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).

本研究揭示了来自南非阿皮斯河的河水及其沉积物中隐孢子虫物种的流行、栖息物种和亚型多样性。隐孢子虫属 淡水及其沉积物中的浓度使用 Ziehl-Neelsen 染色和定量聚合酶链反应 (qPCR) 技术测定。靶向隐孢子虫60 kDa 糖蛋白 (gp60) 基因的新一代测序 (NGS) 。进行了揭示淡水及其沉积物中的物种、亚型科和亚型。虽然结果显示与沉积物 (28%) 相比，水样的流行率 (30%) 更高，但可观察到的隐孢子虫数量属 使用 Ziehl-Neelsen 染色，沉积物样品中的卵囊（范围为每 1 升4.90 至 5.81 log ₁₀卵囊）高于河水样品（范围为每 1 L 4.60 至 5.58 log ₁₀卵囊）。河床沉积物中隐孢子虫的 18S 核糖体核糖核酸 (rRNA) 基因拷贝范围为 6.03 至 7.65 log ₁₀，而在河水中，它被发现在 4.20 至 6.79 log _{10 之间}。亚型结果表明，在河床沉积物中，Cryptosporidium parvum占序列的 40.72%，其次是Cryptosporidium hominis占 23.64%，Cryptosporidium cuniculus占 7.10%，Cryptosporidium meleagridis为 4.44%，最少的是Cryptosporidium wrairi，为 2.59%。河床沉积物中相当大比例的读数 (21.25%) 未分配给任何亚型。河流水样中有 45.63% 的序列属于C. parvum，其次是C. hominis的 30.32%、C . meleagridis 的17.99%和C. cuniculus 的5.88% 。获得的数据令人担忧，因为隐孢子虫属。对水处理过程具有内在抵抗力和低感染剂量，由于水的各种用途（供人类消费、休闲和再利用），这可能对人类健康构成风险。