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Despite widespread application of nucleic acid diagnostics, cultures remain integral in modern laboratories.
Because cultures detect a large number of organism types, it is unlikely that they will disappear from clinical
practice in the near future. Their downside is slow turn-around time, impacted by time to growth and identi-
cation of that growth. The latter is expedited using a new proteomic technology, matrix-assisted laser desorp-
tion ionizationtime of ight mass spectrometry (MALDI-TOF MS).
Keywords. mass spectrometry; bacteria; fungi; MALDI-TOF; matrix-assisted laser desorption ionization-time
of ight.
Despite widespread application of nucleic acid diagnos- catalase) are rapid, but identify limited organism types
tics, cultures remain integral in modern laboratories. (eg, Staphylococcus aureus). Biochemical test panels
Because cultures detect a large number of organism performed manually (eg, API strips, bioMrieux, Dur-
types, it is unlikely that they will disappear from clinical ham, North Carolina) or on automated instruments
practice in the near future. Their downside is slow (eg, VITEK, bioMrieux; BD Phoenix Automated Mi-
turn-around time, impacted by time to growth and crobiology System, BD, Franklin Lakes, New Jersey; Mi-
identication of that growth. The latter is expedited croScan, Siemens Healthcare Diagnostics, Tarrytown,
using a new proteomic technology, matrix-assisted New York) identify more microorganisms, but have
laser desorption ionizationtime of ight mass spec- longer turn-around times and costly consumables, and
trometry (MALDI-TOF MS). often require knowledge of the organism type being
Historically, identication of cultured bacteria and tested (eg, gram-positive cocci). Finally, broad-range
fungi has been a complex, algorithmic task. Textbooks, PCR followed by sequencing accurately identies bacte-
owcharts, and tables have been used to interpret ria and fungi but has a long turn-around time, and is
colony morphology as well as stains and biochemical expensive and performed in select laboratories. With
tests performed on colonies. Phenotypic tests may be MALDI-TOF MS, colonies growing in culture are inex-
contingent on subsequent growth, prolonging time to pensively and accurately identied in minutes, without
identication. Manual biochemical tests (eg, coagulase, a priori knowledge of microorganism type; users do
not even need to know whether a bacterium or a yeast
is being tested. The product of advances in mass spec-
Received 29 January 2013; accepted 5 April 2013; electronically published 17
trometry and bioinformatics, MALDI-TOF MS is revo-
April 2013. lutionizing bacterial and fungal identication in clinical
Correspondence: Robin Patel, MD, Mayo Clinic, Division of Clinical Microbiology,
microbiology [1].
200 First St SW, Rochester, MN 55905 ( patel.robin@mayo.edu).
Clinical Infectious Diseases 2013;57(4):56472
The concept of using mass spectrometry to identify
The Author 2013. Published by Oxford University Press on behalf of the Infectious bacteria (albeit not based on proteomics) was proposed
Diseases Society of America. All rights reserved. For Permissions, please e-mail:
in the 1970s [2]; with the Nobel Prizewinning invention
journals.permissions@oup.com.
DOI: 10.1093/cid/cit247 of MALDI-TOF MS in the 1980s [3, 4], whole-organism
Figure 1. Matrix-assisted laser desorption ionizationtime of ight mass spectrometry (MALDI-TOF MS) workow. A bacterial or fungal colony (typically
single) is picked from a culture plate to a spot on a MALDI-TOF MS target plate (a reusable or disposable plate with a number of test spots) using a
wooden or plastic stick, pipette tip, or loop. One or many isolates may be tested at one time. At our institution, cells are treated with formic acid on the target
plate. The spot is then overlain with 12 L of matrix. Following a short drying period, the plate is placed in the ionization chamber of the mass spectrometer
for analysis (see Figure 2). A mass spectrum is generated and automatically compared against a database of mass spectra by the software, resulting in identi-
cation of the organism (Candida parapsilosis in position A4 in the example). More complex preparatory protein extraction, commonly used in older studies, may
be performed prior to target plate inoculation. Although this yields high-quality mass spectra [46], it is technically cumbersome; direct on-plate testing using
formic acid identies a similar number of organisms [37]. Direct on-plate testing must be avoided with organisms hazardous to microbiology technologists (eg,
Brucella species) [28]. Reproduced by permission of Mayo Foundation for Medical Education and Research. All rights reserved.
