Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Gregorio Marañón (Madrid)
Hospital Admission Unit Gastroenterology
Patient Sex F
Patient Age 49
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Citrobacter freundii
Carbapenamase type(s) KPC-2
MLST 22:aspC(15), clpX(12), fadD(20), mdh(15), arcA(5), dnaG(11), lysP(17)
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 32 R R
AZT 128 R R
MEM 2 I S
IMI 0.5 S S
IMI-RELE ≤0.25 S S
ERT 64 R R
FOSFO <32 S S
GENTA ≤0.25 S S
TOBRA 1 S S
AMK 0.25 S S
CIP 8 R R
COLIS 0.12 WT S
AI2826_v1
AI2826_v1

Sample 30 was assembled with Unicycler_v0.4.6 into 6 scaffolds, 6 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
AI2826_v1_c1 30 22 Browse 35 4804 5082481 1.00
Citrobacter freundii
51.72 Non-mobilizable - - - - - - - - DQ517526 0.21953100 430
AI2826_v1_c2 30 22 Browse 1 134 112775 1.84
Citrobacter freundii
54.75 Conjugative IncFII, rep_cluster_959 000132__HG969996, 002442__AP014954_00001 MOBF NC_019125_00139 MPF_F NC_021871_00015, NC_019125_00135, NC_021817_00013, NC_019342_00064, NZ_AGTD01000004_00091, NZ_AGTD01000004_00094, NC_021817_00023, NC_021817_00021, NZ_AGTD01000004_00096 - - CP011610 0.07866280 748
AI2826_v1_c3 30 22 Browse 7 99 99059 1.75
Citrobacter freundii
52.80 Non-mobilizable IncFIB 000101__NZ_CP012345_00042 - - - - - - CP017059 0.02021370 748
AI2826_v1_c4 30 22 Browse 0 90 65352 1.90
Raoultella electrica
41.11 Non-mobilizable - - - - - - - - CP008900 0.24376100 1082
AI2826_v1_c5 30 22 Browse 2 49 40836 5.86
Aeromonas hydrophila
57.73 Mobilizable IncP, IncU 000172__KU578314_00001, 000210__KF623109_00045 MOBP NC_003124_00014 - - - - KU578314 0.00205363 891
AI2826_v1_c6 30 22 Browse 0 3 3576 25.57
Klebsiella variicola
44.99 Non-mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 - - - - - - CP006637 0.13386400 179