Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections.

Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance. IMPORTANCE: Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.

The Impact of Robotic Therapy on the Self-Perception of Upper Limb Function in Cervical Spinal Cord Injury: A Pilot Randomized Controlled Trial.

BACKGROUND: The aim of the present study was to evaluate the impact of robotic therapy in patients with cervical spinal cord injury (SCI), measured on the basis of the patients' self-perception of limited upper limb function and level of independence in activities of daily living. METHODS: Twenty-six patients with cervical SCI completed the treatment after being randomly assigned to the intervention or control group. The training consisted of 40 experimental sessions 1 h in duration, ideally occurring 5 days/week for 8 weeks. In addition to the conventional daily therapy (30 min), the control group received another 30 min of conventional therapy, whereas the intervention group received 30 min of robotic therapy. Patients were evaluated by means of the Capabilities of Upper Extremity Questionnaire (CUE) and Spinal Cord Independence Measure (SCIM) clinical scales. RESULTS: The improvement in the feeding item of SCIM was significantly higher in the intervention group than in the control group after the treatment (2.00 (0.91) vs. 1.18 (0.89), p = 0.03). The correlation between the CUE and SCIM scales was higher at the ending than at baseline for both groups. CONCLUSIONS: Although both groups improved, the clinical relevance related to the changes observed for both assessments was slightly higher in the intervention group than in the control group.

The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study.

Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.

Comparative study of pressure distribution at the user-cushion interface with different cushions in a population with spinal cord injury.

BACKGROUND: Few studies have offered comparative information on the mechanical characteristics of different wheelchair seat cushions. The objective of the present study was to compare the benefits of the wheelchair seat cushions most frequently used in a population of patients with spinal cord injury in terms of pressure distribution and contact surface at the user-cushion interface. METHODS: Each one of 48 patients with spinal cord injury was seated in his or her own wheelchair on the four models of cushions analyzed (low-profile air, high-profile air, dual-compartment air, and gel and firm foam), which were presented in randomized order. The pressure distribution readings and support surface area of the user-cushion interface were obtained with a matrix of piezocapacitive sensors. FINDINGS: The dual-compartment air cushion yielded lower readings for all pressure parameters analyzed (P(max), P(mean), P(sd), and P(isch)) than the other three cushion models (P<0.05). The best surface parameter results (S(tot), S>60 and %S>60) also were obtained with the dual-compartment air cushion (P<0.05). INTERPRETATION: In the sample analyzed, the dual-compartment air cushion was the cushion with the best pressure distribution and largest contact surface of the user-cushion interface compared to the other three cushions studied.