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1.
J Glob Health ; 11: 10002, 2021 Apr 03.
Artículo en Inglés | MEDLINE | ID: mdl-33828849

RESUMEN

Background: This rapid evidence review identifies and integrates evidence from epidemiology, microbiology and fluid dynamics on the transmission of SARS-CoV-2 in indoor environments. Methods: Searches were conducted in May 2020 in PubMed, medRxiv, arXiv, Scopus, WHO COVID-19 database, Compendex & Inspec. We included studies reporting data on any indoor setting except schools, any indoor activities and any potential means of transmission. Articles were screened by a single reviewer, with rejections assessed by a second reviewer. We used Joanna Briggs Institute and Critical Appraisal Skills Programme tools for evaluating epidemiological studies and developed bespoke tools for the evaluation of study types not covered by these instruments. Data extraction and quality assessment were conducted by a single reviewer. We conducted a meta-analysis of secondary attack rates in household transmission. Otherwise, data were synthesised narratively. Results: We identified 1573 unique articles. After screening and quality assessment, fifty-eight articles were retained for analysis. Experimental evidence from fluid mechanics and microbiological studies demonstrates that aerosolised transmission is theoretically possible; however, we found no conclusive epidemiological evidence of this occurring. The evidence suggests that ventilation systems have the potential to decrease virus transmission near the source through dilution but to increase transmission further away from the source through dispersal. We found no evidence for faecal-oral transmission. Laboratory studies suggest that the virus survives for longer on smooth surfaces and at lower temperatures. Environmental sampling studies have recovered small amounts of viral RNA from a wide range of frequently touched objects and surfaces; however, epidemiological studies are inconclusive on the extent of fomite transmission. We found many examples of transmission in settings characterised by close and prolonged indoor contact. We estimate a pooled secondary attack rate within households of 11% (95% confidence interval (CI) = 9, 13). There were insufficient data to evaluate the transmission risks associated with specific activities. Workplace challenges related to poverty warrant further investigation as potential risk factors for workplace transmission. Fluid mechanics evidence on the physical properties of droplets generated by coughing, speaking and breathing reinforce the importance of maintaining 2 m social distance to reduce droplet transmission. Conclusions: This review provides a snap-shot of evidence on the transmission of SARS-CoV-2 in indoor environments from the early months of the pandemic. The overall quality of the evidence was low. As the quality and quantity of available evidence grows, it will be possible to reach firmer conclusions on the risk factors for and mechanisms of indoor transmission.


Asunto(s)
Contaminación del Aire Interior/análisis , Transmisión de Enfermedad Infecciosa/estadística & datos numéricos , Ambiente Controlado , Monitoreo del Ambiente/estadística & datos numéricos , Contaminación del Aire Interior/prevención & control , Transmisión de Enfermedad Infecciosa/prevención & control , Microbiología Ambiental , Humanos
3.
J Med Microbiol ; 70(4)2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33909552

RESUMEN

Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively.Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation.Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC.Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples.Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.


Asunto(s)
Amicacina/farmacología , Antibacterianos/farmacología , Fibrosis Quística/complicaciones , Macrólidos/farmacología , Infecciones por Mycobacterium no Tuberculosas/microbiología , Mycobacterium abscessus/efectos de los fármacos , Fibrosis Quística/microbiología , Farmacorresistencia Bacteriana , Microbiología Ambiental , Humanos , Infecciones por Mycobacterium no Tuberculosas/complicaciones , Sistema Respiratorio/microbiología
4.
Int J Mol Sci ; 22(6)2021 Mar 19.
Artículo en Inglés | MEDLINE | ID: mdl-33808768

RESUMEN

The study aimed to prepare sustainable and degradable elastic blends of epoxidized natural rubber (ENR) with poly(lactic acid) (PLA) that were reinforced with flax fiber (FF) and montmorillonite (MMT), simultaneously filling the gap in the literature regarding the PLA-containing polymer blends filled with natural additives. The performed study reveals that FF incorporation into ENR/PLA blend may cause a significant improvement in tensile strength from (10 ± 1) MPa for the reference material to (19 ± 2) MPa for the fibers-filled blend. Additionally, it was found that MMT employment in the role of the filler might contribute to ENR/PLA plasticization and considerably promote the blend elongation up to 600%. This proves the successful creation of the unique and eco-friendly PLA-containing polymer blend exhibiting high elasticity. Moreover, thanks to the performed accelerated thermo-oxidative and ultraviolet (UV) aging, it was established that MMT incorporation may delay the degradation of ENR/PLA blends under the abovementioned conditions. Additionally, mold tests revealed that plant-derived fiber addition might highly enhance the ENR/PLA blend's biodeterioration potential enabling faster and more efficient growth of microorganisms. Therefore, materials presented in this research may become competitive and eco-friendly alternatives to commonly utilized petro-based polymeric products.


