Integrative genome-centric metagenomics for surface water surveillance: Elucidating microbiomes, antimicrobial resistance, and their associations.

Surface water ecosystems are intimately intertwined with anthropogenic activities and have significant public health implications as primary sources of irrigation water in agricultural production. Our extensive metagenomic analysis examined 404 surface water samples from four different geological regions in Chile and Brazil, spanning irrigation canals (n = 135), rivers (n = 121), creeks (n = 74), reservoirs (n = 66), and ponds (n = 8). Overall, 50.25 % of the surface water samples contained at least one of the pathogenic or contaminant bacterial genera (Salmonella: 29.21 %; Listeria: 6.19 %; Escherichia: 35.64 %). Furthermore, a total of 1,582 antimicrobial resistance (AMR) gene clusters encoding resistance to 25 antimicrobial classes were identified, with samples from Brazil exhibiting an elevated AMR burden. Samples from stagnant water sources were characterized by dominant Cyanobacteriota populations, resulting in significantly reduced biodiversity and more uniform community compositions. A significant association between taxonomic composition and the resistome was supported by a Procrustes analysis (p < 0.001). Notably, regional signatures were observed regarding the taxonomic and resistome profiles, as samples from the same region clustered together on both ordinates. Additionally, network analysis illuminated the intricate links between taxonomy and AMR at the contig level. Our deep sequencing efforts not only mapped the microbial landscape but also expanded the genomic catalog with newly characterized metagenome-assembled genomes (MAGs), boosting the classification of reads by 12.85 %. In conclusion, this study underscores the value of metagenomic approaches in surveillance of surface waters, enhancing our understanding of microbial and AMR dynamics with far-reaching public health and ecological ramifications.

Development of Potential Therapeutic Agents from Black Elderberries (the Fruits of Sambucus nigra L.).

Elderberry (Sambucus nigra L.) is a widespread deciduous shrub, of which the fruits (elderberries) are used in the food industry to produce different types of dietary supplement products. These berries have been found to show multiple bioactivities, including antidiabetic, anti-infective, antineoplastic, anti-obesity, and antioxidant activities. An elderberry extract product, Sambucol®, has also been used clinically for the treatment of viral respiratory infections. As the major components, phenolic compounds, such as simple phenolic acids, anthocyanins and other flavonoids, and tannins, show promising pharmacological effects that could account for the bioactivities observed for elderberries. Based on these components, salicylic acid and its acetate derivative, aspirin, have long been used for the treatment of different disorders. Dapagliflozin, an FDA-approved antidiabetic drug, has been developed based on the conclusions obtained from a structure-activity relationship study for a simple hydrolyzable tannin, ß-pentagalloylglucoside (ß-PGG). Thus, the present review focuses on the development of therapeutic agents from elderberries and their small-molecule secondary metabolites. It is hoped that this contribution will support future investigations on elderberries.

Comprehensive mutational scanning of EGFR reveals TKI sensitivities of extracellular domain mutants.

The epidermal growth factor receptor, EGFR, is frequently activated in lung cancer and glioblastoma by genomic alterations including missense mutations. The different mutation spectra in these diseases are reflected in divergent responses to EGFR inhibition: significant patient benefit in lung cancer, but limited in glioblastoma. Here, we report a comprehensive mutational analysis of EGFR function. We perform saturation mutagenesis of EGFR and assess function of ~22,500 variants in a human EGFR-dependent lung cancer cell line. This approach reveals enrichment of erlotinib-insensitive variants of known and unknown significance in the dimerization, transmembrane, and kinase domains. Multiple EGFR extracellular domain variants, not associated with approved targeted therapies, are sensitive to afatinib and dacomitinib in vitro. Two glioblastoma patients with somatic EGFR G598V dimerization domain mutations show responses to dacomitinib treatment followed by within-pathway resistance mutation in one case. In summary, this comprehensive screen expands the landscape of functional EGFR variants and suggests broader clinical investigation of EGFR inhibition for cancers harboring extracellular domain mutations.

A descriptive analysis of otolaryngology presence on the social media platform TikTok.

Objective: In recent years, the video sharing app TikTok has become a new venue for health care providers and medical educators. Research on health care information within the app has primarily focused on cosmetic and plastic surgery content. TikTok could potentially be a tool used to educate the public on otolaryngology-related topics. This study is the first to analyze the quality and quantity of otolaryngology-related TikTok content. Methods: A cross-sectional study of TikTok accounts using otolaryngology-related hashtags within the preceding 6 months was conducted on February 4, 2023. Deductive qualitative analysis was performed between two coders to identify themes of the accounts and their content. Results: A total of 47 accounts were selected for analysis. Facial plastic surgery was the most represented specialty (n = 20; 43%) and pediatric otolaryngology the least represented (n = 1; 2%). Content posted was primarily educational in nature (n = 30; 64%) and 66% (n = 31) of content creators advertised contact information in their account biography. The majority of accounts were in English (n = 30; 64%) and originated in the United States (n = 30; 64%). More accounts were run by male (n = 29; 62%) than female content creators. Conclusion: Otolaryngology is a broad specialty with unequal representation of the related subspecialties on TikTok, a popular social media platform. The majority of current content focuses on patient education in facial plastic surgery. Future studies are warranted to examine the potential growth and impact of otolaryngology content on this video-based platform. Level of Evidence: 2.

Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa.

Since its emergence in the beginning of the 90's, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, blaTEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1-4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.

Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health.

The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.

Noncanonical open reading frames encode functional proteins essential for cancer cell survival.

Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects. We found that one of these ORFs, G029442-renamed glycine-rich extracellular protein-1 (GREP1)-encodes a secreted protein highly expressed in breast cancer, and its knockout in 263 cancer cell lines showed preferential essentiality in breast cancer-derived lines. The secretome of GREP1-expressing cells has an increased abundance of the oncogenic cytokine GDF15, and GDF15 supplementation mitigated the growth-inhibitory effect of GREP1 knockout. Our experiments suggest that noncanonical ORFs can express biologically active proteins that are potential therapeutic targets.

Correlation between the BACTEC MGIT 960 culture system with Genotype MTBDRplus and TB-SPRINT in multidrug resistant Mycobacterium tuberculosis clinical isolates from Brazil.

BACKGROUND: The accurate detection of multidrug-resistant tuberculosis (MDR-TB) is critical for the application of appropriate patient treatment and prevention of transmission of drug-resistant Mycobacterium tuberculosis isolates. The goal of this study was to evaluate the correlation between phenotypic and molecular techniques for drug-resistant tuberculosis diagnostics. Molecular techniques used were the line probe assay genotype MTBDRplus and the recently described tuberculosis-spoligo-rifampin-isoniazid typing (TB-SPRINT) bead-based assay. Conventional drug susceptibility testing (DST) was done on a BACTECTM MGIT 960 TB. METHOD: We studied 80 M. tuberculosis complex (MTC) clinical isolates from Minas Gerais state, of which conventional DST had classified 60 isolates as MDR and 20 as drug susceptible. FINDINGS: Among the 60 MDR-TB isolates with MGIT as a reference, sensitivity, specificity, accuracy, and kappa for rifampicin (RIF) resistance using TB-SPRINT and MTBDRplus, were 96.7% versus 93.3%, 100.0% versus 100.0%, 97.5% versus 95.0% and 0.94 versus 0.88, respectively. Similarly, the sensitivity, specificity, accuracy, and kappa for isoniazid (INH) resistance were 85.0% and 83.3%, 100.0% and 100.0%, 88.8% and 87.5% and 0.74 and 0.71 for both tests, respectively. Finally, the sensitivity, specificity, accuracy, and kappa for MDR-TB were 85.0% and 83.3%, 100.0% and 100.0%, 88.8% and 87.5% and 0.74 and 0.71 for both tests, respectively. MAIN CONCLUSIONS: Both methods exhibited a good correlation with the conventional DST. We suggest estimating the cost-effectiveness of MTBDRplus and TB-SPRINT in Brazil.

Correlation between the BACTEC MGIT 960 culture system with Genotype MTBDRplus and TB-SPRINT in multidrug resistant Mycobacterium tuberculosis clinical isolates from Brazil

BACKGROUND The accurate detection of multidrug-resistant tuberculosis (MDR-TB) is critical for the application of appropriate patient treatment and prevention of transmission of drug-resistant Mycobacterium tuberculosis isolates. The goal of this study was to evaluate the correlation between phenotypic and molecular techniques for drug-resistant tuberculosis diagnostics. Molecular techniques used were the line probe assay genotype MTBDRplus and the recently described tuberculosis-spoligo-rifampin-isoniazid typing (TB-SPRINT) bead-based assay. Conventional drug susceptibility testing (DST) was done on a BACTECTM MGIT 960 TB. METHOD We studied 80 M. tuberculosis complex (MTC) clinical isolates from Minas Gerais state, of which conventional DST had classified 60 isolates as MDR and 20 as drug susceptible. FINDINGS Among the 60 MDR-TB isolates with MGIT as a reference, sensitivity, specificity, accuracy, and kappa for rifampicin (RIF) resistance using TB-SPRINT and MTBDRplus, were 96.7% versus 93.3%, 100.0% versus 100.0%, 97.5% versus 95.0% and 0.94 versus 0.88, respectively. Similarly, the sensitivity, specificity, accuracy, and kappa for isoniazid (INH) resistance were 85.0% and 83.3%, 100.0% and 100.0%, 88.8% and 87.5% and 0.74 and 0.71 for both tests, respectively. Finally, the sensitivity, specificity, accuracy, and kappa for MDR-TB were 85.0% and 83.3%, 100.0% and 100.0%, 88.8% and 87.5% and 0.74 and 0.71 for both tests, respectively. MAIN CONCLUSIONS Both methods exhibited a good correlation with the conventional DST. We suggest estimating the cost-effectiveness of MTBDRplus and TB-SPRINT in Brazil.

