Spectrum and antimicrobial resistance in acute exacerbation of chronic obstructive pulmonary disease with pneumonia: a cross-sectional prospective study from Vietnam.

BACKGROUND: Respiratory infections have long been recognized as a primary cause of acute exacerbation of chronic obstructive pulmonary disease (AE-COPD). Additionally, the emergence of antimicrobial resistance has led to an urgent and critical situation in developing countries, including Vietnam. This study aimed to investigate the distribution and antimicrobial resistance of bacteria in patients with AE-COPD using both conventional culture and multiplex real-time PCR. Additionally, associations between clinical characteristics and indicators of pneumonia in these patients were examined. METHODS: This cross-sectional prospective study included 92 AE-COPD patients with pneumonia and 46 without pneumonia. Sputum specimens were cultured and examined for bacterial identification, and antimicrobial susceptibility was determined for each isolate. Multiplex real-time PCR was also performed to detect ten bacteria and seven viruses. RESULTS: The detection rates of pathogens in AE-COPD patients with pneumonia were 92.39%, compared to 86.96% in those without pneumonia. A total of 26 pathogenic species were identified, showing no significant difference in distribution between the two groups. The predominant bacteria included Klebsiella pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae, followed by Acinetobacter baumannii and Streptococcus mitis. There was a slight difference in antibiotic resistance between bacteria isolated from two groups. The frequency of H. influenzae was notably greater in AE-COPD patients who experienced respiratory failure (21.92%) than in those who did not (9.23%). S. pneumoniae was more common in patients with stage I (44.44%) or IV (36.36%) COPD than in patients with stage II (17.39%) or III (9.72%) disease. ROC curve analysis revealed that C-reactive protein (CRP) levels could distinguish patients with AE-COPD with and without pneumonia (AUC = 0.78). CONCLUSION: Gram-negative bacteria still play a key role in the etiology of AE-COPD patients, regardless of the presence of pneumonia. This study provides updated evidence for the epidemiology of AE-COPD pathogens and the appropriate selection of antimicrobial agents in Vietnam.

Cyclotides: The next generation in biopesticide development for eco-friendly agriculture.

Chemical pesticides remain the predominant method for pest management in numerous countries. Given the current landscape of agriculture, the development of biopesticides has become increasingly crucial. The strategy empowers farmers to efficiently manage pests and diseases, while prioritizing minimal adverse effects on the environment and human health, hence fostering sustainable management. In recent years, there has been a growing interest and optimism surrounding the utilization of peptide biopesticides for crop protection. These sustainable and environmentally friendly substances have been recognized as viable alternatives to synthetic pesticides due to their outstanding environmental compatibility and efficacy. Numerous studies have been conducted to synthesize and identify peptides that exhibit activity against significant plant pathogens. One of the peptide classes is cyclotides, which are cyclic cysteine-rich peptides renowned for their wide range of sequences and functions. In this review, we conducted a comprehensive analysis of cyclotides, focusing on their structural attributes, developmental history, significant biological functions in crop protection, techniques for identification and investigation, and the application of biotechnology to enhance cyclotide synthesis. The objective is to emphasize the considerable potential of cyclotides as the next generation of plant protection agents on the global scale.

Experience of Peripheral Blood CD34+ Stem Cells Collection in Autoimmune Patients.

BACKGROUND: Autologous Hematopoietic Stem Cell Transplantation with or without CD34+ selection is being used successfully to treat patients with severe and refractory autoimmune disease. This study describes our experience of CD34+ stem cell mobilization, harvesting and selection in autoimmune patients based on conditions in Vietnam - the developing country. METHODS: Eight autoimmune patients (four patients with Myasthenia Gravis and four patients with Systemic Lupus Erythematosus) underwent PBSC mobilization with granulocyte colony-stimulating factor (G-CSF) and cyclophosphamide. The apheresis was performed on a Terumo BCT Spectra Optia machine. CD34+ hematopoetic stem cells were collected from the leukapheresis by CliniMACS Plus device using CD34 Enrichment KIT. CD34+ cells, T and B lymphocytes were counted on a FACS BD Canto II device. RESULTS: Eight patients (4 MG and 4 SLE) including 5 females and 3 males were involved in this study. The mean age of the patients was 33.13 ± 16.64 years (ranging from 13 to 58 years). The average number of days for mobilization was 7.9 ± 1.6 days, whereas the average number of days for harvesting was 1.5 ± 0.5 days. There was no difference in the number of days for mobilization and harvesting between the MG and SLE groups. The number of CD34+ cells in peripheral blood (PB) on the day of harvesting was 108.37 ± 59.64 x 106 cells/L. There was a significant difference in white blood cell (WBC), neutrophil, monocyte, and platelet cell counts between before and after mobilization. On the day of stem cell harvesting, variables such as WBC, neutrophil, lymphocyte, monocyte, platelet, CD34+ cell counts, and hemoglobin were not different between the MG and SLE groups. The CD34+ recovery percentage following the CD34+ selection procedure was 68.8%, whereas almost 99.9% of the T and B lymphocytes, and NK cells in the PBSC products were eliminated. CONCLUSIONS: Very first attempts in mobilizing, harvesting, and selecting CD34+ stem cells were successful, paving the way for autoimmune patients to have autologous hematopoietic stem cell transplantation in Vietnam.

