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1.
Environ Int ; 138: 105667, 2020 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-32234679

RESUMO

Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health challenge. While traditionally associated with pathogens in clinical environments, it is becoming increasingly clear that non-clinical environments may also be reservoirs of ARGs. The recent improvements in rapid and affordable next generation sequencing technologies along with sophisticated bioinformatics platforms has the potential to revolutionize diagnostic microbiology and microbial surveillance. Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. However, different platforms may significantly vary and therefore, it is crucial to choose the tools that are most suitable for the specific analysis being conducted. This review provides a detailed account of available bioinformatics platforms for identification and characterization of ARGs and associated genetic elements within single bacterial isolates and complex environmental samples. It focuses primarily on currently available ARG databases, employing a comprehensive benchmarking pipeline to identify ARGs in four bacterial genomes (Aeromonas salmonicida, Bacillus cereus, Burkholderia sp. and Escherichia coli) and three shotgun metagenomes (human gut, poultry litter and soil) providing insight into which databases should be used for different analytical scenarios.

2.
PLoS Biol ; 18(4): e3000698, 2020 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-32243442

RESUMO

Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high-impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions-a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.

4.
Water Res ; 164: 114906, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31377529

RESUMO

Reuse of municipal wastewater is a growing global trend, but currently there is lack of consensus regarding the potential dissemination of antibiotic resistance elements by treated wastewater irrigation. We tracked intI1, a proxy for anthropogenic pollution, and an assemblage of antibiotic resistance genes associated with mobile elements and/or wastewater (blaGES, blaOXA2, blaOXA10, blaTEM, blaCTX-M-32 and qnrS) in treated wastewater effluents, effluent stabilization reservoirs, and along irrigation water-soil-crop continua in experimental lysimeters and large-scale commercial fields. While several of the targeted antibiotic resistance genes were profuse in effluents, there was almost no correlation between gene abundance in irrigation water and those detected in soil, and no evidence of systematic gene transfer to irrigated soil or crops. In contrast, soil intI1 abundance correlated strongly to irrigation water levels in lysimeters and sandy field soils, but this was not the case for clay-rich soils or for most of the analyzed crops, suggesting that intI1 may not always be a reliable marker for tracking the impact of treated wastewater irrigation. We hypothesize that "ecological boundaries" expedited by biotic and abiotic factors constrain dissemination of antibiotic resistance elements, and assert that a more holistic perception of these factors is crucial for understanding and managing antibiotic resistance dissemination.


Assuntos
Integrons , Águas Residuárias , Irrigação Agrícola , Resistência Microbiana a Medicamentos , Genes Bacterianos , Solo , Eliminação de Resíduos Líquidos
5.
Water Res ; 162: 320-330, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-31288142

RESUMO

There is increasing public concern regarding the fate of antibiotic resistance genes (ARGs) during wastewater treatment, their persistence during the treatment process and their potential impacts on the receiving water bodies. In this study, we used quantitative PCR (qPCR) to determine the abundance of nine ARGs and a class 1 integron associated integrase gene in 16 wastewater treatment plant (WWTP) effluents from ten different European countries. In order to assess the impact on the receiving water bodies, gene abundances in the latter were also analysed. Six out of the nine ARGs analysed were detected in all effluent and river water samples. Among the quantified genes, intI1 and sul1 were the most abundant. Our results demonstrate that European WWTP contribute to the enrichment of the resistome in the receiving water bodies with the particular impact being dependent on the effluent load and local hydrological conditions. The ARGs concentrations in WWTP effluents were found to be inversely correlated to the number of implemented biological treatment steps, indicating a possible option for WWTP management. Furthermore, this study has identified blaOXA-58 as a possible resistance gene for future studies investigating the impact of WWTPs on their receiving water.


