Antibiotic characteristics of clinical isolates of multi-drug resistant Stenotrophomonas maltophilia strains in the military hospital Vietnam

Stenotrophomonas maltophilia (S. maltophilia) is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. This framework was used to analyze 50 specimens for cultures were collected from patients in the military hospital in Hanoi, Vietnam, between 2015 and 2017. Three of the 30 MDR S. maltophilia isolates identified by Vitek technology in hospital were confirmed using 16S rRNA gene sequencing. The alignment sequences were analyzed in RAxML version 8.2.10 to estimate the best maximum likelihood phylogenetic tree, with 1,000 bootstrap replicates, estimated GTRGAMMA model and the rapid bootstrapping algorithm. Over 70% of S. maltophilia isolates were resistant to β-lactams (such as carbapenem, penicilline, monobactam, amoxicillin, cephem, and β-lactam); Aminoglycosides (such as gentamycine and tobramycin); Miscellaneous (such as fosfomycin and chloramphenicol). In particularly, all of this strain isolates were resistant to β-lactams and Aminoglycosides high annual increasing/ frequency from 2015 to 2017 year. Three resistant strains with most antibiotics (S. maltophilia 17-87M, 17-95M and 17-90N) were randomly selected to test the association between genotype and phenotypic resistance. The results were shown a significantly different in antibiotic genes expression among three strains and a few difference in phenotypic resistance. These data in light of current models of bacterial speciation, which fit these data well, are stressing the implications of species delimitation in ecological, evolutionary and clinical research

Analyzing 16S rRNA sequences from Vietnamese pathogenic Leptospira strains and in-silico prediction of potential antigenic epitopes on LipL21, LipL32 outer membrane lipoproteins

Leptospirosis, a zoonosis caused by Leptospira, is recognized as an emergent infectious disease. In currently, the lack of adequate diagnostic tools, vaccines are an attractive intervention strategy. In this experiment, a 550 bp fragment of large ribosomal RNA gene (16S rRNA) was sequenced and constructed phylogenetic tree from a panel of six Vietnamese pathogenic strains of Leptospira spirochetes (e.g., Pomona, Canicola, Mitis, Ictero haemohagiae, Bataviae, and Grippotyphosa). The results showed a close relationship of L.Pomona_VN and L.Hardjo (bootstrap: 99%). L.Canicola_VN and L.Ictero haemohagiae_VN appeared to be weak related to the classic L.Canicola, L. Grippotyphosa, these assemblage have a bootstrap support of 62%. The other strains (L.Mitis_VN and L.Grippotyphosa_VN) were appeared monophyletic, while their sister group (L.Bataviae_VN) relationship found only weak support (bootstrap: 62%). We also selected six genes [e.g. the immunoglobulin like proteins A and B (LigA and LigB genes), outer membrane protein (OmpL1 gene), and lipopolysaccharide (LipL32, LipL41, and LipL21 genes)] and checked gene expression in these Leptospira strains by polymerase chain reaction (PCR) method. There were three genes (e.g., LipL32, LipL21, and LigA genes) expressed in all strains, OmpL1 gene occured in 4 strains (L.Bataviae_VN, L.Canicola_VN, L.Grippotyphosa_VN and L.Mitis_VN), whereas LipL41 and LigB genes did not appear in any Leptospira strains. A multi-antigenic epitope potential of two gene (Lip L21 and Lip L32) was predicted by bioinformatic tools for designing a recombinant vaccine against leptospirosis. There were 3 multi-epitope regions (1 region and 95 antigenic epitope for B and T cells of LipL21 peptide; 2 regions and 124 antigenic epitope for both B and T cells of LipL32 peptide). It should be more of the deeply molecular biology studies to confirm the level agglutinating, antigen cleavage, peptide specificity matrices as well as neutralizing antibodies in the immune responses of DNA vaccine of these genes

Antimicrobial resistance gene expression associated with multidrug resistant Salmonella spp. isolated from retail meat in Hanoi, Vietnam

The purpose of this study was to further characterize the multi-antimicrobial resistance and antibiotic resistance gene expression associated with multi-drug resistance (MDR) in Salmonella spp. isolates from retail meats in Hanoi, Vietnam. A total of 14 Salmonella spp. belonging to 9 serotypes (e.g., Warragul, London, Derby, Indiana, Meleagridis, Give, Rissen, Assine, and Typhimurium) were tested for sensitivity to 8 antibiotics. Resistance to at least one antibiotic was shown in 13 strains (92.85%). The multiple antimicrobial resistances accounted for 64.29% of isolates (9/14). One hundred percent of MDR isolates possessed antibiotic resistant genes, in which 17, 16 and 11 genes were found in Salmonella (Salm) Typhimurium S360, S384, S181 respectively; 12 genes in each strain as Indiana, Warragul, and Meleagridis; 11 genes in Give, 8 genes in Derby and 6 genes in Rissen. Three antibiotic resistance genes (ssaQ, aadA, and gyrB) were present in all isolates, whereas Cephalosporin-resistant gene (e.g., CTX-M3-like) was not detected in any isolates. The results suggest that retail meats could constitute a source of human exposure to multi-drug resistant Salmonella and future research should focus on the impact of these MDR source on the human genome. [Int Microbiol 20(2): 85-93 (2017)]Keywords: Salmonella spp. · multidrug resistance · retail mea

