High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal.

BACKGROUND: Viral aetiologies are the most common cause of central nervous system (CNS) infections. Approximately one-half of CNS infections remain of undetermined origin. High-throughput sequencing (HTS) brought new perspectives to CNS infection investigations, allowing investigation of viral aetiologies with an unbiased approach. HTS use is still limited to specific clinical situations. OBJECTIVES: The aim of this review was to evaluate the contribution and pitfalls of HTS for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis in CNS patient samples. SOURCES: PubMed was searched from 1 January 2008 to 2 August 2018 to retrieve available studies on the topic. Additional publications were included from a review of full-text sources. CONTENT: Among 366 studies retrieved, 29 used HTS as a diagnostic technique. HTS was performed in cerebrospinal fluid and brain biopsy samples of 307 patients, including immunocompromised, immunocompetent paediatric, and adult cases. HTS was performed retrospectively in 18 studies and prospectively in 11. HTS led to the identification of a potential causal virus in 41 patients, with 11 viruses known and ten not expected to cause CNS infections. Various HTS protocols were used. IMPLICATIONS: The additional value of HTS is difficult to quantify because of various biases. Nevertheless, HTS led to the identification of a viral cause in 13% of encephalitis, meningoencephalitis, and meningitis cases in which various assays failed to identify the cause. HTS should be considered early in clinical management as a complement to routine assays. Standardized strategies and systematic studies are needed for the integration of HTS in clinical management.

Alterations of gut barrier and gut microbiota in food restriction, food deprivation and protein-energy wasting.

Increasing evidence shows that gut microbiota composition is related to changes of gut barrier function including gut permeability and immune function. Gut microbiota is different in obese compared to lean subjects, suggesting that gut microbes are also involved in energy metabolism and subsequent nutritional state. While research on gut microbiota and gut barrier has presently mostly focused on intestinal inflammatory bowel diseases and more recently on obesity and type 2 diabetes, this review aims at summarizing the present knowledge regarding the impact, in vivo, of depleted nutritional states on structure and function of the gut epithelium, the gut-associated lymphoid tissue (GALT), the gut microbiota and the enteric nervous system. It highlights the complex interactions between the components of gut barrier in depleted states due to food deprivation, food restriction and protein energy wasting and shows that these interactions are multidirectional, implying the existence of feedbacks.

Intrapartum Group B streptococcus detection by rapid polymerase chain reaction assay for the prevention of neonatal sepsis.

Group B streptococcus (GBS) is a leading cause of infectious neonatal morbidity and mortality. Timely and accurate identification of colonized mothers is imperative so that antibioprophylaxis can be implemented during labour to reduce the risk of neonatal sepsis. We planned our study to analyse the diagnostic accuracy of an intrapartum PCR assay to identify GBS-colonized women and to allow the implementation of correct (i.e. at least 4 h) intrapartum antibiotic prophylaxis based on the PCR results. We included 695 women in labour who were tested for rectovaginal GBS carriage by culture and PCR. Women were also screened at 35-37 weeks of gestation. Intrapartum GBS colonization was 19.3%. Assay sensitivity was 81.0% for antenatal culture and 85.0% for intrapartum PCR; p 0.72. GBS colonization (n = 107) was known at least 4 h before delivery in 68 (64%) and 73 (68%) women based on antenatal culture and intrapartum PCR, respectively. Among 43 women delivering preterm, correct status was known at least 4 h before delivery in 10 (23%) and 32 (74%) women according to antenatal culture and intrapartum PCR, respectively. These results support the concept that GBS screening can be performed routinely during labour in a clinical setting. The intrapartum approach is at least as accurate as the antenatal screening, with the additional advantage of identifying women delivering preterm or not followed during pregnancy.

Cost-effectiveness of universal MRSA screening on admission to surgery.

Policy-makers have recommended universal screening to reduce nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infection. Risk profiling of MRSA carriers and rapid PCR tests are now available, yet cost-effectiveness data are limited. The present study assessed the cost-effectiveness of universal PCR screening on admission to surgery. A decision analysis model from the hospital perspective compared costs and the probability of any MRSA infection across three strategies: (i) PCR screening; (ii) screening for risk factors (prior hospitalization or antibiotic use) combined with pre-emptive isolation and contact precautions pending chromogenic agar results; and (iii) no screening. Clinical data were taken from studies at a Swiss teaching hospital as well as from published literature. Costs were derived from hospital accounting systems. Compared to no screening, the PCR strategy resulted in higher costs (CHF 10503 vs. 10358) but a lower infection probability (0.0041 vs. 0.0088), producing a base-case incremental cost-effectiveness ratio of CHF 30784 per MRSA infection avoided. The risk factor strategy was more costly yet less effective than PCR, although, after varying epidemiologic inputs, the costs and effects of both screening strategies were similar. Sensitivity analyses suggested that on-admission prevalence of MRSA carriage predicts cost-effectiveness, alongside the probability of cross-transmission, and the costs of MRSA infection, screening and contact precautions. Although reducing the risk of MRSA infection, universal PCR screening is not strongly cost-effective at our centre. However, local epidemiology plays a critical role. Settings with a higher prevalence of MRSA colonization may find universal screening cost-effective and, in some cases, cost-saving.

