Gut Microbial Signatures Associated with Cryptosporidiosis: A Case Series

Abstract

Cryptosporidium spp. are zoonotic protozoan parasites with a global prevalence, with both gastrointestinal and pulmonary involvement. Though symptoms can often be relatively mild, they can become severe and even fatal in children under five, the elderly, and in immunocompromised individuals, making cryptosporidiosis a leading cause of morbidity and mortality in fragile populations. Furthermore, there is an urgent clinical need for alternative therapies against cryptosporidiosis, as currently available FDA-approved treatments are ineffective in the immunocompromised. Recent evidence in animal models suggests that the gut microbiota (GM) can influence both host and parasite biology to influence the course of Cryptosporidium infection. Here, we present GM profiles in five cases of cryptosporidiosis, associated with varying underlying pathologies. We found that moderate-severe cryptosporidiosis was characterized by a reduction in alpha-diversity and an enrichment of Enterococcus spp., while decreases in Bifidobacterium, Gemmiger, and Blautia were detectable in the milder manifestations of the disease. Our results suggest that severe cryptosporidiosis is associated with a stronger change on the GM than is age or underlying pathology. Together with previously published studies in animal models, we believe that these results suggest that the GM could be a potential therapeutic target for human patients as well, particularly in the immunocompromised for whom anti-Cryptosporidium treatment remains largely ineffective.

Keywords: Cryptosporidium; chronic immunodeficiency; cryptosporidiosis; gut microbiota; metataxonomic sequencing.

Figure 1

GM alpha-diversity in patients with mild and moderate–severe Cryptosporidium infections. (A–E) Alpha-diversity, as measured by Simpson’s index, in Crypto 1 (A), Crypto 2 (B), Crypto 3 (C), Crypto 4 (D) and Crypto 5 (E), compared to age-matched CTRLs. Statistical analysis: Mann–Whitney U-test, * p < 0.05. Patients with moderate to severe cryptosporidiosis (A,C,D) were characterized by a reduction in alpha-diversity measurements, while mildly affected patients (B,E) had comparable alpha-diversity measurements compared to age-matched CTRLs. In red: individual Cryptosporidium-positive replicates. In blue: individual CTRL replicates.

Figure 2

GM composition of patients with moderate–severe cryptosporidiosis. (A–C) Stacked bar charts representing the relative abundance of bacterial genera in each Crypto 1 (A), Crypto 3 (B), and Crypto 4 (C) replicate and each individual age-matched CTRL. Genera detected under 1% relative abundance were grouped together and represented collectively as “other”. Moderately–severely affected patients were characterized by an overabundance of a single bacterial genus in all profiled samples.

Figure 3

GM composition of patients with mild cryptosporidiosis. The GM of mildly affected patients are diverse and somewhat similar to that of their respective healthy CTRLs. (A,B) Stacked bar charts representing the relative abundance of bacterial genera in each Crypto 2 (A) and Crypto 5 (B) replicate and each individual age-matched CTRL. Genera detected under 1% relative abundance were grouped together and represented collectively as “other”.

Figure 4

Beta-diversity analyses of Crypto-positive and CTRL samples. Dendrogram representing similarity between healthy CTRLs (blue) and a single sample from each Cryptosporidium-positive patient (red) as calculated by Bray–Curtis dissimilarity. Green: patients treated with antibiotics. Purple: patients with moderate–severe cryptosporidiosis. Orange: patients with mild cryptosporidiosis.