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Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology.

ABSTRACT: Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious diseases. The present study compares two HTS methods, 16S rRNA marker gene sequencing (metataxonomics) and whole metagenomic shotgun sequencing (metagenomics), in their respective abilities to match the same diagnosis as traditional culture methods (culture inference) for patients with ventilator associated pneumonia (VAP). The metagenomic analysis was able to produce the same diagnosis as culture methods at the species-level for five of the six samples, while the metataxonomic analysis was only able to produce results with the same species-level identification as culture for two of the six samples. These results indicate that metagenomic analyses have the accuracy needed for a clinical diagnostic tool, but full integration in diagnostic protocols is contingent on technological improvements to decrease turnaround time and lower costs.

SUBMITTER: Hilton SK

PROVIDER: S-EPMC4823605 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology.

Hilton Sarah K SK Castro-Nallar Eduardo E Pérez-Losada Marcos M Toma Ian I McCaffrey Timothy A TA Hoffman Eric P EP Siegel Marc O MO Simon Gary L GL Johnson W Evan WE Crandall Keith A KA

Frontiers in microbiology 20160407

Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious diseases. The present study compares two HTS methods, 16S rRNA marker gene sequencing (metataxonomics) and whole metagenomic shotgun sequencing (metagenomics), in their respective abilities to match the sa ...[more]

PMID: 27092134

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Project description:Enhanced quantitative urine culture (EQUC) detects live microorganisms in the vast majority of urine specimens reported as "no growth" by the standard urine culture protocol. Here, we evaluated an expanded set of EQUC conditions (expanded-spectrum EQUC) to identify an optimal version that provides a more complete description of uropathogens in women experiencing urinary tract infection (UTI)-like symptoms. One hundred fifty adult urogynecology patient-participants were characterized using a self-completed validated UTI symptom assessment (UTISA) questionnaire and asked "Do you feel you have a UTI?" Women responding negatively were recruited into the no-UTI cohort, while women responding affirmatively were recruited into the UTI cohort; the latter cohort was reassessed with the UTISA questionnaire 3 to 7 days later. Baseline catheterized urine samples were plated using both standard urine culture and expanded-spectrum EQUC protocols: standard urine culture inoculated at 1 ?l onto 2 agars incubated aerobically; expanded-spectrum EQUC inoculated at three different volumes of urine onto 7 combinations of agars and environments. Compared to expanded-spectrum EQUC, standard urine culture missed 67% of uropathogens overall and 50% in participants with severe urinary symptoms. Thirty-six percent of participants with missed uropathogens reported no symptom resolution after treatment by standard urine culture results. Optimal detection of uropathogens could be achieved using the following: 100 ?l of urine plated onto blood (blood agar plate [BAP]), colistin-nalidixic acid (CNA), and MacConkey agars in 5% CO2 for 48 h. This streamlined EQUC protocol achieved 84% uropathogen detection relative to 33% detection by standard urine culture. The streamlined EQUC protocol improves detection of uropathogens that are likely relevant for symptomatic women, giving clinicians the opportunity to receive additional information not currently reported using standard urine culture techniques.

Project description:Analysis of time-evolving data is crucial to understand the functioning of dynamic systems such as the brain. For instance, analysis of functional magnetic resonance imaging (fMRI) data collected during a task may reveal spatial regions of interest, and how they evolve during the task. However, capturing underlying spatial patterns as well as their change in time is challenging. The traditional approach in fMRI data analysis is to assume that underlying spatial regions of interest are static. In this article, using fractional amplitude of low-frequency fluctuations (fALFF) as an effective way to summarize the variability in fMRI data collected during a task, we arrange time-evolving fMRI data as a subjects by voxels by time windows tensor, and analyze the tensor using a tensor factorization-based approach called a PARAFAC2 model to reveal spatial dynamics. The PARAFAC2 model jointly analyzes data from multiple time windows revealing subject-mode patterns, evolving spatial regions (also referred to as networks) and temporal patterns. We compare the PARAFAC2 model with matrix factorization-based approaches relying on independent components, namely, joint independent component analysis (ICA) and independent vector analysis (IVA), commonly used in neuroimaging data analysis. We assess the performance of the methods in terms of capturing evolving networks through extensive numerical experiments demonstrating their modeling assumptions. In particular, we show that (i) PARAFAC2 provides a compact representation in all modes, i.e., subjects, time, and voxels, revealing temporal patterns as well as evolving spatial networks, (ii) joint ICA is as effective as PARAFAC2 in terms of revealing evolving networks but does not reveal temporal patterns, (iii) IVA's performance depends on sample size, data distribution and covariance structure of underlying networks. When these assumptions are satisfied, IVA is as accurate as the other methods, (iv) when subject-mode patterns differ from one time window to another, IVA is the most accurate. Furthermore, we analyze real fMRI data collected during a sensory motor task, and demonstrate that a component indicating statistically significant group difference between patients with schizophrenia and healthy controls is captured, which includes primary and secondary motor regions, cerebellum, and temporal lobe, revealing a meaningful spatial map and its temporal change.

Project description:ImportanceSutureless gastroschisis repair offers an alternative to the traditional sutured method and has been associated with decreased intubation time. Published study results are inconsistent regarding the advantages of sutureless closure.ObjectiveTo compare the clinical outcomes of sutureless and sutured gastroschisis repair.Design, setting, and participantsA single-center cohort review was performed of all consecutive patients (n = 97) who underwent gastroschisis repair from February 1, 2007, to April 30, 2017, at the University of California, San Francisco. Patients' medical records were evaluated for clinical characteristics and outcomes. Cases with incomplete data during initial hospitalization were excluded.Main outcomes and measuresLength of hospital stay, time to full enteral feeds, total parenteral nutrition duration, days requiring intravenous analgesia, days intubated, wound infection rate, antibiotic treatment duration, rate of umbilical hernias that required an operation, and readmission rate.ResultsIn total, 97 patients (47 [48%] were female and 50 [52%] were male with a mean [SD] age of 2.8 [2.8] days) underwent gastroschisis repair, of which 7 were excluded for incomplete medical record. Of the 90 patients included in the study, 50 (56%) underwent sutured closure and 40 (44%) underwent sutureless closure. No statistical difference was found between the sutured and sutureless groups in length of hospital stay (mean [SD] days, 43.9 [40.4] vs 36.7 [21.2]; P = .71), time to full enteral feeds (mean [SD] days, 31.4 [20.2] vs 27.9 [17.3]; P = .22), total parenteral nutrition duration (mean [SD] days, 33.5 [29.8] vs 27.4 [18.2]; P = .23), wound infection rates (14 [28%] vs 10 [25%]; P = .81), and readmission rates (5 [10%] vs 7 [18%]; P = .36). The sutureless group, compared with the sutured group, had substantially fewer days receiving antibiotics (mean [SD], 7.2 [6.4] vs 12.4 [13.2]; P = .003), fewer days intubated (mean [SD], 2.8 [3.3] vs 6.8 [1.3]; P = .001), fewer days receiving intravenous analgesia (mean [SD], 4.2 [4.0] vs 7.1 [4.5]; P = .003), and fewer patients that required silo reduction (25 [63%] vs 48 [96%]; P < .001). Sutureless closures, compared with the sutured technique, had considerably more umbilical hernias requiring surgical repair (5 [13%] vs 0; P = .02).Conclusions and relevanceSutureless repair of gastroschisis appears to be associated with a statistically significant reduction in mechanical ventilation duration and pain medication requirements but may increase umbilical hernia risk. Multicenter randomized clinical trials are necessary to determine the true advantages of the sutureless approach.

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Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology.

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Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology.

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