10.6084/m9.figshare.6741326.v1
Joana Sabino-Pinto
Joana
Sabino-Pinto
E. Tobias Krause
E.
Tobias Krause
Molly C. Bletz
Molly
C. Bletz
An Martel
An
Martel
Frank Pasmans
Frank
Pasmans
Sebastian Steinfartz
Sebastian
Steinfartz
Miguel Vences
Miguel
Vences
Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi: Supplementary material
Brill Online
2018
Batrachochytrium dendrobatidis
B. salamandrivorans
chytridiomycosis
epidemiology
pathogen survey
Prepman
Qiagen
Ecology not elsewhere classified
2018-07-04 11:21:17
Journal contribution
https://brill.figshare.com/articles/journal_contribution/Detectability_vs_time_and_costs_in_pooled_DNA_extraction_of_cutaneous_swabs_a_study_on_the_amphibian_chytrid_fungi_Supplementary_material/6741326
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, <i>Batrachochytrium dendrobatidis</i> and <i>B. salamandrivorans </i>(<i>Bsal</i>). 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 <i>Bsal</i>,
for which pooled DNA extraction had so far not been tested and massive
monitoring efforts in putatively unaffected regions are underway.