Enteric pathogens and Carbapenem resistance genes are widespread in the fecal contaminated soils of cattle farms in the United States
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Aanderud, 2018, Stoichiometric shifts in soil C:N:P promote bacterial taxa dominance, maintain biodiversity, and deconstruct community assemblages, Front. Microbiol., 9, 10.3389/fmicb.2018.01401
An, 2018, Tracking antibiotic resistome during wastewater treatment using high throughput quantitative PCR, Environ. Int., 117, 10.1016/j.envint.2018.05.011
Anderson, 2008, A new method for non-parametric multivariate analysis of variance, Austral. Ecol., 26, 32, 10.1046/j.1442-9993.2001.01070.x
Baker-Austin, 2006, Co-selection of antibiotic and metal resistance, Trends Microbiol., 14, 176, 10.1016/j.tim.2006.02.006
Barbera, 2019, EPA-ng: massively parallel evolutionary placement of genetic sequences, Syst. Biol., 68, 365, 10.1093/sysbio/syy054
Bolyen, 2018, Reproducible, interactive, scalable, and extensible microbiome data science using QIIME2, Nat. Biotechnol., 37, 852, 10.1038/s41587-019-0209-9
Bonardi, 2019, Carbapenemase-producing bacteria in food-producing animals, wildlife and environment: a challenge for human health, Italian J. Food Saf., 8, 7956
Cadena, 2018, Tetracycline and sulfonamide antibiotic resistance genes in soils from nebraska organic farming operations, Front. Microbiol., 9, 10.3389/fmicb.2018.01283
Callahan, 2016, DADA2: High-resolution sample inference from Illumina amplicon data, Nat. Methods, 13, 581, 10.1038/nmeth.3869
Cantón, 2011, Co-resistance: an opportunity for the bacteria and resistance genes, Curr. Opin. Pharmacol., 11, 477, 10.1016/j.coph.2011.07.007
Chen, 2019, Loss of soil microbial diversity exacerbates spread of antibiotic resistance, Soil Ecol. Lett., 1, 3, 10.1007/s42832-019-0011-0
Cheng, 2013, Abundance and persistence of antibiotic resistance genes in livestock farms: a comprehensive investigation in eastern China, Environ. Int., 61, 1, 10.1016/j.envint.2013.08.023
Czech, 2019, Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples, PLoS One, 14
D’Costa, 2011, Antibiotic resistance is ancient, Nature, 477, 457, 10.1038/nature10388
Davies, 2010, Origins and Evolution of Antibiotic Resistance, Microbiol. Mol. Biol. R, 74, 417, 10.1128/MMBR.00016-10
Djordjevic, 2013, Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota, Front. Microbiol., 4, 10.3389/fmicb.2013.00086
Douglas, 2020, PICRUSt2 for prediction of metagenome functions, Nat. Biotechnol., 38, 685, 10.1038/s41587-020-0548-6
Economou, 2015, Agriculture and food animals as a source of antimicrobial- resistant bacteria, Infect. Drug Resist., 8, 49, 10.2147/IDR.S55778
Elmund, 1971, Role of excreted chlortetracycline in modifying the decomposition process in feedlot waste, B Environ. Contam. Tox., 6, 129, 10.1007/BF01540093
Empadinhas, 2004, A gene from the mesophilic bacterium dehalococcoides ethenogenes encodes a novel mannosylglycerate synthase, J. Bacteriol., 186, 4075, 10.1128/JB.186.13.4075-4084.2004
Fair, 2014, Antibiotics and bacterial resistance in the 21st century, Perspect. Medicin. Chem., 6, 25, 10.4137/PMC.S14459
Forsberg, 2012, The shared antibiotic resistome of soil bacteria and human pathogens, Science, 337, 1107, 10.1126/science.1220761
Ghanbari, 2019, The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline, Sci. Rep.-UK, 9, 4062, 10.1038/s41598-019-40496-8
González-Plaza, 2019, Antibiotic-manufacturing sites are hot-spots for the release and spread of antibiotic resistance genes and mobile genetic elements in receiving aquatic environments, Environ. Int., 130, 10.1016/j.envint.2019.04.007
Green, 2014, Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples, Appl. Environ. Microbiol., 80, 3086, 10.1128/AEM.04137-13
Guan, 2003, Pathogen survival in swine manure environments and transmission of human enteric illness–a review, J. Environ. Qual., 32, 383, 10.2134/jeq2003.3830
Haugland, 2005, Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis, Water Res., 39, 559, 10.1016/j.watres.2004.11.011
