Suitability of loci for multiple-locus variable-number of tandem-repeats analysis of Cryptosporidium parvum for inter-laboratory surveillance and outbreak investigations.

Cryptosporidium parvum is the major cause of livestock and zoonotically-acquired human cryptosporidiosis. The ability to track sources of contamination and routes of transmission by further differentiation of isolates would assist risk assessment and outbreak investigations. Multiple-locus variable-number of tandem-repeats (VNTR) analysis provides a means for rapid characterization by fragment sizing and estimation of copy numbers, but structured, harmonized development has been lacking for Cryptosporidium spp. To investigate potential for application in C. parvum surveillance and outbreak investigations, we studied nine commonly used VNTR loci (MSA, MSD, MSF, MM5, MM18, MM19, MS9-Mallon, GP60 and TP14) for chromosome distribution, repeat unit length and heterogeneity, and flanking region proximity and conservation. To investigate performance in vitro, we compared these loci in 14 C. parvum samples by capillary electrophoresis in three laboratories. We found that many loci did not contain simple repeat units but were more complex, hindering calculations of repeat unit copy number for standardized reporting nomenclature. However, sequenced reference DNA enabled reproducible fragment sizing and inter-laboratory allele assignation based on size normalized to that of the sequenced fragments by both single round and nested polymerase chain reactions. Additional Cryptosporidium loci need to be identified and validated for robust inter-laboratory surveillance and outbreak investigations.

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.

Validation of fragment analysis by capillary electrophoresis to resolve mixed infections by Cryptosporidium parvum subpopulations.

The potential of capillary electrophoresis (CE)-based DNA fragment analysis to identify mixed infections by Cryptosporidium parvum subpopulations was validated using high-resolution slab-gel electrophoresis. A selection of genomic DNA samples from C. parvum isolates with CE electropherogram profiles indicative of two concurrent alleles at one or more of six mini and microsatellite loci (MSB, MS5, ML1, ML2, TP14, 5B12) were analysed. These loci were PCR-amplified and products separated on precast Spreadex EL600 slab gels. ML1 PCR products differing by as little as 3 bp in length were visible after Spreadex gel electrophoresis and fragments were clearly separated for all but the ML2 and 5B12 loci, which generated stutter bands. No stuttering was seen for the remaining markers, having three or more nucleotide motifs in the repeat region. For each sample, the two bands of interest were excised separately, DNA extracted and re-amplified by PCR. Sequencing of these PCR products revealed the expected sequences for both alleles at most samples, except for the longest ML2 and 5B12 alleles which generated indeterminate sequences. Two novel MS5 alleles were successfully sequenced after PCR re-amplification. These findings demonstrate the utility of high-resolution Spreadex gels for analysing the polymorphism of satellite markers of Cryptosporidium isolates and support the validity of CE as a reliable and sensitive tool for detecting mixed Cryptosporidium subpopulations in a single-host infection.

Identification of clinical isolates of α-hemolytic streptococci by 16S rRNA gene sequencing, matrix-assisted laser desorption ionization-time of flight mass spectrometry using MALDI Biotyper, and conventional phenotypic methods: a comparison.

Fifty-six α-hemolytic streptococcal isolates were identified using MALDI Biotyper MS (Bruker Daltonics), API 20 Strep (bioMérieux), and BD Phoenix (Becton, Dickinson). The gold standard for identification was 16S rRNA gene sequence analysis with 16S-23S rRNA intergenic spacer sequencing. The following percentages of isolates were correctly identified to the species level: MALDI Biotyper, 46%; BD Phoenix, 35%; and API 20 Strep, 26%.

Detection and characterization of Cryptosporidium cuniculus by real-time PCR.

