Rongchang Yang

Specific and quantitative detection and identification of Cryptosporidium hominis and C. parvum in clinical and environmental samples.

Cryptosporidium is an enteric protozoan parasite that is resistant to inactivation by commonly used drinking water disinfectants. Between 2004 and 2010, it was responsible for 60% of all waterborne protozoan parasitic outbreaks reported worldwide. Most sporadic infections in humans and almost all outbreaks are caused by Cryptosporidium parvum and Cryptosporidium hominis. We report the development and validation of a quantitative qPCR assay using minor groove binder (MGB)-probes targeting a unique Cryptosporidium specific protein-coding gene, that directly detects, quantitates and identifies C. hominis and C. parvum in environmental and faecal samples. An internal amplification control (IAC) was also developed and included in this assay. The qPCR assay was compared with an 18S nested PCR assay for sensitivity and specificity. The analytical sensitivity for the qPCR assay was 1 oocyst and 1-10 oocysts for the 18S assay. Evaluation of analytical specificity of the qPCR assay revealed no cross-reactions with other genera and detected all C. parvum and C. hominis isolates correctly. The diagnostic sensitivity and specificity of the qPCR was 100% compared to 96.9% and 98.4%, respectively for the 18S assay. The qPCR assay was also highly reproducible with RSD (relative standard deviation) values of 1.4-9.4%, when the assay was performed by four different technicians. When tested on water samples, the qPCR assay was more sensitive than the 18S assay, detecting positives in 37 of 138 water samples compared to 35 for the 18S locus. This qPCR assay should be a valuable tool for the detection and differentiation of C. hominis and C. parvum in both clinical and environmental samples.

Prevalence and molecular characterisation of Cryptosporidium and Giardia species in pre-weaned sheep in Australia

A total of 477 faecal samples from pre-weaned sheep from 5 different farms in the south west of Western Australia were screened for the presence of Cryptosporidium and Giardia using PCR. There were substantial differences in prevalence between the farms and overall prevalence was 24.5% and 11.1%, respectively for Cryptosporidium and Giardia. At the 18S locus, 66 Cryptosporidium positives were identified, the majority of which were C. bovis (n=52), followed by the cervid genotype (n=10) and C. parvum (n=2). At a second diagnostic locus, using C. parvum and C. hominis-specific qPCR primers, 63 C. parvum positives were identified, some of which were co-infections with C. bovis. The C. parvum/C. hominis qPCR was more sensitive than the nested 18S PCR at detecting C. parvum. This may be due to the low numbers of oocysts present, as quantitation data indicated that all the C. parvum detected were present in low numbers (1-10 oocysts). It may also be that using C. parvum-specific primers is necessary to determine the true prevalence of C. parvum. Amongst Giardia positive isolates, G. duodenalis genotype E (livestock) was the most prevalent (36/53), with G. duodenalis genotype A detected in five positive isolates. There were also 11 mixed A and E infections detected. The findings of the present study indicate that pre-weaned lambs are not an important source of zoonotic Giardia genotypes in Australia but may be an important source of zoonotic Cryptosporidium.

Comparison of next-generation droplet digital PCR (ddPCR) with quantitative PCR (qPCR) for enumeration of Cryptosporidium oocysts in faecal samples

Clinical microbiology laboratories rely on quantitative PCR for its speed, sensitivity, specificity and ease-of-use. However, quantitative PCR quantitation requires the use of a standard curve or normalisation to reference genes. Droplet digital PCR provides absolute quantitation without the need for calibration curves. A comparison between droplet digital PCR and quantitative PCR-based analyses was conducted for the enteric parasite Cryptosporidium, which is an important cause of gastritis in both humans and animals. Two loci were analysed (18S rRNA and actin) using a range of Cryptosporidium DNA templates, including recombinant plasmids, purified haemocytometer-counted oocysts, commercial flow cytometry-counted oocysts and faecal DNA samples from sheep, cattle and humans. Each method was evaluated for linearity, precision, limit of detection and cost. Across the same range of detection, both methods showed a high degree of linearity and positive correlation for standards (R(2)⩾0.999) and faecal samples (R(2)⩾0.9750). The precision of droplet digital PCR, as measured by mean Relative Standard Deviation (RSD;%), was consistently better compared with quantitative PCR, particularly for the 18S rRNA locus, but was poorer as DNA concentration decreased. The quantitative detection of quantitative PCR was unaffected by DNA concentration, but droplet digital PCR quantitative PCR was less affected by the presence of inhibitors, compared with quantitative PCR. For most templates analysed including Cryptosporidium-positive faecal DNA, the template copy numbers, as determined by droplet digital PCR, were consistently lower than by quantitative PCR. However, the quantitations obtained by quantitative PCR are dependent on the accuracy of the standard curve and when the quantitative PCR data were corrected for pipetting and DNA losses (as determined by droplet digital PCR), then the sensitivity of both methods was comparable. A cost analysis based on 96 samples revealed that the overall cost (consumables and labour) of droplet digital PCR was two times higher than quantitative PCR. Using droplet digital PCR to precisely quantify standard dilutions used for high-throughput and cost-effective amplifications by quantitative PCR would be one way to combine the advantages of the two technologies.