Asunto(s)
Productos Biológicos/química , Compuestos Epoxi/química , Poliésteres/química , Goma/química , Biodegradación Ambiental , Celulosa/química , Microbiología Ambiental , Estructura Molecular , Polímeros/química , Resistencia a la Tracción
5.
BMC Bioinformatics ; 22(1): 117, 2021 Mar 10.
Artículo en Inglés | MEDLINE | ID: mdl-33691615

RESUMEN

BACKGROUND: Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. RESULTS: Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. CONCLUSION: AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .


Asunto(s)
Farmacorresistencia Microbiana/genética , Microbiología Ambiental , Genes Bacterianos , Metadatos , Metagenómica , Ecosistema , Internet , Metagenoma , Programas Informáticos
6.
Sci Rep ; 11(1): 5887, 2021 03 15.
Artículo en Inglés | MEDLINE | ID: mdl-33723303

RESUMEN

Based on the current knowledge of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission, wearing a mask has been recommended during the COVID-19 pandemic. Bacterial filtration efficiency (BFE) measurements enable designing and regulating medical masks to prevent bioaerosol dissemination; however, despite the simplicity of these measurements, several scientific questions remain unanswered regarding BFE tests. Here, we investigated (1) the impact of substituting 100-mm Petri dishes with 90-mm disposable Petri dishes, (2) the impact of colony-counting methods on the bioaerosol aerodynamic size, and (3) the impact of colony-counting methods on the total viable particle counts. We demonstrated that disposable 90-mm Petri dishes can be used to replace the 100-mm dishes. We also showed that an automatic high-resolution colony counter can be used to directly count viable particles on collection substrates and to measure the bioaerosol size parameters. Our results enable possible modernization of the outdated testing methods recommended in the US and European standards for BFE measurements. Specifically, use of a modernized colony counter should be clearly regulated and permitted to avoid the counting of positive holes. The median aerodynamic diameter appears to be the most relevant parameter for characterizing bioaerosol size.


Asunto(s)
Bacterias , Filtración/normas , Máscaras/normas , Carga Bacteriana , Microbiología Ambiental , Filtración/métodos , Humanos , Máscaras/microbiología , Tamaño de la Partícula , Porosidad
7.
Methods Mol Biol ; 2278: 61-70, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33649948

RESUMEN

Bifidobacteria are commensal microorganisms able to colonize several ecological niches. Since their discovery, culture-dependent methods combined with the most modern next-generation sequencing techniques have contributed to shed light on the ecological, functional and genomic features of bifidobacteria, purporting them as microorganisms with probiotic traits. Thanks to their acclaimed health-promoting effects, several members of the Bifidobacterium genus have been included in a variety of functional foods and drugs. In this context, the functional relevance of bifidobacteria in the gut explains ongoing efforts to isolate novel and potentially beneficial strains. For this purpose, development of effective and selective isolation protocols in concert with knowledge on the physiological characteristics of bifidobacterial are fundamental requirements for their recovery and discovery from their natural environments, in particular from fecal samples.


Asunto(s)
Bifidobacterium/aislamiento & purificación , Microbiología Ambiental , Heces/microbiología , Animales , Bifidobacterium/crecimiento & desarrollo , Técnicas de Cultivo de Célula/métodos , Medios de Cultivo/química , Microbioma Gastrointestinal , Humanos
8.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33739918

