Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci

Background: Cryptosporidium is a protozoan parasite that causes diarrheal illness in a wide range of hosts including humans. Two species, C. parvum and C. hominis are of primary public health relevance. Genome sequences of these two species are available and show only 3-5% sequence divergence. We investigated this sequence variability, which could correspond either to sequence gaps in the published genome sequences or to the presence of species-specific genes. Comparative genomic tools were used to identify putative species-specific genes and a subset of these genes was tested by PCR in a collection of Cryptosporidium clinical isolates and reference strains. Results: The majority of the putative species-specific genes examined were in fact common to C. parvum and C. hominis. PCR product sequence analysis revealed interesting SNPs, the majority of which were species-specific. These genetic loci allowed us to construct a robust and multi-locus analysis. The Neighbour-Joining phylogenetic tree constructed clearly discriminated the previously described lineages of Cryptosporidium species and subtypes. Conclusions: Most of the genes identified as being species specific during bioinformatics in Cryptosporidium sp. are in fact present in multiple species and only appear species specific because of gaps in published genome sequences. Nevertheless SNPs may offer a promising approach to studying the taxonomy of closely related species of Cryptosporidia

Cryptosporidium

The protozoan Cryptosporidium is notorious for its resistance to chlorine disinfection, a mainstay of water treatment. Human infections, mainly of the small intestine, arise from consumption of faecally contaminated food or water, environmental exposure, and person-to-person or animal-to-person spread. Acute gastrointestinal symptoms can be prolonged but are usually self-limiting. Problems arise with immune-deficient, including malnourished, people including chronic diarrhoea, hepato-biliary tree and extra-gastrointestinal site infection, and few options for treatment or prevention exist. Although genomics has enabled refined classification, identification of chemotherapeutic targets and vaccine candidates, and putative factors for host adaption and pathogenesis, their confirmation has been hampered by a lack of biological tools

Sporadic Human Cryptosporidiosis Caused by Cryptosporidium cuniculus, United Kingdom, 2007–2008

To investigate sporadic human cryptosporidiosis trends in the United Kingdom, we tested 3,030 Cryptosporidium spp.–positive fecal samples, submitted for routine typing in 2007–2008, for C. cuniculus. C. cuniculus prevalence was 1.2%; cases were mostly indigenous and occurred across all age groups. Most occurred during August–October and may be linked to exposure opportunities

Direct sequencing of Cryptosporidium in stool samples for public health

The protozoan parasite Cryptosporidium is an important cause of diarrheal disease (cryptosporidiosis) in humans and animals, with significant morbidity and mortality especially in severely immunocompromised people and in young children in low-resource settings. Due to the sexual life cycle of the parasite, transmission is complex. There are no restrictions on sexual recombination between sub-populations, meaning that large-scale genetic recombination may occur within a host, potentially confounding epidemiological analysis. To clarify the relationships between infections in different hosts, it is first necessary to correctly identify species and genotypes, but these differentiations are not made by standard diagnostic tests and more sophisticated molecular methods have been developed. For instance, multilocus genotyping has been utilized to differentiate isolates within the major human pathogens, Cryptosporidium parvum and Cryptosporidium hominis. This has allowed mixed populations with multiple alleles to be identified: recombination events are considered to be the driving force of increased variation and the emergence of new subtypes. As yet, whole genome sequencing (WGS) is having limited impact on public health investigations, due in part to insufficient numbers of oocysts and purity of DNA derived from clinical samples. Moreover, because public health agencies have not prioritized parasites, validation has not been performed on user-friendly data analysis pipelines suitable for public health practitioners. Nonetheless, since the first whole genome assembly in 2004 there are now numerous genomes of human and animal-derived cryptosporidia publically available, spanning nine species. It has also been demonstrated that WGS from very low numbers of oocysts is possible, through the use of amplification procedures. These data and approaches are providing new insights into host-adapted infectivity, the presence and frequency of multiple sub-populations of Cryptosporidium spp. within single clinical samples, and transmission of infection. Analyses show that although whole genome sequences do indeed contain many alleles, they are invariably dominated by a single highly abundant allele. These insights are helping to better understand population structures within hosts, which will be important to develop novel prevention strategies in the fight against cryptosporidiosis

