Browsing by Author "Chen, Chaoqi"

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    AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
    Liang, Xiao; Akers, Kyle; Keenum, Ishi M.; Wind, Lauren L.; Gupta, Suraj; Chen, Chaoqi; Aldaihani, Reem; Pruden, Amy; Zhang, Liqing; Knowlton, Katharine F.; Xia, Kang; Heath, Lenwood S. (2021-03-10)
    Background Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
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    Artificial topography changes the growth strategy of Spartina alterniflora, case study with wave exposure as a comparison
    Hong, Hualong; Dai, Minyue; Lu, Haoliang; Liu, Jingchun; Zhang, Jie; Chen, Chaoqi; Xia, Kang; Yan, Chongling (Springer Nature, 2017-11-17)
    This paper reports findings about the growth of Spartina alterniflora (Loisel.) near an engineered coastal protection defences to discover the potential influences on vegetation growth from the artificial topography. Impacts of the artificial topography on the sediment element composition were detected by comparing the fixed effects caused by artificial topography and wave exposure using linear mixed models. Surficial sediments under the impacts of artificial topography contain elevated levels of biogenic elements and heavy metals, including C (and organic carbon), N, S, Al, Fe, Mn, Cu, Zn, As, Cd, Cr, Ni, and Pb. The results showed that element enrichment caused by artificial topography reduced the vegetation sexual reproduction. Contrary to the potential inhibition caused by direct wave exposure, which was due to the biomass accumulation limit, the inhibition caused by artificial topography was related to the transition of growth strategy. The contents of Cu, Mn, N, Ni, S and As in the sediments were critical in considering the relationship between the change in the sediment element composition and the alteration in the plant growth. Our study emphasizes the importance of rethinking the impacts of coastal development projects, especially regarding the heterogeneity of sediment element composition and its ecological consequences.
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    Culturable antibiotic-resistant fecal coliform bacteria in soil and surface runoff after liquid dairy manure surface application and subsurface injection
    Hilaire, Sheldon Shervon; Chen, Chaoqi; Radolinski, Jesse; Leventhal, Talia; Preisendanz, Heather; Kleinman, Peter J. A.; Maguire, Rory O.; Stewart, Ryan D.; Saporito, Lou S.; Xia, Kang (Wiley, 2022-02-05)
    Land application of manure, while beneficial to soil health and plant growth, can lead to an overabundance of nutrients and introduction of emerging contaminants into agricultural fields. Compared with surface application of manure, subsurface injection has been shown to reduce nutrients and antibiotics in surface runoff. However, less is known about the influence of subsurface injection on the transport and persistence of antibiotic-resistant microorganisms. We simulated rainfall to field plots at two sites (one in Virginia and one in Pennsylvania) 1 or 7 d after liquid dairy manure surface and subsurface application (56 Mg ha–1) and monitored the abundance of culturable antibiotic-resistant fecal coliform bacteria (ARFCB) in surface runoff and soils for 45 d. We performed these tests at both sites in spring 2018 and repeated the test at the Virginia site in fall 2019. Manure subsurface injection, compared with surface application, resulted in less ARFCB in surface runoff, and this reduction was greater at Day 1 after application compared with Day 7. The reductions of ARFCB in surface runoff because of manure subsurface injection were 2.5–593 times at the Virginia site in spring 2018 and fall 2019 and 4–5 times at the Pennsylvania site in spring 2018. The ARFCB were only detectable in the 0-to-5-cm soil depth within 14 d of manure surface application but remained detectable in the injection slits of manure subsurface-injected plots even at Day 45. This study demonstrated that subsurface injection can significantly reduce surface runoff of ARFCB from manure-applied fields.
