Molecular epidemiology of a Parainfluenza Type 3 virus outbreak: Informing infection control measures on adult hematology wards.

OBJECTIVES: Parainfluenza virus type 3 (PIV3) outbreaks among hematology patients are associated with high morbidity and mortality. Prompt implementation of infection prevention (IP) measures has proven to be the most efficacious approach for controlling PIV3 outbreaks within this patient population. The most suitable IP measures can vary depending on the mode of virus transmission, which remains unidentified in most outbreaks. We describe the molecular epidemiology of an outbreak of PIV3 among hematology patients and the development of a new method that allows for the differentiation of outbreak and community strains, from which a closed outbreak could be inferred. METHODS: Patients were screened for respiratory viruses using multiplex-PCR. PIV3 positive samples with a cycle threshold (Ct)-value of <31 underwent a retrospective characterization via an in-house developed sequence analysis of the hemagglutinin-neuraminidase (HN) gene. RESULTS: Between July and September 2022, 31 hematology patients were identified with PIV3. Although infection control measures were implemented, the outbreak persisted for nine weeks. Sequencing the HN gene of 27 PIV3 strains from 27 patients revealed that all outbreak strains formed a distinct cluster separate from the control strains, suggestive of a nosocomial transmission route. CONCLUSIONS: Sequencing the HN gene of PIV3 strains in an outbreak setting enables outbreak strains to be distinguished from community strains. Early molecular characterization of PIV3 strains during an outbreak can serve as a tool in determining potential transmission routes. This, in turn, enables rapid implementation of targeted infection prevention measures, with the goal of minimizing the outbreak's duration and reducing associated morbidity and mortality.

The Effects of Yeast Protein on Gut Microbiota in Mice When Compared with Soybean Protein and Whey Protein Isolates.

Different protein sources can impact gut microbiota composition and abundance, and also participate in health regulation. In this study, mice were gavaged with yeast protein (YP), soybean protein isolate (SPI), and whey protein isolate (WPI) for 28 days. Body weights showed similar patterns across different protein administration groups. The ileum in YP-supplemented mice exhibited good morphology, and tight-junction (TJ) proteins were slightly upregulated. Immunoglobulin (Ig)A, IgM, and IgG levels in the ileum of different protein groups were significantly increased (p < 0.05). Interleukin (IL)-10 levels were significantly increased, whereas IL-6 levels were significantly reduced in the YP group when compared with the control (C) (p < 0.05). Glutathione peroxidase (GSH-Px) levels in the ileum were significantly increased in the YP group (p < 0.05). These results indicate that YP potentially improved intestinal immunity and inflammatory profiles. The relative abundances of Parabacteroides, Prevotella, and Pseudobutyrivibrio in the YP group were more enriched when compared with the C and SPI groups, and Parabacteroides was significantly upregulated when compared with the WPI group (p < 0.05). Overall, the results indicate that YP upregulates the beneficial bacteria and improves ileal immunity and anti-inflammatory capabilities.

Substance basis and pharmacological mechanism of heat-clearing herbs in the treatment of ischaemic encephalopathy: a systematic review and network pharmacology.

