Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.

Whole genome sequencing has increasingly become the essential method for studying the genetic mechanisms of antimicrobial resistance and for surveillance of drug-resistant bacterial pathogens. The majority of bacterial genomes sequenced to date have been sequenced with Illumina sequencing technology, owing to its high-throughput, excellent sequence accuracy, and low cost. However, because of the short-read nature of the technology, these assemblies are fragmented into large numbers of contigs, hindering the obtaining of full information of the genome. We develop Pasa, a graph-based algorithm that utilizes the pangenome graph and the assembly graph information to improve scaffolding quality. By leveraging the population information of the bacteria species, Pasa is able to utilize the linkage information of the gene families of the species to resolve the contig graph of the assembly. We show that our method outperforms the current state of the arts in terms of accuracy, and at the same time, is computationally efficient to be applied to a large number of existing draft assemblies.

AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance.

We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz .

Potent IPTG-inducible integrative expression vectors for production of recombinant proteins in Bacillus subtilis.

The IPTG-inducible promoter family, Pgrac, allows high protein expression levels in an inducible manner. In this study, we constructed IPTG-inducible expression vectors containing strong Pgrac promoters that allow integration of the transgene at either the amyE or lacA locus or both loci in Bacillus subtilis. Our novel integrative expression vectors based on Pgrac promoters could control the repression of protein production in the absence and the induction in the presence of an inducer, IPTG. The ß-galactosidase (BgaB) protein levels were 9.0%, 15% and 30% of the total cellular protein in the B. subtilis strains carrying single cassettes with the Pgrac01, Pgrac100 or Pgrac212 promoters, respectively. The maximal induction ratio of Pgrac01-bgaB was 35.5 while that of Pgrac100-bgaB was 7.5 and that of Pgrac212-bgaB was 9. The inducible expression of GFP and BgaB protein was stably maintained for 24 h, with the highest yield of GFP being 24% of cell total protein while the maximum amount of BgaB was found to be 38%. A dual integration of two copies of the gfp+ gene into the B. subtilis genome at the lacA and amyE loci resulted in a yield of about 40% of total cellular protein and a 1.74-fold increase in GFP compared with single-integrated strains containing the same Pgrac212 promoter. The capability of protein production from low to high levels of these inducible integrative systems is useful for fundamental and applied research in B. subtilis.

Neisseria gonorrhoeae FC428 Subclone, Vietnam, 2019-2020.

Among 114 clinical Neisseria gonorrhoeae isolates collected in Vietnam during 2019-2020, we detected 15 of subclone sequence type 13871 of the FC428 clonal complex. Fourteen sequence type 13871 isolates with mosaic penA allele 60.001 were ceftriaxone or cefixime nonsusceptible, and 3/14 were azithromycin nonsusceptible. Emergence of this subclone threatens treatment effectiveness.

The columbamine O-methyltransferase gene (CoOMT) is capable of increasing alkaloid content in transgenic tobacco plants.

BACKGROUND: In the alkaloid biosynthetic pathways of Stephania and Rannunculaceae, columbamine O-methyltransferase (CoOMT) is an important enzyme that catalyses the formation of the tetrahydropalmatin (rotundin) biosynthesis pathway. In this study, the transgenic construct pBI121-35S-CoOMT-cmyc-Kdel was designed successfully. METHODS AND RESULTS: The real-time RT-PCR results proved that the CoOMT transgene was successfully introduced into Nicotiana tabacum L. plants and produced mRNA. Its transcription levels in three transgenic tobacco lines, T0-7, T0-9, and T0-20, in the T0 generation were higher than those in wild-type tobacco plants. By analysing Western blots and ELISAs, three T0 generation transgenic tobacco lines also expressed recombinant CoOMT (rCoOMT) protein with a molecular weight of approximately 40 kDa, and its contents ranged from 0.048 µg mg-1 to 0.177 µg mg-1. These data illustrated that the CoOMT transgene was expressed; thus, the rCoOMT protein synthesis efficiency increased significantly in comparison with that of the wild-type tobacco plants. The total alkaloid contents ranged from 2.12 g 100 g-1 (of dry weight) to 3.88 g 100 g-1 (of dry weight). The T0-20 plant had the highest total alkaloid content (3.88 g 100 g-1 of dry weight), followed by the T0-7 line (2.75 g 100 g-1 of dry weight). The total alkaloid contents of the CoOMT transgenic tobacco lines increased by approximately 1.09-1.83-fold compared to the wild-type tobacco plants. CONCLUSIONS: This is the first study on the transformation and expression of the CoOMT gene in N. tabacum plants. Initial results of the analysis of transgenic plants proved that the transgenic structure pBI121- CoOMT-Cmyc-Kdel can be used for transformation into Stephania plants.

