-
1
-
-
2442449227
-
Genomic islands in pathogenic and environmental microorganisms
-
[1] Dobrindt, U., Hochhut, B., Hentschel, U., Hacker, J., Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2 (2004), 414–424.
-
(2004)
Nat Rev Microbiol
, vol.2
, pp. 414-424
-
-
Dobrindt, U.1
Hochhut, B.2
Hentschel, U.3
Hacker, J.4
-
2
-
-
84891372586
-
The role of aquatic ecosystems as reservoirs of antibiotic resistance
-
[2] Marti, E., Variatza, E., Balcázar, J.L., The role of aquatic ecosystems as reservoirs of antibiotic resistance. Trends Microbiol 22 (2014), 36–41.
-
(2014)
Trends Microbiol
, vol.22
, pp. 36-41
-
-
Marti, E.1
Variatza, E.2
Balcázar, J.L.3
-
3
-
-
23944506044
-
Mobile genetic elements: the agents of open source evolution
-
[3] Frost, L.S., Leplae, R., Summers, A.O., Toussaint, A., Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3 (2005), 722–732.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 722-732
-
-
Frost, L.S.1
Leplae, R.2
Summers, A.O.3
Toussaint, A.4
-
4
-
-
84875939802
-
Extended spectrum β-lactamases, carbapenemases and mobile genetic elements responsible for antibiotics resistance in Gram-negative bacteria
-
[4] El Salabi, A., Walsh, T.R., Chouchani, C., Extended spectrum β-lactamases, carbapenemases and mobile genetic elements responsible for antibiotics resistance in Gram-negative bacteria. Crit Rev Microbiol 39 (2013), 113–122.
-
(2013)
Crit Rev Microbiol
, vol.39
, pp. 113-122
-
-
El Salabi, A.1
Walsh, T.R.2
Chouchani, C.3
-
5
-
-
79952306616
-
Antibiotic resistance genes in the bacteriophage DNA fraction of environmental samples
-
e17549
-
[5] Colomer-Lluch, M., Jofre, J., Muniesa, M., Antibiotic resistance genes in the bacteriophage DNA fraction of environmental samples. PLoS ONE, 6, 2011 e17549.
-
(2011)
PLoS ONE
, vol.6
-
-
Colomer-Lluch, M.1
Jofre, J.2
Muniesa, M.3
-
6
-
-
84886426225
-
Prevalence of antibiotic resistance genes and bacterial community composition in a river influenced by a wastewater treatment plant
-
e78906
-
[6] Marti, E., Jofre, J., Balcázar, J.L., Prevalence of antibiotic resistance genes and bacterial community composition in a river influenced by a wastewater treatment plant. PLoS ONE, 8, 2013 e78906.
-
(2013)
PLoS ONE
, vol.8
-
-
Marti, E.1
Jofre, J.2
Balcázar, J.L.3
-
7
-
-
84943580979
-
METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
-
[7] Bengtsson-Palme, J., Hartmann, M., Eriksson, K.M., Pal, C., Thorell, K., Larsson, D.G., et al. METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Mol Ecol Resour 15 (2015), 1403–1414.
-
(2015)
Mol Ecol Resour
, vol.15
, pp. 1403-1414
-
-
Bengtsson-Palme, J.1
Hartmann, M.2
Eriksson, K.M.3
Pal, C.4
Thorell, K.5
Larsson, D.G.6
-
8
-
-
75549086985
-
ACLAME: A CLAssification of Mobile genetic Elements, update 2010
-
[8] Leplae, R., Lima-Mendez, G., Toussaint, A., ACLAME: A CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res 38:Database issue (2010), D57–61.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.Database issue
, pp. D57-61
-
-
Leplae, R.1
Lima-Mendez, G.2
Toussaint, A.3
-
9
-
-
80052549504
-
Integrative analysis of environmental sequences using MEGAN4
-
[9] Huson, D.H., Mitra, S., Ruscheweyh, H.J., Weber, N., Schuster, S.C., Integrative analysis of environmental sequences using MEGAN4. Genome Res 21 (2011), 1552–1560.
