Response of the Northeast China grain market to climate change based on the gravity model approach.

Scientific evidence has revealed that climate change negatively affects agricultural crop production both regionally and globally. Previous studies have indicated that the role of climate change is significant in some parts of China. Thus, assessing the impact of the future climate on the grain market is vital for ensuring regional and national food security. In this study, regional climate model (RCM 4.5 and 8.5) simulations were employed to investigate the role of future climate change on a major grain-producing market in China (Northeast China). For this purpose, historical (2004-2017) and future (2020-2076) data were applied in the gravity model to examine the effects of climate change on the Northeast China grain market. The results revealed that the maximum temperature is a crucial climate factor that significantly affects the grain market. The analysis revealed that precipitation was positively related and that the temperature was significantly negatively related to domestic consumption and exports of rice, maize, and soybean. Moreover, the analysis of the RCM (4.5 and 8.5) simulations revealed a negative contribution of the maximum temperature to domestic consumption and export levels. Overall, the analysis enhances our understanding of the impacts of climate change on the Northeast China grain market.

Lipid Composition, Cytotoxic and Acetylcholinesterase Inhibition Effects of Two Brown Algae Species Lobophora tsengii and Lobophora australis.

In this paper, the lipid classes, compositions of the neutral lipids, phospholipids and fatty acids, acetylcholinesterase inhibition and cytotoxic activity of two brown algae Lobophora tsengii D. Tien & Z. Sun and Lobophora australis Z. Sun, F. C. Gurgel & H. Kawai have been investigated. The polar lipid class had the highest content in total lipid (TL) (43.47% in L. tsengii and 48.95% in L. australis). Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were the main components in the phospholipids of two studied brown algae with contents varied from 32.27% to 52.33%. Total lipids were rich in PUFA (42.54% of total fatty acids for L. australis and 32.98% for L. tsengii), with EPA (11.46%, 14.30%) and AA (8.0%, 11.96%). L. tsengii methanol extract inhibited acetylcholinesterase (AChE) in in vitro assay with an IC50 value of 25.45 µg/mL. Both Lobophora methanol extracts display cytotoxic effects against four human cancer cell lines (KB, MCF7, HepG2 and A549) with IC50 in the range of 21.11-83.61 µg/mL. Especially, L. australis extract showed a strong cytotoxicity against KB cell lines with IC50 value of 21.11±0.39 µg/mL.

Antiviral activity of SAFER®, a commercial acidifying desiccant powder, against African swine fever virus.

African swine fever (ASF) is one of the deadliest swine diseases, causing significant economic losses, threatening food security, and limiting pig production in affected countries. In the absence of an effective ASF vaccine, prevention and control of ASF depend mainly on effective biosecurity measures. In this study, the efficacy of SAFER®, a powdered disinfectant containing clay, an acid complex, and the active ingredient thyme essential oil, was tested against the ASF virus. The results showed that ASFV isolate (VNUA/HY/ASF1/Vietnam/2019) was inactivated by 3.5 and 5 Log10HAD50/ml after 20 and 120 min of treatment with SAFER®, respectively. When body fluids contaminated with ASFV, such as blood, saliva, urine, and feces, were treated with SAFER® for 20 min, the ASFV titer was reduced by 1.6, 2.2, 2.0, and 2.2 Log10HAD50/ml, respectively.

Factors predicting menstrual irregularity among university students in Ho Chi Minh City, Vietnam: A cross-sectional study.

Background: University students often face menstrual irregularities, particularly among healthcare students, due to rigorous study environments, such as night duties resembling professional staff responsibilities. Objective: This study aimed to examine the prevalence of and factors predicting menstrual irregularities among female students in Ho Chi Minh City, Vietnam. Methods: A cross-sectional study was conducted from April to July 2023 at the University of Medicine and Pharmacy at Ho Chi Minh City (UMP). Data were collected using self-administered questionnaires comprising sections on personal background, menstrual cycles, sleep duration, and academic stress. Descriptive statistics and multiple logistic regression were employed for data analysis. Results: Approximately 48.3% of participants experienced menstrual irregularities. Overweight or obese students were more likely to experience irregularities compared to those of normal weight (AOR = 7.56, 95% CI = 1.34, 80.8). Nursing majors (including nursing, midwifery, and anesthesia resuscitation nursing) showed a higher likelihood of irregularities compared to other majors (AOR = 2.5, 95% CI = 1.35, 4.13). Conclusion: This study highlights a significant prevalence of menstrual irregularities among female students. Interventions in nursing education should focus on promoting healthy lifestyles and regular physical activity to manage weight and mitigate menstrual irregularities.

