C-1 Microbiology Jeff Alder, Ph.D. Vice President, Drug Discovery and Evaluation Cubist Pharmaceuticals

C-1

MicrobiologyMicrobiology

Jeff Alder, Ph.D.Jeff Alder, Ph.D.Vice President, Drug Discovery and EvaluationVice President, Drug Discovery and Evaluation

Cubist PharmaceuticalsCubist Pharmaceuticals

C-2

Analysis of MIC ShiftsAnalysis of MIC Shifts

• Unprecedented microbiology databaseUnprecedented microbiology database– 1,215 1,215 S. aureus S. aureus isolates were tested for MICs isolates were tested for MICs

– First study to examine serial isolate susceptibility in SAB patientsFirst study to examine serial isolate susceptibility in SAB patients

• MIC shifts to MIC shifts to 2 noted 2 noted – Daptomycin- and vancomycin-treated patients Daptomycin- and vancomycin-treated patients

– Different susceptibility criteriaDifferent susceptibility criteria

• Scientific investigations with these isolatesScientific investigations with these isolates– Bacteria, drug, patientBacteria, drug, patient

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Wild-type Distribution of Wild-type Distribution of S. aureusS. aureus Isolates Isolates Includes Daptomycin MICs of 2 Includes Daptomycin MICs of 2 µµg/mLg/mL

No. ofIsolates

MIC90

(µg/mL)Range(µg/mL)

MIC of 2 µg/mLn (%)

Regional Surveys

1998-2003 5,248 0.25 - 1 0.12 -

28 (0.15)

Global Surveillance Studies

1999-2001 2,787 0.25 - 0.5 0.12 -

21 (0.04)

2002 2,623 0.5 0.12 -

22 (0.08)

2003 4,362 0.5 0.12 -

21 (0.02)

2004 5,260 0.5 0.12 -

22 (0.04)

2005 6,374 0.5 0.12 -

23 (0.05)

Total 26,654 NA 0.12 -

217 (0.06)

• MICs of 2 MICs of 2 µµg/mL were observed prior to approval (Sept ’03)g/mL were observed prior to approval (Sept ’03)

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Daptomycin-treated Patients with Post-baseline Daptomycin-treated Patients with Post-baseline Daptomycin MICs of 2 and 4 Daptomycin MICs of 2 and 4

• MIC 4 µg/mL (NMIC 4 µg/mL (N == 1)1)– 1 failure (cRIE; large septic pulmonary emboli, tunnel infection)1 failure (cRIE; large septic pulmonary emboli, tunnel infection)

• MIC 2 µg/mL (NMIC 2 µg/mL (N == 6)6)– 1 success (cBAC; vertebral osteomyelitis, debrided x2) 1 success (cBAC; vertebral osteomyelitis, debrided x2)

– 3 failures (cBAC; IV port infection, septic arthritis, 3 failures (cBAC; IV port infection, septic arthritis, retroperitoneal abscess)retroperitoneal abscess)

– 2 failures (LIE; no valve replacement surgery) 2 failures (LIE; no valve replacement surgery)

• Failed patients did not or could not receive adjunctive Failed patients did not or could not receive adjunctive therapy (e.g., surgery, drainage)therapy (e.g., surgery, drainage)

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Vancomycin-treated Patients with Post-baseline Vancomycin-treated Patients with Post-baseline Vancomycin MICs of Vancomycin MICs of 2 2

• 2 patients by Central Lab testing2 patients by Central Lab testing– 1 success (cRIE)1 success (cRIE)

– 1 failure (cBAC; septic thrombophlebitis)1 failure (cBAC; septic thrombophlebitis)

• 5 additional patients by Local Lab testing5 additional patients by Local Lab testing– 1 failure (LIE; no valve replacement surgery) 1 failure (LIE; no valve replacement surgery)

– 3 failures (cBAC; sternal osteomyelitis, abscesses, ulcers) 3 failures (cBAC; sternal osteomyelitis, abscesses, ulcers)

– 1 failure (uBAC; abdominal wound with mesh) 1 failure (uBAC; abdominal wound with mesh)

• Failed patients did not or could not receive adjunctive Failed patients did not or could not receive adjunctive therapy (e.g., surgery, drainage)therapy (e.g., surgery, drainage)

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Serial Passage Experiments:Serial Passage Experiments:Magnitude of MIC ShiftsMagnitude of MIC Shifts

DaptomycinDaptomycin

CiprofloxacinCiprofloxacin

2020

4040

6060

8080

100100

120120

140140

11 22 33 44 55 66 77 88 99 1010 1111 1212 1313 1414 1515 1616

DayDay

Fo

ld C

han

ge

Fo

ld C

han

ge

[(S

trai

n M

IC/P

aren

t M

IC)-

1][(

Str

ain

MIC

/Par

ent

MIC

)-1]

00

VancomycinVancomycin

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Genes Involved in Genes Involved in S. aureus S. aureus SusceptibilitySusceptibility

Genetic Change*

Isolate Source

Wild-type (Non-exposed)

SAB/SAIEStu

dyClinical

UseSerial

Passage

(MIC 1)

(MIC 2)(MIC 2-

4)(MIC 2-

8)(MIC 2-16)

mprF - yycG - - - rpoB - - - - rpoC - - - -

** Genetic loci identified using whole genome comparisons between CA-MRSA MW2 Genetic loci identified using whole genome comparisons between CA-MRSA MW2 and lab-derived MW2 strains with increasing daptomycin MICsand lab-derived MW2 strains with increasing daptomycin MICs