Characteristics of tuberculosis in the state of Minas Gerais, Brazil: 2002-2009.

OBJECTIVE: To analyze the profile of tuberculosis cases reported between 2002 and 2009 in the state of Minas Gerais, Brazil, according to sociodemographic, clinical, and laboratory characteristics, as well as to comorbidities and mortality. METHODS: This was a descriptive, epidemiological study based on data obtained from the Brazilian Case Registry Database and the Brazilian Mortality Database for the 2002-2009 period. RESULTS: There were 47,285 reported cases of tuberculosis, corresponding to a mean incidence of 22.3/100,000 population. The individuals diagnosed with tuberculosis were predominantly in the 20- to 49-year age bracket and male (62.4% and 67.0%, respectively). Individuals with a low level of education accounted for 18.5% of the cases. New cases, cases of recurrence, and cases of retreatment accounted for 83.7%, 5.7%, 5.7%, respectively. The rates of cure and treatment noncompliance were 66.2% and 11.2%, respectively; multidrug-resistant tuberculosis was identified in 0.2% of the cases; and the mortality rate was 12.9%. The directly observed treatment, short-course (DOTS) strategy was applied in 21.8% of the cases. Sputum smear microscopy and culture were performed in only 73.9% and 12.9% of the cases, respectively. Chest X-rays were performed in 90.5% of the cases. Pulmonary tuberculosis was the predominant form (in 83.9%). Comorbidity with alcoholism, HIV infection, and diabetes mellitus were identified in 17.2%, 8.3%, and 3.8%, respectively. CONCLUSIONS: During the study period, the numbers of new cases, cases of treatment noncompliance, and deaths were high, comorbidities were common, and there was a failure to perform adequately basic tests for the diagnosis of tuberculosis. Multidisciplinary approaches, expanded use of the DOTS strategy, better knowledge of the distribution of tuberculosis, and improvements in the databases are needed in order to achieve better control of the disease in the state of Minas Gerais.

Characteristics of tuberculosis in the state of Minas Gerais, Brazil: 2002-2009 / Características da tuberculose no estado de Minas Gerais entre 2002 e 2009

OBJECTIVE: To analyze the profile of tuberculosis cases reported between 2002 and 2009 in the state of Minas Gerais, Brazil, according to sociodemographic, clinical, and laboratory characteristics, as well as to comorbidities and mortality. METHODS: This was a descriptive, epidemiological study based on data obtained from the Brazilian Case Registry Database and the Brazilian Mortality Database for the 2002-2009 period. RESULTS: There were 47,285 reported cases of tuberculosis, corresponding to a mean incidence of 22.3/100,000 population. The individuals diagnosed with tuberculosis were predominantly in the 20- to 49-year age bracket and male (62.4% and 67.0%, respectively). Individuals with a low level of education accounted for 18.5% of the cases. New cases, cases of recurrence, and cases of retreatment accounted for 83.7%, 5.7%, 5.7%, respectively. The rates of cure and treatment noncompliance were 66.2% and 11.2%, respectively; multidrug-resistant tuberculosis was identified in 0.2% of the cases; and the mortality rate was 12.9%. The directly observed treatment, short-course (DOTS) strategy was applied in 21.8% of the cases. Sputum smear microscopy and culture were performed in only 73.9% and 12.9% of the cases, respectively. Chest X-rays were performed in 90.5% of the cases. Pulmonary tuberculosis was the predominant form (in 83.9%). Comorbidity with alcoholism, HIV infection, and diabetes mellitus were identified in 17.2%, 8.3%, and 3.8%, respectively. CONCLUSIONS: During the study period, the numbers of new cases, cases of treatment noncompliance, and deaths were high, comorbidities were common, and there was a failure to perform adequately basic tests for the diagnosis of tuberculosis. Multidisciplinary approaches, expanded use of the DOTS strategy, better knowledge of the distribution of tuberculosis, and improvements in the databases are needed ...

