Molecular Epidemiology of Escherichia coli Resistant to Carbapenems, Fluoroquinolones, and Aminoglycosides Isolated from One of the Largest Hospitals in Vietnam in 2014-2019.

Introduction: Multidrug-resistant (MDR) Gram-negative bacilli including carbapenem-resistant Gram-negative Enterobacteriaceae (CRE) threaten global health. Little is known, however, about the distribution of antimicrobial resistance genes in MDR isolated from patients in Vietnamese hospitals. In this study, we collected MDR Escherichia coli, defined as E. coli resistance against all fluoroquinolones, aminoglycosides, and carbapenems. Aim: This study was designed to clarify the molecular epidemiology of Escherichia coli isolates resistant to carbapenems, fluoroquinolones, and aminoglycosides isolated from patients admitted to one of the largest hospitals in Vietnam in 2014-2019 based on both whole-genome sequencing (WGS) and phenotypic data. Methodology. Sixty-seven Vietnamese isolates screened by drug resistance by the disk test were subjected to WGS, and their sequences were analyzed to determine their multilocus sequence type (MLST), O-types, H-types, distribution of drug resistance genes, plasmid types, pathogenicity islands (PIs), virulence factor distribution, and phylogenetic evolution using the WGS data. Results: Among the STs detected, ST410 was relatively dominant. Dominant O-types and H-types were O102 and H9 and showed some links, such as those between O102 and H8. The most dominant plasmid type and carbapenemase type were 4 and NDM-5, respectively. MLST, O-types, H-types, plasmid types, and types of carbapenemases were very heterogeneous among the isolates, with no clear correlation between them. Dominant plasmid type carrying drug resistance gene was IncQ1_1. The percentage of isolates positive for drug resistance genes, such as anti-beta-lactams and aminoglycosides, was relatively high because the isolates screened were resistant to carbapenems, fluoroquinolones, and aminoglycosides. Conclusions: MDR E. coli isolates isolated at a high-volume Vietnamese hospital were very heterogeneous, suggesting that they were acquired from different sources, including nosocomial infection, animals, and water. Eradication of MDR E. coli from hospitals and other clinical environments is very challenging because a single measure may be ineffective.

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies.

Different B cell activation patterns in asymptomatic and symptomatic COVID-19 patients

Early and persistent defects in B cell subsets such as memory B cells were shown to be correlated with poor outcomes in COVID-19 patients. This research aimed to develop a molecular pathway model to understand the B cell development in COVID-19. A B cell transcriptomics dataset, obtained from COVID-19 patients, was analyzed on the resulting pathway model to study B cell activation. The pathway showed two distinct gene expression profiles between asymptomatic and symptomatic patients. In asymptomatic patients, there is an increase in transcript levels of antiviral interferon-stimulated genes such as ISG15, IFITM1, and NEAT1 and a driving gene for the extrafollicular pathway CXCR4 indicating a formation of plasmablast. In symptomatic patients, the results suggest an inhibition occurring at the germinal center hinting at a reduction in memory B cell production. Transcripts of driver gene CXCR5 involved in germinal center development is one of the most downregulated genes. This could contribute to the shortage in the formation of memory B cells in COVID-19. Concluding, in SARS-CoV-2 infection, B cells follow different activation routes in asymptomatic and symptomatic patients. In this study, we constructed a pathway that allowed us to analyze and interpret activation patterns of B cells in COVID-19 patients and their link to disease severity. Importantly, the pathway and approach can be reused for further research in COVID-19 or other diseases.

Elucidating the roles of oxygen functional groups and defect density of electrochemically exfoliated GO on the kinetic parameters towards furazolidone detection.

Using electrochemically exfoliated graphene oxide (GO)-modified screen-printed carbon electrodes for the detection of furazolidone (FZD), a nitrofuran antibiotic, was explored. In this study, we designed some GO samples possessing different oxygen functional group content/defect density by using ultrasonic irradiation or microwave techniques as supporting tools. The difference in physical characteristics of GO led to the remarkable change in kinetic parameters (electron transfer rate constant (k s) and transfer coefficient (α)) of electron transfer reactions at K 3/K 4 probes as well as the FZD analyte. Obtained results reveal that the GO-ultrasonic sample showed the highest electrochemical response toward FZD detection owing to the increase in defect density and number of edges in the GO nanosheets under ultrasonic irradiation. The proposed electrochemical nanosensor enabled the monitoring of FZD in the linear range from 1 µM to 100 µM with an electrochemical sensitivity of 1.03 µA µM-1 cm-2. Tuning suitable electronic structures of GO suggests the potentiality of advanced GO-based electrochemical nanosensor development in food-producing animal safety monitoring applications.

