Impact of MALDI TOF on AST

Transcription

1 Impact of MALDI TOF on AST NATHAN READING SENIOR BIOMEDICAL SCIENTIST MICROBIOLOGY SANDWELL AND WEST BIRMINGHAM HOSPITALS NHS ANTIMICROBIAL SUSCEPTIBILITY TESTING METHOD USER DAY 8 TH JULY 2014

2 Overview Context Susceptibility Testing Implications Of MALDI TOF. MALDI TOF and ART practicalities Influencing Antimicrobial Prescribing Faster Sensitivity Testing? Conclusions.

3 About us Large District General Hospital Trust c.900 beds (Split across two hospital sites ) Serves approx 400,000 patients Tertiary referral Ophthalmology inc A&E Unified microbiology lab on single site Previous home of BSAC Standardized Susceptibility Testing Method Development Centre. Key interest in A.S.T.

4 Why MALDI TOF at City Hospital? Efficiency Redesign our workflow Reconfiguration of service providers locally 7 other microbiology laboratories within 10 miles 4 within 5 miles! Improvement of our service for users. Decrease time to detection of pathogens Improved decision support Standardise our ID methods to a single platform Opportunity to get first VITEK MS in U.K. clinical laboratory.

5 Why VITEK MS MALDI TOF at City Hospital? Current VITEK 2 User AST and GN/GP ID Easy integration to attach ID to sensitivity testing using MYLA middleware solution. MYLA also has connectivity to our automated sample processing and blood culture system Middleware is now potentially a powerful management tool Smart Incubators/Sample preparation in the future Very simple ID protocol Minimal extraction (Formic Acid for Yeasts only done on target) Simple sample preparation on disposable targets

6 Why is MALDI TOF important for AST/ART? Accurate identification can be used to predict phenotype Inducible AmpC production. Morganella, Serratia, Enterobacter, Citrobacter, Providencia Ampicillin Resistant, Co amoxyclav Resistant, 3G Ceph Intrinsic Vancomycin Resistance Some Enterococci (VanC) Colistin Resistance Serratia sp Stenotrophomonas, Elizabethkingia, Chryseomonas Carbapenem = R

7 Why is MALDI TOF important for AST/ART? Most breakpoint tables, zone diameter and MIC built using SPECIFIC species. BSAC EUCAST If the species isn t named or part of a group then there is no specific guidance! Use of foot notes and species guidance Aminoglycosides, Ciprofloxacin, Cefuroxime and Salmonella sp. Vancomycin for Coag Neg Staphs vs S.aureus

8 Validation. Do we trust the ID provided? CE/FDA IVD Only database reduced need to validate? Performance claims assured? Non conformity or non performance addressed via regulatory bodies MHRA? UKAS/CPA Stds F1.1, F1.2 and ISO Non CE IVD Database Extensive and robust validation? Implications when using with patients?

9 Validation Approximately 1400 highly characterised strains 93.8% 100% Species ID correct 97.4% 100% Group/Family Level ID Correct 98.5% 100% Genus Level ID Correct Reading et al. ECCMID 2012 Poster P2323 Reading et al. ECCMID 2012 Poster P2332 Symonds et al. ECCMID 2012 Abstract R2637 Symonds et al. Microbiology Poster Session, IBMS Congress 2013, Poster 40

10 Validation Direct Comparison 400 further isolates Parallel testing with current API VITEK 2 Phenotypic/Biochemical/Microscopy No misidentification when compared to traditional Limitations of database Strains not included Slash line ID?

11 Our ROUTINE workflow time saving? When was ID available compared to traditional method? Same 400 isolates REAL WORLD performance Time to Identification Organism Traditional (mean/range)/hours MALDI TOF (mean/range)/hours 19/ / /6 22, 13/ / 0.3 3, 2/ Streptococci 8/ / HACEK 18 / / Yeasts 34 / / / / Staphylococci GNB (Ferm/Non Ferm) Enterococci

12 Our ROUTINE workflow MS is now de facto first line ID No latex for Staphylococci and Streptococcal Grouping No Dnase plate No Germ Tubes API/VITEK 2 only on occasion, Shigella spp, S.typhi. ID set up and results reviewed by bench readers as cultures read. Processed in groups of 16 isolates Organism ID ready for choice of sensitivity testing.