OBJETIVO: Analisar o perfil de casos de tuberculose no estado de Minas Gerais entre 2002 e 2009, segundo características sociodemográficas, clínicas e laboratoriais, assim como presença de comorbidades e mortalidade. MÉTODOS: Estudo epidemiológico descritivo com levantamento de dados dos casos notificados no Sistema de Informação de Agravos de Notificação e Sistema de Informação de Mortalidade entre 2002 e 2009. RESULTADOS: Foram notificados 47.285 casos de tuberculose nos anos estudados, com média de incidência 22,3/100.000 habitantes. Os indivíduos com tuberculose eram predominantemente da faixa etária de 20-49 anos (62,4%), do sexo masculino (67,0%) e tinham baixa escolaridade (18,5%). Casos novos, de recidiva e de retratamento representaram, respectivamente, 83,7%, 5,7% e 5,7% do total de casos. As proporções de cura, abandono do tratamento e tuberculose multirresistente foram, respectivamente, 73,1%, 11,2% e 0,2%, enquanto o coeficiente de mortalidade foi 12,9%. O tratamento diretamente observado (TDO) foi administrado em 21,8% dos casos. A baciloscopia e a cultura de escarro somente foram realizadas em 73.9% e 12,9% dos casos, respectivamente. A radiografia de tórax foi realizada em 90,5% dos casos. A forma pulmonar prevaleceu (83,9%). A comorbidade com alcoolismo, infecção pelo HIV e diabetes mellitus foi identificada em 17,2%, 8,3% e 3,8% dos casos, respectivamente. CONCLUSÕES: No período estudado, o número de casos novos, de abandono e de óbitos foi elevado, as comorbidades foram relevantes, e os exames básicos não foram realizados adequadamente para o diagnóstico da tuberculose. São necessários o trabalho multiprofissional, ampliação da estratégia TDO, maior conhecimento da distribuição ...

Discovery of new anticancer agents from higher plants.

Small organic molecules derived from higher plants have been one of the mainstays of cancer chemotherapy for approximately the past half a century. In the present review, selected single chemical entity natural products of plant origin and their semi-synthetic derivatives currently in clinical trials are featured as examples of new cancer chemotherapeutic drug candidates. Several more recently isolated compounds obtained from plants showing promising in vivo biological activity are also discussed in terms of their potential as anticancer agents, with many of these obtained from species that grow in tropical regions. Since extracts of only a relatively small proportion of the ca. 300,000 higher plants on earth have been screened biologically to date, bioactive compounds from plants should play an important role in future anticancer drug discovery efforts.

Pharmacokinetics of α-mangostin in rats after intravenous and oral application.

SCOPE: The xanthone α-mangostin is one of the major bioactive secondary metabolites in Garcinia mangostana. Until now, in vivo studies on the absorption, bioavailability, disposition, and metabolism of α-mangostin are limited. METHODS AND RESULTS: In the present study, an LC-MS/MS assay has been established for the determination of α-mangostin in rat plasma. The validated method was used successfully to support pharmacokinetic studies in rats after intravenous (i.v.) and oral administration. Both non-compartmental and compartmental analyses were performed, where the two-compartment body model had a good fit with the i.v. data. Following i.v. administration, the disposition of α-mangostin in rat plasma was biphasic, subdivided into a fast distribution and a slow elimination phase. The half-life of the distribution phase was 3 min, and that of the terminal elimination phase 3.5 h, indicating a high tissue binding. However, for oral administration, the bioavailability was so low that it was not possible to obtain a full concentration-time profile. CONCLUSION: Although pure α-mangostin has shown a variety of pharmacological activities in in vitro assays at present it is uncertain if the same magnitude of effects will be achieved in vivo when its low bioavailability is considered.

Knowledge of severe acute respiratory syndrome among community physicians, nurses, and emergency medical responders.

INTRODUCTION: The preparedness levels of front-line clinicians including physicians, nurses, emergency medical responders (EMRs), and other medical staff working in clinics, offices and ambulatory care centers must be assessed, so these personnel are able to deal with communicable and potentially lethal diseases, such as severe acute respiratory syndrome (SARS). In order to determine the knowledge of these clinicians, a survey of their understanding of SARS and their use of educational resources was administered. METHODS: A questionnaire was distributed to physicians, nurses, and EMRs attending conferences on SARS in the summer of 2003. Questions related to information sources, knowledge of SARS, and plans implemented in their workplace to deal with it. Statistical analysis was performed using the Statistical Package for the Social Sciences (10.1 Program, SPSS Inc., Chicago, Illinois). RESULTS: A total of 201 community healthcare providers (HCPs) participated in the study. A total of 51% of the participants correctly identified the incubation period of SARS; 48% correctly identified the symptoms of SARS; and 60% knew the recommended infection control precautions to take for families. There was little difference in knowledge among the physicians, nurses, and EMRs evaluated. Media outlets such as newspapers, journals, television, and radio were reported as the main sources of information on SARS. However, there appears to be a growing use of the Internet, which correlated best with the correct answers on symptoms of SARS. Fewer than one-third of respondents were aware of a protocol for SARS in their workplace. A total of 60% reported that N-95 masks were available in their workplace. CONCLUSION: These findings suggest the need for more effective means of education and training for front-line clinicians, as well as the institution of policies and procedures in medical offices, clinics, and emergency services in the community.