• mprFmprF mutations: mutations: Part of the wild-type distributionPart of the wild-type distribution

• yycGyycG mutations: mutations: First unique change seen in MIC First unique change seen in MIC 4 clinical 4 clinical isolates, but not seen in wild-type isolatesisolates, but not seen in wild-type isolates

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Genes Involved in Genes Involved in S. aureusS. aureus Susceptibility Susceptibility

** Genetic loci identified using whole genome comparisons between CA-MRSA MW2 Genetic loci identified using whole genome comparisons between CA-MRSA MW2 and lab-derived MW2 strains with increasing daptomycin MICsand lab-derived MW2 strains with increasing daptomycin MICs

Genetic Change*

Isolate Source

Wild-type (Non-exposed)

SAB/SAIE Study

Clinical Use

Serial Passage

(MIC 1)

(MIC 2)(MIC 2-

4)(MIC 2-

8)(MIC 2-16)

mprF - yycG - - - rpoB - - - - rpoC - - - -

• mprFmprF mutations: mutations: Part of the wild-type distributionPart of the wild-type distribution

• yycGyycG mutations: mutations: First unique change seen in MIC First unique change seen in MIC 4 clinical 4 clinical isolates, but not seen in wild-type isolatesisolates, but not seen in wild-type isolates

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17661766

10311031

453453250250275275

Pharmacodynamics of Pharmacodynamics of S. aureusS. aureus in Mice in MiceLab-derived Isolates of CA-MRSA MW2 Lab-derived Isolates of CA-MRSA MW2

Median AUC = 543 µg·hr/mL

with the human 6 mg/kg dose

MIC Value (MIC Value (µg/mLµg/mL))

To

tal A

UC

fo

r 3

log

To

tal A

UC

fo

r 3

log

1010 R

edu

ctio

n R

edu

ctio

n

(µg

·hr/

mL

)(µ

g·h

r/m

L)

00

200200

400400

600600

800800

10001000

12001200

14001400

16001600

18001800

20002000

22 44 88 161611 1010 100100

• MICs MICs 2 respond to similar drug exposure (AUC) 2 respond to similar drug exposure (AUC)• MICs MICs 4 require increasing levels of drug exposure 4 require increasing levels of drug exposure

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Efficacy in Mice Against Baseline and Efficacy in Mice Against Baseline and Post-baseline Isolates from the SAB/SAIE StudyPost-baseline Isolates from the SAB/SAIE Study

152152 212212 105105 037037 183183 136136 172172

Patient Number (Daptomycin-treated)Patient Number (Daptomycin-treated)

To

tal P

lasm

a A

UC

fo

r 3

log

To

tal P

lasm

a A

UC

fo

r 3

log

1010 R

edu

ctio

n R

edu

ctio

n

(µg

·hr/

mL

)(µ

g·h

r/m

L)

00

250250

500500

750750

10001000

12501250

15001500

BaselineBaselinePost-baselinePost-baseline

11001100

537537442442

651651

413413

14201420

713713

Patient-specific AUCPatient-specific AUC

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Daptomycin Penetration into Simulated Daptomycin Penetration into Simulated Endocardial VegetationsEndocardial Vegetations

• Daptomycin penetrates into rat fibrin clots; exerts bactericidal activity Daptomycin penetrates into rat fibrin clots; exerts bactericidal activity

Mortin Mortin et alet al. ASM 2003; Tsuji and Rybak. AAC 2005; Caron . ASM 2003; Tsuji and Rybak. AAC 2005; Caron et alet al. AAC 1992.. AAC 1992.

T = 72h;2 doses

T = 72h;No treatment

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• Daptomycin achieved efficacy at simulated 6 mg/kg doseDaptomycin achieved efficacy at simulated 6 mg/kg dose


T = 72h;2 doses


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• Daptomycin achieved efficacy at simulated 6 mg/kg doseDaptomycin achieved efficacy at simulated 6 mg/kg dose

• 1414C-daptomycin achieved homogenous penetration into C-daptomycin achieved homogenous penetration into rabbit vegetationsrabbit vegetations


T = 72h;2 doses


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Global Surveillance Data (MRSA)Global Surveillance Data (MRSA)

Study YearStudy Year

% I

nci

den

ce%

In

cid

ence

00

1010

2020

3030

4040

5050

6060

7070

2000-20012000-2001 20022002 20032003 20042004 20052005

0.120.12

0.250.25

0.50.5

11

22

MICMIC

Jones Jones et alet al. Annual Surveillance Reports. 2002-2005.. Annual Surveillance Reports. 2002-2005.

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Microbiology SummaryMicrobiology Summary

• Additional investigations due to failures at MIC Additional investigations due to failures at MIC 2 2– Bacteria, drug, patientBacteria, drug, patient

• No decisive bacterial or daptomycin factors No decisive bacterial or daptomycin factors – No trends in surveillanceNo trends in surveillance

– Difficult to select for large MIC increasesDifficult to select for large MIC increases

– Incremental genetic changesIncremental genetic changes

– Modeling shows adequate drug exposure and penetration Modeling shows adequate drug exposure and penetration

• Patient-specific factors likely play a rolePatient-specific factors likely play a role– Complicated infections and outcomesComplicated infections and outcomes

– Adjunctive care importantAdjunctive care important

– Similar observations with vancomycinSimilar observations with vancomycin

Documents

C-1 Microbiology Jeff Alder, Ph.D. Vice President, Drug Discovery and Evaluation Cubist Pharmaceuticals