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Salud Publica de Mexico Dec 2020Objetivo. Describir la evidencia sobre la presencia e infectividad de SARS-CoV-2 y otros coronavirus en aguas residuales y su potencial uso como herramienta de...
Objetivo. Describir la evidencia sobre la presencia e infectividad de SARS-CoV-2 y otros coronavirus en aguas residuales y su potencial uso como herramienta de vigilancia epidemiológica. Material y métodos. Búsqueda de publicaciones en PubMed y medRxiv desde enero 2003 hasta el 8 de junio de 2020 de acuerdo con la guía de revisiones rápidas de Cochrane. Resultados. Se incluyeron 29 publicaciones. El ARN de SARS-CoV-2 no infectivo se encontró en agua residual hospitalaria, agua residual cruda, tratada y lodos de plantas de tratamiento. Los niveles cuantitativos de ARN viral en agua residual presentan relación con el número de casos de Covid-19. SARS-CoV-1 y otros coronavirus permanecieron infectivos en agua residual cruda hasta por dos días. Conclusiones. Hasta esta revisión no existe evidencia sobre la presencia de virus infectivos de SARS-CoV-2 en agua residual cruda o tratada. La cuantificación de ARN de SARS-CoV-2 en agua residual es útil para la vigilancia epidemiológica.
Topics: Coronavirus; Mexico; RNA, Viral; Severe acute respiratory syndrome-related coronavirus; SARS-CoV-2; Virulence; Wastewater; Wastewater-Based Epidemiological Monitoring; Water Microbiology
PubMed: 33984206
DOI: 10.21149/11783 -
International Journal of Hygiene and... Sep 2020Heat treatment, or thermal disinfection, is one of the simplest disinfection methods, and is widely used in the water, sanitation, and food sectors, especially in low... (Meta-Analysis)
Meta-Analysis Review
Heat treatment, or thermal disinfection, is one of the simplest disinfection methods, and is widely used in the water, sanitation, and food sectors, especially in low resource settings. Pathogen reductions achieved during heat treatment are influenced by a combination of temperature and exposure time. The objective of this paper was to construct updated time-temperature pathogen inactivation curves to define "safety zones" for the reduction of four pathogen groups (bacteria, viruses, protozoan (oo)cysts, and helminth eggs) during heat treatment in a variety of matrices. A systematic review and meta-analysis were conducted to determine the times needed to achieve specified levels of pathogen reduction at different temperatures. Web of Science was searched using a Boolean string to target studies of heat treatment and pasteurization systems that exposed pathogens in water, wastewater, biosolids, soil, or food matrices to temperatures between 20 °C and 95 °C. Data were extracted from tables or figures and regression was used to assess the relationship between time and temperature. Our findings indicate that the temperatures and times needed to achieve a 1-log reduction of all pathogen groups are likely higher and longer, respectively, than previously reported. The type of microorganism and the matrix significantly impact T values reported at different temperatures. At high temperatures, the time-temperature curves are controlled by thermally stable viruses such as hepatitis A virus. Data gaps include the lack of data on protozoa, and the lack of data on all pathogen groups at low temperatures, for long exposure times, and with high log reductions. The findings from this study can be used by engineers, food safety specialists for the planning and design of engineered water, sanitation, and food pasteurization and treatment systems.
Topics: Disinfection; Food Microbiology; Hot Temperature; Pasteurization; Temperature; Viruses
PubMed: 32814236
DOI: 10.1016/j.ijheh.2020.113595 -
Clinical Microbiology and Infection :... Nov 2023The clinical features and predictors of Clostridioides difficile infection overlap with many conditions. (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
The clinical features and predictors of Clostridioides difficile infection overlap with many conditions.
OBJECTIVES
We performed a systematic review to evaluate the diagnostic utility of clinical features (clinical examination, risk factors, laboratory tests, and radiographic findings) associated with C. difficile.
METHODS
Systematic review and meta-analysis of diagnostic features for C. difficile.
DATA SOURCES
MEDLINE, EMBASE, CINAHL, and Cochrane databases were searched up to September 2021.
STUDY ELIGIBILITY CRITERIA
Studies that reported clinical features of C. difficile, a valid reference standard test for confirming diagnosis of C. difficile, and a comparison among patients with a positive and negative test result.
PARTICIPANTS
Adult and paediatric patients across diverse clinical settings.
OUTCOMES
Sensitivity, specificity, likelihood ratios.