Strong Negative Association between Cesarean Delivery and Early Initiation of Breastfeeding Practices among Vietnamese Mothers-A Secondary Analysis of the Viet Nam Sustainable Development Goal Indicators on Children and Women Survey.

Early initiation of breastfeeding (EIBF) involves feeding a newborn with the mother's breast milk within the first hour of delivery. The prevalence of EIBF in Vietnam has recently shown a downward trend. The present study aimed to demonstrate the current prevalence of EIBF practices and identify factors associated with EIBF among Vietnamese mothers with children under 24 months of age. This study was a secondary analysis of data from the Viet Nam Sustainable Development Goal Indicators on Children and Women (SDGCW) survey 2020-2021. The study participants included 1495 mothers extracted from the SDGCW dataset. Descriptive statistics and logistic regression analyses were performed. The prevalence of EIBF practice was 25.5% among all mothers, 31.9% among vaginal-delivery mothers groups, and 9.0% among cesarean-section mothers groups. Factors negatively associated with EIBF were younger age (0.18 times), cesarean delivery (0.25 times), and absence of skin-to-skin contact with newborns immediately after birth (0.43 times). The prevalence of EIBF among Vietnamese mothers was found to be substantially low, especially among those who underwent cesarean delivery. EIBF should be promoted among younger mothers and those who underwent cesarean delivery.

Reliability of online dental final exams in the pre and post COVID-19 era: A comparative study.

Amidst the fourth COVID-19 wave in Viet Nam, national lockdowns necessitated the closure of numerous dental schools. To assess DDS (Doctor of Dental Surgery) graduation exams, this study analyzed their 2021 implementation in comparison to onsite exams conducted in 2020 and 2022 at the Faculty of Odonto-Stomatology, University of Medicine and Pharmacy at Ho Chi Minh City, Viet Nam (FOS-UMPH). The final online examination comprises two main sessions: a synchronous online examination using FOS-UMPH e-Learning for theories (consisting of 200 MCQs and 3 written tests with 3 clinical situations needed be solved) and a synchronous online examination using Microsoft Teams for practicum (comprising of 12 online OSCE stations). The final grades were evaluated using the same metrics in face-to-face final examinations in 2022 and 2020. A total of 114, 112 and 95 students were recruited for the first-time exams in 2020, 2021 and 2022, respectively. In order to analyze the reliability, histogram and k-mean clustering were employed. The histograms from 2020, 2021 and 2022 showed a striking similarity. However, fewer students failed in 2021 and 2022 (13% and 12.6%, respectively) compared to 2020 (28%), with clinical problem-solving part grades (belonging to theory session) being notably higher in 2021 and 2022. Intriguingly, the MCQ Score results showed the identical patterns. The courses of orthodontics, dental public health, and pediatrics subjects (in the group of prevention and development dentistry) stood out for their exceptional accuracy across both sessions. After examining data gathered over three years, we identified three distinct clusters: the first comprised of scattered average and low scores, the second characterized by high scores but unstable and scattered and the third cluster boasting consistently high and centered scores. According to our study, online and onsite traditional graduation exam results are relatively equivalent, but additional measures are necessary to standardize the final examination and adapt to the new normal trend in dental education.