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    Effect of antibiotic use and composting on antibiotic resistance gene abundance and resistome risks of soils receiving manure-derived amendments
    Chen, Chaoqi; Pankow, Christine A.; Oh, Min; Heath, Lenwood S.; Zhang, Liqing; Du, Pang; Xia, Kang; Pruden, Amy (Elsevier, 2019-05-03)
    Manure-derived amendments are commonly applied to soil, raising questions about whether antibiotic use in livestock could influence the soil resistome (collective antibiotic resistance genes (ARGs)) and ultimately contribute to the spread of antibiotic resistance to humans during food production. Here, we examined the metagenomes of soils amended with raw or composted manure generated from dairy cows administered pirlimycin and cephapirin (antibiotic) or no antibiotics (control) relative to unamended soils. Initial amendment (Day 1) with manure or compost significantly increased the diversity (richness) of ARGs in soils (p < 0.01) and resulted in distinct abundances of individual ARG types. Notably, initial amendment with antibiotic-manure significantly increased the total ARG relative abundances (per 16S rRNA gene) in the soils (2.21×unamended soils, p < 0.001). After incubating 120 days, to simulate a wait period before crop harvest, 282 ARGs reduced 4.33- fold (median) up to 307-fold while 210 ARGs increased 2.89-fold (median) up to 76-fold in the antibioticmanure- amended soils, resulting in reduced total ARG relative abundances equivalent to those of the unamended soils. We further assembled the metagenomic data and calculated resistome risk scores, which was recently defined as a relative index comparing co-occurrence of sequences corresponding to ARGs, mobile genetic elements, and putative pathogens on the same scaffold. Initial amendment of manure significantly increased the soil resistome risk scores, especially when generated by cows administered antibiotics, while composting reduced the effects and resulted in soil resistomes more similar to the background. The risk scores of manure-amended soils reduced to levels comparable to the unamended soils after 120 days. Overall, this study provides an integrated, high-resolution examination of the effects of prior antibiotic use, composting, and a 120-day wait period on soil resistomes following manure-derived amendment, demonstrating that all three management practices have measurable effects and should be taken into consideration in the development of policy and practice for mitigating the spread of antibiotic resistance.
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    Effect of composting and soil type on dissipation of veterinary antibiotics in land-applied manures
    Chen, Chaoqi; Ray, Partha P.; Knowlton, Katharine F.; Pruden, Amy; Xia, Kang (2018)
    The objective of this study was to determine the fate of commonly used veterinary antibiotics in their naturally excreted form when manure-based amendments are applied to soil. Beef cattle were administered sulfamethazine, tylosin, and chlortetracycline and dairy cows were treated with pirlimycin. The resulting manure was composted for 42 d under static or turned conditions and applied at agronomic N rates to sandy, silt, and silty clay loam soils and compared with amendment with corresponding raw manures in sacrificial microcosms over a 120-day period. Antibiotic dissipation in the raw manure-amended soils followed bi-phasic first order kinetics. The first phase half-lives for sulfamethazine, tylosin, chlortetracycline, and pirlimycin ranged from 6.0 to 18, 2.7 to 3.7, 23 to 25, and 5.5–8.2 d, respectively. During the second phase, dissipation of sulfamethazine was negligible, while the half-lives for tylosin, chlortetracycline, and pirlimycin ranged from 41 to 44, 75 to 144, and 87–142 d, respectively. By contrast, antibiotic dissipation in the compost-amended soils followed single-phase first order kinetics with negligible dissipation of sulfamethazine and half-lives of tylosin and chlortetracycline ranging from 15 to 16 and 49–104 d, respectively. Pirlimycin was below the detection limit in the compost-amended soils. After incubating 120 d, antibiotics in compost-amended soils (up to 3.1 μg kg−1) were significantly lower than in manure-amended soils (up to 19 μg kg−1, p < .0001), with no major effect of soil type on the dissipation. Risk assessment suggested that composting can reduce antibiotic resistance selection potential in manure-amended soils.
