Outbreak of Diarrhea Caused by a Novel Cryptosporidium hominis Subtype During British Military Training in Kenya.

Background: We report clinical, epidemiological, and laboratory features of a large diarrhea outbreak caused by a novel Cryptosporidium hominis subtype during British military training in Kenya between February and April 2022. Methods: Data were collated from diarrhea cases, and fecal samples were analyzed on site using the multiplex polymerase chain reaction (PCR) BioFire FilmArray. Water was tested using Colilert kits (IDEXX, UK). DNA was extracted from feces for molecular characterization of Cryptosporidium A135, Lib13, ssu rRNA, and gp60 genes. Results: One hundred seventy-two of 1200 (14.3%) personnel at risk developed diarrhea over 69 days. One hundred six primary fecal samples were tested, and 63/106 (59.4%; 95% CI, 0.49%-0.69%) were positive for Cryptosporidium spp. Thirty-eight had Cryptosporidium spp. alone, and 25 had Cryptosporidium spp. with ≥1 other pathogen. A further 27/106 (25.5%; 95% CI, 0.18%-0.35%) had non-Cryptosporidium pathogens only, and 16/106 (15.1%; 95% CI, 0.09%-0.23%) were negative. C. hominis was detected in 58/63 (92.1%) Cryptosporidium spp.-positive primary samples, but the others were not genotypable. Twenty-seven C. hominis specimens were subtypable; 1 was gp60 subtype IeA11G3T3, and 26 were an unusual subtype, ImA13G1 (GenBank accession OP699729), supporting epidemiological evidence suggesting a point source outbreak from contaminated swimming water. Diarrhea persisted for a mean (SD) of 7.6 (4.6) days in Cryptosporidium spp. cases compared with 2.3 (0.9) days in non-Cryptosporidium cases (P = .001). Conclusions: Real-time multiplex PCR fecal testing was vital in managing this large cryptosporidiosis outbreak. The etiology of a rare C. hominis gp60 subtype emphasizes the need for more genotypic surveillance to identify widening host and geographic ranges of novel C. hominis subtypes.

Preliminary investigation of a significant national Cryptosporidium exceedance in the United Kingdom, August 2023 and ongoing.

Routine laboratory surveillance has identified an unprecedented and ongoing exceedance of Cryptosporidium spp. across the United Kingdom, notably driven by C. hominis transmission, since 14 August 2023. Information from 477 reported cases in England and Wales, followed up with a standardised exposure questionnaire as of 25 September 2023, identified foreign travel in 250 (54%) of 463 respondents and swimming in 234 (66%) of 353 cases. A significant, common exposure has not yet been identified in first analyses.

A comparison of qPCR and microscopy for the detection and enumeration of Cryptosporidium oocysts from drinking water.

Introduction. Cryptosporidium presents one of the main waterborne public health threats due to its resistance to chlorine disinfection and ability to cause large-scale outbreaks. The standard method used in the UK water industry for detection and enumeration of Cryptosporidium is based on fluorescence microscopy and is laborious and expensive. Molecular methods such as quantitative polymerase chain reaction (qPCR) can be more amenable to streamlining through automation, improving workflows and standardizing procedures.Hypothesis. The null hypothesis was that there was no difference in the detection or enumeration between the standard method and a qPCR.Aim. We aimed to develop and evaluate a qPCR for the detection and enumeration of Cryptosporidium in drinking water, and to compare the assay with the standard method used in the UK.Methodology. We first developed and evaluated a qPCR method by incorporating an internal amplification control and calibration curve into a real-time PCR currently used for Cryptosporidium genotyping. Then we compared the qPCR assay with the standard method of immunofluorescent microscopy for the detection and enumeration of 10 and 100 Cryptosporidium oocysts in 10 l of artificially contaminated drinking water.Results. The results demonstrated that detection of Cryptosporidium by this qPCR was reliable at low numbers of oocysts; however, enumeration was less reliable and more variable than immunofluorescence microscopy.Conclusions. Despite these results, qPCR offers practical advantages over microscopy. There is potential for the use of PCR-based methods for Cryptosporidium analysis if parts of the upstream sample preparation are revised, and alternative technologies for enumeration (such as digital PCR) are also explored to improve analytical sensitivity.