Risk factors for treatment failure in orthopedic device-related methicillin-resistant Staphylococcus aureus infection.

The purpose of this study was to determine the clinical and microbiological risk factors for treatment failure of methicillin-resistant Staphylococcus aureus (MRSA) orthopedic device-related infection (ODRI). A retrospective cohort study of patients with MRSA ODRI who were treated at Geneva University Hospitals between 2000 and 2008 was undertaken. Stored MRSA isolates were retrieved for genetic characterization and determination of the vancomycin minimum inhibitory concentration (MIC). Fifty-two patients were included, of whom 23 (44%) had joint arthroplasty and 29 (56%) had osteosynthesis. All 41 of the retrieved MRSA isolates were susceptible to vancomycin (MIC

Immuno-detection of Staphylococcus aureus biofilm on a cochlear implant.

CASE PRESENTATION: A 46-year-old man suffering from progressive deafness since childhood received a Clarion 90 K cochlear implant with the HiRes preformed electrode in his left ear in October 2006. A persistent Staphylococcus aureus infection failed to be treated with corticoids, amoxicillin/ clavulanate, ciprofloxaxin, and rifampin. The processor was removed on July 2007. INTERVENTIONS: The removed cochlear implant processor was treated with different reagents, with the aim of detecting a S. aureus and S. aureus biofilm: (1) fluorescein-coupled Fc of anti-human serum, (2) polyclonal anti-polysaccharide intercellular adhesion antibodies coupled to Alexa Fluor 568 goat anti-rabbit immunoglobulin (Ig)G, (3) crystal violet, (4) methylene blue, (5) acridine orange, (6) Gram stain, and (7) live/dead fluorescent stain. RESULTS: S. aureus and the major constituent of the S. aureus biofilm, the polysaccharide intercellular adhesion, were detected on the surface of the implant. S. aureus was isolated after a simple contact between the implant and a solid growth medium. The ability of the isolated S. aureus strain to produce biofilm in vitro was confirmed. INTERPRETATION: S. aureus biofilm was documented on the implant. Initial bacterial colonization could be related to the pocket of the removable magnet. Colonies of S. aureus without biofilm were found attached to the electrode wire. CONCLUSION: We report one case of a S. aureus biofilm infection documented on a cochlear implant, as assessed by immuno-microscopy. The biofilm was likely responsible for the persistent infection which manifested for many months after the implant surgery and could explain the unusual bacterial phenotypic resistance against administered antimicrobial agents.

Intracellular residency is frequently associated with recurrent Staphylococcus aureus rhinosinusitis.

AIM: The prevalence of intracellular Staphylococcus aureus organisms in the nasal mucosa of patients with recurrent infectious rhinosinusitis episodes was studied. METHOD: Twenty-seven consecutive adult patients who failed medical management of chronic rhinosinusitis (CRS) of multiple origins, associated or not with nasal polyposis, were consecutively enrolled for endonasal sinus surgery (including partial middle turbinectomy, middle antrostomy, ethmoidectomy, sphenoidotomy) and followed for a 12-month post-operative period. RESULTS: Seventeen of these patients showed the presence of intracellular S. aureus as detected by confocal laser scan immunofluorescence microscopy in epithelial cells of surgical intranasal biopsy specimens. Nine of the patients with and two without intracellular bacteria yielded S. aureus in endoscopically guided cultures of middle meatus secretions, despite the recent administration of prophylactic antibiotics. Eleven of the 17 patients with intracellular S. aureus relapsed for rhinosinusitis within the 12-month follow-up period. Molecular typing of sequential S. aureus isolates demonstrated the persistence of unique patient-specific S. aureus clonotypes in nine of the patients with intracellular bacteria during the 12-month follow-up. CONCLUSION: The presence of intracellular S. aureus in epithelial cells of the nasal mucosa is a significant risk factor for recurrent episodes of rhinosinusitis due to persistent bacterial clonotypes, which appear refractory to antimicrobial and surgical therapy.

A novel H(+) conductance in eosinophils: unique characteristics and absence in chronic granulomatous disease.