Bio-AgNPs-based electrochemical nanosensors for the sensitive determination of 4-nitrophenol in tomato samples: the roles of natural plant extracts in physicochemical parameters and sensing performance.

The present work reports efficient electrochemical nanosensors for the sensitive monitoring of 4-nitrophenol (4-NP) in tomato samples using various biosynthesized silver nanoparticles (bio-AgNPs). Three different bio-AgNP types were synthesized using natural plant extracts, including green tea (GT) leaf, grapefruit peel (GP), and mangosteen peel (MP), aiming to investigate their effects on the formation of bio-AgNPs, as well as the analytical performance of 4-NP. Based on the obtained results, it was found that the phytochemical content in various plant extracts directly influenced the physicochemical parameters of the created bio-AgNPs, such as particle size, crystallinity, and distribution. More importantly, these parameters have decisive effects on the electrocatalytic activity, conductivity, and electrochemical sensing performance of electrodes modified with them for 4-NP detection. Among the three bio-AgNPs evaluated, the GT-AgNPs (using green tea leaf extract) with uniform shape, small size without aggregation, and high crystallinity showed the best analytical performance for 4-NP determination. The electrode-modified GT-AgNPs exhibited a good 4-NP analytical performance with an electrochemical sensitivity of 1.25 µA µM-1 cm-2 and a detection limit of 0.43 µM in the detection range from 0.5 to 50 µM. The practical applicability of the sensor was also studied in tomato samples, promising satisfactory results toward 4-NP detection in other real samples.

Assessment of Climate Change and Human Activities on Vegetation Development in Northeast China.

Vegetation in Northeast China (NEC) has faced dual challenges posed by climate change and human activities. However, the factors dominating vegetation development and their contribution remain unclear. In this study, we conducted a comprehensive evaluation of the response of vegetation in different land cover types, climate regions, and time scales to water availability from 1990 to 2018 based on the relationship between normalized difference vegetation index (NDVI) and the standardized precipitation evapotranspiration index (SPEI). The effects of human activities and climate change on vegetation development were quantitatively evaluated using the residual analysis method. We found that the area percentage with positive correlation between NDVI and SPEI increased with time scales. NDVI of grass, sparse vegetation, rain-fed crop, and built-up land as well as sub-humid and semi-arid areas (drylands) correlated positively with SPEI, and the correlations increased with time scales. The negatively correlated area was concentrated in humid areas or areas covered by forests and shrubs. Vegetation water surplus in humid areas weakens with warming, and vegetation water constraints in drylands enhance. Moreover, potential evapotranspiration had an overall negative effect on vegetation, and precipitation was a controlling factor for vegetation development in semi-arid areas. A total of 53% of the total area in NEC showed a trend of improvement, which is mainly attributed to human activities (93%), especially through the implementation of ecological restoration projects in NEC. The relative role of human activities and climate change in vegetation degradation areas were 56% and 44%, respectively. Our findings highlight that the government should more explicitly consider the spatiotemporal heterogeneity of the influence of human activities and water availability on vegetation under changing climate and improve the resilience of regional water resources. The relative proportions and roles map of climate change and human activities in vegetation change areas provide a basis for government to formulate local-based management policies.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.

Epidemiology of Enterobacter cloacae strains producing a carbapenemase or metallo-beta-lactamase in Vietnamese clinical settings in 2014-2017.

Introduction. Little is known about the epidemiology of Enterobacter cloacae strains producing a carbapenemase or metallo-beta-lactamase in Vietnamese hospitals.Aim. This study analysed E. cloacae strains resistant to imipenem or meropenem that had been isolated from patients admitted to one of the largest hospitals in Vietnam in 2014-2017.Methodology. Eighteen Vietnamese (VN) strains were subjected to whole-genome sequencing and their sequences compared with those of 17 E. cloacae strains carrying a carbapenemase or metallo-beta-lactamase in the database (db strains).Results. Although the distribution of virulence factors did not differ significantly between VN and db strains, all 18 VN isolates harboured blaNDM-1, phylogenetic analysis revealed a high clonality of the VN strains. Bayesian phylogenetic analysis suggested that the VN strains speciated relatively recently.Conclusions. Several prevalent clones of carbapenem-resistant E. cloacae have circulated within Vietnamese hospitals. Adequate measures are needed to prevent their further spread.

Antibiotic Resistance, Biofilm Formation, and Intracellular Survival As Possible Determinants of Persistent or Recurrent Infections by Staphylococcus aureus in a Vietnamese Tertiary Hospital: Focus on Bacterial Response to Moxifloxacin.