REFERENCE STANDARD
Stool nucleic acid amplification tests, enzyme immunoassays, cell cytotoxicity assay, and stool toxigenic culture.
ASSESSMENT OF RISK OF BIAS
Rational Clinical Examination Series and Quality Assessment of Diagnostic Accuracy Studies-2.
METHODS OF DATA SYNTHESIS
Univariate and bivariate analyses.
RESULTS
We screened 11 231 articles of which 40 were included, enabling the evaluation of 66 features for their diagnostic utility for C. difficile (10 clinical examination findings, 4 laboratory tests, 10 radiographic findings, prior exposure to 13 antibiotic types, and 29 clinical risk factors). Of the ten features identified on clinical examination, none were significantly clinically associated with increased likelihood of C. difficile infection. Some features that increased likelihood of C. difficile infection were stool leukocytes (LR+ 5.31, 95% CI 3.29-8.56) and hospital admission in the prior 3 months (LR+ 2.14, 95% CI 1.48-3.11). Several radiographic findings also strongly increased the likelihood of C. difficile infection like ascites (LR+ 2.91, 95% CI 1.89-4.49).
DISCUSSION
There is limited utility of bedside clinical examination alone in detecting C. difficile infection. Accurate diagnosis of C. difficile infection requires thoughtful clinical assessment for interpretation of microbiologic testing in all suspected cases.
Topics: Humans; Clostridium Infections; Clostridioides difficile; Risk Factors; Sensitivity and Specificity; Feces; Adult; Child
PubMed: 37327874
DOI: 10.1016/j.cmi.2023.06.010 -
Advances in Nutrition (Bethesda, Md.) Jan 2023Food fermentation using sourdough-i.e., consortia of lactic bacteria and yeasts-is increasingly considered among the public as a natural transformation yielding... (Review)
Review
Food fermentation using sourdough-i.e., consortia of lactic bacteria and yeasts-is increasingly considered among the public as a natural transformation yielding nutritional benefits; however, it is unclear whether its alleged properties are validated by science. The aim of this study was to systematically review the clinical evidence related to the effect of sourdough bread on health. Bibliographic searches were performed in 2 different databases (The Lens and PubMed) up to February 2022. Eligible studies were randomized controlled trials involving adults, healthy or not, given any type of sourdough bread compared with those given any type of yeast bread. A total of 573 articles were retrieved and investigated, of which 25 clinical trials met the inclusion criteria. The 25 clinical trials included a total of 542 individuals. The main outcomes investigated in the retrieved studies were glucose response (N = 15), appetite (N = 3), gastrointestinal markers (N = 5), and cardiovascular markers (N = 2). Overall, it is currently difficult to establish a clear consensus with regards to the beneficial effects of sourdough per se on health when compared with other types of bread because a variety of factors, such as the microbial composition of sourdough, fermentation parameters, cereals, and flour types potentially influence the nutritional properties of bread. Nonetheless, in studies using specific strains and fermentation conditions, significant improvements were observed in parameters related to glycemic response, satiety, or gastrointestinal comfort after bread ingestion. The reviewed data suggest that sourdough has great potential to produce a variety of functional foods; however, its complex and dynamic ecosystem requires further standardization to conclude its clinical health benefits.
Topics: Humans; Ecosystem; Lactobacillus; Yeasts; Fermentation; Bread; Flour; Randomized Controlled Trials as Topic
PubMed: 36811591
DOI: 10.1016/j.advnut.2022.10.003 -
Periodontology 2000 Feb 2024Three years into the coronavirus disease 2019 (COVID-19) pandemic, there are still growing concerns with the emergence of different variants, unknown long- and... (Meta-Analysis)
Meta-Analysis
Three years into the coronavirus disease 2019 (COVID-19) pandemic, there are still growing concerns with the emergence of different variants, unknown long- and short-term effects of the virus, and potential biological mechanisms underlying etiopathogenesis and increased risk for morbidity and mortality. The role of the microbiome in human physiology and the initiation and progression of several oral and systemic diseases have been actively studied in the past decade. With the proof of viral transmission, carriage, and a potential role in etiopathogenesis, saliva and the oral environment have been a focus of COVID-19 research beyond diagnostic purposes. The oral environment hosts diverse microbial communities and contributes to human oral and systemic health. Several investigations have identified disruptions in the oral microbiome in COVID-19 patients. However, all these studies are cross-sectional in nature and present heterogeneity in study design, techniques, and analysis. Therefore, in this undertaking, we (a) systematically reviewed the current literature associating COVID-19 with changes in the microbiome; (b) performed a re-analysis of publicly available data as a means to standardize the analysis, and (c) reported alterations in the microbial characteristics in COVID-19 patients compared to negative controls. Overall, we identified that COVID-19 is associated with oral microbial dysbiosis with significant reduction in diversity. However, alterations in specific bacterial members differed across the study. Re-analysis from our pipeline shed light on Neisseria as the potential key microbial member associated with COVID-19.
