Genomic insights into an extensively drug-resistant and hypervirulent Burkholderia dolosa N149 isolate of a novel sequence type (ST2237) from a Vietnamese patient hospitalised for stroke.

OBJECTIVES: Burkholderia dolosa is a clinically important opportunistic pathogen in inpatients. Here we characterised an extensively drug-resistant and hypervirulent B. dolosa isolate from a patient hospitalised for stroke. METHODS: Resistance to 41 antibiotics was tested with the agar disc diffusion, minimum inhibitory concentration, or broth microdilution method. The complete genome was assembled using short-reads and long-reads and the hybrid de novo assembly method. Allelic profiles obtained by multilocus sequence typing were analysed using the PubMLST database. Antibiotic-resistance and virulence genes were predicted in silico using public databases and the 'baargin' workflow. B. dolosa N149 phylogenetic relationships with all available B. dolosa strains and Burkholderia cepacia complex strains were analysed using the pangenome obtained with Roary. RESULTS: B. dolosa N149 displayed extensive resistance to 31 antibiotics and intermediate resistance to 4 antibiotics. The complete genome included three circular chromosomes (6 338 630 bp in total) and one plasmid (167 591 bp). Genotypic analysis revealed various gene clusters (acr, amr, amp, emr, ade, bla and tet) associated with resistance to 35 antibiotic classes. The major intrinsic resistance mechanisms were multidrug efflux pump alterations, inactivation and reduced permeability of targeted antibiotics. Moreover, 91 virulence genes (encoding proteins involved in adherence, formation of capsule, biofilm and colony, motility, phagocytosis inhibition, secretion systems, protease secretion, transmission and quorum sensing) were identified. B. dolosa N149 was assigned to a novel sequence type (ST2237) and formed a mono-phylogenetic clade separated from other B. dolosa strains. CONCLUSIONS: This study provided insights into the antimicrobial resistance and virulence mechanisms of B. dolosa.

Evaluation of the safety and immune stimulatory effects of multi-strain Lab Mix product on laboratory animals.

Background & aims: Probiotics are alive and beneficial bacteria used as food complements with sufficient amounts to improve and balance the intestinal flora in the human gastrointestinal tract and inhibit harmful microorganisms. In this study, we conducted experiments to evaluate he safety and the effect of one of our probiotics on selected biochemical parameters in animal models. Methods: LabMix is a probiotic product containing three bacterial strains, including Lactobacillus acidophilus LA 304.17, Lactobacillus casei LC 304.08, and Bifidobacterium bifidum BF 304.98, with a density of 9 × 109 CFU/g and being mixed with suitable excipients. In this study, we conducted experiments to evaluate LabMix's acute ttoxicity in mice as well as subchronic toxicity in rats. Results: The LD50 dose in mice of this product could not be determined since no death or disorder was recorded. In rats receiving LabMix with doses of 2.52 × 109 CFU/kg and 12.6 × 109 CFU/kg continuously for 28 days, this product caused no significant changes in the amount of red and white blood cells and platelets. Similarly, no significant changes were recorded in serum concentrations of hemoglobin, alanine aminotransferase (ALT), aspartate aminotransferase (AST), glucose, protein, cholesterol, bilirubin, and creatinine. Besides, LabMix products also did not cause any changes in the histology of the liver, kidney, and spleen in rats. Moreover, LabMix was well tolerated without affecting the normal growth and feeding of rats. Furthermore, LabMix also decreased serum cytokines and increased serum and gut mucosal IgA antibodies. Conclusions: LabMix product is possibly considered safe for human., and this sproduct reduced the release of pro-inflammatory cytokines (IL-6 and TNF-α), but increased IgA levels. However, it is necessary to further evaluate the product's effectiveness in the preclinical phase as well as in further phases before mass production and commercialization.

Radiological risk assessment of outdoor222Rn and220Rn around rare earth element and uranium mines from northern Vietnam.

