Assessment of VITEK® MS IVD database V3.0 for identification of Nocardia spp. using two culture media and comparing direct smear and protein extraction procedures.

We assessed the performance of the VITEK® MS IVD V3.0 matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI-ToF MS) V3.0 database for the identification of Nocardia spp. as compared with targeted DNA sequencing. A collection of 222 DNA sequence-defined Nocardia spp. strains encompassing 18 different species present or not in the database was tested. Bromocresol purple agar (BCP) and Columbia agar +5% sheep's blood (COS) culture media were used together with two different preparation steps: direct smear and a "3 attempts" procedure that covered (1) spotting of an extract, (2) new spotting of the same extract, and (3) spotting of a new extract. The direct smear protocol yielded low correct identification rates (≤ 15% for both media) whereas protein extraction yielded correct identification results (> 67% regardless of the media used.). The use of 2 additional attempts using repeat or new extracts increased correct identification rates to 87% and 91% for BCP and COS, respectively. When using the 3 attempts procedure, the best identification results, independent of media types, were obtained for N. farcinica and N. cyriacigeorgica (100%). Identification attempts 2 and 3 allowed to increase the number of correct identifications (BCP, +20%; COS, +13%). The enhancement in performance during attempts 2 and 3 was remarkable for N. abscessus (81% for both media) and low prevalence species (BCP, 70%; COS, 85%). Up to 3.4% and 2.4% of the strains belonging to species present in the database were misidentified with BCP and COS media, respectively. In 1.9% of the cases for BCP and 1.4% for COS, these misidentifications concerned a species belonging to the same phylogenetic complex. Concerning strains that are not claimed in the V3.0 database, N. puris and N. goodfellowi generated "No identification" results and 100% of the strains belonging to N. arthritidis, N.cerradoensis, and N. altamirensis yielded a misidentification within the same phylogenetic complex. Vitek® MS IVD V3.0 is an accurate and useful tool for identification of Nocardia spp.

Emergence of Clostridium difficile tcdC variant 078 in Marseille, France.

The purpose of this investigation was to evaluate the epidemiology of hypervirulent Clostridium difficile ribotypes from January 2013 to February 2017 in the Marseille area of southern France. By using the Xpert Clostridium difficile Epi polymerase chain reaction (PCR) assay and sequencing the tcdC gene, we characterised C. difficile isolates from symptomatic patients diagnosed with C. difficile infection (CDI) in Marseille university hospitals. We first tested retrospectively 278 C. difficile samples isolated from January 2013 to December 2014 and observed a high prevalence of isolates with tcdC mutations and deletions previously described in both hypervirulent ribotypes RT027 and RT078 (16.4% and 10.7%, respectively). We highlighted the co-circulation of these two hypervirulent C. difficile tcdC variants (tV) with distinct epidemiological characteristics. While an RT027 outbreak occurred mainly as healthcare-associated infection in the elderly, CDI caused by tV078 occurred mainly in a younger population as community-associated infection. From January 2016, a systematic survey of these two hypervirulent C. difficile ribotypes revealed the emergence of CDI caused by tV078, currently being more prevalent than RT027 in the Marseille area. The present study is the first report of the emergence of CDI caused by tV078 in southern France. We showed the simultaneous circulation and sequential spread of hypervirulent ribotypes, such as RT027 and tV078. This emphasises the need for an efficient surveillance system for CDI with ribotyping and an optimised management of CDI caused by hypervirulent strains.

Multigene testing of moderate-risk genes: be mindful of the missense.