BACKGROUND AND OBJECTIVE: Ischaemic encephalopathy is a common cerebrovascular disease caused by insufficient blood supply to the cerebral vessels. The ischaemic encephalopathy is closely associated with the development of many chronic diseases such as obesity, hypertension and diabetes. Neurotrophic therapy has become the main therapeutic strategy for ischaemic encephalopathy. However, neurotrophic drugs only slightly recover the neurological function of patients, and their long-term efficacy is uncertain. Previous reports revealed that the active ingredients of natural medicines play important roles in the treatment of cerebral ischemia. In this study, we reviewed clearing herbs with anti-ischaemic encephalopathy functions using the data from quantitative statistical and network pharmacological exploration methods. We also discussed the different bioactive components and pharmacological effects of these herbs. METHODS: First, we collected Chinese herbal prescriptions against ischaemic encephalopathy in four databases. Then, we statistically analysed the frequency of application of heat-clearing herbs to obtain the commonly used heat-clearing herbs against ischaemic encephalopathy, and classified them according to their efficacy according to the statistical results, to summarize the mechanism of anti-ischaemic effects of different bioactive components; Second, the network database was used to obtain the above components of heat-clearing Chinese medicines and their corresponding targets of action, disease targets of ischaemic stroke; Venny 2.1.0 was used to obtain component-disease target intersections; Cytoscape was used to construct the 'Drug-Active Ingredient-Target Network Graph '; DAVID was used for GO and KEGG enrichment analysis. RESULTS: Literature and database screening involved 149 prescriptions, with a total of 269 flavours of Chinese medicines and 20 flavours of single-flavour heat-clearing Chinese medicines; The top nine in terms of frequency of use were Radix Paeoniae Rubra、Rehmanniae Radix Praeparata、Figwort Root、Cortex Moutan、Scutellariae Radix、Coptidis Rhizoma、Gardeniae Fructus、Cassiae Semen、Lonicerae Japonicae Flos. The common components obtained from network pharmacology were beta-sitosterol, quercetin, and stigmasterol, which mainly act on key targets such as RELA, AKT1, JUN, PRKACA, PTGS2, RAF1 and CHUK; and their active ingredients are mainly involved in signalling pathways such as Calcium, PI3K-Ak, MAPK, cAMP, IL-17, HIF-1, TNF, T-cell receptor, NF-kappa B and JAK-STAT. CONCLUSIONS: Heat-clearing herbs are useful and promising for the protection against and prevention of ischemic encephalopathy. The results of the network pharmacological studies are similar to the mechanisms of anti-ischemic encephalopathy of the active ingredients of the purgative herbs we have listed; Thin either directly protects cerebrovascular tissues by improving vascular permeability and reducing the area of infarcted tissues, or produces protective effects through molecular signaling pathways. It can be seen that the components of heat-clearing Chinese medicines can exert cerebroprotective effects through multiple pathways, which provides us with a reference for further development and study of heat-clearing Chinese medicines in the treatment of ischemic cerebrovascular diseases.

Association Between VEGF-460C/T Gene Polymorphism and Risk of Diabetic Retinopathy in Type 2 Diabetes Mellitus: A Meta-Analysis.

The aim of the study was to investigate the relationship between VEGF-460C/T polymorphism and susceptibility to diabetic retinopathy (DR) in type 2 diabetes mellitus (T2DM) by meta-analysis. A comprehensive search was conducted across six databases until September 2023 to identify studies examining the association between VEGF-460C/T polymorphism and susceptibility to DR. Data process was performed by Stata 15.0 software. Eight studies were included, involving 1463 patients with DR. In the overall analysis, the difference was statistically significant only in the homozygous model (CC vs. TT: OR=1.86, p=0.048). A subgroup analysis of 6 papers with genotype frequency satisfying HWE in the control group indicated significant differences among the allele (C vs. T: OR=1.34, p=0.037), recessive (CC vs. CT+TT: OR=1.96, p=0.022) and homozygous (CC vs. TT: OR=2.28, p=0.015) models. However, in the dominant and heterozygous models, the difference was not statistically significant. The sensitivity of the HWE-based subgroup analysis showed that the conclusions in other gene models except the heterozygote model were not robust. This meta-analysis indicated that VEGF-460C/T gene polymorphism is associated with susceptibility to DR in T2DM. Allele C and genotype CC at the VEGF-460C/T locus are associated with an increased risk of DR in T2DM. However, considering that the results are not robust, more trials involving more rigorous design are needed to verify the findings of this review in the future.

Antihypertensive Effect, ACE Inhibitory Activity, and Stability of Umami Peptides from Yeast Extract.