ダイズ種子エポキシド加水分解酵素変異体の作出及びその性質検討

Epoxide hydrolases (EH) catalyze hydrolysis of epoxides to the corresponding vicinal diols. By site-directed mutagenesis, a total of 22 mutants were constructed, followed by analyzing their kinetics. Through these experiments, mutation of G32, S39, and D58, located at a highly conserved region of EHs known to date, led to a 2-fold higher specific activity than that of wild-type.エポキシド水解酵素は, エポキシドを加水分解し, ジオールに変換する触媒作用を示す. ダイズエポキシド水解酵素の22種の部位特異的変異体の作出を試み, 6種の可溶性変異酵素が得られた. 得られた変異酵素の内, ゲノム上極めて高度に保存されている領域に変異を有する 3種の酵素については, 野生型酵素の 2倍近い酵素活性が得られた. 野生型酵素及び変異酵素のCDスペクトルを測定した結果, 顕著な差異は見られなかった. 変異による酵素活性の上昇はアミノ酸変異による微少な変化を反映しているものと予想された

Development of a solar/LED lighting system for a plant tissue culture room

As the green energy, sunlight provides a friendly-environment and reduces electricity used for lighting. Our target is to enhance the use of natural energy and minimize the consumption of electricity for improving indoor environments. For this reason, a hybrid lighting system, combining sunlight with LEDs for plant tissue culture, are presented. The optical fiber daylighting system consists of three main parts: concentration, collimation beam, and transportation. The concentration part is formed by Fresnel lenses to collect and focus the sunlight into a small area by a non-imaging optical effect. The collimation part consists of optical filters and collimator lenses; the optical filters are used to reflect the ultraviolet (UV) and near infrared (NIR) regions, therefore, only the visible range of the solar light can be transmitted. The transportation part is a large-core optical fiber bundle. To increase the coupling efficiency, the collimator lens is used to expand and to collimate the focused light beam. The collimated light beam is then transported by the optical fiber bundle into a plant tissue culture room. In order to keep the plant tissue culture room at a constant illumination, a lighting control system based on LEDs is used to compensate variations of the natural light. In this paper, a prototype of optical fiber daylighting system and our proposed application will be presented.Ánh sáng mặt trời, một nguồn năng lượng xanh, được sử dụng cho chiếu sáng nhằm mang lại nguồn ánh sáng thân thiện với môi trường và giảm điện năng. Mục tiêu của chúng tôi là tăng cường sử dụng năng lượng tự nhiên và linh kiện tiêu thụ điện thấp để cải thiện môi trường ánh sáng trong nhà và giảm tiêu thụ điện cho chiếu sáng. Vì lý do này, một hệ thống chiếu sáng kết hợp ánh sáng mặt trời với đèn LED để nuôi cấy mô thực vật sẽ được trình bày. Hệ thống chiếu sáng ban ngày bằng sợi quang bao gồm ba phần chính:Bộ phận thu nhận và hội tụ ánh sáng, bộ phận chuẩn trực chùm sáng và bộ phận vận chuyển ánh sáng mặt trời tới nơi cần chiếu sáng. Phần tập trung được hình thành bởi một thấu kính Fresnel để thu thập và hội tụ ánh sáng mặt trời vào một vùng nhỏ bằng hiệu ứng quang học không tạo ảnh. Bộ phận chuẩn trực chumg sáng bao gồm bộ lọc quang học và thấu kính chuẩn trực. Bộ phận vận chuyển là các bó sợi quang lõi lớn. Bộ lọc quang học được sử dụng để phản xạ vùng cực tím (UV) và vùng hồng ngoại gần (NIR), chỉ cho phần ánh sáng nhìn thấy truyền qua. Để tăng hiệu quả ghép nối, thấu kính chuẩn trực được sử dụng để mở rộng và chuẩn trực chùm ánh sáng hội tụ. Chùm sáng chuẩn trực sau đó được vận chuyển bởi bó sợi quang vào phòng nuôi cấy mô thực vật. Để giữ cho phòng nuôi cấy mô thực vật được chiếu sáng liên tục, một hệ thống điều khiển ánh sáng dựa trên đèn LED để bù lại sự biến đổi của ánh sáng tự nhiên. Trong bài báo này, một nguyên mẫu của hệ thống chiếu sáng ban ngày bằng sợi quang và ứng dụng đề xuất của hệ thống sẽ được trình bày

