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MALDI TOF Mass Spectrometry A New Era in Diagnostic
Microbiology
Dr Barry Wong, Scientific Officer (Medical) Microbiology Laboratory, United Christian Hospital
19 May 2015
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2021
1995
1973
United Christian Hospital
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Traditional Microbiology
How to identify the pathogen??
Colony characteristics Direct microscopy
Biochemical tests
Antigen detection
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protein bacterial cell
DNA
genome proteome
DNA fingerprint
3000 5000 7000 9000 11000 13000
Mass ( m/ z)
2117. 3
0
10
20
30
40
50
60
70
80
90
100
% Intensity
V o y a g e r S p e c # 1 = > A d v B C ( 3 2 , 0 . 5 , 1 . 0 ) = > N F 0 . 7 [ B P = 4 4 2 3 . 9 , 2 1 1 7 ]
44
24
.2
94
76
.2
48
61
.0
88
23
.5
58
97
.8
62
71
.2
80
54
.3
66
29
.0
74
24
.9
12
27
1.4
47
38
.6
69
84
.6
83
83
.8
67
86
.7
65
33
.3
90
75
.2
31
32
.3
61
37
.3
72
09
.8
89
03
.3
86
10
.6
10
11
0.8
47
65
.4
10
97
5.2
40
26
.9
45
35
.6
33
11
.8
10
49
3.9
34
91
.4
96
11
.5
mass fingerprint
Species identification
Microbial taxonomy: genomics vs proteomics
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Technology advancement
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What is MALDI TOF MS?
MALDI-TOF MS(Matrix Assisted Laser Desorption / Ionization – Time-Of-Flight Mass Spectrometry). Mass Spectrometry (MS) is an analytical technique to determine the elemental composition of a sample. The MS principle consists of ionizing chemical compounds to generate charge molecules and to measure their mass-to-charge ratio. The first attempt of using MS technology started in 1970s and was mainly used for Chemical Pathology. A type of MS which can allow the screening proteins directly from intact bacteria.
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Technology breakthrough in 1996….
The use of MALDI-TOF for the whole cell fingerprinting and identification of bacteria from cell surface proteins, ribosomal proteins, high abundance
cold-shock protein, and acid resistance proteins 6
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Matrix Assisted Laser Desorption / Ionization – Time-Of-Flight
The analyte with matrix was dried on a target plate
Matrix
Analyte (organism)
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Target plate
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Matrix Assisted Laser Desorption / Ionization – Time-Of-Flight
High energy laser
The laser fired at the matrix dried sport and cause desorption: matrix absorbs the energy from laser and becomes ionized (by addition of a proton)
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Matrix Assisted Laser Desorption / Ionization – Time-Of-Flight
The matrix will transfer the proton to the analyte molecule making it becomes a positive charge [M-H]+ ion.
Finally, laser causes the sample and matrix volatilize
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Matrix Assisted Laser Desorption / Ionization – Time-Of-Flight
The ions formed are accelerated by a high voltage supply and allow to drift down a flight tube where they are separated according to their mass
The positively charged proteins draft in the flight tube, with the smaller proteins draft faster
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MALDI-TOF is a technology that can develop a protein pattern from an unknown isolate. This unknown pattern is used to match with known library and presents with a score for that isolate to facilitate species identification.
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Target preparation MALDI-TOF
measurement Bacterial identification
Workflow of MALDI TOF
12 96 tests / 1 hour
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Meaning of score value
Meaning of consistency category A, B, C Category Description
A Species consistency: The best match was classified as green. Further green matches are of the same species as the first one. First yellow match are at least the same genus as the first one.
B Genus consistency: The best match was classified as green or yellow. Further green or yellow matches are of the same genus as the first one. The conditions of species consistency are not fulfilled.
