A predictive score for the result of carbapenem-resistant Enterobacterales and vancomycin-resistant enterococci screening

BACKGROUND

The duration of extensively drug-resistant bacteria (XDR) carriage depends on several factors for which the information can be difficult to recover.

AIM

To determine whether past screening and clinical results of patients can predict the results of subsequent screening.

METHODS

In total, 256 patients were retrospectively included from 10 healthcare centres in France from January 2014 to January 2022. We created a predictive clearance score, ranging from -5 to +7, that included the number of XDR species and the type of resistance detected in the sample, as well as the time from the last positive sample, the number of previous consecutive negative samples, and obtaining at least one negative PCR result in the collection. This score could be used for the upcoming rectal screening of a patient carrying an XDR as soon as the last screening sample was negative.

FINDINGS

The negative predictive value was >99% for score ≤0. The median time to achieve XDR clearance was significantly shorter for a score of 0 (443 days (259-705)) than that based on previously published criteria.

CONCLUSION

This predictive score shows high performance for the assessment of XDR clearance. Relative to previous guidelines, it could help to lift specific infection prevention and control measures earlier. Nevertheless, the decision should be made according to other factors, such as antimicrobial use and adherence to hand hygiene.

Environmental detection of SARS-CoV-2 in hospital rooms in different wards of an University Hospital

Background

Methods

Results

Conclusion

P–016 Using artificial intelligence to predict semen upgrading after microsurgical varicocele repair

Study question

Can we use artificial intelligence models to predict semen upgrading after microsurgical varicocele repair?

Summary answer

A machine learning model performed well in predicting clinically meaningful post-varicocelectomy semen upgrade using pre-operative hormonal, clinical, and semen analysis data.

What is known already

Varicocele repair is recommended in the presence of a clinical varicocele together with at least one abnormal semen parameter, and male infertility. Unfortunately, up to 50% of men who meet criteria for repair will not see meaningful benefit in outcomes despite successful surgery. Nomograms exist to help predict success, but these are based out of single-center databases, do not incorporate hormonal data, and are rarely designed to predict pre-defined, clinically meaningful improvements in semen parameters.

Study design, size, duration

Data were collected from an international, multi-center retrospective cohort. A total of 240 men were identified. Data from 160 men from Miami, USA and 80 men from Toronto, Canada were included. Data was collected from 2006 to 2020.

Participants/materials, setting, methods

We collected pre and postoperative clinical data following varicocele surgery. Clinical upgrading was defined as an increase in sperm concentration that would allow a couple to access new reproductive technologies/techniques. The tiers used for upgrading were 0–1million/cc (Intracytoplasmic Sperm Injection), 1–5 million (In Vitro Fertilization), 5–15 million (Intrauterine Insemination), and >15 million (Natural conception). Artificial intelligence models were trained and tested using R to predict which patients upgraded after surgery.

Main results and the role of chance

51% of men underwent bilateral varicocele repair. The majority of men had grade 2 varicocele on the left, and (when present) a grade 1 varicocele on the right. Overall, 47% of men experienced an upgrade following varicocele surgery, 47% did not change, and 6% downgraded. The data from Miami were used to create a random forest model for predicting clinically significant upgrade in sperm concentration. The most informative model parameters were preoperative FSH, sperm concentration, and surgical laterality. The model identified three clinical categories: men with unfavorable, intermediate, and favorable features to predict varicocele upgrade. On external validation using data from Toronto, the model accurately predicted upgrade in 87% of men with favorable features, and in 49% and 36% of men with intermediate and unfavorable features, respectively. Overall, the model performed well on external validation with an AUC of 0.72 and good calibration.

Calibration plots, using cross-validation, define how well the predicted probabilities match the actual probability of sperm concentration upgrade. The random forest model was run twelve times. All model characteristics are the mean of ten model runs with the highest and lowest performing runs removed.

The model was translated to an online calculator that can be used by clinicians.

Limitations, reasons for caution

One limitation to our study is that we were not able to predict total motile sperm count (TMSC), which has been shown to perform slightly better than concentration at predicting assisted reproduction outcomes. By focusing on clinically significant upgrading, this difference should be minimized.

Wider implications of the findings: Predicting the chances of clinically significant semen upgrading after varicocele repair is essential for patients and clinicians to understand. Several men undergo surgery with no subsequent benefit, which may lead to a delay in definitive treatment with IVF/IUI. Understanding their chances will help couples make better informed decisions moving forward.

Trial registration number

Not applicable

Biofilms in hospital effluents as a potential crossroads for carbapenemase-encoding strains

