Large-scale molecular epidemiological survey of Giardia and Cryptosporidium in Victoria, Australia (2020–2024), reveals novel subtypes and outbreak-associated lineages

Abstract

Cryptosporidium and Giardia are major causes of gastrointestinal illness globally. In Australia, cryptosporidiosis is nationally notifiable, yet molecular characterization is not routinely undertaken, limiting outbreak detection, source attribution, and zoonotic risk assessment. This limitation became apparent in 2024, when Australia experienced a 273% increase in cryptosporidiosis notifications, the third-highest rise globally. We conducted a molecular epidemiological investigation of Cryptosporidium and Giardia in fecal samples from humans with gastroenteritis in Victoria, Australia, between 2020 and 2024. Positive samples were sequenced using SSU and gp60 for Cryptosporidium and tpi for G..