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Advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs

  • SERGE MORAND (a1) (a2)


DNA barcoding is now a common tool in parasitology and epidemiology, which require good methods for identification not only of parasites and pathogens but vectors and reservoirs. This special issue presents some advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. DNA barcoding found new applications in disease ecology, conservation parasitology, environmental parasitology and in paleoparasitology. New technologies such as next-generation sequencing and matrix-assisted laser desorption–ionization time-of-flight have made it now possible to investigate large samples of specimens. By allowing the investigation of parasites at the interface between environment, biodiversity, animal and human health, barcoding and biobanking have important policy outcomes as well as ethics and legal implications. The special issue ‘Advances and challenges in the barcoding of parasites, vectors and reservoirs’ illustrates some recent advances and proposes new avenues for research in barcoding in parasitology.

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Corresponding author

*Corresponding author: CNRS ISEM, CIRAD ASTRE, Université de Montpellier, Montpellier, France and Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand. E-mail:


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Aivelo, T. and Medlar, A. (2018). Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals. Parasitology 145, 609622.
Allard, M. W. (2016). The future of Whole-Genome Sequencing for public health and the clinic. Journal of Clinical Microbiology 54, 19461948.
Bass, D., Stentiford, G. D., Littlewood, D. T. J. and Hartiakinen, H. (2015). Diverse applications of environmental DNA methods in parasitology. Trends in Parasitology 31, 499513.
Beebe, N. W. (2018). DNA barcoding mosquitoes: advice for potential prospectors. Parasitology 145, 623634.
Bitome-Essono, P. Y., Ollomo, B., Arnathau, C., Durand, P., Mokoudoum, N. D., Yacka-Mouele, L., Okouga, A. P., Boundenga, L., Mve-Ondo, B., Obame-Nkoghe, J., Mbehang-Nguema, P., Njiokou, F., Makanga, B., Wattier, R., Ayala, D., Ayala, F. J., Renaud, F., Rougeron, V., Bretagnolle, F. and Prugnolle, F. (2017). Tracking zoonotic pathogens using blood-sucking flies as ‘flying syringes’. ELife 6, e22069.
Boon, N. A. M., Van de Broeck, F., Faye, D., Volckaert, F. A. M., Mboup, S., Katja Polman, K. and Huyse, T. (2018) Barcoding hybrids: heterogeneous distribution of Schistosoma haematobium x Schistosoma bovis hybrids across the Senegal River Basin. Parasitology 145, 635646.
Buschmann, T. (2017). DNABarcodes: an R package for the systematic construction of DNA sample tags. Bioinformatics (Oxford, England), 920922. doi: 10.1093/bioinformatics/btw759.
Caira, J. N. and Littlewood, D. T. J. (2013). Worms, platyhelminthes. Encyclopedia of Biodiversity, vol. 7 (ed. Levin, S. A.), pp. 437469. Academic Press, Waltham, MA.
Chamberlain, S. (2017). bold: Interface to Bold Systems API. R package version 0.5.0.
Chan, A., Chiang, L-P., Hapuarachchi, H. C., Tan, C.-H., Pang, S.-C., Lee, R., Lee, K.-S., Ng, L.-C. and Lam-Phua, S.-G. (2014). DNA barcoding: complementing morphological identification of mosquito species in Singapore. Parasites and Vectors 7, 569.
Côté, N. M.-L and Le Bailly, M. (2018) Paleoparasitology and paleogenetics: review and perspectives for the study of ancient human parasites. Parasitology 145, 657665.
Danesi, P., da Rold, G., Rizzoli, A., Hauffe, H. C., Marangon, S., Samerpitak, K., Demanche, C., Guillot, J., Capelli, G. and de Hoog, S. G. (2016) Barcoding markers for Pneumocystis species in wildlife. Fungal Biology 120, 191206.
Desquesnes, M., Kamyingkird, K., Yangtara, S., Milocco, C., Ravel, S., Wang, M.-H., Lun, Z.-R., Morand, S. and Jittapalapong, S. (2011) Specific primers for PCR amplification of the ITS1 (ribosomal DNA) of Trypanosomal lewisi. Infection, Genetics and Evolution 11, 13611367.
Diarra, A. Z., Almeras, L., Laroche, M., Berenger, J.-M., Koné, A. K., Bocoum, Z., Dabo, A., Doumbo, O., Raoult, D. and Parola, P. (2017). Molecular and MALDI-TOF identification of ticks and tick-associated bacteria in Mali. PLoS Neglected Tropical Diseases 11, e0005762.
Ermakov, O. A., Simonov, E., Surin, V. L., Titov, S. V., Brandler, O. V., Ivanova, N. V. and Borisenko, A. V. (2016). Implications of hybridisation, numts, and overlooked diversity for DNA barcoding of Eurasian ground squirrels. PLoS ONE 10, e0117201.
