Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi

Sabino-Pinto J, Krause T, Bletz MC, Martel A, Pasmans F, Steinfartz S, Vences M (2018)
Amphibia-Reptilia 40(1): 29-39.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Sabino-Pinto, Joana; Krause, TobiasUniBi ; Bletz, Molly C.; Martel, An; Pasmans, Frank; Steinfartz, Sebastian; Vences, Miguel
Abstract / Bemerkung
AbstractEpidemiology relies on understanding the distribution of pathogens which often can be detected through DNA-based techniques, such as quantitative Polymerase Chain Reaction (qPCR). Typically, the DNA of each individual sample is separately extracted and undergoes qPCR analysis. However, when performing field surveys and long-term monitoring, a large fraction of the samples is generally expected to be negative, especially in geographical areas still considered free of the pathogen. If pathogen detection within a population – rather than determining its individual prevalence – is the focus, work load and monetary costs can be reduced by pooling samples for DNA extraction. We test and refine a user-friendly technique where skin swabs can be pooled during DNA extraction to detect the amphibian chytrid fungi,Batrachochytrium dendrobatidisandB. salamandrivorans(Bsal). We extracted pools with different numbers of samples (from one to four swabs), without increasing reaction volumes, and each pool had one sample inoculated with a predetermined zoospore amount. Pool size did not reduce the ability to detect the two fungi, except if inoculated with extremely low zoospore amounts (one zoospore). We confirm that pooled DNA extraction of cutaneous swabs can substantially reduce processing time and costs without minimizing detection sensitivity. This is of relevance especially for the new emerging pathogenBsal, for which pooled DNA extraction had so far not been tested and massive monitoring efforts in putatively unaffected regions are underway.
Stichworte
Animal Science and Zoology
Erscheinungsjahr
2018
Zeitschriftentitel
Amphibia-Reptilia
Band
40
Ausgabe
1
Seite(n)
29-39
ISSN
0173-5373
eISSN
1568-5381
Page URI
https://pub.uni-bielefeld.de/record/2942184

Zitieren

Sabino-Pinto J, Krause T, Bletz MC, et al. Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi. Amphibia-Reptilia. 2018;40(1):29-39.
Sabino-Pinto, J., Krause, T., Bletz, M. C., Martel, A., Pasmans, F., Steinfartz, S., & Vences, M. (2018). Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi. Amphibia-Reptilia, 40(1), 29-39. doi:10.1163/15685381-20181011
Sabino-Pinto, J., Krause, T., Bletz, M. C., Martel, A., Pasmans, F., Steinfartz, S., and Vences, M. (2018). Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi. Amphibia-Reptilia 40, 29-39.
Sabino-Pinto, J., et al., 2018. Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi. Amphibia-Reptilia, 40(1), p 29-39.
J. Sabino-Pinto, et al., “Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi”, Amphibia-Reptilia, vol. 40, 2018, pp. 29-39.
Sabino-Pinto, J., Krause, T., Bletz, M.C., Martel, A., Pasmans, F., Steinfartz, S., Vences, M.: Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi. Amphibia-Reptilia. 40, 29-39 (2018).
Sabino-Pinto, Joana, Krause, Tobias, Bletz, Molly C., Martel, An, Pasmans, Frank, Steinfartz, Sebastian, and Vences, Miguel. “Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi”. Amphibia-Reptilia 40.1 (2018): 29-39.

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