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Volumn 8, Issue 4, 2017, Pages

An in Vitro chicken gut model demonstrates transfer of a multidrug resistance plasmid from Salmonella to commensal Escherichia coli

Author keywords

Antimicrobial resistance; Enteric pathogens; Escherichia coli; Horizontal gene transfer; Plasmids; Salmonella

Indexed keywords

CEFOTAXIME; RNA 16S; ANTIINFECTIVE AGENT;

EID: 85029222100     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00777-17     Document Type: Article
Times cited : (58)

References (67)
  • 1
    • 85070568472 scopus 로고    scopus 로고
    • The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2014
    • European Food Safety Authority and European Centre for Disease Prevention and Control. 2015. The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2014. EFSA J 13:4329–4528.
    • (2015) EFSA J , vol.13 , pp. 4329-4528
  • 2
    • 38049000353 scopus 로고    scopus 로고
    • Comparison of antimicrobial resistance genes in nontyphoidal salmonellae of serotypes Enteritidis, Hadar, and Virchow from humans and food-producing animals in England and Wales
    • Hopkins KL, Batchelor MJ, Anjum M, Davies RH, Threlfall EJ. 2007. Comparison of antimicrobial resistance genes in nontyphoidal salmonellae of serotypes Enteritidis, Hadar, and Virchow from humans and food-producing animals in England and Wales. Microb Drug Resist 13:281–288. https://doi.org/10.1089/mdr.2007.779.
    • (2007) Microb Drug Resist , vol.13 , pp. 281-288
    • Hopkins, K.L.1    Batchelor, M.J.2    Anjum, M.3    Davies, R.H.4    Threlfall, E.J.5
  • 3
    • 84900834533 scopus 로고    scopus 로고
    • Microbiota of the chicken gastrointestinal tract: Influence on health, productivity and disease
    • Stanley D, Hughes RJ, Moore RJ. 2014. Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease. Appl Microbiol Biotechnol 98:4301-4310. https://doi.org/10.1007/s00253-014-5646-2.
    • (2014) Appl Microbiol Biotechnol , vol.98 , pp. 4301-4310
    • Stanley, D.1    Hughes, R.J.2    Moore, R.J.3
  • 5
    • 84939865017 scopus 로고    scopus 로고
    • Impact of ciprofloxacin and clindamycin administration on Gram-negative bacteria isolated from healthy volunteers and characterization of the resistance genes they harbor
    • Card RM, Mafura M, Hunt T, Kirchner M, Weile J, Rashid MU, Weintraub A, Nord CE, Anjum MF. 2015. Impact of ciprofloxacin and clindamycin administration on Gram-negative bacteria isolated from healthy volunteers and characterization of the resistance genes they harbor. Antimicrob Agents Chemother 59:4410–4416. https://doi.org/10.1128/AAC.00068-15.
    • (2015) Antimicrob Agents Chemother , vol.59 , pp. 4410-4416
    • Card, R.M.1    Mafura, M.2    Hunt, T.3    Kirchner, M.4    Weile, J.5    Rashid, M.U.6    Weintraub, A.7    Nord, C.E.8    Anjum, M.F.9
  • 6
    • 84866010135 scopus 로고    scopus 로고
    • Collateral effects of antibiotics on mammalian gut microbiomes
    • Looft T, Allen HK. 2012. Collateral effects of antibiotics on mammalian gut microbiomes. Gut Microbes 3:463-467. https://doi.org/10.4161/gmic.21288.
    • (2012) Gut Microbes , vol.3 , pp. 463-467
    • Looft, T.1    Allen, H.K.2
  • 7
    • 84874782497 scopus 로고    scopus 로고
    • Chicken faecal microbiota and disturbances induced by single or repeated therapy with tetracycline and streptomycin
    • Videnska P, Faldynova M, Juricova H, Babak V, Sisak F, Havlickova H, Rychlik I. 2013. Chicken faecal microbiota and disturbances induced by single or repeated therapy with tetracycline and streptomycin. BMC Vet Res 9:30. https://doi.org/10.1186/1746-6148-9-30.
