A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia.

IMPORTANCE: The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative detection of 20 relevant bacterial species from bronchoalveolar lavage samples.

Significant Change in Marine Plankton Structure and Carbon Production After the Addition of River Water in a Mesocosm Experiment.

Rivers are known to be major contributors to eutrophication in marine coastal waters, but little is known on the short-term impact of freshwater surges on the structure and functioning of the marine plankton community. The effect of adding river water, reducing the salinity by 15 and 30%, on an autumn plankton community in a Mediterranean coastal lagoon (Thau Lagoon, France) was determined during a 6-day mesocosm experiment. Adding river water brought not only nutrients but also chlorophyceans that did not survive in the brackish mesocosm waters. The addition of water led to initial increases (days 1-2) in bacterial production as well as increases in the abundances of bacterioplankton and picoeukaryotes. After day 3, the increases were more significant for diatoms and dinoflagellates that were already present in the Thau Lagoon water (mainly Pseudo-nitzschia spp. group delicatissima and Prorocentrum triestinum) and other larger organisms (tintinnids, rotifers). At the same time, the abundances of bacterioplankton, cyanobacteria, and picoeukaryote fell, some nutrients (NH4+, SiO43-) returned to pre-input levels, and the plankton structure moved from a trophic food web based on secondary production to the accumulation of primary producers in the mesocosms with added river water. Our results also show that, after freshwater inputs, there is rapid emergence of plankton species that are potentially harmful to living organisms. This suggests that flash flood events may lead to sanitary issues, other than pathogens, in exploited marine areas.

Digital antimicrobial susceptibility testing using the MilliDrop technology.

We present the MilliDrop Analyzer (MDA), a droplet-based millifluidic system for digital antimicrobial susceptibility testing (D-AST), which enables us to determine minimum inhibitory concentrations (MICs) precisely and accurately. The MilliDrop technology was validated by using resazurin for fluorescence readout, for comparison with standard methodology, and for conducting reproducibility studies. In this first assessment, the susceptibility of a reference Gram-negative strain Escherichia coli ATCC 25922 to gentamicin, chloramphenicol, and nalidixic acid were tested by the MDA, VITEK®2, and broth microdilution as a reference standard. We measured the susceptibility of clinically relevant Gram-positive strains of Staphylococcus aureus to vancomycin, including vancomycin-intermediate S. aureus (VISA), heterogeneous vancomycin-intermediate S. aureus (hVISA), and vancomycin-susceptible S. aureus (VSSA) strains. The MDA provided results which were much more accurate than those of VITEK®2 and standard broth microdilution. The enhanced accuracy enabled us to reliably discriminate between VSSA and hVISA strains.

Occurrence and removal of butyltin compounds in a waste stabilisation pond of a domestic waste water treatment plant of a rural French town.

The aim of this study was to investigate the fate and behaviour of butyltin pollutants, including monobutyltin (MBT), dibutylin (DBT), and tributyltin (TBT), in waste stabilisation ponds (WSP). The study was conducted as part of a baseline survey and included five sampling campaigns comprising bottom sludge and the water column from each pond from a typical WSP in France. Butyltins were detected in all raw wastewater and effluents, reflecting their widespread use. Our results revealed high affinity between butyltins and particulate matter and high accumulation of butyltins in the sludge taken from anaerobic ponds. The dissolved butyltins in the influent ranged from 21.5 to 28.1 ng(Sn).L(-1) and in the effluent, from 8.8 to 29.3 ng(Sn).L(-1). The butyltin concentrations in the sludge ranged from 45.1 to 164 and 3.6-8.1 ng(Sn).g(-1) respectively in the first and last ponds. Our results showed an average treatment efficiency of 71% for MBT, 47% for DBT, 55% for TBT. Laboratory sorption experiments enabled the calculation of a distribution coefficient (Kd = 75,000 L.kg-1) between TBT and particulate matter from the WSPs. The Kd explained the accumulation and persistence of the TBT in the sludge after settling of particulate matter. The continuous supply of contaminated raw wastewater and the sorption-desorption processes in the ponds led to incomplete bio- and photolytic degradation and to the persistence of butyltins in dissolved and particulate matrices throughout the survey period. It is thus recommended to use shallow ponds and to pay particular attention when sludge is used for soil amendment.

