Pharmacogenomic Analysis of CYP3A5*3 and Tacrolimus Trough Concentrations in Vietnamese Renal Transplant Outcomes.

Purpose: CYP3A5 polymorphisms have been associated with variations in the pharmacokinetics of tacrolimus (Tac) in kidney transplant patients. Our study aims to quantify how the CYP3A5 genotype influences tacrolimus trough concentrations (C0) in a Vietnamese outpatient population by selecting an appropriate population pharmacokinetic model of Tac for our patients. Patients and Methods: The external dataset was obtained prospectively from 54 data of adult kidney transplant recipients treated at the 103 Military Hospital. All published Tac population pharmacokinetic models were systematically screened from PubMed and Scopus databases and were selected based on our patient's available characteristics. Mean absolute prediction error (MAPE), mean prediction error, and goodness-of-fit plots were used to identify the appropriate model for finding the formula that identifies the influence of CYP3A5 genotype on the pharmacokinetic data of Vietnamese patients. Results: The model of Zhu et al had a good predictive ability with MAPE of 19.29%. The influence of CYP3A5 genotype on tacrolimus clearance was expressed by the following formulas: CL/F=27,2×[(WT/70)0,75]×[(HCT/0,35)-0,501]×[(POD/180)0,0306]×CYP3A5(L/h). The simulation result showed that Tac C0 was significantly higher in patients not expressing CYP3A5 (p< 0.001). Conclusion: The incorporation of the CYP3A5 phenotype into Zhu's structural model has significantly enhanced our ability to predict Tacrolimus trough levels in the Vietnamese population. This study's results underscore the valuable role of CYP3A5 phenotype in optimizing the forecast of Tac concentrations, offering a promising avenue to assist health-care practitioners in their clinical decision-making and ultimately advance patient care outcomes.

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered.

UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.

First foods in a packaged world: Results from the COMMIT consortium to protect young child diets in Southeast Asia.

Although commercially produced complementary foods (CPCFs) are increasingly sold throughout Southeast Asia, concerns have been raised about CPCFs nutritional quality, labelling practices and the strength and scope of national CPCF regulations. The Consortium for Improving Complementary Foods in Southeast Asia (COMMIT), composed of UN agencies and civil society organizations, was formed to assess the nutrient gap in the diets of young children and the consumer, product and policy landscapes for CPCFs in seven Southeast Asian countries. Results from a nutrient gap assessment indicate that the diets of children aged 6-23 months are suboptimal and deficient in micronutrients. A consumer survey revealed that caretakers commonly use CPCFs, are conscious of the importance of nutrition and are influenced by label claims. Results from a CPCF benchmarking showed that many products sold in Southeast Asia contained added sugar or sweeteners, had a high total sugar and/or high sodium content and that no CPCF product adhered to all recommended labelling practices. Further, a legal review of national binding legal measures relevant to CPCFs showed minimal alignment with available global guidance. Urgent actions are necessary to strengthen national regulations related to CPCF nutrient composition and labelling practices. To speed progress, COMMIT developed a compendium of existing standards and global guidance to help countries align their national regulations with CPCF composition, labelling and production recommendations. Advocacy to garner public support for new or improved CPCF regulations, as well as strong government monitoring and enforcement of regulations, is crucial to support efforts to safeguard and improve the diets of older infants and young children in Southeast Asia.

Overpromoted and underregulated: National binding legal measures related to commercially produced complementary foods in seven Southeast Asian countries are not fully aligned with available guidance.

The market for commercially produced complementary foods (CPCF) is rapidly expanding in Southeast Asia; however, the existence and content of mandatory national policies, standards and legislation (binding legal measures) for CPCF in the region is unclear. To assess the status of national binding legal measures for CPCF in Southeast Asia, a legal and policy desk review was conducted in seven countries (Cambodia, Laos People's Democratic Republic, Indonesia, Malaysia, Philippines, Thailand and Viet Nam). The alignment of the national binding legal measures relevant to CPCF was assessed against guidance on CPCF nutrient composition and labelling requirements provided by Codex Alimentarius and the World Health Organization (WHO). Each of the seven countries had at least two national binding legal measures related to the nutrient composition or labelling of CPCF; however, there was limited alignment with the guidance from Codex and WHO. No country was fully aligned with the three CPCF-specific Codex standards/guidelines and only one country was in full alignment with the recommendations related to the protection of breastfeeding from the 'WHO Guidance on ending the inappropriate promotion of foods for infants and young children'. The findings of the review indicate that the existing national binding legal measures are insufficient to ensure that the CPCF sold as suitable for older infants and young children are nutritionally adequate and labelled in a responsible manner that does not mislead caregivers. Improved and enforced national binding legal measures for CPCF, in alignment with global guidance, are required to ensure that countries protect, promote and support optimal nutrition for children 6-36 months of age.

