Cepheid GeneXpert clinical value and product details 佑康公司 楊瑞萍 Kelly.

Cepheid GeneXpert clinical value and product details

佑康公司 楊瑞萍 Kelly

2 |INTERNATIONAL DISTRIBUTOR MEETING INTERNAL USE ONLY Product availability based on timing of FDA submission in US*Exclusively distributed worldwide by Instrumentation Laboratories

The System Approach:

It’s All about the Efficiency

Cepheid GeneXpert Product offerOct.2009 – CE IVD Menu of Xpert Assays

• Xpert MRSA , Preventing MRSA infections and transmission• Xpert MRSA/SA Nasal , Pre-surgical screening to prevent surgical site infections• Xpert MRSA/SA BC , Diagnosing S.aureus blood stream infections• Xpert MRSA/SA SSTI , Diagnosing S.aureus skin and soft tissues infections• Xpert C.difficile , Diagnosing CDI (Clostridium difficile infection)• Xpert vanA/vanB , Preventing VRE spread and outbreaks

• Xpert MTB/RIF , Diagnosing tuberculosis and drug resistance• Xpert GBS , GBS screening to prevent neonatal Group B Strep disease• Xpert EV , Diagnosing Enterovirus meningitis

• Xpert BCR ABL , CML treatment monitoring• Xpert Factor II and V , Deep venous thrombosis

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GeneXpert® Platform Strategic Reach

GX-IGX-I GX-IVGX-IV GX-XVIGX-XVI InfinityInfinity

GeneXpert ModuleGeneXpert Module

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Our System ApproachVersus a random competitor

Gen-Probe• Fixed Analyzer Format• Old “batch” Technology• 4 Assays On-board• 1 Test on Menu• Narrow Future Menu Focus• Single Technology (dated)• Labor Intensive• Low Test / m2

Cepheid• Scalable Configuration• Total Random Access• Limited only by Menu• 13 Tests on Menu• Broad Future Menu• Multiple Technologies• Easy to Use• High Tests / m2

VS.ANALYZERSystem

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Patient Care Continuum

Time & ResourcesTriage Dispo

Admit

ExamLab

Imaging

Consult

Transfer

Pharma

7 |INTERNATIONAL DISTRIBUTOR MEETING INTERNAL USE ONLY

Patient Care Continuum

Time & ResourcesTriage Dispo

Admit

ExamLab

Imaging

Consult

Transfer

Pharma

Overall Reduction due to Elimination

of Waste

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• 金黃色葡萄球菌是臨床上相當重要的致病菌，抗藥性金黃色葡萄球菌（ MRSA ）也被歸類為超級細菌之一，近 10 年來曾在社區出現流行，尤其造成兒童感染嚴重病例不少，甚至造成死亡。

• 林口長庚兒童醫院兒童感染科醫師陳志榮在 2005 到 2008 年研究，針對 6000 多名孩童採鼻腔檢體分析，結果發現，台灣 5 歲（含）以下健康兒童，有 7.8% 鼻腔帶菌，且帶菌率在 3 年間顯著上升。

• 值得注意的是，前陣子 H1N1 新型流感疫情高峰時，臨床發現患者續發細菌性肺炎也是近 10 年來最嚴峻的，其中有些就是 MRSA 細菌感染引起。

• 此外，陳志榮分析院內 2004 年到 2006 年間重覆感染 MRSA 的病童與感染菌株，共有48 位孩童有 2 次以上 MRSA 感染，且 7 成是由同一株 MRSA 引起，甚至有病童在相隔超過 11 個月後再次感染 MRSA ，仍是同一株細菌，顯示細菌未被根除，仍在鼻腔等處帶菌，等待孩童免疫力低下時，又再度造成感染。

• 這項研究顯示，大多數的重複感染來自於病患自身所帶的細菌，因此，醫師積極主動篩檢，並有效投藥去除帶菌，例如鼻腔抹藥或以特定殺菌劑讓患者洗澡，才是杜絕大部分MRSA 重複感染的有效方法。

