Posey: The Imipact of Genomics Era on Mtb Research. 2/26/16- TB Genomics MOLECULAR EPIDEMIOLOGY

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1 The Impact of Genomics Era on Mycobacterium tuberculosis Jamie Posey, PhD pplied Team Lead National enter for HIV/IDS, Viral Hepatitis, STD, and TB Prevention Division of Tuberculosis Elimination NGS Platforms MOLEULR EPIDEMIOLOGY 1

2 luster 1 ~ 1 Patients DRUG RESISTNE onventional Drug Susceptibility Testing q Growth based Time consuming (week to month) Laborious Infrastructure q Liquid or solid media Equivalent concentrations? q ritical concentration q Minimum inhibitory concentration 2

3 Drug Resistant Survey q Based on phenotypic assays Some countries perform routine DST Resource-limited areas (once every 3-5 years) Lack infrastructure q an we use molecular assays? Do we have the knowledge What tools are needed q Rifamycin resistance Role of mutations rpob Surveillance q Frequency of mutations Population level ssay development q Importance of data alculate sensitivity and specificity of assays Silent mutations How much phenotypic resistance is missed What is the affect on patient outcome Fusion Primers for Ion Torrent PGM RRDR 3

4 Rifampin Resistant Determining Region (RRDR) of rpob rpob Surveillance q 14 months >1, isolates q Mutations 411 isolates (35 unique mutations) Ser531Leu (184 isolates) Silent mutations (94 isolates) RESERH 4

5 reas to ddress q Identify new mechanisms of drug resistance Existing and new drugs q Identify preexisting resistance Repurposed and new drugs q Microevolution in the patient q ompensatory mutations B B B B B 19 B 58 bp G 31998G upstream Rv29 T T acn T 5143T Rv47c G T T Rv12 T T T Rv27c G T T PE_PGRS T 5 G G Rv398c T mmpl1 G G fabg1 T pks pks9 G 171 bp T28776 upstream of Rv1838c Rv2112c T G Rv2142c G G ubie T 46 bp T upstream Rv2339 T T rpob G G G rpo G G G Rv698 G G95686 G Rv811c G PE_PGRS T G betp G T PE_PGRS T G G 17 G G Rv997 G T Rv184 T T T Rv114 G T bpob T T Rv1139c G T T fdx T G Rv2449c G Rv2631 G Rv2819c G ech lepb T PPE PPE Rv355 G Rv388 T G36847 Rv323c PPE56 T G PPE spou pap3 G 5 bp upstream G Rv3585 G G G tag G Rv1272c T G G PE_PGRS 59 T Rv3633 G top bfrb G 5

6 Identify New Mechanisms of Resistance fabg1 inh L23L silent mutation in mab confers isoniazid resistance on Mycobacterium tuberculosis. ndo H, Miyoshi-kiyama T, Watanabe S, Kirikae T. inh Transcript Levels LINIL MNGEMENT 6

7 Starting Material Sputum Dx ulture Subculture WGS versus Targeted pproach q WGS Need a culture High molecular weight DN (1 5 ug) nalyze about 9 99% of genome Low to medium throughput q Targeted loci ould possibly start with processed sputum PR based Lower quality and quantity of DN Only analyze the areas amplified High throughput Sensitivity and Specificity of Loci Drug Gene(s) Sensitivity (%) Specificity (%) RIF rpob INH inh, katg EMB embb FQ gyr KN rrs, eis MK rrs P rrs, tly MDR rpob, inh, katg

8 Retrospective DR Study and MDDR Service Sensitivity and Specificity of Loci Drug Gene(s) Sensitivity (%) Specificity (%) RIF rpob INH inh, katg EMB embb FQ gyr KN rrs, eis MK rrs P rrs, tly Molecular Detection of Drug Resistance q Original assay 8 single PR reactions Sanger DN sequencing 16 sequencing reactions q High throughput assay NGS Ion Torrent PGM Multiplex PR Barcoded 96 samples per assay Targeted Loci DRUG Gene Region Rifampin rpob 176 and RRDR Isoniazid katg 315 inh Promoter Ethambutol embb ERDR Pyrazinamide pnc Promoter and ORF Fluoroquinolones gyr QRDR gyrb QRDR Kanamycin eis Promoter rrs 141 mikacin rrs 141 apreomycin rrs 141 tly Promoter and ORF 8