RESUMEN

Introduction. Carbapenem resistance in Acinetobacter baumannii (A. baumannii) is an emerging global threat.Gap statement. The adaptation strategies of A. baumannii for this emergence as a nosocomial pathogen has been less studied.Aim. This prospective study analysed a sustained outbreak of carbapenem resistant Acinetobacter baumannii (CRAB) in the intensive care unit (ICU) with reference to antimicrobial resistance and virulence in the colonizing and pathogenic isolates under carbapenem stress.Results. The CRAB isolates from initial and sustained outbreak were found harbouring multiple carbapenemase genes. These genes included bla OXA-23 ,bla IMP, bla VIM and bla NDM. From NICU environment three phenotypically carbapenem susceptible isolates were found carrying bla OXA-23, bla IMP, bla VIM genes. Prior imipenem therapy was one of the risk factors (P=0.0016). The outbreak was polyclonal. Under imipenem stress, outbreak isolates showed no loss of carbapenemase genes against stress free conditions (23.7±1.33 days). Biofilm formation increased with imipenem concentration, with outbreak isolates producing highest biomass. While the pathogens showed a slow growth rate on imipenem exposure, the colonisers grew rapidly (P <0.0001).Methods. Sustained outbreak of CRAB was identified in the ICU (July 2015 to December 2017). Risk factors for acquisition of CRAB was studied. A. baumannii isolates were also collected from the environments of ICU and neonatal ICU (NICU) and blood cultures of septic neonates. Isolates were characterized based on antimicrobial susceptibility, genetic profile, integrons carriage and clonality. Biofilm formation and growth kinetics were studied under varying carbapenem stress.Conclusion. Intense carbapenem exposure in the ICU facilitates persistence of CRAB by several adaptations causing sustained outbreaks.


Asunto(s)
Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/fisiología , Adaptación Fisiológica , Carbapenémicos/farmacología , Infección Hospitalaria/microbiología , Brotes de Enfermedades , Farmacorresistencia Bacteriana Múltiple/fisiología , Infecciones por Acinetobacter/tratamiento farmacológico , Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/patogenicidad , Adulto , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Biopelículas/efectos de los fármacos , Biopelículas/crecimiento & desarrollo , Carbapenémicos/uso terapéutico , Infección Hospitalaria/tratamiento farmacológico , Infección Hospitalaria/epidemiología , Farmacorresistencia Bacteriana Múltiple/efectos de los fármacos , Farmacorresistencia Bacteriana Múltiple/genética , Microbiología Ambiental , Femenino , Genes Bacterianos , Humanos , Imipenem/farmacología , Imipenem/uso terapéutico , Integrones/genética , Unidades de Cuidados Intensivos , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Estudios Prospectivos , Factores de Riesgo , Virulencia , beta-Lactamasas/genética , beta-Lactamasas/metabolismo
9.
Methods Mol Biol ; 2246: 207-224, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33576991

RESUMEN

Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) is an imaging method used to identify microorganisms in environmental samples based on their phylogeny. CARD-FISH can be combined with nano-scale secondary ion mass spectrometry (nanoSIMS) to directly link the cell identity to their activity, measured as the incorporation of stable isotopes into hybridized cells after stable isotope probing. In environmental microbiology, a combination of these methods has been used to determine the identity and growth of uncultured microorganisms, and to explore the factors controlling their activity. Additionally, FISH-nanoSIMS has been widely used to directly visualize microbial interactions in situ. Here, we describe a step-by-step protocol for a combination of CARD-FISH, laser marking, and nanoSIMS analysis on samples from aquatic environments.


Asunto(s)
Hibridación Fluorescente in Situ/métodos , Espectrometría de Masa de Ion Secundario/métodos , Isótopos de Carbono/metabolismo , Microbiología Ambiental , Marcaje Isotópico/métodos , Microbiota/genética , Microbiota/fisiología , Isótopos de Nitrógeno/metabolismo , Filogenia
10.
Methods Mol Biol ; 2246: 291-299, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33576997

RESUMEN

Fluorescent in situ hybridization (FISH) on environmental samples has become a standard technique to identify and enumerate microbial populations. However, visualization and quantification of cells in environmental samples with complex matrices is often challenging to impossible, and downstream protocols might also require the absence of organic and inorganic particles for analysis. Therefore, quite often microbial cells have to be detached and extracted from the sample matrix prior to use in FISH. Here, details are given for a routine protocol to extract intact microbial cells from environmental samples using density gradient centrifugation. This protocol is suitable and adaptable for a wide range of environmental samples.


