Uncovering the Genetic Diversity of Giardia Isolates from Outbreaks in New Zealand

Abstract BackgroundGiardia is one of the most common causes of diarrhoea in the world and is a notifiable disease in New Zealand. Recent advances in molecular techniques, such as PCR and Sanger sequencing, have greatly improved our understanding of the taxonomic classification and epidemiology of this parasite. However, there has been an inability to identify shared subtypes between samples from the same epidemiologically linked cases, due to samples showing multiple dominant subtypes within the same outbreak when characterised using Sanger sequencing. MethodsHere, NGS was employed to uncover the genetic diversity within samples from sporadic and outbreak cases of giardiasis that occurred in New Zealand between 2010 and 2018. ResultsThis strategy exposed the significant diversity of subtypes of Giardia present in each sample. The utilisation of NGS and metabarcoding at the glutamate dehydrogenase (gdh) locus enabled the identification of shared subtypes between samples from shared outbreaks, providing a better understanding of the epidemiology of outbreaks of giardiasis in New Zealand.ConclusionsNext-generation sequencing technologies provides a superior tool, when compared to consensus sequencing technologies, for capturing the genetic diversity of Giardia within hosts. This study showed that infections in humans are frequently mixed, with multiple subtypes present in each host.