C No consistency: Neither species nor genus consistency. Check for synonyms of names or microbial mixtures. 13
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All green matches belong to the same species
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Class A report – Species consistent result
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All the green matches belong to the same genus
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Class B report – Genus consistent result
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One green and three yellow matches belong to different genus
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Class C report – Non consistent result
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Limitation in data base • E. coli / Shigella
• Streptococcus pneumoniae / S. mitis / S. oralis
• Salmonella species
• Raoultella ornithinolytica / Klebsiella oxytoca
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Need supplementary tests
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Evaluation data • From 15 Jan to 15 April 2015
• 431 bacteria and yeasts
• Clinical isolates and ATCC strains
• < 3 days isolates
• Positive blood culture (94):
– Positive bottles in the morning, use BA for MALDT testing in the afternoon (~5-6 hrs incubation)
• Compared with conventional tests, commercial kits and gene sequencing
• Agar: BA, CHO, MH, MHBA, HTM, SAB
Results Number (percentage)
Species Level
382 (88.6%)
Genus Level
45 (10.4%)
Mismatch with conventional tests
4 (1%)
18 99% identified to genus + species level
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MALDT TOF result -Organism (no) Species level No. (%) Genus level No. (%) Wrong ID No. (%) Comment/In house result
E. Coli (18) 18 (100%) 0 (0%) 0 (0%) Closely related with Shigella
Enterobacter cloacae (3) 3 (100%) 0 (0%) 0 (0%)
Enterobacter kobei (2) 0 2 (100%) 0 (0%) E. cloacae, E. species
Enterobacter aerogenes (2) 2 (100%) 0 (0%) 0 (0%)
Enterobacter gergoviae (1) 0 (0%) 1 (100%) 0 (0%) E. aerogenes
Citrobacter freundii (7) 7 (100%) 0 (0%) 0 (0%)
Citrobacter koseri (3) 3 (100%) 0 (0%) 0 (0%)
Citrobacter youngae (1) 0 1 (100%) 0 (0%) Citrobacter species
Achromobacter xylosoxidans (1) 1 (100%) 0 (0%) 0 (0%)
Klebsiella pneumoniae (9) 9 (100%) 0 (0%) 0 (0%)
Klebsiella oxytoca (3) 3 (100%) 0 (0%) 0 (0%)
Raoultella ornithinolytica (2) 0 (0%) 0 (0%) 2 (100%) Klebsiella oxytoca
Morganella morganii (6) 6 (100%) 0 (0%) 0 (0%)
Proteus mirabilis (7) 7 (100%) 0 (0%) 0 (0%)
Proteus vulgaris (4) 4 (100%) 0 (0%) 0 (0%)
Providencia alcalifaciens (1) 1 (100%) 0 (0%) 0 (0%)
Providencia rettegeri (2) 2 (100%) 0 (0%) 0 (0%)
Providencia stuartii (1) 1 (100%) 0 (0%) 0 (0%)
Plesiomonas shigelloides (2) 2 (100%) 0 (0%) 0 (0%)
Acinetobacter baumannii (3) 3 (100%) 0 (0%) 0 (0%)
Acinetobacter guillouiae (1) 0 (0%) 1 (100%) 0 (0%) Acinetobacter species
Acinetobacter tandoii (1) 0 (0%) 1 (100%) 0 (0%) Acinetobacter species
Acinetobacter ursingii (1) 0 (0%) 1 (100%) 0 (0%) Acinetobacter species
Aeromonas caivae (2) 2 (100%) 0 (0%) 0 (0%) Aeromonas caivae by API, report as Aeromonas sp
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MALDT TOF result -Organism (no) Species level No. (%) Genus level No. (%) Wrong ID No. (%) Comment/In house result
Aeromonas hydrophila (3) 3 (100%) 0 (0%) 0 (0%) Aeromonas hydrophila by API, report as Aeromonas sp
Aeromonas veronii (1) 0 (0%) 1 (100%) 0 (0%) Aeromonas species
