Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Hadfield, Stephen J ^a   Pachebat, Justin A ^b   Swain, Martin T ^b   Robinson, Guy ^a   Cameron, Simon J S ^b   Alexander, Jenna ^b   Hegarty, Matthew J ^b   Elwin, Kristin ^a   Chalmers, Rachel M ^a  

^a SINGLETON HOSPITAL   (United Kingdom)

^b ABERYSTWYTH UNIVERSITY   (United Kingdom)

Author keywords

Cryptosporidium; Illumina; Immunomagnetic separation; Nextera XT; Stool; Whole genome sequencing

Indexed keywords

RNA 18S; PROTOZOAL DNA;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BACTERIAL GENOME; BACTERIUM ISOLATE; CONTROLLED STUDY; CRYPTOSPORIDIOSIS; CRYPTOSPORIDIUM HOMINIS; CRYPTOSPORIDIUM HOMINIS GP60 SUBTYPE IAA14R3; CRYPTOSPORIDIUM HOMINIS GP60 SUBTYPE IBA10G2; CRYPTOSPORIDIUM HOMINIS TU502 V1; CRYPTOSPORIDIUM PARVUM; CRYPTOSPORIDIUM PARVUM GP60 SUBTYPE IIAA15G2R1; CRYPTOSPORIDIUM PARVUM GP60 SUBTYPE IIAA17G1R1; CRYPTOSPORIDIUM PARVUM GP60 SUBTYPE IIAA18G2R1; CRYPTOSPORIDIUM PARVUM GP60 SUBTYPE IIAA19G1R2; CRYPTOSPORIDIUM PARVUM GP60 SUBTYPE IIDA22G1; DNA EXTRACTION; FECES ANALYSIS; GENE SEQUENCE; HUMAN; IMMUNOMAGNETIC SEPARATION; MICROSCOPY; NEXT GENERATION SEQUENCING; NONHUMAN; OOCYST; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; WHOLE GENOME SEQUENCING; CRYPTOSPORIDIUM; FECES; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; METABOLISM; NUCLEOTIDE SEQUENCE; PARASITOLOGY; PILOT STUDY;

ANIMALIA; CRYPTOSPORIDIUM; CRYPTOSPORIDIUM HOMINIS; CRYPTOSPORIDIUM PARVUM;

BASE SEQUENCE; CRYPTOSPORIDIUM; CRYPTOSPORIDIUM PARVUM; DNA, PROTOZOAN; FECES; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; OOCYSTS; PILOT PROJECTS;

EID: 84940054261     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1805-9     Document Type: Article

References (32)