Promoting Respectful Maternity Care by Reducing Unnecessary Episiotomies: Experiences from Centers of Excellence for Breastfeeding in Vietnam.

(1) Background: Routine episiotomy is not recommended by international guidelines; however, it occurs at a high rate in Vietnam. (2) Methods: A process to reduce unnecessary episiotomies was developed and implemented as part of the Centers of Excellence for Breastfeeding initiative, which aims to deliver high-quality breastfeeding and early essential newborn care services within a supportive policy environment. The aim of this project report is to outline the steps undertaken to reduce episiotomies, the experience in pilot hospitals, and the process towards changing policy. (3) Results: During the 14 months following the change in episiotomy policy, pilot hospital records showed no infant death or injury. Monthly monitoring data from four pilot hospitals showed that the prevalence of episiotomy was substantially lower than the average in national hospitals in Vietnam. Facilitators to reducing the episiotomy rate include the incentive of Centers of Excellence for Breastfeeding designation and supportive hospital leadership. Challenges include the ambiguity of Vietnam's national guideline on episiotomy and lack of routine monitoring on the episiotomy rate and indications. (4) Discussion: Our experience suggests that through training and routine monitoring hospitals can apply a policy of selective episiotomy and reduce the practice, particularly among multiparous women, and improve breastfeeding rates.(5) Conclusions: Sharing our experience of implementing this process and offering four areas for action will hopefully contribute to expanded use of mother-friendly, evidence-based care as policy and routine practice in Vietnam and similar settings.

Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon.

Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.

How, not if, is the question mycologists should be asking about DNA-based typification.

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.

Comparing genomic variant identification protocols for Candida auris.

Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 Candida auris isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results. Although these pipelines used different variant callers and filtering criteria, we found high overall agreement of SNPs from each pipeline. This concordance correlated with site quality, as SNPs discovered by a few pipelines tended to show lower mapping quality scores and depth of coverage than those recovered by all pipelines. We observed that the major differences between pipelines were due to variation in read trimming strategies, SNP calling methods and parameters, and downstream filtration criteria. We calculated specificity and sensitivity for each pipeline by aligning three isolates with chromosomal level assemblies and found that the GATK-based pipelines were well balanced between these metrics. Selection of trimming methods had a greater impact on SAMtools-based pipelines than those using GATK. Phylogenetic trees inferred by each pipeline showed high consistency at the clade level, but there was more variability between isolates from a single outbreak, with pipelines that used more stringent cutoffs having lower resolution. This project generated two truth datasets useful for routine benchmarking of C. auris variant calling, a consensus VCF of genotypes discovered by 10 or more pipelines across these 35 diverse isolates and variants for 2 samples identified from whole-genome alignments. This study provides a foundation for evaluating SNP calling pipelines and developing best practices for future fungal genomic studies.

Corrigendum: First do no harm overlooked: Analysis of COVID-19 clinical guidance for maternal and newborn care from 101 countries shows breastfeeding widely undermined.

[This corrects the article DOI: 10.3389/fnut.2022.1049610.].

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics.

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.

Dnabarcoder: An open-source software package for analysing and predicting DNA sequence similarity cutoffs for fungal sequence identification.