Resistance is notoriously high in Asia but may not entirely explain therapeutic failures. Specific modes of bacterial life, such as biofilm or intracellular survival, may also contribute to the persistent and/or recurrent character of infections. Most Staphylococcus aureus isolates form biofilm and many survive and even thrive intracellularly. We collected 36 nonduplicate S. aureus isolates (including 18 methicillin-resistant S. aureus) from patients with clinical evidence of persistent or recurrent infections in a large tertiary Vietnamese hospital. We examined their antibiotic resistance profile (minimal inhibitory concentration determination) and clonal relatedness (spa and agr typing, pulsed field gel electrophoresis profiles). We then assessed the activity of moxifloxacin in both biofilms and infected phagocytes (moxifloxacin previously proved to be one of the most active antibiotics against reference strains in these models). spa-types t189 and t437 and agr group I were the most frequent. Among the 36 isolates, 30 were multidrug resistant but 30 were recovered from patients having received an active drug. All tested isolates produced biofilm and survived inside phagocytes. At its human Cmax, moxifloxacin was inactive on biofilms made by moxifloxacin-susceptible as well as moxifloxacin-resistant isolates. It caused only a modest intracellular colony-forming unit decrease against moxifloxacin-susceptible isolates and was inactive against those resistant to moxifloxacin. While our data confirm for this collection the high resistance levels and prevalence of endemic spa- or agr- types in Asia, they show that tolerance in both biofilm and phagocytes are correlated and markedly limit moxifloxacin activity, which goes in line with the suggested role of these modes of life in persistence or recurrence of infections.

Antimicrobial susceptibility of Burkholderia pseudomallei isolates in Northern Vietnam.

OBJECTIVES: The antimicrobial susceptibility pattern of clinical Burkholderia pseudomallei (B. pseudomallei) in Vietnam has not been reported since the first publication in 2008. The present study aimed to determine the antimicrobial susceptibility pattern of B. pseudomallei isolated in a tertiary referral centre in Hanoi from January 2012 to December 2017. METHODS: A total of 312 B. pseudomallei isolates obtained from melioidosis patients admitted to a 2000-bed general hospital were analysed by the Etest method. Interpretation of the susceptibility testing results were reported using Clinical and Laboratory Standards Institute guidelines. RESULTS: All isolates were susceptible to ceftazidime, imipenem and amoxicillin-clavulanate (100%) with MIC90s relatively low (2µg/mL). Two isolates had intermediate resistance to doxycycline (0.6%) and 34 isolates were resistant to trimethoprim/sulfamethoxazole (10.9%). CONCLUSION: The results of this study suggest that currently recommended antibiotics for melioidosis treatment can be empirically used, but continuously monitoring antimicrobial susceptibility should be a concern.

Occurrence of antibiotic residues and antibiotic-resistant bacteria in effluents of pharmaceutical manufacturers and other sources around Hanoi, Vietnam.

Pharmaceutical manufacturers in Vietnam are producing a wide variety of antibiotics for human and veterinary use. Consequently, the water discharged from those facilities can contain residues of antibiotics, which could have adverse impact on the environment. However, studies on the occurrence of antibiotics in the wastewater from pharmaceutical manufacturers in Vietnam are almost non-existent. In this study, water samples were collected at around the outlets of four pharmaceutical manufacturing plants as well as from a hospital and an aquaculture farm around Hanoi in 2016 and 2017. Fifteen antibiotics from four major classes (ß-lactam, quinolones, macrolides, sulfonamides) were monitored, using a validated LC-MS/MS method, based on their number of registrations at the Ministry of Health. Ten antibiotics, ampicillin, cefuroxime, cefotaxime, clarithromycin, azithromycin, sulfamethoxazole, trimethoprim, ofloxacin, norfloxacin, and ciprofloxacin were detected in the samples at different concentrations. Notably, sulfonamides and quinolones were occasionally detected at very high concentration, such as sulfamethoxazole (252 µg/L), trimethoprim (107 µg/L), ofloxacin (85 µg/L), and ciprofloxacin (41 µg/L). In this study, concentrations of antibiotic residues in effluent of pharmaceutical plants were higher than those from other sources. The antibiotic-resistance tests indicated the widespread resistance to common antibiotics like quinolone and sulfonamides in the collected samples. This finding suggests that wastewater from pharmaceutical manufacturers could be an important source of antibiotics and antibiotic-resistant bacteria in the aquatic environment of Vietnam.

Emergence of colistin-resistant Escherichia coli clinical isolates harboring mcr-1 in Vietnam.