1. Chalmers RM, Davies AP. Mini-review: clinical cryptosporidiosis. Exp Parasitol. 2010;124:138-46.
2. Kotloff KL, Nataro JP, Blackwelder WC, Nasrin D, Farag TH, Panchalingam S, et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet. 2013;382:209-22.
3. Xu P, Widmer G, Wang Y, Ozaki LS, Alves JM, Serrano MG, et al. The genome of Cryptosporidium hominis. Nature. 2004;431:1107-12.
4. Abrahamsen MS, Templeton TJ, Enomoto S, Abrahante JE, Zhu G, Lancto CA, et al. Complete genome sequence of the apicomplexan. Cryptosporidium parvum. Science. 2004;304:441-5.
5. Guy RA, Payment P, Krull UJ, Horgen PA. Real-Time PCR for Quantification of Giardia and Cryptosporidium in environmental water samples and sewage. Appl Environ Microbiol. 2003;69:5178-85.
6. Widmer G, Lee Y, Hunt Y, Martinelli A, Tolkoff M, Bodi K. Comparative genome analysis of two Cryptosporidium parvum isolates with different host range. Infect Genet Evol. 2012;12:1213-21.
7. Li N, Xiao L, Alderisio K, Elwin K, Cebelinski E, Chalmers R, et al. Subtyping Cryptosporidium ubiquitum, a zoonotic pathogen emerging in humans. Emerg Infect Dis. 2014;20:217-24.
8. Widmer G, Akiyoshi D, Buckholt MA, Feng X, Rich SM, Deary KM, et al. Animal propagation and genomic survey of a genotype 1 isolate of Cryptosporidiurn parvum. Mol Biochem Parasitol. 2000;108:187-97.
9. Baishanbo A, Gargala G, Delaunay A, François A, Ballet JJ, Favennec L. Infectivity of Cryptosporidium hominis and Cryptosporidium parvum genotype 2 isolates in immunosuppressed Mongolian gerbils. Infect Immun. 2005;73:5252-5.
10. Guo Y, Li N, Lysén C, Frace M, Tang K, Sammons S, et al. Isolation and enrichment of Cryptospordiium DNA and verification of DNA purity for whole genome sequencing. J Clin Microbiol. 2015;53(2):641-7.
11. Seth-Smith HMB, Harris SR, Skilton RJ, Radebe FM, Golparian D, Shipitsyna E, et al. Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture. Genome Res. 2013;23:855-66.
12. Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc. 2012;7:1260-84.
13. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357-9.
14. Otto TD, Dillon GP, Degrave WS, Berriman M. RATT: Rapid Annotation Transfer Tool. Nucl Acids Res. 2011;39:e57.
15. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-10.
16. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, et al. Database resources of the National Center for Biotechnology Information. Nucl Acids Res. 2007;35 suppl 1:D5-D12.
17. Strong WB, Gut J, Nelson RG. Cloning and sequence analysis of a highly polymorphic Cryptosporidium parvum gene encoding a 60-Kilodalton glycoprotein and characterization of Its 15- and 45-kilodalton zoite surface antigen products. Infect Immun. 2000;68:4117-34.
18. Alves M, Xiao L, Sulaiman I, Lal AA, Matos O, Antunes F. Subgenotype analysis of Cryptosporidium isolates from humans, cattle, and zoo ruminants in Portugal. J Clin Microbiol. 2003;41:2744-7.
19. Bouzid M, Chalmers RM, Tyler KM, Elwin K, Hunter PR. Multilocus analysis of Cryptosporidium provides evidence for ecological adaption driving genetically divergent subpopulations. BMC Microbiol. 2010;10:213.
20. Bouzid M, Heavens D, Elwin K, Chalmers RM, Hadfield S, Hunter PR, et al. Whole Genome Amplification (WGA) for archiving and genotyping of clinical isolates of Cryptosporidium species. Parasitology. 2010;137:27-36.
21. Esteban JA, Salas M, Blanco L. Fidelity of F29 DNA Polymerase: comparison between protein-primed initiation and DNA polymerization. J Biol Chem. 1993;268:2713-26.
22. Hadfield SJ, Robinson G, Elwin K, Chalmers RM. Detection and differentiation of Cryptosporidium spp. in human clinical samples by use of real-time PCR. J Clin Microbiol. 2011;49:918-24.
23. Tosini F, Drumo R, Elwin K, Chalmers RM, Pozio E, Cacciò SM. The CpA135 gene as a marker to identify Cryptosporidium species infecting humans. Parasitol Int. 2010;59:606-9.
24. Robinson G, Wright S, Elwin K, Hadfield SJ, Katzer F, Bartley PM, et al. Re-description of Cryptosporidium cuniculus Inman and Takeuchi, 1979 (Apicomplexa: Cryptosporidiidae); morphology, biology and phylogeny. Int J Parasitol. 2010;40:1539-48.
25. Elwin K, Hadfield SJ, Robinson G, Chalmers RM. The epidemiology of sporadic human infections with unusual cryptosporidia detected during routine typing in England and Wales, 2000 to 2008. Epidemiol Infect. 2011;140:673-83.
26. Upton SJ. vitro cultivation. In: Fayer R, editor. Cryptosporidium and Cryptosporidiosis. Boca Raton, FL: CRC Press; 1997. p. 181-207.
27. Jones AW, Cameron SJ, Thatcher R, Beecroft MS, Mur LA, Davison G. Effects of bovine colostrum supplementation on upper respiratory illness in active males. Brain Behav Immun. 2014;39:194-203.
28. Kim EJ, Huws SA, Lee MR, Wood JD, Muetzel SM, Wallace RJ, et al. Fish oil increases the duodenal flow of long chain polyunsaturated fatty acids and trans-11 18:1 and decreases 18:0 in steers via changes in the rumen bacterial community. J Nutr. 2008;138:889-96.
29. Le Blancq SM, Khramtsov NV, Zamani F, Upton SJ, Wu TW. Ribosomal RNA gene organization in Cryptosporidium parvum. Mol Biochem Parasitol. 1997;90:463-78.
30. Assefa S, Keane TM, Otto TD, Newbold C, Berriman M. ABACAS: Algorithm-Based Automatic Contiguation of Assembled Sequences. Bioinformatics. 2009;25:1968-9.
31. Tsai IJ, Otto TD, Berriman M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol. 2010;11:R41.
32. Otto TD, Sanders M, Berriman M, Newbold C. Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics. 2010;26:1704-7.