Evaluating e-learning on an international scale: An audit of computer simulation learning materials in the field of dentistry.

BACKGROUND/PURPOSE: Global networking and e-learning courses are an effective strategy for sharing educational content and there is potential scope to use e-learning technology in dental education. Therefore, this study aimed to explicate the challenges encountered in international e-learning use and decipher optimum solutions for disseminating course/systems on an international scale. MATERIALS AND METHODS: An e-learning course with four computer-assisted simulation materials developed among international faculties was provided to dental undergraduates at dental schools in Japan and Vietnam in 2020. A post-questionnaire survey plus pre- and post-tests were conducted to obtain learners' feedback and assess the success of the course's implementation. RESULTS: Altogether, 41 students participated, with a response rate of 78.8%. The mean post-test score was significantly higher than that of the pre-test (p < 0.001). Students from both groups felt that e-learning was beneficial, useful for their future, and should be continued. CONCLUSION: This study showed that e-learning/course provision could be achieved at an international level by using a common online system, which is beneficial for students to gain a wider perspective and global dental education. Learners indicated that they learned without any major problems in learning operations. This type of educational material creation and course implementation is extremely important in global networking and dental education in the present era; and communication and cooperation between the faculties was important for course provision. More countries should be included in future studies to ensure that it has global application.

Costs and Cost-Effectiveness of mCME Version 2.0: An SMS-Based Continuing Medical Education Program for HIV Clinicians in Vietnam.

BACKGROUND: The Mobile Continuing Medical Education (mCME) 2.0 project was a randomized controlled trial that found that a 6-month text message-based CME intervention improved both the use of online medical training resources and medical knowledge among a cadre of HIV clinicians in Vietnam. This companion study analyzed intervention costs and cost-effectiveness. METHODS: We conducted (1) a financial analysis based on costs incurred during the trial's planning and implementation; (2) an economic analysis to consider resource utilization; and (3) cost-effectiveness analyses to estimate cost inputs relative to impact: increase in self-study (measured by visits to online courses) and increase in knowledge (measured by exam score improvement) (in 2016 US$). Finally, we estimated the economic cost of a 9-month national program and a 10-year scaled-up model (in 2021 US$). RESULTS: The total financial cost of the intervention was US$49,552; the main cost drivers were personnel time (71.4%) and technology inputs (14.9%). The total economic cost was estimated at US$92,212, with the same key cost inputs (representing 77.7% and 8.0%, respectively, of total costs). The financial cost per 10% increase in accessing online courses was US$923, while the cost of improving knowledge, measured by a 10% improvement in mean exam score across the study population, was US$32,057 (US$605 per intervention clinician). The comparable total economic cost of each improvement, respectively, was US$1,770 and US$61,452 (US$1,159 per intervention clinician). A future 9-month national program was estimated to cost US$37,403, while the full 10-year scaled-up program was estimated at US$196,446. CONCLUSIONS: This analysis indicates that leveraging mobile technology could be a feasible way to provide distance learning to health professions across Vietnam at a relatively low cost. Given the need for practical ways to expand CME in resource-constrained regions of the world, this approach warrants further study and possible adoption.

Role of Immunotherapy in Pulmonary Angiosarcoma: A Case Report.

Pulmonary angiosarcoma is a rare clinical entity with a poor prognosis and no established therapeutic strategies. We present the first case to our knowledge of metastatic pulmonary angiosarcoma, treated with checkpoint inhibitor immunotherapy, and have an excellent response. Until now, patient has been treated with immunotherapy for 1 year, and his disease is stable and well-tolerated.

Physical Activity and Plasma Glucose Control among Diabetic Patients Attending Outpatients Clinics in Hanoi, Vietnam.