Rapid, low cost and sensitive detection of Calreticulin mutations by a PCR based amplicon length differentiation assay for diagnosis of myeloproliferative neoplasms.

BACKGROUND: Calreticulin (CALR) gene mutations are currently recommended as biomarkers in diagnosis of patients with myeloproliferative neoplasms (MPN) with Jak2 V617F negative phenotype. Our aim was to establish a rapid, low cost and sensitive assay for identification of CALR gene mutations and to validate the diagnostic performance of the established assay in a patient cohort with different clinical MPN phenotypes. METHODS: One hundred five Philadelphia-negative MPN patients, including polycythemia vera (PV), essential thrombocythaemia (ET), and primary myelofibrosis (PMF) were initially screened for JAK2 mutations by amplification-refractory mutation system (ARMS-PCR) methodology and were further subjected to detection of CALR gene mutations by our in-house assay, a PCR based amplicon length differentiation assay (PCR-ALDA). The PCR-ALDA methodology was compared with real time PCR and Sanger sequencing methods. Furthermore, the analytical sensitivity of the assay was established. RESULTS: PCR - ALDA approach was able to detect and discriminate the pseudo-positive samples containing more than 1% CALR mutant alleles. CALR mutations were not detected in 63 Jak2 V617F positive cases in all three methods. In contrast, amongst 42 Jak2 V617F negative cases, both PCR-ALDA and Sanger sequencing coherently identified 12 CALR mutants compared to 10 CALR mutants detected by real-time PCR method. CONCLUSION: PCR-ALDA can be utilized as an easy-to-use, rapid, low cost and sensitive tool in the detection of CALR mutations in Philadelphia-negative MPN patients.

Molecular Epidemiology of Helicobacter pylori Infection in a Minor Ethnic Group of Vietnam: A Multiethnic, Population-Based Study.

The Helicobacter pylori-induced burden of gastric cancer varies based on geographical regions and ethnic grouping. Vietnam is a multiethnic country with the highest incidence of gastric cancer in Southeast Asia, but previous studies focused only on the Kinh ethnic group. A population-based cross-sectional study was conducted using 494 volunteers (18-78 years old), from 13 ethnic groups in Daklak and Lao Cai provinces, Vietnam. H. pylori status was determined by multiple tests (rapid urease test, culture, histology, and serology). cagA and vacA genotypes were determined by PCR-based sequencing. The overall H. pylori infection rate was 38.1%. Multivariate analysis showed that variations in geographical region, age, and ethnicity were independent factors associated with the risk of H. pylori acquisition. Therefore, multicenter, multiethnic, population based study is essential to assess the H. pylori prevalence and its burden in the general population. Only the E De ethnicity carried strains with Western-type CagA (82%) and exhibited significantly lower gastric mucosal inflammation compared to other ethnic groups. However, the histological scores of Western-type CagA and East-Asian-type CagA within the E De group showed no significant differences. Thus, in addition to bacterial virulence factors, host factors are likely to be important determinants for gastric mucosal inflammation and contribute to the Asian enigma.

Search for novel candidate mutations for metronidazole resistance in Helicobacter pylori using next-generation sequencing.