MRSA 超菌 孩童鼻腔帶菌高2011/04/19 中央社記者陳麗婷台北 19日電

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• C.difficile （梭狀芽胞桿菌）是最常見可被辨識出來會導致感染愛滋病患者腹瀉的細菌

• 細菌性腹瀉的發生率為每年每 1000 人中有 7.2 人，且直接和患者的免疫力被抑制有關連

• 在引起疾病的有機物中， C.difficile （梭狀芽胞桿菌）佔了 54%, ，賀氏菌(Shigella species) 佔了 14%

• 主要的復發危險因子有年紀增長，使用抗生素及住院治療

• 及時檢測成本效益 : 降低抗生素使用、 減少腸道檢查 ( 結腸鏡檢查、 影像診斷學 ) 以及不必要手術干預

• C.difficle 感染平均將增加病患在醫院 5-6天的留置時間，將增加病患在醫院的醫療成本

• Xpert C.difficle 除針對懷疑 CDI 感染患者作快速篩檢之外， 更能針對 GDH(+) 檢體進行確認 C.difficle產毒菌種是否存在

C.difficile

Xpert MTB Agenda

• Background: tuberculosis infection and disease

• Current testing algorithms

• Clinical value of Xpert MTB/RIF

• Xpert MTB/RIF: product details

• Xpert MTB/RIF: latest clinical experience

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Tuberculosis: an important public health concern

• Bacterial disease, airborne – transmitted caused by M.tuberculosis

• 1/3 world population latently infected: 2 billion people

• ~9.3 million of new cases in 2007 and 1.8 million deaths

• TB the second most deadly infectious disease worldwide after HIV/AIDS.

• Most of the cases occur in the developing world.

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TB burden, Taiwan

結核病一直是台灣最嚴重的傳染疾病，到國民所得已超過一萬三千美元的今天，每年仍有將近約一萬三千名的新發個案，其嚴重性比所有其他傳染病的總和還大。 ( 行政院衛生署 結核病十年減半第二期計畫書 )

How Much Does TB Cost?

Sources:* 中國醫藥大學馬作金強助理教授 -住院治療結核病患之成本效益評估研究

20120.68 元 (OPD)* ； 166983.35 元 (山地鄉 )*

Average cost of treating a case of TB

X

14265Annual incidence in Taiwan

=

＄約 2 億 8 千 7 百萬 (OPD)Annual cost in Taiwan

PAGE | 14

Tuberculosis infection versus active disease

Inhalation (1–5 μm Ø)

droplet infection

No infection 10–30% infection

90% LTBI 5–10% ACTIVE TB within 2 years 10% TB during lifetime

10% TB within 1 year if HIV+

85% pulmonary TB15% extrapulmonary TB

33% pulmonary TB33% extrapulmonary TB33% both

HIV- HIV+

14265 人 / 2008 年 TB新案數

14265*1/3= 4755 人

4755*5%=237.75(2年新增開放性 TB病患 )

1st line and 2nd line antibiotics

 Usual treatment regimens for new cases:- 2 months therapy with 4 drugs: rifampicin + Isoniazid + pyrazinamide + ethambutol - followed by a 4 months treatment with rifampicin + isoniazid 

PAGE | 16

Drug resistant TB

• Jeopardizing TB control programmes

• MDR TB = Resistance to at least Isoniazid (INH) and Rifampicin (RIF)

• XDR TB = Resistance to al least isoniazid and rifampicin + any of the fluoroquinolones + any of the three injectable drugs : Amikacin, Capreomycin , Kanamycin

PAGE | 17

RIF resistance as surrogate marker for MDR TB

• RIF resistance as a mono resistance not very frequent (5-15% of them)

• 80-95% of RIF resistant strains are also resistant to INH

Current diagnostics and patient management

PAGE | 19

The problem with current testing methods

• Smear test (AFB):• Insensitive, WHO and national guidelines recommend 2

to 3 smear tests to be performed by suspected patient• Requires highly skilled technician• Time consuming: 1-2 hours

