Status and prospects of DNA barcoding in medically important parasites and vectors

Trends in Parasitology

Volumn 30, Issue 12, 2014, Pages 582-591

  Ondrejicka, Danielle A ^a   Locke, Sean A ^a   Morey, Kevin ^a   Borisenko, Alex V ^a   Hanner, Robert H ^a  

^a UNIVERSITY OF GUELPH   (Canada)

Author keywords

Endoparasites and ectoparasites; Neglected tropical disease; Pathogens; Species delineation; Specimen identification; Vectors

Indexed keywords

MITOCHONDRIAL DNA;

AEDES; AEDES ALBOPICTUS; AEDES TRIVITTATUS; ANCYLOSTOMA DUODENALE; ASCARIS; ASCARIS LUMBRICOIDES; CLONORCHIS SINENSIS; COMPARATIVE STUDY; COQUILLETTIDIA PERTURBANS; CULEX QUINQUEFASCIATUS; DNA BARCODING; DNA HYBRIDIZATION; ECTOPARASITE; FASCIOLA HEPATICA; NECATOR AMERICANUS; NEMATODE; NEXT GENERATION SEQUENCING; NONHUMAN; PARASITE; PARASITE VECTOR; PLATYHELMINTH; REVIEW; SCHISTOSOMA; TRICHURIS TRICHIURA; TROPICAL DISEASE; ANIMAL; DISEASE CARRIER; GENETICS; HUMAN; PARASITOLOGY; PROCEDURES; TRENDS;

ANIMALS; DISEASE VECTORS; DNA BARCODING, TAXONOMIC; HUMANS; PARASITES; PARASITOLOGY;

EID: 84922797217     PISSN: 14714922     EISSN: 14715007     Source Type: Journal    
DOI: 10.1016/j.pt.2014.09.003     Document Type: Review

References (104)

