VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.

Oxidative Stress and Cardiovascular Risk in Type 1 Diabetes Mellitus: Insights From the DCCT/EDIC Study

Background

Hyperglycemia leading to increased oxidative stress is implicated in the increased risk for the development of macrovascular and microvascular complications in patients with type 1 diabetes mellitus.

Methods and Results

A random subcohort of 349 participants was selected from the DCCT / EDIC (Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications) cohort. This included 320 controls and 29 cardiovascular disease cases that were augmented with 98 additional known cases to yield a case cohort of 447 participants (320 controls, 127 cases). Biosamples from DCCT baseline, year 1, and closeout of DCCT , and 1 to 2 years post‐ DCCT ( EDIC years 1 and 2) were measured for markers of oxidative stress, including plasma myeloperoxidase, paraoxonase activity, urinary F 2α isoprostanes, and its metabolite, 2,3 dinor‐8 iso prostaglandin F 2α . Following adjustment for glycated hemoblobin and weighting the observations inversely proportional to the sampling selection probabilities, higher paraoxonase activity, reflective of antioxidant activity, and 2,3 dinor‐8 iso prostaglandin F 2α , an oxidative marker, were significantly associated with lower risk of cardiovascular disease (−4.5% risk for 10% higher paraoxonase, P <0.003; −5.3% risk for 10% higher 2,3 dinor‐8 iso prostaglandin F 2α , P =0.0092). In contrast, the oxidative markers myeloperoxidase and F 2α isoprostanes were not significantly associated with cardiovascular disease after adjustment for glycated hemoblobin. There were no significant differences between DCCT intensive and conventional treatment groups in the change in all biomarkers across time segments.

Conclusions

Heightened antioxidant activity (rather than diminished oxidative stress markers) is associated with lower cardiovascular disease risk in type 1 diabetes mellitus, but these biomarkers did not change over time with intensification of glycemic control.

Clinical Trial Registration

URL : https://www.clinicaltrials.gov . Unique identifiers: NCT 00360815 and NCT 00360893.

Abstract P6-05-11: DEPArray™ enables recovery of pure tumor cells from heterogeneous fine needle aspirates for routine downstream NGS analysis

Introduction: We have previously shown reliability in isolating pure populations of cells from complex tissues using the DEPArray™. Fine Needle Aspiration (FNA) is a quick and simple procedure often performed to make a diagnosis or rule out conditions such as cancer. Although FNA is also used to assess response to treatment, the procedure is often deemed insufficient in yield and purity of tumor cells. Here we provide preliminary results showing 100% efficiency in recovering pure tumor cell populations from FNA samples of patients affected by Metastatic Breast Cancer and known to have low tumor burden (&lt;20%) prior to using the DEPArray™ platform.

Method: FNA paraffin embedded sections (50 microns thickness) from metastases originating from breast (n=3) primary tumors were evaluated. Each FFPE curl was processed to yield single cells followed by DEPArray™ sorting based on cytokeratin (Ker), vimentin (Vim) and nuclear staining. The recovered cell populations were directly lysed in the collection tube prior to PCR-based target enrichment for next generation sequencing using Ion AmpliSeq™ CHPv2.

Results: DEPArray™ analysis allowed identification of 3 well separated cell populations, including tumor (Ker+/Vim-), stromal (Vim+/Ker) and putative EMT (Ker+/Vim+) cells. Overall, only 21% (4.3% to 42.7% range) of the total (mean of 6335) cells analyzed were of tumor (KER+/Vim-) origin. Groups of pure cells (mean 105 cells, range 15-200) for each population were recovered for sequence analysis. In one breast cancer FNA sample, we observed TP53 LoH but only in the recovered tumor (KER+) cells and not in the unsorted, stromal (VIM+), or EMT (KER+/VIM+) populations. In addition, a PIK3CA missense somatic heterozygous variant was identified in both the tumor and putative EMT populations but not in stromal cells, confirming this as a somatic mutation.

Conclusion: DEPArray™ allows resolution of two main limitations associated with FNA samples obtained for genomic analysis: too few target cells and unwanted admixture of normal cells. DEPArray™ allows for phenotypic distinction between the sorted cells prior to recovery; thus, enabling sequence analysis that is suitable for detecting genomic aberrations such as CNVs and LoH, which cannot be evaluated as precisely in an unsorted sample. Clearly, the DEPArray™ platform brings precision to detection, quantification and recovery of pure target cells that are suitable for subsequent downstream molecular analysis that can improve cancer diagnosis and personalized treatment strategies for breast cancer patients.

Citation Format: Sero V, Forcato C, Bolognesi C, Buson G, Medoro G, Yazdani M, Blevins A, Manaresi N, Bischoff FZ. DEPArray™ enables recovery of pure tumor cells from heterogeneous fine needle aspirates for routine downstream NGS analysis. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-05-11.

Prevention of skin colonization and subsequent bacteremia with CDC-JK organisms in patients with cancer

A 10-year experience with a program designed to reduce the incidence of bacteremias in the cancer patient, specifically those caused by Corynebacterium CDC-JK, is presented. Retrospective chart reviews identified patients at risk and generated the hypothesis that special attention to body hygiene may play a significant role. Implementation of a skin hygiene program resulted in a significant decrease in the incidence of CDC-JK bacteremias in Memorial Hospital patients.