Healy-Profitós, 2016, Neighborhood diversity of potentially pathogenic bacteria in drinking water from the city of Maroua, Cameroon, J. Water Health, 14, 559, 10.2166/wh.2016.204
Hoar, 2001, An examination of risk factors associated with beef cattle shedding pathogens of potential zoonotic concern, Epidemiol. Infect., 127, 147, 10.1017/S0950268801005726
Hsu, 2014, Prevalence of sulfonamide-resistant bacteria, resistance genes and integron-associated horizontal gene transfer in natural water bodies and soils adjacent to a swine feedlot in northern Taiwan, J. Hazard. Mater., 277, 34, 10.1016/j.jhazmat.2014.02.016
Huijbers, 2015, Role of the environment in the transmission of antimicrobial resistance to humans: a review, Environ. Sci. Technol., 49, 11993, 10.1021/acs.est.5b02566
Hurst, 2019, Trends in antimicrobial resistance genes in manure blend pits and long-term storage across dairy farms with xomparisons to antimicrobial usage and residual concentrations, Environ. Sci. Technol., 53, 2405, 10.1021/acs.est.8b05702
Ibekwe, 2002, Multiplex fluorogenic real-time PCR for detection and quantification of Escherichia coli O157:H7 in dairy wastewater wetlands, Appl. Environ. Microbiol., 68, 4853, 10.1128/AEM.68.10.4853-4862.2002
Jay-Russell, M. (2013). What is the risk from wild animals in food-borne pathogen contamination of plants? CAB Rev, 8, 040. https://doi.org/10.1079/PAVSNNR20138040.
Jutkina, 2018, Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations, Sci. Total Environ., 616-617, 172, 10.1016/j.scitotenv.2017.10.312
Kahan, 1979, Thienamycin, a new beta-lactam antibiotic I. discovery, taxonomy, isolation and physical properties, J. Antibiot. (Tokyo), 32, 1, 10.7164/antibiotics.32.1
Kildare, 2007, 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach, Water Res., 41, 3701, 10.1016/j.watres.2007.06.037
Klase, 2019, The microbiome and antibiotic resistance in integrated fishfarm water: Implications of environmental public health, Sci. Total Environ., 649, 1491, 10.1016/j.scitotenv.2018.08.288
Klous, 2016, Human–livestock contacts and their relationship to transmission of zoonotic pathogens, a systematic review of literature, One Health, 2, 65, 10.1016/j.onehlt.2016.03.001
Kyselková, 2013, Cow excrements enhance the occurrence of tetracycline resistance genes in soil regardless of their oxytetracycline content, Chemosphere, 93, 2413, 10.1016/j.chemosphere.2013.08.058
Lawhorn, 2004, Biosynthesis of the thiamin pyrimidine: the reconstitution of a remarkable rearrangement reaction, Org. Biomol. Chem., 17, 2538, 10.1039/b405429f
Li, 2014, Functional potential of soil microbial communities in the Maize Rhizosphere, PLoS One, 9
Louca, 2018, Efficient comparative phylogenetics on large trees, Bioinformatics, 34, 1053, 10.1093/bioinformatics/btx701
Malaviya, 2012, Continuous butanol production with reduced byproducts formation from glycerol by a hyper producing mutant of Clostridium pasteurianum, Appl. Microbiol. Biotechnol., 93, 1485, 10.1007/s00253-011-3629-0
Mandal, 2015, Analysis of composition of microbiomes: a novel method for studying microbial composition, Microb. Ecol. Health Dis., 26, 27663
Martens, 2002, Microbial production of vitamin B12, Appl. Microbiol. Biotechnol., 58, 275, 10.1007/s00253-001-0902-7
Martin, 2016, The evolving role of coliforms as indicators of unhygienic processing conditions in dairy foods, Front. Microbiol., 7, 1549, 10.3389/fmicb.2016.01549
McDaniel, 2014, Humans and cattle: a review of bovine zoonoses, Vector Borne Zoonotic Dis., 14, 1, 10.1089/vbz.2012.1164
Mieszkin, 2010, Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real-time PCR, J. Appl. Microbiol., 108, 974, 10.1111/j.1365-2672.2009.04499.x
Nesme, 2014, Large- scale metagenomic-based study of antibiotic resistance in the environment, Curr. Biol., 24, 1096, 10.1016/j.cub.2014.03.036
Paulson, 2013, Differential abundance analysis for microbial marker-gene surveys, Nat. Methods, 10, 1200, 10.1038/nmeth.2658
