- Antibiotic resistance genes
- mRNA, miRNA, and lncRNA as disease biomarkers
- Pathogen detection in human samples and food
- Genotyping using animal and blood samples
Antibiotic resistance genes in manure and sewage
Manure and sewage samples often contain antibiotic-resistant bacteria. These bacteria may be present in both manure and sewage runoff, as well as in locations where large quantities of organic fertilizer are used. The antibiotic-resistant bacteria can then be transferred to crops and produce, and potentially introduced into humans. Numerous studies have utilized the SmartChip Real-Time PCR System to study antibiotic resistance in manure and sewage samples.
In one study, researchers analyzed the intestinal contents of fish from fish farms (Muziasari et al. 2017). By utilizing a 364-primer panel on the SmartChip system, they identified 28 antibiotic resistance genes that were present in the fish feces and then discovered that those same genes were present in the farm sediments. Although the composition of antibiotic-resistant bacteria varied slightly between individual fish, the same 28 genes were present in all sediment samples, indicating an environmental selection process. No antibiotic-resistant genes were detected outside of the intestines, such as on the gills of the fish.
Chen, Q.-L., An, X.-L., Zheng, B.-X., Ma, Y.-B. & Su, J.-Q. Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize. Sci. Total Environ. 645, 1230–1237 (2018).
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, 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).
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).
Huang, X. et al. Higher temperatures do not always achieve better antibiotic resistance gene removal in anaerobic digestion of swine manure. Appl. Environ. Microbiol. 85, e02878–18 (2019).
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
Lu, X.-M., Li, W.-F. & Li, C.-B. Characterization and quantification of antibiotic resistance genes in manure of piglets and adult pigs fed on different diets. Environ. Pollut. 229, 102–110 (2017).
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. 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).
Qian, X. et al. Diversity, abundance, and persistence of antibiotic resistance genes in various types of animal manure following industrial composting. J. Hazard. Mater. 344, 716–722 (2018).
Stedtfeld, R. D. et al. Antimicrobial resistance Dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol. Ecol. 92, 1–9 (2016).
Stedtfeld, R. D. et al. Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. J. Environ. Manage. 198, 213–220 (2017).
Su, J. Q. et al. Antibiotic resistome and its association with bacterial communities during sewage sludge composting. Environ. Sci. Technol. 49, 7356–7363 (2015).
Tang, M. et al. Abundance and distribution of antibiotic resistance genes in a full-scale anaerobic-aerobic system alternately treating ribostamycin, spiramycin and paromomycin production wastewater. Environ. Geochem. Health (2017). doi:10.1007/s10653-017-9987-5
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, H. et al. The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome. ISME J. 11, 100–111 (2017).
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).
Xie, W.-Y. et al. Changes in antibiotic concentrations and antibiotic resistome during commercial composting of animal manures. Environ. Pollut. 219, 182–190 (2016).
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).
Zhao, Y. et al. Feed additives shift gut microbiota and enrich antibiotic resistance in swine gut. Sci. Total Environ. 621, 1224–1232 (2018).
Zhou, X. et al. Turning pig manure into biochar can effectively mitigate antibiotic resistance genes as organic fertilizer. Sci. Total Environ. 649, 902–908 (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).
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