Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection.

Low-abundance members of microbial communities are difficult to study in their native habitats. This includes Escherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenic Escherichia coli (UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverse E. coli in gastrointestinal communities, we developed E. coli PanSelect which uses a set of probes designed to specifically recognize and capture E. coli's broad pangenome from sequencing libraries. We demonstrated the ability of E. coli PanSelect to enrich, by orders of magnitude, sequencing data from diverse E. coli using a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes between E. coli residing in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gut E. coli are responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of native in vivo biology of E. coli in other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.

Strain Tracking with Uncertainty Quantification.

The ability to detect and quantify microbiota over time has a plethora of clinical, basic science, and public health applications. One of the primary means of tracking microbiota is through sequencing technologies. When the microorganism of interest is well characterized or known a priori, targeted sequencing is often used. In many applications, however, untargeted bulk (shotgun) sequencing is more appropriate; for instance, the tracking of infection transmission events and nucleotide variants across multiple genomic loci, or studying the role of multiple genes in a particular phenotype. Given these applications, and the observation that pathogens (e.g. Clostridioides difficile, Escherichia coli, Salmonella enterica) and other taxa of interest can reside at low relative abundance in the gastrointestinal tract, there is a critical need for algorithms that accurately track low-abundance taxa with strain level resolution. Here we present a sequence quality- and time-aware model, ChronoStrain, that introduces uncertainty quantification to gauge low-abundance species and significantly outperforms the current state-of-the-art on both real and synthetic data. ChronoStrain leverages sequences' quality scores and the samples' temporal information to produce a probability distribution over abundance trajectories for each strain tracked in the model. We demonstrate Chronostrain's improved performance in capturing post-antibiotic E. coli strain blooms among women with recurrent urinary tract infections (UTIs) from the UTI Microbiome (UMB) Project. Other strain tracking models on the same data either show inconsistent temporal colonization or can only track consistently using very coarse groupings. In contrast, our probabilistic outputs can reveal the relationship between low-confidence strains present in the sample that cannot be reliably assigned a single reference label (either due to poor coverage or novelty) while simultaneously calling high-confidence strains that can be unambiguously assigned a label. We also include and analyze newly sequenced cultured samples from the UMB Project.

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women.

Recurrent urinary tract infections (rUTIs) are a major health burden worldwide, with history of infection being a significant risk factor. While the gut is a known reservoir for uropathogenic bacteria, the role of the microbiota in rUTI remains unclear. We conducted a year-long study of women with (n = 15) and without (n = 16) history of rUTI, from whom we collected urine, blood and monthly faecal samples for metagenomic and transcriptomic interrogation. During the study 24 UTIs were reported, with additional samples collected during and after infection. The gut microbiome of individuals with a history of rUTI was significantly depleted in microbial richness and butyrate-producing bacteria compared with controls, reminiscent of other inflammatory conditions. However, Escherichia coli gut and bladder populations were comparable between cohorts in both relative abundance and phylogroup. Transcriptional analysis of peripheral blood mononuclear cells revealed expression profiles indicative of differential systemic immunity between cohorts. Altogether, these results suggest that rUTI susceptibility is in part mediated through the gut-bladder axis, comprising gut dysbiosis and differential immune response to bacterial bladder colonization, manifesting in symptoms.

StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities.

Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x.

Safety and effectiveness of selective carotid angioplasty prior to cardiac surgery: a single-centre matched case-control study.

OBJECTIVES: Reducing the rate of postoperative stroke after cardiac surgery remains challenging, especially in patients with occlusive cerebrovascular disease. Angioplasty in all patients with high-grade carotid artery stenosis has not been shown to be effective in reducing the post-surgical stroke rate. In this study, we present the initial results of a different approach using selective carotid angioplasty only in patients with poor intracranial collaterals. METHODS: We conducted a single-centre study to assess the safety of this procedure. The postangioplasty complication rate of the study group was compared to that of patients who were scheduled for symptomatic carotid artery angioplasty. To determine the effectiveness of this procedure, the post-cardiac surgery complication rate of the study group was compared with that of the matched case controls. RESULTS: Twenty-two patients were treated with selective carotid angioplasty without developing persistent major neurological complications. All patients except 1 patient subsequently underwent surgery without developing persistent major neurological disabilities. Two patients died of cardiogenic shock within 30 days. CONCLUSIONS: Selective carotid angioplasty prior to cardiac surgery in patients with a presumed high risk of stroke was relatively safe and effective in this study group. Although this strategy does not prevent stroke in these high-risk patients, data suggest that this approach shifts the postoperative type of stroke from a severe haemodynamic stroke towards a minor embolic stroke with favourable neurological outcomes. Larger studies are needed to determine whether this strategy can effectively eliminate the occurrence of haemodynamic stroke after cardiac surgery.