Bioactive peptides from foods have garnered considerable attention as viable supplements for hypertensive patients. Herein, the antihypertensive effect and mechanism of umami peptides from yeast extract were investigated based on the pharmacophore model, simulated digestion, spontaneously hypertensive rat (SHR) model, and molecular docking. Notably, umami peptide LLLLPKP exhibited favorable angiotensin I-converting enzyme (ACE) inhibitory activity (IC50 = 10.22 µM) in vitro and regulated blood pressure in the SHR model with excellent durability. Remarkably, LLLLPKP showed the highest Fitvalue (4.022) of the pharmacophore model, indicating its similar pharmacological effects as ACE inhibitors. During the simulated gastrointestinal digestion, the ACE inhibition rate of LLLLPKP was merely reduced by 5.89%, but it was enzymatically cleaved into 14 peptide segments. The C-terminal sequence comprising L (4), P (5), K (6), and P (7) exhibited robust stability and a notable presence within the peptide segments postdigestion. Meanwhile, according to molecular docking, these four residues within LLLLPKP were responsible for all interactions with key sites within active pockets S1 and S2 and the active pocket of Zn2+. In light of these findings, LLLLPKP is a highly promising antihypertensive peptide. Developing this umami peptide with antihypertensive effects holds substantial importance for the long-term treatment of hypertension.

ACE inhibitory activity and salt-reduction properties of umami peptides from chicken soup.

Angiotensin-I-converting enzyme (ACE) inhibitory activity and salt-reduction properties of umami peptides identified in chicken soup were investigated. The ACE inhibition rate of TPLVDR (91.22%) and AEINKILGN (81.26%) was significantly higher than other umami peptides, and their semi-inhibitory concentration was 0.017 mM and 0.034 mM, respectively. After in vitro digestion, the inhibitory activity of AEINKILGN and TPLVDR decreased, but the original sequences were still detected. The docking results showed that AEINKILGN and TPLVDR mainly interacted with Zn2+ and key sites (His353, Lys511and Glu411) in the active pockets of ACE through hydrogen bonds, which was crucial to the ACE inhibitory activity. Based on response surface methodology and sensory analysis, saltiness and palatability models were established to investigate the salt-reduction effect. The optimal level of AEINKILGN was about 1.16 mg/mL in 0.44% salt solution. And the TPLVDR was applicable to the low salt solution (0.1-0.2%) at a concentration from 0.23 to 0.29 mg/mL.

Prevalence of myopia among senior students in Fenghua, Eastern China, before and during the COVID-19 pandemic.

Background: Myopia is a common cause of vision impairment worldwide. In China, the prevalence, the affected population, and the onset age of myopia are prominent issues. Prevention and intervention of myopia are great public health concerns. Methods: This school-based retrospective study retrieved visual acuity and refractive data of senior students (grade 12th) from six high schools in Fenghua City, Zhejiang Province, eastern China, from 2016 and 2022. Noncycloplegic autorefraction was performed for refractive status. Students were divided into three subgroups by their school types. The overall myopia prevalence, as well as the prevalence of low myopia, moderate myopia, and high myopia, were calculated separately for each year. Statistical analyzes were performed using SPSS 25.0 and Graphpad Prism software. Results: The mean myopia prevalence in Fenghua was 84.5% (95% CI: 84.0-85.0%), and a slightly downward trend was found in myopia prevalence after 2019, but the change was not statistically significant (p = 0.078). The overall prevalence of myopia was 79.6, 85.2, and 86.1% in vocational high schools, general high schools, and key high schools, respectively, with statistically significant differences (p < 0.001). The prevalence of myopia among senior students in the vocational high school was significantly lower than that in the other two high schools. There's no significant change in the overall prevalence of myopia (84.7% vs. 84.3%, p = 0.265) before and during the COVID-19 pandemic, and it remained statistically insignificant after stratifying by gender (male p = 0.207, female p = 0.918) or school types (vocational high school p = 0.112; general high school p = 0.299; key high school p = 0.393). Conclusion: The prevalence of myopia among senior students in Fenghua is relatively high, and the COVID-19 pandemic has no significant impact on it. The prevalence of myopia among vocational high school students is lower than that of general high school and key high school. Attention should be paid to the effects of educational pressure on the prevalence of myopia among students.

