Population structure of natural and propagated isolates of Cryptosporidium parvum, C. hominis and C. meleagridis

Abstract

The three protozoan species Cryptosporidium parvum, C. meleagridis and C. hominis (phylum Apicomplexa) are enteric pathogens of humans. The former two species are zoonotic and the latter is thought to infect only humans. To better characterize the structure and transmission of natural and laboratory-propagated isolates, we analyzed a collection of archived human and animal isolates of these three species by deep-sequencing polymerase chain reaction products amplified from a polymorphic sequence on chromosome 1. Thousands of screened 200-nucleotide sequences were analyzed to compare the diversity among samples, to assess the impact of laboratory propagation on population complexity and to identify taxonomically mixed isolates. Contrary to our expectation, repeated propagation in animals did not reduce intra-isolate diversity nor was diversity associated with host species. Significantly, in most samples, sequences characteristic of a different species were identified. The presence of C. hominis alleles in C. parvum and C. meleagridis isolates confirms earlier reports of mixed isolates and raises the possibility that the host range of C. hominis is broader than typically assumed. In a genetically divergent isolate of C. parvum, a majority of sequences was found to be recombinant, suggesting that this genotype originated from a C. parvum × C. hominis recombination event.

Next Generation Sequencing uncovers within-host differences in the genetic diversity of Cryptosporidium gp60 subtypes

“…The relative contribution of each type of population structure appears to vary between regions and hosts, and may reflect the prevailing ecological transmission dynamics (Mallon et al, 2003;Tanriverdi et al, 2008;Widmer and Sullivan, 2010;Herges et al, 2012;Widmer et al, 2015). The finding of only one C. hominis subtype by both Sanger and NGS in the kangaroo-derived DNA samples may reflect a clonal population structure operating locally in kangaroo populations from the main Sydney drinking water catchment.…”

“…hominis indicates a flexible reproductive strategy with panmictic (where genetic exchange occurs at random with limited or no sub-structuring), clonal and epidemic population structures (Mallon et al, 2003;Morrison et al, 2008;Tanriverdi et al, 2008;Widmer and Sullivan, 2010;Drumo et al, 2012;De Waele et al, 2013;Ramo et al, 2015Ramo et al, , 2016Widmer et al, 2015). The relative contribution of each type of population structure appears to vary between regions and hosts, and may reflect the prevailing ecological transmission dynamics (Mallon et al, 2003;Tanriverdi et al, 2008;Widmer and Sullivan, 2010;Herges et al, 2012;Widmer et al, 2015).…”

Direct Sequencing of Cryptosporidium in Stool Samples for Public Health

“…To generate sufficient DNA, oocysts may be propagated through animals, but Cryptosporidium populations have been shown to change through natural host-based preferential selection of individual subtypes or further recombination into new subtypes. For example, the "isolate" that provided the first reference C. hominis genome in 2004 (TU502) was subsequently serially propagated in gnotobiotic pigs over many years resulting in a different subtype in 2012, which was likely due to the original population being overgrown by another contaminating isolate (76). Additionally, the availability of host animals appropriate to the Cryptosporidium species in question ( Table 1), and the ethics, time and cost resources that are associated with propagation are prohibitive.…”

“…Cama et al used MLST to characterize differences in Iowa reference C. parvum isolates that had been maintained in different laboratories and described differences that were likely the results of passages through calves infected with exogenous C. parvum (107). This genetic drift in reference isolates was also seen with the TU502 reference C. hominis isolate between 2005 and 2012 following multiple animal passages (76). Therefore, the implications of MOI for surveillance and outbreak investigations are uncertain.…”

Annotated draft genome sequences of three species ofCryptosporidium:Cryptosporidium meleagridisisolate UKMEL1,C. baileyiisolate TAMU-09Q1 andC. hominisisolates TU502_2012 and UKH1

“…In fact, high-throughput sequencing of a polymorphic locus demonstrated the presence of multiple alleles in laboratory and natural Cryptosporidium isolates (Widmer et al. 2015). …”