The potential of circHIPK3 as a biomarker in chronic myeloid leukemia.

Chronic myeloid leukemia (CML) is a myeloproliferative disorder characterized by leukocytosis and left shift. The primary molecular alteration is the BCR::ABL1, chimeric oncoprotein with tyrosine kinase activity, responsible for the initial oncogenesis of the disease. Therapy of CML was revolutionized with the advent of tyrosine kinase inhibitors, but it is still not considered curative and may present resistance and serious adverse effects. Discoveries in CML inaugurated a new era in cancer treatment and despite all the advances, a new biomarker is needed to detect resistance and adverse effects. Circular RNAs (circRNAs) are a special type of non-coding RNA formed through a process called backsplicing. The majority of circRNAs are derived from protein-coding genes. CircHIPK3 is formed from the second exon of the HIPK3 gene and has been found in various pathologies, including different types of cancer. New approaches have demonstrated the potential of circular RNAs in cancer research, and circHIPK3 has shown promising results. It is often associated with cellular regulatory pathways, suggesting an important role in the molecular dynamics of tumors. The identification of biomarkers is an important tool for therapeutic improvement; thus we review the role of circHIPK3 and its potential as a biomarker in CML.

An overview of actionable and potentially actionable TSC1 and TSC2 germline variants in an online Database.

Tuberous Sclerosis Complex (TSC) is caused by loss of function germline variants in the TSC1 or TSC2 tumor suppressor genes. Genetic testing for the detection of pathogenic variants in either TSC1 or TSC2 was implemented as a diagnostic criterion for TSC. However, TSC molecular diagnosis can be challenging due to the absence of variant hotspots and the high number of variants described. This review aimed to perform an overview of TSC1/2 variants submitted in the ClinVar database. Variants of uncertain significance (VUS), missense and single nucleotide variants were the most frequent in clinical significance (37-40%), molecular consequence (37%-39%) and variation type (82%-83%) categories in ClinVar in TSC1 and TSC2 variants, respectively. Frameshift and nonsense VUS have potential for pathogenic reclassification if further functional and segregation studies were performed. Indeed, there were few functional assays deposited in the database and literature. In addition, we did not observe hotspots for variation and many variants presented conflicting submissions regarding clinical significance. This study underscored the importance of disseminating molecular diagnostic results in a public database to render the information largely accessible and promote accurate diagnosis. We encourage the performance of functional studies evaluating the pathogenicity of TSC1/2 variants.

SARS-CoV-2 Variants of Concern: Presumptive Identification via Sanger Sequencing Analysis of the Receptor Binding Domain (RBD) Region of the S Gene.

Variants of concern (VOCs) of SARS-CoV-2 are viral strains that have mutations associated with increased transmissibility and/or increased virulence, and their main mutations are in the receptor binding domain (RBD) region of the viral spike. This study aimed to characterize SARS-CoV-2 VOCs via Sanger sequencing of the RBD region and compare the results with data obtained via whole genome sequencing (WGS). Clinical samples (oro/nasopharyngeal) with positive RT-qPCR results for SARS-CoV-2 were used in this study. The viral RNA from SARS-CoV-2 was extracted and a PCR fragment of 1006 base pairs was submitted for Sanger sequencing. The results of the Sanger sequencing were compared to the lineage assigned by WGS using next-generation sequencing (NGS) techniques. A total of 37 specimens were sequenced via WGS, and classified as: VOC gamma (8); delta (7); omicron (10), with 3 omicron specimens classified as the BQ.1 subvariant and 12 specimens classified as non-VOC variants. The results of the partial Sanger sequencing presented as 100% in agreement with the WGS. The Sanger protocol made it possible to characterize the main SARS-CoV-2 VOCs currently circulating in Brazil through partial Sanger sequencing of the RBD region of the viral spike. Therefore, the sequencing of the RBD region is a fast and cost-effective laboratory tool for clinical and epidemiological use in the genomic surveillance of SARS-CoV-2.

Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child.

