Distribution and Quantification of Antibiotic Resistant Genes and Bacteria across Agricultural and Non-Agricultural Metagenomes

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Durso, Lisa M ^a   Miller, Daniel N ^a   Wienhold, Brian J ^a  

^a USDA Agricultural Research Service Lincoln Nebraska   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BETA LACTAM ANTIBIOTIC; BETA LACTAMASE; MULTIDRUG RESISTANCE PROTEIN; QUINOLINE DERIVED ANTIINFECTIVE AGENT; TETRACYCLINE; VANCOMYCIN;

AGRICULTURAL SPECIES; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENE; BACTERIAL VIRULENCE; BACTERIUM IDENTIFICATION; BETA LACTAMASE GENE; CONCENTRATION RESPONSE; CONTROLLED STUDY; DRUG EFFECT; FOOD CHAIN; GENE FUNCTION; GENE LOCATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; HETEROZYGOTE; MARINE ENVIRONMENT; METAGENOME; MICROBIAL COMMUNITY; MULTIDRUG RESISTANT EFFLUX PUMP GENE; NONHUMAN; QUANTITATIVE ANALYSIS; RESISTANCE TO ANTIBIOTIC AND TOXIC COMPOUND GENE; SPECIES HABITAT;

AGRICULTURE; ANIMALS; ANTI-BACTERIAL AGENTS; BACTERIA; BETA-LACTAMASES; CROPS, AGRICULTURAL; DRUG RESISTANCE, MICROBIAL; ECOLOGY; ECOSYSTEM; FLUOROQUINOLONES; FOOD CHAIN; GENES, BACTERIAL; HUMANS; METAGENOME; METAGENOMICS; PRINCIPAL COMPONENT ANALYSIS; TETRACYCLINE; VANCOMYCIN;

ANIMALIA;

EID: 84868318290     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048325     Document Type: Article

References (31)

1. Collignon P, Powers JH, Chiller TM, Aidara-Kane A, Aarestrup AFM, (2009) World Health Organization ranking of antimicrobials according to their importance in human medicine: a critical step for developing risk management strategies for the use of antimicrobials in food production animals. Clin Infect Dis 49: 132-141.
2. Crippen TL, Poole TL, (2009) Conjugative transfer of plasmid-located antibiotic resistance genes within the gastrointestinal tract of lesser mealworm larvae, Alphitobius diaperinius (Coleoptera: Tenebrionidae). Foodborne Pathog Dis 7: 907-915.
3. Schjørring S, Krogfelt K (2010) Assessment of bacterial antibiotic resistance transfer in the gut. Int J Microbiol. doi:10.1155/2011/312956.
4. Stecher B, Denzler R, Maier L, Bernet F, Sanders MJ, et al. (2012) Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proc Natl Acad Sci U S A 109: 1269-1274.
5. Teuber M, (2001) Veterinary use and antibiotic resistance. Curr Opin Microbiol 4: 493-499.
6. Brichta-Harhay DM, Arthur TM, Bosilevac JM, Kalchayanand N, Shackelford SD, et al. (2001) Diversity of multidrug-resistant Salmonella enterica strains associated with cattle at harvest in the United States. Appl Environ Microbiol 77: 1783-1796.
7. Haley CA, Dargatz DA, Bush EJ, Erdman MM, Fedorka-Cray PJ, (2012) Salmonella Prevalence and antimicrobial susceptibility from the National Animal Health Monitoring System Swine 2000 and 2006 studies. J Food Prot 75: 428-436.
8. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, et al. (2005) Comparative metagenomics of microbial communities. Science 208: 554-557.
9. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, et al. (2008) Functional metagenomic profiling of nine biomes. Nature 452: 629-633.
10. Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, et al. (2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 4: 198.
11. Durso LM, Harhay GP, Bono JL, Smith TPL, (2011) Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach. J Microbiol Methods 84: 278-282.
12. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II global ocean sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
13. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, et al. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560-565.
14. Brulc JM, Antonopoulos DA, Berg Miller ME, Wilson MK, Yannarell AC, et al. (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 106: 1948-1953.
15. Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, et al. (2008) Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 3: e2945.
16. Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, et al. (2010) Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME J 5: 639-649.
17. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. (2006) The marine viromes of four oceanic regions. PLoS Biol 4: e368.
18. Ng C, DeMaere MZ, Williams TJ, Lauro FM, Raftery M, et al. (2010) Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica. ISME J 4: 1002-1019.
19. Jung JY, Lee SH, Kim JM, Park MS, Bae J, et al. (2011) Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl Environ Microbiol 77: 2264-2274.
20. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14: 169-181.
21. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The Metagenomics RAST server- A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
22. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-5702.
23. Raphael E, Wong LK, Riley LW, (2011) Extended-spectrum beta-lactamase gene sequences in Gram-negative saprophytes on retail organic and nonorganic spinach. Appl. Environ Microbiol 77: 1601-1607.
24. Thaller MC, Migliore L, Marquez C, Tapia W, Ceden V, et al. (2010) Tracking acquired antibiotic resistance in commensal bacterial fo Galapagos Land iguanas: No Man, No Resistance. PLoS ONE 5(2): e8989 doi:10.1371/journal.pone.0008989.
25. Collingnon P, Angulo FJ, (2006) Fluoroquinolone-resistant Escherichia coli: Food for thought. J Clin Infect Dis 194: 8-10.
26. Empey WA, Scott WJ (1939) Investigations on chilled beef. part I.-microbial contamination acquired in the meatworks. Council for Scientific and Industrial Research, Commonweatlh of Austrailia Bulletin no.126. Melbourne, Australia.
27. Arthur TM, Bosilevac JM, Brichta-Harhay DM, Kalchayanand N, King DA, et al. (2008) Source tracking of Escherichia coli O157:H7 and Salmonella contamination in the lairage environment at commercial U.S. beef processing plants and identification of an effective intervention. J Food Prot 71: 1752-1760.
28. Durso LM, Harhay GP, Smith TP, Bono JL, DeSantis TZ, et al. (2011) Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces. Foodborne Pathog Dis 8: 647-649.
29. Wright GD, (2007) The antibiotic resistome: The nexus of chemical and genetic diversity. Nat Rev Microbiol 5: 175-186.
30. D'Costa VM, King CE, Kalan L, Morar M, Sung WWL, et al. (2011) Antibiotic resistance in ancient. Nature 477: 457-461.
31. Dantas G, Sommer MOA, Oluwasegun RD, Church GM, (2008) Bacteria subsisting on antibiotics. Science 320: 100-103.