-
1
-
-
84949314542
-
New insights in antibiotic resistance of Lactobacillus species from fermented foods
-
Abriouel, H., Casado Muñoz, M.D.C, Lerma, L.L., Montoro, P.B., Bockelmann, W., Pichner, R., Kabisch, J., Cho, G.S., Franz, C.M.A.P., Gálvez, A., Benomar, N., 2015. New insights in antibiotic resistance of Lactobacillus species from fermented foods. Food Res. Int. 78, 465–481. doi:10.1016/j.foodres.2015.09.016
-
(2015)
Food Res. Int.
, vol.78
, pp. 465-481
-
-
Abriouel, H.1
Casado Muñoz, M.D.C.2
Lerma, L.L.3
Montoro, P.B.4
Bockelmann, W.5
Pichner, R.6
Kabisch, J.7
Cho, G.S.8
Franz, C.M.A.P.9
Gálvez, A.10
Benomar, N.11
-
2
-
-
85021256187
-
In silico genomic insights into aspects of food safety and defense mechanisms of a potentially probiotic Lactobacillus pentosus MP-10 isolated from brines of naturally fermented Aloreña green table olives
-
Abriouel, H., Montoro, B.P., Casado Muñoz, M.D.C., Knapp, C.W., Gálvez, A., Benomar, N., 2017. In silico genomic insights into aspects of food safety and defense mechanisms of a potentially probiotic Lactobacillus pentosus MP-10 isolated from brines of naturally fermented Aloreña green table olives. PLoS One. 12, e0176801. doi:10.1371/journal.pone.0176801
-
(2017)
PLoS One
, vol.12
-
-
Abriouel, H.1
Montoro, B.P.2
Casado Muñoz, M.D.C.3
Knapp, C.W.4
Gálvez, A.5
Benomar, N.6
-
3
-
-
34247631733
-
Tetracycline resistance mediated by tet(W), tet(M), and tet(O) genes of Bifidobacterium isolates from humans
-
Aires, J., Doucet-Populaire, F., Butel, M.J., 2007. Tetracycline resistance mediated by tet(W), tet(M), and tet(O) genes of Bifidobacterium isolates from humans. Appl. Environ. Microbiol. 73, 2751–2754. doi:10.1128/AEM.02459-06
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 2751-2754
-
-
Aires, J.1
Doucet-Populaire, F.2
Butel, M.J.3
-
4
-
-
52949139102
-
Analysis of tetracycline resistance tet(W) genes and their flanking sequences in intestinal Bifidobacterium species
-
Ammor, M.S., Flórez, A.B., Álvarez-Martín, P., Margolles, A., Mayo, B., 2008. Analysis of tetracycline resistance tet(W) genes and their flanking sequences in intestinal Bifidobacterium species. J. Antimicrob. Chemother. 62, 688–693. doi:10.1093/jac/dkn280
-
(2008)
J. Antimicrob. Chemother.
, vol.62
, pp. 688-693
-
-
Ammor, M.S.1
Flórez, A.B.2
Álvarez-Martín, P.3
Margolles, A.4
Mayo, B.5
-
5
-
-
85040949299
-
GenBank
-
Benson, D.A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Ostell, J., Pruitt, K.D., Sayers, E.W., 2018. GenBank. Nucleic Acids Res. 46, D41–D47. doi:10.1093/nar/gkx1094
-
(2018)
Nucleic Acids Res.
, vol.46
, pp. D41-D47
-
-
Benson, D.A.1
Cavanaugh, M.2
Clark, K.3
Karsch-Mizrachi, I.4
Ostell, J.5
Pruitt, K.D.6
Sayers, E.W.7
-
6
-
-
85023162253
-
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets
-
Bertelli, C., Laird, M.R., Williams, K.P., Simon Fraser University Research Computing Group, Lau, B.Y., Hoad, G., Winsor, G.L., Brinkman, F.S.L.L., 2017. IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 45, W30–W35. doi:10.1093/nar/gkx343
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. W30-W35
-
-
Bertelli, C.1
Laird, M.R.2
Williams, K.P.3
Simon Fraser University Research Computing Group4
Lau, B.Y.5
Hoad, G.6
Winsor, G.L.7
Brinkman, F.S.L.L.8
-
7
-
-
33750598302
-
Multiple genetic elements carry the tetracycline resistance gene tet(W) in the animal pathogen Arcanobacterium pyogenes
-
Billington, S.J., Jost, B.H., 2006. Multiple genetic elements carry the tetracycline resistance gene tet(W) in the animal pathogen Arcanobacterium pyogenes. Antimicrob. Agents Chemother. 50, 3580–3587. doi:10.1128/AAC.00562-06
-
(2006)
Antimicrob. Agents Chemother.
, vol.50
, pp. 3580-3587
-
-
Billington, S.J.1
Jost, B.H.2
-
8
-
-
0032859055
-
Association of alterations in ParC and GyrA proteins with resistance of clinical isolates of Enterococcus faecium to nine different fluoroquinolones
-
Brisse, S., Fluit, A.D.C., Wagner, U., Heisig, P., Milatovic, D., Verhoef, J., Scheuring, S., Köhrer, K., Schmitz, F.-J., 1999. Association of Alterations in ParC and GyrA Proteins with Resistance of Clinical Isolates of Enterococcus faecium to Nine Different Fluoroquinolones. Antimicrob. Agents Chemother. 43, 2513–2516.
-
(1999)
Antimicrob. Agents Chemother.
, vol.43
, pp. 2513-2516
-
-
Brisse, S.1
Fluit, A.D.C.2
Wagner, U.3
Heisig, P.4
Milatovic, D.5
Verhoef, J.6
Scheuring, S.7
Köhrer, K.8
Schmitz, F.-J.9
-
9
-
-
0018405342
-
Mechanism of aminoglycoside antibiotic resistance in anaerobic bacteria: Clostridium perfringens and Bacteroides fragilis
-
Bryan, L.E., Kowand, S.K., Van Den Elzen, H.M., 1979. Mechanism of aminoglycoside antibiotic resistance in anaerobic bacteria: Clostridium perfringens and Bacteroides fragilis. Antimicrob. Agents Chemother. 15, 7–13.
-
(1979)
Antimicrob. Agents Chemother.
, vol.15
, pp. 7-13
-
-
Bryan, L.E.1
Kowand, S.K.2
Van Den Elzen, H.M.3
-
10
-
-
74049108922
-
BLAST+: architecture and applications
-
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L., 2009. BLAST+: Architecture and applications. BMC Bioinformatics 10, 421. doi:10.1186/1471-2105-10-421
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
11
-
-
85059753645
-
Genus-wide assessment of antibiotic resistance in Lactobacillus spp
-
Campedelli, I., Mathur, H., Salvetti, E., Clarke, S., Rea, M.C., Torriani, S., Ross, R.P., Hill, C., O'Toole, P.W., 2019. Genus-wide assessment of antibiotic resistance in Lactobacillus spp. Appl. Environ. Microbiol. 85, e01738-18. doi:10.1128/AEM.01738-18
-
(2019)
Appl. Environ. Microbiol.
, vol.85
, pp. e01738-18
-
-
Campedelli, I.1
Mathur, H.2
Salvetti, E.3
Clarke, S.4
Rea, M.C.5
Torriani, S.6
Ross, R.P.7
Hill, C.8
O'Toole, P.W.9
-
12
-
-
84903160552
-
In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing
-
Carattoli, A., Zankari, E., Garciá-Fernández, A., Larsen, M.V., Lund, O., Villa, L., Aarestrup, F.M., Hasman, H., 2014. In silico detection and typing of plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing. Antimicrob. Agents Chemother. 58, 3895–3903. doi:10.1128/AAC.02412-14
-
(2014)
Antimicrob. Agents Chemother.