Cryptosporidium cuniculus was originally detected in rabbits and has been identified as an emerging human pathogen, but the occurrence, prevalence, and epidemiology in human and rabbit populations are poorly understood. As identification of C. cuniculus can be time-consuming and costly using existing molecular assays, a real-time polymerase chain reaction (PCR)-based method targeting specific markers for this species was developed. The assay is based on amplification of the C. cuniculus-specific 60-kDa glycoprotein (GP60) gene using two PCRs targeting subtype families Va and Vb. PCR product formation was monitored by SYBR Green I fluorescence measurement followed by post-amplification melt curve analysis; high resolution melt curve analysis was found to give increased sensitivity over standard melt curve analysis. The real-time PCR correctly identified all 41 C. cuniculus isolates (40 from humans, one from a rabbit) tested, with subtype family in agreement with GP60 gene sequencing. Specificity was demonstrated by lack of detection of nine other Cryptosporidium species and genotypes, including 88 isolates of the closely related species, Cryptosporidium hominis. The PCRs were performed in separate tubes to maximize the possibility of detecting mixed Va-Vb infections; however, none were detected. The potential for multiplexing the reactions was also demonstrated, furthering the utility of the assay for large-scale occurrence and prevalence studies.

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.

Detection and differentiation of Cryptosporidium spp. in human clinical samples by use of real-time PCR.

Real-time PCR has the potential to streamline detection and identification of Cryptosporidium spp. in human clinical samples. In the present article, we report the first such assay to allow not only detection and differentiation of the most common human pathogens, Cryptosporidium hominis and Cryptosporidium parvum, but also simultaneous amplification of a region of the small subunit (SSU) rRNA gene, permitting direct sequence analysis to identify any Cryptosporidium species. An internal control is incorporated to identify the presence of PCR inhibitors. Analytical sensitivity was determined to be as low as 200 oocysts per gram of feces processed, equivalent to 2 oocysts per PCR. The C. hominis and C. parvum PCRs specifically detected only species/genotypes in their respective target clades. Diagnostic sensitivity and specificity, evaluated against a widely used conventional nested SSU rRNA gene PCR as a nominated gold standard using a panel of 258 (151 positive and 107 negative) samples, were 100% and 99.1%, respectively. The assay agreed with PCR-restriction fragment length polymorphism analysis of the Cryptosporidium oocyst wall protein gene for 134 of 136 (98.5%) samples tested prospectively and typed two additional isolates. The real-time PCR assay was sensitive, specific, and reproducible and significantly improved laboratory work flow and turnaround times.

Zoonotic linkage and variation in Cryptosporidium parvum from patients in the United Kingdom.

Relationships between patient exposure risks and variation within the Cryptosporidium parvum 60 kDa glycoprotein (GP60) gene were explored in samples isolated from human cases of cryptosporidiosis (n=69) in England and Wales. GP60 family IIa predominated (n=56), followed by IId (n=9). One case was IIc, a newly named genotype IIcA5G3j, and isolates from three cases did not amplify with the GP60 primers. Cases with GP60 family IIa were more likely than IId to have visited a farm, or had contact with farm animals or with their faeces in the 2 weeks prior to illness. Within GP60 family IIa, genotypes IIaA15G2R1 and IIaA17G1R1 predominated (22 cases each); nine other IIa genotypes accounted for 12 cases. The IId genotypes were mainly IIdA17G1 and IIdA18G1 (3 each). Cases with IIaA17G1R1 were particularly linked to zoonotic exposures: visiting a farm or having farm animal contact in the 2 weeks prior to illness. These findings provide further evidence of zoonotic pathways for the transmission of C. parvum isolates.

Whole genome amplification (WGA) for archiving and genotyping of clinical isolates of Cryptosporidium species.

Clinical and environmental isolates of pathogens are often unique and may be unculturable, yielding a very limited amount of DNA for genetic studies. Cryptosporidium in particular are difficult to propagate. Whole genome amplification (WGA) is a valuable technique for amplifying genomic material. In this study, we tested 5 WGA commercial kits using Cryptosporidium clinical isolates. DNA of 5 C. hominis and 5 C. parvum clinical isolates and C. parvum IOWA reference strain were used. The majority of the samples were amplified by all of the kits tested. The integrity and fidelity of the amplified genomic DNA were assessed by sequence analysis of several PCR products of varying length. We found evidence that one kit in particular may be more error prone while another seemed the more suitable kit for Cryptosporidium clinical samples, generating high molecular weight DNA from all the samples with high fidelity. Thus WGA was found to be a useful technique for producing amplified DNA suitable for downstream genotyping techniques and archiving of Cryptosporidium clinical isolates.

