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SmartChip系统文献案例

浏览下列文献，了解SmartChip Real-Time PCR System在环境微生物抗生素耐药基因研究中的应用。

医院来源样本中抗生素耐药基因的追踪

医院中可能含有大量的耐药细菌，因此进行常规监测以防止爆发事件是至关重要的。2013年，一项研究报道，在美国，每年有＞2,000,000例疾病由耐药细菌造成，＞23,000个死亡病例和这些细菌相关联。众多发表的研究显示，利用SmartChip Real-Time PCR System，对医院中各个位置来源的样本进行抗生素耐药性追踪，包括空调系统滤芯、医院废水、处理厂等。

有报道，利用SmartChip系统对来自医院、农场、城市、乡村的空调滤芯进行了ARGs分析（Li, Y et al. 2019）。使用一个包含296个ARGs引物的SmartChip检测方案，研究人员从所有类型样本中共检测到了177个ARGs。在医院和农场来源的样本中检测到较多的ARGs，分别是146个和154个。这一结果与预期一致，因为抗生素在这些地区的应用更为广泛。然而，从鉴定到的ARGs类别来看，不同地点来源的样本都是相似的。这表明，在医院和农场工作的人可能将抗生素耐药细菌带回到城市和乡村中。

文献案例（Citations）

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).

Li, Y. et al. Prevalence of antibiotic resistance genes in air-conditioning systems in hospitals, farms, and residences. Int. J. Environ. Res. Public Health 16: 683 (2019).

Parnanen, K. M. M. et al. Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Sci. Adv. 5: eaau9124 (2019).

Wang, Q., Wang, P. & Yang, Q. Occurrence and diversity of antibiotic resistance in untreated hospital wastewater. Sci. Total Environ. 621: 990-999 (2018).

Zheng, H. S. et al. Electro-peroxone pretreatment for enhanced simulated hospital wastewater treatment and antibiotic resistance genes reduction. Environ. Int. 115: 70-78 (2018).

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, Y.-G. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol. 2, 16270 (2017).

Stedtfeld, R. D. et al. Antimicrobial resistance Dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol. Ecol. 92: 1-9 (2016).

水体样本中抗生素耐药基因的鉴定

目前，在各种不同的水源中，如未正确处理的废水，都能够发现抗生素耐药性细菌。这些细菌也可能存在于溪流、江河、湖泊、海洋等自然环境中。而饮用水也有被污染的风险，对健康造成危害。众多已发表的研究利用SmartChip Real-Time PCR System对各种水体样本进行了抗生素耐药性分析。

在一项研究中，研究人员对来自人的粪便和皮肤样本、来自污水处理系统的水体样本和来自河流的水体样本进行了分析（Zhou et al. 2018）。研究人员使用一个包含296个ARGs引物的SmartChip检测方案，在人类来源样本中鉴定了234个特异性ARGs。污水样本中ARGs丰度是河水样本的7倍。进一步调查发现，污水样本中鉴定到的53个ARGs与人粪便样本直接相关联，表明肠道中的抗生素耐药细菌与环境水体中的耐药细菌存在直接联系。

另一项来自赫尔辛基大学研究团队的研究，是利用SmartChip系统对采集自欧洲七国数十个城市废水处理厂的水体样本进行了大规模qPCR研究，样本类型包括未经处理的原始废水样本和经过处理后排出的水体样本（Parnanen et al. 2019）。研究人员据此发现，抗生素处方率更高的国家，其废水中更有可能存在ARGs。这项首例跨欧洲的检测研究为抗生素耐药性监测与追踪方法开创了先例。

文献案例（Citations）

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).

Chen, Y. et al. High-throughput profiling of antibiotic resistance gene dynamic in a drinking water river-reservoir system. Water Res. 149: 179-189 (2019).

Parnanen, K. M. M. et al. Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Sci. Adv. 5: eaau9124 (2019).

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).

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).

Jiao, Y. N. et al. Biomarkers of antibiotic resistance genes during seasonal changes in wastewater treatment systems. Environ. Pollut. 234: 79-87 (2018).

Jong, M. C. et al. Co-optimization of sponge-core bioreactors for removing total nitrogen and antibiotic resistance genes from domestic wastewater. Sci. Total Environ. 634: 1417-1423 (2018).

Liu, L. et al. Large-scale biogeographical patterns of bacterial antibiotic resistome in the waterbodies of China. Environ. Int. 117: 292-299 (2018).

Zheng, J. et al. High-throughput profiling of seasonal variations of antibiotic resistance gene transport in a peri-urban river. Environ. Int. 114: 87-94 (2018).

Zhou, Z. C. et al. Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments. Environ. Int. 121: 1155-1161 (2018).

Zhang, M. et al. Co-selection of antibiotic resistance via copper shock loading on bacteria from a drinking water bio-filter. Environ. Pollut. 233: 132-141 (2018).

Zheng, J., Chen, T. & Chen, H. Antibiotic resistome promotion in drinking water during biological activated carbon treatment: Is it influenced by quorum sensing Sci. Total Environ. 612: 1-8 (2018).

Zhu, Y. G. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol. 2: 16270 (2017).

Zheng, J. et al. High-throughput profiling and analysis of antibiotic resistance genes in East Tiaoxi River, China. Environ. Pollut. 230: 648-654 (2017).

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).

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 39: 1595-1605 (2017).

