Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Ramón y Cajal (Madrid)
Hospital Admission Unit None
Patient Sex M
Patient Age 65
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) NDM-1
MLST 101:gapA(2), infB(6), mdh(1), pgi(5), phoE(4), rpoB(1), tonB(6)
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 >256 R R
CAZ-AVI >256 R R
CEF 8 SDD R
AZT 128 R R
MEM 4 R I
IMI 2 I S
IMI-RELE 2 I S
ERT 2 R R
FOSFO <32 S S
GENTA >256 R R
TOBRA >256 R R
AMK 128 R R
CIP 128 R R
COLIS <0.06 WT S
AI2898_v1
AI2898_v1

Sample 176 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
AI2898_v1_c1 176 101 Browse 30 5028 5400154 1.00
Klebsiella pneumoniae
57.22 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP015754 0.21089700 1583
AI2898_v1_c2 176 101 Browse 7 123 119298 1.70
Klebsiella pneumoniae
53.72 Conjugative IncFII, rep_cluster_1418 000124__KP125893_00142, 000759__NC_013950_00034 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_019165_00034, NC_021654_00016, NC_022609_00081, NC_014312_00128, NC_019389_00068, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_019389_00080, NC_019155_00032 - - KF295829 0.01683910 1587
AI2898_v1_c3 176 101 Browse 24 98 96925 1.10
Klebsiella pneumoniae
49.58 Non-mobilizable IncFIB 000107__CP014778_00094 - - - - - - CP010390 0.03562200 770
AI2898_v1_c4 176 101 Browse 5 41 38201 1.92
Klebsiella pneumoniae
52.64 Mobilizable IncFIB 000097__NC_025166_00051 MOBP NC_021576_00050 - - - - CP021947 0.01450760 1219
AI2898_v1_c5 176 101 Browse 0 7 5838 14.41
Klebsiella pneumoniae
49.47 Mobilizable - - MOBP NC_017723_00002 - - - - FJ696405 0.12449100 330
AI2898_v1_c6 176 101 Browse 0 3 4713 5.53
Klebsiella pneumoniae
43.39 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - CP018358 0.06454370 204
AI2898_v1_c7 176 101 Browse 0 5 4052 11.13
Klebsiella pneumoniae
53.65 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 MOBP NC_016979_00005 - - MOBP CP018941 CP018740 0.00031257 95
AI2898_v1_c8 176 101 Browse 0 3 3479 6.56
Klebsiella pneumoniae
45.65 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - CP000652 0.00036121 193