1. WHO Working to Overcome the Global Impact of Neglected Tropical Diseases: First WHO Report on Neglected Tropical Diseases 2010, WHO.
2. Fenwick A. The global burden of neglected tropical diseases. Public Health 2012, 126:233-236.
3. Perkins S.L., et al. Do molecules matter more than morphology? Promises and pitfalls in parasites. Parasitology 2011, 138:1664-1674.
4. Reuben R. Illustrated keys to species of Culex (Culex) associated with Japanese encephalitis in Southeast Asia (Diptera: Culicidae). Mosq. Syst. 1994, 26:75-96.
5. Valkiunas G., et al. Parasite misidentifications in GenBank: how to minimize their number?. Trends Parasitol. 2008, 24:247-248.
6. Wong S.S., et al. Molecular diagnosis in clinical parasitology: when and why?. Exp. Biol. Med. (Maywood) 2014, 10.1177/1535370214523880.
7. Bensch S., et al. MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages. Mol. Ecol. Resour. 2009, 9:1353-1358.
8. Aurrecoechea C., et al. EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res. 2010, 38:D415-D419.
9. Valentini A., et al. DNA barcoding for ecologists. Trends Ecol. Evol. 2009, 24:110-117.
10. Hebert P.D.N., et al. Biological identifications through DNA barcodes. Proc. Biol. Sci. 2003, 270:313-321.
11. Hebert P.D.N., et al. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. Biol. Sci. 2003, 270(Suppl. 1):S96-S99.
12. Besansky N.J., et al. DNA barcoding of parasites and invertebrate disease vectors: what you don't know can hurt you. Trends Parasitol. 2003, 19:545-546.
13. Kwong S., et al. An update on DNA barcoding: low species coverage and numerous unidentified sequences. Cladistics 2012, 28:639-644.
14. Kvist S. Barcoding in the dark? A critical view of the sufficiency of zoological DNA barcoding databases and a plea for broader integration of taxonomic knowledge. Mol. Phylogenet. Evol. 2013, 69:39-45.
15. Frewin A.C., et al. DNA barcoding for plant protection: applications and summary of available data for arthropod pests. CAB Rev. 2013, 8:1-13.
16. Fišer Pečnikar Ž., Buzan E.V. 20 Years since the introduction of DNA barcoding: from theory to application. J. Appl. Genet. 2014, 55:43-52.
17. Taylor H.R., Harris W.E. An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol. Ecol. Resour. 2012, 12:377-388.
18. Teletchea F. After 7 years and 1000 citations: comparative assessment of the DNA barcoding and the DNA taxonomy proposals for taxonomists and non-taxonomists. Mitochondrial DNA 2010, 21:206-226.
19. Frézal L., Leblois R. Four years of DNA barcoding: current advances and prospects. Infect. Genet. Evol. 2008, 8:727-736.
20. Betson M., et al. A molecular epidemiological investigation of Ascaris on Unguja, Zanzibar using isoenyzme analysis, DNA barcoding and microsatellite DNA profiling. Trans. R. Soc. Trop. Med. Hyg. 2011, 105:370-379.
21. Foster P.G., et al. Phylogenetic analysis and DNA-based species confirmation in Anopheles (Nyssorhynchus). PLoS ONE 2013, 8:e54063.
22. Laurito M., et al. COI barcode versus morphological identification of Culex (Culex) (Diptera: Culicidae) species: a case study using samples from Argentina and Brazil. Mem. Inst. Oswaldo Cruz 2013, 108(Suppl. 1):110-122.
23. Cohnstaedt L.W., et al. Phylogenetics of the phlebotomine sand fly group Verrucarum (Diptera: Psychodidae: Lutzomyia). Am. J. Trop. Med. Hyg. 2011, 84:913-922.
24. Zapata S., et al. A study of a population of Nyssomyia trapidoi (Diptera: Psychodidae) caught on the Pacific coast of Ecuador. Parasit. Vectors 2012, 5:144.
25. Gómez G., et al. Wing geometric morphometrics and molecular assessment of members in the Albitarsis complex from Colombia. Mol. Ecol. Resour. 2013, 13:1082-1092.
26. Loaiza J.R., et al. Novel genetic diversity within Anopheles punctimacula s.l.: phylogenetic discrepancy between the barcode cytochrome c oxidase I (COI) gene and the rDNA second internal transcribed spacer (ITS2). Acta Trop. 2013, 128:61-69.
27. Brabec J., et al. Substitution saturation and nuclear paralogs of commonly employed phylogenetic markers in the Caryophyllidea, an unusual group of non-segmented tapeworms (Platyhelminthes). Int. J. Parasitol. 2012, 42:259-267.
28. Huyse T., et al. Hybridisation between the two major African schistosome species of humans. Int. J. Parasitol. 2013, 43:687-689.
29. Huyse T., et al. Bidirectional introgressive hybridization between a cattle and human schistosome species. PLoS Pathog. 2009, 5:e1000571.
30. Webster B.L., et al. A revision of the interrelationships of Schistosoma including the recently described Schistosoma guineensis. Int. J. Parasitol. 2006, 36:947-955.
31. Ashford R., Crewe W. An Annotated Checklist of the Protozoa, Helminths and Arthropods for which We are Home 2003, CRC Press.
32. Eldridge B.F., Edman J.D. Medical Entomology: A Textbook on Public Health and Veterinary Problems Caused by Arthropods 2000, Kluwer Academic.
33. Goddard J. Physician's Guide to Arthropods of Medical Importance 2003, CRC Press. 4th edn.
34. Marquardt W.C. Biology of Disease Vectors 2005, Elsevier.
