Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Central de Asturias (Oviedo)
Hospital Admission Unit Urology
Patient Sex M
Patient Age 63
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Citrobacter freundii
Carbapenamase type(s) OXA-48
MLST 18:aspC(10), clpX(14), fadD(17), mdh(12), arcA(5), dnaG(5), lysP(14)
EDTA Assay (if any) None
PCR Result (if any) None
Agent MIC CLSI EUCAST
Piper 256 R R
P/T 128 R R
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 0.5 S S
IMI-RELE ≤0.12 S S
ERT 1 I R
FOSFO <32 S S
GENTA 128 R R
TOBRA 256 R R
AMK 8 S S
CIP >128 R R
COLIS <0.06 WT S
AI2668_v1
AI2668_v1

Sample 244 was assembled with Unicycler_v0.4.6 into 7 scaffolds, 7 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
AI2668_v1_c1 244 18 Browse 37 4658 4964029 1.00
Citrobacter freundii
51.89 Non-mobilizable - - - - - - - - LK056646 0.21953100 429
AI2668_v1_c2 244 18 Browse 13 313 287088 1.52
Enterobacter hormaechei
46.95 Conjugative rep_cluster_1088, IncH 000139__NC_012555_00001, 000338__NC_021819 MOBH NC_012555_00231 MPF_F NC_005211_00200, NC_005211_00207, NC_005211_00005, NC_009838_00006, NC_005211_00012, NC_021845_00017, NC_005211_00030 MOBH NC_017484 CP008825 0.00865422 429
AI2668_v1_c3 244 18 Browse 9 150 142948 1.97
Citrobacter freundii
53.06 Non-mobilizable IncFIB 000101__NZ_CP012345_00042 - - - - - - CP017059 0.00977265 748
AI2668_v1_c4 244 18 Browse 0 128 110089 1.67
Enterobacter hormaechei
50.80 Non-mobilizable IncFIB 000102__NC_003385_00128 - - - - - - KX015668 0.02398290 86
AI2668_v1_c5 244 18 Browse 1 86 63570 3.25
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
AI2668_v1_c6 244 18 Browse 0 3 3810 21.24
Enterobacter sp.
55.83 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 MOBP NC_011404_00002 - - MOBP HQ328804 KU302806 0.03844950 107
AI2668_v1_c7 244 18 Browse 0 2 1335 16.67
-, Citrobacter freundii, Cronobacter sakazakii, Salmonella enterica
48.16 Mobilizable - - - - - - MOBP NZ_AFSD01000008 CP002129 0.19173100 248