Different latent class models were used and evaluated for assessing the accuracy of campylobacter diagnostic tests: overcoming imperfect reference standards?

In the absence of perfect reference standard, classical techniques result in biased diagnostic accuracy and prevalence estimates. By statistically defining the true disease status, latent class models (LCM) constitute a promising alternative. However, LCM is a complex method which relies on parametric assumptions, including usually a conditional independence between tests and might suffer from data sparseness. We carefully applied LCMs to assess new campylobacter infection detection tests for which bacteriological culture is an imperfect reference standard. Five diagnostic tests (culture, polymerase chain reaction and three immunoenzymatic tests) of campylobacter infection were collected in 623 patients from Bordeaux and Lyon Hospitals, France. Their diagnostic accuracy were estimated with standard and extended LCMs with a thorough examination of models goodness-of-fit. The model including a residual dependence specific to the immunoenzymatic tests best complied with LCM assumptions. Asymptotic results of goodness-of-fit statistics were substantially impaired by data sparseness and empirical distributions were preferred. Results confirmed moderate sensitivity of the culture and high performances of immunoenzymatic tests. LCMs can be used to estimate diagnostic tests accuracy in the absence of perfect reference standard. However, their implementation and assessment require specific attention due to data sparseness and limitations of existing software.

90Y-ibritumomab tiuxetan, fludarabine, busulfan and antithymocyte globulin reduced-intensity allogeneic transplant conditioning for patients with advanced and high-risk B-cell lymphomas.

BACKGROUND: Patients with advanced B-cell non-Hodgkin's lymphoma (NHL) refractory to initial chemotherapy or relapsing after autologous stem-cell transplantation have a poor prognosis. Allogeneic stem-cell transplantation after reduced-intensity conditioning (RIC) regimen can be a therapeutic option. However, the high incidence of relapse remains a challenging issue. We speculated that the incorporation of (90)Y-Ibritumomab tiuxetan into a fludarabine-based RIC regimen would improve the lymphoma control without overwhelming toxicity. Our aim was to evaluate the safety of (90)Y-Ibritumomab tiuxetan in association with such a regimen in a prospective multicenter phase II trial. PATIENTS AND METHODS: Thirty-one patients with advanced lymphoma from five distinct institutions were included between February 2008 and October 2010. Thirty patients in complete or partial response after failure of a median of 3 (range, 2-4) previous chemotherapy regimens including autologous transplant in 29 were evaluable for nonrelapse mortality (NRM) at day 100 post-transplant that was the primary end point. RESULTS: With a median follow-up of 32 months (range, 29-60 months), the 2-year event-free and overall survivals of the whole study group were both 80% [95 confidence interval (CI) 60.8% to 90.5%). The 100-day and 2-year post-transplant cumulative incidences of NRM were 3.3% (95% CI 0.2% to 14.9%) and 13.3% (95% CI 5.4% to 33.2%), respectively. The 2-year cumulative incidence of relapse was 6.7% (95% CI 1.7% to 25.4%). The cumulative incidences of grade II-IV and extensive chronic graft-versus-host disease were 27% and 14%, respectively. CONCLUSIONS: For chemosensitive advanced high-risk B-cell lymphoma, the addition of (90)Y-Ibritumomab tiuxetan to a RIC regimen based on fludarabine, busulfan and antithymocyte globulin followed by allogeneic transplant is safe and highly effective. clinicaltrials.gov: NCT00607854.

Comparison of transient elastography (FibroScan), FibroTest, APRI and two algorithms combining these non-invasive tests for liver fibrosis staging in HIV/HCV coinfected patients: ANRS CO13 HEPAVIH and FIBROSTIC collaboration.