The accuracy and precision of fungal molecular identification and classification are challenging, particularly in environmental metabarcoding approaches as these often trade accuracy for efficiency given the large data volumes at hand. In most ecological studies, only a single similarity cutoff value is used for sequence identification. This is not sufficient since the most commonly used DNA markers are known to vary widely in terms of inter- and intraspecific variability. We address this problem by presenting a new tool, dnabarcoder, to predict local similarity cutoffs and measure the resolving powers of a biomarker for sequence identification for different clades of fungi. It was shown that the predicted similarity cutoffs varied significantly between the clades of a recently released ITS DNA barcode data set from the CBS culture collection of the Westerdijk Fungal Biodiversity Institute. When classifying a large public fungal ITS data set-the UNITE database-against the barcode data set, the local similarity cutoffs assigned fewer sequences than the traditional cutoffs used in metabarcoding studies. However, the obtained accuracy and precision were significantly improved. Our study showed that it might be better to extract the ITS region from the ITS barcodes to optimize taxonomic assignment accuracy. Furthermore, 15.3, 25.6, and 26.3% of the fungal species of the barcode data set were indistinguishable by full-length ITS, ITS1, and ITS2, respectively. Except for these indistinguishable species, the resolving powers of full-length ITS, ITS1, and ITS2 sequences were similar at the species level. Nevertheless, the complete ITS region had a better resolving power at higher taxonomic levels.

Awareness, Perceptions, Gaps, and Uptake of Maternity Protection among Formally Employed Women in Vietnam.

Maternity protection is a normative fundamental human right that enables women to combine their productive and reproductive roles, including breastfeeding. The aim of this study is to examine the uptake of Vietnam's maternity protection policy in terms of entitlements and awareness, perceptions, and gaps in implementation through the lens of formally employed women. In this mixed methods study, we interviewed 494 formally employed female workers, among whom 107 were pregnant and 387 were mothers of infants and conducted in-depth interviews with a subset of these women (n = 39). Of the 494 women interviewed, 268 (54.3%) were working in blue-collar jobs and more than 90% were contributing to the public social insurance fund. Among the 387 mothers on paid maternity leave, 51 (13.2%) did not receive cash entitlements during their leave. Among the 182 mothers with infants aged 6-11 months, 30 (16.5%) returned to work before accruing 180 days of maternity leave. Of 121 women who had returned to work, 26 (21.5%) did not receive a one-hour paid break every day to express breastmilk, relax, or breastfeed, and 46 (38.0%) worked the same or more hours per day than before maternity leave. Although most women perceived maternity leave as beneficial for the child's health (92.5%), mother's health (91.5%), family (86.2%), and society (90.7%), fewer women perceived it as beneficial for their income (59.5%), career (46.4%), and employers (30.4%). Not all formally employed women were aware of their maternity protection rights: women were more likely to mention the six-month paid maternity leave (78.7%) and one-hour nursing break (62.3%) than the other nine entitlements (2.0-35.0%). In-depth interviews with pregnant women and mothers of infants supported findings from the quantitative survey. In conclusion, although Vietnam's maternity protection policy helps protect the rights of women and children, our study identified implementation gaps that limit its effectiveness. To ensure that all women and their families can fully benefit from maternity protection, there is a need to increase awareness of the full set of maternity entitlements, strengthen enforcement of existing policies, and expand entitlements to the informal sector.

Genetic and phenotypic diversity of fecal Candida albicans strains in irritable bowel syndrome.

Irritable bowel syndrome (IBS) is a common disorder characterized by chronic abdominal pain and changes in bowel movements. Visceral hypersensitivity is thought to be responsible for pain complaints in a subset of patients. In an IBS-like animal model, visceral hypersensitivity was triggered by intestinal fungi, and lower mycobiota α-diversity in IBS patients was accompanied by a shift toward increased presence of Candida albicans and Saccharomyces cerevisiae. Yet, this shift was observed in hypersensitive as well as normosensitive patients and diversity did not differ between IBS subgroups. The latter suggests that, when a patient changes from hyper- to normosensitivity, the relevance of intestinal fungi is not necessarily reflected in compositional mycobiota changes. We now confirmed this notion by performing ITS1 sequencing on an existing longitudinal set of fecal samples. Since ITS1 methodology does not recognize variations within species, we next focused on heterogeneity within cultured healthy volunteer and IBS-derived C. albicans strains. We observed inter- and intra-individual genomic variation and partial clustering of strains from hypersensitive patients. Phenotyping showed differences related to growth, yeast-to-hyphae morphogenesis and gene expression, specifically of the gene encoding fungal toxin candidalysin. Our investigations emphasize the need for strain-specific cause-and-effect studies within the realm of IBS research.

Lower Plasma Albumin, Higher White Blood Cell Count and High-Sensitivity C-Reactive Protein are Associated with Femoral Artery Intima-Media Thickness Among Newly Diagnosed Patients with Type 2 Diabetes Mellitus.