13 Our ROUTINE workflow Lab Aspects Decrease turnaround times Bacterial Identification available earlier. Standardised identification platform Reduction of identification methods Reduction of training requirements Reduction of reagent requirements Reduced transport & packaging sustainability Reduced storage space/refrigeration requirements Increased throughput capacity Addresses pathology reconfiguration requirements Locally and Nationally

14 Efficient susceptibility testing Effective Identification Only test appropriate isolates. Reduction of wastage Non S.aureus strains but Staphylococcal Latex Positive, Dnase equivocal/positive Staphylococcus lugdunensis Oxidase positive non Pseudomonas non fermenters Only test appropriate antibiotics Specific panels based on Genus vs general broad panels

15 Our workflow savings/improvements?s. aureus Latex and DNase 2 3 Isolates per day through Vitek 2 NOT S. aureus Cost approximately 5.00 per isolate (Purity plate, Vitek 2 Consumables, Staff Time) 1 week study 11 Isolates non S. aureus Extrapolated saving 2800 p.a.?s. pneumoniae Optochin/Bile Solubility Approximately 1.15 per isolate (Plate, Discs, Staff Time) Approximately 20% not S.pneumoniae Extroplated saving 350 p.a.

16 Efficient susceptibility testing Can choose most appropriate testing method Automated Vitek 2 Staphylococci, Enterobacteriacae, Pseudomonads, Enterococci BSAC Standardized Disc Method Streptococci (AHS, BHS, S.pneumoniae) Neisseria meningitidis, N. gonorrhoeae Moraxella catarrhalis, Haemophilus influenzae Gradient Strips / Referral Everything else!

17 Workflow capacity extension Prior to MALDI April 2009 November 2011 VITEK 2 at 75% 100% Mon Fri ID and Sensitivity Testing Ongoing workload increases Post MALDI November 2011 Present Vitek 2 at 75% 100% Mon Fri Sensitivity Testing Only Second instrument not required

18 WORKFLOW EFFICIENCY STAFFING AST Pre Vitek 2 1 WTE Senior BMS, 2 WTE Band 6 BMS 1 WTE Lab Support Work AST Post Vitek 2 Pre MALDI 1 WTE Senior BMS, 1 WTE Band 6 BMS 0.5 WTE Lab Support Worker AST Post Vitek 2 Post MALDI 1 WTE Band 6 BMS 0.5 WTE Lab Support Worker

19 Problems? Testing without guidelines/methodology? Accurate ID better characterisation of infecting species Increased likelihood of reported isolate Needs susceptibility testing How? Discs x EUCAST/BSAC more for CLSI but zone diameter cut offs limited Vitek/Phoenix x Sensititre/Microscan ISO Microbroth? Yes but No interpretation Off line read?

20 Problems? Testing without guidelines/methodology? Agar/Broth MIC Yes Need antibiotics Adequate controls Time consuming Specialist equipment/reference Gradient Strips Yes Care with some antibiotics Cost and Range

21 Problems? Testing without guidelines/methodology? How to interpret? Breakpoint tables BSAC/EUCAST Anaerobe tables EUCAST species non specific table ECOFF s via EUCAST website Look at MIC distributions Look to Case Reports

22 How do we speed up advice for Sepsis? Sample cultured 24 hours ID Set up 24 hours 48 Hours to correct antibiotic guidance Sample cultured 24 hours Identification Available 24 hours to correct antibiotic guidance Blood culture sampled 24hours Flags Positive Gram Stain 24 hours. Subculture 48 hrs ID

23 Extending the use of MALDI TOF. ECCMID 2011, Milan Poster P % Spiked Bottles Fothergill A. et.al. J.Clin.Microbiol. March 2013;51: % Clinical Samples

24 Reading et.al. ECCMID 2013 Berlin, E Poster ep769

25 Impact of Direct Blood Culture ID using MALDI TOF. MALDI TOF direct identification, would have led to modification of empirical therapy of 18 patients (12.32%) If TNase media not used then potential for a further 47 patients to have been positively impacted. Total potential impact 67/146 patients (44.5%) All 16 bottles of AmpC producing Enterobacteriaceae species from 8 patients were correctly identified at the species level by MALDI TOF. Direct identification for Enterobacter spp. would have lead to broadening of antibiotic in 6 patients. In 5 of these patients, there was delay in starting appropriate antibiotics for 48 hrs. One patient with Enterobacter spp. bacteraemia died 24 hrs. after starting inappropriate antibiotic for sepsis. Identification on day 1 likely to have had a definite impact on patient management.