Penakalapati, 2017, Exposure to animal feces and human health: a systematic review and proposed research priorities, Environ. Sci. Technol., 51, 11537, 10.1021/acs.est.7b02811
Pérez-Valera, 2019, Native soil microorganisms hinder the soil enrichment with antibiotic resistance genes following manure applications, Sci. Rep., 9, 6760, 10.1038/s41598-019-42734-5
Potter, 2016, The rapid spread of carbapenem-resistant Enterobacteriaceae, Drug Resist. Updat., 29, 30, 10.1016/j.drup.2016.09.002
Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic. Acids. Res., 41, D590, 10.1093/nar/gks1219
Queenan, 2007, Carbapenemases: the Versatile β-Lactamases, Clin. Microbiol. Rev., 20, 440, 10.1128/CMR.00001-07
2019
Rådström, 1991, Genetic analyses of sulfonamide resistance and its dissemination in gram-negative bacteria illustrate new aspects of R plasmid evolution, Antimicrob. Agents Chemother., 35, 1840, 10.1128/AAC.35.9.1840
Ransom-Jones, 2017, Lignocellulose-degrading microbial communities in landfill sites represent a repository of unexplored biomass-degrading diversity, Msphere, 2, e00300, 10.1128/mSphere.00300-17
Robinson, 2016, Antibiotic resistance is the quintessential one health issue, Trans. R. Soc. Trop. Med. Hyg., 110, 377, 10.1093/trstmh/trw048
Seiler, 2012, Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture, Front. Microbiol., 3, 339, 10.3389/fmicb.2012.00399
Simon, 2017, Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats, ISME J., 11, 1483, 10.1038/ismej.2016.198
Slobodkin, 2014, The family peptostreptococcaceae, 291
Streit, 2003, Biotin in microbes, the genes involved in its biosynthesis, its biochemical role and perspectives for biotechnological production, Appl. Microbiol. Biotechnol., 61, 21, 10.1007/s00253-002-1186-2
Subirats, 2017, Real-time PCR assays for the detection and quantification of carbapenemase genes (bla KPC, bla NDM, and bla OXA-48) in environmental samples, Environ. Sci. Pollut. Res. Int., 24, 6710, 10.1007/s11356-017-8426-6
Tyrrell, 2019, Antibiotic resistance in grass and soil, Biochem. Soc. Trans., 47, 477, 10.1042/BST20180552
1995
USDA. (2016). USDA “One Health” Approach – Fact Sheet. Retrieved from https://www.usda.gov/sites/default/files/documents/fact-sheet-one-health-06-16-2016.pdf.
2011
2017
Vikram, 2018, Functional blaKPC-2 sequences are present in U.S. beef cattle feces regardless of antibiotic use, Foodborne Pathog. Dis., 15, 444, 10.1089/fpd.2017.2406
Wang, 2015, Antibiotic resistance genes in manure-amended soil and vegetables at harvest, J. Hazard. Mater., 299, 215, 10.1016/j.jhazmat.2015.05.028
Webb, 2016, Carbapenem-resistant bacteria recovered from faeces of dairy cattle in the high plains region of the USA, PLoS One, 11, 10.1371/journal.pone.0147363
Wein, 2019, Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance, Nat. Commun., 10, 2595, 10.1038/s41467-019-10600-7
Winkelmann, 2002, Microbial siderophore-mediated transport, Biochem. Soc. Trans., 30, 691, 10.1042/bst0300691
Wittum, 2010, CTX-M-type extended-spectrum β-lactamases present in Escherichia coli from the feces of cattle in Ohio, United States, Foodborne Pathog. Dis., 7, 1575, 10.1089/fpd.2010.0615
USDA. (2017). Death loss in U.S. cattle and calves due to predator and nonpredator causes, 2015. Retrieved from https://www.aphis.usda.gov/animal_health/nahms/general/downloads/cattle_calves_deathloss_2015.pdf.
World Organization for Animal Health (OIE). (2015). OIE list of antimicrobial agents of veterinary medicine 2015. Retrieved from https://www.oie.int/fileadmin/Home/eng/Our_scientific_expertise/docs/pdf/Eng_OIE_Lis t_antimicrobials_May2015.pdf.
Xie, 2017, Antibiotics and antibiotic resistance from animal manures to soil: a review, Eur. J. Soil Sci., 69, 181, 10.1111/ejss.12494
Ye, 2009, A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes, PLoS Comput. Biol., 5, 10.1371/journal.pcbi.1000465
Yutin, 2013, A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia, Environ. Microbiol., 15, 2631, 10.1111/1462-2920.12173