Impact of the COVID-19 restrictions on the epidemiology of Cryptosporidium spp. in England and Wales, 2015-2021: a time series analysis.

Introduction. In England and Wales, cryptosporidiosis cases peak in spring and autumn, associated with zoonotic/environmental exposures (Cryptosporidium parvum, spring/autumn) and overseas travel/water-based activities (Cryptosporidium hominis, autumn). Coronavirus disease 2019 (COVID-19) restrictions prevented social mixing, overseas travel and access to venues (swimming pools/restaurants) for many months, potentially increasing environmental exposures as people sought alternative countryside activities.Hypothesis. COVID-19 restrictions reduced incidence of C. hominis cases and potentially increased incidence of C. parvum cases.Aim. To inform/strengthen surveillance programmes, we investigated the impact of COVID-19 restrictions on the epidemiology of C. hominis and C. parvum cases.Methodology. Cases were extracted from the Cryptosporidium Reference Unit (CRU) database (1 January 2015 to 31 December 2021). We defined two periods for pre- and post-COVID-19 restrictions implementation, corresponding to before and after the first UK-wide lockdown on 23 March 2020. We conducted a time series analysis, assessing differences in C. parvum and C. hominis incidence, trends and periodicity between these periods.Results. There were 21 304 cases (C. parvum=12 246; C. hominis=9058). Post-restrictions implementation incidence of C. hominis dropped by 97.5 % (95 % CI: 95.4-98.6 %; P<0.001). The decreasing incidence trend pre-restrictions was not observed post-restrictions implementation due to lack of cases. No periodicity change was observed post-restrictions implementation. There was a strong social gradient; there was a higher proportion of cases in deprived areas. For C. parvum, post-restrictions implementation incidence fell by 49.0 % (95 % CI: 38.4-58.3 %; P<0.001). There was no pre-restrictions incidence trend but an increasing incidence trend post-restrictions implementation. A periodicity change was observed post-restriction implementation, peaking 1 week earlier in spring and 2 weeks later in autumn. The social gradient was the inverse of that for C. hominis. Where recorded, 22 % of C. hominis and 8 % of C. parvum cases had travelled abroad.Conclusion. C. hominis cases almost entirely ceased post-restrictions implementation, reinforcing that foreign travel seeds infections. C. parvum incidence fell sharply but recovered post-restrictions implementation, consistent with relaxation of restrictions. Future exceedance reporting for C. hominis should exclude the post-restriction implementation period but retain it for C. parvum (except the first 6 weeks post-restrictions implementation). Infection prevention and control advice should be improved for people with gastrointestinal illness (GI) symptoms to ensure hand hygiene and swimming pool avoidance.

Development and evaluation of a real-time PCR for genotyping of Cryptosporidium spp. from water monitoring slides.

Cryptosporidium is an important cause of gastroenteritis globally and the main agent of waterborne outbreaks caused by protozoan parasites. Water monitoring for Cryptosporidium oocysts is by detection and enumeration using stained slide microscopy. Species identification (known as genotyping) may be undertaken post hoc and remains a specialist test, only undertaken in some laboratories. The benchmark method is nested PCR-sequencing of part of the SSU rRNA gene, but not all slides are typable and the workflow is cumbersome. We report the development, in-house validation and application of a real-time PCR-sequencing assay based on that gene, using a hydrolysis probe, for the detection and genotyping of all Cryptosporidium spp. The assay was investigated in two formats; a high volume DNA template for analysing all the DNA extracted from Cryptosporidium-positive water monitoring slides with <5 oocysts seen, and a lower volume DNA template permitting several technical replicates from slides with ≥5 oocysts seen where multiple species are more likely to be present. Each format conformed to the MIQE guidelines for amplification dynamics and was specific for Cryptosporidium spp. With high sensitivity, being capable of detecting and genotyping single oocysts by sequencing of a 435 bp amplicon. When 65 water monitoring slides with <5 oocysts seen were tested, slide typeability varied by sending laboratory (n = 9), and ranged from 22 to 60%. Typeability was 75% for slides with ≥5 oocysts seen that were submitted by a single laboratory. The laboratory workflow was improved by using real-time PCR, and decreased the time to result compared with nested PCR-sequencing. In practical application, there was no loss of typeability when the ≥5 oocysts assay was applied to all slides, irrespective of the number of oocysts present.