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    Fe3 +-saturated montmorillonite effectively deactivates bacteria in wastewater
    Qin, Chao; Chen, Chaoqi; Shang, Chao; Xia, Kang (Elsevier, 2018)
    Existing water disinfection practices often produce harmful disinfection byproducts. The antibacterial activity of Fe3 +-saturated montmorillonite was investigated mechanistically using municipal wastewater effluents. Bacterial deactivation efficiency (bacteria viability loss) was 92 ± 0.64% when a secondary wastewater effluent was mixed with Fe3 +-saturated montmorillonite for 30 min, and further enhanced to 97 ± 0.61% after 4 h. This deactivation efficiency was similar to that when the same effluent was UV-disinfected before it exited a wastewater treatment plant. Comparing to the secondary wastewater effluent, the bacteria deactivation efficiency was lower when the primary wastewater effluent was exposed to the same dose of Fe3 +-saturated montmorillonite, reaching 29 ± 18% at 30 min and 76 ± 1.7% at 4 h. Higher than 90% bacterial deactivation efficiency was achieved when the ratio between wastewater bacteria population and weight of Fe3 +-saturated montmorillonite was at < 2 × 103 CFU/mg. Furthermore, 99.6–99.9% of total coliforms, E. coli, and enterococci in a secondary wastewater effluent was deactivated when the water was exposed to Fe3 +-saturated montmorillonite for 1 h. Bacterial colony count results coupled with the live/dead fluorescent staining assay observation suggested that Fe3 +-saturated montmorillonite deactivated bacteria in wastewater through two possible stages: electrostatic sorption of bacterial cells to the surfaces of Fe3 +-saturated montmorillonite, followed by bacterial deactivation due to mineral surface-catalyzed bacterial cell membrane disruption by the surface sorbed Fe3 +. Freeze-drying the recycled Fe3 +-saturated montmorillonite after each usage resulted in 82 ± 0.51% bacterial deactivation efficiency even after its fourth consecutive use. This study demonstrated the promising potential of Fe3 +-saturated montmorillonite to be used in applications from small scale point-of-use drinking water treatment devices to large scale drinking and wastewater treatment facilities.
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    MetaCompare: a computational pipeline for prioritizing environmental resistome risk
    Oh, Min; Pruden, Amy; Chen, Chaoqi; Heath, Lenwood S.; Xia, Kang; Zhang, Liqing (2018-07)
    The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means of comparing and prioritizing risks represented by various environmental compartments is lacking. Here, we introduce MetaCompare, a publicly available tool for ranking 'resistome risk', which we define as the potential for antibiotic resistance genes (ARGs) to be associated with mobile genetic elements (MGEs) and mobilize to pathogens based on metagenomic data. A computational pipeline was developed in which each ARG is evaluated based on relative abundance, mobility, and presence within a pathogen. This is determined through the assembly of shotgun sequencing data and analysis of contigs containing ARGs to determine if they contain sequence similarity to MGEs or human pathogens. Based on the assembled metagenomes, samples are projected into a 3-dimensionalhazard space and assigned resistome risk scores. To validate, we tested previously published metagenomic data derived from distinct aquatic environments. Based on unsupervised machine learning, the test samples clustered in the hazard space in a manner consistent with their origin. The derived scores produced a well-resolved ascending resistome risk ranking of: wastewater treatment plant effluent, dairy lagoon, and hospital sewage.
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    Metagenomic tracking of antibiotic resistance genes through a pre-harvest vegetable production system: an integrated lab-, microcosm- and greenhouse-scale analysis
    Keenum, Ishi M.; Wind, Lauren L.; Ray, Partha P.; Guron, Giselle K. P.; Chen, Chaoqi; Knowlton, Katharine F.; Ponder, Monica A.; Pruden, Amy (Wiley, 2022-05-18)
    Prior research demonstrated the potential for agricultural production systems to contribute to the environmental spread of antibiotic resistance genes (ARGs). However, there is a need for integrated assessment of critical management points for minimizing this potential. Shotgun metagenomic sequencing data were analysed to comprehensively compare total ARG profiles characteristic of amendments (manure or compost) derived from either beef or dairy cattle (with and without dosing antibiotics according to conventional practice), soil (loamy sand or silty clay loam) and vegetable (lettuce or radish) samples collected across studies carried out at laboratory-, microcosm- and greenhouse-scale. Vegetables carried the greatest diversity of ARGs (n = 838) as well as the most ARG-mobile genetic element co-occurrences (n = 945). Radishes grown in manure- or compost-amended soils harboured a higher relative abundance of total (0.91 and 0.91 ARGs/16S rRNA gene) and clinically relevant ARGs than vegetables from other experimental conditions (average: 0.36 ARGs/16S rRNA gene). Lettuce carried the highest relative abundance of pathogen gene markers among the metagenomes examined. Total ARG relative abundances were highest on vegetables grown in loamy sand receiving antibiotic-treated beef amendments. The findings emphasize that additional barriers, such as post-harvest processes, merit further study to minimize potential exposure to consumers.