26 Impact of Direct Blood Culture ID using MALDI TOF. Impact of Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry on the Clinical Management of Patients With Gram negative Bacteremia: A Prospective Observational Study Clerc. O et al. Clin Infect Dis. (2013) 56. (8): MALDI TOF identification led to a modification of empirical therapy in 71 of all 202 cases (35.1%), and in 16 of 27 cases (59.3%) of monomicrobial bacteremia caused by AmpC producing Enterobacteriaceae.

27 Extending the use of MALDI in AST. Identification of organism in positive blood cultures Wider range of organisms vs. FISH Microscopy and CE Marked Multiplexed Molecular SEPSIS Assays Cheaper Very quick 30mins! Same day effective clinical advice Tailored therapy knowledge based vs. best guess. Better patient outcomes? Contaminant vs. Pathogen De escalate therapy earlier Pharmacy savings? Tailored direct sensitivity testing vs. wider range of panels Reduces cost.

28 Resistance testing 6 18 hours

29 Faster sensitivity testing Molecular Limited Targets Target deviation/novel variants Genotype doesn t always predict Phenotype EUCAST Expert rules for Cephs/Carbs If it tests S then in theory can treat.????? Expensive Skilled workflow GeneXpert, BD Max

30 Faster sensitivity testing Digital Microscopy Micro fluidics Sensitivity testing reported down to 1 2 hours Early Disc reading 6 8 hours post inoculation Needs re evaluated zone diameters EUCAST Eurostar Rapid Disk Method ECCMID 2013 Sundqvist M et al, P1541 Automated zone reading built into Smart Incubators BD Kiestra/ Copan/ Biomerieux Driven by smart image software with expert rules? Read when ready?

31 Rapid phenotypic tests? HMRZ 86 BioRad Beta Lacta Mast Cica Beta Carba NP Test Rosco Rapid Carb Screen Rapidec Carba NP

32 Antibiotic resistance screening. MALDI-TOF - Detection of Metabolites produced after enzyme hydrolysis + Enzyme Antibiotic E Enzyme hydrolysis Studies: B lactam antibiotics Ampicillin, Ertapenem, Meropenem, 3 G Cephs

33 The first useful MALDI-TOF MS resistance test MBT_MSBL assay + 18 Da - 44 Da Functional assay, detection of hydrolysis of betalactam antibiotics Rapid: 1-4 hours Simple pipetting protocol Same instrument like for identification get it into rou ne! A number of publications show performance 05 August

34 MBT_MSBL assay Bacterial suspension in antibiotic solution Incubation 1-4 h, 37 C centrifugation supernatant Target preparation Data interpretation MALDI Biotyper 05 August

35 Ampicillin hydrolysis 350,1 372,1 379, Intens. [a.u.] DH ,2 368,1 390,0 412, Intens. [a.u.] ESBL strain 0 x , ESBL strain/ clavulanic acid 324,2 372,1 Intens. [a.u.] 394,1 [Mhydr CO2+H] + [M+H] + [Mhydr+H] + [M+Na] + [Mhydr+Na] + [M+2Na] + [Mhydr+2Na] m/z 05/08/

