Functional Screening of Antibiotic Resistance Genes from a Representative Metagenomic Library of Food Fermenting Microbiota

BioMed Research International

Volumn 2014, Issue , 2014, Pages

  Devirgiliis, Chiara ^a   Zinno, Paola ^a   Stirpe, Mariarita ^a,b   Barile, Simona ^a   Perozzi, Giuditta ^a  

^a ISTITUTO NAZIONALE DELLA NUTRIZIONE   (Italy)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; BACTERIUM ISOLATION; CHEESE; DNA EXTRACTION; FERMENTATION; GENETIC SCREENING; LACTIC ACID BACTERIUM; LACTOBACILLUS HELVETICUS; METAGENOMICS; MICROFLORA; MOLECULAR CLONING; NONHUMAN; STREPTOCOCCUS SALIVARIUS; STREPTOCOCCUS THERMOPHILUS; DAIRY PRODUCT; FOOD CONTROL; GENE LIBRARY; GENETICS; METAGENOME; MICROBIOLOGY;

BACTERIA (MICROORGANISMS); LACTOBACILLUS HELVETICUS; STREPTOCOCCUS THERMOPHILUS;

CHEESE; DAIRY PRODUCTS; DRUG RESISTANCE, MICROBIAL; FERMENTATION; FOOD MICROBIOLOGY; GENE LIBRARY; GENETIC TESTING; GENOME, BACTERIAL; METAGENOME; MICROBIOTA;

EID: 84935878291     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/290967     Document Type: Article

References (49)