• Culture• Highly sensitive• Slow: 4 to 6 weeks

• Current/previous Nucleic Acid Amplification methods:• Time consuming and requiring highly skilled personnel• Highly specific• Not optimal on clinical samples:

• Highly sensitive on smear positive samples (95-100%)• Until now not so sensitive on smear negative samples (60-75%)

• Very sensitive on culture:• For identification• For drug susceptibility testing

Lowënstein medium

PAGE | 20

Focus on PCR: new CDC recommendations

“CDC recommends that Nucleic Acid Amplification testing be performed:

• on at least one respiratory specimen• from each patient with signs and symptoms

of pulmonary TB for whom a diagnosis of TB is being considered but has not yet been established,

• and for whom the test result would alter case management or TB control activities, such as contact investigations.”1

1. MMWR. Updated Guidelines for the Use of Nucleic Acid Amplification Tests in the Diagnosis of Tuberculosis. Jan 19, 2009

PAGE | 21

Unmet Needs

• Early detection of disease• TB cases diagnosed without aetiology (smear-, current PCR not

sensitive enough)• Limitation of spread• Detection in HIV cases

• Detection of MDR / XDR TB• Rapid implementation of the appropriate therapy• Limitation of spread of resistance• Optimisation of expensive isolation facilities

The value of Xpert MTB/RIF

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The value of Xpert MTB/RIF:

• Xpert MTB/RIF detects simultaneously the tuberculosis complex and rifampicin resistance

• Xpert MTB/RIF significantly enhances diagnosis and therapeutic decision making in pulmonary tuberculosis

• Xpert MTB/RIF combines rapidity and high sensitivity in a simply performed test

PAGE | 24

Molecular Beacon

Target

Hybrid

The Xpert MTB/RIF Molecular Beacon Assay

5 Probes bind to wild type

Probes do not bind to mutant sequence

1 Probe for SPC (B. globigii)

6 fluorescent dyes detected simultaneously

5’-3’-

-3’-5’

A

B

C D

E

rpoB gene

Sensitivity and Specificity

• Sensitivity in smear negative, culture positive (S-C+) was 90.9% (70/77)

• Sensivity in smear positive, culture positive (S+C+). was 100% (275/275)

• Specificity of the assay was 98.3%

• Sensitivity observed for Rifampicin resistance was 96.7%

• Specificity observed for Rifampicin resistance was 98.6%

Smear Positive

Culture Positive

Culture Negative

Culture Positive

Xpert Positive

70 5 275

Xpert Negative

7 289 0

Smear negative

Specimen Processing

Routine Bacteriology Mycobacteriology

BSL2 BSL3

2 min 3 hrs (batch)

Incubate 1-2 days Incubate up to 8 wks

Culture Detection and Identification

Routine Bacteriology MycobacteriologyBSL2 BSL3

Myobacterial Culture Methods

MGIT liquid medium 7H11 agar

Specimen pellet

LJ slant

Average TTD: 3 wks

MGIT 960320 tubes per unit

Positive

Automated Liquid Culture Systems

Average TTD: 7days

Solid Media

1. Absolute conc.2. Proportion method3. Resistance ratio

Drug Susceptibility Testing Methods for M. tuberculosis

MGIT 960

Average TAT: 8 wks 2-3 weeks

Specimen Processing is Required for NAATs

BSL3

2 hrs (batched) DNA extraction

Real-Time PCR

Specimen Processing is Required for NAATs

BSL3

2 hrs (batched) DNA extraction

Real-Time PCR

It’s About Time to Stop Transmission!

