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MEDI CAL MICRO BIO LO GY INVITED ARTICLE

Melvin P. Weinstein and L. Barth Reller, Section Editors

Matrix-Assisted Laser Desorption Ionization


Time of Flight Mass Spectrometry in Clinical
Microbiology
Robin Patel
Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology and Division of Infectious Diseases, Department of Medicine, Mayo
Clinic, Rochester, Minnesota

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

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proteomics became possible. It took until the 1990s for develop- triuoroacetic acid) isolates microbial molecules from each
ment of libraries of reference spectra and software for bacterial other; microbial and matrix molecules on the target plate are
identication, and until the past few years for commercialization desorbed, with the majority of energy being absorbed by the
of the technology [1, 5]. MALDI-TOF MS, used for a few years matrix, converting it to an ionized state. Through random colli-
in European clinical microbiology laboratories, and being rap- sion in the gas phase, charge is transferred from matrix to mi-
idly adopted worldwide, is likely to antiquate most biochemical crobial molecules; analytes within the mass range specied are
microbial identication in the near future. measured, the most abundant being ribosomal proteins. The
The simplest MALDI-TOF MS applications test bacterial or cloud of ionized microbial proteins is funneled through a posi-
yeast colonies without elaborate preparation and using minimal tively charged electrostatic eld into a time of ight or TOF
consumables, providing rapid and low-cost identication. mass analyzer, a tube under vacuum. The ions travel toward an
Testing begins by picking an unknown colony from a culture ion detector with small analytes traveling fastest, followed by
plate to a spot on a MALDI-TOF MS target plate (Figure 1). progressively larger analytes. A mass spectrum is generated,
The cells may be treated on the target plate (we use formic representing the number of ions of a given mass impacting the
acid) and are ultimately overlain with 12 L of matrix. Follow- ion detector over time.
ing a short drying period, the plate is placed in the ionization Analytes are not individually characterized; instead, the gen-
chamber of the mass spectrometer (Figure 2). erated mass spectrum provides a prole (ngerprint) of the
MALDI refers to the matrix, which assists in the desorp- unknown microorganism. Generated mass spectra are unique
tion and ionization of microbial analytes through pulses of to individual microorganism types, with peaks specic to
energy from an ultraviolet N2 laser. The matrix (eg, -cyano-4- genera, species, and even strains. The test isolates mass spec-
hydroxycinnamic acid dissolved in 50% acetonitrile and 2.5% trum is automatically compared to a database of reference

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.

