PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level

Plasmid prediction may be of great interest when studying bacteria of medical importance such as Enterobacteriaceae as well as Staphylococcus aureus or Enterococcus. Indeed, many resistance and virulence genes are located on such replicons with major impact in terms of pathogenicity and spreading capacities. Beyond strain outbreak, plasmid outbreaks have been reported in particular for some extended-spectrum beta-lactamase- or carbapenemase-producing Enterobacteriaceae. Several tools are now available to explore the ‘plasmidome’ from whole-genome sequences with various approaches, but none of them are able to combine high sensitivity and specificity. With this in mind, we developed PlaScope, a targeted approach to recover plasmidic sequences in genome assemblies at the species or genus level. Based on Centrifuge, a metagenomic classifier, and a custom database containing complete sequences of chromosomes and plasmids from various curated databases, PlaScope classifies contigs from an assembly according to their predicted location. Compared to other plasmid classifiers, PlasFlow and cBar, it achieves better recall (0.87), specificity (0.99), precision (0.96) and accuracy (0.98) on a dataset of 70 genomes of Escherichia coli containing plasmids. In a second part, we identified 20 of the 21 chromosomal integrations of the extended-spectrum beta-lactamase coding gene in a clinical dataset of E. coli strains. In addition, we predicted virulence gene and operon locations in agreement with the literature. We also built a database for Klebsiella and correctly assigned the location for the majority of resistance genes from a collection of 12 Klebsiella pneumoniae strains. Similar approaches could also be developed for other well-characterized bacteria.

Liver transplantation for alcoholic hepatitis: A systematic review with meta-analysis

Background

The rate of alcohol relapse among patients who underwent liver transplantation for alcoholic hepatitis (AH) is not precisely known.

Aim

Synthesize the available evidence on liver transplantation for AH to assess alcohol relapse and 6-month survival.

Methods

Meta-analysis of trials evaluating liver transplantation for AH, either clinically severe or diagnosed on the explant.

Results

Eleven studies were included. The pooled estimate rate for alcohol relapse was 0.22 (95% CI = 0.12–0.36) in overall analysis with high heterogeneity between studies (I² = 76%), 0.20 (95% CI = 0.07–0.43) in the subgroup analysis including patients with clinically severe AH (I² = 84%), 0.14 (95% CI = 0.08–0.23) among patients with clinically severe AH in sensitivity analysis excluding the discrepant studies that did not use stringent selection criteria for liver transplantation (I² = 0%), and 0.15 (95% CI = 0.07–0.27) for recurrent harmful alcohol consumption among patients with clinically severe AH (I² = 3%). The risk of alcohol relapse was not different between AH transplanted patients and patients with alcoholic cirrhosis who underwent elective liver transplantation in sensitivity analysis excluding the discrepant studies (OR = 1.68, 95%CI = 0.79–3.58, p = 0.2, I² = 16%). The pooled estimate rate for 6-month survival was 0.85 (95% CI = 0.77–0.91, I² = 49%), and 0.80 among patients transplanted for clinically severe AH (95% CI = 0.69–0.88, I² = 30%). AH transplanted patients had similar 6-month survival to patients with alcoholic cirrhosis who underwent elective liver transplantation (OR = 2.00, 95% CI = 0.95–4.23, p = 0.07, I² = 0%).

Conclusion

Using stringent selection criteria, 14% of patients with clinically severe AH have alcohol relapse after liver transplantation. The percentage of alcohol relapse of AH transplanted patients is similar than that of patients who underwent elective liver transplantation.

Endoscopic and surgical ampullectomy for non-invasive ampullary tumors: Short-term outcomes