Assuntos
Antibacterianos , Águas Residuárias , Resistência Microbiana a Medicamentos , Europa (Continente) , Genes Bacterianos , Inquéritos e Questionários
6.
Front Microbiol ; 10: 146, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30804916

RESUMO

The ß-lactams are the largest group of clinically applied antibiotics, and resistance to these is primarily associated with ß-lactamases. There is increasing understanding that these enzymes are ubiquitous in natural environments and henceforth, elucidating the global diversity, distribution, and mobility of ß-lactamase-encoding genes is crucial for holistically understanding resistance to these antibiotics. In this study, we screened 232 shotgun metagenomes from ten different environments against a custom-designed ß-lactamase database, and subsequently analyzed ß-lactamase homologs with a suite of bioinformatic platforms including cluster and network analyses. Three interrelated ß-lactamase clusters encompassed all of the human and bovine feces metagenomes, while ß-lactamases from soil, freshwater, glacier, marine, and wastewater grouped within a separate "environmental" cluster that displayed high levels of inter-network connectivity. Interestingly, almost no connectivity occurred between the "feces" and "environmental" clusters. We attributed this in part to the divergence in microbial community composition (dominance of Bacteroidetes and Firmicutes vs. Proteobacteria, respectively). The ß-lactamase diversity in the "environmental" cluster was significantly higher than in human and bovine feces microbiomes. Several class A, B, C, and D ß-lactamase homologs (bla CTX-M, bla KPC, bla GES) were ubiquitous in the "environmental" cluster, whereas bovine and human feces metagenomes were dominated by class A (primarily cfxA) ß-lactamases. Collectively, this study highlights the ubiquitous presence and broad diversity of ß-lactamase gene precursors in non-clinical environments. Furthermore, it suggests that horizontal transfer of ß-lactamases to human-associated bacteria may be more plausible from animals than from terrestrial and aquatic microbes, seemingly due to phylogenetic similarities.

7.
Environ Microbiol ; 21(3): 1068-1085, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30637927

RESUMO

A hallmark of the Gram-positive bacteria, such as the soil-dwelling bacterium Bacillus subtilis, is their cell wall. Here, we report that d-leucine and flavomycin, biofilm inhibitors targeting the cell wall, activate the ß-lactamase PenP. This ß-lactamase contributes to ampicillin resistance in B. subtilis under all conditions tested. In contrast, both Spo0A, a master regulator of nutritional stress, and the general cell wall stress response, differentially contribute to ß-lactam resistance under different conditions. To test whether ß-lactam resistance and ß-lactamase genes are widespread in other Bacilli, we isolated Bacillus species from undisturbed soils, and found that their genomes can encode up to five ß-lactamases with differentiated activity spectra. Surprisingly, the activity of environmental ß-lactamases and PenP, as well as the general stress response, resulted in a similarly reduced lag phase of the culture in the presence of ß-lactam antibiotics, with little or no impact on the logarithmic growth rate. The length of the lag phase may determine the outcome of the competition between ß-lactams and ß-lactamases producers. Overall, our work suggests that antibiotic resistance genes in B. subtilis and related species are ancient and widespread, and could be selected by interspecies competition in undisturbed soils.

8.
Front Microbiol ; 9: 1176, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29937755

RESUMO

Plasmids harboring qnr genes confer resistance to low fluoroquinolone concentrations. These genes are of significant clinical, evolutionary and environmental importance, since they are widely distributed in a diverse array of natural and clinical environments. We previously extracted and sequenced a large (∼185 Kbp) qnrB-harboring plasmid, and several small (∼8 Kbp) qnrS-harboring plasmids, from Klebsiella pneumoniae isolates from municipal wastewater biosolids, and hypothesized that these plasmids provide host bacteria a selective advantage in wastewater treatment plants (WWTPs) that often contain residual concentrations of fluoroquinolones. The objectives of this study were therefore to determine the effect of residual fluoroquinolone concentrations on the growth kinetics of qnr plasmid-harboring bacteria; and on the copy number of qnr plasmids and expression of qnr genes. Electrotransformants harboring either one of the two types of plasmids could grow at ciprofloxacin concentrations exceeding 0.5 µg ml-1, but growth was significantly decreased at concentrations higher than 0.1 µg ml-1. In contrast, plasmid-free strains failed to grow even at 0.05 µg ml-1. No differences were observed in plasmid copy number under the tested ciprofloxacin concentrations, but qnr expression increased incrementally from 0 to 0.4 µg ml-1, suggesting that the transcription of this gene is regulated by antibiotic concentration. This study reveals that wastewater-derived qnr plasmids confer a selective advantage in the presence of residual fluoroquinolone concentrations and provides a mechanistic explanation for this phenomenon.