Metronidazole resistance is a key factor associated with Helicobacter pylori treatment failure. Although this resistance is mainly associated with mutations in the rdxA and frxA genes, the question of whether metronidazole resistance is caused by the inactivation of frxA alone is still debated. Furthermore, it is unclear whether there are other mutations involved in addition to the two genes that are associated with resistance. A metronidazole-resistant strain was cultured from the metronidazole-susceptible H. pylori strain 26695-1 by exposure to low concentrations of metronidazole. The genome sequences of both susceptible and resistant H. pylori strains were determined by Illumina next-generation sequencing, from which putative candidate resistance mutations were identified. Natural transformation was used to introduce PCR products containing candidate mutations into the susceptible parent strain 26695-1, and the metronidazole MIC was determined for each strain. Mutations in frxA (hp0642), rdxA (hp0954), and rpsU (hp0562) were confirmed by the Sanger method. The mutated sequence in rdxA was successfully transformed into strain 26695-1, and the transformants showed resistance to metronidazole. The transformants containing a single mutation in rdxA showed a low MIC (16 mg/liter), while those containing mutations in both rdxA and frxA showed a higher MIC (48 mg/liter). No transformants containing a single mutation in frxA or rpsU were obtained. Next-generation sequencing was used to identify mutations related to drug resistance. We confirmed that the mutations in rdxA are mainly associated with metronidazole resistance, and mutations in frxA are able to enhance H. pylori resistance only in the presence of rdxA mutations. Moreover, mutations in rpsU may play a role in metronidazole resistance.

Pathogenesis of Helicobacter pylori Infection.

Three decades have passed since Warren and Marshall described the successful isolation and culture of Helicobacter pylori, the Gram-negative bacterium that colonizes the stomach of half the human population worldwide. Although it is documented that H. pylori infection is implicated in a range of disorders of the upper gastrointestinal tract, as well as associated organs, many aspects relating to host colonization, successful persistence, and the pathophysiological mechanisms of this bacteria still remain controversial and are constantly being explored. Unceasing efforts to decipher the pathophysiology of H. pylori infection have illuminated the crucially important contribution of multifarious bacterial factors for H. pylori pathogenesis, in particular the cag pathogenicity island (PAI), the effector protein CagA, and the vacuolating cytotoxin VacA. In addition, recent studies have provided insight into the importance of the gastrointestinal microbiota on the cumulative pathophysiology associated with H. pylori infection. This review focuses on the key findings of publications related to the pathogenesis of H. pylori infection published during the last year, with an emphasis on factors affecting colonization efficiency, cagPAI, CagA, VacA, and gastrointestinal microbiota.

Discovery of novel mutations for clarithromycin resistance in Helicobacter pylori by using next-generation sequencing.

OBJECTIVES: Resistance to clarithromycin is the most important factor causing failure of Helicobacter pylori eradication. Although clarithromycin resistance is mainly associated with three point mutations in the 23S rRNA genes, it is unclear whether other mutations are associated with this resistance. METHODS: Two types of clarithromycin-resistant strains (low- and high-resistance strains) were obtained from clarithromycin-susceptible H. pylori following exposure to low clarithromycin concentrations. The genome sequences were determined with a next-generation sequencer. Natural transformation was used to introduce the candidate mutations into strain 26695. Etest and an agar dilution method were used to determine the MICs. RESULTS: High-resistance strains contained the mutation A2143G in the 23S rRNA genes, whereas low-resistance strains did not. There were seven candidate mutations in six genes outside of the 23S rRNA genes. The mutated sequences in hp1048 (infB), hp1314 (rpl22) and the 23S rRNA gene were successfully transformed into strain 26695 and the transformants showed an increased MIC of and low resistance to clarithromycin. The transformants containing a single mutation in infB or rpl22 (either a 9 bp insertion or a 3 bp deletion) or the 23S rRNA gene showed low MICs (0.5, 2.0, 4.0 and 32 mg/L, respectively) while the transformants containing double mutations (mutation in the 23S rRNA genes and mutation in infB or rpl22) showed higher MICs (>256 mg/L). CONCLUSIONS: Next-generation sequencing can be a useful tool for screening mutations related to drug resistance. We discovered novel mutations related to clarithromycin resistance in H. pylori (infB and rpl22), which have synergic effects with 23S rRNA resulting in higher MICs.

The reproductive biology of Ellochelon vaigiensis from the Vietnamese Mekong Delta.

