Cryptosporidium parvum is a zoonotic protozoan parasite that causes food and waterborne gastrointestinal disease and whose major animal reservoirs are cattle and small ruminants. We report here on a draft whole-genome sequence of a zoonotic isolate of C. parvum isolated from a person with cryptosporidiosis.
ABSTRACT
Cryptosporidium parvum is a zoonotic protozoan parasite that causes food and waterborne gastrointestinal disease and whose major animal reservoirs are cattle and small ruminants. We report here on a draft whole-genome sequence of a zoonotic isolate of C. parvum isolated from a person with cryptosporidiosis.
ANNOUNCEMENT
Cryptosporidium parvum is one of the two major species of the protozoan parasite Cryptosporidium that infect humans and cause gastrointestinal disease (1). C. parvum is considered zoonotic and has a wide host range, in which cattle and small ruminants are the predominant reservoir hosts (2). However, some subtypes of C. parvum, such as the IIc gp60 subgroup, are considered to be human adapted (2), because they are mainly reported in humans, with only a few reports in European hedgehogs (3). Whole-genome sequencing (WGS) provides a means for comparing isolates to identify markers important in distinguishing routes of transmission and potential virulence traits for better epidemiological analysis and risk assessment. The objective of this work was to sequence a zoonotic isolate of C. parvum.
We sequenced a human isolate of C. parvum, UKP1, isolated at the Public Health England and Public Health Wales Cryptosporidium Reference Unit and identified as gp60 type IIaA17G1R1 (GenBank accession no. JX971701). This subtype has a global distribution and has been observed in humans, cattle, pigs, and sheep (4, 5). Zoonotic linkages with cases in England and Wales have been demonstrated with IIaA17G1R1 (4). Oocysts were semipurified from stool using a salt flotation and hypochlorite treatment. DNA was extracted with the QIAamp DNA extraction kit (Qiagen, Hilden, Germany) and whole-genome amplified with the REPLI-g kit (Qiagen) before 454 GS FLX Titanium and Illumina HiSeq 2500 sequencing. A total of 472.6 Mbp, representing 1.6 million reads, were obtained from the 454 GS FLX Titanium sequencing, and 12.8 Gbp, representing 26 million reads, were produced on an Illumina MiSeq instrument. The quality of the reads was examined using FastQC (6). Illumina and 454 reads were mapped against a reference C. parvum isolate (GenBank accession no. NZ_AAEE00000000) using Bowtie 2 v. 2.3.3.1 (7), and the mapped reads were then de novo assembled using SPAdes v. 3.11.0 (8). The initial assembly was used in a second round of assembly using the --trusted-contigs flag with SPAdes. Iterative polishing of the assembly was done by mapping the reads back to the assembly with Bowtie 2 and correcting them with Pilon 1.22 (9). The 8 C. parvum chromosomes assembled into 14 contigs with a total genome size of 8,881,956 bp, a G+C content of 30.20%, an N50 value of 1,092,230 bp, and a largest contig length of 1,333,759 bp.
Data availability.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. PYCJ00000000, and raw sequence reads are available under the BioProject no. PRJNA439211.
ACKNOWLEDGMENTS
We are grateful to Brian Boyle (Genomics Sequencing Platform, IBIS, Université de Laval, Quebec City, Quebec, Canada) for whole-genome amplification and generating the 454 and Illumina sequence data.
Funding for this work was provided by the Public Health Agency of Canada.
REFERENCES
- 1.Ryan U, Hijjawi N. 2015. New developments in Cryptosporidium research. Int J Parasitol 45:367–373. doi: 10.1016/j.ijpara.2015.01.009. [DOI] [PubMed] [Google Scholar]
- 2.Feng Y, Ryan UM, Xiao L. 2018. Genetic diversity and population structure of Cryptosporidium. Trends Parasitol doi: 10.1016/j.pt.2018.07.009. [DOI] [PubMed] [Google Scholar]
- 3.Krawczyk AI, van Leeuwen AD, Jacobs-Reitsma W, Wijnands LM, Bouw E, Jahfari S, van Hoek AHAM, van der Giessen JWB, Roelfsema JH, Kroes M, Kleve J, Dullemont Y, Sprong H, de Bruin A. 2015. Presence of zoonotic agents in engorged ticks and hedgehog faeces from Erinaceus europaeus in (sub) urban areas. Parasit Vectors 8:210–216. doi: 10.1186/s13071-015-0814-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Chalmers RM, Smith RP, Hadfield SJ, Elwin K, Giles M. 2011. Zoonotic linkage and variation in Cryptosporidium parvum from patients in the United Kingdom. Parasitol Res 108:1321–1325. doi: 10.1007/s00436-010-2199-x. [DOI] [PubMed] [Google Scholar]
- 5.Smith RP, Clifton-Hadley FA, Cheney T, Giles M. 2014. Prevalence and molecular typing of Cryptosporidium in dairy cattle in England and Wales and examination of potential on-farm transmission routes. Vet Parasitol 204:111–119. doi: 10.1016/j.vetpar.2014.05.022. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Andrews S. 2010. FastQC. A quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
- 7.Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi: 10.1038/nmeth.1923. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PloS One 9:e112963. doi: 10.1371/journal.pone.0112963. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
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Data Availability Statement
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. PYCJ00000000, and raw sequence reads are available under the BioProject no. PRJNA439211.