OBJECTIVES: Combining noninvasive tests increases diagnostic accuracy for staging liver fibrosis in hepatitis C virus (HCV)-infected patients, but this strategy remains to be validated in HIV/HCV coinfection. We compared the performances of transient elastography (TE), Fibrotest (FT), the aspartate aminotransferase-to-platelet ratio index (APRI) and two algorithms combining TE and FT (Castera) or APRI and FT (SAFE) in HIV/HCV coinfection. METHODS: One hundred and sixteen HIV/HCV-coinfected patients (64% male; median age 44 years) enrolled in two French multicentre studies (the HEPAVIH cohort and FIBROSTIC) for whom TE, FT and APRI data were available were included in the study. Diagnostic accuracies for significant fibrosis (METAVIR F ≥ 2) and cirrhosis (F4) were evaluated by measuring the area under the receiver-operating characteristic curve (AUROC) and calculating percentages of correctly classified (CC) patients, taking liver biopsy as a reference. RESULTS: For F ≥ 2, both TE and FT (AUROC = 0.87 and 0.85, respectively) had a better diagnostic performance than APRI (AUROC = 0.71; P < 0.005). Although the percentage of CC patients was significantly higher with Castera's algorithm than with SAFE (61.2% vs. 31.9%, respectively; P < 0.0001), this percentage was lower than that for TE (80.2%; P < 0.0001) or FT (73.3%; P < 0.0001) taken separately. For F4, TE (AUROC = 0.92) had a better performance than FT (AUROC = 0.78; P = 0.005) or APRI (AUROC = 0.73; P = 0.025). Although the percentage of CC patients was significantly higher with the SAFE algorithm than with Castera's (76.7% vs. 68.1%, respectively; P < 0.050), it was still lower than that for TE (85.3%; P < 0.033). CONCLUSIONS: In HIV/HCV-coinfected patients, TE and FT have a similar diagnostic accuracy for significant fibrosis, whereas for cirrhosis TE has the best accuracy. The use of the SAFE and Castera algorithms does not seem to improve diagnostic performance.

[Statistical and epidemiological methods used in biomedical research: implications for initial medical education]. / Méthodes biostatistiques et épidémiologiques employées pour la recherche biomédicale : implications pour la formation médicale initiale.

BACKGROUND: The main source of key medical information consists in original articles published in peer-reviewed biomedical journals. Reported studies use increasingly sophisticated statistical and epidemiological approaches that first require a solid understanding of core methods. However, such understanding is not widely shared among physicians. Our aim was to assess whether the basic statistical and epidemiological methods used in original articles published in general biomedical journals are taught during the first years of the medical curriculum in France. METHODS: We selected original articles published in The New England Journal of Medicine, The Lancet, and The Journal of the American Medical Association, over a period of six months in 2007 and in 2008. A standardized statistical content checklist was used to extract the necessary information in the "Abstract", "Methods", "Results", footnotes of tables, and legends of figures. The methods used in the selected articles were compared to the national program and the public health program of biostatistics and epidemiology taught during the first six years of medical school. RESULTS: The 237 analyzed original articles all used at least one statistical or epidemiological method. Descriptive statistics, confidence interval and Chi(2) or Fisher tests, methods used in more than 50% of articles, were repeatedly taught throughout the medicine curriculum. Measures of association, sample size, fit and Kaplan-Meier method, used in 40 to 50% of articles, were specifically taught during training sessions on critical reading methods. Cox model (41% of articles) and logistic regression (24% of articles) were never taught. The most widely used illustrations, contingency tables (92%) and flowcharts (48%), were not included in the national program. CONCLUSION: More teaching of the core methods underlying the understanding of sophisticated methods and illustrations should be included in the early medical curriculum so that physicians can read the scientific literature critically for their medical education.

Comparison of open and robotic-assisted partial nephrectomy approaches using multicentric data (UroCCR-47 study).