COVID or no COVID: Interpreting inconclusive SARS-CoV-2 qPCR results in different populations and platforms.

Introduction: High cycle threshold values (Ct) value) results for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be true infections or false-positive results. Misinterpretation of results has negative consequences. Goal of this study was to evaluate quantitative real-time polymerase chain reaction (qPCR) results with high Ct-values, to reach a point where a correct interpretation can be given. Methods: High Ct-value results of SARS-CoV-2 in respiratory samples taken between April 2020 and January 2021 were analysed. Three different SARS-CoV-2 qPCR assays (in-house, Alinity M and Xpert Xpress) were used for screening patients and healthcare workers (HCW). High Ct-value results were defined as "inconclusive". The Ct-value cut-off for the interpretation of the test as "positive" and "inconclusive" were based on quality assurance panel results and manufacturers' instructions. Results: Out of totally 50.295 samples tested for SARS-CoV-2, the in-house and Alinity M qPCR together yielded 379 inconclusive results. A second sample existed for 217 samples, allowing dynamics of the PCR in time. Of these, 187 were negative (86%), 11 again inconclusive (5%) and 19 positive (9%). Sixteen out of 19 persons with a positive result were HCW, 14 (74%) had a link to a SARS-CoV-2 infected person. The majority of inconclusive results detected with the Xpert Xpress (n=45 of 3603), were related to individuals with a known history of SARS-CoV-2 infection (n=28, 62%). Conclusion: This study shows the importance of re-testing inconclusive SARS-CoV-2 qPCR results. Only then, the correct (true or false) interpretation can be given, leading to the right measures.

Decoding the Effect of Age on the Taste Perception of Chicken Breast Soup Based on LC-QTOF-MS/MS Combined with a Chemometric Approach.

A nontargeted fingerprinting approach combined with the chemometrics method and sensory analysis was used to assess the differences in taste-chemical compositions of chicken breast soup with different ages and their sensory qualities. The sensory evaluation results showed that the overall taste as well as the sourness, saltiness, and umami scores of the soup were increased with the age of chicken. Fifty-nine compounds were identified from four soup samples by liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (LC-QTOF-MS/MS), and their total content was the highest in the 90 wk soup samples. Six upregulated compounds (carnosine, hypoxanthine, inosine, inosine 5'-monophosphate (5'-IMP), adenosine 5'-monophosphate (5'-AMP), and lactic acid) were identified as potential contributors to the taste characteristics of the 90 wk soup samples by orthogonal projections to latent structures-discriminant analysis (OPLS-DA). Additional experiments showed that 5'-AMP particularly contributed to the sourness of the soup, while carnosine contributed to the saltiness and umami of the soup.

Better antimicrobial resistance data analysis and reporting in less time.

Objectives: Insights about local antimicrobial resistance (AMR) levels and epidemiology are essential to guide decision-making processes in antimicrobial use. However, dedicated tools for reliable and reproducible AMR data analysis and reporting are often lacking. We aimed to compare traditional data analysis and reporting versus a new approach for reliable and reproducible AMR data analysis in a clinical setting. Methods: Ten professionals who routinely work with AMR data were provided with blood culture test results including antimicrobial susceptibility results. Participants were asked to perform a detailed AMR data analysis in a two-round process: first using their software of choice and next using our newly developed software tool. Accuracy of the results and time spent were compared between both rounds. Finally, participants rated the usability using the System Usability Scale (SUS). Results: The mean time spent on creating the AMR report reduced from 93.7 to 22.4 min (P < 0.001). Average task completion per round changed from 56% to 96% (P < 0.05). The proportion of correct answers in the available results increased from 37.9% in the first to 97.9% in the second round (P < 0.001). Usability of the new tools was rated with a median of 83.8 (out of 100) on the SUS. Conclusions: This study demonstrated the significant improvement in efficiency and accuracy in standard AMR data analysis and reporting workflows through open-source software. Integrating these tools in clinical settings can democratize the access to fast and reliable insights about local microbial epidemiology and associated AMR levels. Thereby, our approach can support evidence-based decision-making processes in the use of antimicrobials.

