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

Abstract

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.

Increasing Antimicrobial Resistance and Potential Human Bacterial Pathogens in an Invasive Land Snail Driven by Urbanization

“…For instance, tetracycline resistance genes are ubiquitous and abundant in the human gut worldwide, , aminoglycoside and beta-lactam resistant genes have been shown to be the most abundant ARG types in urban park soil with reclaimed water irrigation, and multidrug resistance genes, vancomycin, and beta-lactam resistant genes are the most diverse and dominant ARGs in collembola. , However, ARGs conferring resistance to multidrug, beta-lactam, and MLS resistance genes were found to be dominant in the gut microbiome of the giant African snails we studied. Our study revealed that multidrug resistance accounted for 60% of the total ARG abundance in giant African snails, exceeding other environmental samples such as urban streams, livestock manure, and untreated urban sewage . This high ratio of multidrug resistance in giant African snails sets it apart from related studies and calls for further attention, especially given the increasing prevalence of multidrug-resistant pathogenic bacteria worldwide, which poses significant challenges to disease control …”

“…24,73 However, ARGs conferring resistance to multidrug, beta-lactam, and MLS resistance genes were found to be dominant in the gut microbiome of the giant African snails we studied. Our study revealed that multidrug resistance accounted for 60% of the total ARG abundance in giant African snails, exceeding other environmental samples such as urban streams, 74 livestock manure, 69 and untreated urban sewage. 75 This high ratio of multidrug resistance in giant African snails sets it apart from related studies and calls for further attention, especially given the increasing prevalence of multidrug-resistant pathogenic bacteria worldwide, which poses significant challenges to disease control.…”

“…Furthermore, a comparison of our results to a similar study that examined livestock manure revealed that the giant African giant snail had a higher diversity of ARG subtypes (601) than broilers (545), swine (427), laying (419), dairy cow (288), and cattle (232). Moreover, the relative abundance of total ARG in giant African snails was comparable to that of broiler manure (1.59 copies per 16S rRNA gene), which exhibited the highest relative abundance among the animal samples tested . Therefore, giant African snails could be an underappreciated reservoir for ARGs that has the potential to transfer AMR from soil and other environmental substrates to humans.…”

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

“…Specifically, AMX is the most commonly used human and animal antibiotic among 36 different drug types in China ( Liu et al, 2019 ), with doses up to 500 mg/kg used in pig feed ( Liu et al, 2018 ). 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 ).…”

Metagenomic insights for antimicrobial resistance surveillance in soils with different land uses in Brazil

“…Even though the soil microbiota naturally presents a large and robust diversity of ARGs in its intrinsic resistome, land use transformation due to anthropic activities, such as the excessive use of antibiotics in livestock production [4], antibiotic-enriched manure application [5,6], and excessive use of xenobiotics in crops [7,8], along with increasing levels of deforestation for farming or urban purposes, can alter bacterial communities and disseminate ARGs throughout the environment [9]. In these highly modified sites, soil bacteria more frequently are in close proximity to commensal and pathogenic ones, which could lead to an increased horizontal ARG transfer rate among them, followed by a dominance of organisms with acquired resistance in comparison to intrinsically resistant bacteria [10].…”