Introduction: Low albumin levels, high levels of high-sensitivity C-reactive protein (hs-CRP), and high white blood cell count were risk factors for changes in arterial intima-media thickness (IMT). Femoral artery IMT damages were one of the common peripheral artery type 2 diabetes. This study was conducted to determine the association between femoral artery IMT and plasma albumin, hs-CRP levels, and white blood cell count in newly diagnosed patients with type 2 diabetes mellitus (nT2D). Materials and Methods: From January 2015 to May 2020, 306 patients with nT2D were recruited for this cross-sectional descriptive study at Vietnam's National Endocrinology Hospital. We measured IMT by Doppler ultrasound. Results: There was a statistically significant difference in albumin, hs-CRP levels, hs-CRP-to-albumin ratio, and white blood cell counts between three different IMT groups namely normal IMT, thick IMT, and atherosclerosis (p = 0.003, p = 0.001, p = 0.001 and p = 0.049, respectively). In the multivariate linear regression analysis, white blood cell count, and hs-CRP levels showed a significantly positive correlation to IMT (standardized B and p of 0.17, 0.015 and 0.163, 0.024, respectively), but albumin levels were a significantly negative correlation to IMT (standardized B = -0.151, p = 0.029). The multivariate logistic regression analysis showed that albumin (OR = 0.79, 95% CI 0.65-0.90, p = 0.018), hs-CRP (OR = 1.09, 95% CI 1.01-1.18, p = 0.026), and white blood cell count (OR = 1.36, 95% CI 1.03-1.81, p = 0.033) had correlation to atherosclerosis of femoral artery. Conclusion: Reduced plasma albumin, elevated hs-CRP, and white blood cell count associated with IMT increased the odds for atherosclerosis of femoral artery among nT2D.

A review of front-of-pack nutrition labelling in Southeast Asia: Industry interference, lessons learned, and future directions.

Front-of-pack nutrition labelling is an evidence-based nutrition intervention that is recommended by the World Health Organization and other health agencies as an effective non-communicable disease prevention strategy. To date, the types of front-of-pack labels that have been identified as being most effective have yet to be implemented in Southeast Asia. This has been partly attributed to extensive industry interference in nutrition policy development and implementation. This paper outlines the current state of food labelling policy in the region, describes observed industry interference tactics, and provides recommendations for how governments in Southeast Asia can address this interference to deliver best-practice nutrition labelling to improve diets at the population level. The experiences of four focal countries - Malaysia, Thailand, the Philippines, and Viet Nam - are highlighted to provide insights into the range of industry tactics that are serving to prevent optimal food labelling policies from being developed and implemented. Funding: This research was supported by the United Kingdom Global Better Health Programme, which is managed by the United Kingdom Foreign, Commonwealth and Development Office and supported by PricewaterhouseCoopers in Southeast Asia.

First do no harm overlooked: Analysis of COVID-19 clinical guidance for maternal and newborn care from 101 countries shows breastfeeding widely undermined.

Background: In March 2020, the World Health Organization (WHO) published clinical guidance for the care of newborns of mothers with COVID-19. Weighing the available evidence on SARS-CoV-2 infection against the well-established harms of maternal-infant separation, the WHO recommended maternal-infant proximity and breastfeeding even in the presence of maternal infection. Since then, the WHO's approach has been validated by further research. However, early in the pandemic there was poor global alignment with the WHO recommendations. Methods: We assessed guidance documents collected in November and December 2020 from 101 countries and two regional agencies on the care of newborns of mothers with COVID-19 for alignment with the WHO recommendations. Recommendations considered were: (1) skin-to-skin contact; (2) early initiation of breastfeeding; (3) rooming-in; (4) direct breastfeeding; (5) provision of expressed breastmilk; (6) provision of donor human milk; (7) wet nursing; (8) provision of breastmilk substitutes; (9) relactation; (10) psychological support for separated mothers; and (11) psychological support for separated infants. Results: In less than one-quarter of country guidance were the three key breastfeeding facilitation practices of skin-to-skin contact, rooming-in, and direct breastfeeding recommended. Donor human milk was recommended in under one-quarter of guidance. Psychological support for mothers separated from their infants was recommended in 38%. Few countries recommended relactation, wet nursing, or psychological support for infants separated from mothers. In three-quarters of country guidance, expressed breastmilk for infants unable to directly breastfeed was recommended. The WHO and the United Kingdom's Royal College of Obstetricians and Gynecologists were each cited by half of country guidance documents with the United States Centers for Disease Control and Prevention directly or indirectly cited by 40%. Conclusion: Despite the WHO recommendations, many COVID-19 maternal and newborn care guidelines failed to recommend skin-to-skin contact, rooming-in, and breastfeeding as the standard of care. Irregular guidance updates and the discordant, but influential, guidance from the United States Centers for Disease Control may have been contributory. It appeared that once recommendations were made for separation or against breastfeeding they were difficult to reverse. In the absence of quality evidence on necessity, recommendations against breastfeeding should not be made in disease epidemics.