BACKGROUND: With the progression of the Coronavirus disease pandemic, the number of mutations in the viral genome has increased, showing the adaptive evolution of severe acute respiratory syndrome coronavirus 2 in humans and intensification in transmissibility. Long-term infections also allow the development of viral diversity. In this study, we report the case of a child with severe combined immu presenting a prolonged severe acute respiratory syndrome coronavirus 2 infection. We aimed to analyze 3 naso-oropharyngeal swab samples collected between August and December 2021 to describe the amino acid changes present in the sequence reads that may have a role in the emergence of new viral variants. METHODS: The whole genome from clinical samples was sequenced through high throughput sequencing and analyzed using a workflow to map reads and then find variations/single-nucleotide polymorphisms. In addition, the samples were isolated in cell culture, and a plaque forming units assay was performed, which indicates the presence of viable viral particles. RESULTS: The results obtained showed that the virus present in all samples is infectious. Also, there were 20 common mutations among the 3 sequence reads, found in the ORF1ab and ORF10 proteins. As well, a considerable number of uncommon mutations were found. CONCLUSIONS: In conclusion, we emphasize that genomic surveillance can be a useful tool to assess possible evolution signals in long-term patients.

The antibiotic resistome in Escherichia coli isolated from human, food, and animal sources.

AIMS: The aim of this study was to analyze and compare the prevalence and distribution of resistance genes in Escherichia coli genomes isolated from human clinical samples and animal-based foods worldwide. METHODS AND RESULTS: We download from NCBI Pathogen Detection Database the corresponding metadata of the 7,123 E. coli genome to access the information about the antimicrobial resistance gene content. The geographic location and the source of isolation were also obtained and compiled with the antimicrobial resistance gene for statistical analysis, results and discussion. Our criteria considered four groups for analyzing the antimicrobial resistance gene distribution. The first group of genomes from invasive clinical human (ICH) samples from countries with Human Development Index (HDI) ≥ 0.850; the second group of ICH from countries with an HDI ≤ 0.849; the third group of animal-based foods (ABF) from countries with HDI ≥ 0.850 and the fourth group of ABFs from countries with HDI ≤ 0.849. The most prevalent genes in the first group were blaCTX-M-134 (96.53%) and blaCTX-M-27 (86.35%). In the second group, ere(A) (95.96%), soxS (94.49%), qepA8 (90.81%), blaCTX-M-15 (85.66%), and fosA3 (80.88%). In the third group, the most frequently detected were aadA12 (98.5%), ant(3") (89.92%), and blaCARB-2 (87.2%). In the fourth group, aadA12 and aac(3)-IV were identified in 100% of the analyzed genomes. CONCLUSIONS: It was clear that the use of aminoglycosides in animal production is increasing the selective pressure on micro-organisms in both groups of countries since genes linked to aminoglycoside resistance are related to E. coli from ABF samples. The genomic profile of E. coli from HDI ≥ 0.850 countries indicates a selective pressure aimed at cephalosporins given the high prevalence in both sources.

HPLC-MS/MS method for determination of betamethasone in human plasma with application to a dichorionic twin pregnancy pharmacokinetic and placental transfers studies

Abstract Betamethasone (BET) is a synthetic glucocorticoid recommended for pregnant women at imminent risk of preterm birth before 34 weeks to reduce neonatal complications. There are different techniques to describe BET plasma quantification. However, none quantified the plasmatic concentration of BET in dichorionic (DC) twin pregnancies using LC-MS. Our objectives were to develop and validate a method for quantifying BET by LC-MS for pharmacokinetic (PK) and placental transfer studies in DC twin pregnancies. Blood samples were collected after intramuscular administration of a single BET dose containing 6 mg disodium phosphate + 6 mg acetate. BET was determined in plasma by liquid-liquid extraction. The method showed linearity in the range of 2-250 ng/mL, as well as precision and accuracy with a coefficient of variation and relative standard errors ≤ 15%. Additionally, the method presented selectivity and did not present matrix or carry-over effect. Stability tests also presented coefficient of variation and relative standard errors ≤ 15%. This is the first study which describe maternal and fetal plasma concentrations of BET in a DC twin pregnancy. The BET PK parameters were AUC0-∞, CL/F, Vd/F, Cmax, Tmax of 292.20 h*ng/mL, 39.08 L/h, 278.72 L, 25.55 ng/mL and 0.58 h, respectively. The placental transfer ratios of umbilical vein/maternal vein and intervillous space/maternal vein were 0.14 and 0.19 and 0.40 and 0.27 for both twins, respectively. However, a clinical study with more subjects is imperative to confirm this higher concentration of BET in the intervillous space

Enhanced elimination of betamethasone in dichorionic twin pregnancies.