Molecular characterization of Cryptosporidium and Giardia in pre-weaned calves in Western Australia and New South Wales.

A total of 364 fecal specimens from randomly selected pre-weaned calves, aged up to 4 months, from 5 different farms in the south of Western Australia and 1 farm from New South Wales were screened for the presence of Cryptosporidium and Giardia using PCR. There were substantial differences in prevalence between the farms and the overall prevalence was 22.3% (81/364) and 26.9% (98/364) respectively for Cryptosporidium and Giardia. For Cryptosporidium, 70 positives were identified at the 18S locus. At a unique diagnostic locus, an additional 12 C. parvum positives were identified. Sequence analysis at the 18S ribosomal RNA locus was successful for 59 of the 70 positive isolates; of these 14 were C. parvum, 28 were C. bovis, 15 were C. ryanae, 1 was pig genotype II and 1 was a mixed C. ryanae/C. parvum infection. Sub-typing analysis at the glycoprotein 60 (gp60) locus for 24 C. parvum isolates identified all as IIa; 17 were A17G2R1, 1 was A18G3R1 and 6 were A20G3R1. For Giardia, 75 positives were identified at the 18S locus and an additional 23 positives were identified at the gdh locus. The majority of the isolates sequenced were assemblage E, however assemblage A and B and mixed A and E and A, B and E infections as well as the quenda genotype were identified. The findings of the present study indicate that pre-weaned calves are not an important source of zoonotic Giardia species in Australia but may be an important source of zoonotic Cryptosporidium.

Identification of rare and novel Cryptosporidium GP60 subtypes in human isolates from Jordan

Little is known about the epidemiology of Cryptosporidium in Jordan and no genotyping studies have been conducted on Cryptosporidium isolates from humans or animals from Jordan. Genotyping of 44 Cryptosporidium isolates from Jordanian children at the 18S rRNA locus and a unique diagnostic locus identified four Cryptosporidium species; C. parvum (22), C. hominis (20), C. meleagridis (1) and C. canis (1). Sub-genotype analysis of 29 isolates at the 60-kDa glycoprotein (GP60) locus identified three C. parvum, two C. hominis subtype families and one C. meleagridis subtype. Several rare and novel subtypes were identified indicating unique endemicity and transmission of Cryptosporidium in Jordan.

Longitudinal investigation of protozoan parasites in meat lamb farms in southern Western Australia.

In this study, 96 faecal samples were collected from pregnant Merino ewes, at two broad-acre, commercial sheep farms in southern Western Australia, on two separate occasions (16 and 2 weeks prior to lambing). Following lambing, 111 (Farm A) and 124 (Farm B) female crossbred lambs (2-6 weeks old), were individually identified using ear tags (a numbered tag and a radio-frequency tag). A total of 1155 faecal samples were collected only from these individually identified lambs on five separate sampling occasions. All samples were screened using PCR to detect Cryptosporidium (18S rRNA and actin loci) and Giardia duodenalis (glutamate dehydrogenase and triosephosphate isomerise loci). The overall prevalences (lambs positive for a parasite on at least one of the five samplings) at Farm A and B were 81.3% and 71.4%, respectively for Cryptosporidium and similarly 67.3% and 60.5% for Giardia, respectively. Cryptosporidium and Giardia prevalences at individual samplings ranged between 18.5 and 42.6% in lambs and were <10% in the ewes. Cryptosporidium xiaoi was the most prevalent species detected at all five samplings and was also isolated from lamb dam water on Farm B. Cryptosporidium ubiquitum was most commonly detected in younger lambs and Cryptosporidium parvum was detected in lambs at all five samplings, typically in older lambs and as part of a mixed species infection with C. xiaoi. A novel, possibly new genotype (sheep genotype I), was identified in six Cryptosporidium isolates from Farm B. Giardia duodenalis assemblage E was the most common genotype detected at all five samplings, with greater proportions of assemblage A and mixed assemblage A and E infections identified in older lambs. This longitudinal study identified high overall prevalences of Cryptosporidium and Giardia in lambs grazed extensively on pastures, while reinforcing that sampling a random selection of animals from a flock/herd on one occasion (point prevalence), underestimates the overall prevalence of these parasites in the flock/herd across an extended time period. Based on these findings, grazing lambs were identified as a low risk source of zoonotic Cryptosporidium and Giardia species/genotypes, with these protozoa detected at all five samplings in some lambs, indicating that these individuals were either unable to clear the naturally acquired protozoan infections or were repeatedly re-infected from their environment or other flock members.