Evaluation test and analysis of a microneedle and iontophoresis based medical device "CELLADEEP Patch" in skin improvement on ex vivo human-derived skin tissue models.

BACKGROUND: Microneedles are tiny needles, typically ranging from tens to hundreds of micrometers in length, used in various medical procedures and treatments. The tested medical device named "CELLADEEP Patch" a dissolvable microneedle therapy system (MTS), made of hyaluronic acid and collagen. And the iontophoresis technique is also applied in the system. The study aimed to evaluate the effectiveness of the "CELLADEEP Patch" in skin improvement. METHODS: Ex vivo human-derived skin tissue models were used in this study and they were divided into three different groups, namely, the Untreated Group, the Negative Control Group, and the Test Group respectively. The Untreated Group received no treatment measures, the Negative Control Group was exposed to ultraviolet B radiation (UVB) irradiation, and the Test Group was exposed to UVB irradiation and treated with "CELLADEEP Patch". Skin moisture content, transdermal water loss, and skin elasticity were evaluated by three clinical devices. Additionally, histological staining and related mRNA expression levels were also analyzed. RESULTS: The results of skin moisture content, transdermal water loss, and skin elasticity evaluation consistently illustrated that the application of "CELLADEEP Patch" led to remarkable skin improvement. And the analysis of histological staining images also confirmed the effectiveness of the "CELLADEEP Patch", especially for increasing collagen density. Moreover, the upregulation of Collagen type 1 a (COL1A1) and hyaluronan synthase 3 mRNA expression and the decrease of Matrix metalloproteinase 1 (MMP-1) and Interleukin-1 beta (IL-1ß) mRNA expression reflected its wrinkle improvement, moisturizing and anti-inflammation function. CONCLUSION: "CELLADEPP Patch", the MTS combined with the iontophoresis technique, exhibits its effectiveness in moisturizing, skin elasticity improvement, and anti-inflammatory function when applied to ex vivo human-derived skin tissue models in experiments. The study has contributed to the understanding of the "CELLADEPP Patch" and laid the foundation for subsequent animal experiments and clinical trials.

Association between SARC-F scores and risk of adverse outcomes in older patients with cardiovascular disease: a prospective study at a tertiary hospital in the south of Vietnam.

Introduction: Older patients typically face elevated mortality rates and greater medical resource utilization during hospitalizations compared to their younger counterparts. Sarcopenia, serving as a prognostic indicator, is related to disability, diminished quality of life, and increased mortality. The SARC-F questionnaire, known for its cost-effectiveness, offers a valuable means of assessing sarcopenia. This study aims to explore the association between SARC-F scores and risk of adverse outcomes in elderly patients with cardiovascular disease at a Ho Chi Minh City hospital. Method: Participants aged 60 and above, admitted to the Department of Cardiology - Interventional and Cardiovascular Emergency of Thong Nhat Hospital in Ho Chi Minh City from November 2021 to June 2022, were recruited for the prospective, single-center study. The prognostic outcomes included all-cause death and the initial occurrence of emergency re-hospitalization within 6 months' post-discharge. The Kaplan-Meier analysis compared the overall survival rates between different SARC-F score groups. Results: The study enrolled 285 patients with a median age of 74 (67, 81). During a 6-month follow-up period, there were 14 cases of mortality. A SARC-F score of 4 or higher was significantly associated with an increased risk of all-cause mortality, with HR of 2.02 (95% CI: 1.39-2.92, p < 0.001), and higher incidence of re-hospitalization events with RR of 1.66 (95% CI: 1.06 to 2.59, p = 0.026). Kaplan-Meier survival analysis indicated a notably higher mortality rate in the patients with high SARC-F scores (p < 0.001). Conclusion: In elderly patients with cardiovascular disease, the SARC-F questionnaire could serve as a simple and cost-effective method for detecting mortality and the risk of re-hospitalization.

