Separating the signal from the noise in metagenomic cell-free DNA sequencing.

BACKGROUND: Cell-free DNA (cfDNA) in blood, urine, and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise. RESULTS: Here, we report low biomass background correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high-throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection. CONCLUSIONS: The data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term. Video abstract.

Verification of association of elevated serum IDO enzyme activity with acute rejection and low CD4-ATP levels with infection.

BACKGROUND: Both acute rejection (AR) and major infection events (MIE) can reduce long-term allograft survival. We assessed the simultaneous efficacy of serum and urine biomarker indoleamine 2,3-dioxygenase (IDO) enzyme activity and peripheral blood CD4-ATP levels for AR and MIE association, respectively. METHODS: We prospectively tested 217 blood and 167 urine serial samples, collected monthly for 12 months after transplantation from 29 consecutive children receiving a kidney transplant. The indoleamine 2,3-dioxygenase activity was assessed by mass spectrometry assays using the ratio of product L-kynurenine (kyn) to substrate tryptophan (trp). Kyn/trp ratios and blood CD4 T-cell ATP levels were correlated with AR, MIE, or stable group (no events) in the next 30 days. RESULTS: Using absolute cutoffs and allocating to samples to AR, MIE, or stable group, mean serum kyn/trp ratios were significantly elevated in the group that experienced AR (P=0.0007). Similarly, peripheral blood CD4-ATP levels were significantly lower in the group experiencing MIE (P=0.0351). Urine kyn/trp ratios and blood tacrolimus levels were not different between AR and stable groups. Within-subject analyses, accounting for repeated measures in subjects, also showed that, over time, serum kyn/trp ratios were higher before AR (P=0.031) and blood CD4-ATP levels were lower before MIE (P=0.008). CONCLUSIONS: These results from our pilot discovery group suggest that a panel of biomarkers together can predict overimmunosuppression or underimmunosuppression. Further independent validation in a multicenter cohort is suggested.

Primary focal segmental glomerulosclerosis in nephrotic patients: common complications and risk factors.

BACKGROUND: Focal segmental glomerulosclerosis (FSGS) presents a range of potentially serious complications, including acute kidney injury (AKI), infection and thromboembolism. This study aimed to find out the incidence rates and risk factors for these complications in FSGS patients. METHODS: Patients with biopsy-proven primary FSGS and nephrotic-range proteinuria were included in this study. A short-term (16-week) follow-up was performed to observe the aforementioned complications. Clinical characteristics of patients were recorded upon enrollment. AKI was diagnosed as an absolute increase in serum creatinine of ≥0.3 mg/dL or a percentage increase of ≥50% within 48 hours; infection, by a combination of clinical manifestations, laboratory tests and imaging examinations; and thromboembolism, by imaging methods. Risk factors for complications were evaluated by logistic regression model. RESULTS: The study population included 90 FSGS patients (63 males, mean age 28.9 ± 12.9 years). The incidences of AKI, infection and thromboembolism were 44.4%, 25.6% and 12.2%, respectively. Patients with AKI were more likely to be male, with lower serum albumin, greater proteinuria and more severe acute tubulointerstitial damage. Patients with infection had higher proteinuria and lower serum albumin, globulin and IgG. Circulating endothelial cells (CECs) and von Willebrand factor were higher in patients with thromboembolism. Logistic regression showed that increased urine retinol-binding protein, decreased serum albumin and IgG, and increased CECs and hemoglobin were independent risk factors for AKI, infection and thromboembolism, respectively. CONCLUSIONS: AKI, infection and thromboembolism are common among FSGS patients. Awareness of risk factors and prevention of these complications are important for the prognosis of these patients.

Urine suPAR levels compared with plasma suPAR levels as predictors of post-consultation mortality risk among individuals assumed to be TB-negative: a prospective cohort study.

Plasma levels of the inflammatory biomarker soluble urokinase plasminogen activator (suPAR) have been shown to carry prognostic information in various infectious and inflammatory diseases. The present study aimed to compare the prognostic value of urine suPAR (U-suPAR) to that of plasma suPAR (P-suPAR), thereby exploring the possibility of replacing the blood sample with an easy obtainable urine sample. We enrolled 1,007 adults, older than 15 years of age, with a negative TB diagnosis between April 2004 and December 2006. Levels of U-suPAR and P-suPAR were available in 863 individuals. U-suPAR was measured using a commercial ELISA (suPARnostic®). We found that U-suPAR carried significant prognostic information on mortality for HIV-infected subjects with an area under the ROC curve of 0.75. For HIV-negative individuals, little or no prognostic effect was observed. However, in both HIV positives and negatives, the predictive effect of U-suPAR was found to be inferior to that of P-suPAR.

Urine-based diagnostic technologies.

The worldwide dissemination of infectious agents has created a demand for simple diagnostic tests. Urine-based testing makes use of non-invasive collection of specimens, and there is no need for expensive facilities and equipment, or for highly trained personnel. As urine antibodies retain activity under normal conditions of transport and storage, such tests appear to have widespread application. Urine-based antibody tests have also indicated a compartmentalized antibody response to HIV-1 infection. Urine studies suggest that antibodies to the products of endogenous viral genes may be involved in the pathogenesis of chronic diseases of suspected viral etiology.