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necessary. In the absence of mass spectral entries in a database,
entries may be manually added (assuming availability of requi-
site isolates). The time from putting the target plate into the in-
strument to nal result is fast; for example, the Bruker system
produces results in 3 minutes per isolate. No mass spectrome-
try expertise is required, and the technology is green with re-
usable target plates available and few disposables.
Commercial MALDI-TOF MS systems are available from
Bruker Daltonics Inc (Billerica, Massachusetts) and bioMrieux
Inc. A system used primarily in France (Andromas, Paris,
France), will not be further discussed. The Bruker Biotyper
system is most well studied and includes a mass spectrometer,
software, and library; over the past few years, improved software
and progressively more comprehensive and better curated mass
spectral libraries have been made available. AnagnosTec
(Zossen, Germany) previously marketed a microbial database
called SARAMIS used with Shimadzus AXIMA Assurance
mass spectrometer (Shimadzu, Columbia, Maryland), which
was acquired by bioMrieux in 2010; with this acquisition, the
systems name was changed to VITEK MS RUO. BioMrieux
developed its own database/operating software/algorithms, re-
ferred to as VITEK MS (including a prerelease version of the
VITEK MS v1.1 database [6], the v1 system/v1.1 database [710],
the v2.0 system/v2.0 database and algorithms, and VITEK MS
Plus, which incorporates the VITEK MS v2.0 and SARAMIS
v4.0 databases). Rapidly implemented progressive improve-
Figure 2. Matrix-assisted laser desorption ionizationtime of ight ments in both systems are enhancing the clinical laboratorys
mass spectrometer. The target plate is placed into the ionization chamber ability to identify a range of organisms but render it challenging
of the mass spectrometer. Spots to be analyzed are shot by an ultraviolet for those reading the literature to compare studies due to vari-
N2 laser desorbing microbial and matrix molecules from the target plate.
able software, interpretive rules, databases, mass spectrometers,
The majority of energy is absorbed by the matrix, converting it to an
ionized state. Through random collision in the gas phase, charge is trans- comparators, specimen preparations, organism sets (ie, en-
ferred from matrix to microbial molecules. The cloud of ionized molecules riched for unusual organisms, or not), and so forth. Current
is funneled through a positively charged electrostatic eld into the time of systems databases are generally best for common aerobic
ight mass analyzer, a tube under vacuum. The ions travel toward an ion gram-negative bacilli and gram-positive cocci, and may lack
detector with small analytes traveling fastest, followed by progressively some esoteric organisms, such as certain anaerobes, fungi, and
larger analytes. As ions emerge from the mass analyzer, they collide with
mycobacteria. Given changing nomenclature and ongoing de-
an ion detector generating a mass spectrum representing the number of
ions hitting the detector over time. Although separation is by mass- scription of new species and emerging microorganisms, regular
to-charge ratio, because the charge is typically single for the described ap- and ongoing updates to databases are imperative to ensure clin-
plication, separation is effectively by molecular weight. Reproduced by ical utility. Databases should include entries representing major
permission of Mayo Foundation for Medical Education and Research. All phylogenetic lineages within each species. It is possible for
rights reserved.
users to add their own mass spectral entries to enhance existing
databases or create their own database by including locally im-
portant strains or strains not well represented in commercial
spectra to determine the relatedness of the spectrum to spectra libraries.
in the database; a list of most closely related organisms is gener- The Bruker and bioMrieux MALDI-TOF MS systems differ
ated, each with a numeric ranking (percentage or score) indicat- in databases, algorithms used to identify organisms, and instru-
ing the level of condence in identication. Depending on how mentation. Numeric rankings are reported on different scales,
high the value is, the organism is identied at the family, genus, and are not directly comparable. Brukers Microex LT mass
or species level. As with any identication system, well-curated spectrometer is a desktop instrument, whereas bioMrieuxs is
spectral databases representing comprehensive collections of a larger, oor model. At this time, neither system is approved
correctly named and clinically relevant bacteria and fungi are by the US Food and Drug Administration.

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Table 1. Examples of Recent Evaluations of Matrix-Assisted Laser Desorption IonizationTime of Flight Mass Spectrometry for Routine
Bacterial Identication