, vol.58
, pp. 3895-3903
-
-
Carattoli, A.1
Zankari, E.2
Garciá-Fernández, A.3
Larsen, M.V.4
Lund, O.5
Villa, L.6
Aarestrup, F.M.7
Hasman, H.8
-
13
-
-
84857188863
-
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
-
Carver, T., Harris, S.R., Berriman, M., Parkhill, J., McQuillan, J.A., 2012. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28, 464–469. doi:10.1093/bioinformatics/btr703
-
(2012)
Bioinformatics
, vol.28
, pp. 464-469
-
-
Carver, T.1
Harris, S.R.2
Berriman, M.3
Parkhill, J.4
McQuillan, J.A.5
-
14
-
-
84928898049
-
Human intestinal mucosa-associated Lactobacillus and Bifidobacterium strains with probiotic properties modulate IL-10, IL-6 and IL-12 gene expression in THP-1 cells
-
Čitar, M., Hacin, B., Tompa, G., Štempelj, M., Rogelj, I., Dolinšek, J., Narat, M., Bogovic Matijašić, B., 2015. Human intestinal mucosa-associated Lactobacillus and Bifidobacterium strains with probiotic properties modulate IL-10, IL-6 and IL-12 gene expression in THP-1 cells. Benef. Microbes 6, 325–336. doi:10.3920/BM2014.0081
-
(2015)
Benef. Microbes
, vol.6
, pp. 325-336
-
-
Čitar, M.1
Hacin, B.2
Tompa, G.3
Štempelj, M.4
Rogelj, I.5
Dolinšek, J.6
Narat, M.7
Bogovic Matijašić, B.8
-
15
-
-
33847403528
-
Antibiotic resistance of lactic acid bacteria and Bifidobacterium spp. isolated from dairy and pharmaceutical products
-
D'’Aimmo, M.R., Modesto, M., Biavati, B., 2007. Antibiotic resistance of lactic acid bacteria and Bifidobacterium spp. isolated from dairy and pharmaceutical products. Int. J. Food Microbiol. 115, 35–42. doi:10.1016/j.ijfoodmicro.2006.10.003
-
(2007)
Int. J. Food Microbiol.
, vol.115
, pp. 35-42
-
-
D'Aimmo, M.R.1
Modesto, M.2
Biavati, B.3
-
16
-
-
80053130409
-
Antibiotic resistance is ancient
-
D'’Costa, V.M., King, C.E., Kalan, L., Morar, M., Sung, W.W.L., Schwarz, C., Froese, D., Zazula, G., Calmels, F., Debruyne, R., Golding, G.B., Poinar, H.N., Wright, G.D., 2011. Antibiotic resistance is ancient. Nature 477, 457–461. doi:10.1038/nature10388
-
(2011)
Nature
, vol.477
, pp. 457-461
-
-
D'Costa, V.M.1
King, C.E.2
Kalan, L.3
Morar, M.4
Sung, W.W.L.5
Schwarz, C.6
Froese, D.7
Zazula, G.8
Calmels, F.9
Debruyne, R.10
Golding, G.B.11
Poinar, H.N.12
Wright, G.D.13
-
17
-
-
0037445763
-
Susceptibility of Lactobacillus spp. to antimicrobial agents
-
Danielsen, M., Wind, A., 2003. Susceptibility of Lactobacillus spp. to antimicrobial agents. Int. J. Food Microbiol. 82, 1–11. doi:10.1016/S0168-1605(02)00254-4
-
(2003)
Int. J. Food Microbiol.
, vol.82
, pp. 1-11
-
-
Danielsen, M.1
Wind, A.2
-
18
-
-
77956193448
-
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement
-
Darling, A.E., Mau, B., Perna, N.T., 2010. progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5, e11147. doi:10.1371/journal.pone.0011147
-
(2010)
PLoS One
, vol.5
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
19
-
-
20044385075
-
Antibiotic susceptibility of Lactobacillus and Bifidobacterium species from the human gastrointestinal tract
-
Delgado, S., Flórez, A.B., Mayo, B., 2005. Antibiotic susceptibility of Lactobacillus and Bifidobacterium species from the human gastrointestinal tract. Curr. Microbiol. 50, 202–207. doi:10.1007/s00284-004-4431-3
-
(2005)
Curr. Microbiol.
, vol.50
, pp. 202-207
-
-
Delgado, S.1
Flórez, A.B.2
Mayo, B.3
-
20
-
-
85027975033
-
Lifestyles in transition: evolution and natural history of the genus Lactobacillus
-
Duar, R.M., Lin, X.B., Zheng, J., Martino, M.E., Grenier, T., Pérez-Muñoz, M.E., Leulier, F., Gänzle, M., Walter, J., 2017. Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS Microbiol. Rev. 41, S27–S48. doi:10.1093/femsre/fux030
-
(2017)
FEMS Microbiol. Rev.
, vol.41
, pp. S27-S48
-
-
Duar, R.M.1
Lin, X.B.2
Zheng, J.3
Martino, M.E.4
Grenier, T.5
Pérez-Muñoz, M.E.6
Leulier, F.7
Gänzle, M.8
Walter, J.9
-
21
-
-
85010208913
-
Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria
-
Duranti, S., Lugli, G.A., Mancabelli, L., Turroni, F., Milani, C., Mangifesta, M., Ferrario, C., Anzalone, R., Viappiani, A., van Sinderen, D., Ventura, M., 2017. Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria. Appl. Environ. Microbiol. 83, e02894-16. doi:10.1128/AEM.02894-16
-
(2017)
Appl. Environ. Microbiol.
, vol.83
, pp. e02894-16
-
-
Duranti, S.1
Lugli, G.A.2
Mancabelli, L.3
Turroni, F.4
Milani, C.5
Mangifesta, M.6
Ferrario, C.7
Anzalone, R.8
Viappiani, A.9
van Sinderen, D.10
Ventura, M.11
-
22
-
-
85066956382
-
ECDC/EFSA/EMA second joint report on the integrated analysis of the consumption of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals
-
ECDC/EFSA/EMA, 2017. ECDC/EFSA/EMA second joint report on the integrated analysis of the consumption of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals. EFSA J. 15, 135. doi:10.2903/j.efsa.2017.4872
-
(2017)
EFSA J.
, vol.15
, pp. 135
-
-
ECDC/EFSA/EMA1
-
23
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy, S.R., 2011. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195. doi:10.1371/journal.pcbi.1002195
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Eddy, S.R.1
-
24
-
-
85075008004
-
Opinion of the scientific committee on a request from EFSA related to a generic approach to the safety assessment by EFSA of microorganisms used in food/feed and the production of food/feed additives
-
EFSA, 2005a. Opinion of the Scientific Committee on a request from EFSA related to a generic approach to the safety assessment by EFSA of microorganisms used in food/feed and the production of food/feed additives. EFSA J. 226, 1–12. doi:10.2903/j.efsa.2005.226
-
(2005)
EFSA J.
, vol.226
, pp. 1-12
-
-
EFSA1
-
25
-
-
85043403157
-
Opinion of the scientific panel on additives and products or substances used in animal feed on the updating of the criteria used in the assessment of bacteria for resistance to antibiotics of human or veterinary importance
-
EFSA, 2005b. Opinion of the Scientific Panel on additives and products or substances used in animal feed on the updating of the criteria used in the assessment of bacteria for resistance to antibiotics of human or veterinary importance. EFSA J. 223, 1–12. doi:10.2903/j.efsa.2005.223
-
(2005)
EFSA J.
