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

(2019) AMPHIBIA-REPTILIA. 40(1). p.29-39
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Abstract
Epidemiology 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 dendrobatidis and B. 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 pathogen Bsal, for which pooled DNA extraction had so far not been tested and massive monitoring efforts in putatively unaffected regions are underway.
Keywords
BATRACHOCHYTRIUM-DENDROBATIDIS, SP-NOV, PCR, CHYTRIDIOMYCOSIS, DISEASE, SALAMANDRIVORANS, PROTOCOL, SAMPLES, SPREAD, ASSAYS, Batrachochytrium dendrobatidis, B. salamandrivorans, chytridiomycosis, epidemiology, pathogen survey, Prepman, Qiagen

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MLA
Sabino-Pinto, Joana et al. “Detectability Vs. Time and Costs in Pooled DNA Extraction of Cutaneous Swabs : a Study on the Amphibian Chytrid Fungi.” AMPHIBIA-REPTILIA 40.1 (2019): 29–39. Print.
APA
Sabino-Pinto, J., Krause, E. T., Bletz, M. C., Martel, A., Pasmans, F., Steinfartz, S., & Vences, M. (2019). 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.
Chicago author-date
Sabino-Pinto, Joana, E. Tobias Krause, Molly C. Bletz, An Martel, Frank Pasmans, Sebastian Steinfartz, and Miguel Vences. 2019. “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.
Chicago author-date (all authors)
Sabino-Pinto, Joana, E. Tobias Krause, Molly C. Bletz, An Martel, Frank Pasmans, Sebastian Steinfartz, and Miguel Vences. 2019. “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.
Vancouver
1.
Sabino-Pinto J, Krause ET, Bletz MC, Martel A, Pasmans F, Steinfartz S, et al. Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs : a study on the amphibian chytrid fungi. AMPHIBIA-REPTILIA. 2019;40(1):29–39.
IEEE
[1]
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, no. 1, pp. 29–39, 2019.
@article{8625947,
  abstract     = {Epidemiology 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 dendrobatidis and B. 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 pathogen Bsal, for which pooled DNA extraction had so far not been tested and massive monitoring efforts in putatively unaffected regions are underway.},
  author       = {Sabino-Pinto, Joana and Krause, E. Tobias and Bletz, Molly C. and Martel, An and Pasmans, Frank and Steinfartz, Sebastian and Vences, Miguel},
  issn         = {0173-5373},
  journal      = {AMPHIBIA-REPTILIA},
  keywords     = {BATRACHOCHYTRIUM-DENDROBATIDIS,SP-NOV,PCR,CHYTRIDIOMYCOSIS,DISEASE,SALAMANDRIVORANS,PROTOCOL,SAMPLES,SPREAD,ASSAYS,Batrachochytrium dendrobatidis,B. salamandrivorans,chytridiomycosis,epidemiology,pathogen survey,Prepman,Qiagen},
  language     = {eng},
  number       = {1},
  pages        = {29--39},
  title        = {Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs : a study on the amphibian chytrid fungi},
  url          = {http://dx.doi.org/10.1163/15685381-20181011},
  volume       = {40},
  year         = {2019},
}

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