We compared the outcomes of robotic-assisted partial nephrectomy (RPN) and open partial nephrectomy (OPN) using contemporary data to respond to unmet clinical needs. Data from patients included in the registry who underwent partial nephrectomy between January 01, 2014 and June 30, 2017 within 20 centres of the French Network for Research on Kidney Cancer UroCCR were collected (NCT03293563). Statistical methods included adjusted multivariable analyses. Rates of peri- and post-operative transfusion, and of surgical revision, were lower in the RPN (n = 1434) than the OPN (n = 571) group (2.9% vs. 6.0%, p = 0.0012; 3.8% vs. 11.5%, p < 0.0001; 2.4% vs. 6.7%, p < 0.0001, respectively). In multivariable analyses, RPN was independently associated with fewer early post-operative complications than OPN (overall: odds-ratio [95% confidence interval, CI] = 0.48 [0.35-0.66]; severe: 0.29 [0.16-0.54], p < 0.0001 for both) and shorter hospital stays (34% [30%; 37%], p < 0.0001). RPN was also a significantly associated with a decresedrisk of post-operative acute renal failure, and new-onset chronic kidney disease at 3 and 12 months post-surgery. There were no between-group differences in oncological outcomes. In comparison with OPN, RPN was associated with improved peri- and post-operative morbidity, better functional outcomes, and shorter hospital stays. Our results support the use of RPN, even for large and complex tumours.

A synthetic glycolipid with B-cell mitogenic activity.

A synthetic glycolipid, N-palmitoyl-D-glucosamine, (NPG) was found to be a potent B-cell mitogen, that stimulated spleen cells from nu/nu as well as from normal mice. The proper dispersion of the water insoluble preparation is critical for the elicitation of this mitogenic effect. Limulus lysate clotting assay indicated that the NPG preparation either contains only 0.001% endotoxin contamination, or that NPG itself is 10(-5) times less active in this assay than purified endotoxic LPS. Since such low levels of endotoxin concentration are not mitogenic, it is concluded that synthetic N-palmitoyl-D-glucosamine, when properly dispersed, is itself a B-cell mitogen.

Exogenous acquisition of Pseudomonas aeruginosa in intensive care units: a prospective multi-centre study (DYNAPYO study).

BACKGROUND: Pseudomonas aeruginosa remains one of the most common nosocomial pathogens in intensive care units (ICUs). Although exogenous acquisition has been widely documented in outbreaks, its importance is unclear in non-epidemic situations. AIM: To elucidate the role of exogenous origin of P. aeruginosa in ICU patients. METHODS: A chronological analysis of the acquisition of P. aeruginosa was performed using samples collected in 2009 in the DYNAPYO cohort study, during which patients and tap water were screened weekly. Molecular relatedness of P. aeruginosa isolates was investigated by pulsed-field gel electrophoresis. Exogenous acquisition was defined as identification of a P. aeruginosa pulsotype previously isolated from another patient or tap water in the ICU. FINDINGS: The DYNAPYO cohort included 1808 patients (10,402 samples) and 233 water taps (4946 samples). Typing of 1515 isolates from 373 patients and 375 isolates from 81 tap water samples identified 296 pulsotypes. Analysis showed exogenous acquisition in 170 (45.6%) of 373 patients. The pulsotype identified had previously been isolated from another patient and from a tap water sample for 86 and 29 patients, respectively. The results differed according to the ICU. CONCLUSION: Exogenous acquisition of P. aeruginosa could be prevented in half of patients. The overall findings of this survey support the need for studies on routes of transmission and risk assessment approach to better define how to control exogenous acquisition in ICUs.

Risk factors for colonization and infection by Pseudomonas aeruginosa in patients hospitalized in intensive care units in France.

OBJECTIVE: To assess the role of environment, medical care and individual risks factors for P. aeruginosa colonization and infection. STUDY DESIGN AND SETTING: A French multicentric prospective study involved ten ICUs for a five months period. Every adult patient newly hospitalized in ICUs with no P. aeruginosa carriage up to 48 hours after admission was included and weekly screened before discharge or death. Screening swabs were either rectal, sputum or oropharyngeal samples. Hydric environment was also sampled each week. Data on patient clinical features, environmental and device exposures, and antibiotics supports were regularly collected. Multivariate analysis was performed with a multistate model. RESULTS: The overall prevalence of P. aeruginosa carriage was 15.3% (201/1314). Risk factors associated with patient colonization were: use of inactive antibiotics against P. aeruginosa (HR = 1.60 [1.15-2.21] p<0.01), tap water contamination at the entry in the room (HR = 1.66 [1.01-2.27] p<0.05) and mechanical invasive ventilation (HR = 4.70 [2.66-8.31] p<0.0001). Active antibiotics prevented from colonization (HR = 0.67 [0.48-0.93] p = 0.02) and from infection (HR = 0.64 [0.41-1.01] p = 0.05). Interaction between hydric environment antibiotics support was not statistically associated with patient colonization. CONCLUSION: Hydric contamination and antibiotics pressure seem to remain key independent risk factors in P. aeruginosa colonization. These results advocate the need to carry on preventive and targeted interventions toward healthcare associated infections.

