Multi-pathogens sequence containing plasmids as positive controls for universal detection of potential agents of bioterrorism

BACKGROUND: The limited circulation of many of the agents that are likely to be used in a bioterrorism attack precludes the ready availability of positive controls. This means that only specialized laboratories can screen for the presence of these agents by nucleic amplification assays. Calibrated controls are also necessary for quantitative measurements. Primers and probes to be used in both conventional and real-time PCR assays were designed for the detection of agents likely to be used by a bioterrorist. Three plasmids, each of which contains 4 to 6 specific sequences from agents on the CDC Category A and B list (excluding RNA viruses) were constructed. Two plasmids incorporate the sequences of Category A and B agents, respectively. The third plasmid incorporates sequences from Variola major and organisms that cause rash-like illnesses that may be clinically confused with smallpox. An "exogenic sequence", introducing a NotI restriction site was incorporated in the native sequences of the bioterrorism agents inserted in plasmids. The designed molecular system for detection of bioterrorism agents was tested on each of these agents (except Monkeypox virus, Smallpox virus and 2 Burkholderia species for which no native DNA was available) and a collection of 50 isolates of C. burnetii using constructed plasmids as positive controls. RESULTS: Designed primers and probes allowed molecular detection, in either single or multiplex assays, of agent-specific targets with analytical sensitivities of between 1 and 100 DNA copies. The plasmids could be used as positive controls. False-positive results due to contamination by the positive control were easily detected by sequencing and eliminated by digestion with NotI. CONCLUSION: Plasmid A and B can be used as positive controls in molecular assays for the detection of bioterrorism agents in clinical specimens or environmental samples. Plasmid C can be used as a positive control in differentiation of vesicular rashes. It is also possible to avoid or to ensure immediate detection of false positive results due to contamination by positive controls using these plasmids. These plasmids and the corresponding primers and probes are immediately available for all clinical microbiology laboratories provided they have molecular amplification equipment

Malaria Risk Factors in Dielmo, A Senegalese Malaria-Endemic Village, Between October and November of 2013: A Case-Control Study

International audienceThe incidence of malaria has decreased recently in parts of Africa, coinciding with the widespread use of long-lasting insecticide-treated nets (LLINs) and artemisinin-based combination therapy (ACT). This reduction was also observed in Dielmo, our study area, and it was associated with the use of ACT as the first-line treatment against malaria beginning in 2006 and the implementation of LLINs in 2008. However, an unexplained slight increase in malaria incidence was observed in October and November of 2013. The aim of this study was to identify individual and environmental risk factors for malaria using a case-control study approach. Thirty cases and sixty controls were investigated. The use of LLINs was protective against malaria (adjusted odds ratio [AOR] = 0.10; 95% confidence interval [95% CI] = 0.02–0.45; P = 0.003). The risk of malaria transmission was high among villagers who watched television outside the house or the bedroom during the night (AOR = 8.83; 95% CI = 1.39–56.22; P = 0.021). The use of LLINs should be reinforced by the use of individual protection measures to avoid malaria transmission outside of the home. BACKGROUN

Optimization of Generalized Multichannel Quantum Defect reference functions for Feshbach resonance characterization

This work stresses the importance of the choice of the set of reference functions in the Generalized Multichannel Quantum Defect Theory to analyze the location and the width of Feshbach resonance occurring in collisional cross-sections. This is illustrated on the photoassociation of cold rubidium atom pairs, which is also modeled using the Mapped Fourier Grid Hamiltonian method combined with an optical potential. The specificity of the present example lies in a high density of quasi-bound states (closed channel) interacting with a dissociation continuum (open channel). We demonstrate that the optimization of the reference functions leads to quantum defects with a weak energy dependence across the relevant energy threshold. The main result of our paper is that the agreement between the both theoretical approaches is achieved only if optimized reference functions are used.Comment: submitte to Journal of Physics

Q fever in Bulgaria and Slovakia.

As a result of dramatic political and economic changes in the beginning of the 1990s, Q-fever epidemiology in Bulgaria has changed. The number of goats almost tripled; contact between goat owners (and their families) and goats, as well as goats and other animals, increased; consumption of raw goat milk and its products increased; and goats replaced cattle and sheep as the main source of human Coxiella burnetii infections. Hundreds of overt, serologically confirmed human cases of acute Q fever have occurred. Chronic forms of Q fever manifesting as endocarditis were also observed. In contrast, in Slovakia, Q fever does not pose a serious public health problem, and the chronic form of infection has not been found either in follow-ups of a Q-fever epidemic connected with goats imported from Bulgaria and other previous Q-fever outbreaks or in a serologic survey. Serologic diagnosis as well as control and prevention of Q fever are discussed

Atypical Q Fever in US Soldiers

Q fever is an emerging infectious disease among US soldiers serving in Iraq. Three patients have had atypical manifestations, including 2 patients with acute cholecystitis and 1 patient with acute respiratory distress syndrome. Providers must be aware of Q fever’s signs and symptoms to avoid delays in treatment

Cowpox Virus Transmission from Pet Rats to Humans, France

In early 2009, four human cases of cowpox virus cutaneous infection in northern France, resulting from direct contact with infected pet rats (Rattus norvegicus), were studied. Pet rats, originating from the same pet store, were shown to be infected by a unique virus strain. Infection was then transmitted to humans who purchased or had contact with pet rats