, vol.223
, pp. 1-12
-
-
EFSA1
-
26
-
-
85069214772
-
Technical guidance – update of the criteria used in the assessment of bacterial resistance to antibiotics of human or veterinarly importance
-
EFSA, 2008. Technical guidance – Update of the criteria used in the assessment of bacterial resistance to antibiotics of human or veterinarly importance. EFSA J. 732, 1–15. doi:10.2903/j.efsa.2008.732
-
(2008)
EFSA J.
, vol.732
, pp. 1-15
-
-
EFSA1
-
27
-
-
85061533831
-
The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016
-
EFSA/ECDC, 2018. The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016. EFSA J. 16, 5182. doi:10.2903/j.efsa.2018.5182
-
(2018)
EFSA J.
, vol.16
, pp. 5182
-
-
EFSA/ECDC1
-
28
-
-
85049829783
-
Guidance on the characterisation of microorganisms used as feed additives or as production organisms
-
EFSA-FEEDAP, 2018. Guidance on the characterisation of microorganisms used as feed additives or as production organisms. EFSA J. 16, 5206. doi:10.2903/j.efsa.2018.5206
-
(2018)
EFSA J.
, vol.16
, pp. 5206
-
-
EFSA-FEEDAP1
-
29
-
-
70349947226
-
Identification and characterization of antibiotic resistance genes in Lactobacillus reuteri and Lactobacillus plantarum
-
Egervärn, M., Roos, S., Lindmark, H., 2009. Identification and characterization of antibiotic resistance genes in Lactobacillus reuteri and Lactobacillus plantarum. J. Appl. Microbiol. 107, 1658–1668. doi:10.1111/j.1365-2672.2009.04352.x
-
(2009)
J. Appl. Microbiol.
, vol.107
, pp. 1658-1668
-
-
Egervärn, M.1
Roos, S.2
Lindmark, H.3
-
30
-
-
10444286823
-
Bile-mediated aminoglycoside sensitivity in Lactobacillus species likely results from increased membrane permeability attributable to cholic acid
-
Elkins, C.A., Mullis, L.B., 2004. Bile-mediated aminoglycoside sensitivity in Lactobacillus species likely results from increased membrane permeability attributable to cholic acid. Appl. Environ. Microbiol. 70, 7200–7209. doi:10.1128/AEM.70.12.7200-7209.2004
-
(2004)
Appl. Environ. Microbiol.
, vol.70
, pp. 7200-7209
-
-
Elkins, C.A.1
Mullis, L.B.2
-
31
-
-
84923919905
-
The European committee on antimicrobial susceptibility testing. Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019
-
(Accessed 6 February 2019)
-
EUCAST, 2019. The European Committee on antimicrobial susceptibility testing. Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. http://www.eucast.org Accessed 06 February 2019
-
(2019)
-
-
EUCAST1
-
32
-
-
0003885913
-
Opinion of the scientific committee on animal nutrition on the criteria for assessing the safety of micro-organisms resistant to antibiotics of human clinical and veterinary importance
-
(Accessed 6 February 2019)
-
European Commission, 2003. Opinion of the scientific committee on animal nutrition on the criteria for assessing the safety of micro-organisms resistant to antibiotics of human clinical and veterinary importance. https://ec.europa.eu/food/sites/food/files/safety/docs/animal-feed_additives_rules_scan-old_report_out108.pdf Accessed 06 February 2019
-
(2003)
-
-
European Commission1
-
33
-
-
70349957110
-
Probiotics in food - health and nutritional properties and guidelines for evaluation
-
(Accessed 6 February 2019)
-
FAO/WHO, 2006. Probiotics in food - Health and nutritional properties and guidelines for evaluation. FAO Food Nutr. Pap. 85. http://www.fao.org/3/a-a0512e.pdf Accessed 06 February 2019
-
(2006)
FAO Food Nutr. Pap. 85
-
-
FAO/WHO1
-
34
-
-
0142043308
-
In vitro conjugal transfer of tetracycline resistance from Lactobacillus isolates to other Gram-positive bacteria
-
Gevers, D., Huys, G., Swings, J., 2003. In vitro conjugal transfer of tetracycline resistance from Lactobacillus isolates to other Gram-positive bacteria. FEMS Microbiol. Lett. 225, 125–130. doi:10.1016/S0378-1097(03)00505-6
-
(2003)
FEMS Microbiol. Lett.
, vol.225
, pp. 125-130
-
-
Gevers, D.1
Huys, G.2
Swings, J.3
-
35
-
-
84921632491
-
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology
-
Gibson, M.K., Forsberg, K.J., Dantas, G., 2015. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J. 9, 207–216. doi:10.1038/ismej.2014.106
-
(2015)
ISME J
, vol.9
, pp. 207-216
-
-
Gibson, M.K.1
Forsberg, K.J.2
Dantas, G.3
-
36
-
-
77952265531
-
Genetic basis of tetracycline resistance in Bifidobacterium animalis subsp. lactis
-
Gueimonde, M., Flórez, A.B., van Hoek, A.H.A.M., Stuer-Lauridsen, B., Strøman, P., de los Reyes-Gavilán, C.G., Margolles, A., 2010. Genetic basis of tetracycline resistance in Bifidobacterium animalis subsp. lactis. Appl. Environ. Microbiol. 76, 3364–3369. doi:10.1128/AEM.03096-09
-
(2010)
Appl. Environ. Microbiol.
, vol.76
, pp. 3364-3369
-
-
Gueimonde, M.1
Flórez, A.B.2
van Hoek, A.H.A.M.3
Stuer-Lauridsen, B.4
Strøman, P.5
de los Reyes-Gavilán, C.G.6
Margolles, A.7
-
37
-
-
84885361489
-
Antibiotic resistance in probiotic bacteria
-
Gueimonde, M., Sánchez, B., de los Reyes-Gavilán, C.G., Margolles, A., 2013. Antibiotic resistance in probiotic bacteria. Front. Microbiol. 4, 202. doi:10.3389/fmicb.2013.00202
-
(2013)
Front. Microbiol.
, vol.4
, pp. 202
-
-
Gueimonde, M.1
Sánchez, B.2
de los Reyes-Gavilán, C.G.3
Margolles, A.4
-
38
-
-
84875532661
-
Co-evolution of genomic islands and their bacterial hosts revealed through phylogenetic analyses of 17 groups of homologous genomic islands
-
Guo, F.-B., Wei, W., Wang, X.L., Lin, H., Ding, H., Huang, J., Rao, N., 2012. Co-evolution of genomic islands and their bacterial hosts revealed through phylogenetic analyses of 17 groups of homologous genomic islands. Genet. Mol. Res. 11, 3735–3743. doi:10.4238/2012.October.15.5
-
(2012)
Genet. Mol. Res.
