- Pathogen detection in human samples and food
- Antibiotic resistance genes
- mRNA, miRNA, and lncRNA as disease biomarkers
- Genotyping using animal and blood samples
Uncovering antibiotic resistance genes in soil, sediment, and sludge
A significant amount of research have focused on studying antibiotic resistance in soil, sediment, and sludge samples using the SmartChip Real-Time PCR System. These samples were obtained from a variety of different locales. In some cases, the soil samples were collected from crops and areas that received significant organic fertilization. Other samples were collected from per-urban runoff, where improperly treated wastewater contaminates the ground. Exciting findings have linked metal pollution in soil and antibiotic-resistant bacteria. In all of the studies, the SmartChip system was utilized to monitor large panels of antibiotic resistance genes from the soil samples.
One recent publication sought to understand drivers of antibiotic resistance genes in High Arctic soil (McCann et al. 2019). By isolating soil from eight different relatively remote polar sites, the researchers sought to establish a benchmark for background antibiotic resistance that could be used to track the spread in other environments. By utilizing a 296-primer set panel of antibiotic resistance genes using the SmartChip system, they identified over 131 antibiotic resistance genes, with an average of 66 per sample. In addition, they identified 39 unique antibiotic resistance genes in all the samples, likely representing indigenous antibiotic-resistant bacteria. The other, non-conserved antibiotic resistance genes are likely contaminants from human or animal sources.
Chen, Q. et al. Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil. Environ. Int. 92-93, 1–10 (2016).
Chen, Q. L. et al. Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere. Environ. Sci. Technol. 51, 8149–8157 (2017).
Chen, Q. L. et al. Effect of biochar amendment on the alleviation of antibiotic resistance in soil and phyllosphere of Brassica chinensis L. Soil Biol. Biochem. 119, 74–82 (2018).
Chen, Z. et al. Antibiotic resistance genes and bacterial communities in cornfield and pasture soils receiving swine and dairy manures. Environ. Pollut. 248, 947–957 (2019).
Cheng, J. H., Tang, X. Y. & Cui, J. F. Effect of long-term manure slurry application on the occurrence of antibiotic resistance genes in arable purple soil (entisol). Sci. Total Environ. 647, 853–861 (2019).
Cui, E. P. et al. Amendment soil with biochar to control antibiotic resistance genes under unconventional water resources irrigation: Proceed with caution. Environ. Pollut. 240, 475–484 (2018).
Ding, J. et al. Long-term application of organic fertilization causes the accumulation of antibiotic resistome in earthworm gut microbiota. Environ. Int. 124, 145–152 (2019).
Gou, M. et al. Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils. Sci. Total Environ. 612, 1300–1310 (2018).
Han, X. M. et al. Antibiotic resistance genes and associated bacterial communities in agricultural soils amended with different sources of animal manures. Soil Biol. Biochem. 126, 91–102 (2018).
Hu, H. W. et al. Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes. Environ. Microbiol. 20, 3186–3200 (2018).
Kang, W., Zhang, Y. J., Shi, X., He, J. Z. & Hu, H. W. Short-term copper exposure as a selection pressure for antibiotic resistance and metal resistance in an agricultural soil. Environ. Sci. Pollut. Res. 25, 29314–29324 (2018).
Kanger, K. et al. Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard. bioRxiv 564823 (2019). doi:10.1101/564823
Lin, W., Zhang, M., Zhang, S. & Yu, X. Can chlorination co-select antibiotic-resistance genes? Chemosphere 156, 412–419 (2016).
McCann, C. M. et al. Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems. Environ. Int. 125, 497–504 (2019).
Muurinen, J. et al. Influence of manure application on the environmental resistome under Finnish agricultural practice with restricted antibiotic use. Environ. Sci. Technol. 51, 5989–5999 (2017).
Muziasari, W. I. et al. Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments. FEMS Microbiol. Ecol. 92, fiw052 (2016).
Muziasari, W. I. et al. The resistome of farmed fish feces contributes to the enrichment of antibiotic resistance genes in sediments below Baltic Sea fish farms. Front. Microbiol. 7, 1–10 (2017).
Stedtfeld, R. D. et al. Antimicrobial resistance Dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol. Ecol. 92, 1–9 (2016).
