scholarly journals Exploring the prevalence and distribution patterns of antibiotic resistance genes in bovine gut microbiota using a metagenomic approach

2020 ◽  
Author(s):  
Zhen Zhu ◽  
Mingze Cao ◽  
Weiwei Wang ◽  
Liwei Zhang ◽  
Tenghe Ma ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Beef Cattle ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Distribution Patterns ◽  
Antibiotic Consumption ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Illumina Hiseq

Abstract Background: Antibiotic resistance genes (ARGs) have become recognized contaminants and pose a high public health risk. The animal gut microbiota is a reservoir of ARGs, but the knowledge of the origin and dissemination of ARGs remains unclear.Methods: 30 of the fecal samples were obtained from bovine and were immediately frozen in liquid nitrogen. Total metagenomic DNA was extracted by cetyltrimethylammonium bromide (CTAB) method and sequenced by Illumina HiSeq X Ten platform. After quality control and assembled, the sequence were annotated by NR, CARD and ISfinder. Statistical analysis was performed using SPSS 19.0.Results: A total of 42 ARG types were detected by annotating the metagenomic sequencing data from the Comprehensive Antibiotic Resistance Database (CARD). We found that the diversity and abundance of ARGs in individual yaks were significantly lower than those in dairy and beef cattle. The results of heat map and single-nucleotide polymorphism (SNP) clustering suggest that ARGs from dairy and beef cattle are more similar, while those from yaks cluster separately. Conclusion: The long-term use of antibiotics may contribute to this difference, suggesting that antibiotic consumption is the main cause of ARG prevalence. Furthermore, abundant insertions and integrations were also found in this study, signifying a strong potential for horizontal transfer of ARGs among microbes, especially pathogens.

scholarly journals Diversity and Distribution of Potential Pathogens and Antibiotic Resistance Genes in Anthropogenic Disturbances Aquatic Environment and Their Relationship with Microbial Indicators

2021 ◽  
Author(s):  
Xiang-Long Zhao ◽  
Zhao Qi ◽  
Hao Huang ◽  
Jian Tu ◽  
Xiang-Jun Song ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Antibiotic Resistance Genes ◽  
Chaohu Lake ◽  
Lake Basin ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Potential Health ◽  
Microbial Indicators

Abstract Microbial indicators are often used as alternative indicators of microbial safety in water. However, information regarding the correlation between microbial indicators and ecotoxicological factors such as potential pathogens and antibiotic resistance genes (ARGs) in anthropogenically impacted waters remains highly limited. Combining 16S rRNA and metagenomic sequencing data, we investigated the composition of bacterial community and potential pathogens, ARGs diversity, ARGs host and horizontal gene transfer (HGT) potential in water samples under the influence of different exogenous pollutants in Chaohu Lake basin. The water body that receives a large amount of domestic sewage showed a significant decrease in microbial diversity and a significant enrichment of potential pathogens. A total of 14 main types and 461 subtypes of ARGs were detected in all samples, dominated by multidrug resistance (MDR) efflux pump (53.6%), aminoglycoside (6.0%), fluoroquinolone (5.8%) and polymyxin (5.46%). Host-tracking analysis showed that Escherichia coli and Bacteroides graminisolvens carried a wealth of ARG subtypes. Correlation analysis showed that potential pathogens and some ARG subtypes such as dfrE, sul2, PmrE exhibits significant correlation with indicator bacteria. Overall, next-generation sequencing (NGS) has the ability to conduct preliminary surveys of environmental samples to access potential health risks, thus providing ideas for water resources management.

scholarly journals Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ishi Keenum ◽  
Robert K. Williams ◽  
Partha Ray ◽  
Emily D. Garner ◽  
Katharine F. Knowlton ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Land Application ◽  
Multidimensional Analysis ◽  
Small Scale ◽  
Antibiotic Administration ◽  
Metagenomic Sequencing ◽  
Combined Effects ◽  
Bacterial Microbiota

Abstract Background Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resistance to spread. Here, we carried out a comprehensive parallel examination of the effects of small-scale (> 55 °C × 3 days) static and turned composting of manures from dairy and beef cattle collected during standard antibiotic administration (cephapirin/pirlimycin or sulfamethazine/chlortetracycline/tylosin, respectively), versus from untreated cattle, on “resistomes” (total antibiotic resistance genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, and indicator ARGs enumerated via quantitative polymerase chain reaction. To gain insight into the role of the thermophilic phase, compost was also externally heated to > 55 °C × 15 days. Results Progression of composting with time and succession of the corresponding bacterial microbiota was the overarching driver of the resistome composition (ANOSIM; R = 0.424, p = 0.001, respectively) in all composts at the small-scale. Reduction in relative abundance (16S rRNA gene normalized) of total ARGs in finished compost (day 42) versus day 0 was noted across all conditions (ANOSIM; R = 0.728, p = 0.001), except when externally heated. Sul1, intI1, beta-lactam ARGs, and plasmid-associated genes increased in all finished composts as compared with the initial condition. External heating more effectively reduced certain clinically relevant ARGs (blaOXA, blaCARB), fecal coliforms, and resistome risk scores, which take into account putative pathogen annotations. When manure was collected during antibiotic administration, taxonomic composition of the compost was distinct according to nonmetric multidimensional analysis and tet(W) decayed faster in the dairy manure with antibiotic condition and slower in the beef manure with antibiotic condition. Conclusions This comprehensive, integrated study revealed that composting had a dominant effect on corresponding resistome composition, while little difference was noted as a function of collecting manure during antibiotic administration. Reduction in total ARGs, tet(W), and resistome risk suggested that composting reduced some potential for antibiotic resistance to spread, but the increase and persistence of other indicators of antibiotic resistance were concerning. Results indicate that composting guidelines intended for pathogen reduction do not necessarily provide a comprehensive barrier to ARGs or their mobility prior to land application and additional mitigation measures should be considered.

Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
Bo Li ◽  
Zeng Chen ◽  
Fan Zhang ◽  
Yongqin Liu ◽  
Tao Yan
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Soil Samples ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Metagenomic Sequencing ◽  
Clinical Issue ◽  
Abundance And Diversity

ABSTRACT Widespread occurrence of antibiotic resistance genes (ARGs) has become an important clinical issue. Studying ARGs in pristine soil environments can help to better understand the intrinsic soil resistome. In this study, 10 soil samples were collected from a high elevation and relatively pristine Tibetan area, and metagenomic sequencing and bioinformatic analyses were conducted to investigate the microbial diversity, the abundance and diversity of ARGs and the mobility potential of ARGs as indicated by different mobile genetic elements (MGEs). A total of 48 ARG types with a relative abundance of 0.05–0.28 copies of ARG/copy of 16S rRNA genes were detected in Tibetan soil samples. The observed ARGs were mainly associated with antibiotics that included glycopeptide and rifamycin; the most abundant ARGs were vanRO and vanSO. Low abundance of MGEs and potentially plasmid-related ARGs indicated a low horizontal gene transfer risk of ARGs in the pristine soil. Pearson correlation and redundancy analyses showed that temperature and total organic carbon were the major environmental factors controlling both microbial diversity and ARG abundance and diversity.

scholarly journals Persistence of antibiotic resistance genes in beef cattle backgrounding environment over two years after cessation of operation

PLoS ONE ◽  
2019 ◽  
Vol 14 (2) ◽  
pp. e0212510 ◽  
Author(s):  
Getahun E. Agga ◽  
Kimberly L. Cook ◽  
Annesly M. P. Netthisinghe ◽  
Rebecca A. Gilfillen ◽  
Paul B. Woosley ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Beef Cattle ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes

scholarly journals Metagenomic Profiles of Antibiotic Resistance Genes in Activated Sludge, Dewatered Sludge and Bioaerosols

Water ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1516
Author(s):  
Il Han ◽  
Keunje Yoo
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Activated Sludge ◽  
Resistance Genes ◽  
Wastewater Treatment Plants ◽  
Antibiotic Resistance Genes ◽  
Illumina Hiseq ◽  
Wastewater Treatment Process ◽  
Dewatered Sludge ◽  
Scientific Attention

Wastewater treatment plants (WWTPs) have been considered hotspots for the development and dissemination of antibiotic resistance in the environment. Although researchers have reported a significant increase in bioaerosols in WWTPs, the associated bacterial taxa, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) remain relatively unknown. In this study, we have investigated the abundance and occurrences of ARGs and MGEs, as well as the bacterial community compositions in activated sludge (AS), dewatered sludge (DS) and bioaerosols (BA) in a WWTP. In total, 153 ARG subtypes belonging to 19 ARG types were identified by the broad scanning of metagenomic profiles obtained using Illumina HiSeq. The results indicated that the total occurrences and abundances of ARGs in AS and DS samples were significantly higher than those in BA samples (p < 0.05). However, some specific ARG types related to sulfonamide, tetracycline, macrolide resistance were present in relatively high abundance in BA samples. Similar to many other full-scale WWTPs, the Proteobacteria (58%) and Bacteroidetes (18%) phyla were dominant in the AS and DS samples, while the Firmicutes (25%) and Actinobacteria (20%) phyla were the most dominant in the BA samples. Although the abundance of genes related to plasmids and integrons in bioaerosols were two to five times less than those in AS and DS samples, different types of MGEs were observed in BA samples. These results suggest that comprehensive analyses of resistomes in BA are required to better understand the emergence of both ARGs and MGEs in the wastewater treatment process due to the significant increase of scientific attention toward bioaerosols effects.

Metagenomic profiles and antibiotic resistance genes in gut microbiota of mice exposed to arsenic and iron

Chemosphere ◽  
2014 ◽  
Vol 112 ◽  
pp. 1-8 ◽  
Author(s):  
Xuechao Guo ◽  
Su Liu ◽  
Zhu Wang ◽  
Xu-xiang Zhang ◽  
Mei Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes
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