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

Cryptosporidium species and subtypes identified in human domestic cases through the national microbiological surveillance programme in Sweden from 2018 to 2022

BACKGROUND

The intestinal protozoan parasite Cryptosporidium is an important cause of diarrheal disease worldwide. A national microbiological surveillance programme was implemented in Sweden in 2018 in order to increase knowledge of the molecular epidemiology of human cryptosporidiosis to better understand transmission patterns and potential zoonotic sources. This article summarises the results of the first five years of the surveillance programme.

METHODS

Cryptosporidium-positive faecal and DNA samples from domestically acquired infections were collected from clinical microbiological laboratories in Sweden. Species and subtype determination was performed using 60 kDa glycoprotein and/or small subunit ribosomal RNA gene analysis.

RESULTS

Between 2018 and 2022, 1654 samples were analysed and 11 different species were identified: C. parvum (n = 1412), C. mortiferum (n = 59), C. hominis (n = 56), C. erinacei (n = 11), C. cuniculus (n = 5), C. meleagridis (n = 3), C. equi (n = 2), C. ubiquitum (n = 2), and one each of C. canis, C. ditrichi and C. felis. Subtyping revealed seven subtype families of C. parvum (new subtype families IIy and IIz) and 69 different subtypes (11 new subtypes). The most common C. parvum subtypes were IIdA22G1c, IIdA24G1, IIdA15G2R1 and IIaA16G1R1b. For C. hominis, four different subtype families and nine different subtypes (two new subtypes) were identified. For additional species, two new subtype families (IIIk and VId) and nine new subtypes were identified. All successfully subtyped C. mortiferum cases were subtype XIVaA20G2T1, confirming previous findings in Sweden. Several outbreaks were identified of which the majority were foodborne and a few were due to direct contact with infected animals.

CONCLUSION

Infection with C. parvum is the leading cause of human cryptosporidiosis acquired in Sweden, where more than 90% of domestic cases are caused by this zoonotic species and only a small proportion of cases are due to infection with other species. The rodent-associated C. mortiferum is considered an emerging zoonotic species in Sweden and the number of domestically acquired human cases has surpassed that of infection with C. hominis. A high diversity of species and subtypes, as well as diversity within the same subtype, was detected. Also, cryptosporidiosis appears to affect adults to a great extent in Sweden.

Cryptosporidium parvum: an emerging occupational zoonosis in Finland

BACKGROUND

Cryptosporidiosis has increased in recent years in Finland. We aimed to identify risk factors for human cryptosporidiosis and to determine the significance of Cryptosporidium parvum as a causative agent. Based on notifications to the Finnish Infectious Disease Register (FIDR), we conducted a case-control study and genotyped Cryptosporidium species from patient samples from July to December 2019. We also retrieved the occupational cryptosporidiosis cases from 2011 to 2019 from the Finnish Register of Occupational Diseases (FROD).

RESULTS

Of 272 patient samples analyzed, 76% were C. parvum and 3% C. hominis. In the multivariable logistic regression analysis of 82 C. parvum cases and 218 controls, cryptosporidiosis was associated with cattle contact (OR 81, 95% confidence interval (CI) 26-251), having a family member with gastroenteritis (OR 34, 95% CI 6.2-186), and spending time at one's own vacation home (OR 15, 95% CI 4.2-54). Of the cases, 65% had regular cattle contact. The most common gp60 subtypes identified were IIaA15G2R1 and IIaA13G2R1. In FROD, 68 recognized occupational cryptosporidiosis cases were registered in 2011-2019.

CONCLUSIONS

C. parvum is the most common Cryptosporidium species found in humans in Finland and poses a moderate to high risk of occupational infection for people working with cattle. The number of occupational notifications of cryptosporidiosis increased between 2011 and 2019. Cryptosporidiosis should be recognized as an important occupational disease among persons working with livestock in Finland, criteria to identify occupational cryptosporidiosis need to be created, and occupational safety in cattle-related work should be improved.

Comparison of Three Real-Time PCR Assays Targeting the SSU rRNA Gene, the COWP Gene and the DnaJ-Like Protein Gene for the Diagnosis of Cryptosporidium spp. in Stool Samples

As qualified microscopy of enteric parasitoses as defined by high diagnostic accuracy is difficult to maintain in non-endemic areas due to scarce opportunities for practicing with positive sample materials, molecular diagnostic options provide less investigator-dependent alternatives. Here, we compared three molecular targets for the real-time PCR-based detection of Cryptosporidium spp. From a population of 1000 individuals comprising both Ghanaian HIV (human immunodeficiency virus) patients and military returnees after deployment in the tropics, stool samples were assessed for Cryptosporidium spp. by real-time PCR targeting the small subunit ribosomal RNA (SSU rRNA) gene, the Cryptosporidium oocyst wall (COWP) gene, and the DnaJ-like protein gene (DnaJ), respectively. In declining order, sensitivity of 100% for the SSU rRNA gene PCR, 90.0% for the COWP PCR and 88.8% for the DnaJ PCR, respectively, as well as specificity of 99.6% for the COWP PCR and 96.9% for both the SSU rRNA gene PCR and the DnaJ PCR, respectively, were recorded. Substantial agreement (kappa value 0.663) between the three assays was observed. Further, an accuracy-adjusted Cryptosporidium spp. prevalence of 6.0% was calculated for the study population. In conclusion, none of the assessed real-time PCR assays were associated with perfect test accuracy. However, a combination of highly sensitive SSU rRNA gene PCR for screening purposes and more specific COWP PCR for confirmatory testing should allow reliable diagnosis of Cryptosporidium spp. in stool samples even in low prevalence settings.

