Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry as an Alternative to 16S rRNA Gene Sequencing for Identification of Difficult-To-Identify Bacterial Strains

A. Bizzini; K. Jaton; D. Romo; J. Bille; G. Prod'hom; G. Greub

doi:10.1128/JCM.01463-10

DOI: 10.1128/JCM.01463-10

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Fig. 1.
Identification (ID) yield of MALDI-TOF MS analysis for 410 bacterial isolates identified at the species level by 16S rRNA gene sequencing.

Table 1.

Description of discordant results at the species level between the 16S rRNA gene identification (“gold standard”) and MALDI-TOF MS among strains with a score of x ≥ 2

16S rRNA gene identification (no. of isolates)	MALDI-TOF MS identification (no. of isolates)	Presence in MALDI-TOF MS database (no. of spectra)^{^a}	Commentary (reference)	Result upon additional testing
Achromobacter xylosoxidans (2)	Achromobacter ruhlandii (2)	Yes (4)	This discordance has been observed in a previous study (1).	Positive reduction of nitrate into nitrite indicates that the correct identification is A. ruhlandii. A new MALDI-TOF MS identification with the updated database still yields A. ruhlandii.^{^b}
Acinetobacter junii (1)	Acinetobacter grimontii (1)	Yes (2)	A. grimontii is a heterotypic synonym of A. junii (16).	A new MALDI-TOF MS identification with the updated database still yields A. grimontii.^{^b}
Actinobacillus hominis (1)	Actinobacillus suis (1)	No	A. suis is mainly a pig pathogen and is rarely involved in human infections (10).	Lack of growth on MacConkey agar and α-haemolysis on blood agar indicates that the correct identification is A. hominis. A new MALDI-TOF MS identification with the updated database yields A. equuli.^{^b}
Aerococcus sanguinicola (1)	Aerococcus urinae (1)	Yes (1)	A. urinae and A. sanguinicola are difficult to identify by conventional phenotypic methods (2).	Positive pyrrolidonyl aminopeptidase activity indicates that the correct identification is A. sanguinicola. A new MALDI-TOF MS identification with the updated database now yields A. sanguinicola.^{^b}
Corynebacterium aurimucosum (1)	Corynebacterium minutissimum (1)	Yes (2)	C. aurimucosum is a recently described Corynebacterium species (18).	Positive hippurate hydrolysis indicates that the correct identification is C. aurimucosum. A new MALDI-TOF MS identification with the updated database now yields C. aurimucosum.^{^b}
Corynebacterium glucuronolyticum (3)	Corynebacterium seminale (3)	Yes (1)	C. seminale is a heterotypic synonym of C. glucuronolyticum (7).	A new MALDI-TOF MS identification with the updated database now yields C. glucuronolyticum.^{^b}
Dysgonomonas capnocytophagoides (1)	Dysgonomonas gadei (1)	No	Dysgonomonas are rare human pathogens which have been recently described (11).	Negative catalase reaction indicates that the correct identification is D. capnocytophagoides. A new MALDI-TOF MS identification with the updated database still yields D. gadei.^{^b}
Enterococcus saccharolyticus (1)	Enterococcus phoeniculicola (1)	Yes (1)	E. phoeniculicola has been isolated from a bird; it is not known as a human pathogen (12).	Positive mobility, a vancomycin MIC of 6, and a new biochemical identification by Vitek2 indicates that the isolate is E. casseliflavus. A new MALDI-TOF MS identification with the updated database now yields E. casseliflavus.^{^b}
Kingella kingae (1)	Kingella sp. (1)	Yes (3)	The presence of reference spectra of strains identified only to the genus level is misleading and precludes definitive identification to the species level; such spectra should be discarded from the database.	A new MALDI-TOF MS identification with the updated database now yields K. kingae.^{^b}
Lactobacillus fermentum (1)	Lactobacillus rhamnosus (1)	Yes (3)	Conventional methods often fail to identify lactobacilli at the species level (13).	An API 50 CH carbohydrate strip indicates that the correct identification is L. rhamnosus. A new MALDI-TOF MS identification with the updated database still yields L. rhamnosus.^{^b}
Ochrobactrum anthropi (1)	Ochrobactrum intermedium (1)	Yes (3)	O. anthropi and O. intermedium are phenotypically and genetically closely related pathogens (14).	Resistance to colistin indicates that the correct identification is O. intermedium. A new MALDI-TOF MS identification with the updated database still yields O. intermedium.^{^b}
Pandoraea sputorum (1)	Pandoraea pnomenusa (1)	No	Pandoraea species are difficult to differentiate by conventional and molecular methods (6).	A negative urease test and lack of growth at 42°C indicates that the correct identification is P. sputorum. A new MALDI-TOF MS identification with the updated database still yields P. pnomenusa.^{^b}
Pasteurella pneumotropica (1)	Pasteurella multocida (1)	No	P. pneumotropica is a rare human pathogen, difficult to identify by conventional methods (9).	A negative urease test, lack of growth on MacConkey agar, and coccoid Gram-negative staining indicate that the correct identification is P. multocida. A new MALDI-TOF MS identification with the updated database still yields P. multocida.^{^b}

↵a Presence of the 16S rRNA gene-identified species in the MALDI-TOF MS database. The number of different reference spectra per species is shown in parentheses.
↵b Database updated during the revision process to version 3.1 (5 July 2010), which contains 3,740 spectra.

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Supplemental file 1 - Table S1 (Comparison between 16S rDNA sequencing and MALDI-TOF MS identification techniques for 410 bacterial isolates encompassing 84 different genera and 207 different species)
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