Fully Resolved assembly of Cryptosporidium Parvum

BACKGROUND: Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission. The basis of every genomic study is a high-quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies. FINDINGS: Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on 2 main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single-copy BUSCO genes. CONCLUSIONS: This high-quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional, and association studies

Chapter 8: Meta-analysis of Test Performance When There is a “Gold Standard”

Synthesizing information on test performance metrics such as sensitivity, specificity, predictive values and likelihood ratios is often an important part of a systematic review of a medical test. Because many metrics of test performance are of interest, the meta-analysis of medical tests is more complex than the meta-analysis of interventions or associations. Sometimes, a helpful way to summarize medical test studies is to provide a “summary point”, a summary sensitivity and a summary specificity. Other times, when the sensitivity or specificity estimates vary widely or when the test threshold varies, it is more helpful to synthesize data using a “summary line” that describes how the average sensitivity changes with the average specificity. Choosing the most helpful summary is subjective, and in some cases both summaries provide meaningful and complementary information. Because sensitivity and specificity are not independent across studies, the meta-analysis of medical tests is fundamentaly a multivariate problem, and should be addressed with multivariate methods. More complex analyses are needed if studies report results at multiple thresholds for positive tests. At the same time, quantitative analyses are used to explore and explain any observed dissimilarity (heterogeneity) in the results of the examined studies. This can be performed in the context of proper (multivariate) meta-regressions

Evaluation of Recombinant Oocyst Protein CP41 for Detection of Cryptosporidium-Specific Antibodies

Cryptosporidium is an important cause of diarrhea in developed and developing countries, and its epidemiology is of interest. The methodologies used in the detection of Cryptosporidium-specific antibodies vary widely, which complicates comparison of results. This study assesses the performance of a Cryptosporidium recombinant protein (rCP41) in a serological assay compared to that of a crude antigen preparation. The 41-kDa protein from the oocyst wall was previously cloned and expressed in Escherichia coli. Sera from 192 healthy adults from the Texas Medical Center (Houston) were tested for anti-Cryptosporidium antibody reactivity using both crude and recombinant antigen preparations in an enzyme-linked immunosorbent assay. Immunoglobulin G reactivity was highly concordant (88%; P < 0.0001) between the two antigen preparations, with 110 positive (57%) and 59 negative (31%) by both tests. Regression analysis revealed a high correlation between the absorbance values generated with both antigen preparations and suggests that the rCP41 may be used in place of crude antigen. These results indicate that the use of the recombinant CP41 antigen in a standardized serodiagnostic assay could provide a reliable and cost-effective method for assessing human exposure to Cryptosporidium

Combined Use of Enzyme-Linked Immunosorbent Assay and Flow Cytometry To Detect Antibodies to Trypanosoma cruzi in Domestic Canines in Texas

Canines may be sentinels and/or reservoirs for human Trypanosoma cruzi exposures. This study adapted a method originally designed for human diagnostics to detect serum immunoglobulin G to T. cruzi in canines. The method combined an enzyme-linked immunosorbent assay (ELISA) for screening and flow cytometry detection of anti-live trypomastigote antibodies (ALTA) for confirmation. The assays were optimized by using known positive and negative control canine sera, and cutoff values were established. The ELISA and ALTA assay easily distinguished between reactive (positive controls) and nonreactive (negative controls) sera and were used to test sera collected in a cross-sectional seroprevalence survey of 356 domestic canines from Harris County, Tex., and the surrounding area. Fifty-three (14.9%) of 356 asymptomatic canines in the survey were positive by ELISA, and 5 (1.4%) were confirmed positive with the ALTA assay, with an additional 4 (1.1%) canines classified as “suspect positive.” Thus, the overall prevalence of T. cruzi antibodies in this population was 2.6%. This is the first U.S. study to use the combination of ELISA and ALTA to detect serum antibodies to T. cruzi and the first report of the prevalence of T. cruzi infection in domestic canines in the Houston, Tex. (Harris County), region. Our results demonstrate that the combination of ELISA and ALTA has been successfully adapted for use in testing canines for serological evidence of T. cruzi infection. Seroprevalence survey results suggest that T. cruzi antibody-positive domestic canines in the peridomestic setting are present in the Houston, Tex., region and further suggest that T. cruzi is enzootic in the region

Building geochemically based quantitative analogies from soil classification systems using different compositional datasets.