Asunto(s)
Hibridación Fluorescente in Situ/métodos , Microbiología Ambiental , Microbiota/genética
11.
Sci Rep ; 11(1): 4699, 2021 02 25.
Artículo en Inglés | MEDLINE | ID: mdl-33633273

RESUMEN

COVID-19 reaffirms the vital role of superspreaders in a pandemic. We propose to broaden the research on superspreaders through integrating human mobility data and geographical factors to identify superspreading environment. Six types of popular public facilities were selected: bars, shopping centres, karaoke/cinemas, mega shopping malls, public libraries, and sports centres. A historical dataset on mobility was used to calculate the generalized activity space and space-time prism of individuals during a pre-pandemic period. Analysis of geographic interconnections of public facilities yielded locations by different classes of potential spatial risk. These risk surfaces were weighed and integrated into a "risk map of superspreading environment" (SE-risk map) at the city level. Overall, the proposed method can estimate empirical hot spots of superspreading environment with statistical accuracy. The SE-risk map of Hong Kong can pre-identify areas that overlap with the actual disease clusters of bar-related transmission. Our study presents first-of-its-kind research that combines data on facility location and human mobility to identify superspreading environment. The resultant SE-risk map steers the investigation away from pure human focus to include geographic environment, thereby enabling more differentiated non-pharmaceutical interventions and exit strategies to target some places more than others when complete city lockdown is not practicable.


Asunto(s)
/transmisión , /epidemiología , Control de Enfermedades Transmisibles , Microbiología Ambiental , Hong Kong/epidemiología , Humanos , Instalaciones Públicas , Restaurantes , Factores de Riesgo , Instalaciones Deportivas y Recreativas
13.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33599604

RESUMEN

Over a decade ago, a multidrug-resistant nosocomial fungus Candida auris emerged worldwide and has since become a significant challenge for clinicians and microbiologists across the globe. A resilient pathogen, C. auris survives harsh disinfectants, desiccation and high-saline environments. It readily colonizes the inanimate environment, susceptible patients and causes invasive infections that exact a high toll. Prone to misidentification by conventional microbiology techniques, C. auris rapidly acquires multiple genetic determinants that confer multidrug resistance. Whole-genome sequencing has identified four distinct clades of C. auris, and possibly a fifth one, in circulation. Even as our understanding of this formidable pathogen grows, the nearly simultaneous emergence of its distinct clades in different parts of the world, followed by their rapid global spread, remains largely unexplained. We contend that certain host-pathogen-environmental factors have been evolving along adverse trajectories for the last few decades, especially in regions where C. auris originally appeared, until these factors possibly reached a tipping point to compel the evolution, emergence and spread of C. auris. Comparative genomics has helped identify several resistance mechanisms in C. auris that are analogous to those seen in other Candida species, but they fail to fully explain how high-level resistance rapidly develops in this yeast. A better understanding of these unresolved aspects is essential not only for the effective management of C. auris patients, hospital outbreaks and its global spread but also for forecasting and tackling novel resistant pathogens that might emerge in the future. In this review, we discuss the emergence, spread and resistance of C. auris, and propose future investigations to tackle this resilient pathogen.


Asunto(s)
Candida/fisiología , Candidiasis/microbiología , Enfermedades Transmisibles Emergentes/microbiología , Farmacorresistencia Fúngica Múltiple , Microbiología Ambiental , Antiinfecciosos/farmacología , Antiinfecciosos/uso terapéutico , Candida/clasificación , Candida/aislamiento & purificación , Candida/patogenicidad , Candidiasis/epidemiología , Candidiasis/transmisión , Enfermedades Transmisibles Emergentes/epidemiología , Enfermedades Transmisibles Emergentes/transmisión , Infección Hospitalaria/epidemiología , Infección Hospitalaria/microbiología , Infección Hospitalaria/transmisión , Salud Global , Humanos , Virulencia
14.
Nat Commun ; 12(1): 1101, 2021 02 17.
Artículo en Inglés | MEDLINE | ID: mdl-33597520

RESUMEN

It is widely hypothesised that primeval life utilised small organic molecules as sources of carbon and energy. However, the presence of such primordial ingredients in early Earth habitats has not yet been demonstrated. Here we report the existence of indigenous organic molecules and gases in primary fluid inclusions in c. 3.5-billion-year-old barites (Dresser Formation, Pilbara Craton, Western Australia). The compounds identified (e.g., H2S, COS, CS2, CH4, acetic acid, organic (poly-)sulfanes, thiols) may have formed important substrates for purported ancestral sulfur and methanogenic metabolisms. They also include stable building blocks of methyl thioacetate (methanethiol, acetic acid) - a putative key agent in primordial energy metabolism and thus the emergence of life. Delivered by hydrothermal fluids, some of these compounds may have fuelled microbial communities associated with the barite deposits. Our findings demonstrate that early Archaean hydrothermal fluids contained essential primordial ingredients that provided fertile substrates for earliest life on our planet.


