Antibiotic Resistance in Marine Microbial Communities Proximal to a Florida Sewage Outfall System.
Ontology highlight
ABSTRACT:
SUBMITTER: Griffin DW
PROVIDER: S-EPMC7148511 | biostudies-literature | 2020 Mar
REPOSITORIES: biostudies-literature
Publications
Antibiotic Resistance in Marine Microbial Communities Proximal to a Florida Sewage Outfall System.
Griffin Dale W DW Banks Kenneth K Gregg Kurtis K Shedler Sarah S Walker Brian K BK
Antibiotics (Basel, Switzerland) 20200311 3
Water samples were collected at several wastewater treatment plants in southeast Florida, and water and sediment samples were collected along and around one outfall pipe, as well as along several transects extending both north and south of the respective outfall outlet. Two sets of samples were collected to address potential seasonal differences, including 38 in the wet season (June 2018) and 42 in the dry season (March 2019). Samples were screened for the presence/absence of 15 select antibioti ...[more]
Similar Datasets
Project description:Antibiotic resistance poses a serious threat to global public health, and antibiotic resistance determinants can enter natural aquatic systems through discharge of wastewater effluents. Hospital wastewater in particular is expected to contain high abundances of antibiotic resistance genes (ARGs) compared to municipal wastewater because it contains human enteric bacteria that may include antibiotic-resistant organisms originating from hospital patients, and can also have high concentrations of antibiotics and antimicrobials relative to municipal wastewater. Viruses also play an important role in wastewater treatment systems since they can influence the bacterial community composition through killing bacteria, facilitating transduction of genetic material between organisms, and modifying the chromosomal content of bacteria as prophages. However, little is known about the fate and connections between ARGs, viruses, and their associated bacteria in hospital wastewater systems. To address this knowledge gap, we characterized the composition and persistence of ARGs, dsDNA viruses, and bacteria from influent to effluent in a pilot-scale hospital wastewater treatment system in Israel using shotgun metagenomics. Results showed that ARGs, including genes conferring resistance to antibiotics of high clinical relevance, were detected in all sampling locations throughout the pilot-scale system, with only 16% overall depletion of ARGs per genome equivalent between influent and effluent. The most common classes of ARGs detected throughout the system conferred resistance to aminoglycoside, cephalosporin, macrolide, penam, and tetracycline antibiotics. A greater proportion of total ARGs were associated with plasmid-associated genes in effluent compared to in influent. No strong associations between viral sequences and ARGs were identified in viral metagenomes from the system, suggesting that phage may not be a significant vector for ARG transfer in this system. The majority of viruses in the pilot-scale system belonged to the families Myoviridae, Podoviridae, and Siphoviridae. Gammaproteobacteria was the dominant class of bacteria harboring ARGs and the most common putative viral host in all samples, followed by Bacilli and Betaproteobacteria. In the total bacterial community, the dominant class was Betaproteobacteria for each sample. Overall, we found that a variety of different types of ARGs and viruses were persistent throughout this hospital wastewater treatment system, which can be released to the environment through effluent discharge.
| S-EPMC7042388 | biostudies-literature
Project description:The structure and composition of bacterial communities can compromise antibiotic efficacy. For example, the secretion of β-lactamase by individual bacteria provides passive resistance for all residents within a polymicrobial environment. Here, we uncover that collective resistance can also develop via intracellular antibiotic deactivation. Real-time luminescence measurements and single-cell analysis demonstrate that the opportunistic human pathogen Streptococcus pneumoniae grows in medium supplemented with chloramphenicol (Cm) when resistant bacteria expressing Cm acetyltransferase (CAT) are present. We show that CAT processes Cm intracellularly but not extracellularly. In a mouse pneumonia model, more susceptible pneumococci survive Cm treatment when coinfected with a CAT-expressing strain. Mathematical modeling predicts that stable coexistence is only possible when antibiotic resistance comes at a fitness cost. Strikingly, CAT-expressing pneumococci in mouse lungs were outcompeted by susceptible cells even during Cm treatment. Our results highlight the importance of the microbial context during infectious disease as a potential complicating factor to antibiotic therapy.