Temporal and spatial variability of organotins in an intermittent Mediterranean river.

Organotin compounds (OTs) are exclusively anthropogenic and have been widely used for their biocidal properties and as stabilizers in various industrial applications. Hence organotins are common pollutants. Their high toxicity has led to their entry on the EU water framework's priority substances' list. However, few studies are available regarding their behaviour in surface waters, in particular, in intermittent Mediterranean rivers. The Vène is an intermittent river located in Languedoc-Roussillon, southern France. It is the main tributary of an important shellfish farming site: the Thau lagoon. The present study aims at establishing the presence of OTs on a 1.5 km long reach of the river into which a waste water treatment plant (WWTP) discharges. The study is carried out during steady-state flow conditions over two consecutive years and investigates potential OTs sources in everyday domestic activities. Routine field monitoring was carried out over a 5 month period during the springs of 2008 and 2009. The results establish the presence of butyltins and octyltins throughout the 1.5 km long reach at concentrations exceeding the maximum allowable concentration levels imposed by the water framework directive. The WWTP is recognized as an important OTs point source; however, using trace and rare earth elements as tracers, an urban stormwater sewage gutter is identified as a secondary source. Its impact on the river's pollutant loads is however variable in time because of flow intermittency. The paper discusses the need for specific monitoring and management schemes for intermittent rivers.

Adherence to antiretroviral therapy, virological response, and time to resistance in the Dakar cohort.

In 1998, with the launch of the Senegalese Initiative for Antiretroviral Access (ISAARV), Senegal became one of the first African countries to propose an antiretroviral access program. Our objective in this paper is to study the time to any first drug resistance, as well as predictors of the time to resistance. We propose a joint model to study the effect of adherence to the HAART therapy, and virological response on the time to resistance mutations. A logistic mixed model is used to model the time-dependent adherence process; and a Markov model is used to study the virological response. Given the presence of missing data in the adherence process and in the virological response, the latent adherence and virological states are then included in the linear predictor of the time to resistance model. The proposed time to resistance model takes into account interval-censored data as well as null hazard periods, during which the viral replication is very low. A Bayesian approach is used for accommodating with missing data and for prediction. We also propose model checking tools to study model adequacy.

Diversity of risk of mother-to-child HIV-1 transmission according to feeding practices, CD4 cell count, and haemoglobin concentration in a South African cohort.

OBJECTIVE: To estimate the probabilities of intrapartum and postpartum HIV-1 mother-to-child-transmission according to various feeding practices (formula feeding, exclusive breastfeeding, or mixed-feeding) and to other mother and infant covariates. METHODS: We used the promotion time model extended to multiple exposures to study the probability of infection attributable to each transmission occasion. Blood samples from 551 infants from Durban (South Africa) born to HIV-1 positive untreated mothers between 1995 and 1998 were sequentially tested until 15 months. RESULTS: The probability of infection attributable to in utero and intrapartum transmission was 21.88% (18.71-25.20) and was not significantly associated with the feeding practice. The probability of infection attributable to postnatal transmission through exclusive breastfeeding was negligible -0.7% (0-2.5) for 6 months of exclusive breastfeeding-- in comparison with that observed with mixed-feeding -6.15% (3.16-9.57) for 6 months of mixed-feeding. Maternal CD4 cell count and gestational age were significant predictors of intrapartum transmission probability while maternal CD4 cell count and maternal haemoglobin concentration were significant predictors of postpartum transmission probability. CONCLUSION: Decisions about appropriate infant feeding practices should take into account the difference in postpartum transmission risk between exclusive and mixed-feeding. Mixed-feeding should be all the more avoided that mothers have poor immunological statuses and low haemoglobin concentrations.

Application of the promotion time cure model with time-changing exposure to the study of HIV/AIDS and other infectious diseases.