Detection of Cryptosporidium species and sources of contamination with Cryptosporidium hominis during a waterborne outbreak in north west Wales.

As part of investigations into the cause of a waterborne outbreak of Cryptosporidium hominis infection linked to a mains water supply, surface waters and wastewater treatment plants were tested for Cryptosporidium spp. Oocyst counts in base flow surface water samples ranged from nil to 29 per 10 l. Oocyst counts in effluent from a community wastewater treatment plant were up to 63 fold higher and breakout from one septic tank five logs higher. There were no peak (storm) flow events during the investigation. C. hominis, four named genotypes (cervine, muskrat II, rat, W19) and six new small subunit ribosomal RNA gene sequences were identified. Four of the new sequences were closely related to Cryptosporidium muskrat genotype I, one was closely related to the fox genotype and one to Cryptosporidium canis. C. hominis was found extensively in the catchment, but only at sites contaminated by wastewater, and in the treated water supply to the affected area. All were gp60 subtype IbA10G2, the outbreak subtype. Multiple routes of contamination of the reservoir were identified, resulting in persistent detection of low numbers of oocysts in the final water. This work demonstrates the utility of genotyping Cryptosporidium isolates in environmental samples during outbreak investigations.

Validation of Multiplex Serology for human hepatitis viruses B and C, human T-lymphotropic virus 1 and Toxoplasma gondii.

Multiplex Serology is a high-throughput technology developed to simultaneously measure specific serum antibodies against multiple pathogens in one reaction vessel. Serological assays for hepatitis B (HBV) and C (HCV) viruses, human T-lymphotropic virus 1 (HTLV-1) and the protozoan parasite Toxoplasma gondii (T. gondii) were developed and validated against established reference assays. For each pathogen, between 3 and 5 specific antigens were recombinantly expressed as GST-tag fusion proteins in Escherichia coli and tested in Monoplex Serology, i.e. assays restricted to the antigens from one particular pathogen. For each of the four pathogen-specific Monoplex assays, overall seropositivity was defined using two pathogen-specific antigens. In the case of HBV Monoplex Serology, the detection of past natural HBV infection was validated based on two independent reference panels resulting in sensitivities of 92.3% and 93.0%, and specificities of 100% in both panels. Validation of HCV and HTLV-1 Monoplex Serology resulted in sensitivities of 98.0% and 95.0%, and specificities of 96.2% and 100.0%, respectively. The Monoplex Serology assay for T. gondii was validated with a sensitivity of 91.2% and specificity of 92.0%. The developed Monoplex Serology assays largely retained their characteristics when they were included in a multiplex panel (i.e. Multiplex Serology), containing additional antigens from a broad range of other pathogens. Thus HBV, HCV, HTLV-1 and T. gondii Monoplex Serology assays can efficiently be incorporated into Multiplex Serology panels tailored for application in seroepidemiological studies.

Geographic linkage and variation in Cryptosporidium hominis.

UK Cryptosporidium hominis isolates have previously shown slight PCR fragment length polymorphism at multiple loci. To further investigate transmission, we conducted a case-control study and sequenced the GP60 locus from 115 isolates. Nine subtypes were identified; IbA10G2 predominated. Having a non-IbA10G2 subtype was significantly linked to recent travel outside Europe.

Cryptosporidium genotypes and subtypes in lambs and goat kids in Spain.

