DELAMANID SUSCEPTIBILITY TESTING IN AN AUTOMATED LIQUID CULTURE SYSTEM

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1 DELAMANID SUSCEPTIBILITY TESTING IN AN AUTOMATED LIQUID CULTURE SYSTEM Daniela Maria Cirillo San Raffaele Scientific Institute, Milan

2 COI/CA OSR as signed MTA with Janssen and Otzuka as SRL and is involved in the development of MGIT test for delamanid OSR has received reimbursement for participation to the reproducibility study sponsored by Janssen OSR is leading the SRLN project partially financed by Otzuka for the development of DLM DST in MGIT

3 DELAMANID (DLM) Delamanid is a nitromidoxazole compound that specifically impairs the bio-synthesis of methoxy- and keto-mycolic acids, by disrupting metabolism of the cell wall (Matsumoto M, 2006, Plos Med). Active on both replicating and not bacilli (Matsumoto M, 2006, Plos Med). Like other Nitroimidazoles, DLM require activation by mycobacterial F420-dependent deazaflavin-dependent nitroreductase (Rv3547 or Ddn) (Matsumoto M. et al., Plos One 2006) Mechanism of resistance: Mutations in genes involved in coenzyme F420 biosynthesis and metabolism [fbia (Rv3261), fbib (Rv3262), fbic (Rv1173), fgd1 (Rv0407)] has been proposed as possible mechanisms of resistance to DLM (Choi KP et al., J. Bacteriol. 2002) Spontaneous rate of resistance to delamanid in in he range of 6.44 x x 10-5 (EMA, 2013)

4 DELAMANID - DELTYBA Well tolerated in TB patients, associated to higher favourable treatment outcomes and significantly lower mortality, not associated with clinically relevant drug-drug interactions (Blair HA, 2015,Drugs; Gler MT, 2012, Engl J Med). Conditional approval by WHO in 2014 for MDR-XDR TB treatment Deltyba has received marketing authorization by the European Medicine Agency and the Japanese Ministry of Health, Labor and Welfare in 2014 (Ryan NJ, 2014, Drugs). Delamanid is available in the UK, Germany and other European Countries for the management of MDR-TB patients and has received conditional approval by the world health organization (WHO).

5 AIMS To develop a standardized protocol for rapid Delamanid (DLM) susceptibility testing (DST) using the semi-automated BACTEC MGIT 960 To define a breakpoint able to accurately discriminate between susceptibility and resistance of Mycobacterium tuberculosis (MTB) towards DLM.

6 EXPERIMENTAL PLAN Validation of the resazurin microtiter assay (REMA) and MGIT MIC against the 7H11 agar based protocol (APM) on a panel of 19 Otsuka precharacterized strains Determination of MIC distribution in REMA and MGIT of clinical isolates never exposed to the drug. Results confirmed by APM WGS of study strains to explore genetic polymorphisms in the five genes involved in the F420 mediated activation

7 7H11/REMA/MGIT µg/ml RESISTANT STRAINS SUSCEPTIBLE STRAINS A break point of 0,2 µg/ml has been proposed by Otsuka based on previous work on a collection of wt and resistant mutant in vitro generated strains The break point has been discussed with the EUCAST committee (0,06 µg/ml)

8 DLM mic Determination of DLM MIC for a panel of 19 reference strains using REMA (from 0,0005 to 32 mg/l), MGIT and 7H11 (from 0,0005 to 16 mg/l) Otsuka has independently established a 7H11-based DST method for testing strains and based on MIC performed on a collection of wt and resistant mutant in vitro generated strains defined a Breakpoint of 0,2 mg/l.

9 MGIT-REMA ON OTSUKA PANEL Code #strain MIC (OTSK) REMA 7H11 MGIT 1 MGIT 2 OTSK N0268 R > 32 > 16 > 16 > 16 OTSK N1002 R OTSK N0185 R > 32 > 16 > 16 > 16 OTSK N0652 R 0,5 1 0,25 0,25 OTSK N0339 S 0,03 0,004 0,016 0,008 OTSK N0085 S 0,008 0,016 0,008 0,004 OTSK N0001 S 0,016 0,016 0,016 0,008 OTSK N0082 S 0,016 0,016 0,008 0,008 OTSK N0299 S 0,008 0,016 0,016 0,01 OTSK N0156 S 0,004 0,004 0,004 0,008 OTSK N0400 S 0,008 0,004 0,004 0,016 OTSK N0117 S 0,008 0,008 0,016 0,008 OTSK N0110 S 0,004 0,016 0,008 0,008 OTSK N0678 S 0,008 0,002 0,004 0,008 OTSK N0097 S 0,008 0,004 0,016 0,016 OTSK N0667 S 0,004 0,004 0,004 0,004 OTSK N0946 S 0,008 0,004 0,004 0,004 OTSK N0193 S 0,03 0,125 0,03 0,03 H37RV S 0,004 0,016 0,004 0,008

