MALDI-TOF MS in Clinical Microbiology

Comparative study of MALDI-TOF MS and VITEK 2 in bacteria

identification
Ling Guo, Liyan Ye, Qiang Zhao, Yanning Ma, Jiyong Yang, Yanping Luo

Department of Microbiology, General Hospital of PLA, Beijing 100853, China

Correspondence to: Yanping Luo. Department of Microbiology, PLA General Hospital, 28 Fuxing Road, Beijing 100853, China. Email: [email protected].

Background: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF

MS) has recently been introduced in diagnostic microbiology laboratories for the identification of bacterial
and yeast strains isolated from clinical samples. This study aimed to evaluate the accuracy of MALDI-TOF
MS in clinical microbiology diagnosis by comparing it with commonly-used VITEK 2 or gene sequencing.
Methods: The performances of MALDI-TOF MS and VITEK 2 were compared retrospectively for
identifying routine isolates. Discrepancies were analyzed by gene sequencing analysis of the 16S genes.
Results: For 1,025 isolates, classified as 55 species of 25 genera, 1,021 (99.60%) isolates were accurately
identified at the genus level, and 957 (93.37%) isolates at the species level by using MALDI-TOF
MS. A total of 949 (92.59%) isolates were completely matched by both methods. Both methods found
76 unmatched isolates among which one strain had no definite identification by MALDI-TOF MS and
VITEK 2 respectively. However, MALDI-TOF MS made no errors at the genus level while VITEK 2 made
6 (0.58%) errors at the genus level. At the species level, the identification error rates for MALDI-TOF MS
and VITEK 2 were 5.56% and 6.24%, respectively.
Conclusions: With a lower identification error rate, MALDI-TOF MS has better performance than
VITEK 2 in identifying bacteria found routinely in the clinical laboratory. It is a quick and cost-effective
technique, and has the potential to replace conventional phenotype methods in identifying common bacterial
isolates in clinical microbiology laboratories.

Keywords: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS);
VITEK2; bacteria identification

Submitted Jan 18, 2014. Accepted for publication Feb 26, 2014.
doi: 10.3978/j.issn.2072-1439.2014.02.18
View this article at: http://www.jthoracdis.com/article/view/2351/2939

Introduction molecular methods are not routinely used for bacterial

identification. A faster and easier technique for microbial
Traditionally, bacterial and fungal identifications in clinical
identification would greatly enhance the conventional
microbiology laboratories are mainly carried out according
laboratory in providing more timely feedback to clinic.
to phenotype characteristics, including identifications of This is especially true in cases when patients are critically
culture media, colony morphology, gram stain and various ill suffering from infectious diseases and where therapeutic
biochemical reactions (1). Although all of these methods intervention is urgently needed.
can achieve high accuracies, it usually takes minimum Matrix-assisted laser desorption ionization-time of flight
one day or longer to complete the whole identification mass spectrometry (MALDI-TOF MS) can be used to
process. Molecular methods, such as real-time PCR, gene obtain protein fingerprinting from whole bacterial cells (2).
sequencing and microarray analysis, are quick methods for Through comparing these fingerprints to a reference
bacterial and fungal identification, but they come at a very database by the use of various algorithms, bacteria can be
high cost and require highly-trained technicians. Therefore, rapidly identified. The earliest application of this technique

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Journal of Thoracic Disease, Vol 6, No 5 May 2014 535

for bacterial identification dates back to 1975 (3), while the before adding 1 μL VITEK MS-CHCA matrix. Finally,
first related article was published in 1996 (Holland, et al.) (4). the mass spectra acquired for each sample were compared
Studies in this field have been progressively advancing for to the known mass spectra contained in the database for,
the last decade (5). Until now, domestic comparative studies and given a confidence score according to how close the
on mass spectrometry and other methods are relatively few. acquired spectra matched those contained in the database.
In order to compare the performance differences between ATCC8739 was used as the quality control strain.
MALDI-TOF MS and VITEK 2, the latter being the
most-used automated identification technique in current
Gene sequencing
microbiology laboratories, we employed the two systems
in parallele to identify and analyze 1,025 isolates routinely Discrepancies between VITEK 2 and MALDI-TOF MS were
isolated in 2012 at a microbiology laboratory of PLA resolved by 16S rRNA gene sequencing. The results would be
General Hospital. considered valid if the homologous rate was above 99%.