Spatiotemporal epidemiology of cryptosporidiosis in the Republic of Ireland, 2008-2017: development of a space-time "cluster recurrence" index

Background

Ireland frequently reports the highest annual Crude Incidence Rates (CIRs) of cryptosporidiosis in the EU, with national CIRs up to ten times the EU average. Accordingly, the current study sought to examine the spatiotemporal trends associated with this potentially severe protozoan infection.

Methods

Overall, 4509 cases of infection from January 2008 to December 2017 were geo-referenced to a Census Small Area (SA), with an ensemble of geo-statistical approaches including seasonal decomposition, Local Moran’s I, and space–time scanning used to elucidate spatiotemporal patterns of infection.

Results

One or more confirmed cases were notified in 3413 of 18,641 Census SAs (18.3%), with highest case numbers occurring in the 0–5-year range (n = 2672, 59.3%). Sporadic cases were more likely male (OR 1.4) and rural (OR 2.4), with outbreak-related cases more likely female (OR 1.4) and urban (OR 1.5). Altogether, 55 space–time clusters (≥ 10 confirmed cases) of sporadic infection were detected, with three “high recurrence” regions identified; no large urban conurbations were present within recurrent clusters.

Conclusions

Spatiotemporal analysis represents an important indicator of infection patterns, enabling targeted epidemiological intervention and surveillance. Presented results may also be used to further understand the sources, pathways, receptors, and thus mechanisms of cryptosporidiosis in Ireland.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06598-3.

A novel genotyping method for Cryptosporidium hominis

Cryptosporidiosis remains the leading protozoan induced cause of diarrhoea-associated mortality worldwide. Cryptosporidium hominis, the anthroponotically transmitted species within the Cryptosporidium genus, contributes significantly to the global burden of infection, accounting for the majority of clinical cases in many countries. This study applied high resolution melting analysis, a post-real-time PCR application, to the differentiation of six globally prevalent C. hominisgp60-subtypes. This novel method targeted three microsatellite, tandem repeat containing genetic markers, gp60, the genetic marker upon which current Cryptosporidium subtype nomenclature is based, MSB, and MSE, by which to differentiate between C. hominis isolates. This multi-locus approach successfully differentiated between all six C. hominisgp60-subtypes studied, some of which, such as IbA10G2, are known to exhibit global ubiquity. Thus, this method has the potential to be universally employed as a sensitive, cost effective and highly reproducible means to rapidly differentiate between C. hominisgp60-subtypes. Such a method would be of particular utility in epidemiological studies and outbreak scenarios, providing cost effective, clinically accessible alternative to DNA sequencing. The success of this preliminary study also supports further analysis of an expanded C. hominisgp60-subtype range and the potential expansion of the multi-locus panel in order to improve the discriminatory power of this approach.

Development of a novel, high resolution melting analysis based genotyping method for Cryptosporidium parvum

This study employed the post-real-time PCR application, high resolution melting (HRM) analysis, in order to differentiate between characterised clinical and reference Cryptosporidium parvum samples obtained from Cork University Hospital (Cork, Ireland) and the Cryptosporidium Reference Unit (Swansea, Wales). A sample set composed of 18 distinct C. parvum gp60-subtypes of the IIa gp60-subtype family (an allele family accounting for over 80% of all cryptosporidiosis cases in Ireland) was employed. HRM analysis-based interrogation of the gp60, MM5 and MS9-Mallon tandem repeat loci was found to completely differentiate between 10 of the 18 studied gp60-subtypes. The remaining eight gp60-subtypes were differentiated into three distinct groupings, with the designations within these groupings resolved to two to three potential gp60-subtypes. The current study aimed to develop a novel, reproducible, real-time PCR based multi-locus genotyping method to distinguish between C. parvum gp60-subtypes. These preliminary results support the further expansion of the multi-locus panel in order to increase the discriminatory capabilities of this novel method.

Socio-economic factors associated with the incidence of Shiga-toxin producing Escherichia coli (STEC) enteritis and cryptosporidiosis in the Republic of Ireland, 2008–2017

The Republic of Ireland (ROI) currently reports the highest incidence rates of Shiga-toxin producing Escherichia coli (STEC) enteritis and cryptosporidiosis in Europe, with the spatial distribution of both infections exhibiting a clear urban/rural divide. To date, no investigation of the role of socio-demographic profile on the incidence of either infection in the ROI has been undertaken. The current study employed bivariate analyses and Random Forest classification to identify associations between individual components of a national deprivation index and spatially aggregated cases of STEC enteritis and cryptosporidiosis. Classification accuracies ranged from 78.2% (STEC, urban) to 90.6% (cryptosporidiosis, rural). STEC incidence was (negatively) associated with a mean number of persons per room and percentage of local authority housing in both urban and rural areas, addition to lower levels of education in rural areas, while lower unemployment rates were associated with both infections, irrespective of settlement type. Lower levels of third-level education were associated with cryptosporidiosis in rural areas only. This study highlights settlement-specific disparities with respect to education, unemployment and household composition, associated with the incidence of enteric infection. Study findings may be employed for improved risk communication and surveillance to safeguard public health across socio-demographic profiles.