Molecular epidemiology of Giardia duodenalis in the high-income world

Giardia duodenalis is a gastrointestinal parasite that infects most mammals, including humans. Outcome of infection ranges from asymptomatic carriage to severe clinical disease, leading to digestive abnormalities lasting years beyond infection. In high-income countries, this parasite was once primarily thought to be contracted by individuals with a history of foreign travel. Recent evidence suggests that endemic infection is an important factor in the epidemiology of giardiasis, and consequently human patients without a history of travel should be screened for Giardia to aid in the understanding of endemic infection. The first objective of the present study was to undertake a literature review of human giardiasis outbreaks to determine the primary routes of transmission in high-income countries. Outbreaks were categorised by transmission route, which included waterborne, foodborne, travel, person-to-person, zoonotic and direct faecal exposure. Waterborne transmission emerged as the route associated with the highest number of outbreak studies, followed by person-to-person transmission. This review highlighted the need for increased screening protocols in high-income countries and investigation into transmission routes other than travel. Being able to discern between different sub-types of Giardia, termed assemblages, is an important aspect of transmission analysis since different assemblages show varying levels of host-specificity, with some capable of infecting both humans and animals. Current Giardia typing methods rely largely on PCR of marker loci and sequencing of amplicons, however these suffer from poor amplification success rates particularly when applied to non-human assemblages. In this study, recently published genomic data was used to modify and optimise one such Giardia marker to increase sensitivity. Using this improved marker, the success rate across multiple assemblages increased markedly and it was subsequently applied to type a large collection of UK human and companion animal field samples. This revealed an appreciable presence of zoonotic assemblages in the companion animal population and highlighted them as potential source of human infection. This study adds to the knowledge on Giardia epidemiology in the context of a high-income country and provides improved genotyping methodology which can be applied to future studies

Molecular epidemiology of Giardia infections in the genomic era

Giardia duodenalis is a major gastrointestinal parasite of humans and animals across the globe. It is also of interest from an evolutionary perspective as it possesses many features that are unique among the eukaryotes, including its distinctive binucleate cell structure. While genomic analysis of a small number of isolates has provided valuable insights, efforts to understand the epidemiology of the disease and the population biology of the parasite have been limited by the molecular tools currently available. We review these tools and assess the impact of affordable and rapid genome sequencing systems increasingly being deployed in diagnostic settings. While these technologies have direct implications for public and veterinary health, they will also improve our understanding of the unique biology of this fascinating parasite

A scoping review of risk factors and transmission routes associated with human giardiasis outbreaks in high-income settings

The flagellated pathogen Giardia duodenalis is one of the leading causes of parasitic gastrointestinal illness worldwide. In many higher income countries, such as the United Kingdom, the disease is often perceived as being travel-related, likely leading to the under-reporting of sporadic cases and outbreaks. A summary of the literature describing outbreaks and risk factors in higher income countries is necessary to improve our understanding of this pathogen and identify existing knowledge gaps. Initial literature searches were carried out in September 2016 and updated at regular intervals until November 2021, using appropriate search terms in Medline, Embase and PubMed databases. A total of 75 papers met the inclusion criteria, revealing that the consumption of contaminated water and contact with young children of diaper-wearing age were the most common transmission routes leading to outbreaks of giardiasis. Of the ten studies where food was primarily associated with outbreaks, food handlers accounted for eight of these. Another reported transmission route was direct contact with fecal material, which was reported in six studies as the primary transmission route. Travel-associated giardiasis was considered the sole transmission route in two studies, whereas multiple transmission routes contributed to giardiasis outbreaks in eleven studies. The evidence around zoonotic transmission was less clear and hampered by the lack of robust and regularly applied parasite molecular typing techniques. This literature review summarizes the findings of Giardia outbreak investigations and epidemiological studies in high-income countries. Transmission routes are identified and discussed to highlight the associated risk factors. These data also indicate gaps in our current knowledge that include the need for robust, in-depth molecular studies and have underscored the importance of water as a transmission route for Giardia cysts. These future molecular studies will improve our understanding of Giardia epidemiology and transmission pathways in higher income countries to prevent spread of this significantly under-reported pathogen