Methods Standards for identification

Bacteria isolates In cases where the isolate was correctly identified at

the species level or at the generic level by both VITEK
A total of 1,025 isolates, composed of 1,020 bacterial strains
MS and VITEK 2, the results were considered to be in
and 5 fungal strains representing 25 different genera were
accordance with one another. In instances that the two
selected for analysis. These bacteria were routinely isolated
methods produced different results, or if the results from
from clinical patients, such as Pseudomonas spp, Acinetobacter
one method were not definite, 16S rRNA gene sequencing
spp that cause lung infections, Enterobacteriaceae that cause
was used to resolve identification discrepancies. For isolates
blood and urinary tract infections. In addition, there are also
misidentified at the genus level, the results were considered
some bacteria which grow slowly but have clinical significance
a major mistake in the identification analysis. For isolates
such as Eikenella corrodens, Listeria monotytogens, Haemophilus
misidentified at species level but correctly identified at the
infuenzae, etc.
genus level, the results were considered a minor mistake.
Results not able to distinguish two different bacteria of the
VITEK 2 identification same genus also were considered as minor mistakes (6,7).

GP, GN, YST, ANC and NH were selected to run

identification analysis according to the different strains to Results
be tested. The identification rate was expected to be above
Identification results by MALDI-TOF MS
93% by VITEK 2 (bioMérieux) (5), with quality control by
stages via ATCC25922, ATCC27853 and ATCC25923. Among the 1,025 total isolates, 1,021 (99.60%) isolates were
accurately identified at the genus level and 957 (93.37%)
isolates at the species level by MALDI-TOF MS.
MALDI-TOF MS identification

Strains were identified by MALDI-TOF MS using the

Matched results by the two identification methods
VITEK MS system (bioMérieux). Loops were used to select
and smear the subject isolates onto the sample spots on the Identification results for 949 (92.59%) isolates, belonging
target slide. Then 1 μL VITEK MS-CHCA matrix was to 23 genera and 48 species, were in agreement (see Table 1)
applied over the sample and air dried until the matrix and using both methods.
sample co-crystallized. The target slide with all prepared
samples then was loaded into the VITEK MS system to
Unmatched results by the two identification methods
acquire the mass spectra of whole bacterial cell protein,
mainly composed of ribosomal protein, for each sample. Among the 1,025 isolates, 76 (7.4%) isolates produced
In the case of yeasts, 0.5 μL VITEK MS-FA was added to discordant results between the two identification methods.
each sample on the target slide and allowed to air dry it One strain had no definitive identification for each

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536 Guo et al. Comparative study of MALDI-TOF MS and VITEK 2 in bacteria identification