, vol.11
, pp. 3735-3743
-
-
Guo, F.-B.1
Wei, W.2
Wang, X.L.3
Lin, H.4
Ding, H.5
Huang, J.6
Rao, N.7
-
39
-
-
85013459726
-
Characterization of antibiotic resistance genes from Lactobacillus isolated from traditional dairy products
-
Guo, H., Pan, L., Li, L., Lu, J., Kwok, L., Menghe, B., Zhang, H., Zhang, W., 2017. Characterization of antibiotic resistance genes from Lactobacillus isolated from traditional dairy products. J. Food Sci. 82, 724–730. doi:10.1111/1750-3841.13645
-
(2017)
J. Food Sci.
, vol.82
, pp. 724-730
-
-
Guo, H.1
Pan, L.2
Li, L.3
Lu, J.4
Kwok, L.5
Menghe, B.6
Zhang, H.7
Zhang, W.8
-
40
-
-
84891552789
-
ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
-
Gupta, S.K., Padmanabhan, B.R., Diene, S.M., Lopez-Rojas, R., Kempf, M., Landraud, L., Rolain, J.M., 2014. ARG-annot, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob. Agents Chemother. 58, 212–220. doi:10.1128/AAC.01310-13
-
(2014)
Antimicrob. Agents Chemother.
, vol.58
, pp. 212-220
-
-
Gupta, S.K.1
Padmanabhan, B.R.2
Diene, S.M.3
Lopez-Rojas, R.4
Kempf, M.5
Landraud, L.6
Rolain, J.M.7
-
41
-
-
77949601825
-
CD-HIT suite: a web server for clustering and comparing biological sequences
-
Huang, Y., Niu, B., Gao, Y., Fu, L., Li, W., 2010. CD-HIT Suite: A web server for clustering and comparing biological sequences. Bioinformatics 26, 680–682. doi:10.1093/bioinformatics/btq003
-
(2010)
Bioinformatics
, vol.26
, pp. 680-682
-
-
Huang, Y.1
Niu, B.2
Gao, Y.3
Fu, L.4
Li, W.5
-
42
-
-
33846900427
-
Antibiotic resistances of starter and probiotic strains of lactic acid bacteria
-
Hummel, A.S., Hertel, C., Holzapfel, W.H., Franz, C.M.A.P., 2007. Antibiotic resistances of starter and probiotic strains of lactic acid bacteria. Appl. Environ. Microbiol. 73, 730–739. doi:10.1128/AEM.02105-06
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 730-739
-
-
Hummel, A.S.1
Hertel, C.2
Holzapfel, W.H.3
Franz, C.M.A.P.4
-
43
-
-
77952621710
-
Intra- and interlaboratory performances of two commercial antimicrobial susceptibility testing methods for bifidobacteria and nonenterococcal lactic acid bacteria
-
Huys, G., D'’Haene, K., Cnockaert, M., Tosi, L., Danielsen, M., Flórez, A.B., Mättö, J., Axelsson, L., Korhonen, J., Mayrhofer, S., Egervärn, M., Giacomini, M., Vandamme, P., 2010. Intra- and interlaboratory performances of two commercial antimicrobial susceptibility testing methods for bifidobacteria and nonenterococcal lactic acid bacteria. Antimicrob. Agents Chemother. 54, 2567–2574. doi:10.1128/AAC.00407-10
-
(2010)
Antimicrob. Agents Chemother.
, vol.54
, pp. 2567-2574
-
-
Huys, G.1
D'Haene, K.2
Cnockaert, M.3
Tosi, L.4
Danielsen, M.5
Flórez, A.B.6
Mättö, J.7
Axelsson, L.8
Korhonen, J.9
Mayrhofer, S.10
Egervärn, M.11
Giacomini, M.12
Vandamme, P.13
-
44
-
-
85074565463
-
-
International Organization for Standardization Geneva
-
ISO 10932, 2010. Geneva: International Organization for Standardization.
-
(2010)
ISO 10932
-
-
-
45
-
-
33845678684
-
Horizontal transfer of tet(M) and erm(B) resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis JH2-2 in the gastrointestinal tract of gnotobiotic rats
-
Jacobsen, L., Wilcks, A., Hammer, K., Huys, G., Gevers, D., Andersen, S.R., 2007. Horizontal transfer of tet(M) and erm(B) resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis JH2-2 in the gastrointestinal tract of gnotobiotic rats. FEMS Microbiol. Ecol. 59, 158–166. doi:10.1111/j.1574-6941.2006.00212.x
-
(2007)
FEMS Microbiol. Ecol.
, vol.59
, pp. 158-166
-
-
Jacobsen, L.1
Wilcks, A.2
Hammer, K.3
Huys, G.4
Gevers, D.5
Andersen, S.R.6
-
46
-
-
85016050964
-
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
-
Jia, B., Raphenya, A.R., Alcock, B., Waglechner, N., Guo, P., Tsang, K.K., Lago, B.A., Dave, B.M., Pereira, S., Sharma, N.A., Doshi, S., Courtot, M., Lo, R., Williams, L.E., Frye, G., Elsayegh, T., Sardar, D., Westman, E.L., Pawlowski, A.C., Johnson, A.T., Brinkman, F.S.L.L., Wright, G.D., McArthur, A.G., 2017. CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45, D566–D573. doi:10.1093/nar/gkw1004
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D566-D573
-
-
Jia, B.1
Raphenya, A.R.2
Alcock, B.3
Waglechner, N.4
Guo, P.5
Tsang, K.K.6
Lago, B.A.7
Dave, B.M.8
Pereira, S.9
Sharma, N.A.10
Doshi, S.11
Courtot, M.12
Lo, R.13
Williams, L.E.14
Frye, G.15
Elsayegh, T.16
Sardar, D.17
Westman, E.L.18
Pawlowski, A.C.19
Johnson, A.T.20
Brinkman, F.S.L.L.21
Wright, G.D.22
McArthur, A.G.23
more..
-
47
-
-
32044447914
-
Antibiotic susceptibility patterns and resistance genes of starter cultures and probiotic bacteria used in food
-
Kastner, S., Perreten, V., Bleuler, H., Hugenschmidt, G., Lacroix, C., Meile, L., 2006. Antibiotic susceptibility patterns and resistance genes of starter cultures and probiotic bacteria used in food. Syst. Appl. Microbiol. 29, 145–155. doi:10.1016/j.syapm.2005.07.009
-
(2006)
Syst. Appl. Microbiol.
, vol.29
, pp. 145-155
-
-
Kastner, S.1
Perreten, V.2
Bleuler, H.3
Hugenschmidt, G.4
Lacroix, C.5
Meile, L.6
-
48
-
-
33746911189
-
Comparative analysis of sequences flanking tet(W) resistance genes in multiple species of gut bacteria
-
Kazimierczak, K.A., Flint, H.J., Scott, K.P., 2006. Comparative analysis of sequences flanking tet(W) resistance genes in multiple species of gut bacteria. Antimicrob. Agents Chemother. 50, 2632–2639. doi:10.1128/AAC.01587-05
-
(2006)
Antimicrob. Agents Chemother.
, vol.50
, pp. 2632-2639
-
-
Kazimierczak, K.A.1
Flint, H.J.2
Scott, K.P.3
-
49
-
-
0346409069
-
Antibacterial activities of Lactobacillus crispatus ATCC 33820 and Lactobacillus gasseri ATCC 33323
-
Kim, J., Rajagopal, S.N., 2001. Antibacterial activities of Lactobacillus crispatus ATCC 33820 and Lactobacillus gasseri ATCC 33323. J. Microbiol. 39, 146–148.
