Collection CNM
Isolation Year 2016
Isolation Location Hospital Infanta Leonor (Madrid)
Hospital Admission Unit None
Patient Sex M
Patient Age 80
Community/Hospital/LTCF acquisition Hospital
Biological Sample of Isolation wound
Infection or Colonization C
Outbreak None
Genus/Species
Citrobacter freundii
Carbapenamase type(s) KPC-2
MLST 515:aspC(26), clpX(5), fadD(17), mdh(15), arcA(~40), dnaG(9), 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 16 R R
IMI 4 R I
IMI-RELE ≤0.12 S S
ERT 128 R R
FOSFO <32 S S
GENTA 0.5 S S
TOBRA 4 S R
AMK 4 S S
CIP 16 R R
COLIS <0.06 WT S
AI3058_v1
AI3058_v1

Sample 359-B was assembled with Unicycler_v0.4.6 into 37 scaffolds, 3 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
AI3058_v1_c1 359-B 515 Browse 19 2909 3060796 1.00
Citrobacter freundii
51.64 Non-mobilizable - - - - - - - - CP007734 0.26302200 1586
AI3058_v1_c2 359-B 515 Browse 5 556 602328 1.09
Citrobacter freundii
51.74 Non-mobilizable - - - - - - - - CP003223 0.26302200 80
AI3058_v1_c3 359-B 515 Browse 4 478 481840 1.13
Citrobacter freundii
52.10 Non-mobilizable - - - - - - - - AP014806 0.26302200 1549
AI3058_v1_c4 359-B 515 Browse 3 313 342563 1.11
Citrobacter freundii
52.79 Non-mobilizable - - - - - - - - CP008701 0.21953100 1229
AI3058_v1_c5 359-B 515 Browse 0 234 244272 1.11
Citrobacter freundii
51.67 Non-mobilizable - - - - - - - - CP018459 0.21089700 4650
AI3058_v1_c6 359-B 515 Browse 1 122 132223 1.13
Citrobacter freundii
52.47 Non-mobilizable - - - - - - - - CP018674 0.19173100 1713
AI3058_v1_c7 359-B 515 Browse 16 128 117229 0.81
Salmonella enterica
53.08 Conjugative IncFIB, IncN 000107__CP014778_00094, 000155__CP018649 MOBC NC_014725_00039 MPF_T NC_011092_00100, NC_011092_00102, NC_011092_00103 - - HQ332785 0.01497590 991
AI3058_v1_c8 359-B 515 Browse 0 74 84784 1.13
Citrobacter freundii
53.06 Non-mobilizable - - - - - - - - CP017452 0.18676100 1715
AI3058_v1_c9 359-B 515 Browse 0 62 48499 1.74
Escherichia coli, Klebsiella oxytoca
51.39 Conjugative IncN 000152__NZ_CP011646_00085 MOBF NC_015872_00034 MPF_T NC_015872_00033, NC_015872_00005, NC_015872_00006, NC_015872_00007, NC_015872_00010, NC_015872_00011 - - CP010382 0.00186568 937
AI3058_v1_c10 359-B 515 Browse 1 48 38347 5.68
Aeromonas hydrophila
58.48 Mobilizable IncP, IncU 000172__KU578314_00001, 000210__KF623109_00045 MOBP NC_003124_00014 - - - - KU578314 0.00075568 891
AI3058_v1_c11 359-B 515 Browse 1 34 37142 1.11
Citrobacter freundii
53.05 Non-mobilizable - - - - - - - - CP006253 0.14383000 1446
AI3058_v1_c12 359-B 515 Browse 0 21 17339 1.14
Citrobacter freundii
49.43 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c13 359-B 515 Browse 0 20 14503 2.61
Citrobacter freundii
56.19 Non-mobilizable - - - - - - - - CP021835 0.26302200 966
AI3058_v1_c14 359-B 515 Browse 0 14 13625 9.20
Salmonella enterica
49.91 Mobilizable ColRNAI_rep_cluster_1857 000012__CP000801 MOBP NC_019092_00012 - - MOBP NC_013372 CP020846 0.04100300 210
AI3058_v1_c15 359-B 515 Browse 0 6 6648 2.85
Salmonella enterica
50.72 Non-mobilizable - - - - - - - - CP020846 0.02614300 210
AI3058_v1_c16 359-B 515 Browse 0 5 3389 1.38
Citrobacter freundii
43.23 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c17 359-B 515 Browse 0 0 3193 5.51
Citrobacter freundii
51.96 Non-mobilizable - - - - - - - - CP006253 0.12449100 1446
AI3058_v1_c18 359-B 515 Browse 0 1 2760 2.69
Escherichia coli
50.33 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c19 359-B 515 Browse 0 4 2522 1.77
Citrobacter freundii, Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae
54.40 Non-mobilizable - - - - - - - - CP019907 0.08878330 940
AI3058_v1_c20 359-B 515 Browse 0 4 2263 1.33
Salmonella enterica
43.66 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c21 359-B 515 Browse 0 0 1696 5.37
Citrobacter freundii, Citrobacter sp.