Transcriptome and metabolome reveal the effects of three canopy types on the flavonoids and phenolic acids in 'Merlot' (Vitis vinifera L.) berry pericarp.

The flavonoids and phenolic acids in grape berries greatly influence the quality of wine. Various methods are used to shape and prune grapevines, but their effects on the flavonoids and phenolic acids remain unclear. The flavonoids and phenolic acids in the berry pericarps from grapevines pruned using three types of leaf canopy, namely, V-shaped, T-shaped, and vertical shoot-positioned (VSP) canopies, were compared in this study. Results showed that the V-shaped canopy was more favorable for the accumulation of flavonoids and phenolic acids. Transcriptome and metabolome analyses revealed that the differentially expressed genes (DEGs) and differentially regulated metabolites (DRMs) were significantly enriched in the flavonoid and phenylpropanoid biosynthesis pathways. A total of 96 flavonoids and 32 phenolic acids were detected among the DRMs. Their contents were higher in the V-shaped canopy than in the T-shaped and VSP canopies. Conjoint analysis of transcriptome and metabolome showed that nine DEGs (e.g., cytochrome P450 98A9 and 98A2) were significantly correlated to nine phenolic acids (e.g., gentisic acid and neochlorogenic acid) and three genes (i.e., chalcone isomerase, UDP-glycosyltransferase 88A1, and caffeoyl-CoA O-methyltransferase) significantly correlated to 15 flavonoids (e.g., baimaside and tricin-7-O-rutinoside). These genes may be involved in the regulation of various flavonoids and phenolic acids in grape berries, but their functions need validation. This study provides novel insights into the effects of leaf canopy on flavonoids and phenolic acids in the skin of grape berries and reveals the potential regulatory networks involved in this phenomenon.

The Impact of Food Additives on the Abundance and Composition of Gut Microbiota.

The gut microbiota has been confirmed as an important part in human health, and is even take as an 'organ'. The interaction between the gut microbiota and host intestinal environment plays a key role in digestion, metabolism, immunity, inflammation, and diseases. The dietary component is a major factor that affects the composition and function of gut microbiota. Food additives have been widely used to improve the color, taste, aroma, texture, and nutritional quality of processed food. The increasing variety and quantity of processed food in diets lead to increased frequency and dose of food additives exposure, especially artificial food additives, which has become a concern of consumers. There are studies focusing on the impact of food additives on the gut microbiota, as long-term exposure to food additives could induce changes in the microbes, and the gut microbiota is related to human health and disease. Therefore, the aim of this review is to summarize the interaction between the gut microbiota and food additives.

Recent Progress in the Study of Taste Characteristics and the Nutrition and Health Properties of Organic Acids in Foods.

Organic acids could improve the food flavor, maintain the nutritional value, and extend the shelf life of food. This review summarizes the detection methods and concentrations of organic acids in different foods, as well as their taste characteristics and nutritional properties. The composition of organic acids varies in different food. Fruits and vegetables often contain citric acid, creatine is a unique organic acid found in meat, fermented foods have a high content of acetic acid, and seasonings have a wide range of organic acids. Determination of the organic acid contents among different food matrices allows us to monitor the sensory properties, origin identification, and quality control of foods, and further provides a basis for food formulation design. The taste characteristics and the acid taste perception mechanisms of organic acids have made some progress, and binary taste interaction is the key method to decode multiple taste perception. Real food and solution models elucidated that the organic acid has an asymmetric interaction effect on the other four basic taste attributes. In addition, in terms of nutrition and health, organic acids can provide energy and metabolism regulation to protect the human immune and myocardial systems. Moreover, it also exhibited bacterial inhibition by disrupting the internal balance of bacteria and inhibiting enzyme activity. It is of great significance to clarify the synergistic dose-effect relationship between organic acids and other taste sensations and further promote the application of organic acids in food salt reduction.

