Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario Ramón y Cajal (Madrid)
Hospital Admission Unit None
Patient Sex M
Patient Age 71
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation urine
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) OXA-48
MLST 11:gapA(3), infB(3), mdh(1), pgi(1), phoE(1), rpoB(1), tonB(4)
EDTA Assay (if any) MBL positive with EDTA, possible NDM
PCR Result (if any) OXA-48 positive, NDM negative
Agent MIC CLSI EUCAST
Piper >256 R R
P/T >256 R R
CTX >128 R R
CAZ >128 R R
CAZ-AVI >128 R R
CEF >128 R R
AZT >128 R R
MEM 16 R R
IMI 16 R R
IMI-RELE 16 R R
ERT 32 R R
FOSFO 256 R R
GENTA 256 R R
TOBRA 32 R R
AMK 8 S S
CIP >128 R R
COLIS <0.06 WT S
AI2879_v1
AI2879_v1

Sample 146 was assembled with Unicycler_v0.4.6 into 8 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
AI2879_v1_c1 146 11 Browse 33 5010 5350199 1.00
Klebsiella pneumoniae
57.41 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP015754 0.20360400 1583
AI2879_v1_c2 146 11 Browse 32 211 208690 1.22
Klebsiella pneumoniae
52.93 Non-mobilizable IncFII, IncFIB 000107__CP014778_00094, 000113__CP022035, 000132__HG969996 - - MPF_F NC_019165_00034, NC_021654_00016, NC_022609_00081, NC_014312_00128, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_019389_00080, NC_019155_00032, NC_021654_00004 - - CP009777 0.00302611 767
AI2879_v1_c3 146 11 Browse 1 84 65499 3.32
Klebsiella pneumoniae
51.43 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 - - KX523901 0.00007159 681
AI2879_v1_c4 146 11 Browse 7 53 51281 2.57
Klebsiella pneumoniae
50.41 Conjugative IncR 000204__CP008701_00115 MOBF, MOBP NC_015599_00019, NC_021576_00050 MPF_T NC_022375_00024 MOBF NZ_CP012928 CP014299 0.02581150 730
AI2879_v1_c5 146 11 Browse 2 10 9903 2.67
Klebsiella pneumoniae
55.73 Non-mobilizable - - - - - - - - KT988019 0.03038260 1095
AI2879_v1_c6 146 11 Browse 0 2 2534 1.14
Klebsiella pneumoniae
48.86 Non-mobilizable - - - - - - - - JF785550 0.08624910 455
AI2879_v1_c7 146 11 Browse 0 0 380 2.18
Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae
54.74 Non-mobilizable - - - - - - - - NC_010064 0.06236750 742
AI2879_v1_c8 146 11 Browse 0 1 356 2.22
-
51.12 Non-mobilizable - - - - - - - - NC_010064 0.06158390 742