Ganwu Li Assistant Professor Veterinary Diagnostic Lab at Iowa State University
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- Ashlie Pope
- 5 years ago
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1 Applications of NGS in Clinical Microbiology Ganwu Li Assistant Professor Veterinary Diagnostic Lab at Iowa State University
2 Detect and Identify Pathogens
3 Total reads FastQC and host reads remove Clean reads Kraken Classification by using standard Kraken Database Visualized by Krona Identification of mixed infections Discovery uncharacterized virus Filter reads of interested taxon De novo assemble
4 Identification of Uncharacterized Virus from PEDV Positive Fecal Samples
5 Identification of Mixed-Infections from PEDV Positive Fecal Samples
6 NGS Applications in Viral Comparison (1) MN orf5 OH Can the sequence of single gene provide the breadth of evidence needed for differentiating the whole virus? No!
7 NGS Applications in Viral Comparison (2) Eurasia lineage NA lineage CK/Iowa/2015 (H5N2) TK/Iowa/2015 (H5N2)
8 NGS Application in Public Health Risk Assessment PB2 PB1 PA HA NP NA M NS HA1:S138A M1:T215A NS1: P42S H5N2 Increased pathogenicity
9 NGS Application in Detection of Cell Line Contamination
10 PRRSV Clinical Serum Samples Sample ID Ct Value # Total reads # Reads mapped % reads mapped Full length genome Total Longest bases contig assembled Total gaps Gap Gap Gap Gap <150 <750 <1500 >= % Yes VD_S _S % Yes _S % Yes S4099_S % Yes _S % Yes S5342_S % Yes PRRpig1S % Yes S0652A_S % Yes PRRpig11_S % Yes S5432_S % Yes S4969_S % No S4825_S % No S2154_S % No S _S % No S0652B_S % No
11 PRRSV Clinical Lung Samples Sample ID Ct Value # Total reads # Reads mapped % reads mapped Full length genome Total bases Longest assembled contig Total gaps Gap Gap Gap Gap <150 <750 <1500 >= _S % Yes _S % Yes _S % Yes _S % Yes A_S % Yes _S % No _S % No _S % No _S % No _S % No _S % No A_S % No 71759A_S % No 70451A_S % No
12 PEDV 04/ /2016
13 Bacterial Genomic Epidemiology 95 Hemolytic E. coli from ISU VDL LT: 58.9% (56/96) STa: 31.3% (30/96) STb: 54.2% (52/95) EASTA: 36.5% (35/95) (64/96)(67.4%) Stx1 :3.1% (3/95) (17/95) (17.9%) STX2=STX2e: 21.1% (20/95) 987p:0% F41: 0% K99: 0% K88: 40% F18: 43.2% Paa: 36.8% Novel adhesin: 33.7%
14 Bacterial Resistome Analysis Beta-Lactose Agly Rif Phe Tmt MLS Flq Sul Tet Sample AMPH_Ecoli_Bla AmpC1_Ecoli_BlaAmpC2_EcCMY_Bla CTX-M-1_BOXA-1_BlaPenicillin_Binding_Protein_Ecoli_BlaSCO-1_BlaSHV-OKP-LENTEM-1D_Bla Aac3-IIa_AGly Aac3-Iva_AAac3-VIa_ Aac6-IIc_AAacAad_AAadA4-5_AAadA_AGl AadB_AGlyAph3''Ia_AAph4-Ia_AArmA_AGlRmtE_AGl Sat-2A_AGly StrA_AGly StrB_AGly Arr_Rif CatA1_PheCatA2_PheCatBx_PheCmlA_PheFloR_Phe DfrA19_TmDfrA1_TmtDfrA5_TmtDfrA7_TmtDfrA8_TmtDfrA_Tmt EreA_MLSErm42_MLErmB_MLSMefB_MLSMphA_MLMphB_MLSMphE_MLSMsrE_MLSOqxA_Flq OqxBgb_FQnrB_Flq SulIII_Sul SulII_Sul SulI_Sul TetA_Tet TetB_Tet TetC_Tet TetD_Tet TetM_Tet TetR_Tet 714_S1 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* TetA_ _S10 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* 714_S11 AMPH_615* AmpC1_167 AmpC2_346 Penicillin_Binding_Protein_Ecoli_836 TEM198_135* TetB_1213* 714_S12 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* AadA2_165 Aph3Ia_1218* CmlA1_1537* MefB_123 SulIII_1498 TetB_1213* 714_S13 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836SCO1_881 TEM198_135* Aac3IIa_882 AadA1pm_1597*? Aph3''Ia_1217 StrA_151* StrB_1614 FloR_1212* DfrA8_179 SulII_1219 SulI_1616 TetA_1545*? TetC_ _S14 AMPH_615* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* AadA1pm_1597*? CmlA1_1537*? MefB_123 SulIII_1498 TetB_1213* 714_S15 AMPH_615 AmpC1_167* AmpC2_34CMY33_398* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3IId_884* AadA7_1683 AadA2_165* Aph3''Ia_1217*? StrA_151 StrB_1614 DfrA12_189 MphA_1663 SulI_1616 TetB_1213* 714_S16 AMPH_615* AmpC1_167* AmpC2_346* CMY22_387*? Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3VIa_1452* AadA1pm_1597*? Aph3Ia_1218* StrA_151* StrB_1614 FloR_1212* SulII_1219* SulI_1616 TetA_1545*? 714_S17 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aph3Ia_1218* TetA_ _S18 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* TetA_ _S19 AMPH_615* AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836* TEM135_985* TetA_ _S2 AMPH_615* AmpC1_167* AmpC2_346* CMY31_396* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3Iva_1489* Aac3VIa_1452* AadA22_167* Aph3Ia_1218* Aph4Ia_161 RmtE_647* StrA_151* StrB_1614 FloR_1212*? SulII_1219 SulI_1616 TetA_1545TetB_1213* TetM_831* 714_S20 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM54_917* Aac3Iva_1489* StrA_151 StrB_1614 TetA_ _S21 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* AadA2_165 Aph3Ia_1218* CmlA1_1537* SulIII_1498 TetA_ _S22 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S23 AMPH_615* AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836 AadA2_165 Aph3Ia_1218*? StrA_151* StrB_1614 CmlA1_1537* FloR_1212* DfrA1_319 SulIII_1498 SulII_1219* SulI_1616 TetA_1545*? TetB_1213* 714_S24 AMPH_615* AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836* TEM198_135* AadA5_1497 Aph3''Ia_1217 ArmA_65 StrA_151* StrB_1614 FloR_1212* DfrA1_319* MphE_788*MsrE_33 SulII_1219 SulI_1616 TetA_ _S3 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* AadA6_1682*? DfrA14_322* MphE_788*MsrE_33 SulII_1219 SulI_1616 TetA_1545* TetD_ _S4 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* 714_S5 AMPH_615* AmpC1_167*? AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135*? Aac3Iva_1489* AadA2_165 Aph4Ia_161* StrA_151* StrB_1614 CmlA1_1537* SulIII_1498? SulII_ _S6 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S7 AMPH_615* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836* TEM7_925* StrA_151* StrB_1614 SulII_1219* TetA_ _S8 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* AadA2_165 CmlA1_1537* SulIII_1498 TetA_ _S9 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TetB_1213* 718_S1 AMPH_615* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836* StrA_151* StrB_1614 FloR_1212* SulII_1219 TetA_1545*? 718_S10 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3IIa_882* Aac3Iva_1489* AadA5_1497 Aph3''Ia_1217*? Aph4Ia_161 DfrA17_316 MphA_1663 SulI_1616 TetB_1213* 718_S11 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3Iva_1489* AadA22_167* Aph3''Ia_1217*? Aph4Ia_161 SulI_1616 TetB_1213* 718_S12 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* AadA2_165 Aph3Ia_1218* CmlA1_1537* MefB_123 SulIII_1498 TetB_1213* 718_S13 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM15_956* TetA_ _S14 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S15 AMPH_615* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836* AadA6_1682* CatA2_1182* SulI_1616 TetB_1213* 718_S16 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S17 AMPH_615* AmpC1_167* AmpC2_346* CMY33_398 Penicillin_Binding_Protein_Ecoli_836 AadA2_165 Aph3Ia_1218*? StrA_151* StrB_1614 CmlA1_1537* FloR_1212* DfrA1_319 SulIII_1498 SulII_1219* SulI_1616 TetA_1545*? TetB_1213* 718_S18 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* DfrA5_324 TetA_ _S19 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* 718_S2 AMPH_615* AmpC1_167* AmpC2_346* CMY33_398*? Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3Iva_1489* AadA1pm_1597*? Aph3''Ia_1217* Aph4Ia_161 Sat2A_188 StrA_151 StrB_1614 SulII_1219 TetB_1213* 718_S20 AMPH_615* AmpC1_167* AmpC2_346* CTXM32_156 Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S21 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S22 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* Aph3''Ia_1217* StrA_151 StrB_1614 TetB_1213* 718_S23 AMPH_615* AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836 AadA2_165 Aph3Ia_1218*? StrA_151* StrB_1614 CmlA1_1537* FloR_1212* DfrA1_319 SulIII_1498 SulII_1219* SulI_1616 TetA_1545*? TetB_1213* 718_S24 AMPH_615* AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836 AadA2_165 Aph3Ia_1218*? StrA_151* StrB_1614 CmlA1_1537* FloR_1212* DfrA1_319 SulIII_1498 SulII_1219 SulI_1616 TetA_1545*? TetB_1213* 718_S3 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM34_99* Aac3IIa_882* AadA5_1497AadA2_165 Aph3Ia_1218* CmlA1_1537* MphA_1663 SulIII_1498 SulI_1616 TetA_ _S4 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TetA_ _S5 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* StrA_151 StrB_1614 SulII_1219 TetB_1213* 718_S6 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* 718_S7 AMPH_615* AmpC1_167* AmpC2_346* OXA1_52 Penicillin_Binding_Protein_Ecoli_836* Aac3Iva_1489* Aac6Ibcr_1678* AadA2_165 Aph3Ia_1218* Aph4Ia_161 Arr3_275 CatB4_62 CmlA1_1537* FloR_1212* DfrA12_189 SulIII_1498 SulII_1219 SulI_1616 TetA_ _S8 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* 718_S9 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S1 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3VIa_1452* AadA2_165 Aph3Ia_1218*? CmlA1_1537* SulIII_1498 SulI_1616 TetB_1213* 723_S10 AMPH_615* AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836* Aph3''Ia_1217* StrA_151 StrB_1614 SulII_1219* TetB_1213* 723_S11 AMPH_615* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TetB_1213* 723_S12 AMPH_615* AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836 AadA2_165 Aph3Ia_1218*? StrA_151* StrB_1614 CmlA1_1537* FloR_1212* DfrA1_319 SulIII_1498 SulII_1219 SulI_1616 TetA_1545*? TetB_1213* 723_S13 AMPH_615* AmpC1_167 AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836 AadA2_165 StrA_151 CmlA1_1537* SulIII_1498 TetB_1213* TetM_831* 723_S14 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S15 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* AadA2_165* Aph3Ia_1218* CmlA1_1537* SulIII_1498 TetA_ _S16 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* Aac3Iva_1489* AadA2_165* Aph3''Ia_1217* Aph4Ia_161 DfrA12_189 SulI_1616 TetA_ _S17 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* AadA2_165 Aph3Ia_1218*? StrA_151 StrB_1614 CmlA1_1537* SulIII_1498 TetB_1213* 723_S18 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* 723_S19 AMPH_615* AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aph3Ia_1218* StrA_151* StrB_1614 FloR_1212* SulII_1219 TetA_ _S2 AMPH_615 AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836* StrA_151 StrB_1614 TetB_1213* 723_S20 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* AadA3_161* Aph3Ia_1218* CmlA1_1537* SulIII_1498? TetA_ _S21 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* 723_S22 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S23 AMPH_615 AmpC1_167* AmpC2_346 Penicillin_Binding_Protein_Ecoli_836 AadA5_1497 StrA_151* StrB_1614 CatA1_147* DfrA17_316 SulII_1219* SulI_1616 TetB_1213*? 723_S24 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aph3Ia_1218* TetA_ _S3 AMPH_615* AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836 AadA2_165 Aph3Ia_1218*? StrA_151* StrB_1614 CmlA1_1537* FloR_1212* DfrA1_319 SulIII_1498 SulII_1219 SulI_1616 TetA_1545*? TetB_1213* 723_S4 AMPH_615* AmpC1_167 AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* SulII_1219 TetB_1213* 723_S5 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* TetA_ _S6 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM76_929* Aac3Iva_1489* AadA2_165 Aph4Ia_161* StrA_151* StrB_1614 CmlA1_1537* SulIII_1498 SulII_1219 TetB_1213*? 