To provide information on the transmission dynamics of cryptosporidial infections in domestic small ruminants and the potential role of sheep and goats as a source for human cryptosporidiosis, Cryptosporidium-positive isolates from 137 diarrheic lambs and 17 goat kids younger than 21 days of age were examined by using genotyping and subtyping techniques. Fecal specimens were collected between 2004 and 2006 from 71 sheep and 7 goat farms distributed throughout Aragón (northeastern Spain). Cryptosporidium parvum was the only species identified by restriction analyses of PCR products from small-subunit rRNA genes from all 154 microscopy-positive isolates and the sequencing of a subset of 50 isolates. Sequence analyses of the glycoprotein (GP60) gene revealed extensive genetic diversity within the C. parvum strains in a limited geographical area, in which the isolates from lambs exhibited 11 subtypes in two subtype families (IId and IIa) and those from goat kids displayed four subtypes within the family IId. Most isolates (98%) belonged to the subtype family IId, whereas only three isolates belonged to the most widely distributed family, IIa. Three of the four most prevalent subtypes (IIdA17G1a, IIdA19G1, and IIdA18G1) were previously identified in humans, and five subtypes (IIdA14G1, IIdA15G1, IIdA24G1, IIdA25G1, and IIdA26G1) were novel subtypes. All IId subtypes were identical to each other in the nonrepeat region, except for subtypes IIdA17G1b and IIdA22G1, which differed by a single nucleotide polymorphism downstream of the trinucleotide repeats. These findings suggest that lambs and goat kids are an important reservoir of the zoonotic C. parvum subtype family IId for humans.

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.

Detection of IgG antibodies in sera from patients with Cryptosporidium parvum and Cryptosporidium hominis.

OBJECTIVES: Detection of anti-Cryptosporidium immunoglobulin G (IgG) antibodies in human sera has been used to demonstrate population exposure to this gastro-intestinal protozoan parasite. We characterised the dynamics of IgG antibody responses to two Cryptosporidium parvum (IOWA isolate) sporozoite antigens (15/17 kDa and 27 kDa) using longitudinal sera taken from laboratory-confirmed cryptosporidiosis cases in England and Wales. The effect of the infecting Cryptosporidium species was also investigated. METHODS: A mini-gel Western blot was used to test sera from ten Cryptosporidium stool-positive diarrhoea patients, taken soon after diagnosis and at 3 month intervals. RESULTS: Overall responses to the 15/17 kDa antigen complex were stronger and over a greater range than those to the 27 kDa antigen, but declined between 181 and 240 days and were barely detectable thereafter. Responses to the 27 kDa antigen were much weaker but remained detectable for a greater length of time. No differences were detected in either antibody response to infection with C. hominis or C. parvum. CONCLUSIONS: The assay appears to be applicable for the study of recent exposure to C. parvum or C. hominis in the United Kingdom population, with strong responses to the 15/17 kDa antigen occurring within 6 months of infection.

Cryptosporidium viatorum n. sp. (Apicomplexa: Cryptosporidiidae) among travellers returning to Great Britain from the Indian subcontinent, 2007-2011.

A novel Cryptosporidium genotype was identified, among travellers with gastro-intestinal symptoms returning to Great Britain from the Indian subcontinent, for which we propose the name Cryptosporidium viatorum n. sp. The epidemiology of these cases was distinctly different from those with Cryptosporidium parvum and Cryptosporidium hominis. Of the 10 cases identified involving C. viatorum, most were in the first quarter of the year. One occurred in 2007, one in 2008, three in 2010 and five to end March 2011. The median age was 19 years but most were in the 20-29 years age group and seven were male. The symptoms included diarrhoea, abdominal pain, nausea, vomiting and fever. Compared with cases due to C. hominis and C. parvum, vomiting was reported less often, although the duration of gastro-intestinal symptoms was longer. The cases of C. viatorum were all travellers to the Indian subcontinent, whereas cases of C. hominis and C. parvum were more likely to have travelled elsewhere. Cryptosporidium viatorum isolates had indistinguishable sequences at each of the 70 kDa heat shock protein (HSP70), actin and ssrRNA loci which did not match any published previously and, although phylogenetically most similar to Cryptosporidium fayeri, they were distinct (<98% similarity) at the ssrRNA, HSP70 and actin genes. Morphologically, oocysts were typical of predominantly human-infecting species. Cryptosporidium viatorum n. sp. is proposed and work is warranted to investigate further the public health significance and occurrence elsewhere of this emerging parasite.

