Comparison of MALDI-TOF MS, Housekeeping Gene Sequencing, and 16S rRNA Gene Sequencing for Identification of Aeromonas Clinical Isolates
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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 analyzed65 Aeromonas isolates recovered from patients at a university hospital in Koreabetween 1996 and 2012. The isolates were recovered from frozen states and testedusing 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.
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 analyzed65 Aeromonas isolates recovered from patients at a university hospital in Koreabetween 1996 and 2012. The isolates were recovered from frozen states and testedusing 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.
참고문헌 (26)
- Steinberg J, "Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases", pp.465~478 (2010), Churchill Livingstone
- Janda JM, "The genus Aeromonas: taxonomy, pathogenicity, and infection", Clin Microbiol Rev, 23, pp.35~73 (2010)
- Benagli C, "A rapid MALDI-TOF MS identification database at genospecies level for clinical and environmental Aeromonas strains", PLoS One, 7, pp.e48441~ (2012)
- Nhung PH, "Use of the novel phylogenetic marker dnaJ and DNA-DNA hybridization to clarify interrelationships within the genus Aeromonas", Int J Syst Evol Microbiol, 57(Pt 6), pp.1232~1237 (2007)
- Küpfer M, "Genetic relationships of Aeromonas strains inferred from 16S rRNA, gyrB and rpoB gene sequences", Int J Syst Evol Microbiol, 56(Pt 12), pp.2743~2751 (2006)
- Lamy B, "Identification of Aeromonas isolates by matrix-assisted laser desorption ionization time-of-flight mass spectrometry", Diagn Microbiol Infect Dis, 71, pp.1~5 (2011)
- Murray PR, "Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: usefulness for taxonomy and epidemiology", Clin Microbiol Infect, 16, pp.1626~1630 (2010)
- Yáñez MA, "Phylogenetic analysis of members of the genus Aeromonas based on gyrB gene sequences", Int J Syst Evol Microbiol, 53(Pt 3), pp.875~883 (2003)
- Korczak B, "Phylogeny of the family Pasteurellaceae based on rpoB sequences", Int J Syst Evol Microbiol, 54(Pt 4), pp.1393~1399 (2004)
- Tamura K, "MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods", Mol Biol Evol, 28, pp.2731~2739 (2011)
- Mellmann A, "Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria", J Clin Microbiol, 46, pp.1946~1954 (2008)
- Chong Y, "Cultural and biochemical characteristics of clinical isolates of Aeromonas hydrophila", Yonsei Med J, 21, pp.52~57 (1980)
- Kwak CG, "Species and antimicrobial susceptibility of Aeromonas strains isolated from patients and environmental sources", Korean J Infect Dis, 19, pp.167~177 (1987)
- Janda JM, "Evolving concepts regarding the genus Aeromonas: an expanding Panorama of species, disease presentations, and unanswered questions", Clin Infect Dis, 27, pp.332~344 (1998)
- Soler L, "Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes", Int J Syst Evol Microbiol, 54(Pt 5), pp.1511~1519 (2004)
- Horneman AJ, "Manual of Clinical Microbiology", pp.658~665 (2011), ASM Press
- Martinez-Murcia AJ, "Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridizations", Int J Syst Bacteriol, 42, pp.412~421 (1992)
- Blondiaux N, "MALDI-TOF mass spectrometry to identify clinical bacterial isolates: evaluation in a teaching hospital in Lille", Pathol Biol (Paris), 58, pp.55~57 (2010)
- Saavedra MJ, "Updated phylogeny of the genus Aeromonas", Int J Syst Evol Microbiol, 56(Pt 10), pp.2481~2487 (2006)
- Abbott SL, "The genus Aeromonas: biochemical characteristics, atypical reactions, and phenotypic identification schemes", J Clin Microbiol, 41, pp.2348~2357 (2003)
- Morandi A, "Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains", J Bacteriol, 187, pp.6561~6564 (2005)
- Donohue MJ, "The development of a matrix-assisted laser desorption", ionization mass spectrometry-based method for the protein fingerprinting and identification of Aeromonas species using whole cells, 2006, pp.65, 380~389
- Martínez-Murcia A, "Phylogenetic evidence suggests that strains of Aeromonas hydrophila subsp. dhakensis belong to the species Aeromonas aquariorum sp. nov", Curr Microbiol, 58, pp.76~80 (2009)
- Sandrin TR, "MALDI TOF MS profiling of bacteria at the strain level: a review", Mass Spectrom Rev, 32, pp.188~217 (2013)
- Shin GW, "Severe sepsis due to Aeromonas aquariorum in a patient with liver cirrhosis", Jpn J Infect Dis, 66, pp.519~522 (2013)
- Puthucheary SD, "Molecular characterization of clinical isolates of Aeromonas species from Malaysia", PLoS One, 7, pp.e30205~ (2012)