723_S7 AMPH_615* AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836 AadA2_165 Aph3Ia_1218*? StrA_151* StrB_1614 CmlA1_1537* FloR_1212* DfrA1_319 SulIII_1498 SulII_1219* SulI_1616 TetA_1545*? TetB_1213* 723_S8 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* AadA1pm_1597*? StrA_151 StrB_1614 DfrA1_319* SulI_1616 TetA_ _S9 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* AadA1pm_1597*? Aph3Ia_1218* CmlA1_1537* SulIII_1498 TetA_ _S1 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* 724_S10 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3Iva_1489* AadA22_167* Aph3''Ia_1217*? Aph4Ia_161 SulI_1616 TetB_1213* 724_S11 AMPH_615 AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836* AadA2_165AadB_185 Aph3Ia_1218*? StrA_151 StrB_1614 CmlA5_1538* SulIII_1498 SulII_1219 TetB_1213* 724_S12 AMPH_615 AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836* Aac3Iva_1489* AadA2_165 Aph3''Ia_1217*? Aph4Ia_161* StrA_151 StrB_1614 CmlA1_1537* FloR_1212 DfrA12_189 MphA_1663 SulIII_1498 SulII_1219 SulI_1616 TetA_1545*? TetB_1213* 724_S13 AMPH_615* AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836* TEM33_98* Aac3IId_884* AadA5_1497 Aph3Ia_1218* StrA_151* StrB_1614 DfrA17_316 MphA_1663 SulII_1219* SulI_1616 TetB_1213* 724_S14 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM7_925* Aac3IId_884* AadA7_1683 AadA2_165* Aph3''Ia_1217*? StrA_151 StrB_1614 DfrA12_189 MphA_1663 SulI_1616 TetB_1213* 724_S15 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TetA_ _S16 AMPH_615* AmpC1_167* AmpC2_346* OXA1_52 Penicillin_Binding_Protein_Ecoli_836* Aac3Iva_1489* Aac6Ibcr_1678* AadA2_165* Aph3Ia_1218* Aph4Ia_161 Arr3_275 CatB4_62 CmlA1_1537* FloR_1212* DfrA12_189 OqxA_144OqxBgb_49 SulIII_1498 SulII_1219 SulI_1616 TetA_ _S17 AMPH_615* AmpC1_167* AmpC2_346* OXA1_52 Penicillin_Binding_Protein_Ecoli_836* Aac3Iva_1489* Aac6Ibcr_1678* AadA2_165* Aph3Ia_1218* Aph4Ia_161 Arr3_275 CatB4_62 CmlA1_1537* FloR_1212* DfrA12_189 SulIII_1498 SulII_1219 SulI_1616 TetA_ _S18 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* 724_S19 AMPH_615* AmpC1_167 AmpC2_346 Penicillin_Binding_Protein_Ecoli_836 TEM198_135* AadA1pm_1597*? CmlA1_1537*? MefB_123 SulIII_1498 TetB_1213* 724_S2 AMPH_615* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM15_999* AadA2_165 CmlA5_1538* DfrA15b_321* SulI_1616 TetA_ _S20 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* StrA_151 StrB_1614 TetB_1213* 724_S21 AMPH_615 AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836* AadB_185 StrA_151 StrB_1614 CmlA5_1538 FloR_1212* SulII_1219 TetA_1545*? TetB_1213* 724_S22 AMPH_615 AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836* AadA1pm_1597*? AadB_185 StrA_151* StrB_1614 CmlA5_1538* FloR_1212* SulIII_1498 SulII_1219 TetA_1545*? 724_S23 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* SHV12_1288 TEM33_98* Aac3Iva_1489* Aac6IIc_1195 Aac6Ib_1677*? AadA2_165 Aph3''Ia_1217*? Aph4Ia_161 StrA_151 StrB_1614 DfrA19_122* DfrA12_189* EreA_839* QnrB2_11 SulIII_1498 SulII_1219 SulI_1616 TetB_1213* TetD_ _S24 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* AadA2_165* CmlA1_1537* DfrA12_189 ErmB_841*? SulIII_ _S3 AMPH_615 AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836* 724_S4 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* TetA_ _S5 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S6 AMPH_615* AmpC1_167* AmpC2_346* CMY44_49 Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3VIa_1452* AadA1pm_1597*? Aph3''Ia_1217*? StrA_151* StrB_1614 FloR_1212* SulII_1219 SulI_1616 TetA_ _S7 AMPH_615* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM33_98* AadA4_1496* SulII_1219 SulI_1616 TetB_1213* 724_S8 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* TetA_ _S9 AMPH_615* AmpC1_167* AmpC2_346* CMY33_398*? Penicillin_Binding_Protein_Ecoli_836* TEM198_135* SulII_1219 TetA_ _S1 AMPH_615 AmpC1_167* AmpC2_346* CMY44_49* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* Aac3Iva_1489* AadA6_1682* AadA2_165 Aph4Ia_161 StrA_151* StrB_1614 DfrA14_322* DfrA12_189* MphB_1639 SulIII_1498 SulII_1219 SulI_1616 TetA_1545*? 