35. Mullen G.R., Durden L.A. Medical and Veterinary Entomology 2009, Academic Press.
36. Service M. Medical Entomology for Students 2012, Cambridge University Press. 5th edn.
37. Taylor L.H., et al. Risk factors for human disease emergence. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2001, 356:983-989.
38. US Environmental Protection Agency Contaminant Candidate List 3 Microbes: Screening to the PCCL 2008, Office of Water.
39. Woolhouse M.E.J., Gowtage-Sequeria S. Host range and emerging and reemerging pathogens. Emerg. Infect. Dis. 2005, 11:1842-1847.
40. Goddard J. Arthropods, tongue worms, leeches, and arthropod-borne diseases. Tropical Infectious Diseases 2006, 1370-1385. Elsevier. 2nd edn. R.L. Guerrant (Ed.).
41. Phillips A.J., et al. Tyrannobdella rex n. gen. n. sp. and the evolutionary origins of mucosal leech infestations. PLoS ONE 2010, 5:e10057.
42. Liu D. Introductory remarks. Detection of Human Parasitic Pathogens 2013, 1-12. Taylor & Francis. D. Liu (Ed.).
43. Boykin L.M., et al. Species delimitation and global biosecurity. Evol. Bioinform. Online 2012, 8:1-37.
44. Ratnasingham S., Hebert P.D.N. A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE 2013, 8:e66213.
45. John D.T. Markell and Voge's Medical Parasitology 2006, Elsevier. 9th edn.
46. Fürst T., et al. Global burden of human food-borne trematodiasis: a systematic review and meta-analysis. Lancet Infect. Dis. 2012, 12:210-221.
47. Truog R.D., et al. Research ethics. Paying patients for their tissue: the legacy of Henrietta Lacks. Science 2012, 337:37-38.
48. Walker K., Lynch M. Contributions of Anopheles larval control to malaria suppression in tropical Africa: review of achievements and potential. Med. Vet. Entomol. 2007, 21:2-21.
49. Higa Y. Dengue vectors and their spatial distribution. Trop. Med. Health 2011, 39:17-27.
50. Molyneux D.H., et al. "Rapid-impact interventions": how a policy of integrated control for Africa's neglected tropical diseases could benefit the poor. PLoS Med. 2005, 2:e336.
51. Ferguson H.M., et al. Ecology: a prerequisite for malaria elimination and eradication. PLoS Med. 2010, 7:e1000303.
52. Kabatereine N.B., et al. How to (or not to) integrate vertical programmes for the control of major neglected tropical diseases in sub-Saharan Africa. PLoS Negl. Trop. Dis. 2010, 4:e755.
53. Bayoh M., et al. Anopheles gambiae: historical population decline associated with regional distribution of insecticide-treated bed nets in western Nyanza Province. Malar. J. 2010, 9:62.
54. Choi H.W., et al. The effectiveness of insecticide-impregnated bed nets in reducing cases of malaria infection: a meta-analysis of published results. Am. J. Trop. Med. Hyg. 1995, 52:377-382.
55. Hajibabaei M., et al. Critical factors for assembling a high volume of DNA barcodes. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2005, 360:1959-1967.
56. Prosser S.W.J., et al. Advancing nematode barcoding: a primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes. Mol. Ecol. Resour. 2013, 13:1108-1115.
57. Moszczynska A., et al. Development of primers for the mitochondrial cytochrome c oxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminths. Mol. Ecol. Resour. 2009, 9(Suppl. s1):75-82.
58. Pawlowski J., et al. CBOL Protist Working Group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 2012, 10:e1001419.
59. Gjerde B. Characterisation of full-length mitochondrial copies and partial nuclear copies (numts) of the cytochrome b and cytochrome c oxidase subunit I genes of Toxoplasma gondii, Neospora caninum, Hammondia heydorni and Hammondia triffittae (Apicomplexa: Sarcocystidae). Parasitol. Res. 2013, 112:1493-1511.
60. Townzen J.S., et al. Identification of mosquito bloodmeals using mitochondrial cytochrome oxidase subunit I and cytochrome b gene sequences. Med. Vet. Entomol. 2008, 22:386-393.
61. Alcaide M., et al. Disentangling vector-borne transmission networks: a universal DNA barcoding method to identify vertebrate hosts from arthropod bloodmeals. PLoS ONE 2009, 4:e7092.
62. Gariepy T.D., et al. Identifying the last supper: utility of the DNA barcode library for bloodmeal identification in ticks. Mol. Ecol. Resour. 2012, 12:646-652.
63. Muturi C.N., et al. Tracking the feeding patterns of tsetse flies (Glossina genus) by analysis of bloodmeals using mitochondrial cytochrome genes. PLoS ONE 2011, 6:e17284.
64. Rukke B.A., et al. Confirming Hypoderma tarandi (Diptera: Oestridae) human ophthalmomyiasis by larval DNA barcoding. Acta Parasitol. 2014, 59:301-304.
65. Fukuda M., et al. Zoonotic onchocerciasis in Hiroshima, Japan, and molecular analysis of a paraffin section of the agent for a reliable identification. Parasite 2011, 18:185-188.
66. WHO Global Strategic Framework for Integrated Vector Management 2004, WHO.
67. Colwell, et al. Vector-borne parasitic zoonoses: emerging scenarios and new perspectives. Vet. Parasitol. 2011, 182:14-21.
68. Randolph S.E., Rogers D.J. The arrival, establishment and spread of exotic diseases: patterns and predictions. Nat. Rev. Microbiol. 2010, 8:361-371.