9 Workflow mplify targets (page 15) Genomic DN Partially digest primer sequences (page 17) mplify targets using Ion mpliseq Primer Pool Ligate adapters to the amplicons and purify (page 17) Partially digest primer sequences Option 1: Equalize the library (page 19) Option 2: Quantify the unamplified library by qpr (page 21) Option 3: Quantify the amplified library with the Qubit 2. Fluorometer or gilent 21 Bioanalyzer instrument (page 23) dapters P1 OR Barcode dapters X P1 X OR Ligate adapters P1 Nonbarcoded library P1 Barcoded library ombine libraries (optional) and proceed to template preparation. Pilot Study q 8 and 48 samples q Use crude DN preps q ompare Ion Torrent data to Sanger sequence Number of Reads Per Sample Sample Number of Reads MLB2 1,39 MLB18 55,99 MLB36 4,246 MLB138 5,715 MLB149 51,144 MLB176 4,525 MLB27 98,238 MLB224 5,865 9

10 > SNP Report MID Ref'Pos Type Ref'Base alled'bassnp'% Feature'Name mino'cdepth MLB SNP G 97.7% embb G MLB SNP G 99.2% embb L355L 1658 MLB SNP 95.9% embb E MLB SNP G 9.9% gyr S95T 22 MLB SNP G 9.3% gyr S95T 944 MLB SNP G 72.% gyr S95T 1 MLB SNP G 84.% gyr D94G 1 MLB SNP G 9.% gyr S95T 964 MLB SNP G 89.8% gyr S95T 2538 MLB SNP G 91.8% gyr S95T 1279 MLB SNP G 89.2% gyr S95T 869 MLB SNP T 99.5% gyr 9V 83 MLB SNP G 99.6% katg S315T 138 MLB SNP G 99.6% katg S315T 2475 MLB SNP G 99.3% katg S315T 957 MLB SNP T 78.3% pnc V139M 272 MLB SNP G 99.8% pnc Y13H 846 MLB SNP G 98.7% pnc 17V 1475 MLB SNP G 78.9% pnc V MLB SNP T 6.% rpob L452P 25 MLB SNP T 99.1% rpob S45L 9 MLB SNP T 99.5% rpob S45L 1577 SNP Report MLB SNP T 99.1% rpob S45L 68 MLB SNP G 99.8% rrs 551 MLB SNP G 35.% rrs 2 MLB SNP G 99.8% rrs 1658 MLB SNP G 93.1% tly L11L 159 MLB SNP G 96.4% tly L11L 863 MLB SNP G 97.4% tly L11L 76 MLB SNP G 98.9% tly G195D 89 MLB SNP G 97.% tly L11L 943 MLB SNP G 96.6% tly L11L 1511 MLB SNP G 97.4% tly L11L 1337 MLB SNP G 96.3% tly L11L 934 MLB SNP G 96.5% tly L11L 818 1

11 Number of Reads Per Sample (48) 48, 32, 16, 3 overage Depth 25 # Reads overage Depth # Reads

12 Summary and Next Steps q Pilot project 8 samples completed and 1% agreement with Sanger data 48 samples analyzing data q Quality and quantity of DN q Determine the minimal coverage and number of reads q Scale up to 96 samples q Test processed specimens METGENOMIS Starting Material Sputum Dx ulture Subculture 12

13 Synthetic Dilution Series Strategy Pure gdn dilution to extinction Mtb, STE, diff gdn/grn dilution to extinction in complex background Mtb/Sputum STE/Stool Influenza/549 RN O43 oronavirus/549 RN Targeted enrichment study Background depletion study Mtb Sputum Synthetic Sets reate seven sets of dilutions (1 x 5 µl ea.) in a constant background of Sputum gdn (25 ng µl -1 ) Mtb IS611 RT-PR Dilution Unspiked Sputum t >4 Dilution 1 1% Mtb t 13. ±.16 Dilution 2 1% Mtb t 16.7 ±.12 Dilution 3.1% Mtb t 2.1 ±.5 Dilution 4.1% Mtb t 23.5 ± t 4 Dilution 5.1% Mtb t 27.1 ±.15 Dilution 6.1% Mtb t 3.4 ±.12 5 aliquots of each dilution sampled at random assayed in triplicate RT-PR DN Targeted Sequence Enrichment Strategy ommercial and lab developed kits gilent SureSelect Roche NimbleGen Seqap NuGEN Select ustom assays Three initial designs for each approach Mtb H37Rv STE O157:H7 Sakai Influenza H3N2 /Texas/5/212 13