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

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supplementation will improve anaerobic identication to a Compared to standard methods, MALDI-TOF MS improves
level previously possible only with 16S ribosomal RNA gene se- turn-around time for bacterial and fungal identication by an
quencing or gas liquid chromatography. average of 1.45 days [42], and, because only a small amount of
MALDI-TOF MS can accurately identify Francisella tularen- organism is required, testing can be performed directly from
sis and Brucella species; however, the Biotyper library does not single colonies on primary culture plates, whereas other
contain and will not identify these organisms. Use of Brukers methods may require subculture. Tests for screening for some
Security Relevant database enables Brucella species and F. enteric pathogens (eg, triple sugar iron agar for Salmonella
tularensis identication [28]. species) may be eliminated [43].
A handful of investigators have reported using MALDI-TOF MALDI-TOF MS reagent costs are approximately $0.35/test;
MS for mycobacteria. This requires special processing to kill implementation reduces reagent and labor costs for identica-
tested organisms (for safety), disrupt clumped cells, and break tion, in one model, by 57% within 1 year [42]. An estimated
down cell envelopes. Current commercial libraries inadequately 87% of isolates are identied on the rst day (compared with
address the clinically relevant Mycobacterium species, but with 9% with standard techniques), with nal identications a day
appropriate library construction, MALDI-TOF MS should be earlier for most organisms, and several days earlier for bio-
able to identify most, with a few caveats expected. Members of chemically inert, fastidious, or slow-growing organisms [42].
the Mycobacterium tuberculosis complex are identied at the DNA sequencing expenses are avoided for some esoteric organ-
complex level [29]; some species (eg, Mycobacterium abscessus/ isms, waste disposal is decreased, and quality control and labo-
massiliense; Mycobacterium mucogenicum/phocaicum; Myco- ratory technologist training/labor for replaced/retired tests are
bacterium chimaera/intracellulare) may not be well differentiat- eliminated [44].
ed from one another [29], and identication from liquid media Adoption of MALDI-TOF MS impacts laboratory workow [9].
may be more challenging than from colonies on solid media [30]. Time at the bench assessing primary cultures is relatively unaf-
Beyond bacteria, MALDI-TOF MS can identify yeast, out- fected, with subcultures needed for susceptibility testing. Gram
performing some conventional phenotypic systems, and distin- staining of colonies may not always be needed, as this informa-
guishing Candida dubliniensis and albicans; Candida rugosa tion is not required for MALDI-TOF MS. For some organisms
and pararugosa; Candida norvegensis, krusei, and inconspicua; (eg, S. aureus), rapid tests performed at the bench will remain.
Candida parapsilosis, orthopsilosis, and metapsilosis [31]; and MALDI-TOF MS has limitations (Table 2). Unlike publically
(with database supplementation) Cryptococcus neoformans and available sequence databases such as GenBank, MALDI-TOF
gattii [3234]. Dhiman et al evaluated the Biotyper system for MS databases are proprietary. Although low identication per-
identication of 138 common and 103 unusual yeast isolates, centages for some organisms may be improved by user addition
and reported 96% and 85% accurate species-level identication, of mass spectral entries of underrepresented species or strains
respectively [35]. MALDI-TOF MS may outperform current (to cover intraspecies variability) to the database, or even read-
systems to identify esoteric and sometimes misidentied Candida dition of reference strain spectra [26], doing so may be beyond
species, such as Candida famata [31]. Although older studies the capabilities of some laboratories. Because of low scores/per-
used preparatory extraction for yeasts, we and others use the centages, repeat testing is required for approximately 10% of
same direct testing strategy we use for bacteria (Figure 1) [36, 37]. isolates [42]. Growth on some media (eg, colistin-nalidixic acid
Few lamentous fungi are included in current commercial agar) may be associated with low scores/percentages [45], and
databases. Filamentous fungi exhibit variable phenotypes; tiny or mucoid colonies may fail identication [9, 46]. Rened
protein spectra may vary with growth conditions or with the criteria are needed to distinguish closely related species and to
zone of fungal mycelium analyzed. De Carolis et al developed a differentiate them from the next best taxon match [47]. For
library of Aspergillus species, Fusarium species, and Mucorales certain species of organisms, genus- or species-specic (includ-
using the Biotyper system and identied 97% of 94 isolates to ing lowered) cutoffs may be appropriate [13, 16, 48]. Laboratory
the species level [38]. Using the VITEK MS v1 system/v1.1 da- errors may occur, including colony inoculation in erroneous
tabase and direct on-plate testing, Iriart et al identied 82% of target plate locations, testing impure colonies, smearing be-
44 Aspergillus isolates (including all isolates with species in the tween spots, failure to clean target plates, and erroneous result
database) [7]. Theel et al developed a dermatophyte library and entry into laboratory information systems. There is a learning
used it to identify 93% and 60% of 171 dermatophyte isolates curve to applying ideal colony amounts to target plates [9]. In-
to the genus and species levels, respectively, using the Biotyper strument cost is comparable to that of other common laborato-
system [39]. Preliminary studies indicate that Pseudallescheria/ ry equipment; laser, software, hardware, or mass spectrometer
Scedosporium complex species are identiable [40]. Beyond failure require an appropriate service plan. Although MALDI-
fungi, MALDI-TOF MS has been used for Prototheca species TOF MS is generally reproducible, sources of variability in-
identication [41]. clude the mass spectrometer, matrix and solvent composition,

