Real-time PCR assays targeting unique DNA sequences of fish-pathogenic Francisella noatunensis subspecies noatunensis and orientalis

Samuel Duodu, Pär Larsson, Andreas Sjödin, Esteban Soto Martinez, Mats Forsman, Duncan J. Colquhoun

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Specific identification and differentiation of the 2 subspecies of the fish pathogen Francisella noatunensis, namely, F. noatunensis subsp. noatunensis and F. noatunensis subsp. orientalis, remains a major diagnostic challenge. Following whole-genome sequencing and analysis of representatives of all major subclades of the genus Francisella, specific genomic regions were identified for each of the subspecies of this fish pathogen. Two specific real-time quantitative PCR assays, directed at hypothetical genes within these regions were developed. Specificity was confirmed by lack of signal and cross-reactivity with the closest relative, F. philomiragia, and other common bacterial fish pathogens. Both assays, used either as monoplex or multiplex, have a limit of detection of 10 genome equivalents. The quantitative sensitivity of the assays was not affected by the presence of kidney tissues or DNA from Atlantic cod Gadus morhua or tilapia Oreochromis sp.

Original languageEnglish (US)
Pages (from-to)225-234
Number of pages10
JournalDiseases of Aquatic Organisms
Volume101
Issue number3
DOIs
StatePublished - Nov 19 2012
Externally publishedYes

Fingerprint

Francisella
subspecies
targeting
quantitative polymerase chain reaction
pathogen
assay
Gadus morhua
nucleotide sequences
DNA
pathogens
assays
fish
genome
Tilapia (Cichlidae)
Oreochromis
cross reaction
genomics
detection limit
kidneys
gene

Keywords

  • DNA
  • Fish
  • Francisella noatunensis
  • QPCR

ASJC Scopus subject areas

  • Aquatic Science
  • Ecology, Evolution, Behavior and Systematics

Cite this

Real-time PCR assays targeting unique DNA sequences of fish-pathogenic Francisella noatunensis subspecies noatunensis and orientalis. / Duodu, Samuel; Larsson, Pär; Sjödin, Andreas; Soto Martinez, Esteban; Forsman, Mats; Colquhoun, Duncan J.

In: Diseases of Aquatic Organisms, Vol. 101, No. 3, 19.11.2012, p. 225-234.

Research output: Contribution to journalArticle

Duodu, Samuel ; Larsson, Pär ; Sjödin, Andreas ; Soto Martinez, Esteban ; Forsman, Mats ; Colquhoun, Duncan J. / Real-time PCR assays targeting unique DNA sequences of fish-pathogenic Francisella noatunensis subspecies noatunensis and orientalis. In: Diseases of Aquatic Organisms. 2012 ; Vol. 101, No. 3. pp. 225-234.
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