Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing

Samantha J. Lawton, Allison M. Weis, Barbara A Byrne, Heather Fritz, Conor C. Taff, Andrea K. Townsend, Bart C Weimer, Asli Mete, Sarah Wheeler, Walter M Boyce

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens (Gallus gallus domesticus, n = 8), American crows (Corvus brachyrhynchos, n = 17), a mallard duck (Anas platyrhynchos, n = 1), and a western scrub-jay (Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI-TOF MS, the combined results of 16S rDNA sequencing, and the hippurate hydrolysis gene PCR (p = 0.0027, kappa = 1). Likewise, the identifications derived from WGS from a subset of 14 isolates were in 100% agreement with the MALDI-TOF MS identification. In contrast, biochemical testing misclassified 5 isolates of C. jejuni as C. coli, and 16S rDNA sequencing alone was not able to differentiate between C. coli and C. jejuni for 11 sequences (p = 0.1573, kappa = 0.0857) when compared to MALDI-TOF MS and WGS. No agreement was observed between MALDI-TOF MS dendrograms and the phylogenetic relationships revealed by rDNA sequencing or WGS. Our results confirm that MALDI-TOF MS is a fast and reliable method for identifying Campylobacter isolates to the species level from wild birds and chickens, but not for elucidating phylogenetic relationships among Campylobacter isolates.

Original languageEnglish (US)
JournalJournal of Veterinary Diagnostic Investigation
DOIs
StateAccepted/In press - Mar 1 2018

Fingerprint

Campylobacter
matrix-assisted laser desorption-ionization mass spectrometry
wild birds
DNA Sequence Analysis
Birds
Chickens
Mass Spectrometry
Lasers
sequence analysis
chickens
Ribosomal DNA
Corvus brachyrhynchos
Genome
Crows
genome
Anas platyrhynchos
testing
Hydrolysis
hydrolysis
Ducks

Keywords

  • Campylobacter
  • chickens
  • matrix-assisted laser desorption/ionization mass spectrometry
  • wild birds

ASJC Scopus subject areas

  • veterinary(all)

Cite this

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title = "Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing",
abstract = "Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens (Gallus gallus domesticus, n = 8), American crows (Corvus brachyrhynchos, n = 17), a mallard duck (Anas platyrhynchos, n = 1), and a western scrub-jay (Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100{\%} agreement between MALDI-TOF MS, the combined results of 16S rDNA sequencing, and the hippurate hydrolysis gene PCR (p = 0.0027, kappa = 1). Likewise, the identifications derived from WGS from a subset of 14 isolates were in 100{\%} agreement with the MALDI-TOF MS identification. In contrast, biochemical testing misclassified 5 isolates of C. jejuni as C. coli, and 16S rDNA sequencing alone was not able to differentiate between C. coli and C. jejuni for 11 sequences (p = 0.1573, kappa = 0.0857) when compared to MALDI-TOF MS and WGS. No agreement was observed between MALDI-TOF MS dendrograms and the phylogenetic relationships revealed by rDNA sequencing or WGS. Our results confirm that MALDI-TOF MS is a fast and reliable method for identifying Campylobacter isolates to the species level from wild birds and chickens, but not for elucidating phylogenetic relationships among Campylobacter isolates.",
keywords = "Campylobacter, chickens, matrix-assisted laser desorption/ionization mass spectrometry, wild birds",
author = "Lawton, {Samantha J.} and Weis, {Allison M.} and Byrne, {Barbara A} and Heather Fritz and Taff, {Conor C.} and Townsend, {Andrea K.} and Weimer, {Bart C} and Asli Mete and Sarah Wheeler and Boyce, {Walter M}",
year = "2018",
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doi = "10.1177/1040638718762562",
language = "English (US)",
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T1 - Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing

AU - Lawton, Samantha J.

AU - Weis, Allison M.

AU - Byrne, Barbara A

AU - Fritz, Heather

AU - Taff, Conor C.

AU - Townsend, Andrea K.

AU - Weimer, Bart C

AU - Mete, Asli

AU - Wheeler, Sarah

AU - Boyce, Walter M

PY - 2018/3/1

Y1 - 2018/3/1

N2 - Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens (Gallus gallus domesticus, n = 8), American crows (Corvus brachyrhynchos, n = 17), a mallard duck (Anas platyrhynchos, n = 1), and a western scrub-jay (Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI-TOF MS, the combined results of 16S rDNA sequencing, and the hippurate hydrolysis gene PCR (p = 0.0027, kappa = 1). Likewise, the identifications derived from WGS from a subset of 14 isolates were in 100% agreement with the MALDI-TOF MS identification. In contrast, biochemical testing misclassified 5 isolates of C. jejuni as C. coli, and 16S rDNA sequencing alone was not able to differentiate between C. coli and C. jejuni for 11 sequences (p = 0.1573, kappa = 0.0857) when compared to MALDI-TOF MS and WGS. No agreement was observed between MALDI-TOF MS dendrograms and the phylogenetic relationships revealed by rDNA sequencing or WGS. Our results confirm that MALDI-TOF MS is a fast and reliable method for identifying Campylobacter isolates to the species level from wild birds and chickens, but not for elucidating phylogenetic relationships among Campylobacter isolates.

AB - Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens (Gallus gallus domesticus, n = 8), American crows (Corvus brachyrhynchos, n = 17), a mallard duck (Anas platyrhynchos, n = 1), and a western scrub-jay (Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI-TOF MS, the combined results of 16S rDNA sequencing, and the hippurate hydrolysis gene PCR (p = 0.0027, kappa = 1). Likewise, the identifications derived from WGS from a subset of 14 isolates were in 100% agreement with the MALDI-TOF MS identification. In contrast, biochemical testing misclassified 5 isolates of C. jejuni as C. coli, and 16S rDNA sequencing alone was not able to differentiate between C. coli and C. jejuni for 11 sequences (p = 0.1573, kappa = 0.0857) when compared to MALDI-TOF MS and WGS. No agreement was observed between MALDI-TOF MS dendrograms and the phylogenetic relationships revealed by rDNA sequencing or WGS. Our results confirm that MALDI-TOF MS is a fast and reliable method for identifying Campylobacter isolates to the species level from wild birds and chickens, but not for elucidating phylogenetic relationships among Campylobacter isolates.

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