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CryptoGenotyper :
CryptoGenotyper : A new bioinformatics tool for rapid Cryptosporidium identification
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- Yanta, Christine A. (author)
- Publ Hlth Agcy Canada, Natl Microbiol Lab, 110 Stone Rd West, Guelph, ON N1G 3W4, Canada.
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- Bessonov, Kyrylo (author)
- Publ Hlth Agcy Canada, Natl Microbiol Lab, 110 Stone Rd West, Guelph, ON N1G 3W4, Canada.
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- Robinson, Guy (author)
- Singleton Hosp, Cryptosporidium Reference Unit, Publ Hlth Wales, Microbiol & Hlth Protect, Swansea SA2 8QA, W Glam, Wales.;Swansea Univ, Med Sch, Singleton Pk, Swansea SA2 8PP, W Glam, Wales.
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- Troell, Karin (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Natl Vet Inst, S-75189 Uppsala, Sweden.
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- Guy, Rebecca A. (author)
- Publ Hlth Agcy Canada, Natl Microbiol Lab, 110 Stone Rd West, Guelph, ON N1G 3W4, Canada.
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Publ Hlth Agcy Canada, Natl Microbiol Lab, 110 Stone Rd West, Guelph, ON N1G 3W4, Canada Singleton Hosp, Cryptosporidium Reference Unit, Publ Hlth Wales, Microbiol & Hlth Protect, Swansea SA2 8QA, W Glam, Wales.;Swansea Univ, Med Sch, Singleton Pk, Swansea SA2 8PP, W Glam, Wales. (creator_code:org_t)
- Elsevier, 2021
- 2021
- English.
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In: FOOD AND WATERBORNE PARASITOLOGY. - : Elsevier. - 2405-6766. ; 23
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Abstract
Subject headings
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- Cryptosporidium is a protozoan parasite that is transmitted to both humans and animals through zoonotic or anthroponotic means. When a host is infected with this parasite, it causes a gastrointestinal disease known as cryptosporidiosis. To understand the transmission dynamics of Cryptosporidium, the small subunit (SSU or 18S) rRNA and gp60 genes are commonly studied through PCR analysis and conventional Sanger sequencing. However, analyzing sequence chromatograms manually is both time consuming and prone to human error, especially in the presence of poorly resolved, heterozygous peaks and the absence of a validated database. For this study, we developed a Cryptosporidium genotyping tool, called CryptoGenotyper, which has the capability to read raw Sanger sequencing data for the two common Cryptosporidium gene targets (SSU rRNA and gp60) and classify the sequence data into standard nomenclature. The CryptoGenotyper has the capacity to perform quality control and properly classify sequences using a high quality, manually curated reference database, saving users' time and removing bias during data analysis. The incorporated heterozygous base calling algorithms for the SSU rRNA gene target resolves double peaks, therefore recovering data previously classified as inconclusive. The CryptoGenotyper successfully genotyped 99.3% (428/431) and 95.1% (154/162) of SSU rRNA chromatograms containing single and mixed sequences, respectively, and correctly subtyped 95.6% (947/991) of gp60 chromatograms without manual intervention. This new, user-friendly tool can provide both fast and reproducible analyses of Sanger sequencing data for the two most common Cryptosporidium gene targets. Crown Copyright (C) 2021 Published by Elsevier Inc. on behalf of International Association of Food and Waterborne Parasitology.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Infektionsmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Infectious Medicine (hsv//eng)
Keyword
- Genotyping tool
- Sanger sequencing
- SSU rRNA gene
- gp60 gene
- Validated database
- Mixed infections
Publication and Content Type
- ref (subject category)
- art (subject category)
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