Comparison of maldi-tof ms, housekeeping gene sequencing, and 16s rRNA gene sequencing for identification of Aeromonas clinical isolates

Hee Bong Shin, Jihoon Yoon, Yangsoon Lee, Myung Sook Kim, Kyungwon Lee

Research output: Contribution to journalArticle

12 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)550-555
Number of pages6
JournalYonsei medical journal
Volume56
Issue number2
DOIs
Publication statusPublished - 2015 Jan 1

Fingerprint

Aeromonas
Essential Genes
rRNA Genes
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Gastroenteritis
Korea
Sepsis
Patient Care
Costs and Cost Analysis

All Science Journal Classification (ASJC) codes

  • Medicine(all)

Cite this

@article{67b598f9c28f4529a4de98442f1bb2e0,
title = "Comparison of maldi-tof ms, housekeeping gene sequencing, and 16s rRNA gene sequencing for identification of Aeromonas clinical isolates",
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.",
author = "Shin, {Hee Bong} and Jihoon Yoon and Yangsoon Lee and Kim, {Myung Sook} and Kyungwon Lee",
year = "2015",
month = "1",
day = "1",
doi = "10.3349/ymj.2015.56.2.550",
language = "English",
volume = "56",
pages = "550--555",
journal = "Yonsei Medical Journal",
issn = "0513-5796",
publisher = "Yonsei University College of Medicine",
number = "2",

}

Comparison of maldi-tof ms, housekeeping gene sequencing, and 16s rRNA gene sequencing for identification of Aeromonas clinical isolates. / Shin, Hee Bong; Yoon, Jihoon; Lee, Yangsoon; Kim, Myung Sook; Lee, Kyungwon.

In: Yonsei medical journal, Vol. 56, No. 2, 01.01.2015, p. 550-555.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Comparison of maldi-tof ms, housekeeping gene sequencing, and 16s rRNA gene sequencing for identification of Aeromonas clinical isolates

AU - Shin, Hee Bong

AU - Yoon, Jihoon

AU - Lee, Yangsoon

AU - Kim, Myung Sook

AU - Lee, Kyungwon

PY - 2015/1/1

Y1 - 2015/1/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84922780575&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84922780575&partnerID=8YFLogxK

U2 - 10.3349/ymj.2015.56.2.550

DO - 10.3349/ymj.2015.56.2.550

M3 - Article

C2 - 25684008

AN - SCOPUS:84922780575

VL - 56

SP - 550

EP - 555

JO - Yonsei Medical Journal

JF - Yonsei Medical Journal

SN - 0513-5796

IS - 2

ER -