| S-EPMC5189934 | biostudies-literature
Project description:The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.
| S-EPMC6977718 | biostudies-literature
Project description:High-throughput sequencing data of soil microbial communities in non-irrigated and irrigated soils with raw sewage in African cities are presented in this report. These data were collected to study the potential of wastewater use in urban agriculture to disseminate bacterial resistance in soil. Soil samples were collected in three cities in two African countries. Each city had two sectors (irrigated and non-irrigated). After collection, biomass samples were purified, DNA from soil was extracted, quantified and sequenced using multiplex Illumina high-throughput sequencing. The sequence count of the six metagenome datasets ranges from 3,258,523,350 bp to 4,120,454,250 bp; the mean sequence length post quality control average was 149 ± 3 bp. The mechanisms of resistance encoded by the identified antibiotic resistance genes (ARGs) in the metagenomic data were dominated by antibiotic inactivation enzymes (64.7% and 71.9%), followed by antibiotic target replacement (14.7% and 12.5%), antibiotic target protection (11.8% and 9.4%) and efflux pumps (6.3% and 8.8%) in bacterial DNA isolated from irrigated and non-irrigated fields, respectively. The datasets will be useful for the scientific community working in the area of bacterial resistance dissemination from the environment. They can be used for further understanding of bacterial drug-resistance gene prevalence and acquisition in wastewater irrigated soils. The data reported herein was used for the article, titled "Raw wastewater irrigation for urban agriculture in three African cities increases the abundance of transferable antibiotic resistance genes in soil, including those encoding Extended spectrum β-lactamase (ESBLs)" Bougnom et al. (2020) [1].
| S-EPMC6831714 | biostudies-literature
Project description:Recent research has demonstrated that selection for antibiotic resistance occurs at very low antibiotic concentrations in single-species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show that the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low subinhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a 2-order-magnitude concentration range. This is likely to be due to cross protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses of sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment for blaCTX-M genes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far-reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.IMPORTANCE Antibiotic resistance is one of the greatest global issues facing society. Still, comparatively little is known about selection for resistance at very low antibiotic concentrations. We show that the strength of selection for clinically important resistance genes within a complex bacterial community can remain constant across a large antibiotic concentration range (wide selective space). Therefore, largely understudied ecological compartments could be just as important as clinical environments for selection of antibiotic resistance.
| S-EPMC6058293 | biostudies-literature
Project description:Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to thirteen of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual ORF, and distributed along each ~40-160kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having ≤~75% genomic identity. In addition, the array correctly identified target cells added to a background of environmental DNA, with a limit of detection of ~0.1% of the community, corresponding to ~10^3 cells/ml in these samples. Signal correlated to cell concentration with an R2 of 1.0 across six orders of magnitude. In addition the array could track a related strain (at 86% genomic identity to that targeted) with a linearity of R2=0.9999 and a limit of detection of ~1% of the community. Closely related genotypes were distinguishable by differing hybridization patterns across each probe set. This array’s multiple-probe, “genome-proxy” approach and consequent ability to track both target genotypes and their close relatives is important for the array’s environmental application given the recent discoveries of considerable intra-population diversity within marine microbial communities. Keywords: target addition experiment, proof-of-concept for GPL6012
2007-10-31 | GSE9384 | GEO