BACKGROUND: Moderate-risk genes have not been extensively studied, and missense substitutions in them are generally returned to patients as variants of uncertain significance lacking clearly defined risk estimates. The fraction of early-onset breast cancer cases carrying moderate-risk genotypes and quantitative methods for flagging variants for further analysis have not been established. METHODS: We evaluated rare missense substitutions identified from a mutation screen of ATM, CHEK2, MRE11A, RAD50, NBN, RAD51, RINT1, XRCC2 and BARD1 in 1297 cases of early-onset breast cancer and 1121 controls via scores from Align-Grantham Variation Grantham Deviation (GVGD), combined annotation dependent depletion (CADD), multivariate analysis of protein polymorphism (MAPP) and PolyPhen-2. We also evaluated subjects by polygenotype from 18 breast cancer risk SNPs. From these analyses, we estimated the fraction of cases and controls that reach a breast cancer OR≥2.5 threshold. RESULTS: Analysis of mutation screening data from the nine genes revealed that 7.5% of cases and 2.4% of controls were carriers of at least one rare variant with an average OR≥2.5. 2.1% of cases and 1.2% of controls had a polygenotype with an average OR≥2.5. CONCLUSIONS: Among early-onset breast cancer cases, 9.6% had a genotype associated with an increased risk sufficient to affect clinical management recommendations. Over two-thirds of variants conferring this level of risk were rare missense substitutions in moderate-risk genes. Placement in the estimated OR≥2.5 group by at least two of these missense analysis programs should be used to prioritise variants for further study. Panel testing often creates more heat than light; quantitative approaches to variant prioritisation and classification may facilitate more efficient clinical classification of variants.

The Wood equation allows consistent fitting of individual antibody-response profiles of Zika virus or SARS-CoV-2 infected patients.

Antibody kinetic curves obtained during a viral infection are often fitted using aggregated patient data, hiding the heterogeneity of individual humoral immune responses. Individual antibody responses can be modeled using the Wood equation and grouped according to their profile. Such modeling takes into account several important kinetic parameters, such as the day when antibody detection becomes positive [daypos], the day of the maximal response [daymax], the maximum antibody level [levelmax], and the day when antibody detection becomes negative [dayneg]. Potential associations between these profiles and studied factors can then be tested.

Experiences of parents and caregivers in pediatric intensive care units: A qualitative study.

BACKGROUND: In pediatric intensive care units (PICUs), parents and healthcare professionals attend to children who verbally and non-verbally express their pain and suffering, fears, anxieties, desires, and wishes in complex intensive care situations. What can we learn from these experiences to improve the way we can take care of and support children? OBJECTIVES: The main objective of this clinical ethics study was to focus on the experience stories of parents during their child's hospitalization in a PICU, to analyze their discourse, and to propose an ethical perspective. METHOD: The current research collects the experience reports of parents during their child's hospitalization in a PICU and those of the caregivers who treated them. A total of 17 semi-directive interviews were conducted in the PICU of the Nantes University Hospital from November 2017 to June 2019. Each interview lasted around 1 h. The main results of our study are analyzed and informed by the four ethical principles of T. Beauchamp and J. Childress: autonomy, beneficence, non-maleficence, and justice. RESULTS: The interviews highlighted the difficulties encountered by parents during the hospitalization of their children, such as the distance between their home and the hospital, the technicality of PICU environment, and the difficulty in finding their place as parents. For medical and paramedical teams, their main concerns are undoubtedly to improve the coherence and continuity of their stand toward parents, to promote parental autonomy, and to remain fully aware of the profound existential changes that the child's illness brings about for parents: It is the caregivers' duty to take this into account and to respect the parents' rhythm as much as possible. CONCLUSIONS: The main disagreements between healthcare teams and parents, where they exist, are communication problems that are easily controlled, for the most part, by caregivers.

Modeling and evaluation of compliance to water quality regulations in bathing areas on the Daoulas catchment and estuary (France).

The microbiological quality of waters in estuaries determines their acceptability for recreational uses. Microbiological contamination often results from urban wastewater discharges or non-point source pollution (manure spreading), and can cause bathing zones to be closed. European regulations (EC/7/2006) have proposed standards (500 E. coli/100 ml) for the acceptability areas for bathing. In this study, two models were associated to simulate contamination: SWAT on a catchment and MARS 2D in the downstream estuary. After river flow calibration and validation, two scenarios were simulated in SWAT, and E. coli fluxes obtained at the main outlet of the catchment were then introduced into MARS 2D to follow E. coli concentrations in the estuary. An annual evaluation of compliance to bathing area water quality standards was then calculated, linked with daily rainfall classes. Water quality in the estuary was below the standard on 13 days, including 5 days with rainfall superior to 10 mm, due to faecal contamination from soil leaching by rain, and 5 days with rainfall ranging from 0.1 to 5 mm/day, due to the high frequency of this level of rainfall. To conclude, this study allowed us to demonstrate the efficiency of models to gain a better understanding on water quality degradation factors.