Cryptococcal meningitis: outcome in patients with AIDS and patients with neoplastic disease

A retrospective analysis of 41 patients with cryptococcal meningitis and AIDS or neoplastic disease was done. Patients with AIDS were younger and predominantly male; they had a shorter duration of prior illness, higher initial serum cryptococcal antigen titers, and lower initial cerebrospinal fluid white blood cell counts than those with neoplastic disease. The median overall survival for patients with AIDS was 9 months compared with 2 months for those with neoplastic disease (P = .004). Seventy-eight percent of patients with AIDS and 43% of those with neoplastic disease were cured or improved 6 months after diagnosis (P = .039). Toxicity from amphotericin B and flucytosine was similar for both groups. One patient with AIDS relapsed. Multivariate predictors of survival included headache (P = .007) and an AIDS diagnosis (P = .009). Examination of outcomes for other opportunistic infections associated with AIDS and other immunosuppressive illness may distinguish prognostic features for different patient populations.

Aspergillus species from hospital air and from patients

During a seven month period, 367 molds were isolated from hospital air and 23 from patients. Aspergillus niger accounted for 56% of air isolates, but for only 17% of patient isolates. Aspergillus fumigatus was rarely found in air (0.3%), but was the dominant isolate among our patients (44%). We conclude, that different Aspergillus species may have a varied aptitude to colonize immunocompromised patients.

Bacteremia and fungemia in patients with neoplastic disease

This study reviewed 431 episodes of septicemia occurring in 356 patients with cancer at Memorial Sloan-Kettering Cancer Center during 1982. The most frequent organisms causing 273 episodes in 239 non-neutropenic patients were Escherichia coli (20 percent), Staphylococcus aureus (13 percent), polymicrobic (12 percent), Pseudomonas species (8 percent), Klebsiella species (7 percent), Candida species (7 percent), Bacteroides species (6 percent), Enterobacter species (4 percent), and Clostridium species (4 percent). The overall mortality was 31 percent (21 percent with adequate therapy; 50 percent with inadequate therapy). The most frequent organisms causing 158 episodes in 117 neutropenic patients were polymicrobic (21 percent), E. coli (16 percent), Klebsiella species (15 percent), Pseudomonas species (8 percent), Candida species (6 percent), S. aureus (6 percent), Streptococcus faecalis (5 percent), S. epidermidis (4 percent), and Corynebacterium CDC-JK (3 percent). The overall mortality was 52 percent (36 percent with adequate therapy; 88 percent with inadequate therapy). Since a review a decade ago, the spectrum of organisms changed in that the gram-positive organisms, S. faecalis, S. epidermidis, and C. CDC-JK, emerged as important pathogens. Neutropenic patients had a high incidence (42 percent) of septicemia due to multiple organisms, occurring concurrently or sequentially. The overall mortality of these patients was exceptionally high (80 percent). In contrast, the overall mortality of neutropenic patients with single-organism septicemia was comparable to that of non-neutropenic patients with single-organism septicemia (37 percent versus 29 percent).

Bacteremia and fungemia in patients with the acquired immunodeficiency syndrome

Forty-nine episodes of bacteremia and fungemia occurred in 38 of 336 patients with the acquired immunodeficiency syndrome seen at our institution since 1980. There were five types of infections. Infections commonly associated with a T-cell immunodeficiency disorder comprised 16 episodes and included those with Salmonella species, Listeria monocytogenes, Cryptococcus neoformans, and Histoplasma capsulatum. Infections commonly associated with a B-cell immunodeficiency disorder included those with Streptococcus pneumoniae and Haemophilus influenzae. Infections occurring with neutropenia were caused by Pseudomonas aeruginosa, Staphylococcus epidermidis, and Streptococcus faecalis. Other infections occurring in the hospital were caused by Candida albicans, Staphylococcus epidermidis, enteric gram-negative rods, Staphylococcus aureus, and mixed S. aureus and group G streptococcus. Other infections occurring out of the hospital included those with S. aureus, Clostridium perfringens, Shigella sonnei, Pseudomonas aeruginosa, and group B streptococcus. Because two thirds of the septicemias were caused by organisms other than T-cell opportunists, these pathogens should be anticipated during diagnostic evaluation and when formulating empiric therapy.

Severe pneumococcal infection in patients with neoplastic disease

A study of pneumococcal bacteremia in 56 patients with neoplastic disease from January 1, 1972 to June 30, 1980 is presented and compared to an earlier study between 1955 and 1971. Patients at highest risk were those with Hodgkin's disease who had been splenectomized, multiple myeloma and chronic lymphocytic leukemia showing an attack rate of 15.6/1000, 12.5/1000, and 10.8/1000, respectively. The attack rate was more than three times higher among patients with Hodgkin's disease in the present series compared to the previous series. In 32% of cases there was no identifiable source for the infection. Four splenectomized patients with Hodgkin's disease developed pneumococcal meningitis and two died. The overall mortality rate was 32% versus a rate of 18% for those treated with appropriate antibiotics for more than 24 hours. There was a significant improvement in overall survival when compared with our previous series. As before, almost one fourth (24%) of our isolates were not among those included in the pneumococcal vaccine presently available. Antibiotic prophylaxis should be considered in high risk patients.

Pasteurella multocida septicemia. Experience at a cancer hospital

Pasteurella multocida most commonly infects patients with animal contacts. Life-threatening systemic disease is distinctly uncommon in otherwise healthy persons and usually occurs in patients with chronic predisposing disease. Two cases of sepsis occurred in a cancer hospital, and we surmise that specific predisposing factors existed in our patients as in prior reported cases of sepsis in patients without cancer. These factors include animal contact, open wounds, and, most important, advanced hepatic disease.

Arrest and Repair in Experimental Endocarditis Lenta

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