1. E. B. Hansen, "Commercial bacterial starter cultures for fermented foods of the future, " International Journal of FoodMicrobiology, vol. 78, no. 1-2, pp. 119-131, 2002.
2. W. R. Streit and R. A. Schmitz, "Metagenomic-the key to the uncultured microbes, " Current Opinion in Microbiology, vol. 7, no. 5, pp. 492-498, 2004.
3. R. I. Amann, W. Ludwig, and K. Schleifer, "Phylogenetic identification and in situ detection of individual microbial cells without cultivation, " Microbiological Reviews, vol. 59, no. 1, pp. 143-169, 1995.
4. T. S. Lusk, A. R. Ottesen, J. R. White, M. W. Allard, E. W. Brown, and J. A. Kase, "Characterization of microflora in Latinstyle cheeses by next-generation sequencing technology, " BMC Microbiology, vol. 12, article 254, 2012.
5. K. M. Tuohy, C. Gougoulias, Q. Shen, G. Walton, F. Fava, and P. Ramnani, "Studying the human gut microbiota in the trans-omics era-focus on metagenomics and metabonomics, " Current Pharmaceutical Design, vol. 15, no. 13, pp. 1415-1427, 2009.
6. D. Ercolini, "High-throughput sequencing and metagenomics: Moving forward in the culture-independent analysis of food microbial ecology, " Applied and Environmental Microbiology, vol. 79, no. 10, pp. 3148-3155, 2013.
7. S. A. F. T. van Hijum, E. E. Vaughan, and R. F. Vogel, "Application of state-of-art sequencing technologies to indigenous food fermentations, " Current Opinion in Biotechnology, vol. 24, no. 2, pp. 178-186, 2013.
8. C. Devirgiliis, S. Barile, and G. Perozzi, "Antibiotic resistance determinants in the interplay between food and gut microbiota, " Genes and Nutrition, vol. 6, no. 3, pp. 275-284, 2011.
9. C. Devirgiliis, D. Coppola, S. Barile, B. Colonna, andG. Perozzi, "Characterization of the Tn916 conjugative transposon in a food-borne strain of Lactobacillus paracasei, " Applied and Environmental Microbiology, vol. 75, no. 12, pp. 3866-3871, 2009.
10. L. M. Durso, D. N. Miller, and B. J. Wienhold, "Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non-agricultural metagenomes, " PLoS ONE, vol. 7, no. 11, Article ID e48325, 2012.
11. F. Rossi, L. Rizzotti, G. E. Felis, and S. Torriani, "Horizontal gene transfer among microorganisms in food: current knowledge and future perspectives, " Food Microbiology, vol. 42, pp. 232-243, 2014.
12. D. Ercolini, G. Moschetti, G. Blaiotta, and S. Coppola, "The potential of a polyphasic PCR-DGGE approach in evaluating microbial diversity of natural whey cultures for water-buffalo Mozzarella cheese production: bias of culture-dependent and culture-independent analyses, " Systematic and Applied Microbiology, vol. 24, no. 4, pp. 610-617, 2001.
13. C. Devirgiliis, A. Caravelli, D. Coppola, S. Barile, and G. Perozzi, "Antibiotic resistance and microbial composition along the manufacturing process of Mozzarella di Bufala Campana, " International Journal of Food Microbiology, vol. 128, no. 2, pp. 378-384, 2008.
14. D. Ercolini, F. de Filippis, A. La Storia, and M. Iacono, ""Remake" by high-throughput sequencing of the microbiota involved in the production of water Buffalo mozzarella cheese, " Applied and Environmental Microbiology, vol. 78, no. 22, pp. 8142-8145, 2012.
15. M. L. Diaz-Torres, A. Villedieu, N. Hunt et al., "Determining the antibiotic resistance potential of the indigenous oral microbiota of humans using ametagenomic approach, " FEMSMicrobiology Letters, vol. 258, no. 2, pp. 257-262, 2006.
16. J. H. A. Apajalahti, L. K. Sarkilahti, B. R. E. Maki, J. Pekka Heikkinen, P. H. Nurminen, andW. E. Holben, "Effective recovery of bacterialDNAand percent-guanine-plus-cytosine-based analysis of community structure in the gastrointestinal tract of broiler chickens, " Applied and Environmental Microbiology, vol. 64, no. 10, pp. 4084-4088, 1998.
17. M. Pilhofer, A. P. Bauer, M. Schrallhammer et al., "Characterization of bacterial operons consisting of two tubulins and a kinesin-like gene by the novel Two-Step Gene Walking method, " Nucleic Acids Research, vol. 35, no. 20, article e135, 2007.
18. S. Barile, C. Devirgiliis, and G. Perozzi, "Molecular characterization of a novel mosaic tet(S/M) gene encoding tetracycline resistance in foodborne strains of Streptococcus bovis, " Microbiology, vol. 158, no. 9, pp. 2353-2362, 2012.
19. G. Churchward, "Conjugative transposons and related mobile elements, " in Mobile DNA II, N. Craig, R. Craigie, and M. Gellert, Eds., ASM Press, Washington, DC, USA, 2002.
20. G. Dantas, M. O. Sommer, P. H. Degnan, and A. L. Goodman, "Experimental approaches for defining functional roles of microbes in thehumangut, "Annual ReviewofMicrobiology, vol. 67, pp. 459-475, 2013.
21. T. C. Hazen, A. M. Rocha, and S. M. Techtmann, "Advances in monitoring environmental microbes, " Current Opinion in Biotechnology, vol. 24, no. 3, pp. 526-533, 2013.
22. E. C. Pehrsson, K. J. Forsberg, M. K. Gibson, S. Ahmadi, andG. Dantas, "Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs, " Frontiers in Microbiology, vol. 4, article 145, 2013.
23. C. Devirgiliis, P. Zinno, and G. Perozzi, "pdate on antibiotic resistance in foodborne and species, " Frontiers in Microbiology, vol. 4, p. 301, 2013.
24. F. Clementi and L. Aquilanti, "Recent investigations and updated criteria for the assessment of antibiotic resistance in food lactic acid bacteria, " Anaerobe, vol. 17, no. 6, pp. 394-398, 2011.