Topics: Humans; COVID-19; Dysbiosis; Microbiota; Mouth; Oropharynx; Saliva; SARS-CoV-2
PubMed: 37277934
DOI: 10.1111/prd.12489 -
Journal of Hazardous Materials Apr 2022Fumigants have been used for decades to control soil-borne pathogens of high-value crops, and increasing evidence indicates they can affect non-target soil microbial... (Review)
Review
Fumigants have been used for decades to control soil-borne pathogens of high-value crops, and increasing evidence indicates they can affect non-target soil microbial communities. Understanding the impacts of these products on soil microorganisms is of critical importance not only for evaluating their environmental safety, but also because soil microbial communities have a central role in soil quality and nutrient cycling, plant growth, and crop production. Thus, we conducted a systematic review and metanalysis study of fumigant impacts on non-target soil microorganisms. In general, we found that fumigation decreases the bacterial diversity and abundance of total bacteria and nitrogen-cycling genes by approximately 10-50% during the first four weeks after application compared to non-treated soils. These decreases appear transient and tend to diminish or disappear after four weeks. Increases in bacterial diversity and abundance can occur after fumigation but are less common. Fumigant application can also alter bacterial community composition during the first six weeks after treatment by significantly increasing and/or decreasing the relative abundance of bacterial taxa involved in key soil functions such as N-cycling and plant-growth promotion. Knowledge gaps and areas where future research efforts should be prioritized to improve our understanding of the impact of organic fumigants on non-target soil microorganisms are discussed.
Topics: Fumigation; Nitrogen Cycle; Pesticides; Soil; Soil Microbiology
PubMed: 34999405
DOI: 10.1016/j.jhazmat.2021.128149 -
Journal de Mycologie Medicale Apr 2020Limited data are available on the epidemiology and etiology of cryptococcal infections in the Middle East. We aimed to conduct the systematic review and meta-analysis to... (Meta-Analysis)
Meta-Analysis
OBJECTIVE
Limited data are available on the epidemiology and etiology of cryptococcal infections in the Middle East. We aimed to conduct the systematic review and meta-analysis to summarize the epidemiological data on prevalence of Cryptococcus species complexes in trees and their surroundings, bird guano and secretions, animals, and highlight the reported episodes of cryptococcosis in Iran.
MATERIALS AND METHODS
Twelve databases, including PubMed, Science Direct, Scopus, Proquest, Google Scholar, Embase, and the ISI Web of Science, as well as the national databases, from January 1969 to October 2019 were searched. Furthermore, gray literature (e.g., thesis, congress abstracts) was evaluated using Iran Doc and www.thesis.
RESEARCH
ac.ir. Search process was accomplished on English or Persian language articles using the following keywords: "Cryptococcus", "Cryptococcosis", "invasive fungal infection", "Humans", "Birds", "Pigeon", "Animals", "Tree", "Eucalyptus", and "Iran", both alone and in combination.
RESULTS
Overall 36 studies were eligible regarding Cryptococcus and cryptococcosis in Iran. The total prevalence rates of Cryptococcus species in the tree was 4.7% (95% CI: 2.3-7.8), and in bird guano was 20.4% (95% CI: 10.7-32.2). Cryptococcosis in animal, and human were 1.7% (95% CI: 0.01-5.1), and 2.8% (95% CI: 0.7v6.1), respectively. The highest prevalence of Cryptococcus in the trees (14.6%), and bird guano (89.4%) in Khorasan, animals (8.9%) in Chaharmahal and Bakhtiari, and human (4.4%) in Mazandaran provinces were reported.
CONCLUSIONS
Given the significant risk of Cryptococcus species for susceptible humans, mainly HIV-infected patients, it seems quite necessary to adopt concrete preventive strategies to pinpoint the environmental habitats of this yeast.