    • (2013) BMC Vet Res , vol.9 , pp. 30
    • Videnska, P.1    Faldynova, M.2    Juricova, H.3    Babak, V.4    Sisak, F.5    Havlickova, H.6    Rychlik, I.7
  • 8
    • 84907486974 scopus 로고    scopus 로고
    • Antibiotics and the gut microbiota
    • Modi SR, Collins JJ, Relman DA. 2014. Antibiotics and the gut microbiota. J Clin Invest 124:4212-4218. https://doi.org/10.1172/JCI72333.
    • (2014) J Clin Invest , vol.124 , pp. 4212-4218
    • Modi, S.R.1    Collins, J.J.2    Relman, D.A.3
  • 9
    • 84871530299 scopus 로고    scopus 로고
    • Influence of penicillin on microbial diversity of the cecal microbiota in broiler chickens
    • Singh P, Karimi A, Devendra K, Waldroup PW, Cho KK, Kwon YM. 2013. Influence of penicillin on microbial diversity of the cecal microbiota in broiler chickens. Poult Sci 92:272–276. https://doi.org/10.3382/ps.2012-02603.
    • (2013) Poult Sci , vol.92 , pp. 272-276
    • Singh, P.1    Karimi, A.2    Devendra, K.3    Waldroup, P.W.4    Cho, K.K.5    Kwon, Y.M.6
  • 10
    • 84956952169 scopus 로고    scopus 로고
    • Antibiotic treatment affects intestinal permeability and gut microbial composition in Wistar rats dependent on antibiotic class
    • Tulstrup MV, Christensen EG, Carvalho V, Linninge C, Ahrné S, Højberg O, Licht TR, Bahl MI. 2015. Antibiotic treatment affects intestinal permeability and gut microbial composition in Wistar rats dependent on antibiotic class. PLoS One 10:e0144854. https://doi.org/10.1371/journal.pone.0144854.
    • (2015) Plos One , vol.10
    • Tulstrup, M.V.1    Christensen, E.G.2    Carvalho, V.3    Linninge, C.4    Ahrné, S.5    Højberg, O.6    Licht, T.R.7    Bahl, M.I.8
  • 12
    • 85056683369 scopus 로고    scopus 로고
    • EU Summary Report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2013
    • European Food Safety Authority and European Centre for Disease Prevention and Control. 2015. EU Summary Report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2013. EFSA J 13:178.
    • (2015) EFSA J , vol.13 , pp. 178
  • 15
    • 84904559393 scopus 로고    scopus 로고
    • Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella 4,5,12:I:-, Escherichia coli and Klebsiella pneumoniae on a UK pig farm
    • Freire Martín I, AbuOun M, Reichel R, La Ragione RM, Woodward MJ. 2014. Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella 4,5,12:i:-, Escherichia coli and Klebsiella pneumoniae on a UK pig farm. J Antimicrob Chemother 69:2098-2101. https://doi.org/10.1093/jac/dku098.
    • (2014) J Antimicrob Chemother , vol.69 , pp. 2098-2101
    • Freire Martín, I.1    Abuoun, M.2    Reichel, R.3    La Ragione, R.M.4    Woodward, M.J.5
  • 19
    • 84355163054 scopus 로고    scopus 로고
    • Advances and perspectives in in vitro human gut fermentation modeling
    • Payne AN, Zihler A, Chassard C, Lacroix C. 2012. Advances and perspectives in in vitro human gut fermentation modeling. Trends Biotechnol 30:17–25. https://doi.org/10.1016/j.tibtech.2011.06.011.
    • (2012) Trends Biotechnol , vol.30 , pp. 17-25
    • Payne, A.N.1    Zihler, A.2    Chassard, C.3    Lacroix, C.4
  • 20
    • 0038601431 scopus 로고    scopus 로고
    • Effects of cefotaxime and desacetylcefotaxime upon Clostridium difficile proliferation and toxin production in a triple-stage chemostat model of the human gut
    • Freeman J, O’Neill FJ, Wilcox MH. 2003. Effects of cefotaxime and desacetylcefotaxime upon Clostridium difficile proliferation and toxin production in a triple-stage chemostat model of the human gut. J Antimicrob Chemother 52:96-102. https://doi.org/10.1093/jac/dkg267.