Reaching the recommendation on physical activity (PA) for health is highly important to effectively manage blood glucose in patients with type 2 diabetes (T2D). The aims of this study were to assess the level and pattern of PA among T2D outpatients and to relate PA levels to glucose control. A cross-sectional study was conducted in outpatient clinics in Hanoi, Vietnam. PA levels were reported using the Global Physical Activity Questionnaire (GPAQ) version 2.0. Participants meeting the WHO recommendations on PA for health or not were respectively categorized as "sufficiently active" and "insufficiently active". FPG < 7.2 mmol/L was defined as controlled plasma glucose. In total, 407 participants with T2D (55% women, mean (SD) age 61.6 (9.7) years) were included. The fraction of T2D outpatients reporting as insufficiently active was 21%. The lowest amount of energy expenditure was from transport activities (travel from and to places). On multivariate logistic regression, being sufficiently active was associated with a two-fold increased likelihood of having better glycemic control. The findings warrant action plans to increase physical activity in general and in specific active transport for T2D patients in Vietnam.

CD40LG mutations in Vietnamese patients with X-linked hyper-IgM syndrome; catastrophic anti-phospholipid syndrome as a new complication.

BACKGROUND: X-linked hyper-IgM syndrome (XHIGM) is a rare primary immunodeficiency caused by CD40 ligand defects. METHODS: We identified three patients with XHIGM in Ho Chi Minh City, Vietnam. Whole-exome sequencing, immunological analyses and western blot were performed to investigate phenotypic and genotypic features. RESULTS: Despite showing symptoms typical of XHIGM, including recurrent sinopulmonary infections, oral ulcers and otitis media, the diagnosis was significantly delayed. One patient developed anti-phospholipid syndrome, which has been documented for the first time in XHIGM syndrome. Two patients had elevated IgM levels and all of them had low IgG levels. Exome sequencing revealed mutations in the CD40LG gene: one novel splicing mutation c.156+2T>A and two previously characterised mutations (non-frameshift deletion c.436_438delTAC, stop-gain c.654C>A). Due to these mutations, the CD40 ligand was not expressed in any of the three patients, as demonstrated by western blot analysis. CONCLUSION: This is the first report of XHIGM syndrome in Vietnam indicates that an effective diagnostic strategy, such as sequencing analysis, contributes to reliable diagnosis and subsequent therapy.

Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam.

A second cluster of COVID-19 cases imported from Europe occured in Vietnam from early March 2020. We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value <30) admitted to the National Hospital for Tropical Diseases in Hanoi between March 6 and April 15 2020. Whole SARS-CoV-2 genomes from these patients were sequenced using Illumina Miseq and analysed for common genetic variants and relationships to local and globally circulating strains. Results showed that 32 cases were Vietnamese with a median age of 37 years (range 15-74 years), and 23 were male. Most cases were acquired outside Vietnam, mainly from the UK (n = 15), other European countries (n = 14), Russia (n = 6) and countries in Asia (n = 3). No cases had travelled from China. Forty-one cases had symptoms at admission, typically dry cough (n = 36), fever (n = 20), sore throat (n = 14) and diarrhoea (n = 12). Hospitalisation was long with a median of 25 days, most commonly from 20-29 days. All SARS-CoV-2 genomes were similar (92-100% sequence homology) to the reference sequence Wuhan_1 (NC_045512), and 32 strains belonged to the B.1.1 lineage. The three most common variants were linked, and included C3037T, C14408T (nsp12: P323L) and A23403G (S: D614G) mutations. This group of mutations often accompanied variant C241T (39/44 genomes) or GGG 28881..28883 AAC (33/44 genomes). The prevalence of the former reflected probable European origin of viruses, and the transition D614G was dominant in Vietnam. New variants were identified; however, none could be associated with disease severity.

Unpacking the "Black Box": How an SMS-Based Continuing Medical Education Intervention Improved Medical Knowledge Among HIV Clinicians in Vietnam.

