Cryptosporidium species and subtypes in river water and riverbed sediment using next-generation sequencing

Muofhe Grace Mphephu; Mutshiene Deogratias Ekwanzala; Maggy Ndombo Benteke Momba

doi:10.1016/j.ijpara.2020.10.005

Cryptosporidium species and subtypes in river water and riverbed sediment using next-generation sequencing

Int J Parasitol. 2021 Apr;51(5):339-351. doi: 10.1016/j.ijpara.2020.10.005. Epub 2021 Jan 7.

Authors

Muofhe Grace Mphephu¹, Mutshiene Deogratias Ekwanzala¹, Maggy Ndombo Benteke Momba²

Affiliations

¹ Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Private BagX680, Pretoria 0001, South Africa.
² Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Private BagX680, Pretoria 0001, South Africa. Electronic address: mombamnb@tut.ac.za.

PMID: 33421439
DOI: 10.1016/j.ijpara.2020.10.005

Abstract

This study uncovered the prevalence, harboured species, and subtype diversity of Cryptosporidium species in river water and its sediment from the Apies River in South Africa. Cryptosporidium spp. concentrations in freshwater and its sediment were determined using Ziehl-Neelsen staining and quantitative Polymerase Chain Reaction (qPCR) techniques. Next-generation sequencing (NGS) targeting the 60 kDa glycoprotein (gp60) gene of Cryptosporidium spp. was performed to reveal the species, subtype families and subtypes harboured in freshwater and its sediment. Although the results revealed that water samples had a higher prevalence (30%) compared with sediment (28%), the number of observable Cryptosporidium spp. oocysts in sediment samples (ranging from 4.90 to 5.81 log₁₀ oocysts per 1 Liter) was higher than that of river water samples (ranging from 4.60 to 5.58 log₁₀ oocysts per 1 L) using Ziehl-Neelsen staining. The 18S ribosomal ribonucleic acid (rRNA) gene copy of Cryptosporidium in riverbed sediments ranged from 6.03 to 7.65 log₁₀, whereas in river water, it was found to be between 4.20 and 6.79 log₁₀. Subtyping results showed that in riverbed sediments, Cryptosporidium parvum accounted for 40.72% of sequences, followed by Cryptosporidium hominis with 23.64%, Cryptosporidium cuniculus with 7.10%, Cryptosporidium meleagridis with 4.44% and the least was Cryptosporidium wrairi with 2.59%. A considerable percentage of reads in riverbed sediment (21.25%) was not assigned to any subtype. River water samples had 45.63% of sequences assigned to C. parvum, followed by 30.32% to C. hominis, 17.99% to C. meleagridis and 5.88% to C. cuniculus. The data obtained are concerning, as Cryptosporidium spp. have intrinsic resistance to water treatment processes and low infectious doses, which can pose a risk to human health due to the various uses of water (for human consumption, leisure, and reuse).

Keywords: Next-generation sequencing; Protozoa; River water; Riverbed sediments; Subtyping.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cryptosporidiosis*
Cryptosporidium* / genetics
High-Throughput Nucleotide Sequencing
Humans
Oocysts
Rivers