Asunto(s)
Archaea/química , Sulfuro de Hidrógeno/análisis , Metano/análisis , Compuestos de Sulfhidrilo/análisis , Sulfato de Bario/análisis , Planeta Tierra , Ecosistema , Microbiología Ambiental , Evolución Química , Cromatografía de Gases y Espectrometría de Masas , Geografía , Sedimentos Geológicos/química , Factores de Tiempo , Australia Occidental
15.
J Environ Manage ; 284: 112088, 2021 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-33582482

RESUMEN

The pathogen concentration in human excreta needs to be managed appropriately, but a predictive approach has yet to be implemented due to a lack of kinetics models for pathogen inactivation that are available under varied environmental conditions. Our goals were to develop inactivation kinetics models of microorganisms applicable under varied environmental conditions of excreta matrices and to identify the appropriate indicators that can be monitored during disinfection processes. We conducted a systematic review targeting previous studies that presented time-course decay of a microorganism and environmental conditions of matrices. Defined as a function of measurable factors including treatment time, pH, temperature, ammonia concentration and moisture content, the kinetic model parameters were statistically estimated using hierarchical Bayesian modeling. The inactivation kinetics models were constructed for Escherichia coli, Salmonella, Enterococcus, Ascaris eggs, bacteriophage MS2, enterobacteria phage phiX174 and adenovirus. The inactivation rates of a microorganism were predicted using the established model. Ascaris eggs were identified as the most tolerant microorganisms, followed by bacteriophage MS2 and Enterococcus. Ammonia concentration, temperature and moisture content were the critical factors for the Ascaris inactivation. Our model predictions coincided with the current WHO guidelines. The developed inactivation kinetics models enable us to predict microbial concentration in excreta matrices under varied environmental conditions, which is essential for microbiological risk management in emerging resource recovery practices from human excreta.


Asunto(s)
Microbiología Ambiental , Levivirus , Amoníaco , Teorema de Bayes , Humanos , Temperatura
16.
Yakugaku Zasshi ; 141(1): 135-142, 2021.
Artículo en Japonés | MEDLINE | ID: mdl-33390440

RESUMEN

Environmental microorganisms can cause several infections in humans, especially in compromised hosts. Since there are many compromised hosts in a hospital setting, it is important to control environmental pathogens in such scenarios. To disinfect the environment, photocatalysts that produce reactive oxygen in response to light have attracted attention. In the present study, the effects of a visible-light-driven antimicrobial photocatalyst, silver (I) iodide and benzalkonium complex, on bacteria, viruses, and fungi were evaluated in vitro. In addition, uncoated panels and panels coated with the photocatalyst were set up at 11 points in a university campus for 6 months, and the adherent bacteria and fungi were measured. Bacteria, bacterial spores, viruses, and fungi were completely inactivated within 45 min on the photocatalyst-coated surface exposed to approximately 700-lux fluorescent light. In the university setting, there were fewer viable adherent bacteria and fungi on the coated plates. Our findings indicate that the silver (I) iodide and benzalkonium complex photocatalyst can decrease environmental bacteria in vitro and in actual environmental settings, and thus highlight its potential in controlling and disinfecting environmental pathogens.


Asunto(s)
Compuestos de Benzalconio , Desinfección/métodos , Microbiología Ambiental , Fluorescencia , Control de Infecciones/métodos , Yoduros , Luz , Compuestos de Plata , Bacterias/efectos de los fármacos , Compuestos de Benzalconio/farmacología , Hongos/efectos de los fármacos , Yoduros/farmacología , Especies Reactivas de Oxígeno/farmacología , Compuestos de Plata/farmacología , Inactivación de Virus/efectos de los fármacos
17.
mBio ; 12(1)2021 01 19.
Artículo en Inglés | MEDLINE | ID: mdl-33468686

RESUMEN

Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.


