scholarly journals Variability of the Ability of Complex Microbial Communities to Exclude Microbes Carrying Antibiotic Resistance Genes in Rabbits

2019 ◽  
Vol 10 ◽  
Author(s):  
Caroline Stéphanie Achard ◽  
Véronique Dupouy ◽  
Suzanne Siviglia ◽  
Nathalie Arpaillange ◽  
Laurent Cauquil ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes

scholarly journals Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 230
Author(s):  
Shan Wan ◽  
Min Xia ◽  
Jie Tao ◽  
Yanjun Pang ◽  
Fugen Yu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gene Diversity ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Pathogen Transmission ◽  
Transmission Risk ◽  
Antimicrobial Resistance Gene

In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and archaea and fungi were also detected. The genera Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of potential environmental risk in landfills. In addition, KEGG pathway analysis indicated the presence of antibiotic resistance genes typically associated with human antibiotic resistance bacterial strains. These results provide insights into the risk of pathogens in landfills, which is important for controlling the potential secondary transmission of pathogens and reducing workers’ health risk during landfill excavation.

Rare earth oxide nanoparticles promote soil microbial antibiotic resistance by selectively enriching antibiotic resistance genes

2019 ◽  
Vol 6 (2) ◽  
pp. 456-466 ◽  
Author(s):  
Lin Qi ◽  
Yuan Ge ◽  
Tian Xia ◽  
Ji-Zheng He ◽  
Congcong Shen ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Rare Earth ◽  
Microbial Communities ◽  
Resistance Genes ◽  
Soil Microbial Communities ◽  
Antibiotic Resistance Genes ◽  
Rare Earth Oxide ◽  
Oxide Nanoparticles ◽  
Soil Microbial

This study demonstrates that rare earth oxide nanoparticles can enhance soil microbial antibiotic resistance by inducing the enrichment and spread of antibiotic resistance genes in soil microbial communities.

scholarly journals Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California

2019 ◽  
Author(s):  
Brittany J. Suttner ◽  
Eric R. Johnston ◽  
Luis H. Orellana ◽  
Luis M. Rodriguez-R ◽  
Janet K. Hatt ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Health Risk ◽  
Microbial Communities ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Agricultural Runoff ◽  
Public Health Risk ◽  
The Public ◽  
E Coli

ABSTRACTLittle is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens originating from agricultural activities such as Shiga Toxin-producing E. coli (STEC) in such sediments remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley was sampled over a nine-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and comparable to the functional and taxonomic diversity observed in soils. With our sequencing effort (~4 Gbp per library), we were unable to detect any pathogenic Escherichia coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low pathogen abundance. Further, no significant differences were detected in the abundance of human- or cow-specific gut microbiome sequences compared to upstream, more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, a high baseline level of metagenomic reads encoding antibiotic resistance genes (ARGs) was found in all samples and was significantly higher compared to ARG reads in metagenomes from other environments, suggesting that these communities may be natural reservoirs of ARGs. Overall, our metagenomic results revealed that creek sediments are not a major sink for anthropogenic runoff and the public health risk associated with these sediment microbial communities may be low.IMPORTANCECurrent agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food and water-borne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health is assessed by culture-based tests for the intestinal bacterium, E. coli. However, the accuracy of these traditional methods (e.g., low quantification, and false positive signal when PCR-based) and their suitability for sediments remains unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the U.S. in order to assess how agricultural runoff affects the native microbial communities and if the presence of STEC in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.

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