA-48 negative x2
Agent MIC CLSI EUCAST
Piper 8 S S
P/T 4 S S
CTX >128 R R
CAZ >128 R R
CAZ-AVI ≤0.25 S S
CEF >128 R R
AZT >128 R R
MEM ≤0.12 S S
IMI ≤0.12 S S
IMI-RELE ≤0.12 S S
ERT 2 R R
FOSFO <32 S S
GENTA 0.5 S S
TOBRA 0.5 S S
AMK 8 S S
CIP >128 R R
COLIS <0.06 WT S
AI2928_v1
AI2928_v1

Sample 214 was assembled with Unicycler_v0.4.6 into 6 scaffolds, 5 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
AI2928_v1_c1 214 10 Browse 54 4257 4596356 1.00
Escherichia coli
50.90 Non-mobilizable rep_cluster_1527 000882__CP012005_00092 - - - - - - CP010208 0.20360400 2912
AI2928_v1_c2 214 10 Browse 13 110 97068 3.34
Escherichia coli
52.80 Conjugative IncFII, IncFIIA 000136__AP014877_00014, 000121__CP024805 MOBF NC_017627_00068 MPF_F NC_010719_00097, NC_017639_00100, NC_007675_00027, NC_013437_00116, NC_017639_00094, NC_019094_00090, NC_010409_00124, NC_022651_00077, 08-5333_00200, NC_018966_00040, NC_019094_00068, NC_010719_00096 MOBF NZ_CP012164 CP012632 0.00023990 546
AI2928_v1_c3 214 10 Browse 0 59 53489 2.16
Escherichia coli
50.06 Non-mobilizable - - - - - - - - CP021680 0.05698300 1068
AI2928_v1_c4 214 10 Browse 0 51 36062 2.53
Escherichia coli
41.47 Non-mobilizable - - - - - - - - CP016008 0.17817300 585
AI2928_v1_c5 214 10 Browse 0 2 2406 4.62
Escherichia coli
48.75 Non-mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 - - - - - - CP018971 0.05630820 1566
AI2928_v1_c6 214 10 Browse 0 1 2045 7.98
Klebsiella pneumoniae
45.33 Non-mobilizable - - - - - - - - GQ374157 0.12330000 214