Recent advances in biosensors for screening plant pathogens.

Worldwide, plant pathogens have been a considerably important cause of economic loss in agriculture especially in the decades of agricultural intensification. The increasing losses in agriculture due to biotic plant diseases have drawn attention towards the development of plant disease analyzing methods. In this context, biosensors have emerged as significantly important tools which help farmers in on-field diagnosis of plant diseases. Compared to traditional methods, biosensors have outstanding features such as being highly sensitive and selective, cost-effective, portable, fast and user-friendly operation, and so on. There are three common types of biosensors including electrochemical, fluorescent, and colorimetric biosensors. In this review, some common biotic plant diseases caused by fungi, bacteria, and viruses are first summarized. Then, current advances in developing biosensors are discussed.

Rmg10, a novel wheat blast resistance gene derived from Aegilops tauschii.

Wheat blast, caused by Pyricularia oryzae (syn. Magnaporthe oryzae) pathotype Triticum (MoT), is a devastating disease that can result in up to 100% yield loss in affected fields. To find new resistance genes against wheat blast, we screened 199 accessions of Aegilops tauschii Coss., the D genome progenitor of common wheat (Triticum aestivum L.) by seedling inoculation assays with Brazilian MoT isolate Br48, and found 14 resistant accessions. A synthetic hexaploid wheat line (Ldn/KU-2097) derived from a cross between the T. turgidum cultivar 'Langdon' (Ldn) and resistant Ae. tauschii accession KU-2097 exhibited resistance in seedlings and spikes against Br48. In an F2 population derived from 'Chinese Spring' (CS) × Ldn/KU-2097, resistant and susceptible individuals segregated in a 3:1 ratio, suggesting that the resistance from KU-2097 is controlled by a single dominant gene. We designated this gene Rmg10. Genetic mapping using an F2:3 population from the same cross mapped the RMG10 locus to the short arm of chromosome 2D. Rmg10 was ineffective against Bangladesh isolates but effective against Brazilian isolates. Field tests in Bolivia showed increased spike resistance in a synthetic octaploid wheat line produced from a cross between common wheat cultivar 'Gladius' and KU-2097. These results suggest that Rmg10 would be beneficial in farmers' fields in South America.

Adherence to dietary guidelines and associated factors among rural Australian cancer survivors: a cross-sectional study.

PURPOSE: This study aimed to explore levels of adherence to dietary guidelines, and factors associated with dietary guideline adherence, among rural Australian cancer survivors. METHODS: A cross-sectional study was undertaken. We recruited a convenience sample of adults with cancer who attended the chemotherapy day unit or allied health appointments at a rural hospital in Baw Baw Shire, Victoria, Australia, between August 2017 and December 2021. Dietary guideline adherence was assessed by cross-referencing participants' responses to an adapted version of the Dietary Questionnaire for Epidemiological Studies with dietary recommendations in Australian dietary guidelines. Binary logistic regression was used to assess factors associated with dietary guideline adherence for fruits and whole red meats. RESULTS: There were 107 rural cancer survivors (median age, 67 years). Dietary guideline adherence was highest for alcohol (88%) followed by whole red meats (63%), fruits (56%), processed red meats (24%), cereals/breads/grains (7%), and vegetables (4%). Relative to those aged < 65 years, 65-74-year-olds had 5.7-fold greater odds (adjusted odds ratio (aOR) = 5.74, 95% confidence interval (CI) = 1.91-17.17) of adhering to the dietary guideline for fruits. Relative to those who had completed/ceased treatment, participants who were currently receiving treatment had 78% lower odds (aOR = 0.22, 95% CI = 0.09-0.59) of adhering to the dietary guideline for fruits. CONCLUSION: This study contributes preliminary data on adherence to dietary guidelines and associated factors among rural Australian cancer survivors. Dietary guideline adherence varied across food groups and was mostly low, albeit not markedly worse than Australia's national population for the fruits and vegetables groups. The mostly low adherence in our sample suggests a potential need to increase provision of dietary information, supportive care screening, and, wherever necessary, dietetics referrals, assessments, and interventions among rural cancer survivors. Larger, longitudinal studies of adherence to dietary guidelines and/or tailored, cancer-specific dietary recommendations should be undertaken in future.