Cross-sectional household transmission study of Cryptosporidium shows that C. hominis infections are a key risk factor for spread.

BACKGROUND: Infection with the Cryptosporidium parasite causes over 4000 cases of diagnosed illness (cryptosporidiosis) in England and Wales each year. The incidence of sporadic disease has not been sufficiently established, and how frequently this arises from contact with other infected people is not well documented. This project aimed to explore potential transmission in the home and attempt to identify asymptomatic infections, which might play a role in transmission. Risk factors and characteristics associated with spread of infection in the home were described including any differences between Cryptosporidium species. METHODS: The study identified cryptosporidiosis cases from North West England and Wales over a year and invited them and their household to take part. Each household was sent a study pack containing study information and a questionnaire, and stool sample kits to provide samples from consenting household members. Cryptosporidium-positive stool samples, identified by immunofluorescence microscopy, were characterised using molecular methods to help describe any patterns of transmission. Characteristics of households with and without additional cases were described, and compared using odds ratios (OR) and a multivariable logistic regression identified independent risk factors for household transmission. Data collection ran for one year, beginning in September 2018 with an initial pilot phase. RESULTS: We enrolled 128 index cases and their households. Additional illness occurred in over a quarter of homes, each reporting an average of two additional cases. The majority of these were undiagnosed and unreported to surveillance. This burden was even greater in households where the index case was infected with C. hominis versus C. parvum, or the index case was under five years old, with mums and siblings most at risk of secondary infection. Only having an index case of C. hominis was independently associated with transmission in the multivariable model (OR 4.46; p = 0.01). CONCLUSIONS: Cryptosporidium was a considerable burden in the home. At-risk homes were those where the index was less than five years old and/or infected with C. hominis. Of particular risk were female caregivers and siblings. Hygiene advice should be specifically directed here. This work provides evidence for humans as sources of C. hominis infection and that person-person is a key pathway. We recommend that all stools submitted for the investigation of gastrointestinal pathogens are tested for Cryptosporidium to better capture cases, inclusion of speciation data in routine surveillance, and the consideration of specific clinical advice on prevention for high-risk homes.

Cryptosporidium spp surveillance and epidemiology in Ireland: a longitudinal cohort study employing duplex real-time PCR based speciation of clinical cases.

Cryptosporidium is a leading cause of gastroenteritis (cryptosporidiosis), with significant morbidity and mortality worldwide. Irish cryptosporidiosis incidence rates are consistently the highest reported in Europe. A retrospective, longitudinal study of clinical Cryptosporidium isolates was conducted from 2015 to 2018 in Cork, southern Ireland. Overall, 86.5% of cases were attributed to C. parvum, while the remaining 13.5% were caused by C. hominis Despite the widespread implications of this protozoan parasite in sporadic and outbreak-related illness in Ireland, the current dearth of species-level epidemiological surveillance and clinical studies needs to be addressed in order to elucidate the national impact of this enteric pathogen.

Why do we need training? - A "Training school on molecular methods used for foodborne parasite diagnostics in different matrices" is a example of knowledge transfer to foster research quality in EU.

Foodborne parasites with zoonotic potential are of particular concern for human health, being responsible for serious and potentially life threatening diseases. In the last decades, the development of molecular biology techniques have been successfully implemented for clinical diagnosis of FBPs in animal or human samples providing cheaper, less labor intensive, reliable and more sensitive tests. It is apparent from recent publications that unsubstantiated molecular methods for parasite detection that have undergone scant evaluation for sensitivity and specificity are becoming increasingly common. The aim of the organized Training Schools was to transfer knowledge on application, optimization and troubleshooting for methods used to extract, amplify, and sequence nucleic acids from contaminated matrices and isolated FBPs. The organized Training Schools fulfilled the trainees' expectations, whom acquired useful knowledge for their research activities.

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.

Cryptosporidium Diagnostic Assays: Molecular Detection.