-
(2011)
Genome Res
, vol.21
, pp. 1552-1560
-
-
Huson, D.H.1
Mitra, S.2
Ruscheweyh, H.J.3
Weber, N.4
Schuster, S.C.5
-
10
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
[10] Zerbino, D.R., Birney, E., Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18 (2008), 821–829.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
11
-
-
84880509968
-
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
-
[11] Modi, S.R., Lee, H.H., Spina, C.S., Collins, J.J., Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499 (2013), 219–222.
-
(2013)
Nature
, vol.499
, pp. 219-222
-
-
Modi, S.R.1
Lee, H.H.2
Spina, C.S.3
Collins, J.J.4
-
12
-
-
84941729287
-
BiMat: a MATLAB package to facilitate the analysis of bipartite networks
-
[12] Flores, C.O., Poisot, T., Valverde, S., Weitz, J.S., BiMat: a MATLAB package to facilitate the analysis of bipartite networks. Methods Ecol Evol 7 (2016), 127–132.
-
(2016)
Methods Ecol Evol
, vol.7
, pp. 127-132
-
-
Flores, C.O.1
Poisot, T.2
Valverde, S.3
Weitz, J.S.4
-
13
-
-
84925021592
-
Fast and sensitive protein alignment using DIAMOND
-
[13] Buchfink, B., Xie, C., Huson, D.H., Fast and sensitive protein alignment using DIAMOND. Nat Methods 12 (2015), 59–60.
-
(2015)
Nat Methods
, vol.12
, pp. 59-60
-
-
Buchfink, B.1
Xie, C.2
Huson, D.H.3
-
14
-
-
58149183697
-
ARDB—Antibiotic Resistance Genes Database
-
[14] Liu, B., Pop, M., ARDB—Antibiotic Resistance Genes Database. Nucleic Acids Res 37:Database issue (2009), D443–7.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.Database issue
, pp. D443-7
-
-
Liu, B.1
Pop, M.2
-
15
-
-
84879017399
-
The Comprehensive antibiotic resistance database
-
[15] McArthur, A.G., Waglechner, N., Nizam, F., Yan, A., Azad, M.A., Baylay, A.J., et al. The Comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57 (2013), 3348–3357.
-
(2013)
Antimicrob Agents Chemother
, vol.57
, pp. 3348-3357
-
-
McArthur, A.G.1
Waglechner, N.2
Nizam, F.3
Yan, A.4
Azad, M.A.5
Baylay, A.J.6
-
16
-
-
84890923814
-
Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment
-
[16] Chao, Y., Ma, L., Yang, Y., Ju, F., Zhang, X.-X., Wu, W.-M., et al. Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment. Sci Rep, 3, 2013, 3550.
-
(2013)
Sci Rep
, vol.3
, pp. 3550
-
-
Chao, Y.1
Ma, L.2
Yang, Y.3
Ju, F.4
Zhang, X.-X.5
Wu, W.-M.6
-
17
-
-
84945484378
-
Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes
-
[17] Li, B., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J.M., et al. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J 9 (2015), 2490–2502.
-
(2015)
ISME J
, vol.9
, pp. 2490-2502
-
-
Li, B.1
Yang, Y.2
Ma, L.3
Ju, F.4
Guo, F.5
Tiedje, J.M.6
-
18
-
-
84921632491
-
Improved annotation of antibiotic resistance determinants reveals microbial resistome cluster by ecology
-
[18] Gibson, M.K., Forsberg, K.J., Dantas, G., Improved annotation of antibiotic resistance determinants reveals microbial resistome cluster by ecology. ISME J 9 (2015), 207–216.
-
(2015)
ISME J
, vol.9
, pp. 207-216
-
-
Gibson, M.K.1
Forsberg, K.J.2
Dantas, G.3
-
19
-
-
77955902981
-
Ab initio gene identification in metagenomic sequences
-
[19] Zhu, W., Lomsadze, A., Borodovsky, M., Ab initio gene identification in metagenomic sequences. Nucleic Acids Res, 38, 2010, e132.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. e132
-
-
Zhu, W.1
Lomsadze, A.2
Borodovsky, M.3
-
20
-
-
84855245603
-
Antibiotics in feed induce prophages in swine fecal microbiomes
-
[20] Allen, H.K., Looft, T., Bayles, D.O., Humphrey, S., Levine, U.Y., Alt, D., et al. Antibiotics in feed induce prophages in swine fecal microbiomes. MBio, 2, 2011, e00260-11.
