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| SmartChip系統(tǒng)文獻案例 |
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| 瀏覽下列文獻，了解SmartChip Real-Time PCR System在環(huán)境微生物抗生素耐藥基因研究中的應用。 |
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| 醫(yī)院來源樣本中抗生素耐藥基因的追蹤 |
| 醫(yī)院中可能含有大量的耐藥細菌，因此進行常規(guī)監(jiān)測以防止爆發(fā)事件是至關重要的。2013年，一項研究報道，在美國，每年有＞2,000,000例疾病由耐藥細菌造成，＞23,000個死亡病例和這些細菌相關聯(lián)。眾多發(fā)表的研究顯示，利用SmartChip Real-Time PCR System，對醫(yī)院中各個位置來源的樣本進行抗生素耐藥性追蹤，包括空調系統(tǒng)濾芯、醫(yī)院廢水、處理廠等。 |
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| 有報道，利用SmartChip系統(tǒng)對來自醫(yī)院、農場、城市、鄉(xiāng)村的空調濾芯進行了ARGs分析（Li, Y et al. 2019）。使用一個包含296個ARGs引物的SmartChip檢測方案，研究人員從所有類型樣本中共檢測到了177個ARGs。在醫(yī)院和農場來源的樣本中檢測到較多的ARGs，分別是146個和154個。這一結果與預期一致，因為抗生素在這些地區(qū)的應用更為廣泛。然而，從鑒定到的ARGs類別來看，不同地點來源的樣本都是相似的。這表明，在醫(yī)院和農場工作的人可能將抗生素耐藥細菌帶回到城市和鄉(xiāng)村中。 |
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| 文獻案例（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). |
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| 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). |
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| 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). |
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| Wang, Q., Wang, P. & Yang, Q. Occurrence and diversity of antibiotic resistance in untreated hospital wastewater. Sci. Total Environ. 621: 990-999 (2018). |
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| 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). |
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| Zhou, Z.-C. et al. Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments. Environ. Int. 121: 1155-1161 (2018). |
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| Zhu, Y.-G. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol. 2, 16270 (2017). |
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| Stedtfeld, R. D. et al. Antimicrobial resistance Dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol. Ecol. 92: 1-9 (2016). |
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| 水體樣本中抗生素耐藥基因的鑒定 |
| 目前，在各種不同的水源中，如未正確處理的廢水，都能夠發(fā)現(xiàn)抗生素耐藥性細菌。這些細菌也可能存在于溪流、江河、湖泊、海洋等自然環(huán)境中。而飲用水也有被污染的風險，對健康造成危害。眾多已發(fā)表的研究利用SmartChip Real-Time PCR System對各種水體樣本進行了抗生素耐藥性分析。 |
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| 在一項研究中，研究人員對來自人的糞便和皮膚樣本、來自污水處理系統(tǒng)的水體樣本和來自河流的水體樣本進行了分析（Zhou et al. 2018）。研究人員使用一個包含296個ARGs引物的SmartChip檢測方案，在人類來源樣本中鑒定了234個特異性ARGs。污水樣本中ARGs豐度是河水樣本的7倍。進一步調查發(fā)現(xiàn)，污水樣本中鑒定到的53個ARGs與人糞便樣本直接相關聯(lián)，表明腸道中的抗生素耐藥細菌與環(huán)境水體中的耐藥細菌存在直接聯(lián)系。 |
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| 另一項來自赫爾辛基大學研究團隊的研究，是利用SmartChip系統(tǒng)對采集自歐洲七國數(shù)十個城市廢水處理廠的水體樣本進行了大規(guī)模qPCR研究，樣本類型包括未經處理的原始廢水樣本和經過處理后排出的水體樣本（Parnanen et al. 2019）。研究人員據(jù)此發(fā)現(xiàn)，抗生素處方率更高的國家，其廢水中更有可能存在ARGs。這項首例跨歐洲的檢測研究為抗生素耐藥性監(jiān)測與追蹤方法開創(chuàng)了先例。 |
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| 文獻案例（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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| Jiao, Y. N. et al. Biomarkers of antibiotic resistance genes during seasonal changes in wastewater treatment systems. Environ. Pollut. 234: 79-87 (2018). |
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| 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). |
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| Liu, L. et al. Large-scale biogeographical patterns of bacterial antibiotic resistome in the waterbodies of China. Environ. Int. 117: 292-299 (2018). |
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| 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). |
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| Zhou, Z. C. et al. Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments. Environ. Int. 121: 1155-1161 (2018). |
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| 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). |
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| 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). |
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| Zhu, Y. G. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol. 2: 16270 (2017). |
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| Zheng, J. et al. High-throughput profiling and analysis of antibiotic resistance genes in East Tiaoxi River, China. Environ. Pollut. 230: 648-654 (2017). |
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| 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). |
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| 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). |
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| Karkman, A. et al. High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. FEMS Microbiol. Ecol. 92: 1-7 (2016). |
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| Lin, W. et al. Can chlorination co-select antibiotic-resistance genes Chemosphere 156: 412-419 (2016). |
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| 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). |
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| Ouyang, W. Y. et al. Increased levels of antibiotic resistance in urban stream of Jiulongjiang River, China. Appl. Microbiol. Biotechnol. 99: 5697-5707 (2015). |
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| 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). |
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| 污水、糞肥樣本中的抗生素耐藥性篩選 |
| 糞肥和污水類樣本中，經常包含抗生素耐藥性細菌。這些細菌可能同時存在于糞肥和污水徑流中，以及一些大量使用有機肥的地方。然后，這些耐藥細菌可能會轉到農作物、農產品中，并進一步進入人體。許多案例已經使用SmartChip Real-Time PCR System對糞肥、污水樣本中的抗生素抗性開展研究。 |
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| 在一項研究中，研究人員分析了漁場中魚腸道內容物（Muziasari et al. 2017）。利用一個包含364引物的方案，該研究團隊使用SmartChip系統(tǒng)鑒定了28個抗生素抗性基因，它們既在魚的糞便中存在，也在漁場的沉積物中存在。盡管在魚類個體之間耐藥性細菌的組成略有不同，但鑒定到的28個抗性基因在所有沉積物樣本中都存在，表明環(huán)境選擇過程的存在。在腸外位置沒有監(jiān)測到抗生素耐藥性基因，如魚鰓位置。 |