-
(2001)
J. Microbiol.
, vol.39
, pp. 146-148
-
-
Kim, J.1
Rajagopal, S.N.2
-
50
-
-
34447564914
-
Antimicrobial susceptibilities of Lactobacillus, Pediococcus and Lactococcus human isolates and cultures intended for probiotic or nutritional use
-
Klare, I., Konstabel, C., Werner, G., Huys, G., Vankerckhoven, V., Kahlmeter, G., Hildebrandt, B., Müller-Bertling, S., Witte, W., Goossens, H., 2007. Antimicrobial susceptibilities of Lactobacillus, Pediococcus and Lactococcus human isolates and cultures intended for probiotic or nutritional use. J. Antimicrob. Chemother. 59, 900–912. doi:10.1093/jac/dkm035
-
(2007)
J. Antimicrob. Chemother.
, vol.59
, pp. 900-912
-
-
Klare, I.1
Konstabel, C.2
Werner, G.3
Huys, G.4
Vankerckhoven, V.5
Kahlmeter, G.6
Hildebrandt, B.7
Müller-Bertling, S.8
Witte, W.9
Goossens, H.10
-
51
-
-
58149183697
-
ARDB - Antibiotic resistance genes database
-
Liu, B., Pop, M., 2009. ARDB - Antibiotic resistance genes database. Nucleic Acids Res. 37, 443–447. doi:10.1093/nar/gkn656
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 443-447
-
-
Liu, B.1
Pop, M.2
-
52
-
-
84867918293
-
The human microbiome: a hot spot of microbial horizontal gene transfer
-
Liu, L., Chen, X., Skogerbø, G., Zhang, P., Chen, R., He, S., Huang, D.W., 2012. The human microbiome: A hot spot of microbial horizontal gene transfer. Genomics 100, 265–270. doi:10.1016/j.ygeno.2012.07.012
-
(2012)
Genomics
, vol.100
, pp. 265-270
-
-
Liu, L.1
Chen, X.2
Skogerbø, G.3
Zhang, P.4
Chen, R.5
He, S.6
Huang, D.W.7
-
53
-
-
85059797758
-
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
-
Liu, M., Li, X., Xie, Y., Bi, D., Sun, J., Li, J., Tai, C., Deng, Z., Ou, H., 2019. ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res. 47, 660–665. doi:10.1093/nar/gky1123
-
(2019)
Nucleic Acids Res.
, vol.47
, pp. 660-665
-
-
Liu, M.1
Li, X.2
Xie, Y.3
Bi, D.4
Sun, J.5
Li, J.6
Tai, C.7
Deng, Z.8
Ou, H.9
-
54
-
-
33748127928
-
Antimicrobial susceptibility of Bifidobacterium strains from humans, animals and probiotic products
-
Masco, L., Van Hoorde, K., De Brandt, E., Swings, J., Huys, G., 2006. Antimicrobial susceptibility of Bifidobacterium strains from humans, animals and probiotic products. J. Antimicrob. Chemother. 58, 85–94. doi:10.1093/jac/dkl197
-
(2006)
J. Antimicrob. Chemother.
, vol.58
, pp. 85-94
-
-
Masco, L.1
Van Hoorde, K.2
De Brandt, E.3
Swings, J.4
Huys, G.5
-
55
-
-
45749153077
-
Comparison of broth microdilution, Etest, and agar disk diffusion methods for antimicrobial susceptibility testing of Lactobacillus acidophilus group members
-
Mayrhofer, S., Domig, K.J., Mair, C., Zitz, U., Huys, G., Kneifel, W., 2008. Comparison of broth microdilution, Etest, and agar disk diffusion methods for antimicrobial susceptibility testing of Lactobacillus acidophilus group members. Appl. Environ. Microbiol. 74, 3745–3748. doi:10.1128/AEM.02849-07
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 3745-3748
-
-
Mayrhofer, S.1
Domig, K.J.2
Mair, C.3
Zitz, U.4
Huys, G.5
Kneifel, W.6
-
56
-
-
85032658081
-
Safety evaluation of HOWARU® Restore (Lactobacillus acidophilus NCFM, Lactobacillus paracasei Lpc-37, Bifidobacterium animalis subsp. lactis Bl-04 and B. lactis Bi-07) for antibiotic resistance, genomic risk factors, and acute toxicity
-
Morovic, W., Roper, J.M., Smith, A.B., Mukerji, P., Stahl, B., Rae, J.C., Ouwehand, A.C., 2017. Safety evaluation of HOWARU® Restore (Lactobacillus acidophilus NCFM, Lactobacillus paracasei Lpc-37, Bifidobacterium animalis subsp. lactis Bl-04 and B. lactis Bi-07) for antibiotic resistance, genomic risk factors, and acute toxicity. Food Chem. Toxicol. 110, 316–324. doi:10.1016/j.fct.2017.10.037
-
(2017)
Food Chem. Toxicol.
, vol.110
, pp. 316-324
-
-
Morovic, W.1
Roper, J.M.2
Smith, A.B.3
Mukerji, P.4
Stahl, B.5
Rae, J.C.6
Ouwehand, A.C.7
-
57
-
-
85026785962
-
-
Whole-genome sequence of Lactobacillus sakei LT-13 isolated from moto starter of sake. Genome Announc. 5, e00651–17. doi:.
-
Kato, S., Oikawa, T., 2017. Whole-genome sequence of Lactobacillus sakei LT-13 isolated from moto starter of sake. Genome Announc. 5, e00651–17. doi: https://doi.org/10.1128/genomeA.00651-17.
-
(2017)
-
-
Kato, S.1
Oikawa, T.2
-
58
-
-
85056643631
-
-
Transcriptional and functional analysis of Bifidobacterium animalis subsp. lactis exposure to tetracycline. Appl. Environ. Microbiol. 84, e01999–18. doi:.
-
Morovic, W., Roos, P., Zabel, B., Hidalgo-Cantabrana, C., Kiefer, A., Barrangou, R., 2018. Transcriptional and functional analysis of Bifidobacterium animalis subsp. lactis exposure to tetracycline. Appl. Environ. Microbiol. 84, e01999–18. doi: https://doi.org/10.1128/AEM.01999-18.
-
(2018)
-
-
Morovic, W.1
Roos, P.2
Zabel, B.3
Hidalgo-Cantabrana, C.4
Kiefer, A.5
Barrangou, R.6
-
59
-
-
13344280934
-
Antimicrobial susceptibility of bifidobacteria
-
Moubareck, C., Gavini, F., Vaugien, L., Butel, M.J., Doucet-Populaire, F., 2005. Antimicrobial susceptibility of bifidobacteria. J. Antimicrob. Chemother. 55, 38–44. doi:10.1093/jac/dkh495
-
(2005)
J. Antimicrob. Chemother.
, vol.55
, pp. 38-44
-
-
Moubareck, C.1
Gavini, F.2
Vaugien, L.3
Butel, M.J.4
Doucet-Populaire, F.5
-
60
-
-
79954444210
-
Characterization and transfer of antibiotic resistance in lactic acid bacteria from fermented food products
-
Nawaz, M., Wang, J., Zhou, A., Ma, C., Wu, X., Moore, J.E., Millar, B.C., Xu, J., 2011. Characterization and transfer of antibiotic resistance in lactic acid bacteria from fermented food products. Curr. Microbiol. 62, 1081–1089. doi:10.1007/s00284-010-9856-2
-
(2011)
Curr. Microbiol.