Burkholderia cepacia (2) 2 (100%) 0 (0%) 0 (0%)
Burkholderia cenocepacia (3) 3 (100%) 0 (0%) 0 (0%) Burkholderia cepacia
Campylobacter jejuni (2) 2 (100%) 0 (0%) 0 (0%)
Campylobacter coli (2) 2 (100%) 0 (0%) 0 (0%)
Pseudomonas aeruginosa (5) 5 (100%) 0 (0%) 0 (0%)
Salmonella species (11) 0 (0%) 11 (100%) 0 (0%) Confirmed by serology
Serratia marcescens (8) 8 (100%) 0 (0%) 0 (0%)
Stenotrophomonas maltophilia (4) 4 (100%) 0 (0%) 0 (0%)
Vibrio parahaemolyticus (3) 3 (100%) 0 (0%) 0 (0%)
Vibrio vulnificus (3) 3 (100%) 0 (0%) 0 (0%)
Myroides odoratimimus (1) 0 (0%) 1 (100%) 0 (0%) Myroides sp (vitek)
Yersinia enterocolotica (1) 1 (100%) 0 (0%) 0 (0%) RCPA QAP
Elizabethkingia meningoseptica (2) 2 (100%) 0 (0%) 0 (0%)
Chryseobacterium indologenes (1) 0 (0%) 1 (100%) 0 (0%) Chryseobacterium species
Chryseobacterium gleum (1) 0 (0%) 1 (100%) 0 (0%) Chryseobacterium indologenes (Vitek)
Moraxella catarrhalis (3) 3 (100%) 0 (0%) 0 (0%)
Moraxella nonliquefaciens (2) 1 (50%) 1 (50%) 0 (0%) M. nonliquefaciens by sequencing (1) (eye), Moraxella species (1)
Moraxella osloensis (2) 1 (50%) 1 (50%) 0 (0%) Moraxella osloensis (1), Moraxella species (1)
Neisseria mucosa (1) 0 (0%) 1 (100%) 0 (0%) N. sicca (Vitek)
Neisseria gonorrhoeae (6) 6 (100%) 0 (0%) 0 (0%)
Haemophilus influenzae (11) 11 (100%) 0 (0%) 0 (0%) Non-haemolytic
Kingella kingae (1) 1 (100%) 0 (0%) 0 (0%)
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MALDT TOF result -Organism (no) Species level No. (%) Genus level No. (%) Wrong ID No. (%) Comment/In house result
Aerococcus viridans (1) 1 (100%) 0 (0%) 0 (0%)
Aerococcus sanguinicola (1) 1 (100%) 0 (0%) 0 (0%)
Enterococcus avium (3) 3 (100%) 0 (0%) 0 (0%)
Enterococcus faecium (6) 5 (83%) 1 (17%) 0 (0%) Enterococcus species (1) (MSU)
Enterococcus faecalis (17) 17 (100%) 0 (0%) 0 (0%)
Streptococcus agalactiae (10) 10 (100%) 0 (0%) 0 (0%)
Streptococcus constellatus (4) 4 (100%) 0 (0%) 0 (0%)
Streptococcus intermedius (3) 3 (100%) 0 (0%) 0 (0%) Streptococcus intermedius (2), Streptococcus milleri (1)
Streptococcus pneumoniae (14) 14 (100%) 0 (0%) 0 (0%) Closely related with S. mitis / S. oralis
Streptococcus pyogenes (10) 14 (100%) 0 (0%) 0 (0%)
Staphylococcus aureus (12) 12 (100%) 0 (0%) 0 (0%) MRSA (5), MSSA (7)
Staphylococcus epidermidis (11) 4 (36%) 7 (64%) 0 (0%) S. epidermidis (4), CNS (7)
Staphylococcus haemolyticus (3) 2 (67%) 1 (33%) 0 (0%) S. haemolyticus (2), CNS (1)
Staphylococcus lugdunensis (2) 1 (50%) 1 (50%) 0 (0%) S. lugdunensis (1), CNS (1)
Staphylococcus saprophyticus (3) 3 (100%) 0 (0%) 0 (0%)
Candida albicans (11) 11 (100%) 0 (0%) 0 (0%) FAE (4)
Candida glabrata (13) 9 (69%) 4 (31%) 0 (0%) Candida species (4), FAE (5)
Candida parapsilosis (1) 1 (100%) 0 (0%) 0 (0%) FAE
Candida tropicalis (4) 2 (50%) 2 (50%) 0 (0%) Candida species (2), FAE (2)
Cryptococcus neoformans (2) 2 (100%) 0 (0%) 0 (0%) FAE (2)
Bacteroides fragilis (3) 3 (100%) 0 (0%) 0 (0%)
Clostridium difficile (5) 5 (100%) 0 (0%) 0 (0%) Detected by PCR
Clostridium sordellii (2) 2 (100%) 0 (0%) 0 (0%)
Fusobacterium varium (1) 1 (100%) 0 (0%) 0 (0%)
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ATCC strain MALDI-TOF results
ATCC 51299 Enterococcus faecalis
20 ATCC stains identified to species level
ATCC 29212 Enterococcus faecalis
ATCC 12386 Streptococcus agalactiae
ATCC 49619 Streptococcus pneumoniae
ATCC 19615 Streptococcus pyogenes
ATCC BA1708 Staphylococcus aureus
ATCC 43300 Staphylococcus aureus