AIM: No study has evaluated the betamethasone pharmacokinetics in twin pregnancies according to chorionicity. This study aimed to describe and compare the betamethasone pharmacokinetic parameters in singleton and dichorionic (DC) and monochorionic twin pregnancies in the third trimester of pregnancy. METHODS: Twenty-six pregnant women received 2 intramuscular doses of 6 mg of betamethasone sodium phosphate plus 6 mg betamethasone acetate due to preterm labour. Serial blood samples were collected for 24 hours after the first intramuscular dose of betamethasone esters. Betamethasone plasma concentrations were quantified using a validated liquid chromatography-tandem mass spectrometry analytical method, and the pharmacokinetic parameters were obtained employing a noncompartmental model. Preliminary data on the betamethasone placental transfer are also presented. RESULTS: The geometric mean (95% confidence interval) of AUC0-∞ 645.1 (504.3-825.2) vs. 409.8 (311.2-539.6) ng.h/mL and CL/F 17.70 (13.84-22.65) vs. 27.87 (21.17-36.69) were significantly different, respectively, in singleton pregnancies when compared to DC twins. CONCLUSION: Data from this study suggest that the presence of 2 foetoplacental units may increase the betamethasone metabolism by hepatic CYP3A4 and/or placental 11ß-HSD2 enzymes. Pharmacokinetic-pharmacodynamic clinical studies are needed to investigate whether these betamethasone pharmacokinetic changes have clinical repercussions for the newborns and require dose adjustment in DC twin pregnancies.

Global distribution of plasmid-mediated colistin resistance mcr gene in Salmonella: A systematic review.

This systematic review focuses on obtaining the most relevant information from multiple studies that detected a mobilized colistin resistance mcr gene in Salmonella for a better comprehension of its global distribution. A group of strategic and systematic keywords were combined to retrieve research data on the detection frequency of the mcr gene globally from four database platforms (Google Scholar, Science Direct, PubMed and Scielo). Forty-eight studies attended all the eligibility criteria and were selected. China was the country with the highest frequency of Salmonella strains with the mcr gene, and Europe exhibited a wide diversity of countries with positive mcr strains. In addition, animals and humans carried the highest frequency of positive strains for the mcr gene. Salmonella Typhimurium was the most frequent serovar carrying the mcr gene. Apparently, colistin overuse in animal husbandry has increased the selective pressure of antimicrobial resistance, resulting in the emergence of a plasmid-mediated colistin resistance mcr gene in China. The mcr-positive Salmonella strains are recently predominant worldwide, which is probably due to the capacity of this gene to be swiftly horizontally transmissible. The transmission ability of mcr-positive Salmonella strains to humans through the consumption of contaminated animal-based food is a public health concern.

Determination of misoprostol acid in plasma samples by UPLC-MS/MS with application in a maternal-fetal pharmacokinetic study following a low misoprostol dose vaginally to induce labor.

Misoprostol is a prostaglandin E1 synthetic analogous used for elective interruptions of early pregnancy, treatment of incomplete abortion, postpartum hemorrhage and induction of full-term labor. Its a lipophilic drug, passing by extensive and rapid pre-systemic metabolism into the active metabolite, misoprostol acid (MA). The objective of this study was to develop and validate a highly sensitive method for MA determination in plasma using UPLC-MSMS, with application in a study of maternal-fetal pharmacokinetics in healthy parturients women (n = 10) after administration of 25 µg misoprostol vaginally. The method presented linearity of 2-10 pg/mL and acceptable precision, accuracy, plasma and solution stability. The parturients women presented median (interquartile range) values of AUC0-6 of 68.0 (40.8-84.7) pg.h/mL, Cmax of 21.9 (11.9-30.1) pg/mL and Tmax of 2.25 (0.69-5.00) h. The placental transfer of MA was assessed from the umbilical vein/maternal blood ratios of 1.40 (0.91-2.13) and intervillous space/maternal blood ratios of 0.49 (0.15-3.41). In conclusion, this method presented high sensitivity, being able to quantify MA in plasma samples following a low 25 µg misoprostol administered vaginally aimed to induce labor in parturients women. Additionally, this is the first description of the placental transfer of MA after a vaginal administration of misoprostol.

Virulence genes identification and characterization revealed the presence of the Yersinia High Pathogenicity Island (HPI) in Salmonella from Brazil.