Project description:Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a âgenome proxyâ microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to thirteen of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual ORF, and distributed along each ~40-160kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having â¤~75% genomic identity. In addition, the array correctly identified target cells added to a background of environmental DNA, with a limit of detection of ~0.1% of the community, corresponding to ~10^3 cells/ml in these samples. Signal correlated to cell concentration with an R2 of 1.0 across six orders of magnitude. In addition the array could track a related strain (at 86% genomic identity to that targeted) with a linearity of R2=0.9999 and a limit of detection of ~1% of the community. Closely related genotypes were distinguishable by differing hybridization patterns across each probe set. This arrayâs multiple-probe, âgenome-proxyâ approach and consequent ability to track both target genotypes and their close relatives is important for the arrayâs environmental application given the recent discoveries of considerable intra-population diversity within marine microbial communities. Keywords: target addition experiment, proof-of-concept for GPL6012 ***Overall Array design*** The prototype microarray targeted thirteen BAC or fosmid genome fragments (20-160kb) from both bacteria and archaea, recovered from a variety of marine habitats, as well as the cyanobacterium Prochlorococcus MED4. These clones were originally sequenced because of the presence of taxonomic marker or specific functional genes. This array consisted of sets of 70-bp oligonucleotides targeting each genome or genome fragment (Fig. 1), dispersed along the target sequences with no more than one probe per gene, and excluding rRNA genes as targets. The probes were selected solely based on theoretical thermodynamic properties and GC content (~40%); that is, probe selection did not focus on specific genes or regions, but simply produced the âoptimalâ probes for each genome proxy based on the probesâ predicted hybridization properties. rRNA genes were excluded, because this probe design approach, which avoids sequence alignments and considerations of RNA secondary structure, would be unlikely to result in useful rRNA probes. Furthermore, rRNA probes of traditional design could not be included on the array because their appropriate hybridization conditions would be very different from those of this arrayâs probes. ***Microarray probe design*** Microarray 70-mer probes were designed using the program ArrayOligoSelector (Zhu et al., 2003) with the following settings: target %GC = 40%, 1 probe/gene, with the ORFs for each genome fragment as both the input and the database file. The output candidate 70mers were then sorted based on their %GC and those closest to 40% were chosen. In the case of more than the target number of probes having 40%GC, the subset with the lowest free energy of hybridization were selected as probes. Generally, 20 probes were selected per organism. Prochlorococcus MED4 was represented by 60 probes total, 20 each for three different 80kb âgenome-proxyâ regions: 0-80kb, 1.29-1.37Mbp, and 1.58 to 1.66Mbp. Using the same method, a set (n=20) of positive control probes were designed to the genome of the halophillic archaeon Halobacterium salinarum NRC-1. Negative control probes (n=28) were designed to a set of 49 random 1000-base sequences (Stothard, 2000). ***Microarray construction and hybridization*** Oligonucleotides were synthesized (Illumina, San Diego, California), suspended in 3XSSC to a concentration of 40pmol/μl, and spotted on homemade poly-L-lysine-coated glass slides using a QArray 2 microarraying robot (Genetix, Hampshire, England). Six replicates of each probe were spotted. ***Microarray data analysis*** Hybridized arrays were scanned using an Axon Instruments 4000B scanner (Foster City, CA) and the data was normalized and filtered using perl scripts written for the purpose, by the following steps. (1) Signal intensities for each spot were calculated by subtracting the local background (mean F532 â median B532, as calculated by GenePix Pro 5.1 software, Axon Instruments). (2) The median value across replicates was calculated for each probe. (3) For each probe set, the number of probes greater than twice the mean negative control signal was calculated, before further processing. (4) Filter I: Arrays with less than half their positive control probes exceeding twice the mean negative control signal were considered poor quality, low dynamic range, arrays and were excluded from further analysis. (5) Each probe signal was corrected for non-specific binding by subtracting the mean negative control spot signal. (6) The data was then normalized for array-to-array variations in brightness by dividing each probe signal by the mean positive control signal. This positive control signal was the mean signal across the Halobacterium salinarum probes in each hybridization, with identical amounts of H. salinarum DNA having been added to each reaction prior to amplification and labeling. (7) Filter II: In order for a genotype to be considered âpresentâ, at least 45% of its probes had to exceed twice the mean negative control signal. (8) Finally, each genotype signal was calculated as either the MEAN or TUKEY BIWEIGHT across its probe set. ***Experimental Design*** The array was hybridized to laboratory mixtures of cloned environmental genomic DNA targeted by the array, in varying ratios. The use of multiple probes to target many genes