Molecular analysis of Cryptosporidium species in Western Australian human populations (2023–2025), and the emergence of rare C. hominis IeA11G3T3 subtype
Bibliographic record
Abstract
Cryptosporidium species are an important cause of diarrhoeal disease worldwide. Many countries reported declines in cryptosporidiosis incidence during COVID-19 restrictions, followed by marked increases post-COVID. A similar pattern has been observed in Australia, with record-high case numbers reported across multiple states in 2024-2025, including Western Australia (WA), where an outbreak occurred in 2025. Between 1st January - 30th June 2025, WA reported a statewide total of 1110 human cryptosporidiosis cases, which is substantially higher than the previous years. In the present study, a subset of WA cases from 2025 was investigated using contact tracing and molecular typing and compared with subtypes circulating in 2023 and 2024. Sequence analysis of the 18S rRNA and gp60 loci identified three Cryptosporidium species: C. hominis (91.5 %, 108/118), C. parvum (6.8 %, 8/118), and C. meleagridis (1.7 %, 2/118), comprising 13 distinct subtypes, over the three years. Notably, a previously rare C. hominis subtype, IeA11G3T3, emerged in 2023 and by 2025 had become the dominant subtype (92.1 %, 70/76) of samples typed. Multi-locus sequence typing (MLST) of a representative subset of IeA11G3T3 isolates (n = 13) showed that all sequences were identical, except for one isolate from 2024, which contained three insertions: an 18-bp repeat in the cp-47 gene and both a 12-bp and a 6-bp repeat in the dz-hrgp gene. The C. hominis IeA11G3T3 subtype has also recently emerged as a dominant subtype in several other countries, although the factors driving its emergence remain unclear.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".