, vol.62
, pp. 1081-1089
-
-
Nawaz, M.1
Wang, J.2
Zhou, A.3
Ma, C.4
Wu, X.5
Moore, J.E.6
Millar, B.C.7
Xu, J.8
-
61
-
-
85074593232
-
PRJNA402
-
(Accessed 6 February 2019)
-
NCBI BioProject Database, 2006. PRJNA402. https://www.ncbi.nlm.nih.gov/bioproject/ Accessed 06 February 2019
-
(2006)
-
-
NCBI BioProject Database1
-
62
-
-
78751696048
-
Different genetic elements carrying the tet(W) gene in two human clinical isolates of Streptococcus suis
-
Palmieri, C., Princivalli, M.S., Brenciani, A., Varaldo, P.E., Facinelli, B., 2011. Different genetic elements carrying the tet(W) gene in two human clinical isolates of Streptococcus suis. Antimicrob. Agents Chemother. 55, 631–636. doi:10.1128/AAC.00965-10
-
(2011)
Antimicrob. Agents Chemother.
, vol.55
, pp. 631-636
-
-
Palmieri, C.1
Princivalli, M.S.2
Brenciani, A.3
Varaldo, P.E.4
Facinelli, B.5
-
63
-
-
85007189034
-
-
Ruzal, S.M. Draft genome sequence of the probiotic strain Lactobacillus acidophilus ATCC 4356. Genome Announc. 3, e01421–14. doi:.
-
Palomino, M.M., Allievi, M.C., Martin, J.F., Waehner, P.M., Acosta, M.P., Rivas, C.S., Ruzal, S.M., 2015. Draft genome sequence of the probiotic strain Lactobacillus acidophilus ATCC 4356. Genome Announc. 3, e01421–14. doi: https://doi.org/10.1128/genomeA.01421-14.
-
(2015)
-
-
Palomino, M.M.1
Allievi, M.C.2
Martin, J.F.3
Waehner, P.M.4
Acosta, M.P.5
Rivas, C.S.6
-
64
-
-
85053889361
-
Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements
-
Pärnänen, K., Karkman, A., Hultman, J., Lyra, C., Bengtsson-Palme, J., Larsson, D.G.J., Rautava, S., Isolauri, E., Salminen, S., Kumar, H., Satokari, R., Virta, M., 2018. Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nat. Commun. 9, 3891. doi:10.1038/s41467-018-06393-w
-
(2018)
Nat. Commun.
, vol.9
, pp. 3891
-
-
Pärnänen, K.1
Karkman, A.2
Hultman, J.3
Lyra, C.4
Bengtsson-Palme, J.5
Larsson, D.G.J.6
Rautava, S.7
Isolauri, E.8
Salminen, S.9
Kumar, H.10
Satokari, R.11
Virta, M.12
-
65
-
-
85046724253
-
Lactobacillus fermentum L930BB and Bifidobacterium animalis subsp. animalis IM386 initiate signalling pathways involved in intestinal epithelial barrier protection
-
Paveljšek, D., Juvan, P., Košir, R., Rozman, D., Hacin, B., Ivicak-Kocjan, K., Rogelj, I., 2018. Lactobacillus fermentum L930BB and Bifidobacterium animalis subsp. animalis IM386 initiate signalling pathways involved in intestinal epithelial barrier protection. Benef. Microbes 9, 515–525. doi:10.3920/BM2017.0107
-
(2018)
Benef. Microbes
, vol.9
, pp. 515-525
-
-
Paveljšek, D.1
Juvan, P.2
Košir, R.3
Rozman, D.4
Hacin, B.5
Ivicak-Kocjan, K.6
Rogelj, I.7
-
66
-
-
0842287579
-
Analysis of gyrA and parC mutations in enterococci from environmental samples with reduced susceptibility to ciprofloxacin
-
Petersen, A., Jensen, L.B., 2004. Analysis of gyrA and parC mutations in enterococci from environmental samples with reduced susceptibility to ciprofloxacin. FEMS Microbiol. Lett. 231, 73–76. doi:10.1016/S0378-1097(03)00929-7
-
(2004)
FEMS Microbiol. Lett.
, vol.231
, pp. 73-76
-
-
Petersen, A.1
Jensen, L.B.2
-
67
-
-
10744220291
-
The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533
-
Pridmore, R.D., Berger, B., Desiere, F., Vilanova, D., Barretto, C., Pittet, A.-C., Zwahlen, M.-C., Rouvet, M., Altermann, E., Barrangou, R., Mollet, B., Mercenier, A., Klaenhammer, T., Arigoni, F., Schell, M.A., 2004. The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc. Natl. Acad. Sci. U. S. A. 101, 2512–2517. doi:10.1073/pnas.0307327101
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, pp. 2512-2517
-
-
Pridmore, R.D.1
Berger, B.2
Desiere, F.3
Vilanova, D.4
Barretto, C.5
Pittet, A.-C.6
Zwahlen, M.-C.7
Rouvet, M.8
Altermann, E.9
Barrangou, R.10
Mollet, B.11
Mercenier, A.12
Klaenhammer, T.13
Arigoni, F.14
Schell, M.A.15
-
68
-
-
85053201679
-
Antimicrobial susceptibility of bifidobacteria from probiotic milk products and determination of the genetic basis of tetracycline resistance in Enterococcus species after in vitro conjugation with Bifidobacterium animalis subsp. lactis
-
Raeisi, S.N., Ghoddusi, H.B., Juncker Boll, E., Farahmand, N., Stuer-Lauridsen, B., Johansen, E., Sutherland, J.P., Ouoba, L.I.I., 2018. Antimicrobial susceptibility of bifidobacteria from probiotic milk products and determination of the genetic basis of tetracycline resistance in Enterococcus species after in vitro conjugation with Bifidobacterium animalis subsp. lactis. Food Control 94, 205–211. doi:10.1016/j.foodcont.2018.07.016
-
(2018)
Food Control
, vol.94
, pp. 205-211
-
-
Raeisi, S.N.1
Ghoddusi, H.B.2
Juncker Boll, E.3
Farahmand, N.4
Stuer-Lauridsen, B.5
Johansen, E.6
Sutherland, J.P.7
Ouoba, L.I.I.8
-
69
-
-
85074609658
-
Genomic overview of acquired antibiotic resistance mechanisms in Lactobacillus
-
S.M. Ruzal Caister Academic Press Buenos Aires, Argentina
-
Rodríguez, C., Petrelli, L., Ramírez, M.S., Centrón, D., Hebert, E.M., Saavedra, L., 2019. Genomic overview of acquired antibiotic resistance mechanisms in Lactobacillus. In: Ruzal, S.M. (Ed.), Lactobacillus genomics and metabolic engineering. Caister Academic Press, Buenos Aires, Argentina, pp. 185–204. doi:10.21775/9781910190890.10
-
(2019)
Lactobacillus Genomics and Metabolic Engineering
, pp. 185-204
-
-
Rodríguez, C.1
Petrelli, L.2
Ramírez, M.S.3
Centrón, D.4
Hebert, E.M.5
Saavedra, L.6
-
70
-
-
33947159558
-
Lactobacillus gasseri LF221 and K7 — from isolation to application
-
Rogelj, I., Bogovič Matijašić, B., 2006. Lactobacillus gasseri LF221 and K7 — from isolation to application. Biologia (Bratisl). 61, 761–769. doi:10.2478/s11756-006-0154-1
-
(2006)
Biologia (Bratisl)
, vol.61
, pp. 761-769
-
-
Rogelj, I.1
Bogovič Matijašić, B.2
-
71
-
-
84994444665
-
VSEARCH: a versatile open source tool for metagenomics
-
Rognes, T., Flouri, T., Nichols, B., Quince, C., Mahé, F., 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584. doi:10.7717/peerj.2584
-
(2016)
PeerJ
, vol.4
-
-
Rognes, T.1
Flouri, T.2
Nichols, B.3
Quince, C.4
Mahé, F.5
-
72
-
-
54449092724
-
Removal of antibiotic resistance gene-carrying plasmids from Lactobacillus reuteri ATCC 55730 and characterization of the resulting daughter strain, L. reuteri DSM 17938
-
Rosander, A., Connolly, E., Roos, S., 2008. Removal of antibiotic resistance gene-carrying plasmids from Lactobacillus reuteri ATCC 55730 and characterization of the resulting daughter strain, L. reuteri DSM 17938. Appl. Environ. Microbiol. 74, 6032–6040. doi:10.1128/AEM.00991-08
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 6032-6040
-
-
Rosander, A.1
Connolly, E.2
Roos, S.3
-
73
-
-
84999491381
-
Past and future species definitions for bacteria and archaea
-
Rosselló-Móra, R., Amann, R., 2015. Past and future species definitions for bacteria and archaea. Syst. Appl. Microbiol. 38, 209–216. doi:10.1016/j.syapm.2015.02.001
-
(2015)
Syst. Appl. Microbiol.