10 WGS ON OTSUKA PANEL Code #strain MIC ddn (Rv3547) fgd (Rv0407) fbia (Rv3261) fbib (Rv3262) fbic (Rv1173) Lineage OTSK N0268 R Insertion pos: Phe 320 (silent) wt wt wt Beijing OTSK N1002 R pos CA->C DEL Phe 320 (silent) wt wt wt Beijing OTSK N0185 R INSERTION + GTCA (pos: ) wt wt wt Trp678Gly Leu 55 (silent) LAM OTSK N0184 R Pos G->GTCA INS wt wt wt Trp678Gly Leu 55 (silent) LAM OTSK N0652 R Leu107Pro wt wt wt wt LAM OTSK N0339 S wt wt wt wt wt LAM OTSK N0085 S wt wt wt wt wt LAM OTSK N0001 S wt Phe 320 (silent) wt wt wt Beijing OTSK N0082 S wt Phe 320 (silent) wt wt wt Beijing OTSK N0299 S wt wt wt wt Asp375Asn LAM OTSK N0156 S wt Phe 320 (silent) wt wt wt Beijing OTSK N0400 S wt Phe 320 (silent) Val 5 (silent) wt wt EAI "Manila" OTSK N0117 S OTSK N0110 S wt Phe 320 (silent) wt wt wt Beijing OTSK N0678 S wt wt wt wt wt LAM OTSK N0097 S wt wt wt wt Try678Gly Leu 55 (silent) LAM OTSK N0667 S wt wt wt wt Lys 8 (silent) Euro-Am Sup OTSK N0946 S wt wt wt wt wt Euro-Am Sup OTSK N0193 S wt Phe 320 (silent) wt wt wt Beijing

11 SELECTION OF CLINICAL STRAINS: n 288 America 1% XDR 14% Europe 43% Africa 23% pre-xdr 16% Susceptible 29% Asia 33% MDR 32% NO-MDR 9% TUR 1% Euro- America n Ural Superlin 6% eage Ghana 1% Beijing 38% AFRI II 1% LAM Haarlem 10% 10% EAI 8% Delhi- CAS 5%

12 MIC IN REMA AND MGIT DLM MIC [µg/ml] 0,03 0,06 0,125 0,25 0,5 1 Total Susceptible MDR pre-xdr XDR NO_MDR Total number of strains DLM MIC [µg/ml] 0,03 0,06 0,125 0,25 0,5 1 Total Susceptible MDR pre-xdr XDR NO_MDR Total number of strains

13 EXTENDED MIC in REMA and MGIT

14 CORRELATION MGIT-REMA Table 1. Correlation of drug susceptibility results obtained for 221 clinical strains tested both in MGIT and REMA. Conventional breakpoint of 0.2 mg/l determined by agar proportion method was considered when assigning the definition of Susceptible (S) or Resistant (R)

15 CHARACTERIZATION OF THE 4 DLM RESISTANT STRAINS Strain Lineage Phenotipic DST SNP ddn (Rv3547) fbia (Rv3261) DLM_R1 Beijing MDR tgg->tag W88STOP wt Beijing subfamily W148 DLM_R2 Beijing MDR tgg->tag W88STOP wt DLM_R3 Beijing MDR tgg->tag W88STOP wt DLM_R4 Beijing XDR Aag->Tag wt K250STOP 3 Strains resistant harboured a stop codon mutation in ddn (W88STOP) and 1 FbiA (K250STOP).