[Analysis of left-censored quantitative outcome: example of procalcitonin level]. / Analyse d'une variable quantitative censurée à gauche: exemple du taux de procalcitonine.

BACKGROUND: When the sensitivity of an assay used to quantify a marker is poor, some of the values are below the detection limit resulting in left-censoring. Analysis of such data requires appropriate statistical techniques. In this study, we aimed at comparing various methods used to deal with left-censored outcome in regression analysis. METHODS: The application was a real study evaluating the performance of procalcitonin for the diagnosis of bacterial infections among elderly patients. Among 85 patients, eleven had a procalcitonin value below the detection limit. A simulation study was then performed with data sampled according to a Gaussian distribution with parameters estimated on observed data. Various levels of left-censoring were simulated (13, 25 and 50%). A linear regression model was used to explain procalcitonin variations according to another marker, C reactive protein. To handle left-censoring, several methods were used: complete case analysis, simple imputation and multiple imputation methods, and parametric modelling. In the simulation study, estimations according to different methods were compared in terms of bias and mean square error according to each left-censoring level. Estimations obtained with real data were also compared according to the methods used. All analyses were implemented using SAS software. RESULTS: In the simulation study, parametric modelling using maximum likelihood showed best performances whatever the level of censoring. On the other hand, methods using complete cases and simple imputation by the detection limit were highly skewed. On observed data, estimations of the slope varied slightly according to the methods. However the p-values (Wald test) of beta=0 varied from 0.0001 to 0.13 leading to different decisions according to the method used. CONCLUSION: Left-censoring handling in data analysis requires special attention, as different methods may yield results leading to different conclusions.

Fatty acid composition of the lipids of Pseudomonas mildenbergii. Presence of a fatty acid containing two conjugated double bonds.

The whole cell fatty acids of Pseudomonas mildenbergii were extracted and separated, as methyl esters, into non-hydroxylated (60.6%) and hydroxylated (39.4%) esters. The main component of the hydroxy-ester fraction was methyl 3D-hydroxydecanoate. The non-hydroxylated fraction mainly consisted of methyl 2-decenoate, the methyl ester of a C-12 acid having two conjugated double bonds, methyl palmitate, methyl methylene-hexadecanoate and methyl vaccenate.

Glycolipids of brevibacterium vitarumen.

Corynomycolic acids have been identified in the lipids of Brevibacterium vitarumen. The analogy between this strain and typical aerobic Corynebacteria is borne out by these complex lipids, corynomycolic acid being linked as 6,6'-dicorynomycoloyl-trehalose (cord-factor structure) and as 6-monocorynomycoloyl-trehalose.

Magnetisation transfer parameters and stroke outcome.