Peripherally inserted central catheters: a hidden emerging cause of infection outbreaks.

In our institution, between January 2010 and December 2017, 15 140 peripherally inserted central catheters (PICCs) were inserted in 12 314 patients. Using time-series analysis to evaluate the annual historical trend (AHT), we observed a significant increase in bloodstream infections (BSIs; AHT = 24; p < 0.001) and associated deaths (AHT = 3; p 0.02) in patient with PICCs. The risk of experiencing a BSI was significantly higher in patients with PICCs (odds ratio = 9.6; 95% confidence interval, 9.08-10.18; p < 0.001). To reduce PICC-related BSIs and their related mortality, it is important to limit the overuse of PICCs and to implement a 'no PICC' policy by limiting the insertion of PICCs to situations without other available options.

Functional specialization of stable and dynamic microtubules in protein traffic in WIF-B cells.

We found that the magnesium salt of ilimaquinone, named 201-F, specifically disassembled dynamically unstable microtubules in fibroblasts and various epithelial cell lines. Unlike classical tubulin- interacting drugs such as nocodazole or colchicine which affect all classes of microtubules, 201-F did not depolymerize stable microtubules. In WIF-B-polarized hepatic cells, 201-F disrupted the Golgi complex and inhibited albumin and alpha1-antitrypsin secretion to the same extent as nocodazole. By contrast, 201-F did not impair the transport of membrane proteins to the basolateral surface, which was only affected by the total disassembly of cellular microtubules. Transcytosis of two apical membrane proteins-the alkaline phosphodiesterase B10 and dipeptidyl peptidase IV-was affected to the same extent by 201-F and nocodazole. Taken together, these results indicate that only dynamically unstable microtubules are involved in the transport of secretory proteins to the plasma membrane, and in the transcytosis of membrane proteins to the apical surface. By contrast, stable microtubules, which are not functionally affected by 201-F treatment, are involved in the transport of membrane proteins to the basolateral surface. By specifically disassembling highly dynamic microtubules, 201-F is an invaluable tool with which to study the functional specialization of stable and dynamic microtubules in living cells.

Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids.

The worldwide incidence of pulmonary carcinoids is increasing, but little is known about their molecular characteristics. Through machine learning and multi-omics factor analysis, we compare and contrast the genomic profiles of 116 pulmonary carcinoids (including 35 atypical), 75 large-cell neuroendocrine carcinomas (LCNEC), and 66 small-cell lung cancers. Here we report that the integrative analyses on 257 lung neuroendocrine neoplasms stratify atypical carcinoids into two prognostic groups with a 10-year overall survival of 88% and 27%, respectively. We identify therapeutically relevant molecular groups of pulmonary carcinoids, suggesting DLL3 and the immune system as candidate therapeutic targets; we confirm the value of OTP expression levels for the prognosis and diagnosis of these diseases, and we unveil the group of supra-carcinoids. This group comprises samples with carcinoid-like morphology yet the molecular and clinical features of the deadly LCNEC, further supporting the previously proposed molecular link between the low- and high-grade lung neuroendocrine neoplasms.

Mutagenesis rescues spermine and Zn2+ potentiation of recombinant NMDA receptors.