Sealing Treatment of Plasma-Sprayed Cr3C2-NiCr/Al2O3-TiO2 Coating by Aluminum Phosphate Sealant Containing Al2O3 Nanoparticles.

A typical structure of thermal spray coatings consisted of molten particles, semi-molten particles, oxides, pores, and cracks. These factors caused the porosity of sprayed coatings, leading to a significant influence on the coating properties, especially their wear-corrosion resistance. In this study, a post-spray sealing treatment of Cr3C2-NiCr/Al2O3-TiO2 plasma-sprayed coatings was carried out, and then, their corrosion properties were evaluated, before and after the treatment. For the sealing process, aluminum phosphate (APP) containing Al2O3 nanoparticles (~10 nm) was used. The permeability of APP into the sprayed coating was analyzed by SEM-EDS. The treatment efficiency for porosity and corrosion resistance of sprayed coatings was evaluated by electrochemical measurements, such as the potentiodynamic polarization and electrochemical impedance spectroscopy. The wear-corrosion resistance of the coating was examined in 3.5 wt.% NaCl circulation solution containing 0.25% SiO2 particles. The sealing efficiency was evaluated by the percentage of the treated open pores in the coating. The obtained results showed that APP penetrated deeply through the coating and the incorporation of Al2O3 nanoparticles into APP sealant improved the sealing efficiency by 20% of open pores in comparison with the sealant without nano-Al2O3. The effect of the post-treatment on corrosion protection of the sprayed coating has been discussed.

Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam.

Extra-intestinal pathogenic Escherichia coli (ExPEC) ST1193, a globally emergent fluoroquinolone-resistant clone, has become an important cause of bloodstream infections (BSIs) associated with significant morbidity and mortality. Previous studies have reported the emergence of fluoroquinolone-resistant ExPEC ST1193 in Vietnam; however, limited data exist regarding the genetic structure, antimicrobial resistance (AMR) determinants and transmission dynamics of this pandemic clone. Here, we performed genomic and phylogenetic analyses of 46 ST1193 isolates obtained from BSIs and healthy individuals in Ho Chi Minh City, Vietnam, to investigate the pathogen population structure, molecular mechanisms of AMR and potential transmission patterns. We further examined the phylogenetic structure of ST1193 isolates in a global context. We found that the endemic E. coli ST1193 population was heterogeneous and highly dynamic, largely driven by multiple strain importations. Several well-supported phylogenetic clusters (C1-C6) were identified and associated with distinct blaCTX-M variants, including blaCTXM-27 (C1-C3, C5), blaCTXM-55 (C4) and blaCTXM-15 (C6). Most ST1193 isolates were multidrug-resistant and carried an extensive array of AMR genes. ST1193 isolates also exhibited the ability to acquire further resistance while circulating in Vietnam. There were phylogenetic links between ST1193 isolates from BSIs and healthy individuals, suggesting these organisms may both establish long-term colonization in the human intestinal tract and induce infections. Our study uncovers factors shaping the population structure and transmission dynamics of multidrug-resistant ST1193 in Vietnam, and highlights the urgent need for local One Health genomic surveillance to capture new emerging ExPEC clones and to better understand the origins and transmission patterns of these pathogens.

The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks.

Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.

Nanopore Genome Sequencing and Variant Analysis of the Susceptible Candida auris Strain L1537/2020, Salvador, Brazil.

Candida auris has been reported worldwide, but only in December 2020, the first strain from a COVID-19 patient in Brazil was isolated. Here, we describe the genome sequence of this susceptible C. auris strain and performed variant analysis of the genetic relatedness with strains from other geographic localities.