Karkman, A. et al. High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. FEMS Microbiol. Ecol. 92: 1-7 (2016).

Lin, W. et al. Can chlorination co-select antibiotic-resistance genes Chemosphere 156: 412-419 (2016).

Xu, L. et al. High-throughput profiling of antibiotic resistance genes in drinking water treatment plants and distribution systems. Environ. Pollut. 213: 119-126 (2016).

Ouyang, W. Y. et al. Increased levels of antibiotic resistance in urban stream of Jiulongjiang River, China. Appl. Microbiol. Biotechnol. 99: 5697-5707 (2015).

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).

污水、粪肥样本中的抗生素耐药性筛选

粪肥和污水类样本中，经常包含抗生素耐药性细菌。这些细菌可能同时存在于粪肥和污水径流中，以及一些大量使用有机肥的地方。然后，这些耐药细菌可能会转到农作物、农产品中，并进一步进入人体。许多案例已经使用SmartChip Real-Time PCR System对粪肥、污水样本中的抗生素抗性开展研究。

在一项研究中，研究人员分析了渔场中鱼肠道内容物（Muziasari et al. 2017）。利用一个包含364引物的方案，该研究团队使用SmartChip系统鉴定了28个抗生素抗性基因，它们既在鱼的粪便中存在，也在渔场的沉积物中存在。尽管在鱼类个体之间耐药性细菌的组成略有不同，但鉴定到的28个抗性基因在所有沉积物样本中都存在，表明环境选择过程的存在。在肠外位置没有监测到抗生素耐药性基因，如鱼鳃位置。

文献案例（Citations）

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).

Kanger, K. et al. Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard. FEMS Microbiol. Ecol. 96: fiaa006 (2020).

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).

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).

Cheng, J. H. et al. 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).

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).

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).

Chen, Q. L. et al. Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize. Sci. Total Environ. 645: 1230-1237 (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).

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).

Zhao, Y. et al. Feed additives shift gut microbiota and enrich antibiotic resistance in swine gut. Sci. Total Environ. 621: 1224-1232 (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).

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).

Lu, X. M. et al. Characterization and quantification of antibiotic resistance genes in manure of piglets and adult pigs fed on different diets. Environ. Pollut. 229: 102-110 (2017).

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).

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).

Zhu, B. K. et al. Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced Environ. Int. 98: 152-159 (2017).

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).

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: 2137 (2017).

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).

Xie, W. Y. et al. Changes in antibiotic concentrations and antibiotic resistome during commercial composting of animal manures. Environ. Pollut. 219: 182-190 (2016).

Chen, Q. L. 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).

Stedtfeld, R. D. et al. Antimicrobial resistance Dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol. Ecol. 92: fiw020 (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).

土壤、污泥、沉积物样本中的抗生素耐药性基因研究

在土壤、沉积物和污泥样本的抗生素抗性研究中，SmartChip Real-Time PCR System有广泛的应用。样本来自各个不同地点。在一些案例中，有收集自大量施用有机肥的农田地区。还有一些样本采集自地表被未正确处理的废水污染过的城市径流。一些令人兴奋的研究发现，土壤中的金属污染和耐药性细菌有关联。在这些研究中，SmartChip系统被用于对各类土壤样本中的抗生素耐药性基因进行大规模监测。

一项发表的研究，尝试对北极高纬度地区土壤中抗生素耐药基因的驱动因素进行剖析（McCann et al. 2019）。在极地相对偏远的8个位置收集土壤样本，研究人员尝试为背景抗生素耐药性建立基准，可以用于追踪其他环境中抗生素耐药性的传播。使用一个包含296对ARGs引物的方案，研究人员通过SmartChip鉴定了131个ARGs，平均每个样本66个。此外，在所有样本中，研究人员还鉴定到了39个特异性ARGs，很可能代表了本土的抗生素耐药性细菌。其他非保守抗生素耐药基因可能是人源或动物源污染。

文献案例（Citations）

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).

Kanger, K. et al. Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard. FEMS Microbiol. Ecol. 96: fiaa006 (2020).

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. et al. 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).

McCann, C. M. et al. Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems. Environ. Int. 125: 497-504 (2019).

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, H. T. et al. Effects of arsenic on gut microbiota and its biotransformation genes in earthworm Metaphire sieboldi. Environ. Sci. Technol. 53: 3841-3849 (2019).

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. et al. High-throughput characterization of antibiotic resistome in soil amended with commercial organic fertilizers. J. Soils Sediments 19: 641-651 (2019).

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).

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).

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. et al. 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).

Wang, B. et al. 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. Long-term effect of different fertilization and cropping systems on the soil antibiotic resistome. Environ. Sci. Technol. 52: 13037-13046 (2018).

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).

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).

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).

Zhou, Z. C. et al. Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments. Environ. Int. 121: 1155-1161 (2018).

Chen, Q. L. et al. Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere. Environ. Sci. Technol. 51: 8149-8157 (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).

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).

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).

Lin, W., Zhang, M., Zhang, S. & Yu, X. Can chlorination co-select antibiotic-resistance genes Chemosphere 156: 412-419 (2016).

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).

Stedtfeld, R. D. et al. Antimicrobial resistance Dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol. Ecol. 92: 1-9 (2016).

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).

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).

Su, J. Q. et al. Antibiotic resistome and its association with bacterial communities during sewage sludge composting. Environ. Sci. Technol. 49: 7356-7363 (2015).

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).