5/10/13. Mass Spectrometry in diagnostic clin micro: progress and prospects. MS in Diagnostic Microbiology

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1 Mass Spectrometry in diagnostic clin micro: progress and prospects Mark Wilks, Lead Clinical Scientist Barts Health Trust, London UK MALDI-TOF MS in Diagnostic Microbiology State of play: 90-95% of bacteria and yeasts rapidly identified within minutes What s next Filamentous fungi Mycobacteria Detection from positive blood cultures- how and why? Detection of antibiotic resistance: Non MALDI-TOF systems MX PCR and ESI MS - Abbot Plex-ID High MW detection systems MALDI: Matrix Assisted Laser Desorption Ionisation Sample plate hν CH + 377nm N 2 Laser 1. Colony (C) is mixed with excess matrix (M) and dried on a MALDI plate. 2. Laser flash ionises matrix molecules. 3. Sample molecules are ionized by proton transfer from matrix: MH + + C M + CH kv Variable Ground Grid Grid 1

2 Time-of-flight mass analyzer Source Drift region (flight tube) detector V Ions are formed in pulses. Small ions reach the detector before large ones. Measures the time for ions to reach the detector. detector flight tube sample port 2

3 1996 two key papers showing use of MALDI for Bacterial ID, note use of variable low MW ranges, <2KDa molecules include variable metabolic products, another ten years before usable data bases with >2KDa available Low influence of culture conditions Pseudomonas oleovorans grown on different media Psdm. oleovorans B396_Medium Psdm. oleovorans B396_Medium 464 Psdm. oleovorans B396_Medium Psdm. oleovorans B396_Medium 65 Psdm. oleovorans B396_Medium 98 Psdm. oleovorans B396_MRS10 Psdm. oleovorans B396_YPD m/z 3

4 Why does it work? - differences in ribosomal proteins- basic and abundant Intens. [a.u.] E.coli ribosomal Protein m/z RL , RS ,82 RL ,39 RL33meth. 6255,39 RL , RL ,60 RL ,74 RL , RL ,06 RS , m/z Other markers: - RNA chaperones - cold shock proteins - cell division proteins - DNA binding proteins Available MALDI-TOF systems: Saramis Spectral Archiving and Microbial Identification System/ Anagnostec BioM RUO super spectra sum of peak weights compared to mass signals for each super spectra --> confidence value two different matrices Biomerieux Vitek MS IVD CE - Advanced Spectrum classifier - supervised learning of 25K spectra - artificial neural network analysis Bruker MALDI Biotyper IVD CE - multiple spectra from a single strain 1. peaks in sample mass spectra compared to peaks in ref spectra 2. reverse peaks in ref spectra compared to peaks in sample mass 3. spectra signal intensities of matched spectra scores multiplied --> normalised to a value of > log 3.0 Andromadas Nassif Univ of Paris Sud, runs on Bruker MS 4

5 Behaviour of Matrix α-cyano on Target Plates (AnagnosTec, May 2010) Fleximass DS MAB Pictures from Stefan Bugovsky 13 MALDI Biotyper Pilot Vitek MS 15 5

6 Identification of MTB Database limitations but mainly prepn problems cf anaerobes where reverse is true What systems and methods are available Andromas method Marseille group: El Khéchine A, Couderc C, Flaudrops C, Raoult D, et al. (2011) Vitek Bruker Figure 1. MALDI-TOF MS spectra obtained from the M. tuberculosis H37Rv strain using the protocols tested herein. El Khéchine A, Couderc C, Flaudrops C, Raoult D, et al. (2011) Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Identification of Mycobacteria in Routine Clinical Practice. PLoS ONE 6(9): e doi: /journal.pone Database Mycobacteria entries Vitek 9 or 10 species New version < 6 months Bruker 96 Mycobacterial species M tb complex Some sub species too 6

7 Bruker Mycobacteria database Bruker method, alcohol extraction, heat killing and bead beating Database Fungal entries Vitek Bruker 15 spp filamentous fungi 42 genera 123 species Vitek: Barts experience: little success, wait for new version of software or use a Bruker method Bruker: Aspergillus and other filamentous >70% Dermatophytes about 50% success eg Trichophyton tonsurans Try subculturing direct from the colony 7