Su, J. Q. et al. Antibiotic resistome and its association with bacterial communities during sewage sludge composting. Environ. Sci. Technol. 49, 7356–7363 (2015).
Wan, K. et al. Organic carbon: An overlooked factor that determines the antibiotic resistome in drinking water sand filter biofilm. Environ. Int. 125, 117–124 (2019).
Wang, B., Li, G., Cai, C., Zhang, J. & Liu, H. Assessing the safety of thermally processed penicillin mycelial dreg following the soil application: Organic matter's maturation and antibiotic resistance genes. Sci. Total Environ. 636, 1463–1469 (2018).
Wang, F. et al. Influence of soil characteristics and proximity to Antarctic research stations on abundance of antibiotic resistance genes in soils. Environ. Sci. Technol. 50, 12621–12629 (2016).
Wang, F. et al. Long-term effect of different fertilization and cropping systems on the soil antibiotic resistome. Environ. Sci. Technol. 52, 13037–13046 (2018).
Wang, F. H. et al. High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation. Environ. Sci. Technol. 48, 9079–9085 (2014).
Wang, H. T. et al. Effects of arsenic on gut microbiota and its biotransformation genes in earthworm Metaphire sieboldi. Environ. Sci. Technol. acs.est.8b06695 (2019) doi:10.1021/acs.est.8b06695
Waseem, H. et al. Contributions and challenges of high throughput qPCR for determining antimicrobial resistance in the environment: a critical review. Molecules 24, 163 (2019).
Wolters, B. et al. Soil amendment with sewage sludge affects soil prokaryotic community composition, mobilome and resistome. FEMS Microbiol. Ecol. 95, (2018).
Xiang, Q. et al. Spatial and temporal distribution of antibiotic resistomes in a peri-urban area is associated significantly with anthropogenic activities. Environ. Pollut. 235, 525–533 (2018).
Xie, W. Y. et al. Long-term effects of manure and chemical fertilizers on soil antibiotic resistome. Soil Biol. Biochem. 122, 111–119 (2018).
Xie, W. Y. et al. Long-term impact of field applications of sewage sludge on soil antibiotic resistome. Environ. Sci. Technol. 50, 12602–12611 (2016).
Yang, L. et al. Application of biosolids drives the diversity of antibiotic resistance genes in soil and lettuce at harvest. Soil Biol. Biochem. 122, 131–140 (2018).
Zhang, Q. et al. Species-specific response of the soil collembolan gut microbiome and resistome to soil oxytetracycline pollution. Sci. Total Environ. 668, 1183–1190 (2019).
Zhang, Y. J. et al. Salinity as a predominant factor modulating the distribution patterns of antibiotic resistance genes in ocean and river beach soils. Sci. Total Environ. 668, 193–203 (2019).
Zhao, Y. et al. AsChip: A high-throughput qPCR chip for comprehensive profiling of genes linked to microbial cycling of arsenic. Environ. Sci. Technol. 53, 798–807 (2019).
Zhao, Y. et al. Evidence for co-selection of antibiotic resistance genes and mobile genetic elements in metal polluted urban soils. Sci. Total Environ. 656, 512–520 (2019).
Zhou, X., Qiao, M., Su, J. Q. & Zhu, Y. G. High-throughput characterization of antibiotic resistome in soil amended with commercial organic fertilizers. J. Soils Sediments 19, 641–651 (2019).
Zhou, Z. C. et al. Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments. Environ. Int. 121, 1155–1161 (2018).
Zhu, B., Chen, Q., Chen, S. & Zhu, Y. G. Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced? Environ. Int. 98, 152–159 (2017).
Zhu, D. et al. Antibiotics disturb the microbiome and increase the incidence of resistance genes in the gut of a common soil collembolan. Environ. Sci. Technol. 52, 3081–3090 (2018).
Zhu, D. et al. Exposure of a soil collembolan to Ag nanoparticles and AgNO3 disturbs its associated microbiota and lowers the incidence of antibiotic resistance genes in the gut. Environ. Sci. Technol. 52, 12748–12756 (2018).
Zhu, D. et al. Land use influences antibiotic resistance in the microbiome of soil collembolans Orchesellides sinensis. Environ. Sci. Technol. 52, 14088–14098 (2018).
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