Effects of Heavy Metal Exposure from Leather Processing Plants on Serum Oxidative Stress and the Milk Fatty Acid Composition of Dairy Cows: A Preliminary Study.

This study investigated whether unsaturated fatty acids in milk and the oxidative status of cows are affected by heavy metal exposure due to leather processing. The blood lead (Pb) concentrations in cows from two farms in the polluted area were 16.27 ± 8.63 µg/L, respectively, which were significantly (p < 0.05) higher than the blood Pb concentrations in cows from an unpolluted farm (6.25 ± 3.04 µg/L). There were significantly (p < 0.05) lower levels of glutathione S-transferase (GST), glutathione peroxidase (GPX), and glutathione (GSH) in the serum of cows from the polluted area compared to the levels in cows from an unpolluted area. The linoleic acid (C18:2n6c) content in milk from the polluted area was 15% lower than in the control area. There was a significant correlation between linoleic acid in milk with the blood Pb and serum GSH levels. Heavy metals can alter fatty acid synthesis through oxidative stress, which may be the mechanism by which heavy metals affect fatty acid synthesis in milk.

Indeterminate pediatric acute liver failure: Clinical characteristics of a temporal cluster of five children in the Netherlands in the spring of 2022.

There is increasing global concern of severe acute hepatitis of unknown etiology in young children. In early 2022, our center for liver transplantation in the Netherlands treated five children who presented in short succession with indeterminate acute liver failure. Four children underwent liver transplantation, one spontaneously recovered. Here we delineate the clinical course and comprehensive diagnostic workup of these patients. Three of five patients showed a gradual decline of liver synthetic function and had mild neurological symptoms. Their clinical and histological findings were consistent with hepatitis. These three patients all had a past SARS-CoV-2 infection and two of them were positive for adenovirus DNA. The other two patients presented with advanced liver failure and encephalopathy and underwent dialysis as a bridge to transplantation. One of these children spontaneously recovered. We discuss this cluster of patients in the context of the currently elevated incidence of severe acute hepatitis in children.

Threonine Facilitates Cd Excretion by Increasing the Abundance of Gut Escherichia coli in Cd-Exposed Mice.

Cadmium (Cd) can easily enter the body through the food chain and threaten health since Cd pollution is prevalent in the environment. Gut microbiota is necessary for the reduction of metal ions. To reduce Cd-induced harmful impacts and Cd accumulation in the body, we investigated the effect of amino acids on gut microbiota and Cd excretion in (fecal Cd) Cd-exposed mice. The screening of 20 amino acids showed that threonine (Thr) effectively increased fecal Cd, and reduced Cd-induced intestinal structural damage. The abundance of Escherichia-Shigella genus and KF843036_g significantly increased after the oral administration of Thr. As the type species of the Escherichia-Shigella genus, Escherichia coli exhibited high similarity to KF843036_g species and significantly decreased Cd-induced gut damage. Cd contents in the liver, kidney, and gut of Cd-exposed mice were also significantly (p < 0.05) decreased after E. coli treatment, while the contents in the feces were increased. The results demonstrated the potential roles that gut E. coli might play in Thr-mediated Cd excretion in Cd-exposed mice. The findings may provide important data for better understanding the molecular biological mechanism of Thr in reducing Cd accumulation in the body.

The Occurrence, Pathways, and Risk Assessment of Heavy Metals in Raw Milk from Industrial Areas in China.

