Measures to eradicate multidrug-resistant organism outbreaks: How much does it cost?

This study aimed to assess the economic burden of infection control measures that succeeded in eradicating multidrug-resistant organisms (MDROs) in emerging epidemic contexts in hospital settings. The MEDLINE, EMBASE and Ovid databases were systematically interrogated for original English-language articles detailing costs associated with strict measures to eradicate MDROs published between 1 January 1974 and 2 November 2014. This study was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. Overall, 13 original articles were retrieved reporting data on several MDROs, including glycopeptide-resistant enterococci (n = 5), carbapenemase-producing Enterobacteriacae (n = 1), methicillin-resistant Staphylococcus aureus (n = 5), and carbapenem-resistant Acinetobacter baumannii (n = 2). Overall, the cost of strict measures to eradicate MDROs ranged from €285 to €57 532 per positive patient. The major component of these overall costs was related to interruption of new admissions, representing €2466 to €47 093 per positive patient (69% of the overall mean cost; range, 13-100%), followed by mean laboratory costs of €628 to €5849 (24%; range, 3.3-56.7%), staff reinforcement costs of €6204 to €148 381 (22%; range, 3.3-52%), and contact precautions costs of €166 to €10 438 per positive patient (18%; range, 0.7-43.3%). Published data on the economic burden of strict measures to eradicate MDROs are limited, heterogeneous, and weakened by several methodological flaws. Novel economic studies should be performed to assess the financial impact of current policies, and to identify the most cost-effective strategies to eradicate emerging MDROs in healthcare facilities

Inheritance patterns in citation networks reveal scientific memes

Memes are the cultural equivalent of genes that spread across human culture by means of imitation. What makes a meme and what distinguishes it from other forms of information, however, is still poorly understood. Our analysis of memes in the scientific literature reveals that they are governed by a surprisingly simple relationship between frequency of occurrence and the degree to which they propagate along the citation graph. We propose a simple formalization of this pattern and we validate it with data from close to 50 million publication records from the Web of Science, PubMed Central, and the American Physical Society. Evaluations relying on human annotators, citation network randomizations, and comparisons with several alternative approaches confirm that our formula is accurate and effective, without a dependence on linguistic or ontological knowledge and without the application of arbitrary thresholds or filters.Comment: 8 two-column pages, 5 figures; accepted for publication in Physical Review

Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb

<p>Abstract</p> <p>Background</p> <p>A protein annotation database, such as the Universal Protein Resource knowledge base (UniProtKb), is a valuable resource for the validation and interpretation of predicted 3D structure patterns in proteins. Existing studies have focussed on point mutation extraction methods from biomedical literature which can be used to support the time consuming work of manual database curation. However, these methods were limited to point mutation extraction and do not extract features for the annotation of proteins at the residue level.</p> <p>Results</p> <p>This work introduces a system that identifies protein residues in MEDLINE abstracts and annotates them with features extracted from the context written in the surrounding text. MEDLINE abstract texts have been processed to identify protein mentions in combination with taxonomic species and protein residues (F1-measure 0.52). The identified protein-species-residue triplets have been validated and benchmarked against reference data resources (UniProtKb, average F1-measure of 0.54). Then, contextual features were extracted through shallow and deep parsing and the features have been classified into predefined categories (F1-measure ranges from 0.15 to 0.67). Furthermore, the feature sets have been aligned with annotation types in UniProtKb to assess the relevance of the annotations for ongoing curation projects. Altogether, the annotations have been assessed automatically and manually against reference data resources.</p> <p>Conclusion</p> <p>This work proposes a solution for the automatic extraction of functional annotation for protein residues from biomedical articles. The presented approach is an extension to other existing systems in that a wider range of residue entities are considered and that features of residues are extracted as annotations.</p

Mycobacterial PIMs Inhibit Host Inflammatory Responses through CD14-Dependent and CD14-Independent Mechanisms