9.
New Phytol ; 219(1): 363-377, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29417582

RESUMO

Biochar can enhance plant growth and reduce diseases, but frequently the optimal doses for these two benefits do not coincide. An approach is needed that will extend the range of biochar doses resulting in a concurrence of maximum benefits for both plant productivity and disease suppression. A biochar-amended growth medium was pre-conditioned by pre-planting fertigation in order to enhance the indigenous microbial community structure and activity. Cucumber plant performance and resistance against damping-off caused by Pythium aphanidermatum were monitored. Soil microbial activity, as well as bacterial and fungal community structure, were assessed by high-throughput 16S rRNA and ITS1 gene amplicon sequencing. Pre-conditioning enhanced the efficacy of biochar for improving plant performance and suppressing soilborne disease through enriching the medium in beneficial soil microorganisms, increasing microbial and fungal diversity and activity, and eliminating biochar phytotoxic compounds. The pre-conditioning process brought dose-response curves for both growth and disease resistance into sync, resulting in maximum benefits for both. These findings suggest that pre-conditioning should be incorporated as an important stage during biochar application in soil and soilless media.


Assuntos
Carvão Vegetal/farmacologia , Cucumis sativus/microbiologia , Doenças das Plantas/prevenção & controle , Pythium/patogenicidade , Microbiologia do Solo , Bactérias/genética , Cucumis sativus/crescimento & desenvolvimento , Micobioma/genética , Doenças das Plantas/microbiologia , RNA Ribossômico 16S/genética
10.
Water Res ; 123: 448-467, 2017 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-28689129

RESUMO

The use of reclaimed wastewater (RWW) for the irrigation of crops may result in the continuous exposure of the agricultural environment to antibiotics, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). In recent years, certain evidence indicate that antibiotics and resistance genes may become disseminated in agricultural soils as a result of the amendment with manure and biosolids and irrigation with RWW. Antibiotic residues and other contaminants may undergo sorption/desorption and transformation processes (both biotic and abiotic), and have the potential to affect the soil microbiota. Antibiotics found in the soil pore water (bioavailable fraction) as a result of RWW irrigation may be taken up by crop plants, bioaccumulate within plant tissues and subsequently enter the food webs; potentially resulting in detrimental public health implications. It can be also hypothesized that ARGs can spread among soil and plant-associated bacteria, a fact that may have serious human health implications. The majority of studies dealing with these environmental and social challenges related with the use of RWW for irrigation were conducted under laboratory or using, somehow, controlled conditions. This critical review discusses the state of the art on the fate of antibiotics, ARB and ARGs in agricultural environment where RWW is applied for irrigation. The implications associated with the uptake of antibiotics by plants (uptake mechanisms) and the potential risks to public health are highlighted. Additionally, knowledge gaps as well as challenges and opportunities are addressed, with the aim of boosting future research towards an enhanced understanding of the fate and implications of these contaminants of emerging concern in the agricultural environment. These are key issues in a world where the increasing water scarcity and the continuous appeal of circular economy demand answers for a long-term safe use of RWW for irrigation.


