Evolutionary genomics of anthroponosis in Cryptosporidium

Nader, Johanna; Mathers, Thomas C.; Ward, Ben J.; Pachebat, Justin A.; Swain, Martin; Robinson, Guy; Chalmers, Rachel M.; Hunter, Paul R.; Oosterhout, Cock van; Tyler, Kevin M.

doi:10.1038/s41564-019-0377-x

Cited by 114 publications

(155 citation statements)

References 66 publications

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“…Although most C. parvum subtypes are zoonotic, a subspecies that is human-adapted has been proposed as C. parvum anthroponosum [94]. Geographical analysis indicates that the human-adapted species (C. hominis, some C. parvum subtypes) are relatively more prevalent in resource-poor countries, whereas zoonotic C. parvum dominates in North America, Europe, Australia, and parts of the Middle East [95].…”

Section: Transmission Of Cryptosporidiummentioning

confidence: 99%

A One Health Approach to Tackle Cryptosporidiosis

Innes

Chalmers

Wells

et al. 2020

Trends in Parasitology

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152

103

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Section: Transmission Of Cryptosporidiummentioning

confidence: 99%

A One Health Approach to Tackle Cryptosporidiosis

Innes

Chalmers

Wells

et al. 2020

Trends in Parasitology

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152

103

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“…As more genomes are becoming available at an everincreasing rate, researchers are able to explore further the biology and evolution of Cryptosporidium. Recently, Nader et al (87) used 21 whole genome sequences to show the existence of two subspecies lineages of C. parvum (C. parvum parvum and C. parvum anthroponosum) with different host-adapted infectivity. Additionally, they identified some of the historic genetic exchanges that have occurred between these lineages and C. hominis during the evolution of these different species and subspecies, even suggesting rough time-lines for when these events occurred (87,88).…”

Section: Progression Of Whole Genome Sequencing and Assemblymentioning

confidence: 99%

“…The advent of the new techniques to facilitate the DNA extraction, enrichment, sequencing, and assembly of high quality Cryptosporidium genomes from clinical samples, provides an opportunity to greatly expand the number of genomes available. An EU funded collaboration (Aquavalens project, www.aquavalens.org) between several institutions generated 27 assemblies of C. parvum, C. hominis, Cryptosporidium viatorum, C. ubiquitum, C. cuniculus, and C. meleagridis directly from clinical isolates using the DNA extraction and purification protocol described by Hadfield et al (75) and Nader et al (87). Under another EU funded project, COMPARE (https:// www.compare-europe.eu/), 31 new C. parvum and 19 new C. hominis genome assemblies were generated from clinical isolates, using the DNA extraction and purification protocol described by Hadfield et al (75), and the DNA enrichment protocol described by Guo et al (77).…”

Section: Genome Availabilitymentioning

confidence: 99%

Direct Sequencing of Cryptosporidium in Stool Samples for Public Health

Morris

Robinson

Swain

et al. 2019

Front. Public Health

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“…Overall, our approach could be adapted to viruses and bacteria that show recombination or reshuffling of segments as well as clonal propagation [28–31], to other protozoans (e.g. Toxoplasma, Cryprosporidium [32–34]), and to the many fungal pathogens [35], plants [6,7], and animals with mixed mating systems. Due to our treatment of uncertainty, it is especially relevant for a growing number of studies that plan estimate IBD-based relatedness using genotype (versus sequence) data.…”

Section: Introductionmentioning

confidence: 99%

Identity-by-descent relatedness estimates with uncertainty characterise departure from isolation-by-distance betweenPlasmodium falciparumpopulations on the Colombian-Pacific coast

Taylor

Echeverry

Anderson

et al. 2020

Preprint

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18Characterising connectivity between geographically separated biological populations is a common goal in 19 many fields. Recent approaches to understanding connectivity between malaria parasite populations, with 20 implications for disease control efforts, have used estimates of relatedness based on identity-by-descent (IBD). 21 However, uncertainty around estimated relatedness has not been accounted for to date. IBD-based relat-22 edness estimates with uncertainty were computed for pairs of monoclonal Plasmodium falciparum samples 23 collected from five cities on the Colombian-Pacific coast where long-term clonal propagation of P. falciparum 24 is frequent. The cities include two official ports, Buenaventura and Tumaco, that are separated geographically 25 but connected by frequent marine traffic. The fraction of highly-related sample pairs (whose classification 26 accounts for uncertainty) was greater within cities versus between. However, based on both the fraction 27 of highly-related sample pairs and on a threshold-free approach (Wasserstein distances between parasite 28 populations) connectivity between Buenaventura and Tumaco was disproportionally high. Buenaventura- 29Tumaco connectivity was consistent with three separate transmission events involving parasites from five 30 different clonal components (groups of statistically indistinguishable parasites identified under a graph theo-31 retic framework). To conclude, P. falciparum population connectivity on the Colombian-Pacific coast abides 32 by accessibility not isolation-by-distance, potentially implicating marine traffic in malaria transmission with 33 opportunities for targeted intervention. Further investigations are required to test this and alternative hy-34 potheses. For the first time in malaria epidemiology, we account for uncertainty around estimated relatedness 35 (an important consideration for future studies that plan to use genotype versus whole genome sequence data 36 to estimate IBD-based relatedness); we also use a threshold-free approach to compare parasite populations, 37 and identify clonal components in a statistically principled manner. The approaches we employ could be 38 adapted to other recombining organisms with mixed mating systems, thus have broad relevance. 39 1 In many research fields genetic data are used to help characterise connectivity between geographically dis-41 parate biological populations, with numerous applications in conservation, agriculture, and public health. 42Patterns of genetic similarity between pathogen populations help us understand how the disease spreads. 43 Patterns of relatedness (a measure of genetic similarity) between malaria parasites in different human pop-44 ulations, for instance, help characterise the connectivity between them, thus guide the design of targeted 45 public health interventions [1]. 46 Several methods are employed to measure genetic similarity and thus characterise connectivity. Phylo-47 genetic methods, in which genetic distances between individuals are measured in unit...

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Evolutionary genomics of anthroponosis in Cryptosporidium

Cited by 114 publications

References 66 publications

A One Health Approach to Tackle Cryptosporidiosis

A One Health Approach to Tackle Cryptosporidiosis

Direct Sequencing of Cryptosporidium in Stool Samples for Public Health

Identity-by-descent relatedness estimates with uncertainty characterise departure from isolation-by-distance betweenPlasmodium falciparumpopulations on the Colombian-Pacific coast

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