36 MBT_MSBL Publications Hrabák J, Walková R, Studentová V, Chudácková E, Bergerová T. (2011) Carbapenemase activity detection by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 49: Burckhardt I, Zimmermann S. (2011) Using matrix-assisted laser desorption ionization-time of flight mass spectrometry to detect carbapenem resistance within 1 to 2.5 hours. J Clin Microbiol. 49: Sparbier K, Schubert S, Weller U, Boogen C, Kostrzewa M. (2012) MALDI-TOF MS based functional assay for the rapid detection of resistance against ss-lactam antibiotics. J Clin Microbiol. 50: Hrabák J, Studentová V, Walková R, Zemlicková H, Jakubu V, Chudácková E, Gniadkowski M, Pfeifer Y, Perry JD, Wilkinson K, Bergerová T. (2012) Detection of NDM-1, VIM-1, KPC, OXA-48, and OXA-162 carbapenemases by MALDI-TOF mass spectrometry. J Clin Microbiol. [Epub ahead of print] Kempf M, Bakour S, Flaudrops C, Berrazeg M, Brunel JM, Drissi M, Mesli E, Touati A, Rolain JM. (2012). Rapid detection of carbapenem resistance in Acinetobacter baumannii using matrix-assisted laser desorption ionization-time of flight mass spectrometry. PLoS One 7:e31676 Álvarez-Buylla A, Picazo JJ, Culebras E. (2013) Optimized method for Acinetobacter species carbapenemase detection and identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 51(5): Wang L, Han C, Sui W, Wang M, Lu X. (2013) MALDI-TOF MS applied to indirect carbapenemase detection: a validated procedure to clearly distinguish between carbapenemase-positive and carbapenemase-negative bacterial strains. Anal Bioanal Chem. 405(15): Lee W, Chung HS, Lee Y, Yong D, Jeong SH, Lee K, Chong Y. (2013) Comparison of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry assay with conventional methods for detection of IMP-6, VIM-2, NDM-1, SIM-1, KPC-1, OXA-23, and OXA-51 carbapenemase-producing Acinetobacter spp., Pseudomonas aeruginosa, and Klebsiella pneumoniae. Diagn Microbiol Infect Dis. [Epub ahead of print] 05 August

37 Web-based MSBL software prototype STAR_BL 05 August

38 Workflow of the MBT_MSBL assay from positive blood cultures Positive blood culture 1 ml culture Modified Sepsityper protocol Resuspension in antibiotic solution Incubation 1-2 h, 37 C centrifugation supernatant Target preparation Data analysis MALDI Biotyper 05 August

39 MALDI TOF Mass Spectrometry for Rapid Antibiotic Resistance Detection - Mirande,C et al Faropenem Klebsiella pneumoniae 3hrs 37oC + Faropenem Centrifuge 2 min 13,000g Carbapenem-S strains (Neg controls) Carbapenem-R strains (Carbapenemase producers) Carbapenemase E Inactive Faropenem (hydrolysed) Carbapenem-S & m/z Carbapenem-R Decreased intensity of & m/z Additional 304.3, & m/z

40 MBT MS_RESIST Resistance testing with stable isotopes Growing cell perform protein biosynthesis Integration of labeled amino acids resulting in peaks shifts Monitoring growth in the presence of antibiotics by analyzing peak shifts patent allowed & patent pending 05 August

41 Principle of the MS_RESIST normal Lys Control 1 Susceptible heavy Lys antibiotic Resistant heavy Lys Control 2 05 August

42 MBT MS_RESIST S. aureus strains, mass spectra gel view A: Susceptible strain B: resistant strain normal normal heavy + Oxa heavy + Oxa heavy heavy 05 August

43 WHAT ELSE? Typing Genus specific Some evidence of clustering of similar strains Not currently routine Many of the studies on small numbers Specific resistance markers PBP2, Van A/B Current systems in routine not currently Some work on MRSA very early on Confounding studies Carbapenem Resistance in Bateroides fragilis Nagy et al. Delineate strains Carbapenem resistant from sensitive CfiA positive vs CfiA negative

44 Antibiotic resistance screening? Sufficiently robust and accurate for ROUTINE? Good performance with known isolates and in expert labs Maybe good, cost effective option in outbreaks Delineate ESBL/AMPC + Impermeability vs Carbapenemases Less active enzymes? Hydrolysis can be slow Labile substrates Experience of Carbapenemases and AST? Yes/No simplified result. Advantages over molecular confirmation?

45 Conclusions Striving for robust ROUTINE identification Good quality databases which are CE IVD marked Enables trust in identification, secure clinical decisions Need speed of Resistance Testing to catch up New technologies Re evaluation of existing? Ensuring Resistance Testing is performed accurately in context to identification Right method for right organisms

46 THANK