The outdoor222Rn and220Rn concentrations at 320 sampling points at 1 m above the ground in different sites surrounding rare earth element (REE) and uranium mines from northern Vietnam were measured using the RAD7. Results showed that222Rn concentrations were always higher than220Rn concentrations with large variation ranges from 25.7 to 573 Bq m-3and from 18.5 to 385 Bq m-3, respectively. The high correlation between220Rn and228Ra concentrations in surface soil of the studied sites were observed. The highest220Rn and222Rn concentrations are found at the sampling points of the REE NX-Lai Chau site. The220Rn and222Rn activities surrounding the REE mines were found to be higher than those surrounding the uranium mines. The average annual committed effective doses originated from the inhalation of220Rn and222Rn outdoor concentrations is about five times higher than the worldwide average value.

Development of Artificial Neural Network for prediction of radon dispersion released from Sinquyen Mine, Vietnam.

Understanding the radon dispersion released from this mine are important targets as radon dispersion is used to assess radiological hazard to human. In this paper, the main objective is to develop and optimize a machine learning model namely Artificial Neural Network (ANN) for quick and accurate prediction of radon dispersion released from Sinquyen mine, Vietnam. For this purpose, a total of million data collected from the study area, which includes input variables (the gamma data of uranium concentration with 3 × 3m grid net survey inside mine, 21 of CR-39 detectors inside dwellings surrounding mine, and gamma dose at 1 m from ground surface data) and an output variable (radon dispersion) were used for training and validating the predictive model. Various validation methods namely coefficient of determination (R2), Mean Absolute Error (MAE), Root Mean Squared Error (RMSE) were used. In addition, Partial dependence plots (PDP) was used to evaluate the effect of each input variable on the predictive results of output variable. The results show that ANN performed well for prediction of radon dispersion, with low values of error (i.e., R2 = 0.9415, RMSE = 0.0589, and MAE = 0.0203 for the testing dataset). The increase of number of hidden layers in ANN structure leads the increase of accuracy of the predictive results. The sensitivity results show that all input variables govern the dispersion radon activity with different amplitudes and fitted with different equations but the gamma dose is the most influenced and important variable in comparison with strike, distance and uranium concentration variables for prediction of radon dispersion.

First Report on Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus Isolates in Children Admitted to Tertiary Hospitals in Vietnam.

The extensive distribution of multidrug-resistant (MDR) methicillin-resistant Staphylococcus aureus (MRSA) poses a threat to healthcare worldwide. This study aimed to investigate the MDR and molecular patterns of MRSA isolates in children admitted to the two biggest tertiary care pediatric hospitals in northern and southern Vietnam. A total of 168 MRSA strains were collected to determine antibiotic susceptibility by minimum inhibitory concentration tests. Antibiotic-resistant genes, pulsed-field gel electrophoresis, staphylococcal cassette chromosome mec (SCCmec) typing, and multilocus sequence typing were used for the molecular characterization of MRSA. Among the total strains, the MDR rate (51.8%) was significantly higher in the northern hospital than in the southern hospital (73% vs. 39%, p < 0.0001). The MDR-MRSA with the highest rates were "ciprofloxacin-erythromycin-gentamicintetracyclines" (35.6%), followed by "erythromycin-tetracycline-chloramphenicol" (24.1%), and "ciprofloxacin-erythromycin-gentamicin" (19.5%), showing an accumulative total of 79.3%. The most susceptible antibiotics were rifampicin (100%) and vancomycin (100%), followed by doxycycline (94.0%), meropenem (78.0%), and cefotaxime (75.0%). The SCCmecII strains showed greater resistance to gentamicin, ciprofloxacin, tetracycline, meropenem and cephalosporins compared with the other strains. The SCCmecII strains exhibited the highest rate in the tested genes (aacA/aphD: 55.2%, ermA/B/C: 89.7%, and tetK/M: 82.8%). ST5- SCCmecII was the predominant clone in the northern hospital, whereas SCCmecIVa was more pronounced in the southern hospital. In conclusion, our results raised concerns about the predominant MDR-MRSA strains in the pediatric hospitals in Vietnam. The north-south difference in the antibiotic resistance patterns and genetic structure of MRSA suggests different MRSA origins and various uses of antimicrobial agents between the two regions.

Implementation of the World Health Organization Trauma Care Checklist Program in 11 Centers Across Multiple Economic Strata: Effect on Care Process Measures.