Molecular diagnostic assays for Cryptosporidium are usually based on PCR and may detect the entire genus or target specified species. Of the ~40 species, fewer than half have been reported from humans, and most human cases of cryptosporidiosis are caused by Cryptosporidium parvum or Cryptosporidium hominis. Here we describe a nested PCR for the detection of all Cryptosporidium spp. that can then be differentiated by sequencing the PCR amplicons, and a duplex, real-time PCR for the simultaneous detection and differentiation of C. parvum and C. hominis.

Analysis of the Cryptosporidium spp. and gp60 subtypes linked to human outbreaks of cryptosporidiosis in England and Wales, 2009 to 2017.

BACKGROUND: Cryptosporidium spp. are important causes of gastroenteritis that can be transmitted from humans and animals. We elucidated the distribution of species and gp60 subtypes in human outbreaks classified by transmission vehicle. METHODS: We used a combined database of national outbreak surveillance and reference unit data to analyse outbreaks by setting, vehicle, season, and linkage with suspected sources. RESULTS: A total of 178 outbreaks involving 4031 laboratory confirmed cases were identified; 82 (46%) outbreaks involved recreational waters, 74 (42%) animal contact, 4 (2%) environmental contact, 4 (2%) person-to-person spread, 3 (2%) food, 2 (1%) drinking water supplies, and 9 (5%) were of unknown source. The infecting Cryptosporidium sp. was identified in 131 (74%) outbreaks; 69 were C. parvum, 60 C. hominis, and in two outbreaks cases were infected with either species. Animal contact, environmental contact, and food-borne outbreaks were exclusively C. parvum and were mainly in first half of the year. Recreational water outbreaks were predominantly C. hominis and were mainly in the second half of the year. Outbreaks attributed to person-to-person spread were exclusively C. hominis and all occurred in October. Both C. parvum and C. hominis caused drinking waterborne outbreaks. Gp60 subtypes were identified from patients in 48 C. parvum and 38 C. hominis outbreaks, revealing more subtypes among C. parvum (n = 14) than C. hominis (n = 7) outbreaks. Cryptosporidium hominis IbA10G2 predominated (30 outbreaks). Of C. parvum subtypes, IIaA15G2R1 predominated (17 outbreaks), followed by IIaA17G1R1 (12 outbreaks), IIaA19G1R1 (four outbreaks), and other subtypes caused three or fewer outbreaks each. Linkage between cases and suspected sources by gp60 subtype was established in nine animal contact, three swimming pool, and one drinking water outbreak. CONCLUSIONS: The public health benefit of identifying infecting species and subtypes was twofold: (i) identifying and strengthening epidemiologic links between cases; and (ii) indicating possible exposures and sources to inform outbreak management. Gp60 subtype refined the epidemiological investigations, but a multilocus genotyping scheme would provide further benefit. Characterisation of Cryptosporidium spp. and subtypes needs to shift from predominantly supporting outbreak investigations to becoming nationally systematic.

Draft Genome Assembly of a Potentially Zoonotic Cryptosporidium parvum Isolate, UKP1.

Cryptosporidium parvum is a zoonotic protozoan parasite that causes food and waterborne gastrointestinal disease and whose major animal reservoirs are cattle and small ruminants. We report here on a draft whole-genome sequence of a zoonotic isolate of C. parvum isolated from a person with cryptosporidiosis.

Subtype analysis of zoonotic pathogen Cryptosporidium skunk genotype.

Cryptosporidium skunk genotype is a zoonotic pathogen commonly identified in surface water. Thus far, no subtyping tool exists for characterizing its transmission in humans and animals and transport in environment. In this study, a subtyping tool based on the 60kDa glycoprotein (gp60) gene previously developed for Cryptosporidium chipmunk genotype I was used in the characterization of Cryptosporidium skunk genotype in animal and storm runoff samples from a watershed in New York. Altogether, 17 positive samples from this watershed and 5 human and animal specimens from other areas were analyzed. We identified 14 subtypes of Cryptosporidium skunk genotype, 11 of which were seen in the watershed. In phylogenetic analysis, these subtypes belonged to 4 subtype families (XVIa, XVIb, XVIc, and XVId). No host-adapted subtypes were identified and the two subtypes in humans were genetically similar to some in raccoons, otters, and storm runoff samples from the watershed. The characteristics of gp60 protein sequences of the Cryptosporidium skunk genotype are similar to those of other Cryptosporidium species, but only its XVIb subtype family has a putative furin cleavage site. This subtyping tool might be useful in characterizing Cryptosporidium skunk genotype in clinical and environmental samples.