Isolates % Identification
Period of
System No. Type Isolate Collection Genus Level Species Level Country Comparator Reference
Bruker Biotyper 1013 Bacteria 2 mo 99% 97% France Phoenix, API, Biochemical [72]
Bruker Biotyper 468 Bacteria 3 mo 97% 92% Japan MicroScan, API, Phoenix [73]
Bruker Biotyper 2781 Bacteria 1 mo 96% 85% Australia VITEK2, API, Biochemical [74]
Vitek MSa 767 Bacteria 6 wk 95% 87% France VITEK2 [8]
Bruker Biotyper/ 986 Bacteria 3 mo 96%/94% 93%/93% Belgium Bruker Biotyper [6]
Vitek MSb compared to
Vitek MS
a
v1 system/v1.1 database.
b
Prerelease version of v1.1 database.
Generally speaking, MALDI-TOF MS performs at least as Some closely related organisms, such as Escherichia coli and
well as, if not better than, automated biochemical identication Shigella species, are not differentiated. (To avoid potential mis-
for commonly encountered bacteria and yeast (Table 1), and identication, we attempt to avoid testing of suspect E. coli and
better for unusual organisms. We compared the BD Phoenix we perform additional testing if E. coli is suggested.) MALDI-
Automated Microbiology System and Biotyper system using TOF MS accurately detects Enterobacter cloacae complex,
440 common and unusual gram-negative bacilli; the former although it may not discriminate some species within this
correctly identied 83% and 75% of isolates to the genus and complex [9, 17]. Likewise, accurate differentiation of all species
species levels, respectively, whereas MALDI-TOF MS correctly of Acinetobacter may be challenging with current databases, al-
identied 93% and 82% of isolates to the genus and species though Acinetobacter baumannii is identiable [18]. Similar
levels, respectively [11]. We also evaluated the Biotyper system challenges exist with other identication systems. MALDI-TOF
using 217 clinical isolates of staphylococci, streptococci, and MS is exciting because of the breadth and depth of organism
enterococci, 98% and 79% of which were correctly identied to types that can be identied with one platform, including, but
the genus and species levels, respectively [12]. The performance not limited to, Aeromonas species [19], Campylobacter species,
of the 2 commercial systems appears to be similar. Martiny et al Arcobacter butzleri, and Yersinia enterocolitica [20]. MALDI-
reported 93% species-level identications of 1003 routine bac- TOF MS can identify and differentiate Capnocytophaga cani-
terial isolates with both a prerelease version of the VITEK MS morsus from Capnocytophaga cynodegmi [21]. Although typing
v1.1 database and the Biotyper system [6]. within the genus Salmonella is not generally possible, it may be
In most cases, organisms are either correctly identied or possible to distinguish Salmonella enterica subspecies enterica
yield a low score/percentage, indicating that identication has serovar Typhi from other S. enterica serovars [22]. And with
not been achieved; the latter typically implies no match in the user-supplemented databases, HACEK organisms [23], Legion-
database but can occur due to technically poor preparation. ella species [24], and Nocardia species [25] (the last with specif-
Misidentications are unusual but may occur with some closely ic extraction procedures) may be identied.
related organisms. Although a comprehensive review of identi- Jamal et al reported species-level identication of 89% and
cation of specic organisms is beyond the scope of this article, 100% of 274 routinely isolated anaerobic bacteria (enriched in
some generalizations can be made. Identication of staphylo- Bacteroides fragilis) using the Biotyper DB Update v3.3 and the
cocci [13] and -hemolytic streptococci is excellent [14]. The VITEK MS v1 system/v1.1 database, respectively [10]. Identi-
-hemolytic streptococci are more problematic because Strepto- cation of more esoteric anaerobes, including Prevotella species,
coccus mitis and Streptococcus oralis may be poorly differentiat- has been successful in 83% of cases with user supplementation
ed from one another and from Streptococcus pneumoniae, at of Brukers Reference Library 3.2.1.0 [26]. We evaluated a
least with the Bruker system [12, 15]; recent data suggest that diverse collection of 253 clinical anaerobic isolates using the Bi-
VITEK MS may overcome this limitation [8]. Arcanobacterium otyper system and a user-supplemented database; 92% and
haemolyticum, Rhodococcus equi, and all but select closely 71% of isolates were correctly identied to the genus and
related Corynebacterium species are reliably identied [9, 16]. species levels, respectively [27]. Further commercial database