, vol.38
, pp. 209-216
-
-
Rosselló-Móra, R.1
Amann, R.2
-
74
-
-
84898415199
-
Lactobacillus gasseri K7 modulates the blood cell transcriptome of conventional mice infected with Escherichia coli O157: H7
-
Sagaya, F.M., Hacin, B., Tompa, G., Ihan, A., Špela, Š., Černe, M., Hurrell, R.F., Bogovič Matijašić, B., Rogelj, I., Vergères, G., 2014. Lactobacillus gasseri K7 modulates the blood cell transcriptome of conventional mice infected with Escherichia coli O157: H7. J. Appl. Microbiol. 116, 1282–1296. doi:10.1111/jam.12440
-
(2014)
J. Appl. Microbiol.
, vol.116
, pp. 1282-1296
-
-
Sagaya, F.M.1
Hacin, B.2
Tompa, G.3
Ihan, A.4
Špela, Š.5
Černe, M.6
Hurrell, R.F.7
Bogovič Matijašić, B.8
Rogelj, I.9
Vergères, G.10
-
75
-
-
84864351639
-
Distinct adhesion of probiotic strain Lactobacillus casei ATCC 393 to rat intestinal mucosa
-
Saxami, G., Ypsilantis, P., Sidira, M., Simopoulos, C., Kourkoutas, Y., Galanis, A., 2012. Distinct adhesion of probiotic strain Lactobacillus casei ATCC 393 to rat intestinal mucosa. Anaerobe 18, 417–420. doi:10.1016/j.anaerobe.2012.04.002
-
(2012)
Anaerobe
, vol.18
, pp. 417-420
-
-
Saxami, G.1
Ypsilantis, P.2
Sidira, M.3
Simopoulos, C.4
Kourkoutas, Y.5
Galanis, A.6
-
76
-
-
6344291118
-
Molecular basis of bacterial resistance to chloramphenicol and florfenicol
-
Schwarz, S., Kehrenberg, C., Doublet, B., Cloeckaert, A., 2004. Molecular basis of bacterial resistance to chloramphenicol and florfenicol. FEMS Microbiol. Rev. 28, 519–542. doi:10.1016/j.femsre.2004.04.001
-
(2004)
FEMS Microbiol. Rev.
, vol.28
, pp. 519-542
-
-
Schwarz, S.1
Kehrenberg, C.2
Doublet, B.3
Cloeckaert, A.4
-
77
-
-
0034001488
-
Occurrence of the new tetracycline resistance gene tet(W) in bacteria from the human gut
-
Scott, K.P., Melville, C.M., Barbosa, T.M., Flint, H.J., 2000. Occurrence of the new tetracycline resistance gene tet(W) in bacteria from the human gut. Antimicrob. Agents Chemother. 44, 775–777. doi:10.1128/AAC.44.3.775-777.2000
-
(2000)
Antimicrob. Agents Chemother.
, vol.44
, pp. 775-777
-
-
Scott, K.P.1
Melville, C.M.2
Barbosa, T.M.3
Flint, H.J.4
-
78
-
-
85042090683
-
-
Shafeekh Muyyarikkandy, M., Alqahtani, F.H., Mandoiu, I., Amalaradjou, M.A. Draft genome sequence of Lactobacillus rhamnosus NRRL B-442, a potential probiotic strain. Genome Announc. 6, e00556–18. doi:.
-
Shafeekh Muyyarikkandy, M., Alqahtani, F.H., Mandoiu, I., Amalaradjou, M.A., 2018. Draft genome sequence of Lactobacillus rhamnosus NRRL B-442, a potential probiotic strain. Genome Announc. 6, e00556–18. doi: https://doi.org/10.1128/genomeA.00046-18.
-
(2018)
-
-
-
79
-
-
85018773898
-
Antibiotic sensitivity pattern of indigenous lactobacilli isolated from curd and human milk samples
-
Sharma, C., Gulati, S., Thakur, N., Singh, B.P., Gupta, S., Kaur, S., Mishra, S.K., Puniya, A.K., Gill, J.P.S., Panwar, H., 2017. Antibiotic sensitivity pattern of indigenous lactobacilli isolated from curd and human milk samples. 3 Biotech 7, 53. doi:10.1007/s13205-017-0682-0
-
(2017)
3 Biotech
, vol.7
, pp. 53
-
-
Sharma, C.1
Gulati, S.2
Thakur, N.3
Singh, B.P.4
Gupta, S.5
Kaur, S.6
Mishra, S.K.7
Puniya, A.K.8
Gill, J.P.S.9
Panwar, H.10
-
80
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
-
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J.D., Higgins, D.G., 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539. doi:10.1038/msb.2011.75
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 539
-
-
Sievers, F.1
Wilm, A.2
Dineen, D.3
Gibson, T.J.4
Karplus, K.5
Li, W.6
Lopez, R.7
McWilliam, H.8
Remmert, M.9
Söding, J.10
Thompson, J.D.11
Higgins, D.G.12
-
81
-
-
85024923747
-
Assessment of phenotypic and genotypic antibiotic susceptibility of vaginal Lactobacillus sp
-
Štšepetova, J., Taelma, H., Smidt, I., Hütt, P., Lapp, E., Aotäht, E., Mändar, R., 2017. Assessment of phenotypic and genotypic antibiotic susceptibility of vaginal Lactobacillus sp. J. Appl. Microbiol. 123, 524–534. doi:10.1111/jam.13497
-
(2017)
J. Appl. Microbiol.
, vol.123
, pp. 524-534
-
-
Štšepetova, J.1
Taelma, H.2
Smidt, I.3
Hütt, P.4
Lapp, E.5
Aotäht, E.6
Mändar, R.7
-
82
-
-
33745612095
-
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
-
Suzuki, R., Shimodaira, H., 2006. Pvclust: An R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540–1542. doi:10.1093/bioinformatics/btl117
-
(2006)
Bioinformatics
, vol.22
, pp. 1540-1542
-
-
Suzuki, R.1
Shimodaira, H.2
-
83
-
-
84925685116
-
Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260T, a psychrotrophic lactic acid bacterium isolated from silage
-
Tanizawa, Y., Tohno, M., Kaminuma, E., Nakamura, Y., Arita, M., 2015. Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260T, a psychrotrophic lactic acid bacterium isolated from silage. BMC Genomics 16, 240. doi:10.1186/s12864-015-1435-2
-
(2015)
BMC Genomics
, vol.16
, pp. 240
-
-
Tanizawa, Y.1
Tohno, M.2
Kaminuma, E.3
Nakamura, Y.4
Arita, M.5
-
84
-
-
85055818102
-
Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses
-
Tanizawa, Y., Tada, I., Kobayashi, H., Endo, A., Maeno, S., Toyoda, A., Arita, M., Nakamura, Y., Sakamoto, M., Ohkuma, M., Tohno, M., 2018. Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses. Int. J. Syst. Evol. Microbiol. 68, 3512–3517. doi:10.1099/ijsem.0.003020
-
(2018)
Int. J. Syst. Evol. Microbiol.