The Squaretail mullet, Ellochelon vaigiensis, is a commercial fish species distributed throughout the Indo-Pacific region. This species tolerates wide variations in salinity, having been reported from both freshwater and marine habitats. Although economically significant, there is little information on its reproduction, especially in the Vietnamese Mekong Delta (VMD), where it is heavily extracted. Our study elucidates the breeding pattern, seasonality, first length at maturity, as well as potential and relative fecundity of this species. Fish specimens were collected by trawl nets from November 2020 to October 2021 at four estuarine sites within the VMD. We found this species to be a synchronous spawner, with peaks in reproductive activity from June to September. In the populations we surveyed, there was significant dominance of males (1.26:1.00) based on 942 fish samples (526 males and 416 females). The length at 50% maturity for females was significantly higher than for males at all sites and ranged from 10.6 to 19.3 cm. The diameter of the eggs examined for this species exhibited slight variation, from 0.43 to 0.54 mm. The potential fecundity ranged from 246,254 ± 35,878 to 411,970 ± 54,370 eggs, corresponding to female length and weight of 26.7-32.6 cm and 102.97-234.19 g, respectively. Relative fecundity values were highest at Thanh Phu, Ben Tre (6388 ± 605 eggs), and Dong Hai, Bac Lieu (6461 ± 637 eggs), followed by Tran De, Soc Trang (4729 ± 408), and were found to be lowest at Duyen Hai, Tra Vinh (3117 ± 223 eggs). Information on reproductive behavior in this species has far-reaching impacts on sustainable extractions, stock conservation, and aquaculture.

Phylogenics of the genus Glossogobius in the Mekong Delta based on the mitochondrial cytochrome b (cytb) gene.

The Glossogobius species play an essential role in food supply and are distributed widely from the marine to freshwater, especially in the Mekong Delta, Vietnam (VMD). Some of their morphometrics and meristics are observed to vary with species and sampling sites. Therefore, the present study aims to verify if their mitochondrial Cytochrome b (Cytb) gene, one of the popular gene sequences used in fish phylogenic variation assessment, varies with species and sampling sites in the VMD. The Cytb gene size was 1300 bp for GcytbH/GcytbL primer pair and 1045 bp for GluMuq1-F/Mixcyto937-2R. The genetic distances within and among these three fish species groups were 0-11%. The Cytb gene sequences' similarity between this study and the NCBI database was 85.84-100%. The Glossogobius specimens were observed to disperse in small branches of the phylogenetic tree with a low K2P value, suggesting that the Cytb genetic diversity may be low among species.

The use of mtCOI gene sequences in identifying Butis species in the Southwest of Vietnam.

Butis genus is characterised by their small body size and morphological variability, allowing them to adapt to different habitats. This paper analyses the mitochondrial cytochrome C oxidase subunit I gene sequences and morphology of Butis for identification purposes and to understand genetic relationships. The morphological characteristics of Butis koilomatodon differed obviously from Butis humeralis and Butis butis. After classification based on morphology, the total deoxyribonucleic acid of fish samples was isolated, and the mitochondrial cytochrome C oxidase subunit I genes were successfully amplified using the polymerase chain reaction method. At approximately 617bp, the obtained mitochondrial cytochrome C oxidase subunit I gene sequences were highly similar to the reference sequences on Genbank (85.90-100%). The phylogenetic graphic was divided into five distinct groups, where B. koilomatodon was grouped in one group; and B. humeralis and B. butis were grouped together. The results suggest that B. humeralis was an entirely different species from B. butis, with a mean genetic divergence of up to 14%. However, further studies using a combination of other types of deoxyribonucleic acid barcoding together with morphological features should be undertaken to confirm these findings.

Evaluation of polyhydroxyalkanoate (PHA) synthesis by Pichia sp. TSLS24 yeast isolated in Vietnam.

