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Contaminations contaminate common databases

Bensch, Staffan LU ; Inumaru, Mizue ; Sato, Yukita ; Lee Cruz, Larisa ; Cunningham, Andrew A. ; Goodman, Simon J. ; Levin, Iris I. ; Parker, Patricia G. ; Casanueva, Patricia and Hernández, Maria Angeles , et al. (2021) In Molecular Ecology Resources 21(2). p.355-362
Abstract

The polymerase chain reaction (PCR) is a very powerful method to detect and identify pathogens. The high sensitivity of the method, however, comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If not identified as contaminations, these may result in erroneous conclusions on the occurrence of the pathogen, thereby inflating estimates of host range and geographic distribution. In the present paper, we evaluate whether several published records of avian haemosporidian parasites, in either unusual host species or geographical regions, might stem from PCR contaminations rather than novel biological findings. The detailed descriptions of these cases are shedding... (More)

The polymerase chain reaction (PCR) is a very powerful method to detect and identify pathogens. The high sensitivity of the method, however, comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If not identified as contaminations, these may result in erroneous conclusions on the occurrence of the pathogen, thereby inflating estimates of host range and geographic distribution. In the present paper, we evaluate whether several published records of avian haemosporidian parasites, in either unusual host species or geographical regions, might stem from PCR contaminations rather than novel biological findings. The detailed descriptions of these cases are shedding light upon the steps in the work process that might lead to PCR contaminations. By increasing the awareness of this problem, it will aid in developing procedures that keep these to a minimum. The examples in the present paper are from haemosporidians of birds, however the problem of contaminations and suggested actions should apply generally to all kinds of PCR-based identifications, not just of parasites and pathogens.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Haemoproteus, haemosporidian parasites, PCR contamination, plasmodium, sequence databases
in
Molecular Ecology Resources
volume
21
issue
2
pages
355 - 362
publisher
Wiley-Blackwell
external identifiers
  • scopus:85094948824
  • pmid:33037786
ISSN
1755-098X
DOI
10.1111/1755-0998.13272
language
English
LU publication?
yes
id
da79b600-6f4b-4c64-b972-22c48fd2fdf1
date added to LUP
2020-11-23 12:16:29
date last changed
2021-04-16 12:36:36
@article{da79b600-6f4b-4c64-b972-22c48fd2fdf1,
  abstract     = {<p>The polymerase chain reaction (PCR) is a very powerful method to detect and identify pathogens. The high sensitivity of the method, however, comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If not identified as contaminations, these may result in erroneous conclusions on the occurrence of the pathogen, thereby inflating estimates of host range and geographic distribution. In the present paper, we evaluate whether several published records of avian haemosporidian parasites, in either unusual host species or geographical regions, might stem from PCR contaminations rather than novel biological findings. The detailed descriptions of these cases are shedding light upon the steps in the work process that might lead to PCR contaminations. By increasing the awareness of this problem, it will aid in developing procedures that keep these to a minimum. The examples in the present paper are from haemosporidians of birds, however the problem of contaminations and suggested actions should apply generally to all kinds of PCR-based identifications, not just of parasites and pathogens.</p>},
  author       = {Bensch, Staffan and Inumaru, Mizue and Sato, Yukita and Lee Cruz, Larisa and Cunningham, Andrew A. and Goodman, Simon J. and Levin, Iris I. and Parker, Patricia G. and Casanueva, Patricia and Hernández, Maria Angeles and Moreno-Rueda, Gregorio and Rojo, Maria Angeles},
  issn         = {1755-098X},
  language     = {eng},
  number       = {2},
  pages        = {355--362},
  publisher    = {Wiley-Blackwell},
  series       = {Molecular Ecology Resources},
  title        = {Contaminations contaminate common databases},
  url          = {http://dx.doi.org/10.1111/1755-0998.13272},
  doi          = {10.1111/1755-0998.13272},
  volume       = {21},
  year         = {2021},
}