Mobile genetic elements in potential host microorganisms are the key hindrance for the removal of antibiotic resistance genes in industrial-scale composting with municipal solid waste

Tang, Zhurui; Xi, Beidou; Huang, Caihong; Tan, Wenbing; Li, Wenxuan; Zhao, Xinyu; Liu, Kexin; Xia, Xiangqin

doi:10.1016/j.biortech.2019.122723

Cited by 62 publications

(7 citation statements)

References 49 publications

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“…The constant or increased abundance of sulfonamide or trimethoprim resistance genes are often found during composting with various materials, such as swine manure [ 6 , 7 , 56 ], chicken manure [ 57 , 58 ], cow manure [ 12 , 16 ], sewage sludge [ 15 ], and food waste [ 18 ]. Previous correlation analysis showed that the increase in sulfonamide resistance genes was positively correlated with strains that were privileged during the cooling-maturation stages [ 7 , 18 ], and the sulfonamide resistance genes were also often found to be correlated with MGEs, such as intI1 or ISR1 [ 7 , 16 , 57 ]. These results indicate that ARGs may be maintained in other strains due to HGTs.…”

Section: Discussionmentioning

confidence: 99%

“…Clarifying ARG hosts is conducive to controlling ARG dissemination during manure composting. The identification and quantification of potential ARG host bacteria are often based on correlation analysis [7,[15][16][17][18][19][20]. However, because the 16S rDNA amplicon sequencing did not include ARG information, the quantification based on the co-occurrence of ARGs and bacteria could have overestimated the relative abundance of potential ARG hosts.…”

Section: Introductionmentioning

confidence: 99%

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Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

Qiu

Huo

Guo

et al. 2022

Environmental Microbiome

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Background Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts. Results In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86–99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting. Conclusions Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

Qiu

Huo

Guo

et al. 2022

Environmental Microbiome

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“…In recent years, the use of composting technology to reduce ARGs in organic solid waste has become a research hotspot. Although most studies showed that composting can remove ARGs, some studies have demonstrated that composting can not effectively remove ARGs (Liao et al, 2018Tang et al, 2020). The removing effect of ARGs in compost still remains controversial.…”

Section: G R a P H I C Abstract Abstractmentioning

confidence: 99%

Environmental effects and risk control of antibiotic resistance genes in the organic solid waste aerobic composting system: A review

Huang

Tang

et al. 2021

Front. Environ. Sci. Eng.

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Antibiotic resistance genes (ARGs) have been diffusely detected in several kinds of organic solid waste, such as livestock manure, sludge, antibiotic fermentation residues, and food waste, thus attracting great attention. Aerobic composting, which is an effective, harmless treatment method for organic solid waste to promote recycling, has been identified to also aid in ARG reduction. However, the effect of composting in removing ARGs from organic solid waste has recently become controversial. Thus, this article summarizes and reviews the research on ARGs in relation to composting in the past 5 years. ARGs in organic solid waste could spread in different environmental media, including soil and the atmosphere, which could widen environmental risks. However, the conventional composting technology had limited effect on ARGs removal from organic solid waste. Improved composting processes, such as hyperthermophilic temperature composting, could effectively remove ARGs, and the HGT of ARGs and the microbial communities are identified as vital influencing factors. Currently, during the composting process, ARGs were mainly affected by three response pathways, (I) “Microenvironment-ARGs”; (II) “Microenvironment-microorganisms-ARGs”; (III) “Microorganisms-horizontal gene transfer-ARGs”, respectively. Response pathway II had been studied the most which was believed that microbial community was an important factor affecting ARGs. In response pathway III, mainly believed that MGEs played an important role and paid less attention to eARGs. Further research on the role and impact of eARGs in ARGs may be considered in the future. It aims to provide support for further research on environmental risk control of ARGs in organic solid waste.

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“…However, antibiotics usage in animal husbandry ( Zhang et al, 2017a ) can shift animal microbiome, enrich antibiotic resistance genes (ARGs), and subsequently transfer to livestock manure and its products ( Qiu et al, 2022 ). Hence, livestock production is considered an important hotspot and key point-source of antibiotic resistant bacteria (ARB) and ARGs dissemination ( Youngquist et al, 2016 ; Awasthi et al, 2019 ; Deng et al, 2020 ; Lu et al, 2020 ; Tang et al, 2020 ). Previous studies have shown that β-lactam resistance genes are the top three types of ARGs in manure samples from 17 dairy farms in Shanxi Province, China ( Zhou et al, 2016 ; Liu et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Environmental drivers and interaction mechanisms of heavy metal and antibiotic resistome exposed to amoxicillin during aerobic composting

Liu

Li²,

Su³

et al. 2023

Front. Microbiol.

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The environmental accumulation and spread of antibiotic resistance pose a major threat to global health. Aerobic composting has become an important hotspot of combined pollution [e.g., antibiotic resistance genes (ARGs) and heavy metals (HMs)] in the process of centralized treatment and resource utilization of manure. However, the interaction mechanisms and environmental drivers of HMs resistome (MRGs), antibiotic resistance (genotype and phenotype), and microbiome during aerobic composting under the widely used amoxicillin (AMX) selection pressure are still poorly understood. Here, we investigated the dynamics of HMs bioavailability and their MRGs, AMX-resistant bacteria (ARB) and antibiotic resistome (ARGs and intI1), and bacterial community to decipher the impact mechanism of AMX by conducting aerobic composting experiments. We detected higher exchangeable HMs and MRGs in the AMX group than the control group, especially for the czrC gene, indicating that AMX exposure may inhibit HMs passivation and promote some MRGs. The presence of AMX significantly altered bacterial community composition and AMX-resistant and -sensitive bacterial structures, elevating antibiotic resistome and its potential transmission risks, in which the proportions of ARB and intI1 were greatly increased to 148- and 11.6-fold compared to the control group. Proteobacteria and Actinobacteria were significant biomarkers of AMX exposure and may be critical in promoting bacterial resistance development. S0134_terrestrial_group was significantly negatively correlated with blaTEM and czrC genes, which might play a role in the elimination of some ARGs and MRGs. Except for the basic physicochemical (MC, C/N, and pH) and nutritional indicators (NO3−-N, NH4+-N), Bio-Cu may be an important environmental driver regulating bacterial resistance during composting. These findings suggested the importance of the interaction mechanism of combined pollution and its synergistic treatment during aerobic composting need to be emphasized.

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Mobile genetic elements in potential host microorganisms are the key hindrance for the removal of antibiotic resistance genes in industrial-scale composting with municipal solid waste

Cited by 62 publications

References 49 publications

Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

Environmental effects and risk control of antibiotic resistance genes in the organic solid waste aerobic composting system: A review

Environmental drivers and interaction mechanisms of heavy metal and antibiotic resistome exposed to amoxicillin during aerobic composting

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