25. M. S. Ammor, A. B. Florez, and B. Mayo, "Antibiotic resistance in non-enterococcal lactic acid bacteria and bifidobacteria, " Food Microbiology, vol. 24, no. 6, pp. 559-570, 2007.
26. R. Comunian, E. Daga, I. Dupre et al., "Susceptibility to tetracycline and erythromycin of Lactobacillus paracasei strains isolated fromtraditional Italian fermented foods, " International Journal of Food Microbiology, vol. 138, no. 1-2, pp. 151-156, 2010.
27. M. Nawaz, J. Wang, A. Zhou et al., "Characterization and transfer of antibiotic resistance in lactic acid bacteria fromfermented food products, " Current Microbiology, vol. 62, no. 3, pp. 1081-1089, 2011.
28. A. B. Florez, P. Reimundo, S. Delgado et al., "Genome sequence of Lactococcus garvieae IPLA 31405, a bacteriocin-producing, tetracycline-resistant strain isolated from a raw-milk cheese, " Journal of Bacteriology, vol. 194, no. 18, pp. 5118-5119, 2012.
29. L. Feld, E. Bielak, K. Hammer, andA. Wilcks, "Characterization of a small erythromycin resistance plasmid pLFE1 from the food-isolate Lactobacillus plantarum M345, " Plasmid, vol. 61, no. 3, pp. 159-170, 2009.
30. E. Lopez and J. Blazquez, "Effect of subinhibitory concentrations of antibiotics on intrachromosomal homologous recombination in Escherichia coli, " Antimicrobial Agents and Chemotherapy, vol. 53, no. 8, pp. 3411-3415, 2009.
31. A. Zervosen, E. Sauvage, J. Frere, P. Charlier, and A. Luxen, "Development of new drugs for an old target-the penicillin binding proteins, " Molecules, vol. 17, no. 11, pp. 12478-12505, 2012.
32. K. Poole, "Resistance to β-lactam antibiotics, " Cellular and Molecular Life Sciences, vol. 61, no. 17, pp. 2200-2223, 2004.
33. I. Moric, M. Savic, T. Ilic-Tomic et al., "rRNA Methyltransferases and their role in resistance to antibiotics, " Journal of Medical Biochemistry , vol. 29, pp. 165-174, 2010.
34. K. S. Long, J. Poehlsgaard, C. Kehrenberg, S. Schwarz, and B. Vester, "The Cfr rRNA methyltransferase confers resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A antibiotics, " Antimicrobial Agents and Chemotherapy, vol. 50, no. 7, pp. 2500-2505, 2006.
35. M. W. Vetting, L. P. S. de Carvalho, M. Yu et al., "Structure and functions of the GNAT superfamily of acetyltransferases, " Archives of Biochemistry and Biophysics, vol. 433, no. 1, pp. 212-226, 2005.
36. L. P. Tripathi and R. Sowdhamini, "Genome-wide survey of prokaryotic serine proteases: Analysis of distribution and domain architectures of five serine protease families in prokaryotes, " BMC Genomics, vol. 9, article 549, 2008.
37. B. G. Hall andM. Barlow, "Evolution of the serine β-lactamases: past, present and future, " Drug Resistance Updates, vol. 7, no. 2, pp. 111-123, 2004.
38. R. Mehra-Chaudhary, J. Mick, J. J. Tanner, M. T. Henzl, and L. J. Beamer, "Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens, " Proteins, vol. 79, no. 4, pp. 1215-1229, 2011.
39. G. K. Paterson, D. B. Cone, S. E. Peters, andD. J. Maskell, "The enzyme phosphoglucomutase (Pgm) is required by Salmonella enterica serovar Typhimuriumfor O-antigen production, resistance to antimicrobial peptides and in vivo fitness, " Microbiology, vol. 155, no. 10, pp. 3403-3410, 2009.
40. G. A. McKay, D. E. Woods, K. L. MacDonald, and K. Poole, "Role of phosphoglucomutase of Stenotrophomonas maltophilia in lipopolysaccharide biosynthesis, virulence, and antibiotic resistance, " Infection and Immunity, vol. 71, no. 6, pp. 3068-3075, 2003.
41. J. Mahillon and M. Chandler, "Insertion sequences, " Microbiology and Molecular Biology Reviews, vol. 62, no. 3, pp. 725-774, 1998.
42. B. M. Marshall, D. J. Ochieng, and S. B. Levy, "Commensals: underappreciated reservoir of antibiotic resistance, " Microbe, vol. 4, no. 5, pp. 231-238, 2009.
43. L. A. Old and R. R. B. Russell, "Distribution and activity of IS elements in Streptococcus mutans, " FEMS Microbiology Letters, vol. 287, no. 2, pp. 199-204, 2008.
44. V. Martins dos Santos, M. Muller, and W. M. de Vos, "Systems biology of the gut: the interplay of food, microbiota and host at themucosal interface, " Current Opinion in Biotechnology, vol. 21, no. 4, pp. 539-550, 2010.
45. C. A. Schneider, W. S. Rasband, and K. W. Eliceiri, "NIH Image to ImageJ: 25 years of image analysis, " Nature Methods, vol. 9, no. 7, pp. 671-675, 2012.
46. F. di Cello and R. Fani, "A molecular strategy for the study of natural bacterial communities by PCR-based techniques, " Minerva Biotecnologica, vol. 8, no. 3, pp. 126-134, 1996.
47. J. H. Calvo, R. Osta, and P. Zaragoza, "Quantitative PCR detection of pork in raw and heated ground beef and pate, " Journal of Agricultural and Food Chemistry, vol. 50, no. 19, pp. 5265-5267, 2002.
48. S. I. Fujita, Y. Senda, S. Nakaguchi, and T. Hashimoto, "Multiplex PCR using internal transcribed spacer 1 and 2 regions for rapid detection and identification of yeast strains, " Journal of Clinical Microbiology, vol. 39, no. 10, pp. 3617-3622, 2001.
49. R. M. Lopparelli, B. Cardazzo, S. Balzan, V. Giaccone, and E. Novelli, "Real-time TaqMan polymerase chain reaction detection and quantification of cow DNA in pure water buffalo mozzarella cheese: method validation and its application on commercial samples, " Journal of Agricultural and Food Chemistry, vol. 55, no. 9, pp. 3429-3434, 2007.