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Table 2. Advantages and Limitations of Matrix-Assisted Laser fragilis likely to be carbapenem resistant (cA positive) [56]
Desorption IonizationTime of Flight Mass Spectrometry in Clini- may be called out (as markers for possible resistance).
cal Microbiology Although direct testing of clinical specimens is not generally
feasible because of a high limit of detection, urine may be
Advantages Limitations
tested directly due to the high numbers of bacteria present in
Rapid turn-around time Does not provide antimicrobial clinically infected urine (although -defensins 1, 2, and 3 may
susceptibility
impair database matching [57]).
Single colony requirement Requires isolated colony
Automated, high Repeat testing occasionally
Rapid identication of microorganisms growing in blood
throughput required culture bottles is promising, but requires preparatory specimen
Broad applicability to Not cleared by the US Food and processing as blood culture bottles contain macromolecules
bacteria and fungi, Drug Administration
including esoteric
from blood and growth media. Processing is accomplished with
organisms differential centrifugation and washings, selective lysis of blood
Databases may be Identification limited by entries in cells (eg, using water, ammonium chloride, saponin, sodium
expanded by users database; databases vary, not
publicly available
dodecyl sulfate), separator gels, ltration, and so on; commer-
Minimal consumables Laser, hardware, software, mass cial blood culture bottle processing using the Sepsityper
spectrometer failure potential (Bruker Daltonics) is available [5864]. Although results are
testing downtime
valid when obtained, the yield is generally not as good as direct
Cost-effective Instrument cost
colony testing with a higher percentage of gram-negative than
Generalizes to bacteria and Misidentifications: failure to test
yeast pure colonies or to clean target gram-positive organisms being identied [58]; polymicrobial
plates cultures may not be fully characterized (although strategies are
Some closely related organisms being developed). Most Candida species are identiable [65].
not differentiated (eg,
Escherichia coli and Shigella An alternate approach is to subculture positive blood culture
species) bottles to solid media and test growth after a short period (eg,
Growth on some media 24 hours) of incubation [66, 67]. By testing of positive blood
associated with no identification
(without extraction) culture bottles using MALDI-TOF MS, the time to organism
Tiny or mucoid colonies may not identication may be reduced by a day or more, which may
be identified serve as a guide for empirical treatment [68], but antimicrobial
susceptibility is not provided. Recently, MALDI-TOF MS has
been tied with direct antimicrobial susceptibility testing from
technologists, culture conditions, and biological variability; positive blood culture bottles [69, 70], improving time to
quality control strategies are being dened. Notably, MALDI- optimal therapy and decreasing hospital length of stay and
TOF MS may yield different (generally more accurate) identi- costs [71].
cation than current systems [11, 49]. In summary, MALDI-TOF MS is a quantum leap forward
Antimicrobial susceptibility is not directly determined with for rapid and accurate identication of cultured bacteria and
the above-described strategy. By rapid organism identication, fungi in clinical microbiology. This is incontrovertibly bene-
intrinsic antimicrobial resistance characteristics of particular cial to laboratories, and decreased expense is helpful to labora-
species (or typical susceptibility of the identied species based tories and patients alike. MALDI-TOF MS implementation
on local antibiograms) may guide therapy. Some investigators may impact patient outcomes and/or cost of care, depending
have incubated bacteria with antibiotics and measured antibiot- on its application. Further, this new technology may provide
ic degradation using MALDI-TOF MS; this requires specic better denition of the epidemiology, pathogenesis, and antimi-
system conguration and incubation (ie, to allow antibiotic hy- crobial susceptibility of hitherto unrecognized (or misidenti-
drolysis) and applies only to resistance mechanisms associated ed) microorganisms.
with antibiotic degradation (eg, -lactamases) [50]. Although
detection of methicillin resistance in S. aureus has been contro- Notes
versial, this does not appear to be feasible using the Biotyper
Acknowledgments. I thank Dr Nancy L. Wengenack, Scott A. Cun-
software in detection ranges and instrument settings preset for
ningham, Brenda L. Dylla, and Sherry M. Ihde for their thoughtful reviews
microbial identication [51]. Microbial strain typing is under of this manuscript.
development with no current universal protocol; innovations Potential conicts of interest. Author certies no potential conicts of
and advances are expected. With strain typing [52, 53], strains of interest.
The author has submitted the ICMJE Form for Disclosure of Potential
S. aureus likely to be methicillin resistant (eg, USA300 [54]), en- Conicts of Interest. Conicts that the editors consider relevant to the
terococci likely to be vancomycin resistant [55], or Bacteroides content of the manuscript have been disclosed.

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