Identification and typing of Francisella tularensis with a highly automated genotyping assay

D Duncan; A Vogler; M Wolcott; F Li; Derek Sarovich; Dawn Birdsell; Lindsey Watson; T Hall; Rangarajan Sampath; R Housley; L Blyn; S Hofstadler; David Ecker; Paul S Keim; David M Wagner; Mark Eshoo

doi:10.1111/lam.12022

Identification and typing of Francisella tularensis with a highly automated genotyping assay

D Duncan, A Vogler, M Wolcott, F Li, Derek Sarovich, Dawn Birdsell, Lindsey Watson, T Hall, Rangarajan Sampath, R Housley, L Blyn, S Hofstadler, David Ecker, Paul S Keim, David M Wagner, Mark Eshoo

Research output: Contribution to journal › Article › peer-review

Abstract

A PCR assay was developed to genotypically characterize Francisella tularensis and F. novicida. An integrated and partially redundant set of markers was selected to provide positive identification of these species, identify subspecies of F. tularensis and genotype 14 variable number tandem repeat (VNTR) markers. Assay performance was evaluated with 117 Francisella samples. Sample DNA was amplified, and the masses of the PCR products were determined with electrospray ionization/time of flight mass spectrometry (ESI-MS). The base compositions of the PCR amplicons were derived from these high-accuracy mass measurements and contrasted with databased information associated with each of the 25 assay markers. Species and subspecies determinations for all samples were fully concordant with results from established typing methods, and VNTR markers provided additional discrimination among samples. Sequence variants were observed with a number of assay markers, but these did not interfere with sample characterization, and served to increase the genetic diversity detected by the assay.

Original language	English
Pages (from-to)	128-134
Number of pages	7
Journal	Letters in Applied Microbiology
Volume	56
Issue number	2
DOIs	https://doi.org/10.1111/lam.12022
Publication status	Published - 2013

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10.1111/lam.12022

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Duncan, D., Vogler, A., Wolcott, M., Li, F., Sarovich, D., Birdsell, D., Watson, L., Hall, T., Sampath, R., Housley, R., Blyn, L., Hofstadler, S., Ecker, D., Keim, P. S., Wagner, D. M., & Eshoo, M. (2013). Identification and typing of Francisella tularensis with a highly automated genotyping assay. Letters in Applied Microbiology, 56(2), 128-134. https://doi.org/10.1111/lam.12022

@article{5d3a5c95b88d49a8bc2f01d244b358a8,

title = "Identification and typing of Francisella tularensis with a highly automated genotyping assay",

abstract = "A PCR assay was developed to genotypically characterize Francisella tularensis and F. novicida. An integrated and partially redundant set of markers was selected to provide positive identification of these species, identify subspecies of F. tularensis and genotype 14 variable number tandem repeat (VNTR) markers. Assay performance was evaluated with 117 Francisella samples. Sample DNA was amplified, and the masses of the PCR products were determined with electrospray ionization/time of flight mass spectrometry (ESI-MS). The base compositions of the PCR amplicons were derived from these high-accuracy mass measurements and contrasted with databased information associated with each of the 25 assay markers. Species and subspecies determinations for all samples were fully concordant with results from established typing methods, and VNTR markers provided additional discrimination among samples. Sequence variants were observed with a number of assay markers, but these did not interfere with sample characterization, and served to increase the genetic diversity detected by the assay.",

author = "D Duncan and A Vogler and M Wolcott and F Li and Derek Sarovich and Dawn Birdsell and Lindsey Watson and T Hall and Rangarajan Sampath and R Housley and L Blyn and S Hofstadler and David Ecker and Keim, {Paul S} and Wagner, {David M} and Mark Eshoo",

year = "2013",

doi = "10.1111/lam.12022",

language = "English",

volume = "56",

pages = "128--134",

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Duncan, D, Vogler, A, Wolcott, M, Li, F, Sarovich, D, Birdsell, D, Watson, L, Hall, T, Sampath, R, Housley, R, Blyn, L, Hofstadler, S, Ecker, D, Keim, PS, Wagner, DM & Eshoo, M 2013, 'Identification and typing of Francisella tularensis with a highly automated genotyping assay', Letters in Applied Microbiology, vol. 56, no. 2, pp. 128-134. https://doi.org/10.1111/lam.12022

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T1 - Identification and typing of Francisella tularensis with a highly automated genotyping assay

AU - Duncan, D

AU - Vogler, A

AU - Wolcott, M

AU - Li, F

AU - Sarovich, Derek

AU - Birdsell, Dawn

AU - Watson, Lindsey

AU - Hall, T

AU - Sampath, Rangarajan

AU - Housley, R

AU - Blyn, L

AU - Hofstadler, S

AU - Ecker, David

AU - Keim, Paul S

AU - Wagner, David M

AU - Eshoo, Mark

PY - 2013

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AB - A PCR assay was developed to genotypically characterize Francisella tularensis and F. novicida. An integrated and partially redundant set of markers was selected to provide positive identification of these species, identify subspecies of F. tularensis and genotype 14 variable number tandem repeat (VNTR) markers. Assay performance was evaluated with 117 Francisella samples. Sample DNA was amplified, and the masses of the PCR products were determined with electrospray ionization/time of flight mass spectrometry (ESI-MS). The base compositions of the PCR amplicons were derived from these high-accuracy mass measurements and contrasted with databased information associated with each of the 25 assay markers. Species and subspecies determinations for all samples were fully concordant with results from established typing methods, and VNTR markers provided additional discrimination among samples. Sequence variants were observed with a number of assay markers, but these did not interfere with sample characterization, and served to increase the genetic diversity detected by the assay.

U2 - 10.1111/lam.12022

DO - 10.1111/lam.12022

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JO - Letters in Applied Microbiology

JF - Letters in Applied Microbiology

SN - 0266-8254

IS - 2

ER -

Identification and typing of Francisella tularensis with a highly automated genotyping assay

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