Assuntos
Irrigação Agrícola , Antibacterianos , Águas Residuárias , Bactérias , Humanos , Reciclagem , Eliminação de Resíduos Líquidos
11.
Environ Sci Technol ; 51(12): 6709-6718, 2017 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-28422476

RESUMO

Microorganisms carried by dust storms are transported through the atmosphere and may affect human health and the functionality of microbial communities in various environments. Characterizing the dust-borne microbiome in dust storms of different origins or that followed different trajectories provides valuable data to improve our understanding of global health and environmental impacts. We present a comparative study on the diversity of dust-borne bacterial communities in dust storms from three distinct origins (North Africa, Syria and Saudi Arabia) and compare them with local bacterial communities sampled on clear days, all collected at a single location: Rehovot, Israel. Storms from different dust origins exhibited distinct bacterial communities, with signature bacterial taxa. Dust storms were characterized by a lower abundance of selected antibiotic resistance genes (ARGs) compared with ambient dust, asserting that the origin of these genes is local and possibly anthropogenic. With the progression of the storm, the storm-borne bacterial community showed increasing resemblance to ambient dust, suggesting mixing with local dust. These results show, for the first time, that dust storms from different sources display distinct bacterial communities, suggesting possible diverse effects on the environment and public health.


Assuntos
Poeira , Microbiota , África do Norte , Saúde Ambiental , Humanos , Israel , Arábia Saudita
12.
Essays Biochem ; 61(1): 11-21, 2017 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-28258226

RESUMO

Antibiotics are considered to be one of the major medical breakthroughs in history. Nonetheless, over the past four decades, antibiotic resistance has reached alarming levels worldwide and this trend is expected to continue to increase, leading some experts to forecast the coming of a 'post-antibiotic' era. Although antibiotic resistance in pathogens is traditionally linked to clinical environments, there is a rising concern that the global propagation of antibiotic resistance is also associated with environmental reservoirs that are linked to anthropogenic activities such as animal husbandry, agronomic practices and wastewater treatment. It is hypothesized that the emergence and dissemination of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) within and between environmental microbial communities can ultimately contribute to the acquisition of antibiotic resistance in human pathogens. Nonetheless, the scope of this phenomenon is not clear due to the complexity of microbial communities in the environment and methodological constraints that limit comprehensive in situ evaluation of microbial genomes. This review summarizes the current state of knowledge regarding antibiotic resistance in non-clinical environments, specifically focusing on the dissemination of antibiotic resistance across ecological boundaries and the contribution of this phenomenon to global antibiotic resistance.


Assuntos
Resistência Microbiana a Medicamentos , Ecossistema , Atividades Humanas , Animais , Resistência Microbiana a Medicamentos/genética , Genes Bacterianos , Humanos , Modelos Biológicos , Medição de Risco
13.
Sci Rep ; 7: 44382, 2017 03 13.
Artigo em Inglês | MEDLINE | ID: mdl-28287177

RESUMO

Biochar, in addition to sequestering carbon, ameliorating soil, and improving plant performance, can impact foliar and soilborne plant diseases. Nevertheless, the mechanisms associated with suppression of soilborne diseases and improved plant performances are not well understood. This study is designed to establish the relationships between biochar-induced changes in rhizosphere microbial community structure, taxonomic and functional diversity, and activity with soilborne disease suppression and enhanced plant performance in a comprehensive fashion. Biochar suppressed Fusarium crown and root-rot of tomato and simultaneously improved tomato plant growth and physiological parameters. Furthermore, biochar reduced Fusarium root colonization and survival in soil, and increased the culturable counts of several biocontrol and plant growth promoting microorganisms. Illumina sequencing analyses of 16S rRNA gene revealed substantial differences in rhizosphere bacterial taxonomical composition between biochar-amended and non-amended treatments. Moreover, biochar amendment caused a significant increase in microbial taxonomic and functional diversity, microbial activities and an overall shift in carbon-source utilization. High microbial taxonomic and functional diversity and activity in the rhizosphere has been previously associated with suppression of diseases caused by soilborne pathogens and with plant growth promotion, and may collectively explain the significant reduction of disease and improvement in plant performance observed in the presence of biochar.