Salmonella spp. is one of the major agents of foodborne disease worldwide, and its virulence genes are responsible for the main pathogenic mechanisms of this micro-organism. The whole-genome sequencing (WGS) of pathogens has become a lower-cost and more accessible genotyping tool providing many gene analysis possibilities. This study provided an in silico investigation of 129 virulence genes, including plasmidial and bacteriophage genes from Brazilian strains' public Salmonella genomes. The frequency analysis of the four most sequenced serovars and a temporal analysis over the past four decades was also performed. The NCBI sequence reads archive (SRA) database comprised 1077 Salmonella public whole-genome sequences of strains isolated in Brazil between 1968 and 2018. Among the 1077 genomes, 775 passed in Salmonella in silico Typing (SISTR) quality control, which also identified 41 different serovars in which the four most prevalent were S. Enteritidis, S. Typhimurium, S. Dublin, and S. Heidelberg. Among these, S. Heidelberg presented the most distinct virulence profile, besides presenting Yersinia High Pathogenicity Island (HPI), rare and first reported in Salmonella from Brazil. The genes mgtC, csgC, ssaI and ssaS were the most prevalent within the 775 genomes with more than 99% prevalence. On the other hand, the less frequent genes were astA, iucBCD, tptC and shdA, with less than 1% frequency. All of the plasmids and bacteriophages virulence genes presented a decreasing trend between the 2000 s and 2010 s decades, except for the phage gene grvA, which increased in this period. This study provides insights into Salmonella virulence genes distribution in Brazil using freely available bioinformatics tools. This approach could guide in vivo and in vitro studies besides being an interesting method for the investigation and surveillance of Salmonella virulence. Moreover, here we propose the genes mgtC, csgC, ssaI and ssaS as additional targets for PCR identification of Salmonella in Brazil due to their very high frequency in the studied genomes.

The impact of maternal periodontitis in the development of asthma in the offspring.

Clinical and experimental studies show an association between maternal periodontitis and adverse outcomes during gestation. On the other hand, there were no studies evaluating the impact of maternal periodontitis on the offspring. Thus, our objective was to investigate the repercussion of maternal periodontitis on the development of asthma in the offspring. Pregnant rats were submitted or not to periodontitis by ligature technique. Thirty days after birth, the puppies were sensitized and challenged with ovalbumin (OVA) in order to induce asthmatic response. Our results showed that maternal periodontitis reduced cellular infiltrate in the parenchyma of offspring, tracheal responsiveness, lung edema, and anti-OVA antibodies, without alter mucus as well as cytokines production. We concluded that periodontitis has relevant impact on the offspring's immune system, blunting the response to allergic and inflammatory stimulus. This study shows the important role of oral health during pregnancy and opens possibilities for future studies in order to explain the effects of periodontitis during pregnancy in the offspring.

Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades.

Salmonella is a leading human pathogen and a significant public health concern worldwide. Massive food production and distribution have contributed to this pathogen dissemination, which, combined with antimicrobial resistance (AMR), creates new control challenges in food safety. The development of AMR is a natural phenomenon and can occur in the bacterial evolutionary process. However, the overuse and the misuse of antimicrobial drugs in humans and in animals have increased AMR selective pressure. In Brazil, there is an accuracy lack in AMR frequency in Salmonella because too many isolates are under-investigated for genetic and phenotypic AMR by the Brazilian health authorities and the research community. This underreporting situation makes the comprehension of the real level of Salmonella AMR in the country difficult. The present study aimed to use bioinformatics tools for a rapid in silico screening of the genetic antimicrobial resistance profile of Salmonella through whole-genome sequences (WGS). A total of 930 whole-genome sequences of Salmonella were retrieved from the public database of the National Biotechnology Information Center (NCBI). A total of 65 distinct resistance genes were detected, and the most frequent ones were tet(A), sul2, and fosA7. Nine point mutations were detected in total, and parC at the 57 position (threonine → serine) was the highest frequent substitution (26.7%, 249/930), followed by gyrA at the 83 position (serine → phenylalanine) (20.0%, 186/930) and at the 87 position (aspartic acid → asparagine) (15.7%, 146/930). The in silico prediction of resistance phenotype showed that 58.0% (540/930) of the strains can display a multidrug resistance (MDR) profile. Ciprofloxacin and nalidixic acid were the antimicrobial drugs with the highest frequency rates of the predicted phenotype resistance among the strains. The temporal analysis through the last four decades showed increased frequency rates of antimicrobial resistance genes and predicted resistance phenotypes in the 2000s and the 2010s when compared with the 1980s and 1990s. The results presented herein contributed significantly to the understanding of the strategic use of WGS associated with in silico analysis and the predictions for the determination of AMR in Salmonella from Brazil.

Novel frameshift variant of the CFTR gene: S511Lfs*2 from phenotype to molecular predictions.