Study protocol: Early neurological deterioration in patients with minor stroke, frequency, predictors, and outcomes in Vietnam single-centre study.

Early neurological deterioration (END) is progressive neurological deterioration with an increase in NIHSS score of 2 points or more in the first 72 hours from the onset of acute ischemic stroke. END increases the risk of poor clinical outcomes at day 90 of ischemic stroke. We will study the frequency, predictors, and outcomes of patients with END in a case-control study at a comprehensive stroke centre in Vietnam. of the design is a descriptive observational study, longitudinal follow-up of patients with minor stroke hospitalized at the Stroke Center of Bach Mai Hospital from December 1, 2023, to December 1, 2024. Minor stroke patients characterized by NIHSS score ≤ 5 hospitalized within 24 hours of symptom onset will be recruited. The estimated END rate is about 30%, relative accuracy ε = 0.11, 95% reliability, expected 5% of patients lost data or follow-up, and an estimated sample size of 779 patients. This study will help determine the END rate in patients with minor stroke and related factors, thereby building a prognostic model for END. Our study determined the END rate in patients with minor stroke in Vietnam and also proposed risk factors for minor stroke management and treatment.

Identification of Rmg11 in Tetraploid Wheat as a New Blast Resistance Gene with Tolerance to High Temperature.

Wheat blast caused by Pyricularia oryzae pathotype Triticum has spread to Asia (Bangladesh) and Africa (Zambia) from the endemic region of South America. Wheat varieties with durable resistance are needed, but very limited resistance resources are currently available. After screening tetraploid wheat accessions, we found an exceptional accession St19 (Triticum dicoccum, KU-114). Primary leaves of St19 were resistant not only to Brazilian isolate Br48 (a carrier of Type eI of AVR-Rmg8) but also to Br48ΔA8, an AVR-Rmg8 disruptant of Br48, even at 30°C, suggesting that the resistance of St19 is tolerant to high temperature and controlled by a gene or genes other than Rmg8. When an F2 population derived from a cross between St19 and St30 (a susceptible accession of T. paleocolchicum, KU-191) was inoculated with Br48, resistant and susceptible seedlings segregated in a 3:1 ratio, indicating that resistance of St19 is conferred by a single gene. We designated this gene Rmg11. Molecular mapping revealed that the RMG11 locus is located on the short arm of chromosome 7A. Rmg11 is effective not only against other two Brazilian isolates (Br5 and Br116.5) but also against Bangladeshi isolates (T-108 and T-109) at the seedling stage. At the heading stage, lines containing Rmg11 were highly susceptible to the Bangladeshi isolates but moderately resistant to the Brazilian isolates. Stacking of Rmg11 with Rmg8 and the 2NS segment is highly recommended to achieve durable wheat blast resistance.

Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam.

Aeromonas spp. are commonly found in the aquatic environment and have been responsible for motile Aeromonas septicemia (MAS) in striped catfish, resulting in significant economic loss. These organisms also cause a range of opportunistic infections in humans with compromised immune systems. Here, we conducted a genomic investigation of 87 Aeromonas isolates derived from diseased catfish, healthy catfish and environmental water in catfish farms affected by MAS outbreaks in eight provinces in Mekong Delta (years: 2012-2022), together with 25 isolates from humans with bloodstream infections (years: 2010-2020). Genomics-based typing method precisely delineated Aeromonas species while traditional methods such as aerA PCR and MALDI-TOF were unable identify A. dhakensis. A. dhakensis was found to be more prevalent than A. hydrophila in both diseased catfish and human infections. A. dhakensis sequence type (ST) 656 followed by A. hydrophila ST251 were the predominant virulent species-lineages in diseased catfish (43.7 and 20.7 %, respectively), while diverse STs were found in humans with bloodstream infections. There was evidence of widespread transmission of ST656 and ST251 on striped catfish in the Mekong Delta region. ST656 and ST251 isolates carried a significantly higher number of acquired antimicrobial resistance (AMR) genes and virulence factors in comparison to other STs. They, however, exhibited several distinctions in key virulence factors (i.e. lack of type IV pili and enterotoxin ast in A. dhakensis), AMR genes (i.e. presence of imiH carbapenemase in A. dhakensis), and accessory gene content. To uncover potential conserved proteins of Aeromonas spp. for vaccine development, pangenome analysis has unveiled 2202 core genes between ST656 and ST251, of which 78 proteins were in either outer membrane or extracellular proteins. Our study represents one of the first genomic investigations of the species distribution, genetic landscape, and epidemiology of Aeromonas in diseased catfish and human infections in Vietnam. The emergence of antimicrobial resistant and virulent A. dhakensis strains underscores the needs of enhanced genomic surveillance and strengthening vaccine research and development in preventing Aeromonas diseases in catfish and humans, and the search for potential vaccine candidates could focus on Aeromonas core genes encoded for membrane and secreted proteins.