Our aim was to evaluate the association between magnetisation transfer imaging (MTI) parameters measured 30 to 45 days after a cerebrovascular insult and post-stroke functional outcome at the same time. MTI offers the opportunity to depict subtle microstructural changes in infarcted areas. The clinical significance of the heterogeneity of brain damage within ischaemic stroke lesions is unknown. We prospectively included 58 patients with acute middle cerebral artery stroke. Diffusion-weighted imaging was performed within 12 hours after onset and the final infarct was documented by MRI with fluid-attenuated inversion recovery (FLAIR) and MTI at 30 to 45 days follow-up. We evaluated the association between MTI histogram parameters and the clinical outcome assessed by dichotomised (threshold >2) modified rankin scale (mRS) using multivariable logistic regression models adjusted on baseline characteristics. In multivariable analyses, stroke outcome was mostly driven by initial National Institutes of Health Stroke Scale (odds ratio [OR]=1.23; 95% confidence interval [CI]=1.07-1.41; p<0.01) while after adjustment of initial stroke severity magnetisation transfer ratio peak position was the only MRI parameter associated with functional status at 30 to 45 days post-stroke (OR=0.86; 95% CI=0.75-0.98; p=0.02); lower peak position values associated with higher mRS. Conversely, stroke volume measured on FLAIR sequence was not associated with stroke prognosis (p=0.87). The intensity of microstructural changes within the infarct core measured at 30 to 45 days follow-up is independently associated with the functional status evaluated at the same time. MTI and related parameters could be used as surrogate markers of treatment response in stroke clinical trials.

Screening for Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium should it be integrated into routine pregnancy care in French young pregnant women?

Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium screening during pregnancy is not performed routinely in France. We conducted the first prospective study in 1004 women attending for routine antenatal care to determine the prevalence and risk factors for these bacterial infections. The overall prevalence of C. trachomatis, N. gonorrhoeae, and M. genitalium infections was 2.5%, 0%, and 0.8%, respectively. In patients aged 18-24 years, the prevalence increased to 7.9% for C. trachomatis and to 2.4% for M. genitalium. C. trachomatis infection was associated with age ≤24 years or being single or having more than 5 sexual partners in a lifetime. M. genitalium infection was more frequent in patients aged ≤24 years or who had a history of abortion or their first sexual intercourse after 20 years of age. The high prevalence of C. trachomatis in pregnant women aged ≤24 years, mostly asymptomatic, suggests that systematic screening could be beneficial.

A study on the receptor for a mycobacteriophage : phage phlei.

From Mycobacterium phlei, glycolipid fractions have been isolated which inactivate phage Phlei. On the basis of the characteristics of the inactivation (specificity, kinetics, requirement for Ca++) typical of the phage-host cell system, it was concluded that these fractions contain the receptor sites for phage Phlei ; this conclusion was supported by electron microscopic studies. All the active fractions contain four kinds of components : fatty acids, glycerol, sugars (D-lyxose, 6-0-methyl-D-glucose, and low amounts of glucose and mannose), and water-soluble acids. These acids are isolated by degradation of the receptor fractions as oxalic and pyruvic acids. Variations of the ratio oxalic acid/pyruvic acid according to the mode of degradation and the absence of the peak characteristic of the protons of a pyruvic acid residue in the NMR spectrum, suggest that these acids might arise from the splitting of oxaloacetic acid. A tentative structure of the receptor is proposed, in many monoglycerides are linked through keto-acid to a polysaccharide core.

Mycobacterial lipids: a historical perspective.

Mycobacterial lipids have been studied for more than 70 years, due to the fascinating diversity of their structures and biological activities. A historical perspective, and the present status on the structure and activity of major lipids of the outer envelope of mycobacterial cells are presented : mycolic acids, which are main constituents of the cell wall, and glycolipids known for toxic or immunological properties (cord factor, SL, DAT, PGL, GPL, LOS, LAM). As far as possible, it was tried to distinguish between experimentally established knowledge and currently accepted speculations.

[Chemotaxonomy of gram-positive bacteria metabolizing beta-caryophyllene]. / Chimiotaxonomie de bactéries à gram positif métabolisant le beta-caryophyllène.

Chemotaxonomic identification of coryneform bacteria metabolizing b-caryophyllene was attempted. The following phospholipids were identified as main components of the bacterial extracts: cardiolipids, phosphatidylethanolamine, phosphatidylinositol and mannosides of phosphatidylinositol. Saponification of the lipid extracts gave a mixture of hydroxylated and nonhydroxylated fatty acids. Among the latter, oleic and tuberculostearic acids were identified. The hydroxylated fatty acids were analysed by thin-layer chromatography and mass spectrometry (as methyl esters). From the results thus obtained, the strains appeared to be more closely related to the genus Rhodococcus than to the genus Nocardia.