BACKGROUND: Trauma contributes more than ten percent of the global burden of disease. Initial assessment and resuscitation of trauma patients often requires rapid diagnosis and management of multiple concurrent complex conditions, and errors are common. We investigated whether implementing a trauma care checklist would improve care for injured patients in low-, middle-, and high-income countries. METHODS: From 2010 to 2012, the impact of the World Health Organization (WHO) Trauma Care Checklist program was assessed in 11 hospitals using a stepped wedge pre- and post-intervention comparison with randomly assigned intervention start dates. Study sites represented nine countries with diverse economic and geographic contexts. Primary end points were adherence to process of care measures; secondary data on morbidity and mortality were also collected. Multilevel logistic regression models examined differences in measures pre- versus post-intervention, accounting for patient age, gender, injury severity, and center-specific variability. RESULTS: Data were collected on 1641 patients before and 1781 after program implementation. Patient age (mean 34 ± 18 vs. 34 ± 18), sex (21 vs. 22 % female), and the proportion of patients with injury severity scores (ISS) ≥ 25 (10 vs. 10 %) were similar before and after checklist implementation (p > 0.05). Improvement was found for 18 of 19 process measures, including greater odds of having abdominal examination (OR 3.26), chest auscultation (OR 2.68), and distal pulse examination (OR 2.33) (all p < 0.05). These changes were robust to several sensitivity analyses. CONCLUSIONS: Implementation of the WHO Trauma Care Checklist was associated with substantial improvements in patient care process measures among a cohort of patients in diverse settings.

Mycobacterium tuberculosis lineages and anti-tuberculosis drug resistance in reference hospitals across Viet Nam.

BACKGROUND: Mycobacterium tuberculosis, the tuberculosis (TB) pathogen, despite a low level of genetic diversity, has revealed a high variety of biological and epidemiological characteristics linked to their lineages, such as transmissibility, fitness and propensity to acquire drug resistance. This has important implications for the epidemiology of TB. We conducted this first countrywide cross-sectional study to identify the prevalent M. tuberculosis lineages and to assess their epidemiological associations and their relation to drug resistance. The study was conducted among isolates acquired in reference hospitals across Vietnam. Isolates with drug susceptibility testing profiles were identified for their lineages by spoligotyping. Logistic regression was used to investigate the association of M. tuberculosis lineages with location, age and sex of the patients and drug resistance levels. RESULTS: Results showed that the most prevalent lineage was Beijing (55.4 %), followed by EAI (27.5 %), T (6.4 %), LAM (1.3 %), Haarlem (1 %) and Zero type (0.3 %). The proportion of Beijing isolates in the North (70.4 %) and the South (68 %) was higher than in the Centre (28 %) (OR = 1.7 [95 % CI: 1.4-2.0], p < 0.0001), whereas the proportion of EAI isolates in the North (7.1 %) and the South (17 %) was much lower compared with the Centre (59 %) (OR = 0.5 [95 % CI: 0.4-0.6], p < 0.0001). Overall, Beijing isolates were the most likely to be drug-resistant and EAI isolates were the least likely to be drug-resistant, except in the South of Vietnam where EAI is also highly drug-resistant. The proportion of Beijing isolates was significantly higher (p < 0.01), and the proportion of EAI isolates was significantly lower (p < 0.05) in younger patients. The proportion of drug-resistance was higher in isolates collected from male patients and from patients in the middle age groups. CONCLUSIONS: The findings suggest ongoing replacement of EAI lineage, which is mainly more drug-susceptible with highly drug-resistant Beijing lineage in all studied regions of Vietnam. Male patients of working ages should be the focus for better control to prevent the emergence of drug-resistant TB.

Evidence that phytochrome functions as a protein kinase in plant light signalling.

It has been suggested that plant phytochromes are autophosphorylating serine/threonine kinases. However, the biochemical properties and functional roles of putative phytochrome kinase activity in plant light signalling are largely unknown. Here, we describe the biochemical and functional characterization of Avena sativa phytochrome A (AsphyA) as a potential protein kinase. We provide evidence that phytochrome-interacting factors (PIFs) are phosphorylated by phytochromes in vitro. Domain mapping of AsphyA shows that the photosensory core region consisting of PAS-GAF-PHY domains in the N-terminal is required for the observed kinase activity. Moreover, we demonstrate that transgenic plants expressing mutant versions of AsphyA, which display reduced activity in in vitro kinase assays, show hyposensitive responses to far-red light. Further analysis reveals that far-red light-induced phosphorylation and degradation of PIF3 are significantly reduced in these transgenic plants. Collectively, these results suggest a positive relationship between phytochrome kinase activity and photoresponses in plants.