Adaptive response of Pseudomonas aeruginosa under serial ciprofloxacin exposure.

Understanding the evolution of antibiotic resistance is important for combating drug-resistant bacteria. In this work, we investigated the adaptive response of Pseudomonas aeruginosa to ciprofloxacin. Ciprofloxacin-susceptible P. aeruginosa ATCC 9027, CIP-E1 (P. aeruginosa ATCC 9027 exposed to ciprofloxacin for 14 days) and CIP-E2 (CIP-E1 cultured in antibiotic-free broth for 10 days) were compared. Phenotypic responses including cell morphology, antibiotic susceptibility, and production of pyoverdine, pyocyanin and rhamnolipid were assessed. Proteomic responses were evaluated using comparative iTRAQ labelling LC-MS/MS to identify differentially expressed proteins (DEPs). Expression of associated genes coding for notable DEPs and their related regulatory genes were checked using quantitative reverse transcriptase PCR. CIP-E1 displayed a heterogeneous morphology, featuring both filamentous cells and cells with reduced length and width. By contrast, although filaments were not present, CIP-E2 still exhibited size reduction. Considering the MIC values, ciprofloxacin-exposed strains developed resistance to fluoroquinolone antibiotics but maintained susceptibility to other antibiotic classes, except for carbapenems. Pyoverdine and pyocyanin production showed insignificant decreases, whereas there was a significant decrease in rhamnolipid production. A total of 1039 proteins were identified, of which approximately 25 % were DEPs. In general, there were more downregulated proteins than upregulated proteins. Noted changes included decreased OprD and PilP, and increased MexEF-OprN, MvaT and Vfr, as well as proteins of ribosome machinery and metabolism clusters. Gene expression analysis confirmed the proteomic data and indicated the downregulation of rpoB and rpoS. In summary, the response to CIP involved approximately a quarter of the proteome, primarily associated with ribosome machinery and metabolic processes. Potential targets for bacterial interference encompassed outer membrane proteins and global regulators, such as MvaT.

Hierarchical Self-Assembly of Multidimensional Functional Materials from Sequence-Defined Peptoids.

Hierarchical self-assembly represents a powerful strategy for the fabrication of functional materials across various length scales. However, achieving precise formation of functional hierarchical assemblies remains a significant challenge and requires a profound understanding of molecular assembly interactions. In this study, we present a molecular-level understanding of the hierarchical assembly of sequence-defined peptoids into multidimensional functional materials, including twisted nanotube bundles serving as a highly efficient artificial light harvesting system. By employing synchrotron-based powder X-ray diffraction and analyzing single crystal structures of model compounds, we elucidated the molecular packing and mechanisms underlying the assembly of peptoids into multidimensional nanostructures. Our findings demonstrate that incorporating aromatic functional groups, such as tetraphenyl ethylene (TPE), at the termini of assembling peptoid sequences promotes the formation of twisted bundles of nanotubes and nanosheets, thus enabling the creation of a highly efficient artificial light harvesting system. This research exemplifies the potential of leveraging sequence-defined synthetic polymers to translate microscopic molecular structures into macroscopic assemblies. It holds promise for the development of functional materials with precisely controlled hierarchical structures and designed functions.

Anti-Staphylococcus aureus potential of compounds from Ganoderma sp.: A comprehensive molecular docking and simulation approaches.

