Literature DB >> 33037786

Contaminations contaminate common databases.

Staffan Bensch1, Mizue Inumaru2, Yukita Sato2, Larisa Lee Cruz3,4, Andrew A Cunningham5, Simon J Goodman4, Iris I Levin6, Patricia G Parker7, Patricia Casanueva8, Maria-Angeles Hernández9, Gregorio Moreno-Rueda10, Maria-Angeles Rojo8.   

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 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.
© 2020 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.

Entities:  

Keywords:  zzm321990Haemoproteuszzm321990; PCR contamination; haemosporidian parasites; plasmodium; sequence databases

Year:  2020        PMID: 33037786     DOI: 10.1111/1755-0998.13272

Source DB:  PubMed          Journal:  Mol Ecol Resour        ISSN: 1755-098X            Impact factor:   7.090


  6 in total

1.  Avian haemosporidian parasites of accipitriform raptors.

Authors:  Josef Harl; Tanja Himmel; Gediminas Valkiūnas; Mikas Ilgūnas; Nora Nedorost; Julia Matt; Anna Kübber-Heiss; Amer Alic; Cornelia Konicek; Herbert Weissenböck
Journal:  Malar J       Date:  2022-01-05       Impact factor: 2.979

2.  A highly invasive malaria parasite has expanded its range to non-migratory birds in North America.

Authors:  Angela N Theodosopoulos; Kathryn C Grabenstein; Staffan Bensch; Scott A Taylor
Journal:  Biol Lett       Date:  2021-09-08       Impact factor: 3.812

3.  Experimental study of newly described avian malaria parasite Plasmodium (Novyella) collidatum n. sp., genetic lineage pFANTAIL01 obtained from South Asian migrant bird.

Authors:  Elena Platonova; Justė Aželytė; Tatjana Iezhova; Mikas Ilgūnas; Andrey Mukhin; Vaidas Palinauskas
Journal:  Malar J       Date:  2021-02-10       Impact factor: 2.979

4.  Apparent absence of avian malaria and malaria-like parasites in northern blue-footed boobies breeding on Isla Isabel.

Authors:  Federico Roldán-Zurabián; María José Ruiz-López; Josué Martínez de la Puente; Jordi Figuerola; Hugh Drummond; Sergio Ancona
Journal:  Sci Rep       Date:  2022-04-27       Impact factor: 4.996

5.  A widespread survey of avian haemosporidia in deceased wild birds of Japan: the hidden value of personally collected samples.

Authors:  Mizue Inumaru; Isao Nishiumi; Kazuto Kawakami; Yukita Sato
Journal:  J Vet Med Sci       Date:  2022-07-20       Impact factor: 1.105

6.  Dnabarcoder: An open-source software package for analysing and predicting DNA sequence similarity cutoffs for fungal sequence identification.

Authors:  Duong Vu; R Henrik Nilsson; Gerard J M Verkley
Journal:  Mol Ecol Resour       Date:  2022-06-20       Impact factor: 8.678

  6 in total

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