Constitutive expression of a fungus-inducible carboxylesterase improves disease resistance in transgenic pepper plants.

MAIN CONCLUSION: Resistance against anthracnose fungi was enhanced in transgenic pepper plants that accumulated high levels of a carboxylesterase, PepEST in anthracnose-susceptible fruits, with a concurrent induction of antioxidant enzymes and SA-dependent PR proteins. A pepper esterase gene (PepEST) is highly expressed during the incompatible interaction between ripe fruits of pepper (Capsicum annuum L.) and a hemibiotrophic anthracnose fungus (Colletotrichum gloeosporioides). In this study, we found that exogenous application of recombinant PepEST protein on the surface of the unripe pepper fruits led to a potentiated state for disease resistance in the fruits, including generation of hydrogen peroxide and expression of pathogenesis-related (PR) genes that encode mostly small proteins with antimicrobial activity. To elucidate the role of PepEST in plant defense, we further developed transgenic pepper plants overexpressing PepEST under the control of CaMV 35S promoter. Molecular analysis confirmed the establishment of three independent transgenic lines carrying single copy of transgenes. The level of PepEST protein was estimated to be approximately 0.002 % of total soluble protein in transgenic fruits. In response to the anthracnose fungus, the transgenic fruits displayed higher expression of PR genes, PR3, PR5, PR10, and PepThi, than non-transgenic control fruits did. Moreover, immunolocalization results showed concurrent localization of ascorbate peroxidase (APX) and PR3 proteins, along with the PepEST protein, in the infected region of transgenic fruits. Disease rate analysis revealed significantly low occurrence of anthracnose disease in the transgenic fruits, approximately 30 % of that in non-transgenic fruits. Furthermore, the transgenic plants also exhibited resistance against C. acutatum and C. coccodes. Collectively, our results suggest that overexpression of PepEST in pepper confers enhanced resistance against the anthracnose fungi by activating the defense signaling pathways.

Targeted Lesion Generation Through the Skull Without Aberration Correction Using Histotripsy.

This study demonstrates the ability of histotripsy to generate targeted lesions through the skullcap without using aberration correction. Histotripsy therapy was delivered using a 500 kHz, 256-element hemispherical transducer with an aperture diameter of 30 cm and a focal distance of 15 cm fabricated in our lab. This transducer is theoretically capable of producing peak rarefactional pressures, based on linear estimation, (p-)LE, in the free field in excess of 200MPa with pulse durations 2 acoustic cycles. Three excised human skullcaps were used displaying attenuations of 73-81% of the acoustic pressure without aberration correction. Through all three skullcaps, compact lesions with radii less than 1mm were generated in red blood cell (RBC) agarose tissue phantoms without aberration correction, using estimated (p-)LE of 28-39MPa, a pulse repetition frequency of 1Hz, and a total number of 300 pulses. Lesion generation was consistently observed at the geometric focus of the transducer as the position of the skullcap with respect to the transducer was varied, and multiple patterned lesions were generated transcranially by mechanically adjusting the position of the skullcap with respect to the transducer to target different regions within. These results show that compact, targeted lesions with sharp boundaries can be generated through intact skullcaps using histotripsy with very short pulses without using aberration correction. Such capability has the potential to greatly simplify transcranial ultrasound therapy for non-invasive transcranial applications, as current ultrasound transcranial therapy techniques all require sophisticated aberration correction.

A blind reversible robust watermarking scheme for relational databases.

Protecting the ownership and controlling the copies of digital data have become very important issues in Internet-based applications. Reversible watermark technology allows the distortion-free recovery of relational databases after the embedded watermark data are detected or verified. In this paper, we propose a new, blind, reversible, robust watermarking scheme that can be used to provide proof of ownership for the owner of a relational database. In the proposed scheme, a reversible data-embedding algorithm, which is referred to as "histogram shifting of adjacent pixel difference" (APD), is used to obtain reversibility. The proposed scheme can detect successfully 100% of the embedded watermark data, even if as much as 80% of the watermarked relational database is altered. Our extensive analysis and experimental results show that the proposed scheme is robust against a variety of data attacks, for example, alteration attacks, deletion attacks, mix-match attacks, and sorting attacks.