Table 1 Matched results by both MALDI-TOF MS and VITEK 2 MALDI-TOF MS and VITEK 2. However, MALDI-TOF
Bacterial genera Number of strains MS made no errors at the genus level while VITEK 2
Acinetobacter banmannii complex 30 made 6 (0.58%) errors at the genus level. At the species
Corynebacterium jeikeium 1 level, the identification error rates of the two methods were
Citrobacter braakii 2 5.56% and 6.24% for MALDI-TOF MS and VITEK 2
Citrobacter freundii 6 respectively (Table 2).
Citrobacter koseri 1
Escherichia coli 297
Enterobacter aerogenes 13 Discussion and Conclusions
Enterococcus casseliflavus 2
In our laboratory, MALDI-TOF MS is an efficient, quick
Enterococcus faecalis 10
Enterococcus faecium 24
and relatively inexpensive per isolate method for identifying
Enterococcus gallinarum 1 pathogenic microorganisms including bacteria and fungi.
Enterococcus hirae 3 MALDI-TOF MS identification also is largely compatible
Klebsiella oxytoca 10 with a large range of culture media and culture conditions,
Klebsiella pneumonia 66 and is the fastest means to detect microbes in positive
Micrococcus ssp 3 blood culture (8). Furthermore, MALDI-TOF MS has
Morganella morganii 7 broader application prospects in the field of testing for drug
Pseudomonas aeruginosa 126 resistance (9,10).
Pseudomonas putida 1 Shortening the turnaround time to pathogen identification
Stenotrophomonas maltophilia 33 and offering quicker results to the clinic remain the most
Proteus mirabilis 75
important issues needed to be solved in the microbiology
Proteus vul.gr/proteus pen. 9
laboratory. Based on our data, experienced clinicians can treat
Procidencia rettgeri 2
critically infected patients appropriate antibiotic treatment
Staphylococcus aureus 76
given effective and timely identification of pathogenic
Staphylococcus epidermidis 36
Staphylococcus hominisssphominis 37
bacteria. Shortening the turnaround time permits the
Staphylococcus saprophyticus 1 clinician to treat patients faster, ultimately reducing the
Staphylococcus haemolyticus 14 fatality rates, the length of patient stay in the clinic, and
Staphylococcus cohnii 1 healthcare costs associated with patient care. MALDI-TOF
Staphylococcus capitis 5 MS offers one promising solution to shorten the turnaround
Serratia marcescens 23 time and relieve these pressures in the clinic.
Streptococcus parasanguinis 1 In the present study, we chose 1,025 pathogenic bacteria
Streptococcus pneumonia 4 routinely found in our laboratory for identification, and
Streptococcus mitls/Steptococcusoralis 3 compared the performance of MALDI-TOF MS to the VITEK
Streptococcus gallolyticus 1 2 system, the latter which is based on conventional biochemical
Streptococcus gordonii 1
identification that is presently found in most microbiology
Streptococcus sailvarius 1
laboratories. Our results showed that MALDI-TOF
Streptococcus agalatiae 5
MS offered higher identification accuracy and lower error
Streptococcus sanguinis 1
rates at the species level when compared to VITEK 2.
Shewanella algea 3
Vibrio parahaemolyticus 1
Additionally, MALDI-TOF MS dramatically shortened
Candida parapsilosis 2 identification time from 6-8 hours to just a few minutes.
Aeromonasssp 3 MALDI-TOF MS identified 99.60% of isolates to the
Chryseobacterium indologenes 1 genus level and 93.37% of isolates to the species level,
Eikenella corrodens 1 which are slightly higher rates than those previously
Salmonella group 2 reported (5,7,11-14). Van Veen et al., for example, achieved
Listeria monotytogens 1 accuracy rates of 97.1% and 92% to the genus and species
Haemophilus infuenzae 1 levels, respectively. The difference in accuracy is most likely
Burkholderia cepacia 1 due to the different choices of strains. The strains in van
Total 949 Veen’s study included 61 yeast strains, among which 96.7%

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Journal of Thoracic Disease, Vol 6, No 5 May 2014 537

Table 2 Unmatched results by both MALDI-TOF MS and VITEK 2

VITEK MS VITEK 2
Bacterial species Number of strains
Generic errors Species errors Generic errors Species errors
Acinetobacter banmannii 2 2
Acinetobacter jonnosonii 2 2
Citrobacter freundii 1 1
Enterobacter cloacae 46 46 46
Enterococcus faecium 1 1
Pseudomonas putida 1 1
Peudomonas aeruginosa 1 1
Staphylococcus hominis 4 4
Staphylococcus aureus 4 1 3
Staphylococcus epidermidis 1 1
Streptococcus agalactiae 2 2
Streptococcus mitis 3 3 3
Candida guilliermondii 1 1
Rhodotorula mucilaginosa 1 1 1
Achromobacter xylosoxidans 3 3
Chryse.indologenes 1 1 1
Listeria monocytogenes 1 1
Cryptococcus neoformans 1 1
Total 76 0 (0) 57 (5.56%) 6 (0.58%) 6 (6.24%)

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Cite this article as: Guo L, Ye L, Zhao Q, Ma Y, Yang J, Luo

Y. Comparative study of MALDI-TOF MS and VITEK 2 in
bacteria identification. J Thorac Dis 2014;6(5):534-538. doi:
10.3978/j.issn.2072-1439.2014.02.18

© Pioneer Bioscience Publishing Company. All rights reserved. www.jthoracdis.com J Thorac Dis 2014;6(5):534-538