Yonsei Med J.  2015 Mar;56(2):550-555. 10.3349/ymj.2015.56.2.550.

Comparison of MALDI-TOF MS, Housekeeping Gene Sequencing, and 16S rRNA Gene Sequencing for Identification of Aeromonas Clinical Isolates

Affiliations
  • 1Department of Laboratory Medicine and Genetics, Soonchunhyang University College of Medicine, Cheonan, Korea.
  • 2Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea. leekcp@yuhs.ac
  • 3Department of Laboratory Medicine, Hanyang University College of Medicine, Hanyang University Seoul Hospital, Seoul, Korea.

Abstract

PURPOSE
The genus Aeromonas is a pathogen that is well known to cause severe clinical illnesses, ranging from gastroenteritis to sepsis. Accurate identification of A. hydrophila, A. caviae, and A. veronii is important for the care of patients. However, species identification remains difficult using conventional methods. The aim of this study was to compare the accuracy of different methods of identifying Aeromonas at the species level: a biochemical method, matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS), 16S rRNA sequencing, and housekeeping gene sequencing (gyrB, rpoB).
MATERIALS AND METHODS
We analyzed 65 Aeromonas isolates recovered from patients at a university hospital in Korea between 1996 and 2012. The isolates were recovered from frozen states and tested using the following four methods: a conventional biochemical method, 16S rRNA sequencing, housekeeping gene sequencing with phylogenetic analysis, and MALDI-TOF MS.
RESULTS
The conventional biochemical method and 16S rRNA sequencing identified Aeromonas at the genus level very accurately, although species level identification was unsatisfactory. MALDI-TOF MS system correctly identified 60 (92.3%) isolates at the species level and an additional four (6.2%) at the genus level. Overall, housekeeping gene sequencing with phylogenetic analysis was found to be the most accurate in identifying Aeromonas at the species level.
CONCLUSION
The most accurate method of identification of Aeromonas to species level is by housekeeping gene sequencing, although high cost and technical difficulty hinder its usage in clinical settings. An easy-to-use identification method is needed for clinical laboratories, for which MALDI-TOF MS could be a strong candidate.

Keyword

Aeromonas; sequencing; MALDI-TOF MS

MeSH Terms

Aeromonas/classification/*genetics/isolation & purification
DNA, Bacterial/genetics
Genes, Essential/*genetics
Humans
Molecular Typing/*methods
Phylogeny
RNA, Ribosomal, 16S/*genetics
Republic of Korea
Sensitivity and Specificity
Sequence Analysis, DNA/*methods
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods
DNA, Bacterial
RNA, Ribosomal, 16S
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