In this study, a series of secondary metabolites from Ganoderma sp. were screened against Staphylococcus aureus protein targets, including as phosphotransacetylase, clumping factor A, and dihydrofolate reductase, using molecular docking simulations. The chemicals that showed the strongest binding energy with the targeted proteins were ganodermanontriol, lucidumol B, ganoderic acid J, ergosterol, ergosterol peroxide, 7-oxoganoderic acid Z, ganoderic acid AM1, ganosinoside A, ganoderic acid D, and 24R-ergosta-7,2E-diene-3ß,5α,6ß-triol. Interestingly, ganosinoside A showed the greatest affinity for the protein clumping factor A, a result validated by molecular dynamic simulation. Additionally, three natural Ganoderma sp. Strains as Ganoderma lingzhi VNKKK1903, Ganoderma lingzhi VNKK1905A2, and Amauroderma subresinosum VNKKK1904 were collected from Kon Ka Kinh National Park in central land of Vietnam and evaluated for their antibacterial activity against Staphylococcus aureus using an agar well diffusion technique. These results suggest that the fungal extracts and secondary metabolites may serve as valuable sources of antibiotics against Staphylococcus aureus. These findings provided an important scientific groundwork for further exploration of the antibacterial mechanisms of compounds derived from Ganoderma sp. in future research.

Homologous recombination contributes to the repair of acetaldehyde-induced DNA damage.

Acetaldehyde, a chemical that can cause DNA damage and contribute to cancer, is prevalently present in our environment, e.g. in alcohol, tobacco, and food. Although aldehyde potentially promotes crosslinking reactions among biological substances including DNA, RNA, and protein, it remains unclear what types of DNA damage are caused by acetaldehyde and how they are repaired. In this study, we explored mechanisms involved in the repair of acetaldehyde-induced DNA damage by examining the cellular sensitivity to acetaldehyde in the collection of human TK6 mutant deficient in each genome maintenance system. Among the mutants, mismatch repair mutants did not show hypersensitivity to acetaldehyde, while mutants deficient in base and nucleotide excision repair pathways or homologous recombination (HR) exhibited higher sensitivity to acetaldehyde than did wild-type cells. We found that acetaldehyde-induced RAD51 foci representing HR intermediates were prolonged in HR-deficient cells. These results indicate a pivotal role of HR in the repair of acetaldehyde-induced DNA damage. These results suggest that acetaldehyde causes complex DNA damages that require various types of repair pathways. Mutants deficient in the removal of protein adducts from DNA ends such as TDP1-/- and TDP2-/- cells exhibited hypersensitivity to acetaldehyde. Strikingly, the double mutant deficient in both TDP1 and RAD54 showed similar sensitivity to each single mutant. This epistatic relationship between TDP1-/- and RAD54-/- suggests that the protein-DNA adducts generated by acetaldehyde need to be removed for efficient repair by HR. Our study would help understand the molecular mechanism of the genotoxic and mutagenic effects of acetaldehyde.

BM-BronchoLC - A rich bronchoscopy dataset for anatomical landmarks and lung cancer lesion recognition.

Flexible bronchoscopy has revolutionized respiratory disease diagnosis. It offers direct visualization and detection of airway abnormalities, including lung cancer lesions. Accurate identification of airway lesions during flexible bronchoscopy plays an important role in the lung cancer diagnosis. The application of artificial intelligence (AI) aims to support physicians in recognizing anatomical landmarks and lung cancer lesions within bronchoscopic imagery. This work described the development of BM-BronchoLC, a rich bronchoscopy dataset encompassing 106 lung cancer and 102 non-lung cancer patients. The dataset incorporates detailed localization and categorical annotations for both anatomical landmarks and lesions, meticulously conducted by senior doctors at Bach Mai Hospital, Vietnam. To assess the dataset's quality, we evaluate two prevalent AI backbone models, namely UNet++ and ESFPNet, on the image segmentation and classification tasks with single-task and multi-task learning paradigms. We present BM-BronchoLC as a reference dataset in developing AI models to assist diagnostic accuracy for anatomical landmarks and lung cancer lesions in bronchoscopy data.

Rifampicin resistant Mycobacterium tuberculosis in Vietnam, 2020-2022.

