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A modified protocol for the direct identification of positive blood cultures by MALDI-TOF MS.

Rapid identification of organisms in positive blood cultures reported with appropriate antibiotic susceptibility testing is an important function of the clinical microbiology laboratory (1). Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has recently been introduced into clinical microbiology laboratories in New Zealand and overseas. MALDI-TOF uses soft ionisation technology to generate single-charged protein ions, which pass a high vacuum electromagnetic field with different flight times that are captured by a detector to produce an organism's proteomic fingerprint profile. This innovative technique has been called revolutionary in microbiology, being simple, fast, accurate and cost effective (2).

MALDI-TOF is primarily used to identify colonies growing on agar media. However, its ability to identify organisms from broth, such as blood cultures, can lead to a reduction in the turn -around time for targeted treatment of blood stream infection. Several protocols have been reported for the rapid direct detection of microbes from positive blood culture vials, including a centrifugation/washing method, a lysis solution method and a gel-based tube method (3,4,5). The aim of this study was to compare direct MALDI-TOF MS identification of positive blood cultures using an optimised dual protocol, with the conventional method.

From August to November 2014, 52 positive blood culture samples (26 BACTEC plus Aerobic/F blood culture vials, 26 BACTEC lytic 10 Anaerobic/F blood culture vials) were sub-cultured onto agar plates and incubated overnight to obtain bacterial colonies. The colonies were identified by Bruker microflex[TM] LT MALDI-TOF (Bruker Daltonics, Bremen, Germany). Additionally, all blood culture broths were processed directly by the following modified in-house protocol.

Flagged positive blood culture broths (6ml from aerobic vials, 10ml from anaerobic vials) were injected into BD Vacutainer tubes (SSTII gel tube for aerobic vials, non-additive Z tube for anaerobic vial), followed by centrifugation (2,000g and 10 min for aerobic vials; 4,000g and 10 min for anaerobic vials). The supernatant was carefully pipetted off without disturbing the sediment layer below, 2ml distilled water added and gently mixed until cloudy; and 1.5ml of this suspension was then transferred to a micro centrifuge tube and spun at 13,000rpm for two minutes. After decanting off the supernatant, 250 [micro]l of distilled water was added, mixed well and 750 [micro]l of 100% ethanol was then added. After 10 minutes the mixture was centrifuged twice for two minutes at 13,000rpm. The supernatant was again discarded and the pellet dried in a biohazard-cabinet for five minutes until all the ethanol had evaporated. Then, 50 [micro]l 70% formic acid was added, mixed well, and left for five minutes. This was followed by adding 50 [micro]l of acetonitrile, thoroughly mixed and then centrifuged at 13,000rpm for two minutes. Finally, 1 [micro]l of supernatant from the upper part of extraction was spotted onto a target plate in duplicate, air dried for five minutes, then 1 [micro]l matrix HCCa ([alpha]-cyano-4-hydroxycinnamic acid with 50% acetonitrile and 2.5% trifluoroacetic acid) was overlaid and left to dry for 20 minutes. The target plate was then inserted in to the Bruker microflex LT for analysis. (Ion source voltages: 20kv and 18kv; laser shoots: 240 measurements per well; m/z range: 2,000 to 20,000; linear positive mode with delayed extraction).

According to the Bruker direct blood culture ID biotyper score system (species level ID [greater than or equal to] 1.8; genus level ID [greater than or equal to] 1.6) (4), when comparing direct MALDI-TOF identification from blood culture broth with routine MALDI on colonies, the overall concordance in this trial was 69% at the species level and 78% at genus level. 10 of 11 (91%) Staphylococcus aureus and 9 of 9 (100%) Escherichia coli were accurately identified (Table 1). No misidentification was observed.

A correlation was found between the microorganisms' physical characteristics and the optimal protocol parameters. Numerous studies have shown that Gram-negative bacilli ID scores are superior to Gram-positive cocci ID scores, particularly problematic streptococci (3). However, these studies did not use "flexible" assay conditions for those different organisms. With our optimised dual protocol, 6ml broth was used for Gram negative bacteria in aerobic vials as with other protocols, but 10ml broth was used for Gram-positive cocci in anaerobic vials (6). In contrast to 10 minutes at 2,000g centrifugation for Gram-negative bacteria in other studies, in order to harvest enough bacterial pellet for MALDI-TOF we applied 10 minutes at 4,000g to anaerobic vials with Gram-positive cocci, as they have a smaller size and different biomass (7,8). As shown in the table, six Streptococcus pneumoniae and two [alpha]-haemolytic Streptococcus spp. Isolates scored over 2.0 by applying this protocol.

Another important part of the protocol is the optimisation of the manufacturer's recommended ethanol FA/ACN full extraction method. To date, previous studies followed the manufacturer's recommended method, i.e. without an incubation time for ethanol or the FA extraction steps (3,5). However, an additional 10 minute incubation for ethanol protein precipitation and an additional five minutes incubation time for FA cell lysis were found to improve the test performance. Extended conditions, i.e. 20 minutes of 75% ethanol and 10 minutes of FA incubation, may be useful for Gram-positive bacilli which have thick and tough cell walls, such as Clostridium perfringens (See Table).