Prevalence of Cryptosporidium Carriage and Disease in Children With Primary Immune Deficiencies Undergoing Hematopoietic Stem Cell Transplant in Northern Europe.

A prospective cohort study of children with primary immunodeficiencies undergoing hematopoietic stem cell transplant in the United Kingdom investigated the extent and significance of Cryptosporidium carriage in this high risk group. Three of 42 children recruited were infected with Cryptosporidium, a lower proportion than previously described. One had serious disease. The underlying immunodeficiency likely had a bearing on the clinical presentation and possible outcome of infection.

Annotated draft genome sequences of three species of Cryptosporidium: Cryptosporidium meleagridis isolate UKMEL1, C. baileyi isolate TAMU-09Q1 and C. hominis isolates TU502_2012 and UKH1.

Human cryptosporidiosis is caused primarily by Cryptosporidium hominis, C. parvum and C. meleagridis. To accelerate research on parasites in the genus Cryptosporidium, we generated annotated, draft genome sequences of human C. hominis isolates TU502_2012 and UKH1, C. meleagridis UKMEL1, also isolated from a human patient, and the avian parasite C. baileyi TAMU-09Q1. The annotation of the genome sequences relied in part on RNAseq data generated from the oocyst stage of both C. hominis and C. baileyi The genome assembly of C. hominis is significantly more complete and less fragmented than that available previously, which enabled the generation of a much-improved gene set for this species, with an increase in average gene length of 500 bp relative to the protein-encoding genes in the 2004 C. hominis annotation. Our results reveal that the genomes of C. hominis and C. parvum are very similar in both gene density and average gene length. These data should prove a valuable resource for the Cryptosporidium research community.

Molecular Characterization of Cryptosporidium Species and Giardia duodenalis from Symptomatic Cambodian Children.

BACKGROUND: In a prospective study, 498 single faecal samples from children aged under 16 years attending an outpatient clinic in the Angkor Hospital for Children, northwest Cambodia, were examined for Cryptosporidium oocysts and Giardia cysts using microscopy and molecular assays. METHODOLOGY/PRINCIPAL FINDINGS: Cryptosporidium oocysts were detected in 2.2% (11/498) of samples using microscopy and in 7.7% (38/498) with molecular tests. Giardia duodenalis cysts were detected in 18.9% (94/498) by microscopy and 27.7% (138/498) by molecular tests; 82% of the positive samples (by either method) were from children aged 1-10 years. Cryptosporidium hominis was the most common species of Cryptosporidium, detected in 13 (34.2%) samples, followed by Cryptosporidium meleagridis in 9 (23.7%), Cryptosporidium parvum in 8 (21.1%), Cryptosporidium canis in 5 (13.2%), and Cryptosporidium suis and Cryptosporidium ubiquitum in one sample each. Cryptosporidium hominis and C. parvum positive samples were subtyped by sequencing the GP60 gene: C. hominis IaA16R6 and C. parvum IIeA7G1 were the most abundant subtypes. Giardia duodenalis was typed using a multiplex real-time PCR targeting assemblages A and B. Assemblage B (106; 76.8% of all Giardia positive samples) was most common followed by A (12.3%) and mixed infections (5.1%). Risk factors associated with Cryptosporidium were malnutrition (AOR 9.63, 95% CI 1.67-55.46), chronic medical diagnoses (AOR 4.51, 95% CI 1.79-11.34) and the presence of birds in the household (AOR 2.99, 95% CI 1.16-7.73); specifically C. hominis (p = 0.03) and C. meleagridis (p<0.001) were associated with the presence of birds. The use of soap was protective against Giardia infection (OR 0.74, 95% CI 0.58-0.95). CONCLUSIONS/SIGNIFICANCE: This is the first report to describe the different Cryptosporidium species and subtypes and Giardia duodenalis assemblages in Cambodian children. The variety of Cryptosporidium species detected indicates both anthroponotic and zoonotic transmission in this population. Interventions to improve sanitation, increase hand washing after defecation and before preparing food and promote drinking boiled water may reduce the burden of these two parasites.

Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples.