Alternative splicing generates distinct forms of the NMDA receptor subunit NR1. NR1 subunits with an N-terminal insert (termed N1) form receptors in Xenopus oocytes with greatly reduced potentiation by spermine and Zn2+. Oocytes expressing NR1 receptors with N1 exhibited larger NMDA currents than oocytes expressing corresponding receptors without N1. In the present study, we used mutational analysis to investigate structural features of the N1 insert that control current amplitude and spermine and Zn2+ potentiation. Neutralization of positive charges in N1 rescued spermine and Zn2+ potentiation. Positive charges in N1 did not affect spermine or Zn2+ affinity. Neutralization of positive charges in N1 diminished the responses to the level of NR1 receptors lacking N1. The positively charged N1 may increase NMDA currents by causing a conformational change similar to that produced by spermine and Zn2+ in NR1 receptors lacking N1.

The contribution of large genomic deletions at the CDKN2A locus to the burden of familial melanoma.

Mutations in two genes encoding cell cycle regulatory proteins have been shown to cause familial cutaneous malignant melanoma (CMM). About 20% of melanoma-prone families bear a point mutation in the CDKN2A locus at 9p21, which encodes two unrelated proteins, p16(INK4a) and p14(ARF). Rare mutations in CDK4 have also been linked to the disease. Although the CDKN2A gene has been shown to be the major melanoma predisposing gene, there remains a significant proportion of melanoma kindreds linked to 9p21 in which germline mutations of CDKN2A have not been identified through direct exon sequencing. The purpose of this study was to assess the contribution of large rearrangements in CDKN2A to the disease in melanoma-prone families using multiplex ligation-dependent probe amplification. We examined 214 patients from independent pedigrees with at least two CMM cases. All had been tested for CDKN2A and CDK4 point mutation, and 47 were found positive. Among the remaining 167 negative patients, one carried a novel genomic deletion of CDKN2A exon 2. Overall, genomic deletions represented 2.1% of total mutations in this series (1 of 48), confirming that they explain a very small proportion of CMM susceptibility. In addition, we excluded a new gene on 9p21, KLHL9, as being a major CMM gene.

Colonoscopy results of a French regional FOBT-based colorectal cancer screening program with high compliance.

BACKGROUND AND STUDY AIMS: Mass screening for colorectal cancer in France was initiated in pilot regions on the basis of the fecal occult blood test (FOBT) followed by colonoscopy in positive cases. We report the colonoscopy results in one of the first areas to be screened (Ille et Vilaine). PATIENTS AND METHODS: Of the total regional population of 908,449, 187,342 of the 213,635 potential screening candidates who were aged 50 - 74 years were invited for FOBT. Of the 51.3% compliant individuals, 2.6% were positive, and of these 90.7% agreed to undergo colonoscopy (n = 2246). The colonoscopy procedure details, findings, and complications were recorded. Subjects were classified according to the most advanced lesion. Positive predictive values of FOBT were calculated according to sex and age. RESULTS: Colonoscopy was complete in 96.3% of cases. Only 23 adverse events were encountered (1.02%). Colorectal cancer was diagnosed in 237 cases (10.6%, 78.4% of which were clinical stages I - II). The rates of overall adenomas and advanced adenomas were 33.1 % and 21.6 %, respectively. The risk of cancer and advanced adenoma increased significantly in men and in older people. CONCLUSION: The results of mass screening with FOBT followed by colonoscopy in this population-based study are very encouraging in terms of compliance, early findings, and complications. Extension of this program to the whole of France is justified.

Inhomogeneous bulk nematic order reconstruction.

A two-dimensional model within the Q-tensor description of liquid crystals is used to describe the inhomogeneous order reconstruction in a nematic cell driven by tony modulation in the anchoring conditions. Homogeneous and inhomogeneous reconstruction are contrasted: the former is defectless, the latter is defect mediated. While the transition thresholds are comparable in both cases and in good agreement with experimental data, the biaxial wall breaking is considerably slower in the inhomogeneous transition than in the homogeneous one. The shape of the signal given by the electric current flowing through the cell allows us to distinguish the actual path followed by the transition.

The Golgi complex is a microtubule-organizing organelle.