The mcr-1 was first detected on a plasmid in colistin-resistant Escherichia coli from livestock and patients in China. We described here the emergence of colistin-resistant E. coli clinical isolates harboring mcr-1 on the chromosomes in Vietnam. To our knowledge, this is the first report of hospital-acquired E. coli isolates harboring mcr-1 in a medical setting in Vietnam.

Antibiotic Resistance and Antibiotic Resistance Genes in Escherichia coli Isolates from Hospital Wastewater in Vietnam.

The environmental spread of antibiotic-resistant bacteria has been recognised as a growing public health threat for which hospitals play a significant role. The aims of this study were to investigate the prevalence of antibiotic resistance and antibiotic resistance genes (ARGs) in Escherichia coli isolates from hospital wastewater in Vietnam. Wastewater samples before and after treatment were collected using continuous sampling every month over a year. Standard disk diffusion and E-test were used for antibiotic susceptibility testing. Extended-spectrum beta-lactamase (ESBL) production was tested using combined disk diffusion. ARGs were detected by polymerase chain reactions. Resistance to at least one antibiotic was detected in 83% of isolates; multidrug resistance was found in 32%. The highest resistance prevalence was found for co-trimoxazole (70%) and the lowest for imipenem (1%). Forty-three percent of isolates were ESBL-producing, with the blaTEM gene being more common than blaCTX-M. Co-harbouring of the blaCTX-M, blaTEM and qepA genes was found in 46% of isolates resistant to ciprofloxacin. The large presence of antibiotic-resistant E. coli isolates combined with ARGs in hospital wastewater, even post-treatment, poses a threat to public health. It highlights the need to develop effective processes for hospital wastewater treatment plants to eliminate antibiotic resistant bacteria and ARGs.

Multidrug-Resistant Sequence Type 235 Pseudomonas aeruginosa Clinical Isolates Producing IMP-26 with Increased Carbapenem-Hydrolyzing Activities in Vietnam.

Forty clinical isolates of multidrug-resistant Pseudomonas aeruginosa were obtained in a medical setting in Hanoi, Vietnam. Whole genomes of all 40 isolates were sequenced by MiSeq (Illumina), and phylogenic trees were constructed from the single nucleotide polymorphism concatemers. Of these 40 isolates, 24 (60.0%) harbored metallo-ß-lactamase-encoding genes, including blaIMP-15, blaIMP-26, blaIMP-51, and/or blaNDM-1 Of these 24 isolates, 12 harbored blaIMP-26 and belonged to sequence type 235 (ST235). Escherichia coli expressing blaIMP-26 was significantly more resistant to doripenem and meropenem than E. coli expressing blaIMP-1 and blaIMP-15 IMP-26 showed higher catalytic activity against doripenem and meropenem than IMP-1 and against all carbapenems tested, including doripenem, imipenem, meropenem, and panipenem, than did IMP-15. These data suggest that clinical isolates of multidrug-resistant ST235 P. aeruginosa producing IMP-26 with increased carbapenem-hydrolyzing activities are spreading in medical settings in Vietnam.

Detection and Characterization of Clade 1 Reassortant H5N1 Viruses Isolated from Human Cases in Vietnam during 2013.

Highly pathogenic avian influenza (HPAI) H5N1 is endemic in Vietnamese poultry and has caused sporadic human infection in Vietnam since 2003. Human infections with HPAI H5N1 are of concern due to a high mortality rate and the potential for the emergence of pandemic viruses with sustained human-to-human transmission. Viruses isolated from humans in southern Vietnam have been classified as clade 1 with a single genome constellation (VN3) since their earliest detection in 2003. This is consistent with detection of this clade/genotype in poultry viruses endemic to the Mekong River Delta and surrounding regions. Comparison of H5N1 viruses detected in humans from southern Vietnamese provinces during 2012 and 2013 revealed the emergence of a 2013 reassortant virus with clade 1.1.2 hemagglutinin (HA) and neuraminidase (NA) surface protein genes but internal genes derived from clade 2.3.2.1a viruses (A/Hubei/1/2010-like; VN12). Closer analysis revealed mutations in multiple genes of this novel genotype (referred to as VN49) previously associated with increased virulence in animal models and other markers of adaptation to mammalian hosts. Despite the changes identified between the 2012 and 2013 genotypes analyzed, their virulence in a ferret model was similar. Antigenically, the 2013 viruses were less cross-reactive with ferret antiserum produced to the clade 1 progenitor virus, A/Vietnam/1203/2004, but reacted with antiserum produced against a new clade 1.1.2 WHO candidate vaccine virus (A/Cambodia/W0526301/2012) with comparable hemagglutination inhibition titers as the homologous antigen. Together, these results indicate changes to both surface and internal protein genes of H5N1 viruses circulating in southern Vietnam compared to 2012 and earlier viruses.