-
(2011)
MBio
, vol.2
, pp. e00260-11
-
-
Allen, H.K.1
Looft, T.2
Bayles, D.O.3
Humphrey, S.4
Levine, U.Y.5
Alt, D.6
-
21
-
-
40949113443
-
Virus taxonomy—eighth report of the International Committee on Taxonomy of Viruses
-
Elsevier Amsterdam, The Netherlands
-
[21] Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., Ball, L.A., Virus taxonomy—eighth report of the International Committee on Taxonomy of Viruses. 2005, Elsevier, Amsterdam, The Netherlands.
-
(2005)
-
-
Fauquet, C.M.1
Mayo, M.A.2
Maniloff, J.3
Desselberger, U.4
Ball, L.A.5
-
22
-
-
84962182285
-
Virome-associated antibiotic-resistance genes in an experimental aquaculture facility
-
fiw003 [pii]
-
[22] Colombo, S., Arioli, S., Guglielmetti, S., Lunelli, F., Mora, D., Virome-associated antibiotic-resistance genes in an experimental aquaculture facility. FEMS Microbiol Ecol, 92, 2016 fiw003 [pii].
-
(2016)
FEMS Microbiol Ecol
, vol.92
-
-
Colombo, S.1
Arioli, S.2
Guglielmetti, S.3
Lunelli, F.4
Mora, D.5
-
23
-
-
0033862706
-
β-Lactamases: which ones are clinically important?
-
[23] Rice, L.B., Bonomo, R.A., β-Lactamases: which ones are clinically important?. Drug Resist Updat 3 (2000), 178–189.
-
(2000)
Drug Resist Updat
, vol.3
, pp. 178-189
-
-
Rice, L.B.1
Bonomo, R.A.2
-
24
-
-
84896913323
-
Class D β-lactamases: are they all carbapenemases?
-
[24] Antunes, N.T., Lamoureaux, T.L., Toch, M., Stewart, N.K., Frase, H., Vakulenko, S.B., Class D β-lactamases: are they all carbapenemases?. Antimicrob Agents Chemother 58 (2014), 2119–2125.
-
(2014)
Antimicrob Agents Chemother
, vol.58
, pp. 2119-2125
-
-
Antunes, N.T.1
Lamoureaux, T.L.2
Toch, M.3
Stewart, N.K.4
Frase, H.5
Vakulenko, S.B.6
-
25
-
-
79957613599
-
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
[25] Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28 (2011), 2731–2739.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
Kumar, S.6
-
26
-
-
79960004119
-
Interactive Tree of Life v2: online annotation and display of phylogenetic trees made easy
-
[26] Letunic, I., Bork, P., Interactive Tree of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39:Web Server issue (2011), W475–8.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.Web Server issue
, pp. W475-8
-
-
Letunic, I.1
Bork, P.2
-
27
-
-
0034077976
-
OXA-24, a novel class D β-lactamase with carbapenemase activity in an Acinetobacter baumannii clinical strain
-
[27] Bou, G., Oliver, A., Martínez-Beltrán, J., OXA-24, a novel class D β-lactamase with carbapenemase activity in an Acinetobacter baumannii clinical strain. Antimicrob Agents Chemother 44 (2000), 1556–1561.
-
(2000)
Antimicrob Agents Chemother
, vol.44
, pp. 1556-1561
-
-
Bou, G.1
Oliver, A.2
Martínez-Beltrán, J.3
-
28
-
-
80054821662
-
Hydrolytic mechanism of OXA-58 enzyme, a carbapenem-hydrolyzing class D β-lactamase from Acinetobacter baumannii
-
[28] Verma, V., Testero, S.A., Amini, K., Wei, W., Liu, J., Balachandran, N., et al. Hydrolytic mechanism of OXA-58 enzyme, a carbapenem-hydrolyzing class D β-lactamase from Acinetobacter baumannii. J Biol Chem 286 (2011), 37292–37303.
-
(2011)
J Biol Chem
, vol.286
, pp. 37292-37303
-
-
Verma, V.1
Testero, S.A.2
Amini, K.3
Wei, W.4
Liu, J.5
Balachandran, N.6
|