Cystic fibrosis (CF) is a genetic disease caused by variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. There are over 2,000 different pathogenic and non-pathogenic variants described in association with a broad clinical heterogeneity. In this work, we identified a novel variant S511Lfs*2 in CFTR gene that has not been reported in patients with CF. The patient was a female genotyped with c.1000C>T (legacy name: R334W) variant (pathogenic, CF-causing) and the novel variant (S511Lfs*2). We verified the amino acid sequence, the protein structure, and predicted the pathogenicity employing computational analysis. Our findings showed that S511Lfs*2 is a frameshift variant and suggest that it is associated with severe CF phenotype, as it leads to a lack of CFTR protein synthesis, and consequently the loss of its functional activity.

Antimicrobial Resistance in Nontyphoidal Salmonella Isolates from Human and Swine Sources in Brazil: A Systematic Review of the Past Three Decades.

Salmonella is the leading cause of foodborne illnesses worldwide. The widespread use of antimicrobials as prophylactic, therapeutic, and growth promoters in both livestock and human medicine has resulted in selective pressure regarding antimicrobial-resistant (AMR) bacteria. This systematic review summarizes phenotypic antimicrobial resistance profiles in Salmonella isolates from human and swine sources between 1990 and 2018 in Brazil. The 20 studies that matched the eligibility criteria-isolates from pigs and humans from Brazil, between 1990 and 2016, containing information on the number of Salmonella isolates, and applying the disk diffusion susceptibility method-were included. During the assessed period, Salmonella strains isolated from swine sources displayed the highest resistance rates for tetracycline (20.3%) and sulfonamides (17.4%). In contrast, human isolates displayed the highest resistance rates against ampicillin (19.8%) and tetracycline (17%). Salmonella Typhimurium was the most frequent AMR isolate from both swine and human sources, corresponding to 67% of all isolates. From 2001 to 2005, tetracycline and ampicillin were the top antimicrobial resistance compounds, and the most frequently detected in swine and human sources, respectively. A total of 63 and 58 multiple drug resistance profiles were identified in swine and human isolates, respectively. Antimicrobial resistance has decreased throughout the 1990-2016 period, except for gentamicin and nalidixic acid in swine and human isolates, respectively. The results indicate that Salmonella isolated from human and swine display resistance against clinically important antimicrobials, indicating that swine are possibly one of the main vectors for spreading human salmonellosis in Brazil.

Cystic Fibrosis: A Simple and Customized Strategy for Genetic Screening Able to Detect Over 90% of Identified Mutated Alleles in Brazilian Newborns.

INTRODUCTION: The incorporation of molecular genetic testing into cystic fibrosis (CF) screening programs increases the specificity of the diagnostic strategy and has the potential to decrease the rate of false- positive results. In this sense, our objective was to develop a genotyping assay that could detect 25 pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene with high sensitivity and that could be incorporated into the routine of newborn screening, complementing the current existing protocol used in our public health institution. METHODS: A mini-sequencing assay was standardized using single-base extension in a previously genotyped control sample. This strategy was validated in a Brazilian cohort of CF patients by Sanger sequencing. RESULTS: The inclusion of the 25 variants in the current newborn screening program increased the identification rates of two alleles from 33 to 52.43% in CF patients. This new approach was able to detect a total of 37 variants, which represents 93.01% of all mutated alleles described in the last CF Brazilian Register. CONCLUSIONS: Mini-sequencing for the simultaneous detection of 25 CFTR gene variants improves the screening of Brazilian newborns and decreases the number of inconclusive cases. This method uses minimal hands-on time and is suited for rapid screening, which reduces sample processing costs.

Caracterização sensorial e análises físico-químicas de diferentes espécies de peixes durante armazenamento a 0°C / Sensorial description and physicochemical analyzes of different species of fishes during 0°C storage

O consumo de peixe vem aumentando devido aos seus benefícios nutricionais. No entanto, é um produto altamente perecível devido à sua composição. O objetivo do trabalho foi avaliar o comportamento sensorial e físico-químico de três espécies de peixe: xixarro (Trachurus lathami), olho de cão (Priacanthus arenatus) e corvina (Micropogonias furnieri), durante o período de 11 dias de estocagem. Foram realizadas a caracterização sensorial e análises de cocção, pH, amônia, gás sulfídrico e bases voláteis totais. O pH e as bases voláteis totais não apresentaram resultados superiores aos da legislação. A caracterização sensorial indicou que o xixarro sofreu alterações sensoriais mais rapidamente que as outras espécies e as análises físico-químicas feitas não foram suficientes para detectar os primeiros estágios da deterioração.