Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography

Yang, Yuyi; Zan, Li; Song, Wenjing; Du, Li-zhong; Wang, Hongzhi; Zhao, Bo; Liu, Wenzhi; Deng, Danli; Pan, Yun; Lin, Hui; Cao, Xinhua

doi:10.1016/j.envint.2019.03.062

Cited by 105 publications

(30 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The R package v.3.6.3 was used to conduct one‐way analysis of variance (ANOVA) or Kruskal–Wallis one‐way analysis of variance, depending on pass or failure of a Shapiro–Wilk test of normality, to compare differences in relative abundance of ARG or MRG number per 16S rRNA copy, in addition to assessing differences in Shannon index. For network analyses, the observed (O%) and random incidences (R%) of co‐occurrence patterns between antibiotics, biocides and metals were determined following methods described in a previous analysis (Ju et al , 2014, 2016; Yang et al , 2019).…”

Section: Methodsmentioning

confidence: 99%

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Thomas

Oladeinde

Kieran

et al. 2020

Microbial Biotechnology

102

View full text Add to dashboard Cite

Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co-selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), heavy metals (Ash Basins), radionuclides (Pond B) and heavy metal and radionuclides (Tim's Branch). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. Sites with legacies of metal and/or radionuclide contamination displayed significantly lower bacterial diversity compared to the reference site. Metagenomic analysis indicated that multidrug and vancomycin antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) including those associated with copper, arsenic, iron, nickel and zinc were prominent in all soils including the reference site. However, significant differences were found in the relative abundance and diversity of certain ARGs and MRGs in soils with metal/radionuclide contaminated soils compared to the reference site. Co-occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Overall, the study emphasizes the potential risk of human activities on the dissemination of AMR in the environment.

show abstract

Section: Methodsmentioning

confidence: 99%

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Thomas

Oladeinde

Kieran

et al. 2020

Microbial Biotechnology

102

View full text Add to dashboard Cite

show abstract

“…Due to the overuse and misuse of antibiotics in human activities such as agriculture, livestock, and medical treatment, antibiotic resistance has rapidly accelerated in environmental ecosystems [2,3]. Aquatic environments are regarded as a major source for the aggregation and dissemination of antibiotic resistance genes (ARGs) because they are easily influenced by human activities [4,5]. In particular, the emergence of ARGs could significantly increase the spread of antibiotic resistance, especially via mobile genetic elements (MGEs) including plasmids, integrons and insertion sequences [4][5][6].…”

Section: Introductionmentioning

confidence: 99%

“…Aquatic environments are regarded as a major source for the aggregation and dissemination of antibiotic resistance genes (ARGs) because they are easily influenced by human activities [4,5]. In particular, the emergence of ARGs could significantly increase the spread of antibiotic resistance, especially via mobile genetic elements (MGEs) including plasmids, integrons and insertion sequences [4][5][6]. There is growing evidence that wastewater treatment plants (WWTPs) have received special attention in playing a major role in the proliferation of antibiotic resistance into other environmental systems, such as rivers, sediment, and oceans [6].…”

Section: Introductionmentioning

confidence: 99%

Investigation of the Prevalence of Antibiotic Resistance Genes According to the Wastewater Treatment Scale Using Metagenomic Analysis

Yoo

Lee

2021

Antibiotics

View full text Add to dashboard Cite

Although extensive efforts have been made to investigate the dynamics of the occurrence and abundance of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), understanding the acquisition of antibiotic resistance based on the WWTP scale and the potential effects on WWTPs is of relatively less interest. In this study, metagenomic analysis was carried out to investigate whether the WWTP scale could be affected by the prevalence and persistence of ARGs and mobile genetic elements (MGEs). As a result, 152 ARG subtypes were identified in small-scale WWTP samples, while 234 ARG subtypes were identified in large-scale WWTP samples. Among the detectable ARGs, multidrug, MLS (macrolide–lincosamide–streptogramin), sulfonamide, and tetracycline resistance genes had the highest abundance, and large and small WWTPs had similar composition characteristics of ARGs. In MGE analysis, plasmids and integrons were 1.5–2.0-fold more abundant in large-scale WWTPs than in small-scale WWTPs. The profile of bacteria at the phylum level showed that Proteobacteria and Actinobacteria were the most dominant bacteria, representing approximately 70% across large- and small-scale WWTPs. Overall, the results of this study elucidate the different abundances and dissemination of ARGs between large- and small-scale WWTPs, which facilitates the development of next-generation engineered wastewater treatment systems.

show abstract

“…and comprehensively identifying and quantifying ARGs, MRGs, and MGE in different environments [25][26][27]. In addition, pathogenic bacteria affect the risk of resistance transferring to the human microbiome.…”

Section: Metagenomics Methods and Structured Gene Databases Have Becomentioning

confidence: 99%

Metagenomic analysis of effects of oxytetracycline and copper on antibiotic resistance genes and associated pathogenic hosts in swine manure compost

Guo

Wang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: The proliferation of antibiotic resistance genes (ARGs) in compost and their horizontal transfer to human pathogenic bacteria (HPB) may lead to the failure of human antibiotics. However, the antibiotic resistome in compost has not been comprehensively characterized. This study used a metagenomic approach to obtain new insights into the effects of oxytetracycline (OTC) and copper (Cu) on the antibiotic resistome during swine manure composting and the risks posed to human health. Results: The results showed that composting reduced the abundances and diversity of ARGs and HPB in swine manure. In total, 289 ARG subtypes and 19 ARG types were detected in the samples with abundances ranging from 1.08 ´ 10 –1 to 9.39 ´ 10 –1 copies/16S rRNA, which mainly encoded tetracycline, aminoglycoside, and macrolide–lincosamide–streptogramin (MLS) resistance genes. The application of OTC and Cu, especially the combined application, exacerbated the compost resistome risk scores and specific ARG subtypes responded differently. Tetracycline, multidrug, and MLS resistance genes mainly affected resistance profiles of HPB throughout the composting process. HPB and intI1 had significant positive effects on determining the ARG profiles during the composting process, and the co-selective effect of heavy metals may increase the abundances of ARGs via strong positive effects on intI1 . In addition, the effect of mobile genetic elements on the horizontal gene transfer of ARGs should not be ignored. Conclusions: This study of the antibiotic resistome in compost indicates the need for effective regulation of the misuse of livestock and poultry feed additives in order to minimize the spread of the antibiotic resistome in agro-ecosystems and decrease the potential risk to public health. Keywords: Antibiotic resistome; Composting; Metagenome; Pathogenic host; Swine manure

show abstract

Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography

Cited by 105 publications

References 56 publications

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Investigation of the Prevalence of Antibiotic Resistance Genes According to the Wastewater Treatment Scale Using Metagenomic Analysis

Metagenomic analysis of effects of oxytetracycline and copper on antibiotic resistance genes and associated pathogenic hosts in swine manure compost

Contact Info

Product

Resources

About