Topics: Animals; Bird Diseases; Columbidae; Cryptococcosis; Cryptococcus; Eucalyptus; Humans; Invasive Fungal Infections; Iran; Plant Diseases; Prevalence; Trees
PubMed: 31864801
DOI: 10.1016/j.mycmed.2019.100917 -
Current Nutrition Reports Sep 2022Cancers are a leading cause of death in humans and for many other species. Diet has often been associated with cancers, and the microbiome is an essential mediator... (Review)
Review
PURPOSE OF REVIEW
Cancers are a leading cause of death in humans and for many other species. Diet has often been associated with cancers, and the microbiome is an essential mediator between diet and cancers. Here, we review the work on cancer and the microbiome across species to search for broad patterns of susceptibility associated with different microbial species.
RECENT FINDINGS
Some microbes, such as Helicobacter bacteria, papillomaviruses, and the carnivore-associated Fusobacteria, consistently induce tumorigenesis in humans and other species. Other microbes, such as the milk-associated Lactobacillus, consistently inhibit tumorigenesis in humans and other species. We systematically reviewed over a thousand published articles and identified links between diet, microbes, and cancers in several species of mammals, birds, and flies. Future work should examine a larger variety of host species to discover new model organisms for human preclinical trials, to better understand the observed variance in cancer prevalence across species, and to discover which microbes and diets are associated with cancers across species. Ultimately, this could help identify microbial and dietary interventions to diagnose, prevent, and treat cancers in humans as well as other animals.
Topics: Animals; Carcinogenesis; Diet; Humans; Mammals; Microbiota; Neoplasms
PubMed: 35704266
DOI: 10.1007/s13668-022-00420-5 -
International Journal of Molecular... Jul 2023sp. are the most commonly associated pathogens in infective endocarditis, especially within high-income nations. This along with the increasing burden of healthcare,... (Review)
Review
sp. are the most commonly associated pathogens in infective endocarditis, especially within high-income nations. This along with the increasing burden of healthcare, aging populations, and the protracted infection courses, contribute to a significant challenge for healthcare systems. A systematic review was conducted using relevant search criteria from PubMed, Ovid's version of MEDLINE, and EMBASE, and data were tabulated from randomized controlled trials (RCT), observational cohort studies, meta-analysis, and basic research articles. The review was registered with the OSF register of systematic reviews and followed the PRISMA reporting guidelines. Thirty-five studies met the inclusion criteria and were included in the final systematic review. The role of and its interaction with the protective shield and host protection functions was identified and highlighted in several studies. The interaction between infective endocarditis pathogens, vascular endothelium, and blood constituents was also explored, giving rise to the potential use of antiplatelets as preventative and/or curative agents. Several factors allow infections to proliferate within the host with numerous promoting and perpetuating agents. The complex interaction with the hosts' innate immunity also potentiates its virulence. The goal of this study is to attain a better understanding on the molecular pathways involved in infective endocarditis supported by and whether therapeutic avenues for the prevention and treatment of IE can be obtained. The use of antibiotic-treated allogeneic tissues have marked antibacterial action, thereby becoming the ideal substitute in native and prosthetic valvular infections. However, the development of effective vaccines against still requires in-depth studies.
Topics: Humans; Anti-Bacterial Agents; Endocarditis; Endocarditis, Bacterial; Staphylococcal Infections; Staphylococcus; Staphylococcus aureus
PubMed: 37446247
DOI: 10.3390/ijms241311068 -
Gut Microbes Dec 2023Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been... (Review)
Review
Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been published investigating the associations between gut microbiota and disease activity or IBD therapy. We performed a systematic review to investigate the microbiome predictors of response to advanced therapy in IBD. Unlike previous studies, our review focused on predictors of response to therapy; so the included studies assessed microbiome predictors before the proposed time of response or remission. We also provide an update of the available data on mycobiomes and viromes. We highlight key themes in the literature that may serve as future biomarkers of treatment response: the abundance of fecal SCFA-producing bacteria and opportunistic bacteria, metabolic pathways related to butyrate synthesis, and non-butyrate metabolomic predictors, including bile acids (BAs), amino acids, and lipids, as well as mycobiome predictors of response.
Topics: Humans; Gastrointestinal Microbiome; Inflammatory Bowel Diseases; Feces; Fecal Microbiota Transplantation; Biomarkers
PubMed: 38044504
DOI: 10.1080/19490976.2023.2287073