Non-invasive ampullary tumors, may be treated with endoscopic (EA) or surgical ampullectomy (SA). However, evidence on the morbidity of these techniques remains limited. This pilot study aimed to assess and compare morbidity of EA and SA. Patients undergoing EA or SA for non-invasive ampullary tumors were retrospectively analyzed and compared. Outcomes were postoperative complications graded with Clavien Classification and Comprehensive Complication Index (CCI), and length of stay (LoS). A review of the literature was performed to propose an evidence-based algorithm to treat ampullary tumors. A total of 11 EA and 19 SA were identified and analyzed. EA was associated with shorter intervention (51 vs. 191 min, p < 0.001) and decreased blood loss (0 vs. 100 mL, p < 0.001). Postoperative complications were more frequent after surgery compared to endoscopy (9% vs. 68%, p = 0.002). Surgical patients showed a higher CCI (0 vs. 8.7, p < 0.001). LoS was reduced in patients undergoing endoscopy (0 vs. 14 days, p < 0.001), with comparable readmissions rates (p = 0.126). Necessity of subsequent treatment was more frequent after endoscopic, compared to SA (5 vs. 1, p = 0.016). EA was associated with lower morbidity than SA and appeared as an appropriate first-line treatment for non-invasive ampullary tumors. SA remains a valuable alternative after EA failure.

Charge breeder for the SPIRAL1 upgrade: Preliminary results

In the framework of the SPIRAL1 upgrade under progress at the GANIL lab, the charge breeder based on a LPSC Phoenix ECRIS, first tested at ISOLDE has been modified to benefit of the last enhancements of this device from the 1+/n+ community. The modifications mainly concern the 1 + optics, vacuum techniques, and the RF-buffer gas injection into the charge breeder. Prior to its installation in the midst of the low energy beam line of the SPIRAL1 facility, it has been decided to qualify its performances and several operation modes at the test bench of LPSC lab. This contribution shall present preliminary results of experiments conducted at LPSC concerning the 1 + to n+ conversion efficiencies for noble gases as well as for alkali elements and the corresponding transformation times.

How do cumulative live birth rates and cumulative multiple live birth rates over complete courses of assisted reproductive technology treatment per woman compare among registries?

STUDY QUESTION

How do the national cumulative (multiple) live birth rates over complete assisted reproduction technology (ART) courses of treatment per woman in Belgium compare to those in other registries?

SUMMARY ANSWER

Cumulative live birth rates (CLBRs) remain high with a low cumulative multiple live birth rate when compared with other registries and publications.

WHAT IS KNOWN ALREADY

In ART, a reduction in the multiple live birth rate could be achieved by reducing the number of embryos transferred. It has been shown that by doing so, live birth rates per cycle were maintained, particularly when the augmentation effect of attached frozen-thawed cycles was considered.

STUDY DESIGN, SIZE, DURATION

A retrospective cohort study included all patients with a Belgian national insurance number who were registered in the national ART registry (Belrap) and who started a first fresh ART cycle between 1 July 2009 until 31 December 2011 with follow up until 31 December 2012. We analysed 12 869 patients and 38 008 cycles (both fresh and attached frozen cycles).

PARTICIPANTS, MATERIALS, SETTINGS, METHODS

CLBRs per patient who started a first ART cycle including fresh and consecutive frozen cycles leading to a live birth. Conservative estimates of cumulative live birth assumed that patients who did not return for treatment had no chance of achieving an ART-related live birth, whereas optimal estimates assumed that women discontinuing treatment would have the same chance of achieving a live birth as those continuing treatment. A maximum of six fresh ART cycles with corresponding frozen cycles was investigated and compared with other registries and publications.

MAIN RESULTS AND ROLE OF CHANCE

The CLBR was age dependent and declined from 62.9% for women <35 years, to 51.4% for women 35-37 years, to 34.1% for women 38-40 years and 17.7% for women 41-42 years in the conservative analysis after six cycles. In the optimal estimate, the CLBR declined from 85.9% for women <35 years, to 72.0% for women 35-37 years, to 50.4% for women 38-40 years and 36.4% for women 41-42 years. The cumulative multiple live birth rates for the whole population were 5.1 and 8.6% for the conservative and optimal estimate, respectively.

LIMITATIONS, REASONS FOR CAUTION

Conservative and optimal estimates use assumptions for the whole ART population and do not take the individual patient into account.

WIDER IMPLICATIONS OF THE FINDINGS

These data reinforce the validity of the Belgian model of coupling reimbursement of ART costs to a restriction in the number of embryos transferred. Our data can improve decision-making in medical ART practice both on the patient level and for society at large and could provide health care takers and insurance companies with a valid model.

STUDY FUNDING COMPETING INTERESTS

none.