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| 文獻案例（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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| Chen, Q. L. et al. Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize. Sci. Total Environ. 645: 1230-1237 (2018). |
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| Xie, W. Y. et al. Long-term effects of manure and chemical fertilizers on soil antibiotic resistome. Soil Biol. Biochem. 122: 111-119 (2018). |
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| 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). |
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| Zhao, Y. et al. Feed additives shift gut microbiota and enrich antibiotic resistance in swine gut. Sci. Total Environ. 621: 1224-1232 (2018). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| Xie, W. Y. et al. Changes in antibiotic concentrations and antibiotic resistome during commercial composting of animal manures. Environ. Pollut. 219: 182-190 (2016). |
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| 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). |
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| Stedtfeld, R. D. et al. Antimicrobial resistance Dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol. Ecol. 92: fiw020 (2016). |
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| Su, J. Q. et al. Antibiotic resistome and its association with bacterial communities during sewage sludge composting. Environ. Sci. Technol. 49: 7356-7363 (2015). |
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| 土壤、污泥、沉積物樣本中的抗生素耐藥性基因研究 |
| 在土壤、沉積物和污泥樣本的抗生素抗性研究中，SmartChip Real-Time PCR System有廣泛的應用。樣本來自各個不同地點。在一些案例中，有收集自大量施用有機肥的農田地區(qū)。還有一些樣本采集自地表被未正確處理的廢水污染過的城市徑流。一些令人興奮的研究發(fā)現(xiàn)，土壤中的金屬污染和耐藥性細菌有關聯(lián)。在這些研究中，SmartChip系統(tǒng)被用于對各類土壤樣本中的抗生素耐藥性基因進行大規(guī)模監(jiān)測。 |
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| 一項發(fā)表的研究，嘗試對北極高緯度地區(qū)土壤中抗生素耐藥基因的驅動因素進行剖析（McCann et al. 2019）。在極地相對偏遠的8個位置收集土壤樣本，研究人員嘗試為背景抗生素耐藥性建立基準，可以用于追蹤其他環(huán)境中抗生素耐藥性的傳播。使用一個包含296對ARGs引物的方案，研究人員通過SmartChip鑒定了131個ARGs，平均每個樣本66個。此外，在所有樣本中，研究人員還鑒定到了39個特異性ARGs，很可能代表了本土的抗生素耐藥性細菌。其他非保守抗生素耐藥基因可能是人源或動物源污染。 |
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| 文獻案例（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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| McCann, C. M. et al. Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems. Environ. Int. 125: 497-504 (2019). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| 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). |
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| Zhou, X. et al. High-throughput characterization of antibiotic resistome in soil amended with commercial organic fertilizers. J. Soils Sediments 19: 641-651 (2019). |
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| 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). |
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| 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). |
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| Hu, H. W. et al. Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes. Environ. Microbiol. 20: 3186-3200 (2018). |
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| 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). |
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| 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). |
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| 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). |
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| Wolters, B. et al. Soil amendment with sewage sludge affects soil prokaryotic community composition, mobilome and resistome. FEMS Microbiol. Ecol. 95: (2018). |
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| 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). |
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| Xie, W. Y. et al. Long-term effects of manure and chemical fertilizers on soil antibiotic resistome. Soil Biol. Biochem. 122: 111-119 (2018). |
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| 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). |
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| 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). |
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| 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). |
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| 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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| Zhou, Z. C. et al. Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments. Environ. Int. 121: 1155-1161 (2018). |
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| Chen, Q. L. et al. Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere. Environ. Sci. Technol. 51: 8149-8157 (2017). |
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| 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). |
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| 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). |
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| 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). |
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| Stedtfeld, R. D. et al. Antimicrobial resistance Dashboard application for mapping environmental occurrence and resistant pathogens. FEMS Microbiol. Ecol. 92: 1-9 (2016). |
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| 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). |
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| 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). |
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