The effects of offshore petroleum exploitation on microbial community and antibiotic resistome of adjacent marine sediments

Abstract The exploitation of petroleum in offshore areas is becoming more prosperous due to the increasing human demand for oil. However, the effects of offshore petroleum exploitation on the microbial community in the surrounding environment are still not adequately understood. In the present study, variations in the composition, function, and antibiotic resistance of the microbial community in marine sediments adjacent to an offshore petroleum exploitation platform were analyzed by a metagenomics-based method. Significant shifts in the microbial community composition were observed in sediments impacted by offshore petroleum exploitation. Nitrosopumilales was enriched in marine sediments with the activities of offshore petroleum exploitation compared to the control sediments. The abundances of function genes involved in carbon, butanoate, methane, and fatty acid metabolism in sediment microbial communities also increased due to the offshore petroleum exploitation. Offshore petroleum exploitation resulted in the propagation of some antibiotic resistance genes (ARGs), including a multidrug transporter, smeE, and arnA, in marine sediments via horizontal gene transfer mediated by class I integrons. However, the total abundance and diversity of ARGs in marine sediments were not significantly affected by offshore petroleum exploitation. This study is the first attempt to analyze the impact of offshore petroleum exploitation on the spread of antibiotic resistance.

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Microbial Community Composition and Antibiotic Resistance Genes within a North Carolina Urban Water System

Water ◽

10.3390/w10111539 ◽

2018 ◽

Vol 10 (11) ◽

pp. 1539 ◽

Cited By ~ 2

Author(s):

Kevin Lambirth ◽

Matthew Tsilimigras ◽

Anju Lulla ◽

James Johnson ◽

Abrar Al-Shaer ◽

...

Keyword(s):

Antibiotic Resistance ◽

Wastewater Treatment ◽

Microbial Community ◽

Amino Acid ◽

Resistance Genes ◽

Stream Water ◽

Microbial Community Composition ◽

Antibiotic Resistance Genes ◽

Late Winter ◽

Nucleic Acid Metabolism

Wastewater treatment plants (WWTPs) are thought to be potential incubators of antibiotic resistance. Persistence of commonly used antibiotics in wastewater may increase the potential for selection of resistance genes transferred between bacterial populations, some of which might pose a threat to human health. In this study, we measured the concentrations of ten antibiotics in wastewater plant influents and effluents, and in surface waters up- and downstream from two Charlotte area treatment facilities. We performed Illumina shotgun sequencing to assay the microbial community and resistome compositions at each site across four time points from late winter to mid-summer of 2016. Antibiotics are present throughout wastewater treatment, and elevated concentrations of multiple antibiotics are maintained in moving stream water downstream of effluent release. While some human gut and activated sludge associated taxa are detectable downstream, these seem to attenuate with distance while the core microbial community of the stream remains fairly consistent. We observe the slight suppression of functional pathways in the downstream microbial communities, including amino acid, carbohydrate, and nucleic acid metabolism, as well as nucleotide and amino acid scavenging. Nearly all antibiotic resistance genes (ARGs) and potentially pathogenic taxa are removed in the treatment process, though a few ARG markers are elevated downstream of effluent release. Taken together, these results represent baseline measurements that future studies can utilize to help to determine which factors control the movement of antibiotics and resistance genes through aquatic urban ecosystems before, during, and after wastewater treatment.

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Abundance and diversity of phages, microbial taxa and antibiotic resistance genes in the sediments of the river Ganges through metagenomic approach

10.1101/2020.04.29.067819 ◽

2020 ◽

Author(s):

Narender Kumar ◽

Amit Kumar Gupta ◽

Sarabjeet Kour Sudan ◽

Deepika Pal ◽

Vinay Randhawa ◽

...

Keyword(s):

Antibiotic Resistance ◽

Microbial Community ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

River Sediments ◽

Antibiotic Resistance Genes ◽

Ganges River ◽

Illumina Platform ◽

River Ganges ◽

Abundance And Diversity

AbstractIn the present study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community and antibiotic resistance genes. Utilizing data from Illumina platform, 4174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium (128), Propionibacterium (71), Erwinia (70), Ralstonia (56) phages shows the highest abundance and account for approximately 90% of the total identified phages. Additionally, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), Pseudomonadales (∼7.5%) signify the core section. Further, 21869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes) among which 4 ARG types namely multidrug resistance (MDR) (12041 reads, ∼55%), bacitracin (3202 reads, ∼15%), macrolide-lincosamide-streptogramin (MLS) (1744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%) has the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15919 reads). The results unveil the distribution of (pro)-phages; microbial community and various ARGs in the Ganges river sediments. Further research on these identified phage(s) could be used in phage-based therapeutics against pathogenic bacteria.