Galan, M., Pagès, M. and Cosson, J.-F. (2012). Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples. PLoS ONE 7, e48374.
Garcıa-Varela, M. and Pérez-Ponce de León, G. (2015). Advances in the classification of acanthocephalans: evolutionary history and evolution of the parasitism. In Parasite Diversity and Diversification: Evolutionary Ecology Meets Phylogenetics (eds. Morand, S., Krasnov, B. R. and Littlewood, D. T. J.), pp. 182201. Cambridge University Press, Cambridge.
Guernier, V., Allan, K. J. and Goarant, C. (2018). Advances and challenges in barcoding pathogenic and environmental Leptospira. Parasitology 145, 596608.
Hebert, P. D. N., Cywinska, A., Ball, S. L. and deWaard, J. R. (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences 270, 313321.
Hutchinson, R., Jamie, R. and Stevens, J. R. (2018). Barcoding in trypanosomes. Parasitology 145, 563574.
Huver, J. R., Koprivnikar, J., Johnson, P. T. J. and Whyard, S. (2015) Development and application of an eDNA method to detect and quantify a pathogenic parasite in aquatic ecosystems. Ecological Applications 25, 9911002.
Ilina, E. N., Borovskaya, A. D., Malakhova, M. M., Vereshchagin, V. A., Kubanova, A. A., Kruglov, A. N., Svistunova, T. S., Gazarian, A. O., Maier, T., Kostrzewa, M. and Govorun, V. M. (2009). Direct bacterial profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for identification of pathogenic Neisseria. Journal of Molecular Diagnostic 11, 7586.
Joly, D. and Faure, D. (2015). Next-generation sequencing propels environmental genomics to the front line of research. Heredity 114, 429430.
Kocher, A., de Thoisy, B., Catzeflis, F., Valière, S., Bañuls, A. L. and Murienne, J. (2017). iDNA screening: disease vectors as vertebrate samplers. Molecular Ecology 26, 64786486.
Kocher, A., Valière, S., Bañuls, A.-L. and Murienne, J. (2018). High-throughput sequencing of kDNA amplicons for the analysis of Leishmania minicircles and identification of Neotropical species. Parasitology 145, 586595.
Kosoy, M., Mckee, C., Albayrak, L. and Fofanov, Y. (2018). Genotyping of Bartonella bacteria and their animal hosts: current status and perspectives. Parasitology 145, 543562.
Kumlert, R., Chaisiri, K., Anantatat, T., Stekolnikov, A. A., Morand, S., Prasartvit, A., Makepeace, B. L., Sungvornyothin, S. and Paris, D. H. (2018). Autofluorescence microscopy for paired-matched morphological and molecular identification of individual chigger mites (Acari: Trombiculidae), the vectors of scrub typhus. PLoS ONE 13, e0193163.
Lajaunie, C. and Ho, C. W. L. (2018) Pathogens collections, biobanks and related-data in a one health legal and ethical perspective. Parasitology 145, 689697.
Lajaunie, C. and Mazzega, P. (2016). One Health and biodiversity conventions. The emergence of 538 health issues in biodiversity conventions. IUCN Academy of Environmental Law eJournal, Issue 539, 105121.
Lajaunie, C., Morand, S. and Huan, T. B. (2014). Barcoding, biobanking, ebanking for “One Health” projects in South-East Asia: considering ethics and international law. Eubios Journal of Asian and International Bioethics 24, 129131.
Laroche, M., Bérenger, J.-M., Gazelle, G., Blanchet, D., Raoult, D. and Parola, P. (2018). MALDI-TOF MS protein profiling for the rapid identification 1 of Chagas disease triatomine vectors and application to the triatomine fauna of French Guiana. Parasitology 145, 666676.
Latinne, A., Bezé, F., Delhaes, L., Pottier, M., Gantois, N., Nguyen, J., Blasdell, K., Dei-Cas, E., Morand, S. and Chabé, M. (2017). Genetic diversity and evolution of Pneumocystis fungi infecting wild Southeast Asian murid rodents. Parasitology [ahead of print]. doi: 10.1017/S0031182017001883.
Meier, R. (2008). DNA sequences in taxonomy: opportunities and challenges. In The New Taxonomy (ed. Wheeler, Q. D.), Arizona State University Press, Tempe, pp. 95127.
Michelet, L., Delannoy, S., Devillers, E., Umhang, G., Aspan, A., Juremalm, M., Chirico, J., van derWal, F. J., Sprong, H., Boye Pihl, T. P., Klitgaard, K., Bødker, R., Fach, P. and Moutailler, S. (2014). Throughput screening of tick-borne pathogens in Europe. Frontiers Cellular and Infection Microbiology 4, 103.
Muturi, C. N., Ouma, J. O., Malele, I. I., Ngure, R. M., Rutto, J. J., Mithöfer, K. M., Enyaru, J. and Masiga, D. K. (2011). Tracking the feeding patterns of tsetse flies (Glossina genus) by analysis of bloodmeals using mitochondrial cytochromes genes. PLoS ONE 28, e17284.
