title: Discovery of new variable number tandem repeat loci in multiple Cryptosporidium parvum genomes for the surveillance and investigation of outbreaks of cryptosporidiosis.
abstract: Cryptosporidium parvum is a protozoan parasite causing gastro-intestinal disease (cryptosporidiosis) in humans and animals. The ability to investigate sources of contamination and routes of transmission by characterization and comparison of isolates in a cost- and time-efficient manner will help surveillance and epidemiological investigations, but as yet there is no standardised multi-locus typing scheme. To systematically identify variable number tandem repeat (VNTR) loci, which have been shown to provide differentiation in moderately conserved species, we interrogated the reference C. parvum Iowa II genome and seven other C. parvum genomes using a tandem repeat finder software. We identified 28 loci that met criteria defined previously for robust typing schemes for inter-laboratory surveillance, that had potential for generating PCR amplicons analysable on most fragment sizing platforms: repeats ≥6 bp, occurring in tandem in a single repeat region, and providing a total amplicon size of <300 bp including 50 bp for the location of the forward and reverse primers. The qualifying loci will be further investigated in vitro for consideration as preferred loci in the development of a robust VNTR scheme.
authors: Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, SA2 8QA, UK.
authors: Gregorio
authors: G
authors: Pérez-Cordón
authors: Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, SA2 8QA, UK; Swansea University Medical School, Grove Building, Swansea University, Singleton Park, Swansea, SA2 8PP, UK.
authors: Guy
authors: G
authors: Robinson
authors: Norwich Medical School, University of East Anglia, Norwich, UK.
authors: Johanna
authors: J
authors: Nader
authors: Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, SA2 8QA, UK; Swansea University Medical School, Grove Building, Swansea University, Singleton Park, Swansea, SA2 8PP, UK. Electronic address: Rachel.Chalmers@wales.nhs.uk.
authors: Rachel M
authors: RM
authors: Chalmers
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology; D003457:Cryptosporidiosis / Q000453:epidemiology* / Q000469:parasitology; D016785:Cryptosporidium parvum / Q000235:genetics* / Q000254:growth & development; D004196:Disease Outbreaks; D018628:Gene Dosage; D018503:Genome, Protozoan / Q000235:genetics*; D008018:Life Cycle Stages; D018598:Minisatellite Repeats / Q000235:genetics*; D016415:Sequence Alignment
keywords: Cryptosporidium parvum; Multilocus; Variable number tandem repeats