Role of filtration in managing the risk from Cryptosporidium in commercial swimming pools – a review

Most commercial swimming pools use pressurised filters, typically containing sand media, to remove suspended solids as part of the water treatment process designed to keep water attractive, clean and safe. The accidental release of faecal material by bathers presents a poorly quantified risk to the safety of swimmers using the pool. The water treatment process usually includes a combination of maintaining a residual concentration of an appropriate biocide in the pool together with filtration to physically remove particles, including microbial pathogens, from the water. However, there is uncertainty about the effectiveness of treatment processes in removing all pathogens, and there has been growing concern about the number of reported outbreaks of the gastrointestinal disease cryptosporidiosis, caused by the chlorine-resistant protozoan parasite Cryptosporidium. A number of interacting issues influence the effectiveness of filtration for the removal of Cryptosporidium oocysts from swimming pools. This review explains the mechanisms by which filters remove particles of different sizes (including oocyst-sized particles, typically 4–6 μm), factors that affect the efficiency of particle removal (such as filtration velocity), current recommended management practices, and identifies further work to support the development of a risk-based management approach for the management of waterborne disease outbreaks from swimming pools

Unusual Cryptosporidium Genotypes in Human Cases of Diarrhea

Several Cryptosporidium spp. are known to infect humans, but most cases of illness are caused by Cryptosporidium hominis or C. parvum. During a long-term genotyping in the United Kingdom, we identified 3 unusual Cryptosporidium genotypes (skunk, horse, and rabbit) in human patients with diarrhea

Occurrence of Cryptosporidium Oocysts in Leisure Pools in the UK, 2017, and Modelling of Oocyst Contamination Events

Cryptosporidium is a major cause of diarrhoea outbreaks linked to swimming pools, but little is known about the frequency of contamination. The primary aim was to investigate the occurrence and concentration, through sampling and modelling, of Cryptosporidium oocysts in leisure pools. Secondary aims were to compare detections with operational parameters, provide the evidence-base for guidance, and improve sampling capacity and interpretation for public health investigations. Up to 1000 L pool water was sampled during swim sessions once weekly for 10 weeks from 8 August 2017 at six volunteer pools. Oocysts were detected by microscopy in 12/59 (20%) pool water samples, at least once in each pool; 8/12 (66%) detections were in August when bather loads were highest. At three pools, 1 L filter backwash was sampled weekly and oocysts were detected in 2/29 (7%) samples, following detections in pool water. The probabilities of a bather contaminating the pool ranged from 1 in 1000 to over 1 in 10,000. Monte Carlo analysis showed that when high bather numbers caused contamination on over 70% of days, multiple events per day were more likely than single events. In these generally well-managed leisure pools, Cryptosporidium risk related to high bather loads. We conclude that public awareness campaigns for bather hygiene, and reminding pool operators of current guidance for managing faecal accidents, should be ahead of peak swim season

Development of a gp60-subtyping method for Cryptosporidium felis

Background: Feline cryptosporidiosis is an increasing problem, especially in catteries. In humans, close contact with cats could be a potential source of infection although the risk of contracting cryptosporidiosis caused by Cryptosporidium felis is considered to be relatively low. Sequencing of the 60-kDa glycoprotein gene is a commonly used tool for investigation of the genetic diversity and transmission dynamics of Cryptosporidium species. However, until now the sequence of gp60 from C. felis has not been available and genotyping has been limited to less discriminatory markers, such as 18S rRNA, COWP and HSP70. Methods: We have identified the gp60 orthologue within the genome sequence of C. felis, and used the sequence to design a nested PCR for subtyping purposes. A total of 128 clinical isolates of both feline and human origin, were used to evaluate the marker. Results: Sequence analysis revealed large variations between the different samples. The C. felis gp60 lack the characteristic serine-tract found in many other cryptosporidian orthologues, instead it has an insertion of variable length (361-742 nt). Also, two cases of suspected zoonotic transmission of C. felis between cats and humans were successfully confirmed. Conclusions: We have identified the gp60 gene in C. felis and show how this highly variable marker can be used in epidemiological investigations