Collection SERGAS
Isolation Year 2017
Isolation Location Hospital Virgen de la Macarena (Sevilla)
Hospital Admission Unit Internal medicine
Patient Sex F
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 395:gapA(3), infB(1), mdh(2), pgi(4), phoE(1), rpoB(1), tonB(4)
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 >128 R R
CEF >128 R R
AZT >128 R R
MEM 32 R R
IMI 16 R R
IMI-RELE 16 R R
ERT 16 R R
FOSFO >256 R R
GENTA >256 R R
TOBRA >256 R R
AMK >128 R R
CIP 128 R R
COLIS <0.06 WT S
AI2934_v1
AI2934_v1

Sample 220 was assembled with Unicycler_v0.4.6 into 13 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
AI2934_v1_c1 220 395 Browse 30 5147 5410164 1.00
Klebsiella pneumoniae
57.30 Non-mobilizable - - - - - - - - CP007734 0.21953100 1586
AI2934_v1_c2 220 395 Browse 10 149 119538 2.21
Klebsiella pneumoniae
52.38 Conjugative IncR, IncL/M 000148__NC_021488_00028, 000204__CP008701_00115 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 0.01638660 681
AI2934_v1_c3 220 395 Browse 4 115 106240 2.18
Klebsiella pneumoniae
55.05 Conjugative IncFII, IncFIB 000114__CP015527, 000122__JQ418538, 000101__NZ_CP012345_00042 MOBF NC_021501_00073 MPF_F NC_021501_00097, NC_006323_00096, NC_006323_00097, NC_009378_00101, NC_006323_00105, NC_021501_00085, NC_021501_00084, NC_021501_00083, NC_006323_00113, NC_021501_00076, NC_021501_00074 - - KC887916 0.00060662 621
AI2934_v1_c4 220 395 Browse 1 105 84622 1.59
Klebsiella pneumoniae
51.92 Conjugative IncFII, rep_cluster_1418 000759__NC_013950_00034, 000126__FO834904 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 - - CP021946 0.02840570 1585
AI2934_v1_c5 220 395 Browse 0 27 35804 3.28
Klebsiella pneumoniae
58.51 Non-mobilizable - - - - - - - - CP003120 0.26302200 1350
AI2934_v1_c6 220 395 Browse 0 6 5010 13.62
Klebsiella pneumoniae
44.01 Non-mobilizable - - - - - - - - CP018665 0.10604700 207
AI2934_v1_c7 220 395 Browse 0 4 3511 23.62
Klebsiella pneumoniae
54.51 Mobilizable ColRNAI_rep_cluster_1987 000019__CP000651_00005 MOBP NC_001848_00006 - - MOBP CP008720 JQ319770 0.00045892 192
AI2934_v1_c8 220 395 Browse 0 1 1332 2.10
Klebsiella pneumoniae
47.97 Non-mobilizable - - - - - - - - KJ187751 0.14383000 449
AI2934_v1_c9 220 395 Browse 0 0 1073 1.99
Klebsiella michiganensis, Klebsiella pneumoniae
43.24 Non-mobilizable - - - - - - - - MF543359 0.15422300 721
AI2934_v1_c10 220 395 Browse 0 0 436 4.19
Citrobacter sp., Escherichia coli, Klebsiella michiganensis, Klebsiella pneumoniae, Salmonella enterica
58.49 Non-mobilizable - - - - - - - - AY033498 0.08576080 1565
AI2934_v1_c11 220 395 Browse 0 0 363 4.20
-
54.55 Non-mobilizable - - - - - - - - MF543359 0.13857200 721
AI2934_v1_c12 220 395 Browse 0 0 257 2.18
Citrobacter sp., Klebsiella michiganensis, Klebsiella pneumoniae
42.02 Non-mobilizable - - - - - - - - CP018359 0.13694800 201
AI2934_v1_c13 220 395 Browse 0 0 112 4.17
-
54.46 Non-mobilizable - - - - - - - - MF543359 0.18226900 721