Infectious diseases are caused by single or successive contacts with pathogens. Nevertheless, contacts with pathogens do not implicate infection. In 1993, Yakovlev et al. proposed a model to study a population of cancer patients with a cured fraction, a well adapted model to describe an infectious disease with a unique infection occasion. Extensions of this model have been proposed in the recent years. We present a mechanistic formulation in the context of infectious diseases with multiple infection occasions. It is a mixture model that enables to study risk factors associated with infection intensity at each infection occasion and factors shortening the delay from exposure to clinical event. Simulations are performed to evaluate the model fitting and two examples are presented for illustration: an analysis of an HIV-1 mother-to-child transmission data set and an analysis of nosocomial urinary tract infections data set.

Extensive multiallelic analysis of the relationship between HLA-DRB1 and rheumatoid arthritis using a Bayesian partition model.

To analyse the association between individual HLA-DRB1 locus genotypes and rheumatoid arthritis (RA) susceptibility, taking in account the multiallelic nature of the shared epitope (SE). In total, 538 patients and 536 controls were genotyped for 12 alleles of the HLA-DRB1 locus. A Bayesian partition model and multivariate logistic models were used to assess the role of the SE and of its individual components. The SE was associated with RA susceptibility (odds ratio (OR) 2 versus 0 SE copy=9.99 (95 CI 4.69-15.30) and OR 1 versus 0 SE copy=3.16 (95% CI 2.42-4.12)). The Bayesian partition model supplied a permutation of the HLA-DRBA locus alleles ordered by increasing disease risk. Alleles associated with highest risks are those that code for the SE. The individual OR estimations for the HLA-DRB1 locus genotypes went from OR=1.00 (95% CI 1.00-1.25) for the less associated genotype to OR=21.40 (95% CI 8.02-65.79) for the most associated one. In conclusion, the allele order risk and the OR estimations for individual genotypes of the HLA-DRB1 locus were consistent with the SE theory. Using an exploratory statistical method without a priori hypothesis, our study allowed a detailed analysis of the multiallelic nature of the SE.

Mixing and its impact on faecal coliform removal in a stabilisation pond.

Faecal coliform removal in stabilisation ponds is highly dependent on shortest water retention times. Tracer tests have been performed in a 3,300 m2 and 1.0 m deep pond, located in Southern France, to measure the retention times and bring light on the main influencing factors and mechanisms. Tracer concentrations were monitored at the outlet and 60 locations within the pond--at the surface, mid depth and the bottom of the water column. Pond water temperatures were measured at different depths and locations, together with pH, DO and redox potential. Wind velocity and rainfall were recorded. Water quality was monitored at the inlet, outlet and within the pond. Water retention times were shown to be strongly affected by weather conditions. Windy periods appeared to favour mixing regardless of the season. In sunny periods of spring and summer, a clear stratification was observed during daytime and vanished gradually during the night, suggesting alternation of mixed and stratified hydrodynamic patterns. This alternation was shown to influence microorganism contents within and at the outlet of the pond. Accurate prediction of shortest water retention times and disinfection performance requires 3D unsteady state fluid dynamic models that are able to take the influence of wind and water temperature distribution into account.

Annual nutrients export modelling by analysis of landuse and topographic information: case of a small Mediterranean catchment.

The preservation of water bodies from eutrophication implies accurate estimation of phosphorus and nitrogen loads and the control of nutrient production on a catchment scale. In this paper, a simple tool for the modelling of annual nutrient loads is presented. It is implemented in ARC/INFO GIS using Arc Macro Language (AML). The use of a GIS is justified as the spatial characteristics of the catchment area (land use, industrial wastewater location) dictate water quality. The annual nutrient loads are worked out on the catchment scale, using existing GIS routines together with specific routines developed in AML for hydrological and water quality modelling purposes. The catchment area is divided into hydrological subcatchments with relatively homogeneous spatial characteristics. Each subcatchment is linked to a specific nutrient export potential. These nutrient loads, calculated on a subcatchment-by-subcatchment basis, are conveyed to the outlet of the catchment and allow annual nutrient load estimation. A comparison with a water monitoring study is conducted to verify the adequation of modelling results for phosphorus and nitrogen loads.