• Approximately 20% of transmitted infections are caused by smear-negative / culture positive patients1

• Should the patient be isolated until culture results are available?• => cost

• Should the patient be released while awaiting culture results? • => transmission risk

Sources:

1:Behr MA, Warren SA, Salamon H, et al. Transmission of Mycobacterium tuberculosis from patients smear-negative for acid-fast bacilli, Lancet 1999; 353:444–449

Syringe Motor

Motherboard

I-CORE

Uniframe

Valve Drive Motor

Ultrasonic HornModule

Door

GeneXpert® Module

PROCESSING CHAMBERS

REACTION TUBE

VALVE BODY

GeneXpert® Cartridge

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Cartridge Design and Operating Principle

Sonicator Dome

Rotary Valve

Syringe Barrel RT-PCR

Tube

PAGE | 38

Bead Format Reagents

Target-specific reagent bead:

primers; rpoB specific probes; controls

Enzyme reagent bead:

Taq polymerase; dNTPs; Buffers; Mg 2+

Sample Processing Control bead:

Bacillus globigii spores; excipients

Retaining balls

PAGE | 39

Xpert MTB/RIF : biosafety levels required

Based on the CDC recommendations

Novel Technologies Combine Sample Processing and Nucleic Acid Amplification

Sputum treated with “buffer” for 15 min

120 minutes

PAGE | 41

Amplification plot – TB positive/Rif sensitive

MTB Positive Medium, Rif Resistance NOT DETECTED

PAGE | 42

WHO statements

PAGE | 43

WHO endorses new rapid tuberculosis test A major milestone for global TB diagnosis and care

• 2010.12.8 | London | Geneva - Today, WHO endorsed a new and novel rapid test for tuberculosis (TB), especially relevant in countries most affected by the disease. The test could revolutionize TB care and control by providing an accurate diagnosis for many patients in about 100 minutes, compared to current tests that can take up to three months to have results.

• "This new test represents a major milestone for global TB diagnosis and care. It also represents new hope for the millions of people who are at the highest risk of TB and drug-resistant disease." said Dr Mario Raviglione, Director of WHO's Stop TB Department. "We have the scientific evidence, we have defined the policy, and now we aim to support implementation for impact in countries."

PAGE | 44

NEJM – September 2010 – Rapid Molecular Detection of Tuberculosis and Rifampin Resistance

• Large press coverage followed the publication in the US, Europe, many parts of the world

• Dr Mario Raviglione, Director of the World Health Organization's Stop TB Department, said: “The search for faster and more effective means to diagnose TB, which is the second greatest infectious killer of adults worldwide, is a top priority for the global health community. Over the next few days, WHO will convene independent experts to review the full evidence about the field effectiveness of this novel technology and propose it to country programs. These results suggest that it has the potential to revolutionize TB care, and WHO will treat it as a top priority.”

Xpert® MTB/RIF Performance Highlighted inRecent New England Journal Article

• Rapid Molecular Detection of Tuberculosis and Rifampin ResistanceCatharina Boehme, et al. New England Journal of Medicine, 1 Sept,

2010Studied >1,700 Patients• Peru, Azerbaijan, South Africa and India• Smear Positive Patients• 98.2% Sensitivity, 99.2% Specificity• Smear Negative, Culture PositivePatients• 90.2% Sensitivity with Three Samples• 72.5% Sensitivity with One Sample• Patients with Rimfampin Resistance• 97.6% Sensitivity, 98.1% Specificity

Xpert MTB/RIF – Romain Prieur

Impact of Multiple Samples on Sensitivity

Results – Detection of Rifampicin Resistance

Sensitivity Specificity

Overall 99.1% 100%

Lima 100% 100%

Baku 98.1% 100%

Cape Town 93.8% 100%

Durban 100% 100%

Mumbai 99.2% 100%

After discrepant result resolution by sequencing

Results - Comparison with Other NAATs

• The authors noted:• At sites performing alternative nucleic acid amplification testing, the sensitivity of

the automated molecular test performed directly on sputum was higher than that of Amplicor (94.6% vs. 86.8%, P<0.01) and similar to that of ProbeTec (83.7% vs. 83.9%, P = 0.96) performed on extracted DNA from sputum pellets.

• The specificity of the automated molecular test did not differ significantly from that of Amplicor or Probetec

• The Xpert MTB/RIF advantage over other NAATs• Rapid, simple set-up with little hands-on time• Minimal risk of contamination• Simultaneous rifampicin resistance result• On-demand testing – no batch delays

PAGE | 49

JCM – January 2010 – Helb et al.