BACKGROUND: A mobile-based continuing medical education (mCME) intervention implemented over 6 months between 2016 and 2017, consisting of daily SMS multiple choice quizzes and access to online daily readings and CME courses, was shown to be effective in increasing medical knowledge among HIV providers in Vietnam. We hypothesized this improvement was a result of "lateral learning," a process in which the daily SMS quizzes acted as a stimulus for interacting with other study materials. METHODS: We explored how study materials directly provided by the intervention-the daily readings and the online CME courses-and independent study behaviors, such as using medical textbooks and reviewing national guidelines, contributed to medical knowledge as measured by baseline and endline exams. At baseline, there were 53 participants each in the intervention and control groups (N=106). Using linear regression models, we estimated the association between intervention-prompted and independent study behaviors and endline test scores. We also conducted a series of interaction analyses to test the extent to which the effect of daily quiz performance on endline test scores depended on use of the intervention-prompted or independent study materials. Finally, we estimated the proportion of variance in endline test scores explained by each of the intervention-prompted behaviors. RESULTS: The average medical knowledge test score among all participants was 46% at baseline and 54% at endline. Among the intervention group, 82% of the daily quizzes were answered, although only about half were answered correctly. Responding to the daily quizzes (ß=0.24; P=.05), quiz performance (ß=0.42; P<.001), and accessing daily readings (ß=0.22; P=.06) were statistically significantly associated with higher endline test scores. While accessing the online CME courses and some of the independent study behaviors, such as use of medical textbooks, had positive associations with endline test scores, none reached statistical significance. Quiz performance explained 51% of the variation in endline test scores. Interaction analysis found that quiz performance had a stronger, but not statistically significant, association with endline test scores when both daily readings (ß=0.87; P=.08) and online CME courses (ß=0.25; P=.09) were accessed more frequently. CONCLUSION: In mCME interventions, daily SMS quizzes can effectively act as a stimulus for uptake of study behaviors when paired with access to relevant readings and online courses. While further investigation is needed to more fully understand the role of outside study materials, we believe this model has the potential for further use in Vietnam and other low-resource settings.

Benefits and Limitations of Text Messages to Stimulate Higher Learning Among Community Providers: Participants' Views of an mHealth Intervention to Support Continuing Medical Education in Vietnam.

BACKGROUND: A randomized controlled trial was conducted in 2015 to evaluate a mobile continuing medical education (mCME) intervention that provided daily text messages to community-based physicians' assistants (CBPAs) in Thai Nguyen Province, Vietnam. Although the intervention failed to improve medical knowledge over a 6-month period, a companion qualitative study provided insights on the views and experiences of intervention participants. METHODS: We conducted focus group discussions (FGDs) and in-depth interviews (IDIs) among participants randomized to receive text messages containing either simple medical facts or quiz questions. Trained interviewers collected data immediately following the conclusion of the trial in December 2015. Using semi-structured question guides, respondents were queried on their views of the intervention, positive and negative, and perceived impacts of the intervention. During analysis, after learning that the intervention had failed to increase knowledge among participants, we also examined reasons for lack of improvement in medical knowledge. All analyses were performed in NVivo using a thematic approach. RESULTS: A total of 70 CBPAs engaged in one of 8 FGDs or an IDI. One-half were men; average age among all respondents was 40 years. Most (81%) practiced in rural settings and most (51%) focused on general medicine. The mean length of work experience was 3 years. All respondents made positive comments about the intervention; convenience, relevance, and quick feedback (quiz format) were praised. Downsides encompassed lack of depth of information, weak interaction, technology challenges, and challenging/irrelevant messages. Respondents described perceived impacts encompassing increased motivation, knowledge, collegial discussions, Internet use to search for more information, and clinical skills. Overall, they expressed a desire for the intervention to continue and recommended expansion to other medical professionals. Overreliance on the text messages, lack of effective self-study, and technical/language-based barriers may be potential explanations for intervention failure. CONCLUSION: As a form of mCME, daily text messages were well-received by community-level health care providers in Vietnam. This mCME approach appears very promising in low-resource environments or where traditional forms of CME are impractical. Future models might consider enhancements to foster linkages to relevant medical materials, improve interaction with medical experts, and tailor medical content to the daily activities of medical staff.