ATCC 25923 Staphylococcus aureus
ATCC 29213 Staphylococcus aureus
ATCC 12228 Staphylococcus epiderimidis
ATCC 25922 Escherichia coli
ATCC 35218 Escherichia coli
ATCC 49766 Haemophilus influenzae
ATCC 49247 Haemophilus influenzae
ATCC 70063 Klebsiella pneumoniae
ATCC 13883 Klebsiella pneumoniae
ATCC 43069 Neisseria gonorrhoeae
ATCC 12453 Proteus mirabilis
ATCC 27853 Pseudomonas aeruginosa
ATCC 14028 Serratia marcescens
ATCC 13880 Salmonella typhimurium Identified to genus level ATCC 12022 Shigella flexneri
Identified as E. coli ATCC 9290 Shigella sonnei 22
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Positive blood culture bottles
MALDT TOF result -Organism (no) Species level No. (%) Genus level No. (%) Wrong ID No. (%) Comment/In house result
E. Coli (44) 44 (100%) 0 (0%) 0 (0%)
Klebsiella pneumoniae (13) 13 (100%) 0 (0%) 0 (0%)
Proteus mirabilis (5) 5 (100%) 0 (0%) 0 (0%)
Enterobacter aerogenes (2) 2 (100%) 0 (0%) 0 (0%)
Salmonella species (2) 0 (100%) 2 (100%) 0 (0%) Confirmed to group level by API and serology
Serratia marcescens (1) 1 (100%) 0 (0%) 0 (0%)
Bacteroides fragilis (3) 3 (100%) 0 (0%) 0 (0%)
Staphylococcus aureus (9) 9 (100%) 0 (0%) 0 (0%) 8 MSSA, 1 MRSA
Corynebacterium striatum (2) 2 (100%) 0 (0%) 0 (0%)
Clostridium perfringens (1) 1 (100%) 0 (0%) 0 (0%)
Enterococcus avium (1) 1 (100%) 0 (0%) 0 (0%)
Parvimonas micra (1) 1 (100%) 0 (0%) 0 (0%)
Staphylococcus epidermidis (4) 2 (50%) 2 (50%) 0 (0%) S. epidermidis (2), CNS (2)
Staphylococcus hominis (1) 0 (100%) 1 (100%) 0 (0%) CNS
Streptococcus agalactiae (3) 3 (100%) 0 (0%) 0 (0%)
Streptococcus dysgalactiae (1) 1 (100%) 0 (0%) 0 (0%)
Streptococcus mitis (2) 1 (50%) 1 (50%) 0 (0%) S. mitis (1), Viridans strep (1)
Streptococcus oralis (1) 1 (100%) 0 (0%) 0 (0%)
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Special consideration
• E. coli / Shigella – Lactose fermenting – Motility – Serology
• Streptococcus pneumoniae / S. mitis / S. oralis – Optochin susceptibility – Slidex pneumo-kit
• Salmonella species – Serology typing – API 20E for S. typhi, S. paratyphi and blood culture isolates
• Raoultella ornithinolytica / Klebsiella oxytoca – Ornithine decarboxylase test
• Not include in current database: Bacillus anthracis, Brucella species, Burkholderia mallei, Clostridium botulinum, Vibrio cholera
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Implementation date in UCH 15 April 2015
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Challenges
• Staff training • Testing and reporting algorithm • Quality control issues
– BTS, Standard strain, blank control, data transfer
• Equipment and consumable maintenance – Life span of laser, plate
• Re-design workflow • Laboratory accreditation • Integration with other equipment - AST • Laboratory automation • Back up plan
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Positive
• Faster TAT – life threatening diseases – MALDI-TOF + PCR for rapid identification of MRSA in
blood culture – Same date result as for gram stain vs 2-3 days later
• Reduce in consumable cost • Reduce manual work error • Reduce unnecessary workload • Workflow reengineering
– Formation of mega-bench – Extend service hours
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Thank you
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Acknowledgement
Dr Kitty Fung (CONS) Dr Sandy Chau (AC) Mr Ricky Ng (MT) Mr Jason Cheng (AMT) Mr Kelvin Tsui (AMT)
UCH Microbiology Team Members