BACKGROUND: Whole genome sequencing (WGS) of Cryptosporidium spp. has previously relied on propagation of the parasite in animals to generate enough oocysts from which to extract DNA of sufficient quantity and purity for analysis. We have developed and validated a method for preparation of genomic Cryptosporidium DNA suitable for WGS directly from human stool samples and used it to generate 10 high-quality whole Cryptosporidium genome assemblies. Our method uses a combination of salt flotation, immunomagnetic separation (IMS), and surface sterilisation of oocysts prior to DNA extraction, with subsequent use of the transposome-based Nextera XT kit to generate libraries for sequencing on Illumina platforms. IMS was found to be superior to caesium chloride density centrifugation for purification of oocysts from small volume stool samples and for reducing levels of contaminant DNA. RESULTS: The IMS-based method was used initially to sequence whole genomes of Cryptosporidium hominis gp60 subtype IbA10G2 and Cryptosporidium parvum gp60 subtype IIaA19G1R2 from small amounts of stool left over from diagnostic testing of clinical cases of cryptosporidiosis. The C. parvum isolate was sequenced to a mean depth of 51.8X with reads covering 100 % of the bases of the C. parvum Iowa II reference genome (Bioproject PRJNA 15586), while the C. hominis isolate was sequenced to a mean depth of 34.7X with reads covering 98 % of the bases of the C. hominis TU502 v1 reference genome (Bioproject PRJNA 15585). The method was then applied to a further 17 stools, successfully generating another eight new whole genome sequences, of which two were C. hominis (gp60 subtypes IbA10G2 and IaA14R3) and six C. parvum (gp60 subtypes IIaA15G2R1 from three samples, and one each of IIaA17G1R1, IIaA18G2R1, and IIdA22G1), demonstrating the utility of this method to sequence Cryptosporidium genomes directly from clinical samples. This development is especially important as it reduces the requirement to propagate Cryptosporidium oocysts in animal models prior to genome sequencing. CONCLUSION: This represents the first report of high-quality whole genome sequencing of Cryptosporidium isolates prepared directly from human stool samples.

Population structure of natural and propagated isolates of Cryptosporidium parvum, C. hominis and C. meleagridis.

The three protozoan species Cryptosporidium parvum, C. meleagridis and C. hominis (phylum Apicomplexa) are enteric pathogens of humans. The former two species are zoonotic and the latter is thought to infect only humans. To better characterize the structure and transmission of natural and laboratory-propagated isolates, we analyzed a collection of archived human and animal isolates of these three species by deep-sequencing polymerase chain reaction products amplified from a polymorphic sequence on chromosome 1. Thousands of screened 200-nucleotide sequences were analyzed to compare the diversity among samples, to assess the impact of laboratory propagation on population complexity and to identify taxonomically mixed isolates. Contrary to our expectation, repeated propagation in animals did not reduce intra-isolate diversity nor was diversity associated with host species. Significantly, in most samples, sequences characteristic of a different species were identified. The presence of C. hominis alleles in C. parvum and C. meleagridis isolates confirms earlier reports of mixed isolates and raises the possibility that the host range of C. hominis is broader than typically assumed. In a genetically divergent isolate of C. parvum, a majority of sequences was found to be recombinant, suggesting that this genotype originated from a C. parvum × C. hominis recombination event.

Subtyping Cryptosporidium ubiquitum,a zoonotic pathogen emerging in humans.

Cryptosporidium ubiquitum is an emerging zoonotic pathogen. In the past, it was not possible to identify an association between cases of human and animal infection. We conducted a genomic survey of the species, developed a subtyping tool targeting the 60-kDa glycoprotein (gp60) gene, and identified 6 subtype families (XIIa-XIIf) of C. ubiquitum. Host adaptation was apparent at the gp60 locus; subtype XIIa was found in ruminants worldwide, subtype families XIIb-XIId were found in rodents in the United States, and XIIe and XIIf were found in rodents in the Slovak Republic. Humans in the United States were infected with isolates of subtypes XIIb-XIId, whereas those in other areas were infected primarily with subtype XIIa isolates. In addition, subtype families XIIb and XIId were detected in drinking source water in the United States. Contact with C. ubiquitum-infected sheep and drinking water contaminated by infected wildlife could be sources of human infections.