Following the rising concern on environmental issues caused by conventional fossil-based plastics and depleting crude oil resources, polyhydroxyalkanoates (PHAs) are of great interest by scientists and biodegradable polymer market due to their outstanding properties which include high biodegradability in various conditions and processing flexibility. Many polyhydroxyalkanoate-synthesizing microorganisms, including normal and halophilic bacteria, as well as algae, have been investigated for their performance in polyhydroxyalkanoate production. However, to the best of our knowledge, there is still limited studies on PHAs-producing marine yeast. In the present study, a halophilic yeast strain isolated from Spratly Island in Vietnam were investigated for its potential in polyhydroxyalkanoate biosynthesis by growing the yeast in Zobell marine agar medium (ZMA) containing Nile red dye. The strain was identified by 26S rDNA analysis as Pichia kudriavzevii TSLS24 and registered at Genbank database under code OL757724. The amount of polyhydroxyalkanoates synthesized was quantified by measuring the intracellular materials (predicted as poly(3-hydroxybutyrate) -PHB) by gravimetric method and subsequently confirmed by Fourier transform infrared (FTIR) spectroscopic and nuclear magnetic resonance (NMR) spectroscopic analyses. Under optimal growth conditions of 35 °C and pH 7 with supplementation of glucose and yeast extract at 20 and 10 gL-1, the isolated strain achieved poly(3-hydroxybutyrate) content and concentration of 43.4% and 1.8 gL-1 after 7 days of cultivation. The poly(3-hydroxybutyrate) produced demonstrated excellent biodegradability with degradation rate of 28% after 28 days of incubation in sea water.

Expression, crystallization and preliminary X-ray crystallographic analysis of cystathionine γ-synthase (XometB) from Xanthomonas oryzae pv. oryzae.

Cystathionine γ-synthase (CGS) catalyzes the first step in the transsulfuration pathway leading to the formation of cystathionine from O-succinylhomoserine and L-cysteine through a γ-replacement reaction. As an antibacterial drug target against Xanthomonas oryzae pv. oryzae (Xoo), CGS from Xoo (XometB) was cloned, expressed, purified and crystallized. The XometB crystal diffracted to 2.4 Šresolution and belonged to the tetragonal space group I4(1), with unit-cell parameters a=b=165.4, c=241.7 Å. There were four protomers in the asymmetric unit, with a corresponding solvent content of 73.9%.

Crystallization and preliminary diffraction studies of GIM-1, a class B carbapenem-hydrolyzing ß-lactamase.

GIM-1 is a member of the class B carbapenemases (metallo-ß-lactamases; MBLs) and has a wide spectrum of activity against carbapenems, penicillins and extended-spectrum cephalosporins, but not aztreonam. GIM-1 presents an enormous challenge to infection control, particularly in the eradication of Gram-negative pathogens including Enterobacteriaceae, Pseudomonas aeruginosa, Acinetobacter baumannii and nonfermenters. There are presently few or no drugs in late-stage development for these pathogens and GIM-1 is a potential target for the development of antimicrobial agents against pathogens producing MBLs. In this study, GIM-1 was cloned, overexpressed and crystallized. The GIM-1 crystals diffracted to 1.4 Šresolution and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 38.5, b = 67.6, c = 72.8 Å. One molecule is present in the asymmetric unit, with a corresponding V(M) of 1.69 Å(3) Da(-1) and a solvent content of 27.1%.

Population biological traits of Periophthalmus chrysospilos Bleeker, 1853 in the Vietnamese Mekong Delta.

Periophthalmus chrysospilos is an amphibious fish living in mudflats from eastern India to Indonesia, including the Vietnamese Mekong Delta. Population biological traits play an important role in fishery assessment, but understanding is limited for this species. In total 1,031 specimens were caught in two regions covering four provinces, including the TVST (Duyen Hai, Tra Vinh and Tran De, Soc Trang) and BLCM (Dong Hai, Bac Lieu and Dam Doi, Ca Mau). Results found that the sex ratio was close to 1:1. The parameters of the von Bertalanffy in TVST were L∞ = 12.8 cm, K = 0.41 yr-1, t0 = -0.10 yr and in BLCM were 12.7 cm, 0.38 yr-1 and -0.08 yr, respectively. Although the growth coefficient (Φ') in BLCM (1.79), was lower than that in TVST (1.83), the species shared a similar size at first capture (7.9 cm in TVST and 7.9 cm in BLCM). The species suffered from heavy pressure of fishing in TVST as fishing mortality in TVST (2.32 yr-1) was higher than that in BLCM (1.38 yr-1), leading to the higher total mortality (Z = 3.60 yr-1) in TVST compared to BLCM (Z = 2.59 yr-1). By contrast, the species showed similar natural mortality over both sites (1.20 yr-1 in TVST and 1.22 yr-1 in BLCM). The Periophthalmus chrysospilos population was reasonably exploited because E values (0.64 in TVST and 0.53 in BLCM) were lower than E10 (0.706 in BTTV and 0.705 in STBL). Nonetheless, to avoid the consequences of overfishing, some sustainable fisheries practices should be implemented, such as protecting mangrove forests, restricting fishing during the recruitment period, using appropriate fishing tools and increasing mesh size.