Assuntos
Carvão Vegetal/farmacologia , Fertilizantes , Fusarium/efeitos dos fármacos , Lycopersicon esculentum/efeitos dos fármacos , Consórcios Microbianos/efeitos dos fármacos , Bactérias/classificação , Bactérias/efeitos dos fármacos , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Fungos/classificação , Fungos/efeitos dos fármacos , Fungos/genética , Fungos/crescimento & desenvolvimento , Fusarium/crescimento & desenvolvimento , Fusarium/patogenicidade , Sequenciamento de Nucleotídeos em Larga Escala , Lycopersicon esculentum/crescimento & desenvolvimento , Lycopersicon esculentum/microbiologia , Consórcios Microbianos/genética , Doenças das Plantas/prevenção & controle , RNA Ribossômico 16S/genética , Rizosfera , Solo/química , Microbiologia do Solo
14.
New Phytol ; 213(3): 1393-1404, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-27780299

RESUMO

The 'biochar effect' depicts a phenomenon in which biochar soil amendment enhances plant performance by promoting growth and suppressing disease. Although this phenomenon has been observed in numerous studies, the mode of action that explains it is currently unknown. In order to elucidate mechanisms responsible for the 'biochar effect', we comprehensively monitored tomato plant development and resistance to the foliar fungal pathogen Botrytis cinerea, in biochar-amended and nonamended soils using native biochar and washed biochar, striped of labile chemical constituents. We concomitantly assessed bacterial community succession in the rhizosphere by high-throughput 16S rRNA gene amplicon sequencing and carbon-source utilization profiling. Biochar had little impact on plant physiological parameters. However, both native and washed biochar treatments were characterized by higher rhizosphere bacterial diversity and enhanced carbohydrate and phenolic compound utilization rates coupled to stimulation of bacteria known to degrade phenolic compounds. This study indicates that the 'biochar effect' is at least partially dictated by increased diversity and changes in metabolic potential in the rhizosphere microbiome, which is primarily triggered by the recalcitrant carbon backbone of the biochar and tightly bound compounds. It corresponds to the growing consensus that soil amendments which enhance microbial diversity have important benefits to ecosystem functioning.


Assuntos
Biodiversidade , Botrytis/fisiologia , Carvão Vegetal/farmacologia , Lycopersicon esculentum/microbiologia , Desenvolvimento Vegetal/efeitos dos fármacos , Rizosfera , Botrytis/efeitos dos fármacos , Carbono/farmacologia , Suscetibilidade a Doenças , Lycopersicon esculentum/crescimento & desenvolvimento , Doenças das Plantas/microbiologia , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/microbiologia , Solo/química , Fatores de Tempo
15.
Front Microbiol ; 7: 1875, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27965628

RESUMO

The genus Aeromonas is ubiquitous in aquatic environments encompassing a broad range of fish and human pathogens. Aeromonas strains are known for their enhanced capacity to acquire and exchange antibiotic resistance genes and therefore, are frequently targeted as indicator bacteria for monitoring antimicrobial resistance in aquatic environments. This study evaluated temporal trends in Aeromonas diversity and antibiotic resistance in two adjacent semi-intensive aquaculture facilities to ascertain the effects of antibiotic treatment on antimicrobial resistance. In the first facility, sulfadiazine-trimethoprim was added prophylactically to fingerling stocks and water column-associated Aeromonas were monitored periodically over an 11-month fish fattening cycle to assess temporal dynamics in taxonomy and antibiotic resistance. In the second facility, Aeromonas were isolated from fish skin ulcers sampled over a 3-year period and from pond water samples to assess associations between pathogenic strains to those in the water column. A total of 1200 Aeromonas isolates were initially screened for sulfadiazine resistance and further screened against five additional antimicrobials. In both facilities, strong correlations were observed between sulfadiazine resistance and trimethoprim and tetracycline resistances, whereas correlations between sulfadiazine resistance and ceftriaxone, gentamicin, and chloramphenicol resistances were low. Multidrug resistant strains as well as sul1, tetA, and intI1 gene-harboring strains were significantly higher in profiles sampled during the fish cycle than those isolated prior to stocking and these genes were extremely abundant in the pathogenic strains. Five phylogenetically distinct Aeromonas clusters were identified using partial rpoD gene sequence analysis. Interestingly, prior to fingerling stocking the diversity of water column strains was high, and representatives from all five clusters were identified, including an A. salmonicida cluster that harbored all characterized fish skin ulcer samples. Subsequent to stocking, diversity was much lower and most water column isolates in both facilities segregated into an A. veronii-associated cluster. This study demonstrated a strong correlation between aquaculture, Aeromonas diversity and antibiotic resistance. It provides strong evidence for linkage between prophylactic and systemic use of antibiotics in aquaculture and the propagation of antibiotic resistance.