Assessing the feasibility of applying machine learning to diagnosing non-effusive feline infectious peritonitis

Feline infectious peritonitis (FIP) is a severe feline coronavirus-associated syndrome in cats, which is invariably fatal without anti-viral treatment. In the majority of non-effusive FIP cases encountered in practice, confirmatory diagnostic testing is not undertaken and reliance is given to the interpretation of valuable, but essentially non-specific, clinical signs and laboratory markers. We hypothesised that it may be feasible to develop a machine learning (ML) approach which may be applied to the analysis of clinical data to aid in the diagnosis of disease. A dataset encompassing 1939 suspected FIP cases was scored for clinical suspicion of FIP on the basis of history, signalment, clinical signs and laboratory results, using published guidelines, comprising 683 FIP (35.2%), and 1256 non-FIP (64.8%) cases. This dataset was used to train, validate and evaluate two diagnostic machine learning ensemble models. These models, which analysed signalment and laboratory data alone, allowed the accurate discrimination of FIP and non-FIP cases in line with expert opinion. To evaluate whether these models may have value as a diagnostic tool, they were applied to a collection of 80 cases for which the FIP status had been confirmed (FIP: n = 58 (72.5%), non–FIP: n = 22 (27.5%)). Both ensemble models detected FIP with an accuracy of 97.5%, an area under the curve (AUC) of 0.969, sensitivity of 95.45% and specificity of 98.28%. This work demonstrates that, in principle, ML can be usefully applied to the diagnosis of non-effusive FIP. Further work is required before ML may be deployed in the laboratory as a diagnostic tool, such as training models on datasets of confirmed cases and accounting for inter-laboratory variation. Nevertheless, these results illustrate the potential benefit of applying ML to standardising and accelerating the interpretation of clinical pathology data, thereby improving the diagnostic utility of existing laboratory tests

Molecular characterisation of Giardia duodenalis from human and companion animal sources in the United Kingdom using an improved triosephosphate isomerase molecular marker

Giardia duodenalis is a protozoan parasite known for its ability to cause gastrointestinal disease in human and non-human mammals. In the UK, the full impact of this parasite has yet to be fully explored, due to the limited testing which has been undertaken in humans and the low-resolution assemblage-typing methods currently available. Rather than being primarily a travel-associated condition, a recent study has highlighted that an endemic Giardia cycle is present in the UK, although the source of human disease is unclear in the majority of cases. This study focussed on the improvement of one of the commonly used assemblage-typing assays, a nested topoisomerase phosphate (tpi) PCR, to increase the amplification success rate across both human and companion animal samples. After comparing published primers to full Giardia reference genomes, this marker protocol was optimised and then deployed to test a substantial number of human (n ​= ​79) and companion animal (n ​= ​174) samples to gain an insight into the molecular epidemiology of Giardia in the UK. One assemblage A1 and eleven assemblage A2 genotypes were detected in humans, along with and 25 assemblage B genotypes. Assemblage A1 genotypes, known to be human-infective, were found in three feline and one canine sample, while one feline sample contained assemblage A2. Additionally, four feline samples contained assemblage B, which is recognised as potentially human-infective. This study demonstrates the presence of potentially human-infective Giardia genotypes circulating in the companion animal population, notably with 17.4% (8/46) of feline-derived Giardia strains being potentially zoonotic. Using a modified tpi-based genotyping assay, this work highlights the potential for domestic pets to be involved in the endemic transmission of giardiasis in the UK and underlines the need for appropriate hygiene measures to be observed when interacting with both symptomatic and asymptomatic animals. It also serves to underline the requirement for further studies to assess the zoonotic risk of Giardia associated with companion animals in high-income countries