Reproduction ecology of an emerging fishery resource, the amphibious mudskipper Periophthalmus chrysospilos, in the Mekong Delta.

Populations of Periophthalmus chrysospilos, the Gold-spotted mudskipper, within the Mekong Delta are facing extirpation risks due to indiscriminate harvesting for the growing aquarium and food-fish trade. This study provides some of the first information on reproductive ecology-such as spawning type and season, length at first maturity, and batch fecundity-of this species, to be used in their management. The sex ratio of wild populations, based on 1031 individuals (523 males and 508 females) is 1:1. The gonadosomatic index (GSI) values are exhibit a non-normal distribution and changed with gender, season, and site. A combination of GSIs and the monthly appearance of mature gonads suggest that this species reproduces throughout the year, with peak from July to October. This species exhibits sexual and spatial variation in size at first maturity (Lm ) as Lm is 6.2-8.6 cm in males and 6.4-7.3 cm in females. The batch fecundity (F = 2614 to 23,465 eggs/female) exhibits non-normal distribution and varies with site, with the highest values at Dam Doi, Ca Mau (13,336 ± 1,279 SE) and the lowest at Tran De, Soc Trang (6654 ± 851 SE). In addition, batch fecundity is directly proportional to body size due to high determination relationships between batch fecundity and fish size (r 2 > 0.64 for all cases). Information derived on the reproductive biology of this species can inform its conservation, sustainable exploitation, and ex situ propagation.

Feeding ecology of Ellochelon vaigiensis (Quoy & Gaimard, 1825) living in the Mekong Delta, Vietnam.

Ellochelon vaigiensis (squaretail mullet) adapts to a wide salt spectrum, grows quickly and is easy to raise with other species, so it is the object of attention in aquaculture. Information on the biology and ecology of the species, diet, in particular, is still scattered. Here, we explore the feeding habit, feeding intensity, and food composition of the squaretail mullet. A total of 942 fish (526 males and 416 females) were collected from November 2020 to October 2021 at four coastal sites in the Mekong Delta, Vietnam. The squaretail mullet is an algi-omnivorous fish, as their relative gut length (1.81) falls into the range 1-3, and the diet is mostly based on algae. The feeding intensity is high due to the high value of the fullness index (4.39 ± 0.08%). The fullness index did not vary by sampling site and month, while RGL and FI changed depending on sex. Bacillariophyta (49.13%), detritus derived from organic matter (30.37%), and Cyanophyta (18.39%) are the dominant food items in the diet composition of E. vaigiensis, in which detritus is the most important food with the highest IRI index. Besides, Euglenophyta (1.00%), Chlorophyta (0.95%), Paramecium (0.06%), Copepoda (0.04%), Rotatoria (0.03%), Polychaeta (0.02%), and Cladocera (0.01%) are also recorded and ranked based on their biovolume. Some differences in diet composition are observed between immature and mature at different seasons and their interactions. Our results increase the knowledge about the feeding ecology of squaretail mullet and can help the sustainable management of this commercially important fish species.

Foraging ecology of the amphibious mudskipper Periophthalmus chrysospilos (Gobiiformes: Gobiidae).