16.
Environ Sci Technol ; 50(21): 11825-11836, 2016 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-27689892

RESUMO

Integrons are extensively targeted as a proxy for anthropogenic impact in the environment. We developed a novel high-throughput amplicon sequencing pipeline that enables characterization of thousands of integron gene cassette-associated reads, and applied it to acquire a comprehensive overview of gene cassette composition in effluents from wastewater treatment facilities across Europe. Between 38 100 and 172 995 reads per-sample were generated and functionally characterized by screening against nr, SEED, ARDB and ß-lactamase databases. Over 75% of the reads were characterized as hypothetical, but thousands were associated with toxin-antitoxin systems, DNA repair, cell membrane function, detoxification and aminoglycoside and ß-lactam resistance. Among the reads characterized as ß-lactamases, the carbapenemase blaOXA was dominant in most of the effluents, except for Cyprus and Israel where blaGES was also abundant. Quantitative PCR assessment of blaOXA and blaGES genes in the European effluents revealed similar trends to those displayed in the integron amplicon sequencing pipeline described above, corroborating the robustness of this method and suggesting that these integron-associated genes may be excellent targets for source tracking of effluents in downstream environments. Further application of the above analyses revealed several order-of-magnitude reductions in effluent-associated ß-lactamase genes in effluent-saturated soils, suggesting marginal persistence in the soil microbiome.


Assuntos
Integrons/genética , Águas Residuárias , Antibacterianos/farmacologia , Testes de Sensibilidade Microbiana , Dados de Sequência Molecular , Análise de Sequência de DNA , Resistência beta-Lactâmica/genética , beta-Lactamases/metabolismo
17.
J Glob Antimicrob Resist ; 6: 128-135, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27530855

RESUMO

The aim of this study was to determine the phylogenetic diversity of ceftriaxone resistance and the presence of known extended-spectrum ß-lactamase (ESBL) genes in culturable soil resistomes. Libraries of soil bacterial isolates resistant to ceftriaxone were established from six physicochemically diverse soils collected in Hawaii (USA) and Israel. The phylogenetic affiliation, ceftriaxone and multidrug resistance levels, and presence of known ESBL genes of the isolates were determined. The soil bacterial isolates were phylogenetically grouped with the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. Ceftriaxone minimum inhibitory concentrations (MICs) largely followed the phylogeny structure and higher levels of ceftriaxone resistance corresponded to higher multidrug resistance. Three distinct blaTEM variants were detected in soil bacterial isolates belonging to nine different genera. In conclusion, the culturable soil resistomes for ceftriaxone exhibited high phylogenetic diversity and multidrug resistance. blaTEM was the only known ESBL detected in the soil resistomes, and its distribution in different phylogenetic groups suggests its ubiquitous presence and/or possible horizontal gene transfer within the soil microbiomes.


Assuntos
Bactérias/classificação , Ceftriaxona , Farmacorresistência Bacteriana , Microbiologia do Solo , beta-Lactamases/genética , Hawaii , Israel , Filogenia , Solo
18.
J Environ Qual ; 45(2): 377-93, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27065385