Glycolipids from Nocardia rhodochrous grown on glucose.

Nocardia rhodochrous grown on glucose-supplemented medium produced a high yield of a glycolipid fraction (m.p. 65-70 degrees C and [alpha]25D = + 31.4 degrees), identified as 6-(C40-C46) nocardomycoloylglucose. It accounted for approx. 3.4% of the cell dry wt. and 41% of the diethyl ether soluble lipids obtained from ethanol-diethyl ether extract. Dimycoloyltrehalose (cord factor) was found in a very small amount (0.11%).

Risk factors for Pseudomonas aeruginosa acquisition in intensive care units: a prospective multicentre study.

BACKGROUND: Pseudomonas aeruginosa is a major nosocomial pathogen in intensive care units (ICUs); however, endogenous versus exogenous origin of contamination remains unclear. AIM: To identify individual and environmental ICU risk factors for P. aeruginosa acquisition. METHODS: A five-month prospective multicentric study was performed in ten French ICUs. Adult patients hospitalized in ICU for ≥ 24 h were included and screened for P. aeruginosa colonization on admission, weekly and before discharge. P. aeruginosa acquisition was defined by a subsequent colonization or infection if screening swabs on admission were negative. Water samples were obtained weekly on water taps of the ICUs. Data on patient characteristics, invasive devices exposure, antimicrobial therapy, P. aeruginosa water and patient colonization pressures, and ICU characteristics were collected. Hazard ratios (HRs) were estimated using multivariate Cox model. FINDINGS: Among the 1314 patients without P. aeruginosa on admission, 201 (15%) acquired P. aeruginosa during their ICU stay. Individual characteristics significantly associated with P. aeruginosa acquisition were history of previous P. aeruginosa infection or colonization, cumulative duration of mechanical ventilation and cumulative days of antibiotics not active against P. aeruginosa. Environmental risk factors for P. aeruginosa acquisition were cumulative daily ward 'nine equivalents of nursing manpower use score' (NEMS) [hazard ratio (HR): 1.47 for ≥ 30 points; 95% confidence interval (CI): 1.06-2.03] and contaminated tap water in patient's room (HR: 1.76; CI: 1.09-2.84). CONCLUSION: Individual risk factors and environmental factors for which intervention is possible were identified for P. aeruginosa acquisition.

Final cerebral infarct volume is predictable by MR imaging at 1 week.

BACKGROUND AND PURPOSE: Stroke volume, an increasingly used end point in phase II trials, is considered stationary at least 30 days after the ictus. We investigated whether information conveyed by MR imaging measurements of the "final" infarct volume could be assessed as early as the subacute stage (days 3-6), rather than waiting for the chronic stage (days 30-45). MATERIALS AND METHODS: Ninety-five patients with middle cerebral artery stroke prospectively included in a multicenter study underwent MR imaging during the first 12 hours (MR imaging-1), between days 3 and 6 (MR imaging-2), and between days 30 and 45 (MR imaging-3). We first investigated the relationship between subacute (FLAIR-2) and chronic volumes (FLAIR-3), by using a linear regression model. We then tested the relationship between FLAIR volumes (either FLAIR-2 or FLAIR-3) and functional disability, measured by the mRS at the time of MR imaging-3, by using logistic regression. The performances of the models were assessed by using the AUC in ROC. RESULTS: A linear association between log FLAIR-2 and log FLAIR-3 volumes was observed. The proportion of FLAIR-3 variation, explained by FLAIR-2, was high (R(2) = 81%), without a covariate that improved this percentage. Both FLAIR-2 and FLAIR-3 were independent predictors of mRS (OR, 0.79 and 0.73; 95% CI, 0.64-0.97 and 0.56-0.96; P = .026 and .023). The performances of the models for the association between either FLAIR volume and mRS did not differ (AUC = 0.897 for FLAIR-2 and 0.888 for FLAIR-3). CONCLUSIONS: Stroke damage may be assessed by a subacute volume because subacute volume predicts the "true" final volume and provides the same clinical prognosis.