IMP-51, a novel IMP-type metallo-ß-lactamase with increased doripenem- and meropenem-hydrolyzing activities, in a carbapenem-resistant Pseudomonas aeruginosa clinical isolate.

A meropenem-resistant Pseudomonas aeruginosa isolate was obtained from a patient in a medical setting in Hanoi, Vietnam. The isolate was found to have a novel IMP-type metallo-ß-lactamase, IMP-51, which differed from IMP-7 by an amino acid substitution (Ser262Gly). Escherichia coli expressing blaIMP-51 showed greater resistance to cefoxitin, meropenem, and moxalactam than E. coli expressing blaIMP-7. The amino acid residue at position 262 was located near the active site, proximal to the H263 Zn(II) ligand.

Evaluation of the Etest method for detecting colistin susceptibility of multidrug-resistant Gram-negative isolates in Vietnam.

The minimum inhibitory concentrations (MICs) of colistin for 241 multidrug-resistant (MDR) Gram-negative pathogens were determined by the Etest and by the broth microdilution method (BMD). The two methods showed essential agreements of 76% (77/102) for Acinetobacter baumannii, 90% (36/40) for Pseudomonas aeruginosa and 84% (83/99) for Enterobacteriaceae isolates, with categorical agreements of 100%, 98%, and 100%, respectively. Of the 241 isolates, none showed a very major error and one (0.4%) showed a major error. MICs ranged from 0.125 to 0.5 µg/ml for all A. baumannii and most Enterobacteriaceae isolates, and from 1 to 2 µg/ml for most P. aeruginosa isolates. Of the 40 P. aeruginosa isolates, 27 (68%) showed higher colistin MICs by the Etest than by the BMD. In contrast, 77% (78/102) of the A. baumannii and 57% (56/99) of the Enterobacteriaceae isolates showed lower colistin MICs by the Etest than by the BMD. The Etest is a reliable and easy-to-use method to measure colistin MICs of MDR Gram-negative pathogens in clinical laboratories and can be used following validation by microdilution methods.

The efficacy and nephrotoxicity associated with colistin use in an intensive care unit in Vietnam: Use of colistin in a population of lower body weight.

BACKGROUND: There has been a growing need for colistin as a key drug for the treatment of MDR-GNB infection. Information on colistin use in Asian population is limited. METHODS: A retrospective observational study was conducted to assess the efficacy and nephrotoxicity in critically ill adult patients who received intravenous colistin for MDR-GNB infection in the intensive care unit (ICU) at Bach Mai Hospital in Hanoi, Vietnam. Colistin was administered according to the dosing guideline that was based on pharmacokinetic, pharmacodynamic and toxicodynamic principles, adjusted by body weight and creatinine clearance. RESULTS: Twenty-eight eligible patients were included. The mean patient age was 60±20.4 years. The mean body weight was 53±8.6kg. The mean daily dose of colistin was 4.1±1.6 MIU, and the mean cumulative dose of colistin was 48.2±22.8 MIU. Colistin therapies were classified as clinically effective in 19 (67.9%) cases. Six (21.4%) patients developed nephrotoxicity during the study period according to RIFLE criteria. CONCLUSION: A personalized dosing protocol of colistin was effective, with low nephrotoxicity, among critically ill Vietnamese patients with low body weight. Further studies are warranted for assessing the efficacy and toxicity in a larger cohort.

Rapid multiplex immunofluorescent assay to detect antibodies against Burkholderia pseudomallei and taxonomically closely related nonfermenters.

An indirect immunofluorescent assay to detect antibodies against the lipopolysaccharide (LPS) of Burkholderia pseudomallei and taxonomically closely related species was developed with the Luminex system. LPSs of Pseudomonas aeruginosa, Burkholderia cepacia, Burkholderia thailandensis, Burkholderia vietnamiensis, B. pseudomallei, and Burkholderia mallei were successfully conjugated to Luminex microspheres. Antibodies measured against the LPS of B. pseudomallei-conjugated Luminex beads only cross-reacted with those of two genetically closely related species, B. mallei and B. thailandensis (previously classified as non-pathogenic arabinose-negative B. pseudomallei). However, this system could distinguish other closely related species from B. pseudomallei. This assay is able to detect significantly high levels of anti-LPS antibodies of B. pseudomallei in serum from patients with culture-proven melioidosis.