53.01 Non-mobilizable - - - - - - - - CP006253 0.14572700 1446
AI3058_v1_c22 359-B 515 Browse 0 2 1194 1.85
Citrobacter freundii, Enterobacter hormaechei, Klebsiella oxytoca, Klebsiella pneumoniae
52.26 Non-mobilizable - - - - - - - - CP010382 0.14025800 937
AI3058_v1_c23 359-B 515 Browse 0 1 1016 1.56
Citrobacter freundii, Enterobacter hormaechei, Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae
52.85 Non-mobilizable - - - - - - - - CP019907 0.15422300 940
AI3058_v1_c24 359-B 515 Browse 0 1 761 2.73
Citrobacter freundii
56.50 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c25 359-B 515 Browse 0 1 591 1.33
Salmonella enterica
58.04 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c26 359-B 515 Browse 0 1 591 1.25
Citrobacter freundii
56.85 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c27 359-B 515 Browse 0 0 456 1.65
Escherichia coli, Salmonella sp.
56.36 Non-mobilizable - - - - - - - - CP003995 0.08624910 205
AI3058_v1_c28 359-B 515 Browse 0 0 385 1.37
Escherichia coli
55.06 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c29 359-B 515 Browse 0 0 385 1.31
Citrobacter freundii
55.06 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c30 359-B 515 Browse 0 0 378 3.36
Citrobacter freundii, Citrobacter sp.
49.47 Non-mobilizable - - - - - - - - CP006253 0.21089700 1446
AI3058_v1_c31 359-B 515 Browse 0 0 281 3.32
Citrobacter freundii, Enterobacter hormaechei, Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae
65.12 Non-mobilizable - - - - - - - - CP019907 0.21953100 940
AI3058_v1_c32 359-B 515 Browse 0 1 253 2.74
Edwardsiella piscicida, Salmonella enterica
46.64 Non-mobilizable - - - - - - - - CP020845 0.20360400 210
AI3058_v1_c33 359-B 515 Browse 0 0 147 2.38
Citrobacter freundii
51.02 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c34 359-B 515 Browse 0 0 144 1.07
Citrobacter freundii, Citrobacter sp.
36.11 Non-mobilizable - - - - - - - - CP019447 0.26302200 1447
AI3058_v1_c35 359-B 515 Browse 0 0 130 2.20
-
51.54 Non-mobilizable - - - - - - - - CP019447 0.29598100 1447
AI3058_v1_c36 359-B 515 Browse 0 0 123 1.07
-
56.91 Non-mobilizable - - - - - - - - 1.00000000
AI3058_v1_c37 359-B 515 Browse 0 0 120 1.08
Citrobacter freundii, Citrobacter sp.
34.17 Non-mobilizable - - - - - - - - CP019447 0.26302200 1447