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Microbial Community Composition and Antibiotic Resistance Genes Within a North Carolina Urban Water System

10.20944/preprints201809.0255.v1 ◽

2018 ◽

Author(s):

Kevin Lambirth ◽

Matthew Tsilimigras ◽

Anju Lulla ◽

James Johnson ◽

Abrar Al-Shaer ◽

...

Keyword(s):

Antibiotic Resistance ◽

Wastewater Treatment ◽

Microbial Community ◽

Amino Acid ◽

Resistance Genes ◽

Stream Water ◽

Microbial Community Composition ◽

Antibiotic Resistance Genes ◽

Late Winter ◽

Nucleic Acid Metabolism

Wastewater treatment plants (WWTPs) are thought to be potential incubators of antibiotic resistance. Persistence of commonly used antibiotics in wastewater may increase the potential for selection of resistance genes transferred between bacterial populations, some of which may pose a threat to human health. In this study, we measured the concentrations of ten antibiotics in wastewater plant influents and effluents, and in surface waters up- and downstream from two Charlotte area treatment facilities. We performed Illumina shotgun sequencing to assay the microbial community and resistome compositions at each site across four time points from late winter to mid-summer of 2016. Antibiotics are present throughout wastewater treatment, and elevated concentrations of multiple antibiotics are maintained in moving stream water downstream of effluent release. While some human gut and activated sludge associated taxa are detectable downstream, these seem to attenuate with distance while the core microbial community of the stream remains fairly consistent. We observe slight suppression of functional pathways in the downstream microbial communities, including amino acid, carbohydrate and nucleic acid metabolism as well as nucleotide and amino acid scavenging. Nearly all antibiotic resistance genes (ARGs) and potentially pathogenic taxa are removed in the treatment process, though a few ARG markers are elevated downstream of effluent release.  Taken together, these results represent baseline measurements which future studies can utilize to help to determine which factors control the movement of antibiotics and resistance genes through aquatic urban ecosystems before, during and after wastewater treatment.

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2322

Journal of Clinical and Translational Science ◽

10.1017/cts.2017.130 ◽

2017 ◽

Vol 1 (S1) ◽

pp. 35-35

Author(s):

Amy Elizabeth Langdon ◽

Christopher Bulow ◽

Kim Reske ◽

Sherry Sun ◽

Tiffany Hink ◽

...

Keyword(s):

Antibiotic Resistance ◽

Microbial Community ◽

Fecal Microbiota Transplantation ◽

Therapeutic Option ◽

Antibiotic Resistance Gene ◽

Microbial Community Composition ◽

Antibiotic Resistance Genes ◽

Fecal Microbiota ◽

Unifrac Distance ◽

Healthy Donors

OBJECTIVES/SPECIFIC AIMS: Clostridium difficile is the most common cause of infectious antibiotic associated diarrhea. It is often refractory to antimicrobial therapy and fecal microbiota transplantation (FMT) is emerging as a therapeutic option. The objective is to characterize the direct effects of FMT on the gut microbiota. METHODS/STUDY POPULATION: Fecal specimens were obtained from a cohort of 29 subjects with recurrent C. difficile infection who received FMTs from 1 of 4 healthy donors as part of a phase 2 trial (Rebiotix). Fecal specimens were collected from the subject before FMT and up to 6 months post FMT. 16S rRNA sequencing and whole-genome shotgun sequencing were used to assess microbial community composition as compared by weighted Unifrac. RESULTS/ANTICIPATED RESULTS: Before treatment, the microbial community of subjects with C. difficile infection was highly distinct from the composition of the healthy donors in terms of metabolic profile. Quantification of phylogenetic community distance from donor by weighted Unifrac distance showed a significant decrease within the 1st week (Wilcoxon rank sum, p<0.01). This metric was predictive of both treatment failures and antibiotic resistance gene count (LR=22.45, p<0.0001). DISCUSSION/SIGNIFICANCE OF IMPACT: We conclude that distance from donor is a useful metric to quantify FMT success and that FMTs are a promising treatment for otherwise untreatable carriage of antibiotic resistance genes and organisms.

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