725_S10 AMPH_615 AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836* Aac3Iva_1489* AadA2_165 Aph3Ia_1218* Aph4Ia_161* StrA_151 StrB_1614 CmlA1_1537* FloR_1212 DfrA12_189 MphA_1663 SulIII_1498 SulII_1219 SulI_1616 TetA_1545*? TetB_1213* 725_S2 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* 725_S3 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM14_955* AadA5_1497AadA1pm_1597*? Aph3Ia_1218* CmlA1_1537* DfrA17_316 ErmB_841*? MphA_1663 SulIII_1498 SulI_1616 TetA_ _S4 AMPH_615 AmpC1_167* AmpC2_346* CMY33_398 Penicillin_Binding_Protein_Ecoli_836* Aac3VIa_1452* Aph3Ia_1218*? RmtE_647* StrA_151* StrB_1614 FloR_1212* SulII_1219? SulI_1616 TetA_1545 TetM_831* 725_S5 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* Aph3Ia_1218* TetA_ _S6 AMPH_615* AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM198_135* SulII_1219 TetA_ _S7 AMPH_615 AmpC1_167* AmpC2_346* Penicillin_Binding_Protein_Ecoli_836* TEM186_124* Aac3Iva_1489* AadA5_1497AadA2_165* Aph3''Ia_1217 Aph4Ia_161ArmA_65 DfrA1_319* MphE_788*MsrE_33 SulI_ _S8 AMPH_615* AmpC2_346*? CMY33_398 Penicillin_Binding_Protein_Ecoli_836*? 725_S9 AMPH_615* AmpC1_167* AmpC2_346* CMY33_398* Penicillin_Binding_Protein_Ecoli_836* TEM112_963*? AadA2_165 Erm42_164 SulII_1219 TetA_1545
15 Microbiota Analysis
16 Next-Generation Sequencing Center at the Iowa State University Veterinary Diagnostic Laboratory The ISU VDL Next-Generation Sequencing Center offers a range of services based on genomic epidemiological, metagenomics, and transcriptomic analyses using Next- Generation Sequencing Technology combined with bioinformatics analyses. This novel and powerful technology provides a potentially game-changing opportunity in veterinary diagnostic and clinical medicine Services provided: Novel/uncharacterized pathogen detection Mixed infection detection $400.00/library/sample $400.00/library/sample Viral whole genome sequencing $300.00/cell culture isolate sample; $300.00/infected or clinical tissue sample* 16s metagenomics analysis Inquiry Shotgun metagenomics sequencing $300.00/sample ($150.00/sample if sample number is more than 96) Bacterial genomic epidemiological analysis $200.00/strain ($100.00/strain if strain number is more than 96) o Phylogenetic analysis based on maximum-common genome sequence Contact Information o Virulome (a set of virulence genes) analysis o Resistome (a set of antibiotic resistance genes) analysis Turnaround time: 1-2 weeks (bacterial genomic analysis: 1-2 months). The service fee includes costs for NGS library preparation, library sequencing, and bioinformatics analysis, but not the submission fee. *Please inquire if the Ct value of the clinical samples is more than 24. Advantages: The hypothesis-free metagenomics strategy enables NGS to simultaneously detect mixed infections of different microorganisms and identify novel and/or uncharacterized pathogens directly from clinical samples requiring no prior knowledge of the pathogen(s). Compared to traditional epidemiology, genomic epidemiology based on whole genome sequences is the ultimate source of information and may never be superseded. Next-Generation Sequencing Center, Veterinary Diagnostic Laboratory College of Veterinary Medicine Iowa State University 1802 University Blvd., VMRI#1 Ames, IA Phone: liganwu@iastate.edu
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