High prevalence of Beijing and EAI4-VNM genotypes among M. tuberculosis isolates in northern Vietnam: sampling effect, rural and urban disparities.

A total of 221 isolates of M. tuberculosis were sampled from hospitals and the general population in the northern plain of Vietnam, one of the most populated region of the country. Genotypic composition and diversity were characterized, and we investigated how they are affected by sampling (hospital vs. general population), correcting for potential confounding effects (location, age and gender of the patients). Spoligotyping and 12 MIRU-VNTR typing were used as first line. Then 15 MIRU-VNTR standard set was used, making 21 MIRU-VNTR typing for the clustered isolates. Result showed that 8 lineages and 13 sub-lineages were circulating in the region. The most predominant lineages were Beijing (38.5%) and EAI (38.5%). Others appeared with small proportions H (1.4%), LAM (1.8%), T (8.1%), X (0.9%), MANU (2.3%), and Zero (0.4%). Higher clustering rate was found in the hospital samples (17.9% in urban and 19.2% in rural areas) compared to the population ones (0%). The typical Vietnamese EAI4-VNM sub-lineage of EAI lineage accounted for 67% of EAI strains and was associated with older ages. Beijing genotypes were associated with younger, urban population and were characterized by high clustering rates. These characteristics strongly suggest that Beijing strains are invading the population, replacing the local EAI-VNM4, thus predicting a more serious tuberculosis situation in the future in the absence of more effective control strategies.

Trauma quality improvement in low and middle income countries of the Asia-Pacific region: a mixed methods study.

BACKGROUND: Quality Improvement (QI) programs have been shown to be a valuable tool to strengthen care of severely injured patients, but little is known about them in low and middle income countries (LMIC). We sought to explore opportunities to improve trauma QI activities in LMIC, focusing on the Asia-Pacific region. METHODS: We performed a mixed methods research study using both inductive thematic analysis of a meeting convened at the Royal Australasian College of Surgeons, Melbourne, Australia, November 21-22, 2010 and a pre-meeting survey to explore experiences with trauma QI activities in LMIC. Purposive sampling was employed to invite participants with demonstrated leadership in trauma care to provide diverse representation of organizations and countries within Asia-Pacific. RESULTS: A total of 22 experts participated in the meeting and reported that trauma QI activities varied between countries and organizations: morbidity and mortality conferences (56 %), monitoring complications (31 %), preventable death studies (25 %), audit filters (19 %), and statistical methods for analyzing morbidity and mortality (6 %). Participants identified QI gaps to include paucity of reliable/valid injury data, lack of integrated trauma QI activities, absence of standards of care, lack of training in QI methods, and varying cultures of quality and safety. The group highlighted barriers to QI: limited engagement of leaders, organizational diversity, limited resources, heavy clinical workload, and medico-legal concerns. Participants proposed establishing the Asia-Pacific Trauma Quality Improvement Network (APTQIN) as a tool to facilitate training and dissemination of QI methods, injury data management, development of pilot QI projects, and advocacy for quality trauma care. CONCLUSIONS: Our study provides the first description of trauma QI practices, gaps in existing practices, and barriers to QI in LMIC of the Asia-Pacific region. In this study we identified opportunities for addressing these challenges, and that work will be supported by APTQIN.

Antibodies to Helicobacter pylori, CagA, VacA in the patients with gastroenteropathy and in healthy persons

Study was performed on 100 serum samples of patients (15-70 aged) treated of gastro-duodenal diseases and 31 healthy persons by Immunoblot assay. The results showed that: the prevalence of H.pylori positive in patients with gastric ulcer, duodenal ulcer and gastritis was 76.5, 95.8 and 73%, respectively. The prevalence of H. pylori seropositive was found 64.5% in healthy persons. The prevalence of anti-CagA and anti-VacA antibodies was 86.2% and 60.6% (respectively) in patients and was 70% and 40% (respectively) in healthy person.