Soil heterogeneity is a major contributor to the uncertainty in near-surface biogeochemical modeling. We sought to overcome this limitation by exploring the development of a new classification analogy concept for transcribing the largely qualitative criteria in the pedomorphologically based, soil taxonomic classification systems to quantitative physicochemical descriptions. We collected soil horizons classified under the Alfisols taxonomic Order in the U.S. National Resource Conservation Service (NRCS) soil classification system and quantified their properties via physical and chemical characterizations. Using multivariate statistical modeling modified for compositional data analysis (CoDA), we developed quantitative analogies by partitioning the characterization data up into three different compositions: Water-extracted (WE), Mehlich-III extracted (ME), and particle-size distribution (PSD) compositions. Afterwards, statistical tests were performed to determine the level of discrimination at different taxonomic and location-specific designations. The analogies showed different abilities to discriminate among the samples. Overall, analogies made up from the WE composition more accurately classified the samples than the other compositions, particularly at the Great Group and thermal regime designations. This work points to the potential to quantitatively discriminate taxonomically different soil types characterized by varying compositional datasets

High Levels of CXCL10 Are Produced by Intestinal Epithelial Cells in AIDS Patients with Active Cryptosporidiosis but Not after Reconstitution of Immunity

Chemokines play key roles in attracting immune cells to sites of infections. However, few data on chemokine expression in the gut during human infections are available. We examined expression of chemokines in intestinal tissues of AIDS patients during active Cryptosporidium infection and during resolution of such an infection. The chemokines and cytokines in cell lysates from jejunal biopsy tissues were assayed by a 22-multiplex bead immunoassay. CXCL10 (IP-10) and its receptor, CXCR3, in sections were studied by immunohistochemistry. In biopsies from AIDS patients with active cryptosporidiosis, four chemokines (CXCL10, CCL11 [eotaxin], CCL5 [RANTES], and CCL2 [monocyte chemoattractant protein 1]) and three cytokines (interleukin-1α [IL-1α], IL-10, and granulocyte colony-stimulating factor) were detected. The level of CXCL10 was significantly increased in AIDS patients with cryptosporidiosis compared to the level in AIDS patients without cryptosporidiosis or in normal volunteers (median in AIDS patients with cryptosporidiosis, 508 pg/mg protein, compared to 111 pg/mg and 72 pg/mg protein in AIDS patients without cryptosporidiosis and in normal volunteers, respectively [P < 0.05 and P < 0.005, respectively, as determined by a Mann-Whitney test]). The level of CXCL10 correlated with the parasite burden (as measured by the number of Cryptosporidium oocysts in the stools) and also with the IL-1α concentration (Pearson correlation values, 0.961 [P < 0.01] and 0.737 [P < 0.05]). As determined by immunohistochemistry, CXCL10 localized to epithelial cells at the site of infection. Following effective antiparasite and antiretroviral therapy, Cryptosporidium infections resolved, and the levels of CXCL10 decreased to normal levels. We hypothesized that CXCL10 plays an important role in the resolution of cryptosporidiosis by attracting immune effector cells to the site of infection. By contrast, in AIDS patients lacking effector cells, CXCL10 may contribute to the immunopathogenesis by recruiting inflammatory cells

Immune response to a Trichinella spiralis infection in house mice from lines selectively bred for high voluntary wheel running.

Four lines of mice bred for high voluntary wheel running (HR lines) have high baseline circulating corticosterone levels and increased daily energy expenditure as compared with four non-selected control (C) lines. High corticosterone may suppress immune function and competing energy demands may limit ability to mount an immune response. We hypothesized that HR mice have a reduced immune response and therefore a decreased ability to fight an infection by Trichinella spiralis, an ecologically relevant nematode common in mammals. Infections have an acute, intestinal phase while the nematode is migrating, reproducing and traveling throughout the bloodstream, followed by a chronic phase with larvae encysted in muscles. Adult males (generation 55 of the selection experiment) were sham-infected or infected by oral gavage with ~300 J1 T. spiralis larvae. During the chronic phase of infection, mice were given wheel access for 6 days, followed by 2 days of maximum aerobic performance trials. Two weeks post-infection, infected HR had significantly lower circulating immunoglobulin E levels compared with infected C mice. However, we found no statistical difference between infected HR and C mice in numbers of encysted larvae within the diaphragm. As expected, both voluntary running and maximum aerobic performance were significantly higher in HR mice and lower in infected mice, with no line type-by-infection interactions. Results complement those of previous studies suggesting decreased locomotor abilities during the chronic phase of T. spiralis infection. However, despite reduced antibody production, breeding for high voluntary wheel exercise does not appear to have a substantial negative impact on general humoral function