from each organism helped to normalize probe-to-probe heterogeneity, by averaging across all probes in a set (as described below). The evenness of probe response across each genotypeâs set was also used to evaluate the relatedness of hybridizing DNA. To more precisely define the arrayâs phylogenetic range and specificity, it was tested against DNA from Prochlorococcus MED4 and related strains, spanning the known range of Prochlorococcus phylogenetic diversity. To test the effects of hybridization stringency on the specificity and signal of the MED4 probes, Prochlorococcus strains were hybridized at a range of conditions. To test whether the specificity results for Prochlorococcus were comparable for other targeted clades, two genome fragments recovered from closely related phylotypes within the SAR86 clade of the gamma-proteobacteria were represented on the array, and were tested for specificity. To understand the equivalence of probe sets targeting different regions of the same organismâs genome, we targeted three 80kb âgenome proxyâ regions of the Prochlorococcus MED4 genome. One of the regions fell in a genomic âislandâ where inter-strain variability is concentrated (âISL5â in Coleman et al., 2006). To test the array in a complex environmental context, we collected coastal seawater (lacking detectable Prochlorococcus cells by flow cytometry) and added Prochlorococcus cells from strains MED4, MIT9515, MIT9312 and MIT9313 over a range of concentrations from ~101 â 106 cells/ml (Fig. 3). The seawater was then filtered and the DNA extracted, amplified, labeled, and hybridized to the array.
2010-05-25 | E-GEOD-9384 | biostudies-arrayexpress
Project description:The Johor Strait separates the island of Singapore from Peninsular Malaysia. A 1-kilometer causeway built in the early 1920s in the middle of the strait effectively blocks water flowing to/from either side, resulting in low water turnover rates and build-up of nutrients in the inner Strait. We have previously shown that short-term rather than seasonal environmental changes influence microbial community composition in the Johor Strait. Here, we present a temporally-intensive study that uncovers the factors keeping the microbial populations in check. We sampled the surface water at four sites in the inner Eastern Johor Strait every other day for two months, while measuring various water quality parameters, and analysed 16S amplicon sequences and flow-cytometric counts. We discovered that microbial community succession revolves around a common stable state resulting from frequent pulse disturbances. Among these, sporadic riverine freshwater input and regular tidal currents influence bottom-up controls including the availability of the limiting nutrient nitrogen and its biological release in readily available forms. From the top-down, marine viruses and predatory bacteria limit the proliferation of microbes in the water. Harmful algal blooms, which have been observed historically in these waters, may occur only when there are simultaneous gaps in the top-down and bottom-up controls. This study gains insight into complex interactions between multiple factors contributing to a low-resistance but high-resilience microbial community and speculate about rare events that could lead to the occurrence of an algal bloom.
| S-EPMC10244338 | biostudies-literature
Project description:Chlorine disinfection is a key global public health strategy for the prevention and control of diseases, such as COVID-19. However, little is known about effects of low levels of residual chlorine on freshwater microbial communities and antibiotic resistomes. Here, we treated freshwater microcosms with continuous low concentrations of chlorine and quantified the effects on aquatic and zebrafish intestinal microbial communities and antibiotic resistomes, using shotgun metagenome and 16S rRNA gene sequencing. Although chlorine rapidly degraded, it altered the aquatic microbial community composition over time and disrupted interactions among microbes, leading to decreases in community complexity and stability. However, community diversity was unaffected. The majority of ecological functions, particularly metabolic capacities, recovered after treatment with chlorine for 14 d, due to microbial community redundancy. There were also increased levels of antibiotic-resistance gene dissemination by horizontal and vertical gene transfer under chlorine treatment. Although the zebrafish intestinal microbial community recovered from temporary dysbiosis, growth and behavior of zebrafish adults were negatively affected by chlorine. Overall, our findings demonstrate the negative effects of residual chlorine on freshwater ecosystems and highlight a possible long-term risk to public health.
| S-EPMC9758890 | biostudies-literature
Project description:We reported the microbial communities in wastewater between conventional membrane bioreactor (MBR) system and biofilm MBR system using Illumina sequencing.
2019-08-14 | GSE135797 | GEO