On the Out of Distribution Robustness of Foundation Models in Medical Image Segmentation

Constructing a robust model that can effectively generalize to test samples under distribution shifts remains a significant challenge in the field of medical imaging. The foundational models for vision and language, pre-trained on extensive sets of natural image and text data, have emerged as a promising approach. It showcases impressive learning abilities across different tasks with the need for only a limited amount of annotated samples. While numerous techniques have focused on developing better fine-tuning strategies to adapt these models for specific domains, we instead examine their robustness to domain shifts in the medical image segmentation task. To this end, we compare the generalization performance to unseen domains of various pre-trained models after being fine-tuned on the same in-distribution dataset and show that foundation-based models enjoy better robustness than other architectures. From here, we further developed a new Bayesian uncertainty estimation for frozen models and used them as an indicator to characterize the model's performance on out-of-distribution (OOD) data, proving particularly beneficial for real-world applications. Our experiments not only reveal the limitations of current indicators like accuracy on the line or agreement on the line commonly used in natural image applications but also emphasize the promise of the introduced Bayesian uncertainty. Specifically, lower uncertainty predictions usually tend to higher out-of-distribution (OOD) performance.Comment: Advances in Neural Information Processing Systems (NeurIPS) 2023, Workshop on robustness of zero/few-shot learning in foundation model

A real-time RT-PCR for detection of clade 1 and 2 H5N1 Influenza A virus using Locked Nucleic Acid (LNA) TaqMan probes

<p>Abstract</p> <p>Background</p> <p>The emergence and co-circulation of two different clades (clade 1 and 2) of H5N1 influenza viruses in Vietnam necessitates the availability of a diagnostic assay that can detect both variants.</p> <p>Results</p> <p>We developed a single real-time RT-PCR assay for detection of both clades of H5N1 viruses, directly from clinical specimens, using locked nucleic acid TaqMan probes. Primers and probe used in this assay were designed based on a highly conserved region in the <it>HA </it>gene of H5N1 viruses. The analytical sensitivity of the assay was < 0.5 PFU and 10 - 100 ssDNA plasmid copies. A total of 106 clinical samples (58 from patients infected with clade 1, 2.1 or 2.3 H5N1 viruses and 48 from uninfected or seasonal influenza A virus-infected individuals) were tested by the assay. The assay showed 97% concordance with initial diagnostics for H5 influenza virus infection with a specificity of 100%.</p> <p>Conclusions</p> <p>This assay is a useful tool for diagnosis of H5N1 virus infections in regions where different genetic clades are co-circulating.</p

Kinetics of neutralizing antibodies against Omicron variant in Vietnamese healthcare workers after primary immunization with ChAdOx1-S and booster immunization with BNT162b2

We studied the development and persistence of neutralizing antibodies against SARS-CoV-2 ancestral strain, and Delta and Omicron (BA.1 and BA.2) variants in Vietnamese healthcare workers (HCWs) up to 15 weeks after booster vaccination. We included 47 HCWs, including group 1 (G1, N = 21) and group 2 (G2; N = 26) without and with breakthrough Delta variant infection before booster immunization, respectively). The study participants had completed primary immunization with ChAdOx1-S and booster vaccination with BNT162b2. Neutralizing antibodies were measured using a surrogate virus neutralization assay. Of the 21 study participants in G1, neutralizing antibodies against ancestral strain, Delta variant, BA.1, and BA.2 were (almost) abolished at month 8 after the second dose, but all had detectable neutralizing antibodies to the study viruses at week 2 post booster dose. Of the 26 study participants in G2, neutralizing antibody levels to BA.1 and BA.2 were significantly higher than those to the corresponding viruses measured at week 2 post breakthrough infection and before the booster dose. At week 15 post booster vaccination, neutralizing antibodies to BA.1 and BA.2 dropped significantly, with more profound changes observed in those without breakthrough Delta variant infection. Booster vaccination enhanced neutralizing activities against ancestral strain and Delta variant compared with those induced by primary vaccination. These responses were maintained at high levels for at least 15 weeks. Our findings emphasize the importance of the first booster dose in producing cross-neutralizing antibodies against Omicron variant. A second booster to maintain long-term vaccine effectiveness against the currently circulating variants merits further research

Spatiotemporal evolution of SARS-CoV-2 Alpha and Delta variants during large nationwide outbreak of COVID-19, Vietnam, 2021

We analyzed 1,303 SARS-CoV-2 whole-genome sequences from Vietnam, and found the Alpha and Delta variants were responsible for a large nationwide outbreak of COVID-19 in 2021. The Delta variant was confined to the AY.57 lineage and caused >1.7 million infections and >32,000 deaths. Viral transmission was strongly affected by nonpharmaceutical interventions