This study was limited by the small numbers of positive blood cultures. The optimized procedure only requires one to two hours, and can be done the same day the bottles signal as positive. In addition, with the ID, AST testing can occur earlier, which facilitates correct antibiotic selection, particularly where resistance is a concern.

In summary, this pilot study investigated a modified rapid direct identification protocol for positive blood cultures and confirmed it is a promising approach to reduce laboratory turnaround time and consequently to improve blood stream infection management.


The author would like to acknowledge the staff of Labtests Microbiology Department for their encouragement and support. Special thanks Janet Wilson for critical review of the manuscript and the anonymous reviewer for helpful comments.


Michael Sun, BSc BMLSc, Medical Laboratory Scientist Microbiology Department, Labtests, Auckland



(1.) Munson EL, Diekema DJ, Beekmann SE, Chapin KC, Doern GV. Detection and treatment of bloodstream infection: laboratory reporting and antimicrobial management. J Clin Microbiol 2003; 41: 495-497.

(2.) Croxatto A, Prod'hom G, Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 2012; 36: 380-407.

(3.) Drancourt M. Detection of microorganisms in blood specimens using matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a review. Clin Microbiol Infec 2010; 16: 1620-1625.

(4.) Buchan BW, Riebe KM, Ledeboer NA. Comparison of the MALDI Biotyper system using Sepsityper specimen processing to routine microbiological methods for identification of bacteria from positive blood culture bottles. J Clin Microbiol 2012; 50: 346-352.

(5.) Schieffer KM, Tan KE, Stamper PD, Somogyi A, Andrea SB, Wakefield T, et al. Multicenter evaluation of the Sepsityper[TM] extraction kit and MALDI-TOF MS for direct identification of positive blood culture isolates using the BD BACTEC[TM] FX and VersaTREK[R] diagnostic blood culture systems. J Appl Microbiol 2014; 116: 934-941.

(6.) Del Peloso PF, da Costa Leite C, Torres Filho HM, Nunes JD. Direct identification of pathogens in blood cultures by MALDI-TOF. J Infect Control 2013; 2: 128-129.

(7.) Engelkirk, PG, Duben-Engelkirk J. Laboratory Diagnosis of Infectious Disease: Essentials of Diagnostic Microbiology. Lippincott Williams & Wilkins, Baltimore, USA, 2008; 759 pp.

(8.) Karl DM. Determination of in situ microbial biomass, viability, metabolism, and growth. In ER Leadbetter and JS Poindexter, Editors. Bacteria in Nature: Methods and Special Applications in Bacterial Ecology. Plenum Press, New York, USA, 1986; 85-251.

Michael Sun

Labtests, Auckland
Table 1. ID results by direct ID protocol and routine culture
protocol using MALDI-TOF

MALDI-TOF direct blood culture ID results and Biotyper score

                                  Species ID     Species     Genus
                                Score [greater   ID Score   ID Score
                                than or equal    1.9-1.8    1.7-1.6
                                    to] 2

Staphylococcus aureus                 8             2          1
Staphylococcus epidermidis *                        2          1
Staphylococcus capitis *              1
Staphylococcus hominis *              1             1          1
Streptococcus dysgalactiae            1
Streptococcus pneumoniae              6
a-haemolytic streptococcus            2             1          1
Enterococcus faecalis                                          1
Escherichia coli                      9
Clostridium perfringens               1
Polymicrobial contaminated
  sample ([dagger])
Total                                 29            6          5

MALDI-TOF direct blood culture ID results and Biotyper score

                                Unreliable   No Peaks
                                ID (<1.5)

Staphylococcus aureus
Staphylococcus epidermidis *
Staphylococcus capitis *
Staphylococcus hominis *
Streptococcus dysgalactiae
Streptococcus pneumoniae            4
a-haemolytic streptococcus          3           3
Enterococcus faecalis               1
Escherichia coli
Clostridium perfringens
Polymicrobial contaminated                      1
  sample ([dagger])
Total                               8           4

MALDI-TOF direct blood          Routine
culture ID results and          MALDI-TOF
Biotyper score                  Colony ID
                                (number of isolates)

Staphylococcus aureus           Staphylococcus aureus (11)
Staphylococcus epidermidis *    Staphylococcus epidermidis (3)
Staphylococcus capitis *        Staphylococcus capitis (1)
Staphylococcus hominis *        Staphylococcus hominis (3)
Streptococcus dysgalactiae      Streptococcus Dysgalactiae (1)
Streptococcus pneumoniae        Streptococcus Pneumoniae (10)
a-haemolytic streptococcus      a-haemolytic streptococcus
  spp.                            spp. (10)
Enterococcus faecalis           Enterococcus faecalis (2)
Escherichia coli                Escherichia coli (9)
Clostridium perfringens         Clostridium perfringens (1)
Polymicrobial contaminated      Mixed organisms in plates, No
  sample ([dagger])               process (1)
Total                           52

* Coagulase Negative Staphylococcus group. ([dagger]) Not
included in study statistics.
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Title Annotation:SCIENTIFIC LETTER; matrix-assisted laser desorption ionisation time-of-flight mass spectrometry
Author:Sun, Michael
Publication:New Zealand Journal of Medical Laboratory Science
Geographic Code:1USA
Date:Apr 1, 2015
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