Combining local model calibration with the emergent constraint approach to reduce uncertainty in the tropical land carbon cycle feedback

The role of the land carbon cycle in climate change remains highly uncertain. A key source of the projection spread is related to the assumed response of photosynthesis to warming, especially in the tropics. The optimum temperature for photosynthesis determines whether warming positively or negatively impacts photosynthesis, thereby amplifying or suppressing CO2 fertilisation of photosynthesis under CO2-induced global warming. Land carbon cycle models have been extensively calibrated against local eddy flux measurements, but this has not previously been clearly translated into a reduced uncertainty in terms of how the tropical land carbon sink will respond to warming. Using a previous parameter perturbation ensemble carried out with version 3 of the Hadley Centre coupled climate–carbon cycle model (HadCM3C), we identify an emergent relationship between the optimal temperature for photosynthesis, which is especially relevant in tropical forests, and the projected amount of atmospheric CO2 at the end of the century. We combine this with a constraint on the optimum temperature for photosynthesis, derived from eddy covariance measurements using the adjoint of the Joint UK Land Environment Simulator (JULES) land surface model. Taken together, the emergent relationship from the coupled model and the constraint on the optimum temperature for photosynthesis define an emergent constraint on future atmospheric CO2 in the HadCM3C coupled climate–carbon cycle under a common emissions scenario (A1B). The emergent constraint sharpens the probability density of simulated CO2 change (2100–1900) and moves its peak to a lower value of 497 ± 91 compared to 607 ± 128 ppmv (parts per million by volume) when using the equal-weight prior. Although this result is likely to be model and scenario dependent, it demonstrates the potential of combining the large-scale emergent constraint approach with a parameter estimation using detailed local measurements.</p

Point of Care Strategy for Rapid Diagnosis of Novel A/H1N1 Influenza Virus

Within months of the emergence of the novel A/H1N1 pandemic influenza virus (nA/H1N1v), systematic screening for the surveillance of the pandemic was abandoned in France and in some other countries. At the end of June 2009, we implemented, for the public hospitals of Marseille, a Point Of Care (POC) strategy for rapid diagnosis of the novel A/H1N1 influenza virus, in order to maintain local surveillance and to evaluate locally the kinetics of the pandemic.Two POC laboratories, located in strategic places, were organized to receive and test samples 24 h/24. POC strategy consisted of receiving and processing naso-pharyngeal specimens in preparation for the rapid influenza diagnostic test (RIDT) and real-time RT-PCR assay (rtRT-PCR). This strategy had the theoretical capacity of processing up to 36 samples per 24 h. When the flow of samples was too high, the rtRT-PCR test was abandoned in the POC laboratories and transferred to the core virology laboratory. Confirmatory diagnosis was performed in the core virology laboratory twice a day using two distinct rtRT-PCR techniques that detect either influenza A virus or nA/N1N1v. Over a period of three months, 1974 samples were received in the POC laboratories, of which 111 were positive for nA/H1N1v. Specificity and sensitivity of RIDT were 100%, and 57.7% respectively. Positive results obtained using RIDT were transmitted to clinical practitioners in less than 2 hours. POC processed rtRT-PCR results were available within 7 hours, and rtRT-PCR confirmation within 24 hours.The POC strategy is of benefit, in all cases (with or without rtRT-PCR assay), because it provides continuous reception/processing of samples and reduction of the time to provide consolidated results to the clinical practitioners. We believe that implementation of the POC strategy for the largest number of suspect cases may improve the quality of patient care and our knowledge of the epidemiology of the pandemic

Goat-associated Q fever: a new disease in Newfoundland.

In the spring of 1999 in rural Newfoundland, abortions in goats were associated with illness in goat workers. An epidemiologic investigation and a serologic survey were conducted in April 1999 to determine the number of infections, nature of illness, and risk factors for infection. Thirty-seven percent of the outbreak cohort had antibody titers to phase II Coxiella burnetii antigen >1:64, suggesting recent infection. The predominant clinical manifestation of Q fever was an acute febrile illness. Independent risk factors for infection included contact with goat placenta, smoking tobacco, and eating cheese made from pasteurized goat milk. This outbreak raises questions about management of such outbreaks, interprovincial sale and movement of domestic ungulates, and the need for discussion between public health practitioners and the dairy industry on control of this highly infectious organism

High-quality genome sequence and description of Paenibacillus dakarensis sp. nov.

AbstractStrain FF9T was isolated in Dakar (Senegal) from a blood-culture taken from a 16-month-old child. MALDI-TOF analysis did not allow for identification. After sequencing, strain FF9T exhibited 98.18% similarity with the 16SrRNA sequence of Paenibacillus uliginis. A polyphasic study of phenotypic and genomic analyses showed that strain FF9T is Gram variable, catalase-positive, and presents a genome of 4,569,428 bp (one chromosome but no plasmid) with 4,427genes (4,352 protein-coding and 75 RNA genes (including 3 rRNA operons). The G+C content is 45.7%. On the basis of these genomic and phenotypic data analyses, we propose the creation of Paenibacillus dakarensis strain FF9T