14 gilent SureSelect Roche NimbleGen Seqap Roche Targeted Sequence Enrichment Project Workflow MTb gdn + Sputum gdn at different ratios ll 25 ng ul -1 MTb % KP-Based Library Prep Sequence apture MiSeq Sequencing and nalysis 14

15 Mtb Sputum Roche TE nalysis Pre Treatment/ No Enrichment Read ount Normalized Number of Reads Other Mtb Human Q % Mtb DN in Original Sample Mtb Sputum Roche TE analysis Pre Treatment/ No Enrichment No Spike 1% 1%.1% 554, % , 4% , 3% 24328, 4% , 12682, 5% % 1548, % , 5% , 96% 51317, 93% , 95% , 95%.1%.1%.1% 214, % 32365, 5% 14, % , 5% 72, % , 5% 65139, 95% , 95% , 95% Mtb Sputum Roche TE analysis - Pre Treatment/ No Enrichment % Genome overed Percent overage (Reference Base pairs overed) Fold Genome overage verage Read Depth % Mtb in Original Sample Mtb in Original Sample 15

16 Mtb Sputum Roche TE analysis - Pre Treatment/ No Enrichment 1% Mtb H37Rv Genome PosiXon 1% Mtb H37Rv Genome PosiXon.1% Mtb 16 Gene: rrs (16S) 14 Gene: rrl (23S) 12 Gene: rrf (5S) H37Rv Genome PosiXon t decreasing levels of Mtb genome sequence present in samples mappers appear to erroneously attribute other 16S sequence in background sputum to the reference genome Mtb Sputum Roche Post Enrichment nalysis Read ount Normalized Number of Reads Other Mtb Human Q % Mtb in Original Sample Mtb Sputum Roche Post Treatment nalysis No Spike 1%.1% 37984, 1% 43128, 6% , 6% , 9% , 6% , 13% , 85% , 81% , 93%.1%.1%.1% , 7% , 54% , 39% 47228, 8% , 8% , 84% , 9% 11454, 2% , 89% 16

17 Mtb Sputum Roche Post Enrichment nalysis Percent overage (Reference Base Pairs overed) % Genome overage % Mtb in Original Sample Fold Genome overage verage Read Depth % Mtb in Original Sample Mtb Sputum Roche Post Enrichment nalysis No Spike Gene: rrs (16S) Gene: rrl (23S) Gene: rrf (5S) % % %.1%.1% Mtb Sputum Roche TE overage Percent overage (Reference Base pairs overed) No Enrichment % Genome overed % Mtb in Original Sample 1 Percent overage (Reference Base Pairs overed) Post Enrichment % Genome overage % Mtb in Original Sample 17

18 Mtb Sputum Roche verage Depth verage Read Depth No Enrichment Fold Genome overage % Mtb in Original Sample Fold Genome overage verage Read Depth Post Enrichment % Mtb in Original Sample Drug Resistant Genes Drug Resistant Genes 18

19 % Reads % Reads BL R V D94N S95T BL R % Reads % Reads BL R 2 1 D94 S95T BL R 4 1 S95 D94 S95T % Reads % Reads Q R D94G Q R 3 S95T G88 D89G 9V D94N D94G S95T Q R % Reads D94Y D94G S95T Q R % Reads 9V D94N D94 S95T Molecular Epidemiology Drug Resistance Metagenomics 19

20 cknowledgements q q q Laboratory Branch / pplied Team Melisa Willby Paige hopra Paul Grwzybowski Lauren owan Metagenomics Group hris Hopkins Eishita Tyagi Scott Burns ore Facility Mike Frace Scott Sammons Kristen Knipe 2