Asunto(s)
/virología , /aislamiento & purificación , Aguas del Alcantarillado/virología , Secuencia de Bases , California/epidemiología , Microbiología Ambiental , Genoma Viral , Genotipo , Humanos , Metagenoma , Metagenómica , Polimorfismo de Nucleótido Simple , ARN Viral/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Transcriptoma
18.
Viruses ; 13(1)2021 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-33430116

RESUMEN

Virus research has advanced significantly since the discovery of the tobacco mosaic virus (TMV), the characterization of its infection mechanisms and the factors that determine their pathogenicity. However, most viral research has focused on pathogenic viruses to humans, animals and plants, which represent only a small fraction in the virosphere. As a result, the role of most viral genes, and the mechanisms of coevolution between mutualistic viruses, their host and their environment, beyond pathogenicity, remain poorly understood. This review focuses on general aspects of viruses that interact with extremophile organisms, characteristics and examples of mechanisms of adaptation. Finally, this review provides an overview on how knowledge of extremophile viruses sheds light on the application of new tools of relevant use in modern molecular biology, discussing their value in a biotechnological context.


Asunto(s)
Biotecnología , Microbiología Ambiental , Extremófilos/virología , Animales , Virus de Archaea/fisiología , Bacterias/virología , Humanos , Nanomedicina
19.
Viruses ; 13(1)2021 Jan 17.
Artículo en Inglés | MEDLINE | ID: mdl-33477302

RESUMEN

The knowledge about circulation of Human Enteroviruses (EVs) obtained through medical diagnosis in Argentina is scarce. Wastewater samples monthly collected in Córdoba, Argentina during 2011-2012, and then in 2017-2018 were retrospectively studied to assess the diversity of EVs in the community. Partial VP1 gene was amplified by PCR from wastewater concentrates, and amplicons were subject of next-generation sequencing and genetic analyses. There were 41 EVs detected, from which ~50% had not been previously reported in Argentina. Most of the characterized EVs (60%) were detected at both sampling periods, with similar values of intratype nucleotide diversity. Exceptions were enterovirus A71, coxsackievirus B4, echovirus 14, and echovirus 30, which diversified in 2017-2018. There was a predominance of types from EV-C in 2017-2018, evidencing a common circulation of these types throughout the year in the community. Interestingly, high genetic similarity was evidenced among environmental strains of echovirus 30 circulating in 2011-2012 and co-temporal isolates obtained from patients suffering aseptic meningitis in different locations of Argentina. This study provides an updated insight about EVs circulating in an important region of South America, and suggests a valuable role of wastewater-based epidemiology in predicting outbreaks before the onset of cases in the community.


Asunto(s)
Infecciones por Enterovirus/epidemiología , Infecciones por Enterovirus/virología , Enterovirus/genética , Microbiología Ambiental , Monitoreo del Ambiente , Variación Genética , Argentina/epidemiología , Biología Computacional/métodos , Enterovirus/clasificación , Enterovirus/aislamiento & purificación , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Filogenia , Vigilancia en Salud Pública , Carga Viral , Aguas Residuales/microbiología , Aguas Residuales/virología
20.
J Environ Radioact ; 227: 106507, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33321301

RESUMEN

Inspired by microbial diagenesis and mounding, microbial mineralization technology has been widely used in the treatment of heavy metal and radionuclide contamination. S. pasteurii can decompose urea as a source of energy to produce CO32- in the microbial mineralization system. Therefore, strontium-contaminated radioactive wastewater can be effectively treated by combining CO32- with surrounding strontium ions (Sr2+) to form strontium carbonate (SrCO3). Herein, we investigated how the concentration of graphene oxide (GO) and mineralization time influence the morphology of SrCO3 and the mineralization efficiency. GO was used as a crystal regulator to solidify the radionuclide strontium in the microbial mineralization system to obtain large-scale rock-like SrCO3 minerals. The results showed that GO can adsorb the surrounding Sr2+ with oxygen-containing functional groups on its surface to form SrCO3 complexes, directly influencing the morphology and consolidation percentage of SrCO3. Considering the leaching behaviour of nuclides, we further studied the stability of consolidated SrCO3 minerals. The results indicated that the presence of GO improved the stability of the mineralized samples obtained in the microbial mineralization system.


Asunto(s)
Biodegradación Ambiental , Grafito , Monitoreo de Radiación , Estroncio/metabolismo , Microbiología Ambiental , Minerales , Estroncio/química
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