• Part of the data from the pre-registration trials presented from Vietnam and Uganda

• 107 sputum samples from suspected TB cases from Vietnam:• Sensitivity in smear + samples: 100% (n=29)• Sensitivity in smear – samples: 71,7% (n=53) (smear – and

+ve by solid and liquid media)• Specificity 100%

• 64 smear+ samples from Uganda:• Sensitivity of 98.4% for TB and 100% for RIF resistance• Specificity for RIF resistance 100%

• “The Xpert MTB/RIF assay offers the first technical opportunity to bridge this gap, potentially bringing tests for both TB and drug

resistance to levels of the health system where many seek care.

PAGE | 50

ECCMID poster P2032 S. Naidoo (Johannesburg, ZA)

Evaluation of GeneXpert MTB/RIF assay on pulmonary and extra-pulmonary samples in a high-throughput laboratory

• Xpert MTB/RIF was tested on 1140 pulmonary and 361 extra-pulmonary samples and compared to culture (MGIT) ; 970 culture positives

• In pulmonary samples:• Sensitivity for TB complex = 99.8% ; specificity: 94.1%• Sensitivity for RIF resistance: 99.4% ; spec: 98.8%

• In non pulmonary samples:• Sensitivity: 93.5%• Specificity: 99%

Link

PAGE | 51

Other posters presented at ECCMID 2010

P2048 T. Bodmer, A. Ströhle (Berne, CH) Diagnosing pulmonary tuberculosis in a low prevalence setting – the Xpert MTB/RIF test

P2047 - J.S. Lin, C. Lin, R. Hsiao, L. Shih (Changhua, TW) Evaluation of Xpert MTB/RIF assay and amplified Mycobacterium tuberculosis direct test in direct detection of pulmonary M. tuberculosis complex

P2076 K. Kart Yasar, F. Pehlivanoglu, G. Sengoz, E.R. Ince, S. Sandikci (Istanbul, TR) Tuberculosis meningoencephalitis with severe neurologic sequelae in an immigrant family’s child:

Poster presented at ASM 2010

Posters presented at ESM 2010

Detection of M. tuberculosis and rifampicin resistance using a commercial PCR real time technique in respiratory and extrapulmonary samples (T.Tortola, N.Martin…Vall d’Hebron Hosp. in Barcelona, Spain)

Preliminary evaluation of Xpert MTB RIF kit for tuberculosis detection in non-respiratory specimens (M. Casal, M. Causse, Reina Sofia hosp in Cordoba, Spain)

Evaluation of GeneXpert MTB/RIF assay for Mycobacterium Tuberculosis detection and Rifampicin resistance identification in patients with high clinical suspicion of TB. (P.Ioannidis, D. Papaventsis, S. Nikolaou, National reference lab in Athens, Greece)

Molecular diagnosis of tuberculous meningitis: a three day experience (M. Peracchi, L. Fallico, Padua, Italy) + oral presentation respiratory and non respitatory samples

Evaluation of Genexpert MTB/RIF assay for detection of Mycobacterium Tuberculosis and Rifampicin resistance in a routine laboratory setting in Slovenia (Manca Zolnir-Dovc, Golnik, Slovenia)

More to come at ICAAC 2010

Rapid and Efficient detection of Mycobactrium Tuberculosis by the Cepheid Xpert MTB RIF assay (B. Malbruny...R. Leclercq, V. Cattoire, CHU Caen, France)

Effectiveness Analysis of Integrated Nucleic Acid Amplification System for the Rapid Diagnosis of Smear-negative Pulmonary Tuberculosis (L.Muñoz,…F. Alcaide, M. Santin, Hosp Univ. Bellvitge, Barcelona, Spain)

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• 越短的時間得到正確的藥物治療，對結核病患有較佳的預後• 在短時間得到治療，能減低傳染家人及社會的傳播壓力• 病患短時間確診能改變 TB 及 MDR-TB 的傳播• 及時確診是全球結核病控制的重要步驟

NEJM 363;11 Sep 9, 2010

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