8 ID of fungi other than yeasts: Where to sample from? Use of liquid media Use of Rotator 8

9 Positive Blood Cultures range of extraction methods eg Martiny et al EJCMID 2012 Rapid subculture from a +ve BC 9

10 MALDI ID minus AST: so what? secondary benefit of acquiring MALDI use cf expensive MX PCR/array based methods does it effect patient management? is there any patient benefit? any cost savings? - bed days, ITU days decreased antibiotic resistance ass d with deescalation? see Kerremans, Erasmus, Rotterdam MALDI ID minus AST: benefits are obvious? Anecdote 1 GNB seen in film Direct MALDI result N. meningitidis recheck film GNB/GNCB Next day grew N meningitidis--> Ref Lab Patient well, discharged on cefotaxime Anecdote 2 GNB seen in film Direct MALDI results Acinetobacter baumannii Carbapenem added Vlek, Bonten Boel O334 ECCMID 2011 May Milan Alternate months study MALDI Feb 2010 April 2010 Episodes No MALDI- TOF Dec 2009 March 2010 MALDI results ID 50/ % no ID 29/ % Median time for results Switch in antibiotics 16.4 (IQR ) 55% 17.5h 45.2 (IQR ) 58% 24h P=<0.001 P=

11 +BC s: spectrum of severity may mask benefits CoNS - MALDI-TOF excellent speciation, rule out/ rule in --> bacteraemia --> septicaemia --> severe sepsis major determinants of sepsis outcomes are not bacterial ID or AST results passive reporting of ID result no effect probably not antibiotic sens results prompt empirical treatment changes in empirical treatment relate to patient response, and not AST results role of de-escalation? Errors: Barts Health lab re-organisation Reduced error rate in IDs, plate reading MALDI MALDI result plate re-read by another worker Plates are effectively double read Guards against MALDI transcription errors AST Calibrate each plate Negative controls matrix only How do you know it s right? How do you know it s right? Compare with what? Using MALDI-TOF creates it s own problem: move from problems of ID problems of taxonomy 16S sequencing limited information?combination of 16S/rpoB/hsp60?WGS 11

12 The problem of selecting correct databases Saramis database RUO can add own spectra VITEK IVD locked database Vitek separate yeast and bacterial databases e.g. small white colony on blood plate?cns If you select the bacterial database Lactococcus If you select the yeast database Candida albicans Bruker secure database Bruker separate Secure database B. anthracis, S typhi, Brucella, Y. pestis e.g. GNB from a blood culture? Brucella Bruker MALDI good spectrum but no ID Did not have secure database Sent to Barts Health Lab run against secure database Brucella 1 month later, same mistake by our lab, GNB from a BC did not select the right database good spectrum but no ID referred for 16S Brucella!! Vitek: no Brucella? meningo from a BC rough looking colony, score 1.7 should have been reported as Neisseria spp Meningo ref lab- not a meningo Re ID d on by alcohol extraction Bruker meningo 2.3, 2.2 Ref Lab ID: N. cinerea How do you know it s a cinerea?.it s not a meningo 12

13 Direct smear: 2 isolates of Arthrobacter castelli score >2.1 and (++)A category. 16S rdna sequencing: (A) Microbacterium lacticum (99%) (B) Brachybacterium rhamnosum (99%). Alcohol extraction: (A) M. lacticum log score 1.7 for case (A) (B) No reliable ID (log score 1.16). Direct smear: spectra contain large amounts of poly-lysine Database entries also poly-lysine Entry will be replaced in next update ABR testing not AST Hbarak et al Clin Micro Rev 2012 Antibiotic degradation Specific proteins eg. MRSA/MSSA VRE eg vanb E. faecium Modification of target sites aminoglycoside resistance ABR by MALDI : look for cleavage products eg Beta lactams 13

14 Hrabak et al CMR 2013 Merop n Solution K pneumo Non CPase A baumanii NDM-1 A baumanii KPC-2 ceftazidine ertapenem 14

15 Automating detection of antibiotic degradation Plex ID, ESI and not MALDI Abbot Plex ID Arose from US anxieties over bio terrorism Multiplex PCR Separation of products by mass spectrometry Works directly on clinical specimens All viruses, bacteria, fungi, parasites Very expensive,? Cost effective Sepsis and pneumonia trial, Barts, Paris Geneva 15

16 Faix et al NEJM 2009 PlexID ident n of a novel flu before CDC 16

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19 Plex-ID Test for everything on day 1? Worth it in selected patient groups eg Haem Onc, transplant Savings in time to diagnosis Bed days, drugs eg antifungals Infections with more than one pathogen Conventional testing: stop testing after single pathogetn detected No need to guess possible pathogen 19