Nebbak, A., Koumare, S., Willcox, A. C., Berenger, J.-M., Raoult, D., Almeras, L. and Parola, P. (2018). Field application of MALDI-TOF MS on mosquito larvae identification. Parasitology 145, 678688.
Nesi, N., Nakouné, E., Cruaud, C. and Hassanin, A. (2011). DNA barcoding of African fruit bats (Mammalia, Pteropodidae). The mitochondrial genome does not provide a reliable discrimination between Epomophorus gambianus and Micropteropus pusillus. Comptes Rendus Biologie 334, 544554.
Ondrejicka, D. A., Locke, S. A., Morey, K., Borisenko, A. V. and Hanner, R. H. (2014). Status and prospects of DNA barcoding in medically important parasites and vectors. Trends in Parasitology 30, 582591.
Pagès, M., Bazin, E., Galan, M., Chaval, Y., Claude, J., Herbreteau, V., Michaux, J., Piry, S., Morand, S. and Cosson, J. F. (2013). Cytonuclear discordance among Southeast Asian black rats (Rattus rattus complex). Molecular Ecology 22, 10191134.
Poulin, R. and Morand, S. (2004). Parasite Biodiversity. Smithsonian Books, Washington, DC.
Prosser, S. W., Velarde-Aguilar, M. G., León-Règagnon, V. and Hebert, P. D. (2013). Advancing nematode barcoding: a primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes. Molecular Ecological Resources 13, 11081115. Doi: 10.1111/1755-0998.12082.
R Core Team (2018). R: A Language and Environment for Statistical Computing. Vienna, Austria, R Foundation for Statistical Computing.
Rothen, J., Githaka, N., Kanduma, E. G., Olds, C., Pflüger, V., Mwaura, S., Bishop, R. P. and Daubenberger, C. (2016). Matrix-assisted laser desorption/ionization time of flight mass spectrometry for comprehensive indexing of East African ixodid tick species. Parasites and Vectors 9, 151.
Ruiz-Lopez, F., Wilkerson, R. C., Conn, J. E., McKeon, S. N., Levin, D. M., Quĩones, M. L., Póvoa, M. M. and Linton, Y.-M. (2012). DNA barcoding reveals both known and novel taxa in the Albitarsis Group (Anopheles: Nyssorhynchus) of Neotropical malaria vectors. Parasites and Vectors 5, 112.
Sandrin, T. R., Goldstein, J. E. and Schumaker, S. (2013). MALDI TOF MS profiling of bacteria at the strain level: a review. Mass Spectrometry Review 32, 188217.
Shafer, A. B. A., Northrup, J. M., Wikelski, M., Wittemyer, G. and Wolf, B. W. (2016). Forecasting ecological genomics: High-tech animal instrumentation meets high-throughput sequencing. PLoS Biology 14, 111.
Shen, Y.-Y., Chen, X. and Murphy, R. W. (2013) Assessing DNA barcoding as a tool for species identification and data quality control. PLoS ONE 8, e57125.
Šlapeta, J. (2018). DNA barcoding of Cryptosporidium. Parasitology 145, 575585.
Song, H., Buhay, J. E., Whiting, M. F. and Crandall, K. A. (2008) Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the National Academy of Sciences of the United States of America 105, 1348613491.
Stat, M., Huggett, M. J., Bernasconi, R., DiBattista, J. D., Berry, T. E., Newman, S. J., Harvey, E. S. and Bunce, M.(2017). Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment. Scientific Reports 25, 12240.
Stentiford, G. D., Feist, S. W., Stone, D. M., Peeler, E. J. and Bass, D. (2014). Policy, phylogeny, and the parasite. Trends in Parasitology 30, 274281.
Taberlet, P., Coissac, E., Hajibabaei, M. and Rieseberg, L. H. (2012). Environmental DNA. Molecular Ecology 21, 17891793.
Vernooy, R., Haribabu, E., Muller, M. R., Vogel, J. H., Hebert, P. D. N., Schindel, D. E., Shimura, J. and Singer, G. A. (2010) Barcoding life to conserve biological diversity: beyond the taxonomic imperative. PLoS Biology 8, e1000417.
Vogler, A. and Monahan, M. (2006). Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research 45: 110.
Wang, X. C., Liu, C., Huang, L., Bengtsson-Palme, J., Chen, H., Zhang, J. H., Cai, D. and Li, J. Q. (2015). ITS1: a DNA barcode better than ITS2 in eukaryotes? Molecular Ecology Resources 15, 573586.
Waterton, C., Ellis, R. and Wynne, B. (2013). Barcoding Nature. Shifting Cultures of Taxonomy in an age of Biodiversity Loss. Routledge, Oxon.
Wood, J. R. (2018). DNA barcoding of ancient parasites. Parasitology 145, 647656.
Yssouf, A., Almeras, L., Raoult, D. and Parola, P. (2016). Emerging tools for identification of arthropod vectors. Future Microbiology 11, 549566.
Zhang, A.-B., Hao, M.-D., Yangan, C.-Q. and Shi, Z.-Y. (2017) Barcodingr: an integrated R package for species identification using DNA barcodes. Methods in Ecology and Evolution 8, 627634.


Advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs

  • SERGE MORAND (a1) (a2)


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