Impact of the Haga Braincare Strategy on the burden of haemodynamic and embolic strokes related to cardiac surgery.

OBJECTIVES: This study prospectively evaluates the impact of the Haga Braincare Strategy (HBS) on the occurrence of haemodynamic and embolic stroke in a cohort of patients who underwent coronay artery bypass grafting (CABG), valve replacement of a combination of both types of surgery between 2012 and 2015 at the Haga Teaching Hospitals. METHODS: The HBS is a dual strategy based on a preoperative vascular work-up of the cerebral circulation by transcranial Doppler and a perioperative monitoring of the cerebral circulation by cerebral oximetry. Duplex of the carotid arteries and/or computed tomography angiography prior to surgery was performed in high-risk patients. Patients with severe carotid artery stenosis were scheduled for carotid angioplasty prior to surgery or waived from surgery. RESULTS: A total of 1065 patients were included. Poor cerebral haemodynamics were identified by transcranial Doppler in 2.1% of patients (n = 22). Based on the HBS, 3 patients were waived from surgery, 4 received preoperative carotid angioplasty followed by cardiac surgery and the remaining patients were operated while being monitored with bilateral cerebral oximetry sensors. In all, 2.2% of the study group experienced a stroke (n = 23), of which none were classified as haemodynamic. Most of the remaining presumed embolic strokes showed a minor to moderate stroke severity. CONCLUSIONS: In this single-centre prospective follow-up study, surveillance of cerebral perfusion by the HBS eliminated the occurrence of haemodynamic stroke while most of the residual strokes had a good to favourable prognosis.

Duplication of the great saphenous vein: a definition problem and implications for therapy.

BACKGROUND: In the literature there is a range from 1% to 20 % of duplication (up to 20%) of the great saphenous vein (GSV) reported, because there is a lack of an accurate definition of the GSV and objective parameters for an anatomical identification. OBJECTIVE: To investigate the frequency of true duplications of the GSV. MATERIALS AND METHODS: A systematic review of the literature, a retrospective analysis of duplex examinations, and a prospective study of duplex examinations to investigate the frequency of true duplications of the GSV. RESULTS: In the literature review, a great variety of definitions is used for duplication of the GSV. Before the consensus of the Union International de Phlébologie (UIP) in 2006, Only in a small number of studies, the definition of the GSV in the saphenous compartment between the fascial blades is mentioned. CONCLUSION: Phlebographic studies have been the criterion standard for the identification of venous anatomy. Now, duplex is regarded as the criterion standard for accurate detection of the veins. True duplication of the GSV is less common than the previous literature has suggested, namely 1.6% to 2%. It is recommended that the duplicated GSV should be treated to avoid an important risk of recurrence of venous insufficiency.

Complication rate and diagnostic yield of 515 consecutive ultrasound-guided biopsies of renal allografts and native kidneys using a 14-gauge Biopty gun.

Our objective was to evaluate the safety and diagnostic efficacy of the ultrasound-guided renal biopsy procedure using an automated biopsy device (Biopty gun) with a 14-gauge needle. Five hundred fifteen consecutive ultrasound-guided renal biopsies performed in two large university hospitals were retrospectively reviewed. Three hundred forty-five biopsies were performed on renal allografts and 170 on native kidneys. The tissue specimen was adequate for histological evaluation in 95.3% of the cases (94.8% in the transplanted kidney group, 96.5% in the native kidney group). The overall complication rate was 12.2% and was significantly higher in the native kidney group (19.4%) than in the renal allograft group (8.7%). Major complications occurred in 2.7% of the cases (2.9% of the renal allografts and 2.4% of the native kidney biopsies), including one procedure-related death and the loss of the renal allograft in two other patients. Minor complications were noted in 9.5% of the biopsies and there were significantly more in the group of the native kidneys (17.1%) than in the group of the transplanted kidneys (5.8%). Renal biopsy with an automated device using a 14-gauge needle has a high tissue recovery rate, but it is associated with a small risk of serious complications.