We show that the Golgi complex can directly stimulate microtubule nucleation in vivo and in vitro and thus behaves as a potent microtubule-organizing organelle in interphase cells. With the use of nocodazole wash-out experiments in hepatic cells, we found that the occurrence of noncentrosomal, early stabilized microtubules is highly correlated with the subcellular localization of Golgi membranes. With the use of in vitro reconstituted microtubule assembly systems with or without cytosol, we also found that, in contrast to centrosomally attached microtubules, the distal ends of Golgi-attached microtubules are remotely stabilized in a way that requires additional cytosolic component(s). Finally, we demonstrate that Golgi-based microtubule nucleation is direct and involves a subset of gamma-tubulin bound to the cytoplasmic face of the organelle.

"Intestinimonas massiliensis" sp. nov, a new bacterium isolated from human gut.

Here we report the main features of the proposed new bacterial species "Intestinimonas massiliensis" sp. nov. The type strain GD2T (CSUR = P1930) was isolated from the gut microbiota of a healthy patient using a culturomics approach combined with taxonogenomics.

'Bittarella massiliensis' gen. nov., sp. nov. isolated by culturomics from the gut of a healthy 28-year-old man.

We report here the main features of the proposed new bacterial genus Bittarella. The type strain 'Bittarella massiliensis' GD6T (CSUR P2149) was isolated from a stool sample from a healthy French man.

Description of 'Gorbachella massiliensis' gen. nov., sp. nov., 'Fenollaria timonensis' sp. nov., 'Intestinimonas timonensis' sp. nov. and 'Collinsella ihuae' sp. nov. isolated from healthy fresh stools with culturomics.

We report here the main characteristics of 'Gorbachella massiliensis' GD7T gen. nov., sp. nov., 'Fenollaria timonensis' GD5T sp. nov., 'Intestinimonas timonensis' GD4T sp. nov., and 'Collinsella ihuae' sp. nov. GD8T isolated from one fresh stool of a French volunteer. We used a bacterial culturomics approach combined with taxono-genomics.

Imaging of postoperative complications following surgery for lung cancer.

The complications following surgery for lung cancer vary depending upon the comorbidities and the type of surgery. Hemorrhage, infections and pulmonary edemas are not specific to the type of resection but frequently occur following pneumonectomies. Morbidity following pneumonectomies is related to the significant changes in the contents of the intrathoracic space. Pulmonary infarction and torsion are emergency situations that develop following lobectomy. CT shows features of localized congestion and stenosis or occlusion of a vein or bronchus. Rapid identification of severe events, in particular by systematic CT is essential for appropriate management of a postoperative or delayed complication of lung cancer surgery.

A colorimetric nanosensor based on a selective target-responsive aptamer kissing complex.

Herein, we report a novel approach for the design of a colorimetric aptasensor based on functionalized gold nanoparticle probes. This approach relies on the conjugation of nanoparticles by two functional DNA and RNA hairpins that engage specific kissing (loop-loop) interactions in response to the addition of a small analyte ligand, leading to particle aggregation and then red-to-purple colour change of the colloidal solution.

Staphylococcal chromosome cassette evolution in Staphylococcus aureus inferred from ccr gene complex sequence typing analysis.

Staphylococcal chromosome cassette mec (SCCmec) elements within major lineages of healthcare- and community-associated methicillin-resistant Staphylococcus aureus (MRSA) clones were characterised using intra-SCCmec multilocus sequencing. A strong correlation was observed between sequence- and PCR-based typing methods (p <0.001). However, phylogenetic analysis of the SCCmec locus using concatenated sequences evidenced few recombination events. Sequence type (ST)-SCCmec1 was found in SCCmec elements types I and IV, suggesting the evolution of an SCCmecI element into an SCCmecIV element. This coincided with the spread of the clone harbouring this SCCmec element into the community. No correlation was observed between ST-SCCmec lineage and MRSA lineage, confirming multiple acquisitions of SCCmec by S. aureus. This was exemplified by the SCCmecIV ST-SCCmec10 element, which was detected in all of the clonal complexes examined, including healthcare- and community-associated MRSA. The acquisition of this SCCmec element was five- to ten-fold more common than that of others. Models of MRSA clone evolution suggest that this SCCmec was first found in the paediatric clone.