The food composition and feeding ecology of fishes living in the intertidal zone play an essential role in understanding the energetic connectivity between terrestrial and aquatic systems. Periophthalmus chrysospilos is an amphibious fish species occurring in the intertidal zone, but data on its diet and foraging ecology is still poorly known. This study on Ps. chrysospilos was carried out from April 2020 to March 2021 at four sites within the Mekong Delta estuary to define the influence of spatio-temporal factors on the diet of this species. The diet composition and relative gut lengths (RGLs) of Ps. chrysospilos were analysed in relation to four parameters-sex, size, site, and season. A total of 1,031 individuals were collected, and their digestive tract lengths were used to calculate the RGL. The digestive tracts of only 546 individuals were with food items (approximately 1:1 of empty vs full digestive tract) and were subsequently used for further analyses. The ranges in total length and weight in both adult and juvenile individuals were 3.4-10.6 cm and 0.38-14.13 g, respectively. The RGL values varied with season, fish size and site, but was always lower than 1, indicating a predominantly carnivorous diet. The variability of food items found within the digestive tracts demonstrated its adaptability in pursuing prey items within the limits of the littoral zone, and its importance as a conduit of terrestrial-marine connectivity. This species is characterised as an opportunistic mesopredator feeding primarily on Acetes spp., Uca spp., Dolichoderus sp., and rarely on Polychaeta and Actinopterygii. Other items found within the digestive tract are Mollusca, and detritus. The diet composition of Ps. chrysospilos did not vary with season and size, but changed with sex and site parameters. Uca spp. contributed to the sexual variation in dietary component, whereas Mollusca, Uca spp., Dolichoderus sp. and detritus, were drivers for spatial variation in the dietary component. The research provides fundamental information on diet composition and feeding strategy, as well as contributes towards knowledge on foraging ecology and resource use by intertidal animal communities.

Helicobacter pylori type 4 secretion systems as gastroduodenal disease markers.

Although the type 4 secretion system of the integrating and conjugative elements (tfs ICE) is common in Helicobacter pylori, its clinical association with the cag pathogenicity island (cagPAI) have not yet been well-investigated. In this study, Vietnamese patient H. pylori samples (46 duodenal ulcer (DU), 51 non-cardia gastric cancer (NCGC), 39 chronic gastritis (CG)) were fully sequenced using next-generation sequencing and assembled into contigs. tfs3, tfs4, and cagPAI genes were compared with the public database. Most (94%) H. pylori strains possessed a complete cagPAI, which was the greatest risk factor for clinical outcomes, while the prevalences of tfs3 and tfs4 were 45% and 77%, respectively. Complete tfs3 and tfs4 were found in 18.3% and 17.6% of strains, respectively. The prevalence of H. pylori strains with complete tfs3 ICE in DU patients was significantly higher than that in NCGC patients (30.4% vs 11.7%, P < 0.05). In addition, the prevalence of strains with complete tfs3 ICE and cagPAI was significantly higher in DU patients than that in NCGC (28.4% vs 9.8%, P = 0.038) and CG patients (28.2% vs 7.7%, P = 0.024). cagPAI and complete tfs3 increased the risk of DU compared to NCGC (OR = 3.56, 95%CI: 1.1-14.1, P = 0.038) and CG (OR = 4.64, 95%CI: 1.1-27.6, P = 0.024). A complete cluster of tfs3 ICE was associated with gastroduodenal diseases in Vietnam. However, there was a low prevalence of the dupA/complete dupA cluster (15.4%) in the Vietnam strains. The prevalence of cagPAI in Vietnam strains was significantly higher than in US (P = 0.01) and Indonesia (P < 0.0001); the prevalence of the dupA cluster was also higher in the Vietnam strains than in the Indonesian strains (P < 0.05). In addition, the prevalence of ctkA, an accessory gene of tfs3, was significantly different between Vietnam and US strains (28% vs 2%, P = 0.0002). In summary, the acquisition of tfs3/4 ICE was common in H. pylori strains in patients with gastroduodenal disease in Vietnam, and the complete cluster of tfs3 ICE was a reliable marker for the severity of disease in the H. pylori infected population.

Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates.

Genome-wide association studies (GWASs) can reveal genetic variations associated with a phenotype in the absence of any hypothesis of candidate genes. The problem of false-positive sites linked with the responsible site might be bypassed in bacteria with a high homologous recombination rate, such as Helicobacter pylori, which causes gastric cancer. We conducted a small-sample GWAS (125 gastric cancer cases and 115 controls) followed by prediction of gastric cancer and control (duodenal ulcer) H. pylori strains. We identified 11 single nucleotide polymorphisms (eight amino acid changes) and three DNA motifs that, combined, allowed effective disease discrimination. They were often informative of the underlying molecular mechanisms, such as electric charge alteration at the ligand-binding pocket, alteration in subunit interaction, and mode-switching of DNA methylation. We also identified three novel virulence factors/oncoprotein candidates. These results provide both defined targets for further informatic and experimental analyses to gain insights into gastric cancer pathogenesis and a basis for identifying a set of biomarkers for distinguishing these H. pylori-related diseases.