69. Petney T.N. Progress in parasitology. Parasitology Research Monographs 2011, Vol. 2:283-296. Springer-Verlag.
70. Tuite A.R., et al. Effect of latitude on the rate of change in incidence of Lyme disease in the United States. CMAJ Open 2013, 1:E43-E47.
71. Harrus S., Baneth G. Drivers for the emergence and re-emergence of vector-borne protozoal and bacterial diseases. Int. J. Parasitol. 2005, 35:1309-1318.
72. Tatem A.J., et al. Global traffic and disease vector dispersal. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:6242-6247.
73. Stoddard S.T., et al. The role of human movement in the transmission of vector-borne pathogens. PLoS Negl. Trop. Dis. 2009, 3:e481.
74. Tabachnick W.J. Challenges in predicting climate and environmental effects on vector-borne disease episystems in a changing world. J. Exp. Biol. 2010, 213:946-954.
75. Ashfaq M., et al. Analyzing mosquito (Diptera: Culicidae) diversity in Pakistan by DNA barcoding. PLoS ONE 2014, 9:e97268.
76. Abad-Franch F., et al. Ecology, evolution, and the long-term surveillance of vector-borne Chagas disease: a multi-scale appraisal of the tribe Rhodniini (Triatominae). Acta Trop. 2009, 110:159-177.
77. Killeen G.F., et al. Advantages of larval control for African malaria vectors: low mobility and behavioural responsiveness of immature mosquito stages allow high effective coverage. Malar. J. 2002, 1:8.
78. Impoinvil D.E., et al. Comparison of mosquito control programs in seven urban sites in Africa, the Middle East, and the Americas. Health Policy 2007, 83:196-212.
79. Manguin S., et al. Review on global co-transmission of human Plasmodium species and Wuchereria bancrofti by Anopheles mosquitoes. Infect. Genet. Evol. 2010, 10:159-177.
80. Kent R.J. Molecular methods for arthropod bloodmeal identification and applications to ecological and vector-borne disease studies. Mol. Ecol. Resour. 2009, 9:4-18.
81. Müller L., et al. DNA barcoding of sigmodontine rodents: identifying wildlife reservoirs of zoonoses. PLoS ONE 2013, 8:e80282.
82. Lee D-H., et al. DNA barcoding techniques for avian influenza virus surveillance in migratory bird habitats. J. Wildl. Dis. 2010, 46:649-654.
83. Collins R.A., Cruickshank R.H. Known knowns, known unknowns, unknown unknowns and unknown knowns in DNA barcoding: a comment on Dowton et al. Syst. Biol. 2014, 10.1093/sysbio/syu060.
84. Ivanova N.V., et al. Express barcodes: racing from specimen to identification. Mol. Ecol. Resour. 2009, 9(Suppl. s1):35-41.
85. Glenn T.C. Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 2011, 11:759-769.
86. Dowton M., et al. A preliminary framework for DNA barcoding, incorporating the multispecies coalescent. Syst. Biol. 2014, 63:639-644.
87. McCormack J.E., et al. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol. Phylogenet. Evol. 2013, 66:526-538.
88. Caporaso J.G., et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012, 6:1621-1624.
89. Shokralla S., et al. Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Mol. Ecol. Resour. 2014, 14:892-901.
90. Hajibabaei M., et al. Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecol. 2012, 12:28.
91. Yu D. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol. Evol. 2012, 3:613-623.
92. Akande I.S., et al. Polymerase chain reaction (PCR) investigations of prepatent Schistosoma haematobium cercariae incidence in five water bodies, South West, Nigeria. Afr. J. Med. Med. Sci. 2012, 41(Suppl.):75-80.
93. Macuhova K., et al. Contamination, distribution and pathogenicity of Toxocara canis and T. cati eggs from sandpits in Tokyo, Japan. J. Helminthol. 2013, 87:271-276.
94. Taberlet P., et al. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. 2012, 21:2045-2050.
95. Kvist S., et al. Barcoding, types and the Hirudo files: using information content to critically evaluate the identity of DNA barcodes. Mitochondrial DNA 2010, 21:198-205.
96. Folmer O., et al. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 1994, 3:294-299.
97. Puillandre N., et al. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol. Ecol. 2012, 21:1864-1877.
98. Ratnasingham S., Hebert P.D.N. BOLD: the Barcode of Life Data system (http://www.barcodinglife.org). Mol. Ecol. Notes 2007, 7:355-364.
99. Pleijel F., et al. Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Mol. Phylogenet. Evol. 2008, 48:369-371.
100. Hanner R. Data Standards for BARCODE Records in INSDC (BRIs) 2009, Consortium for the Barcode of Life.
101. Rayner J.C., et al. A plethora of Plasmodium species in wild apes: a source of human infection?. Trends Parasitol. 2011, 27:222-229.
102. Liu W., et al. Origin of the human malaria parasite Plasmodium falciparum in gorillas. Nature 2010, 467:420-425.
103. Choi K.S., et al. Population genetic structure of the major malaria vector Anopheles funestus s.s. and allied species in southern Africa. Parasit. Vectors 2012, 5:283.
104. Coetzee M., Koekemoer L.L. Molecular systematics and insecticide resistance in the major African malaria vector Anopheles funestus. Annu. Rev. Entomol. 2013, 58:393-412.