Bacterial resistance to carbapenem, which is mainly due to the successful dissemination of carbapenemase-encoding genes, has become a major health problem. Few studies have aimed to characterize the level of resistance in the environment, notably in hospital wastewater, which is a likely hotspot for exchange of antibiotic resistance genes. In this work, we looked for the presence of imipenem-resistant bacteria and imipenem in the effluent of the teaching hospital of Clermont-Ferrand, France. Selective growth of bacteria from 14-day old biofilms formed in the pipe sewer showed that 22.1% of the isolates were imipenem-resistant and identified as Aeromonas (n = 23), Pseudomonas (n = 10), Stenotrophomonas (n = 4) and Acinetobacter (n = 1). Fifteen of these strains harbored acquired carbapenemase-encoding genes bla_VIM (n = 11), bla_OXA-48 (n = 2), bla_GES (n = 1), bla_NDM (n = 1). All isolates also harbored associated resistances to aminoglycosides, fluoroquinolones and/or tetracyclin. S1-nuclease pulsed-field gel electrophoresis analysis of eight selected isolates showed that four of them harbored one to two plasmids of molecular weight between 48.5 Kb and 194 Kb. In vitro transformation assays evidenced the presence of bla_VIM and bla_NDM on plasmids with the bla_VIM harboring 80 Kb plasmid having conjugative capacity. The predicted environmental concentration of imipenem in the hospital effluent was 3.16 μg/L, suggesting that biofilm bacteria are subjected to sub-MICs of imipenem within the effluent. However, no imipenem molecule was detected in the hospital effluent, probably owing to its instability: in vitro assays indicated that imipenem's biological activity was no longer detectable after 45 h of storage. However, the predictive value of the hazard quotient relative to the development of resistance was >1.0 (HQr = 28.9 ± 1.9), which indicates a possible risk. The presence of carbapenemase-encoding genes in hospital effluent biofilm strains and their ability to transfer are therefore a potential hazard that should not be neglected and points to the need for monitoring antibiotic resistance in hospital wastewater.

The liver fatty acid binding protein--comparison of cavity properties of intracellular lipid-binding proteins

The crystal and solution structures of all of the intracellular lipid binding proteins (iLBPs) reveal a common beta-barrel framework with only small local perturbations. All existing evidence points to the binding cavity and a poorly delimited 'portal' region as defining the function of each family member. The importance of local structure within the cavity appears to be its influence on binding affinity and specificity for the lipid. The portal region appears to be involved in the regulation of ligand exchange. Within the iLBP family, liver fatty acid binding protein or LFABP, has the unique property of binding two fatty acids within its internalized binding cavity rather than the commonly observed stoichiometry of one. Furthermore, LFABP will bind hydrophobic molecules larger than the ligands which will associate with other iLBPs. The crystal structure of LFABP contains two bound oleate molecules and provides the explanation for its unusual stoichiometry. One of the bound fatty acids is completely internalized and has its carboxylate interacting with an arginine and two serines. The second oleate represents an entirely new binding mode with the carboxylate on the surface of LFABP. The two oleates also interact with each other. Because of this interaction and its inner location, it appears the first oleate must be present before the second more external molecule is bound.

Biochemical and crystallographic analyses of a portal mutant of the adipocyte lipid-binding protein

A number of crystallographic studies of the adipocyte lipid-binding protein have established that the fatty acid-binding site is within an internalized water-filled cavity. The same studies have also suggested the existence of a region physically distinct from the fatty acid-binding site which connects the cavity of the protein with the external solvent, hereafter referred to as the portal. In an effort to examine the portal region, we have used site-directed mutagenesis to introduce the mutations V32D/F57H into the murine ALBP cDNA. Mutant protein has been isolated, crystallized, and its stability and binding properties studied by biochemical methods. As assessed by guanidine-HCl denaturation, the mutant form exhibited a slight overall destabilization relative to the wild-type protein under both acid and alkaline conditions. Accessibility to the cavity in both the mutant and wild-type proteins was observed by stopped-flow analysis of the modification of a cavity residue, Cys117, by the sulfhydryl reactive agent 5, 5'-dithiobis(2-nitrobenzoic acid) at pH 8.5. Cys117 of V32D/F57H ALBP was modified 7-fold faster than the wild-type protein. The ligand binding properties of both the V32D/F57H mutant and wild-type proteins were analyzed using a fluorescent probe at pH 6.0 and 8.0. The apparent dissociation constants for 1-anilinonaphthalene-8-sulfonic acid were approximately 9-10-fold greater than the wild-type protein, independent of pH. In addition, there is a 6-fold increase in the Kd for oleic acid for the portal mutant relative to the wild-type at pH 8.0. To study the effect of pH on the double mutant, it was crystallized and analyzed in two distinct space groups at pH 4.5 and 6.4. While in general the differences in the overall main chain conformations are negligible, changes were observed in the crystallographic structures near the site of the mutations. At both pH values, the mutant side chains are positioned somewhat differently than in wild-type protein. To ensure that the mutations had not altered ionic conditions near the binding site, the crystallographic coordinates were used to monitor the electrostatic potentials from the head group site to the positions near the portal region. The differences in the electrostatic potentials were small in all regions, and did not explain the differences in ligand affinity. We present these results within the context of fatty acid binding and suggest lipid association is more complex than that described within a single equilibrium event.

Physiological consequences of DnaK and DnaJ overproduction in Escherichia coli

The physiological consequences of molecular chaperone overproduction in Escherichia coli are presented. Constitutive overproduction of DnaK from a multicopy plasmid containing large chromosomal fragments spanning the dnaK region resulted in plasmid instability. Co-overproduction of DnaJ with DnaK stabilized plasmid levels. To examine the effects of altered levels of DnaK and DnaJ in a more specific manner, an inducible expression system for dnaK and dnaJ was constructed and characterized. Differential rates of DnaK synthesis were determined by quantitative Western blot (immunoblot) analysis. Moderate levels of DnaK overproduction resulted in a defect in cell septation and formation of cell filaments, but co-overproduction of DnaJ overcame this effect. Further increases in the level of DnaK terminated culture growth despite increased levels of DnaJ. DnaK overproduction was found to be bacteriocidal, and this effect was also partially suppressed by DnaJ. The bacteriocidal effect was apparent only with cultures which were allowed to enter stationary phase, indicating that DnaK toxicity is growth phase dependent.