Rapid differentiation of Staphylococcus aureus, Staphylococcus epidermidis and other coagulase-negative staphylococci and meticillin susceptibility testing directly from growth-positive blood cultures by multiplex real-time PCR.

This study evaluated a multiplex real-time PCR method specific for the mecA, femA-SA and femA-SE genes for rapid identification of Staphylococcus aureus, Staphylococcus epidermidis and non-S. epidermidis coagulase-negative staphylococci (CoNS), and meticillin susceptibility testing directly in positive blood cultures that grew Gram-positive cocci in clusters. A total of 100 positive blood cultures produced: 39 S. aureus [12 meticillin-resistant S. aureus (MRSA), 31% of all the S. aureus]; 30 S. epidermidis (56.6% of the CoNS), 8 Staphylococcus capitis (15.1%), 3 Staphylococcus saprophyticus (5.7%), 4 Staphylococcus hominis (7.5%), 3 Staphylococcus haemolyticus (5.7%), 2 Staphylococcus warneri (3.8%), 1 Staphylococcus cohnii (1.9%) and 2 unidentified Staphylococcus spp. (3.8%); and 1 Micrococcus luteus in pure culture. Two blood cultures had no growth on subculture and five blood cultures grew mixed CoNS. For the 95 blood cultures with pure growth or no growth on subculture, there was very good agreement between real-time PCR and the BD Phoenix identification system for staphylococcal species categorization in S. aureus, S. epidermidis and non-S. epidermidis CoNS and meticillin-resistance determination (Cohen's unweighted kappa coefficient κ=0.882). All MRSA and meticillin-susceptible S. aureus were correctly identified by mecA amplification. PCR amplification of mecA was more sensitive for direct detection of meticillin-resistant CoNS in positive blood cultures than testing with the BD Phoenix system. There were no major errors when identifying staphylococcal isolates and their meticillin susceptibility within 2.5 h. Further studies are needed to evaluate the clinical benefit of using such a rapid test on the consumption of glycopeptide antibiotics and the alteration of empiric therapy in the situation of positive blood cultures growing staphylococci, and the respective clinical outcomes.

Re-description of Cryptosporidium cuniculus Inman and Takeuchi, 1979 (Apicomplexa: Cryptosporidiidae): morphology, biology and phylogeny.

To provide re-description of Cryptosporidium cuniculus Inman and Takeuchi, 1979 (synonymous with rabbit genotype), a species closely related to Cryptosporidium hominis, the morphology, natural and experimental host specificity, and genetic characterisation were investigated. The morphology and diagnostic characteristics are typical of other intestinal species of Cryptosporidium, albeit with slightly larger oocysts (5.55-6.40×5.02-5.92 µm; mean 5.98×5.38 µm; length:width=1.1; n=50). Natural hosts appear to be European rabbits (Oryctolagus cuniculus) and humans (Homo sapiens). Experimental infections have been established in weanling rabbits (O. cuniculus), immunosuppressed Mongolian gerbils (Meriones unguiculatus) and immunosuppressed adult Porton strain mice (Mus musculus), but not in neonatal mice. Patterns of infection measured by oocyst shedding are significantly different compared with C. hominis, particularly in rabbits. Histological examination reveals endogenous stages in the brush border of the epithelium of the small intestinal villi, but clinical signs are absent. Inoculation of human HCT-8 cells results in discrete clusters of endogenous stages. A close relationship with C. hominis is inferred from molecular analyses at the ssrRNA, 70 kDa heat shock protein (HSP70), actin, Cryptosporidium oocyst wall protein (COWP), 60 kDa glycoprotein (GP60) genes and a region encoding a product of unknown function (LIB13). Sequences contained limited, consistent polymorphisms at the ssrRNA, HSP70 and actin genes, were identical at the COWP and LIB13 genes and demonstrated two unique families at the GP60 gene. Although genetically closely related, there are significant biological differences between C. cuniculus and C. hominis that support these protozoa being separate species. This is based on the current understanding of these organisms and relies on the assumption that mating between these species would not normally occur. If this is subsequently demonstrated their categorisation may need to be re-addressed.