, vol.68
, pp. 3512-3517
-
-
Tanizawa, Y.1
Tada, I.2
Kobayashi, H.3
Endo, A.4
Maeno, S.5
Toyoda, A.6
Arita, M.7
Nakamura, Y.8
Sakamoto, M.9
Ohkuma, M.10
Tohno, M.11
-
85
-
-
85003550243
-
-
Bogovič Matijašić, B., Rogelj, I. Improved draft genome sequence of probiotic strain Lactobacillus gasseri K7. Genome Announc. 2, e00725–14. doi:.
-
Treven, P., Trmčić, A., Bogovič Matijašić, B., Rogelj, I., 2014. Improved draft genome sequence of probiotic strain Lactobacillus gasseri K7. Genome Announc. 2, e00725–14. doi: https://doi.org/10.1128/genomeA.00725-14.
-
(2014)
-
-
Treven, P.1
Trmčić, A.2
-
86
-
-
79959677612
-
The gut as reservoir of antibiotic resistance: microbial diversity of tetracycline resistance in mother and infant
-
de Vries, L.E., Vallès, Y., Agersø, Y., Vaishampayan, P.A., García-Montaner, A., Kuehl, J. V., Christensen, H., Barlow, M., Francino, M.P., 2011. The gut as reservoir of antibiotic resistance: Microbial diversity of tetracycline resistance in mother and infant. PLoS One 6. doi:10.1371/journal.pone.0021644
-
(2011)
PLoS One
, vol.6
-
-
de Vries, L.E.1
Vallès, Y.2
Agersø, Y.3
Vaishampayan, P.A.4
García-Montaner, A.5
Kuehl, J.V.6
Christensen, H.7
Barlow, M.8
Francino, M.P.9
-
87
-
-
85025816120
-
Analysis of newly detected tetracycline resistance genes and their flanking sequences in human intestinal bifidobacteria
-
Wang, N., Hang, X., Zhang, M., Liu, X., Yang, H., 2017. Analysis of newly detected tetracycline resistance genes and their flanking sequences in human intestinal bifidobacteria. Sci. Rep. 7, 6267. doi:10.1038/s41598-017-06595-0
-
(2017)
Sci. Rep.
, vol.7
, pp. 6267
-
-
Wang, N.1
Hang, X.2
Zhang, M.3
Liu, X.4
Yang, H.5
-
88
-
-
78650575601
-
gplots: various R programming tools for plotting data
-
(Accessed 6 February 2019)
-
Warnes, A.G.R., Bolker, B., Bonebakker, L., Huber, W., Liaw, A., Lumley, T., Magnusson, A., Moeller, S., Schwartz, M., Venables, B., 2015. gplots: Various R programming tools for plotting data. https://cran.r-project.org/web/packages/gplots/index.html Accessed 06 February 2019.
-
(2015)
-
-
Warnes, A.G.R.1
Bolker, B.2
Bonebakker, L.3
Huber, W.4
Liaw, A.5
Lumley, T.6
Magnusson, A.7
Moeller, S.8
Schwartz, M.9
Venables, B.10
-
89
-
-
84876725499
-
Treatment of nonalcoholic steatohepatitis with probiotics. A proof-of-concept study
-
Wong, V.W.S., Wong, G.L.H., Chim, A.M.L., Chu, W.C.W., Yeung, D.K.W., Li, K.C.T., Chan, H.L.Y., 2013. Treatment of nonalcoholic steatohepatitis with probiotics. A proof-of-concept study. Ann. Hepatol. 12, 256–262.
-
(2013)
Ann. Hepatol.
, vol.12
, pp. 256-262
-
-
Wong, V.W.S.1
Wong, G.L.H.2
Chim, A.M.L.3
Chu, W.C.W.4
Yeung, D.K.W.5
Li, K.C.T.6
Chan, H.L.Y.7
-
90
-
-
85009917920
-
Draft genome sequence of Lactobacillus crispatus JCM5810, which can reduce Campylobacter jejuni colonization in chicken intestine
-
e00255–16
-
Wooten, J., Liu, X., Miller, M.J., 2016. Draft genome sequence of Lactobacillus crispatus JCM5810, which can reduce Campylobacter jejuni colonization in chicken intestine. Genome Announc. 4, e00255–16. doi: https://doi.org/10.1128/genomeA.00255-16.
-
(2016)
Genome Announc.
, vol.4
-
-
Wooten, J.1
Liu, X.2
Miller, M.J.3
-
91
-
-
84901809320
-
Antimicrobial Resistance. Global Report on Surveillance
-
World Health Organization Geneva (Accessed 6 February 2019)
-
World Health Organization, 2014. Antimicrobial resistance. Global Report on Surveillance, World Health Organization. Geneva. http://www.who.int/iris/handle/10665/112642 Accessed 06 February 2019
-
(2014)
-
-
World Health Organization1
-
92
-
-
84867587461
-
Identification of acquired antimicrobial resistance genes
-
Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., Aarestrup, F.M., Larsen, M.V., 2012. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644. doi:10.1093/jac/dks261
-
(2012)
J. Antimicrob. Chemother.
, vol.67
, pp. 2640-2644
-
-
Zankari, E.1
Hasman, H.2
Cosentino, S.3
Vestergaard, M.4
Rasmussen, S.5
Lund, O.6
Aarestrup, F.M.7
Larsen, M.V.8
-
93
-
-
85062108870
-
Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments
-
Zeng, J., Pan, Y., Yang, J., Hou, M., Zeng, Z., Xiong, W., 2019. Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments. Environ. Int. 126, 346–354. doi:10.1016/j.envint.2019.02.052
-
(2019)
Environ. Int.
, vol.126
, pp. 346-354
-
-
Zeng, J.1
Pan, Y.2
Yang, J.3
Hou, M.4
Zeng, Z.5
Xiong, W.6
-
94
-
-
85048275789
-
D-Alanyl-D-alanine ligase as a broad-host-range counterselection marker in vancomycin-resistant lactic acid bacteria
-
Zhang, S., Oh, J.-H., Alexander, L.M., Özçam, M., van Pijkerena, J.-P., 2018. D-Alanyl-D-Alanine ligase as a broad-host-range counterselection marker in vancomycin-resistant lactic acid bacteria. J. Bacteriol. 200, e00607-17. doi:10.1128/JB.00607-17
-
(2018)
J. Bacteriol.
, vol.200
, pp. e00607-e00617
-
-
Zhang, S.1
Oh, J.-H.2
Alexander, L.M.3
Özçam, M.4
van Pijkerena, J.-P.5
-
95
-
-
84997832022
-
Complete genome sequence of the probiotic Bifidobacterium thermophilum strain RBL67
-
Jans, C., Lacroix, C., Follador, R., Stevens, M.J.A., 2013. Complete genome sequence of the probiotic Bifidobacterium thermophilum strain RBL67. Genome Announc. 1, e00191–13. doi: https://doi.org/10.1128/genomeA.00191-13.
-
(2013)
Genome Announc
, vol.1
-
-
Jans, C.1
Lacroix, C.2
Follador, R.3
Stevens, M.J.A.4
|