Mycobacteria develop strategies to evade the host immune system. Among them, mycobacterial LAM or PIMs inhibit the expression of pro-inflammatory cytokines by activated macrophages. Here, using synthetic PIM analogues, we analyzed the mode of action of PIM anti-inflammatory effects. Synthetic PIM1 isomer and PIM2 mimetic potently inhibit TNF and IL-12 p40 expression induced by TLR2 or TLR4 pathways, but not by TLR9, in murine macrophages. We show inhibition of LPS binding to TLR4/MD2/CD14 expressing HEK cells by PIM1 and PIM2 analogues. More specifically, the binding of LPS to CD14 was inhibited by PIM1 and PIM2 analogues. CD14 was dispensable for PIM1 and PIM2 analogues functional inhibition of TLR2 agonists induced TNF, as shown in CD14-deficient macrophages. The use of rough-LPS, that stimulates TLR4 pathway independently of CD14, allowed to discriminate between CD14-dependent and CD14-independent anti-inflammatory effects of PIMs on LPS-induced macrophage responses. PIM1 and PIM2 analogues inhibited LPS-induced TNF release by a CD14-dependent pathway, while IL-12 p40 inhibition was CD14-independent, suggesting that PIMs have multifold inhibitory effects on the TLR4 signalling pathway

Assessment of the Performance of the Aptima Bacterial Vaginosis Assay Over a 3-Month Period in a French Hospital

International audienceBacterial vaginosis (BV) is the most common cause of abnormal vaginal discharge. BV represents a dysbiosis with the acquisition of a diverse community of anaerobic bacteria and a reduction in lactobacilli burden. Our objective was to evaluate the Aptima BV assay kit for the diagnosis of BV. From May to August 2019, we enrolled outpatients and inpatients, including nonpregnant women above 18 with vaginosis symptoms, consulting at Nantes University hospital. The Aptima BV assay measures the loads of Gardnerella vaginalis, Atopobium vaginae, and Lactobacillus species in relation to overall bacterial load. The Aptima BV assay was compared to Nugent scoring (NS). A total of 456 women were enrolled, and 347 patients met the inclusion criteria with data available for the analysis. NS was used to classify the samples and 144 (41.5%) samples were classified as normal (NS = 0-3), 45 (13%) as BV (NS = 7-10), 38 (11%) presented an intermediate vaginal microbiota (3 < NS < 7), 79 (22.7%) had various bacteria (excluding vaginal flora), 29 (8.3%) had insufficient bacterial density, and 12 (3.5%) had a predominance of yeasts. The Aptima BV kit displayed a sensitivity of 91.1% and specificity of 94.4% with a positive predictive value (PPV) of 83.7% and a negative predictive (NPV) value of 97.1%. The results of this monocentric retrospective study show that Aptima BV kit has a good diagnostic correlation compared to standard of care for dysbiotic diagnosis cases. IMPORTANCE The possibility exists of the involvement of a new molecular test in the routine algorithm of bacterial vaginosis diagnosis in microbiology laboratories. This manuscript reports on our experience, and we propose an organization combining Nugent scoring and molecular testing, especially for intermediate Nugent scores

Characteristics and outcome of multidrug-resistant tuberculosis in a low-incidence area

International audienceObjectives - To characterize multidrug-resistant tuberculosis (MDR-TB) patients treated in a low endemic area in France and to determine risk factors for resistance. We also analyzed the efficacy and tolerability of tuberculosis (TB) treatment. Methods - Between 2002-2013, all MDR-TB patients diagnosed in western France (hospitals belonging to the GERICCO group) were retrospectively included, with a follow-up period running until 2016. A case-control study (1:2), matched according to age, sex, and year of diagnosis, was performed to assess socio-demographic and clinical data, treatment strategies, and outcomes for the MDR-TB patients and controls treated for drug-susceptible tuberculosis during the same period. Results - Of 134 TB patients, 44 were MDR-TB and 90 were drug-susceptible TB. Of the 44 MDR-TB patients (35 MDR and nine extensively drug-resistant [XDR]), 33 (75%) were males; the median age was 33 years; and 27 (61%) were born in Eastern Europe. Prior treatment failure was more frequently reported for XDR-TB (8/9) in Georgian patients. In multivariate analysis, risk contacts and prior TB history were associated with MDR-TB. Treatment failure was associated with MDR/XDR-TB and miliary TB. Conclusion - In western France, MDR-TB more frequently occurred in recent migrants from high-risk countries with a previous history of at-risk contact with other MDR-TB patients or previous TB treatment failure