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

Unlabelled: Diarrheagenic , 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.

Distribution of Escherichia coli Pathotypes along an Urban-Rural Gradient in Ecuador.

Diarrheal diseases are a leading cause of mortality and morbidity in low- and middle-income countries. Diarrhea is associated with a wide array of etiological agents including bacterial, viral, and parasitic enteropathogens. Previous studies have captured between- but not within-country heterogeneities in enteropathogen prevalence and severity.

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.

Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador.

Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood.

The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample.

The recovery of metagenome-assembled genomes (MAGs) from metagenomic data has recently become a common task for microbial studies. The strengths and limitations of the underlying bioinformatics algorithms are well appreciated by now based on performance tests with mock data sets of known composition. However, these mock data sets do not capture the complexity and diversity often observed within natural populations, since their construction typically relies on only a single genome of a given organism.

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.

Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women.

Background: While the importance of commensal microbes in vaginal health is well appreciated, little is known about the effects of gynecological cancer (GynCa) and radiation therapy (RT) on the vaginal microbiome (VM) of postmenopausal women.

Methods: We studied women with GynCa, pre- (N = 65) and post-RT (N = 25) and a group of healthy controls (N = 67) by sequencing the V4 region of the 16S rRNA gene from vaginal swabs and compared the diversity and composition of VMs between the three groups accounting for potential confounding factors in multivariate analysis of variance.

Results: Comparisons of cancer vs healthy groups revealed that Lactobacillus and Bifidobacterium have significantly higher relative abundance in the healthy group, while the cancer group was enriched in 16 phylogroups associated with bacterial vaginosis (BV) and inflammation, including Sneathia, Prevotella, Peptoniphilus, Fusobacterium, Anaerococcus, Dialister, Moryella, and Peptostreptococcus.

Metagenomic Signatures of Gut Infections Caused by Different Pathotypes.

is a leading contributor to infectious diarrhea and child mortality worldwide, but it remains unknown how alterations in the gut microbiome vary for distinct pathotype infections and whether these signatures can be used for diagnostic purposes. Further, the majority of enteric diarrheal infections are not diagnosed with respect to their etiological agent(s) due to technical challenges. To address these issues, we devised a novel approach that combined traditional, isolate-based and molecular-biology techniques with metagenomics analysis of stool samples and epidemiological data.

Genomic Characterization and Copy Number Variation of Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains.

Bacillus anthracis plasmids pXO1 and pXO2 carry the main virulence factors responsible for anthrax. However, the extent of copy number variation within the species and how the plasmids are related to pXO1/pXO2-like plasmids in other species of the Bacillus cereus group remain unclear. To gain new insights into these issues, we sequenced 412 B.

Draft Genome Sequence of LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids.

We present the genome sequence of LA2007, a strain isolated in 2007 from a fatal pneumonia case in Louisiana. Sequence-based genome analysis revealed that LA2007 carries a plasmid highly similar to pXO1, including the genes responsible for the production and regulation of anthrax toxin.

Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods.

Unlabelled: Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based culture-independent approaches, such as shotgun metagenomics, could sidestep these limitations and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology. However, metagenomics have not yet been validated for foodborne pathogen detection.

Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy.

Taxonomic classification of Clostridium botulinum is based on the production of botulinum neurotoxin (BoNT), while closely related, nontoxic organisms are classified as Clostridium sporogenes. However, this taxonomic organization does not accurately mirror phylogenetic relationships between these species. A phylogenetic reconstruction using 2,016 orthologous genes shared among strains of C.

Physical activity and transcutaneous oxygen pressure in men with spinal cord injury.

This pilot study proposed a method for assessing the status of vascular flow measured by transcutaneous oxygen pressure (TcPO2) in the area of the ischium in people with spinal cord injury (SCI). In a sample of 38 men (two groups: 12 physically active and 26 sedentary) with thoracic SCI, the distribution of the physiological response of the tissues under load during sitting was assessed through analysis of ischium TcPO2 values obtained by an oximeter. TcPO2 baseline, recovery time of TcPO2 after sitting (Trec), the percentage of TcPO2 (%TcPO2) of maximum pressure TcPO2, and mechanic maximal pressure (Pmax) were evaluated.

Comparative ergonomic assessment of manual wheelchairs by paraplegic users.

Purpose: The aim of the present study was to describe and test the reliability of a comprehensive product-centered approach to assessing functional performance and wheelchair user perceptions on device ergonomics and satisfaction of performance. A pilot study was implemented using this approach to evaluate differences among four manual wheelchairs.

Method: Six wheelchair users with complete spinal cord injury (SCI) at the thoracic level and with no previous upper limbs impairment were recruited for this study.

[Application of virtual reality in the motor aspects of neurorehabilitation].

Introduction: Virtual reality allows the user to interact with elements within a simulated scene. In recent times we have been witness to the introduction of virtual reality-based devices as one of the most significant novelties in neurorehabilitation.

Aim: To review the clinical applications of the developments based on virtual reality for the neurorehabilitation treatment of the motor aspects of the most frequent disabling processes with a neurological origin.

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.