RESUMO

The presence of antibiotic drug residues, antibiotic resistant bacteria, and antibiotic resistance genes in agroecosystems has become a significant area of research in recent years and is a growing public health concern. While antibiotics are used in both human medicine and agricultural practices, the majority of their use occurs in animal production where historically they have been used for growth promotion, in addition to the prevention and treatment of disease. The widespread use of antibiotics and the application of animal wastes to agricultural lands play major roles in the introduction of antibiotic-related contamination into the environment. Overt toxicity in organisms directly exposed to antibiotics in agroecosystems is typically not a major concern because environmental concentrations are generally lower than therapeutic doses. However, the impacts of introducing antibiotic contaminants into the environment are unknown, and concerns have been raised about the health of humans, animals, and ecosystems. Despite increased research focused on the occurrence and fate of antibiotics and antibiotic resistance over the past decade, standard methods and practices for analyzing environmental samples are limited and future research needs are becoming evident. To highlight and address these issues in detail, this special collection of papers was developed with a framework of five core review papers that address the (i) overall state of science of antibiotics and antibiotic resistance in agroecosystems using a causal model, (ii) chemical analysis of antibiotics found in the environment, (iii) need for background and baseline data for studies of antibiotic resistance in agroecosystems with a decision-making tool to assist in designing research studies, as well as (iv) culture- and (v) molecular-based methods for analyzing antibiotic resistance in the environment. With a focus on the core review papers, this introduction summarizes the current state of science for analyzing antibiotics and antibiotic resistance in agroecosystems, discusses current knowledge gaps, and develops future research priorities. This introduction also contains a glossary of terms used in the core reivew papers of this special section. The purpose of the glossary is to provide a common terminology that clearly characterizes the concepts shared throughout the narratives of each review paper.


Assuntos
Agricultura , Antibacterianos , Animais , Bactérias , Ecossistema , Humanos
19.
J Environ Qual ; 45(2): 432-40, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27065389

RESUMO

Various culture-based methodologies are used in assessment of antibiotic resistance in samples collected in agroecosystems. Culture-based methods commonly involve isolating target bacteria on general or selective media and assessing growth in response to specific concentrations of antibiotics. The advantages of culture-based methods are multifold. In particular, isolation of bacteria is key to understanding phenotypic characteristics of isolates and their resistance patterns, and most national and international antibiotic resistance monitoring projects are isolate based. This review covers current knowledge of bacterial groups and antibiotics commonly targeted in resistance studies using bacterial culture and discusses the range in methods used, data interpretation, and factors supporting and confounding the use of culture-based methods in assessment of antibiotic resistance. Gaps in knowledge related to study design and resistance databases are discussed. Finally, a case is made for the integration of culture-based and molecular methods to better inform our understanding of antibiotic resistance in agroecosystems.


Assuntos
Agricultura , Antibacterianos/farmacologia , Resistência Microbiana a Medicamentos , Ecossistema , Bactérias , Testes de Sensibilidade Microbiana
20.
Environ Sci Technol ; 50(8): 4194-202, 2016 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-27001166

RESUMO

We evaluated the impact of Saharan dust storms on the local airborne microbiome in a city in the Eastern Mediterranean area. Samples of particles with diameter less than 10 µm were collected during two spring seasons on both dusty and nondusty days. DNA was extracted, and partial 16S rRNA gene amplicons were sequenced using the Illumina platform. Bioinformatic analysis showed the effect of dust events on the diversity of the atmospheric microbiome. The relative abundance of desert soil-associated bacteria increased during dust events, while the relative abundance of anthropogenic-influenced taxa decreased. Quantitative polymerase chain reaction measurements of selected clinically significant antibiotic resistance genes (ARGs) showed that their relative abundance decreased during dust events. The ARG profiles on dust-free days were similar to those in aerosol collected in a poultry house, suggesting a strong agricultural influence on the local ambient profiles. We conclude that dust storms enrich the ambient airborne microbiome with new soil-derived bacteria that disappear as the dust settles, suggesting that the bacteria are transported attached to the dust particles. Dust storms do not seem to be an important vector for transport of probed ARGs.


Assuntos
Microbiologia do Ar , Poeira , Microbiota , Aerossóis/análise , África do Norte , Ar/análise , Bactérias/genética , Biodiversidade , Cidades , Farmacorresistência Bacteriana/genética , Poeira/análise , Monitoramento Ambiental , Israel , Região do Mediterrâneo , Microbiota/genética , RNA Ribossômico 16S , Estações do Ano , Microbiologia do Solo
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