Identification of zoonotic Cryptosporidium and Giardia genotypes infecting animals in Sydney's water catchments

To identify the animal sources for Cryptosporidium and Giardia contamination, we genotyped Cryptosporidium and Giardia spp. in wildlife from Sydneys water catchments using sequence analysis at the 18S rRNA locus for Cryptosporidium and 18S rRNA and glutamate dehydrogenase (gdh) for Giardia. A total of 564 faecal samples from 16 different host species were analysed. Cryptosporidium was identified in 8.5% (48/564) samples from eight host species and Giardia was identified in 13.8% (78/564) from seven host species. Eight species/genotypes of Cryptosporidium were identified. Five G. duodenalis assemblages were detected including the zoonotic assemblages A and B.

High prevalence Giardia duodenalis assemblage B and potentially zoonotic subtypes in sporadic human cases in Western Australia.

Giardia duodenalis is a widespread parasite of mammalian species, including humans. Fecal samples from sporadic human clinical cases of giardiasis in Western Australia were analysed at two loci; 18S rRNA and glutamate dehydrogenase (gdh), and G. duodenalis assemblage B isolates were identified in 75% of isolates. Sequence analyses of 124 isolates at the 18S rRNA locus identified 93 isolates as assemblage B and 31 as assemblage A. Analyses of 109 isolates at the gdh locus identified 44 as B3, 38 as B4 and 27 were A2. Infection with Giardia was highest amongst children <5 years of age, with >56% of infections in this age group. The majority of the isolates were from rural areas (91/124) compared with urban areas (33/124). The assemblage A isolates were completely homogenous genetically at the gdh locus, while assemblage B isolates showed variability at the nucleotide but not at the amino acid level at this locus. Some of the assemblage B3 and B4 subtypes identified in humans were previously identified in marsupials in Australia and in a fox, indicating potential zoonotic transmission.

Longitudinal prevalence, oocyst shedding and molecular characterisation of Cryptosporidium species in sheep across four states in Australia.

The prevalence of Cryptosporidium in sheep in the eastern states of Australia has not been well described, therefore a study of the prevalence, oocyst concentration, species and subtypes of Cryptosporidium were assessed from lamb faecal samples at three sampling periods (weaning, post-weaning and pre-slaughter) from eight farms across South Australia, New South Wales, Victoria and Western Australia. A total of 3412 faecal samples were collected from approximately 1182 lambs across the four states and screened for the presence of Cryptosporidium using a quantitative PCR (qPCR) at the actin locus. Positives were typed at the 18S locus and at a second locus using C. parvum and C. hominis specific qPCR primers. The overall prevalence was 16.9% (95% CI: 15.6-18.1%) and of the 576 positives, 500 were successfully genotyped. In general, the prevalence of Cryptosporidium was higher in WA than the eastern states. Cryptosporidium prevalence peaked at 43.9% and 37.1% at Pingelly (WA2) and Arthur River (WA1), respectively during weaning and at Pingelly (WA2) during pre-slaughter (36.4%). The range of oocyst shedding at weaning overall across all states was 63-7.9×10(6) and the median was 3.2 × 10(4) oocysts g(-1). The following species were identified; C. xiaoi (69%-345/500), C. ubiquitum (17.6%-88/500), C. parvum (9.8%-49/500), C. scrofarum (0.8%-4/500), mixed C. parvum and C. xiaoi (2.4%-12/500), C. andersoni (0.2%-1/500) and sheep genotype 1 (0.2%-1/500). Subtyping of C. parvum and C. ubiquitum isolates identified IIa and IId subtype families within C. parvum (with IId as the dominant subtype) and XIIa within C. ubiquitum. This is the first published description of C. parvum subtypes detected in lambs in Australia.

Giardia genotypes in pigs in Western Australia: prevalence and association with diarrhea.

Little is known of the prevalence of Giardia species and genotypes in pre- and post-weaned domestic pigs. In the present study, a total of 297 pig faecal samples were screened for the presence of Giardia by PCR and genotyped. An overall prevalence of 31.1% (90/289) (25.8, 36.5 CI) was detected. Giardia was detected in 17% (23/123) (11.8-25.6 CI) of pre-weaned piglet faecal samples and 41% (64/156) (33.3-48.7 CI) post-weaned faecal samples analysed. Sequence analysis identified assemblage A and E in pre- and post-weaned pigs. Assemblage F was identified in one post-weaned pig. Assemblage E was the most prevalent assemblage detected.