Objective: We conducted a descriptive analysis of multi-drug resistant tuberculosis (MDR-TB) in Vietnam's two largest cities, Hanoi and Ho Chi Minh city. Methods: All patients with rifampicin resistant tuberculosis were recruited from Hanoi and surrounding provinces between 2020 and 2022. Additional patients were recruited from Ho Chi Minh city over the same time period. Demographic data were recorded from all patients, and samples collected, cultured, whole genome sequenced and analysed for drug resistance mutations. Genomic susceptibility predictions were made on the basis of the World Health Organization's catalogue of mutations in Mycobacterium tuberculosis associated with drug resistance, version 2. Comparisons were made against phenotypic drug susceptibility test results where these were available. Multivariable logistic regression was used to assess risk factors for previous episodes of tuberculosis. Results: 233/265 sequenced isolates were of sufficient quality for analysis, 146 (63 %) from Ho Chi Minh City and 87 (37 %) from Hanoi. 198 (85 %) were lineage 2, 20 (9 %) were lineage 4, and 15 (6 %) were lineage 1. 17/211 (8 %) for whom HIV status was known were infected, and 109/214 (51 %) patients had had a previous episode of tuberculosis. The main risk factor for a previous episode was HIV infection (odds ratio 5.1 (95 % confidence interval 1.3-20.0); p = 0.021). Sensitivity for predicting first-line drug resistance from whole genome sequencing data was over 90 %, with the exception of pyrazinamide (85 %). For moxifloxacin and amikacin it was 50 % or less. Among rifampicin-resistant isolates, prevalence of resistance to each non-first-line drug was < 20 %. Conclusions: Drug resistance among most MDR-TB strains in Vietnam's two largest cities is confined largely to first-line drugs. Living with HIV is the main risk factor among patients with MDR-TB for having had a previous episode of tuberculosis.

Targeted sequencing from cerebrospinal fluid for rapid identification of drug-resistant tuberculous meningitis.

Mortality from tuberculous meningitis (TBM) remains around 30%, with most deaths occurring within 2 months of starting treatment. Mortality from drug-resistant strains is higher still, making early detection of drug resistance (DR) essential. Targeted next-generation sequencing (tNGS) produces high read depths, allowing the detection of DR-associated alleles with low frequencies. We applied Deeplex Myc-TB-a tNGS assay-to cerebrospinal fluid (CSF) samples from 72 adults with microbiologically confirmed TBM and compared its genomic drug susceptibility predictions to a composite reference standard of phenotypic susceptibility testing (pDST) and whole genome sequencing, as well as to clinical outcomes. Deeplex detected Mycobacterium tuberculosis complex DNA in 24/72 (33.3%) CSF samples and generated full DR reports for 22/24 (91.7%). The read depth generated by Deeplex correlated with semi-quantitative results from MTB/RIF Xpert. Alleles with <20% frequency were seen at canonical loci associated with first-line DR. Disregarding these low-frequency alleles, Deeplex had 100% concordance with the composite reference standard for all drugs except pyrazinamide and streptomycin. Three patients had positive CSF cultures after 30 days of treatment; reference tests and Deeplex identified isoniazid resistance in two, and Deeplex alone identified low-frequency rifampin resistance alleles in one. Five patients died, of whom one had pDST-identified pyrazinamide resistance. tNGS on CSF can rapidly and accurately detect drug-resistant TBM, but its application is limited to those with higher bacterial loads. In those with lower bacterial burdens, alternative approaches need to be developed for both diagnosis and resistance detection.

Isothermal amplification-based microfluidic devices for detecting foodborne pathogens: a review.

The gold standard for nucleic acid amplification-based diagnosis is the polymerase chain reaction (PCR). The PCR recognizes the targets such as foodborne pathogens by amplifying their specific genes. The integration of nucleic acid amplification-based assays on microfluidic platforms represents a highly promising solution for convenient, cheap, and effective control of foodborne pathogens. However, the application of the PCR is limited to on-site detection because the method requires sophisticated equipment for temperature control, which makes it complicated for microfluidic integration. Alternatively, isothermal amplification methods are promising tools for integrating microfluidic platforms for on-site detection of foodborne pathogens. This review summarized advances in isothermal amplification-based microfluidic devices for detecting foodborne pathogens. Different nucleic acid extraction approaches and the integration of these approaches in microfluidic platforms were first reviewed. Microfluidic platforms integrated with three common isothermal amplification methods including loop-mediated isothermal amplification, recombinase polymerase amplification, and recombinase-aided amplification were then described and discussed.