Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Universitario La Princesa (Madrid)
Hospital Admission Unit Nephrology and ICU
Patient Sex M
Patient Age 80
Community/Hospital/LTCF acquisition Community
Biological Sample of Isolation blood culture
Infection or Colonization I
Outbreak None
Genus/Species
Klebsiella pneumoniae
Carbapenamase type(s) OXA-48
MLST 39:gapA(2), infB(1), mdh(2), pgi(4), phoE(9), rpoB(1), tonB(14)
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 2 S S
CEF >128 R R
AZT >128 R R
MEM 2 I S
IMI 1 S S
IMI-RELE 1 S S
ERT 4 R R
FOSFO 128 I R
GENTA 32 R R
TOBRA 8 I R
AMK 4 S S
CIP 16 R R
COLIS 0.12 WT S
AI2908_v1
AI2908_v1

Sample 191 was assembled with Unicycler_v0.4.6 into 11 scaffolds, 4 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
AI2908_v1_c1 191 39 Browse 30 4917 5376086 1.00
Klebsiella pneumoniae
57.36 Non-mobilizable - - - - MPF_T NC_010726_00014, NC_005814_00013, NC_010726_00011, NC_013284_00016 - - CP015754 0.21089700 1583
AI2908_v1_c2 191 39 Browse 25 243 242551 1.66
Citrobacter freundii
52.51 Conjugative IncFII, IncFIB 000111__NZ_CP011595_00114, 000101__NZ_CP012345_00042, 000123__CP000858 MOBF NC_019125_00139 MPF_F NC_021817_00020, NC_021871_00015, NC_019125_00135, NC_021817_00013, NC_019342_00064, NZ_AGTD01000004_00091, NC_021871_00025, NZ_AGTD01000004_00094, NC_021871_00022, NC_021817_00023, NC_021817_00021 MOBP NZ_CP016040 KY271404 0.02468310 770
AI2908_v1_c3 191 39 Browse 9 143 140302 0.98
Klebsiella pneumoniae
52.20 Conjugative IncFII, IncFIB 000124__KP125893_00142, 000107__CP014778_00094 MOBF NC_021231_00058 MPF_F NC_021502_00150, NC_019165_00034, NC_021654_00016, NC_011281_00082, NC_022609_00081, NC_014312_00128, NC_019389_00068, NC_023332_00154, NC_014312_00118, NC_014312_00116, NC_021502_00131, NC_019155_00032 - - CP010390 0.02768890 770
AI2908_v1_c4 191 39 Browse 1 84 65499 1.52
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
AI2908_v1_c5 191 39 Browse 0 11 9294 10.43
Klebsiella pneumoniae
55.14 Mobilizable ColRNAI_rep_cluster_1857 000003__NC_002119_00001 MOBC NC_009793_00003 - - - - CP009772 0.00009552 762
AI2908_v1_c6 191 39 Browse 0 4 4471 7.39
Escherichia coli
44.42 Non-mobilizable ColRNAI_rep_cluster_1987, rep_cluster_2050 001473__CP024541, 000019__CP000651_00005 - - - - - - CP018739 0.07371050 207
AI2908_v1_c7 191 39 Browse 0 2 1775 1.62
Rahnella sp.
50.08 Non-mobilizable - - - - - - - - CP014779 0.10765800 3204
AI2908_v1_c8 191 39 Browse 0 0 1724 1.66
-
53.89 Non-mobilizable - - - - - - - - CP021680 0.09946980 1068
AI2908_v1_c9 191 39 Browse 0 1 1600 3.22
Citrobacter amalonaticus
49.19 Non-mobilizable - - - - - - - - CP011654 0.15422300 748
AI2908_v1_c10 191 39 Browse 0 0 455 1.51
-, Enterobacter cloacae, Enterobacter hormaechei, Serratia marcescens
47.69 Non-mobilizable - - - - - - - - CP014779 0.12449100 3204
AI2908_v1_c11 191 39 Browse 0 0 329 1.66
-
54.10 Non-mobilizable - - - - - - - - CP021680 0.17440800 1068