Efficient mechanisms of H(+) ion extrusion are crucial for normal NADPH oxidase function. However, whether the NADPH oxidase-in analogy with mitochondrial cytochromes-has an inherent H(+) channel activity remains uncertain: electrophysiological studies did not find altered H(+) currents in cells from patients with chronic granulomatous disease (CGD), challenging earlier reports in intact cells. In this study, we describe the presence of two different types of H(+) currents in human eosinophils. The "classical" H(+) current had properties similar to previously described H(+) conductances and was present in CGD cells. In contrast, the "novel" type of H(+) current had not been described previously and displayed unique properties: (a) it was absent in cells from gp91- or p47-deficient CGD patients; (b) it was only observed under experimental conditions that allowed NADPH oxidase activation; (c) because of its low threshold of voltage activation, it allowed proton influx and cytosolic acidification; (d) it activated faster and deactivated with slower and distinct kinetics than the classical H(+) currents; and (e) it was approximately 20-fold more sensitive to Zn(2+) and was blocked by the histidine-reactive agent, diethylpyrocarbonate (DEPC). In summary, our results demonstrate that the NADPH oxidase or a closely associated protein provides a novel type of H(+) conductance during phagocyte activation. The unique properties of this conductance suggest that its physiological function is not restricted to H(+) extrusion and repolarization, but might include depolarization, pH-dependent signal termination, and determination of the phagosomal pH set point.

Electron currents generated by the human phagocyte NADPH oxidase.

Electron transport across biological membranes is a well-known feature of bacteria, mitochondria and chloroplasts, where it provides motive forces for vectorial transport processes. In contrast, electron transport is generally not found in the plasma membrane of eukaryotic cells, possibly because it would interfere with electric processes at the plasma membrane. An exception is provided by the phagocyte NADPH oxidase, which generates superoxide (O2.-) through electron transfer from cytosolic NADPH to extracellular oxygen. The enzyme is essential for host defence, and patients with chronic granulomatous disease, who lack the functional enzyme, suffer from severe infections. It has been suggested that electron transfer by the NADPH oxidase might be electrogenic. Here we demonstrate, using the whole-cell patch-clamp technique, the generation of electron currents by the NADPH oxidase in human eosinophil granulocytes. The currents were absent in granulocytes of sufferers of chronic granulomatous disease and under conditions of low oxygen. Generation of electron currents across the plasma membrane of eukaryotic cells has not been observed previously and might be-independently of the generation of superoxide-a physiologically relevant function of the phagocyte NADPH oxidase.

Highly supralinear feedback inhibition of Ca2+ uptake by the Ca2+ load of intracellular stores.

Net Ca2+ uptake into intracellular Ca2+ stores of homogenized cells is transient, even when the extravesicular Ca2+ concentration is kept constant. To study the mechanism underlying the phenomenon, we have investigated 45Ca2+ uptake by HL-60 cell homogenates. The initial rate of Ca2+ uptake as well as the final amount of stored Ca2+ were a function of the extravesicular Ca2+ concentration. However, Ca2+ uptake stopped independently of the extravesicular Ca2+ concentration after approximately 10 min. Studies using Ca2+-ATPase inhibitors demonstrated that the transient nature of the net uptake was not due to Ca2+ efflux. Monovalent cation ionophores did not influence the Ca2+ uptake curves, excluding a relevant involvement of pH and membrane potential. Together with the observation of a continued Ca2+ uptake in the presence of the intralumenal Ca2+ chelator oxalate, these results strongly suggest a feedback inhibition of Ca2+ uptake by the Ca2+ load of intracellular stores. The concentration-inhibition relationship between the Ca2+ load and the rate of Ca2+ uptake was highly supralinear (slope factor >/= 4). IC50 and maximum of the dose-inhibition curve, but not the slope factor were a function of the extravesicular free Ca2+ concentration. A series of three logistic equations derived from our data allowed an appropriate description of the behavior of Ca2+ uptake. Our results suggest, in addition to its well known activation by cytosolic Ca2+ concentration, a highly supralinear feedback inhibition of Ca2+ uptake by the Ca2+ load of intracellular stores. The steepness of the feedback inhibition might have a profound effect on spatial and temporal behavior of the Ca2+ signal.

[Characterization of Ca2+ influx in human neutrophils using the patch clamp technique]. / Caractérisation de l'influx Ca2+ dans les neutrophiles humains par la technique du patch clamp.

In neutrophils, Ca2+ influx across the plasma membrane occurs in response to a variety of agonists. It plays an important role in the regulation of neutrophil function, in particular exocytosis and release of inflammatory mediators. Using the combination of patch clamp and microfluorimetry techniques, we have found the following characteristics of neutrophil Ca2+ influx: (a) neutrophils do not possess voltage-dependent Ca2+ channels; (b) Ca2+ influx is activated by depletion of intracellular Ca2+ stores, either by Ins(1,4,5)P3, or by Ca(2+)-ATPase inhibitors; (c) Ca2+ influx is not activated by [Ca2+]i elevations and not associated with the activation of non-selective cation channels; (d) Ca2+ influx is associated with the activation of a small, voltage-independent current through a highly Ca(2+)-selective conductance. The current was only seen upon depletion of intracellular Ca2+ stores and showed a pharmacological profile similar to the fluorimetrically detected Ca2+ influx.