16 SNPs IN GENES INVOLVED IN DLM ACTIVATION Genome analysis of the 167 DLM susceptible strains revealed eleven polymorphisms in the five genes associated to drug activation ddn, fgd1, fbia, fbib, fbic leading to amino acid exchanges in 39 (22.8%) out of 171 strains (Table 2). gene Nucleotide change Amino-acid change number of strains with the SNP ddn fbia fbib fbic fgd1 Cgg->Tgg R72W 2 gag->gac E83D 1 cag->cgg Q120R 4 acg->atg T302M 2 ctg->cgg K447R 1 aag->agg L448R 1 Ttc->Ctc F220L 8 Acg->Gcg T273A 5 acc->atc T681I 1 aag->atg* K270M* 13 Aag->Gag* K296E* 1 Two of the identified SNPs were previously described as lineage-specific mutation of Haarlem (K270M) and M. africanum WA2 (K296E) genotypes.

17 MULTICENTER STUDY FOR THE VALIDATION OF BREAKPOINT Validation of breakpoint in MGIT using 75 clinical isolates per study site plus 25 isolates from the original panel in four to six SR laboratories ( tests in total)

18 CONCLUSION DST for DLM can be performed in both MGIT and REMA. We propose mg/l as a breakpoint to screen for DLM sensitivity to this new drug Pre-exposure high level resistance was observed on clinical strains Low level resistance was not observed WGS analysis in genes involved in the activation pathways show presence of several SNPs non related to an increased MIC STOPcodons in the same genes are clearly associated to high level of resistance

19 ACKNOWLEDGEMENTS Otsuka Becton Dickinson San Raffaele Scientific Institute,Milano: S. Battaglia E. Borroni A. Cabibbe A. Trovato E. Schena GMBH, Gouting H. Hoffman S. Hoffman L. Nedialkova Research Center, Borstel M. Merkel C. Upatel S.Niemann SRL network WHO - LDR

20 SNPs in genes involved in DLM activation Phenotype Lineage fgd1 fbia fbib fbic ddn Rv3547 nt change MIC MDR Beijing wt wt wt wt Trp88STOP TGG->TGA 32 MDRGenome Beijing analysis wt of the wt167 DLM wt susceptible wt Trp88STOP strains revealed TGG->TGA eleven 32 MDRpolymorphisms Beijing in the wt five genes wt associated wt to drug wt activation Trp88STOPddn, fgd1, TGG->TGA fbia, fbib, 32 DR EAI wt wt wt wt Arg72Trp AGG->TGG 0,002 MDRfbiC leading Ural to amino wtacid exchanges wt in 39 wt (22.8%) wt out of Glu83Asp 171 strains (Table GAG->GAT 2). 0,001 MDR-AG EAI wt wt wt wt Arg72Trp AGG->TGG 0,004 MDR M. africanum WA2 Lys296Glu* wt wt wt wt AAG->GAG 0,001 MDR Harlem Lys270Ser* wt wt wt wt AAG->ATG 0,004 XDR Beijing Lys250STOP wt wt wt wt AAG->TAG 32 MDR-FQ Eur-Am Superlineage wt Thr302Met wt wt wt ACG->ATG 0,001 MDR Eur-Am Superlineage wt Thr302Met wt wt wt ACG->ATG 0,002 DR Eur-Am Superlineage wt Gln120Arg Phe220Leu wt wt CAA->CGA;TTC->TTA 0,0016 DR Eur-Am Superlineage wt Gln120Arg wt wt wt CAA->CGA 0,008 S Eur-Am Superlineage wt Gln120Arg wt wt wt CAA->CGA 0,004 S Eur-Am Superlineage wt Gln120Arg wt wt wt CAA->CGA 0,008 MDR Beijing wt wt Phe220Leu wt wt TTC->TTA 0,004 MDR Delhi/CAS wt wt Lys448Arg wt wt AAG->AGA 0,008 S Eur-Am Superlineage wt wt Leu447Arg wt wt CTA->CGA 0,004 S Eur-Am Superlineage wt wt wt Thr273Ala wt ACT->GCT 0,002 S Eur-Am Superlineage wt wt wt Thr273Ala wt ACT->GCT 0,004 S Eur-Am Superlineage wt wt Phe220Leu Thr273Ala wt TTC->TTA 0,008 S Eur-Am Superlineage wt wt wt Thr273Ala wt ACT->GCT 0,008 S Beijing wt wt wt wt Thr681Ile ACC->ATC 0,004 Two of the identified SNPs were previously described as lineage-specific mutation of Haarlem (K270M) and M. africanum WA2 (K296E) genotypes.