This study evaluated chromium (Cr), arsenic (As), cadmium (Cd), and lead (Pb) contamination in raw milk from industrial areas in China, identified the possible pathways of heavy metals from the environment to raw milk, and made a risk assessment of the consumption of heavy metals from milk consumption. The Cr, As, Cd, and Pb concentrations in raw milk, water and silage were analyzed using inductively coupled plasma mass spectrometry. The Cr and As in soil were analyzed by flame atomic absorption spectrometry and atomic fluorescence spectrometry, respectively. Cd and Pb in soil were determined by a Graphite furnace atomic absorption spectrophotometer. The Cr and As concentrations in milk from industrial areas were 2.41 ± 2.12 and 0.44 ± 0.31 µg/kg, respectively, which were significantly higher (p < 0.01) than those from non-industrial areas, which had levels of 1.10 ± 0.15 and 0.25 ± 0.09 µg/kg, respectively. Chromium was mainly transferred through the soil-silage-milk pathway, As was transferred through the water-silage-milk pathway, while Cd was mainly transferred through the soil (water)-silage-milk pathway. The contributions of each metal to the overall hazard index (HI) followed a descending order of As, Cr, Pb, and Cd, with values of 46.64%, 25.54%, 24.30%, and 3.52%, respectively. Children were at higher risk than adults.

Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium.

BACKGROUND: Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is often used for molecular typing. Long-read sequencing is more rapid and provides useful information about the genome's structural composition but lacks the precision required for SNP-based typing and cgMLST. Here we compared prophages among 50 complete E. faecium genomes belonging to different lineages to explore whether a phage signature would be usable for typing and identifying an outbreak caused by VRE. As a proof of principle, we investigated if long-read sequencing data would allow for identifying phage signatures and thereby outbreak-related isolates. RESULTS: Analysis of complete genome sequences of publicly available isolates showed variation in phage content among different lineages defined by MLST. We identified phage present in multiple STs as well as phages uniquely detected within a single lineage. Next, in silico phage typing was applied to twelve MinION sequenced isolates belonging to two different genetic backgrounds, namely ST117/CT24 and ST80/CT16. Genomic comparisons of the long-read-based assemblies allowed us to correctly identify isolates of the same complex type based on global genome architecture and specific phage signature similarity. CONCLUSIONS: For rapid identification of related VRE isolates, phage content analysis in long-read sequencing data is possible. This allows software development for real-time typing analysis of long-read sequencing data, which will generate results within several hours. Future studies are required to assess the discriminatory power of this method in the investigation of ongoing outbreaks over a longer time period.

Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks.

Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis. Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content. Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster's closest related isolates. The vanB-carrying transposon Tn1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes. Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB-carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients.

Predominance of CTX-M-15-producing ST131 strains among ESBL-producing Escherichia coli isolated from asylum seekers in the Netherlands.

OBJECTIVES: Numerous studies show increased prevalence of MDR bacteria amongst asylum seekers, but data on the molecular profiles of such strains are limited. We aimed to evaluate the molecular profiles of ESBL-producing Escherichia coli (ESBL-E. coli) strains isolated from asylum seekers and investigate their phylogenetic relatedness. METHODS: WGS data of ESBL-E. coli isolates from asylum seekers, retrieved from 1 January to 31 December 2016, were analysed to assess MLST STs, fim types, phylogroups and resistance genes. Fifty-two ESBL-E. coli isolates from the Dutch-German border region were used for genome comparison purposes as a control group. RESULTS: Among 112 ESBL-E. coli isolates from asylum seekers, originating mostly from Syria (n = 40) and Iraq (n = 15), the majority belonged to ST131 (21.4%) and ST10 (17.0%). The predominant gene for ß-lactam resistance was blaCTX-M-15 (67.9%), followed by the often co-detected blaTEM-1B (39.3%). No mcr or carbapenemase genes were detected. The majority of the strains belonged to phylogroups B2 (38.4%) and A (32.1%), carrying fimH27 (25%) and fimH30 (19.6%). A core genome MLST minimum spanning tree did not reveal clusters containing strains from the asylum seekers and the control group. Five clusters were formed within the asylum seeker group, by strains isolated from people originating from different countries. CONCLUSIONS: The most frequently isolated clones in this study were isolated on a regular basis within the Dutch population before the increase in the asylum seeker population. No mcr- or carbapenemase-producing clones were detected among the asylum seeker population. Minor clustering was observed amongst the asylum seeker strains.