    • (2003) J Antimicrob Chemother , vol.52 , pp. 96-102
    • Freeman, J.1    O’Neill, F.J.2    Wilcox, M.H.3
  • 21
    • 84866175132 scopus 로고    scopus 로고
    • Higher-level production of volatile fatty acids in vitro by chicken gut microbiotas than by human gut microbiotas as determined by functional analyses
    • Lei F, Yin Y, Wang Y, Deng B, Yu HD, Li L, Xiang C, Wang S, Zhu B, Wang X. 2012. Higher-level production of volatile fatty acids in vitro by chicken gut microbiotas than by human gut microbiotas as determined by functional analyses. Appl Environ Microbiol 78:5763–5772. https://doi.org/10.1128/AEM.00327-12.
    • (2012) Appl Environ Microbiol , vol.78 , pp. 5763-5772
    • Lei, F.1    Yin, Y.2    Wang, Y.3    Deng, B.4    Yu, H.D.5    Li, L.6    Xiang, C.7    Wang, S.8    Zhu, B.9    Wang, X.10
  • 22
    • 84899465304 scopus 로고    scopus 로고
    • In vitro continuous fermentation model (PolyFermS) of the swine proximal colon for simultaneous testing on the same gut microbiota
    • Tanner SA, Zihler Berner A, Rigozzi E, Grattepanche F, Chassard C, Lacroix C. 2014. In vitro continuous fermentation model (PolyFermS) of the swine proximal colon for simultaneous testing on the same gut microbiota. PLoS One 9:e94123. https://doi.org/10.1371/journal.pone.0094123.
    • (2014) Plos One , vol.9
    • Tanner, S.A.1    Zihler Berner, A.2    Rigozzi, E.3    Grattepanche, F.4    Chassard, C.5    Lacroix, C.6
  • 23
    • 84957921581 scopus 로고    scopus 로고
    • Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model
    • Aguirre M, Eck A, Koenen ME, Savelkoul PH, Budding AE, Venema K. 2016. Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model. Res Microbiol 167:114-125. https://doi.org/10.1016/j.resmic.2015.09.006.
    • (2016) Res Microbiol , vol.167 , pp. 114-125
    • Aguirre, M.1    Eck, A.2    Koenen, M.E.3    Savelkoul, P.H.4    Budding, A.E.5    Venema, K.6
  • 24
    • 84982161453 scopus 로고    scopus 로고
    • A single-batch fermentation system to simulate human colonic microbiota for high-throughput evaluation of prebiotics
    • Takagi R, Sasaki K, Sasaki D, Fukuda I, Tanaka K, Yoshida K, Kondo A, Osawa R. 2016. A single-batch fermentation system to simulate human colonic microbiota for high-throughput evaluation of prebiotics. PLoS One 11:e0160533. https://doi.org/10.1371/journal.pone.0160533.
    • (2016) Plos One , vol.11
    • Takagi, R.1    Sasaki, K.2    Sasaki, D.3    Fukuda, I.4    Tanaka, K.5    Yoshida, K.6    Kondo, A.7    Osawa, R.8
  • 26
    • 0025065314 scopus 로고
    • Estimating the rate of plasmid transfer: An end-point method
    • Simonsen L, Gordon DM, Stewart FM, Levin BR. 1990. Estimating the rate of plasmid transfer: an end-point method. J Gen Microbiol 136: 2319–2325. https://doi.org/10.1099/00221287-136-11-2319.
    • (1990) J Gen Microbiol , vol.136 , pp. 2319-2325
    • Simonsen, L.1    Gordon, D.M.2    Stewart, F.M.3    Levin, B.R.4
  • 28
    • 84902850177 scopus 로고    scopus 로고
    • The interplay between Campylobacter and Helicobacter species and other gastrointestinal microbiota of commercial broiler chickens
    • Kaakoush NO, Sodhi N, Chenu JW, Cox JM, Riordan SM, Mitchell HM. 2014. The interplay between Campylobacter and Helicobacter species and other gastrointestinal microbiota of commercial broiler chickens. Gut Pathog 6:18. https://doi.org/10.1186/1757-4749-6-18.
    • (2014) Gut Pathog , vol.6 , pp. 18
    • Kaakoush, N.O.1    Sodhi, N.2    Chenu, J.W.3    Cox, J.M.4    Riordan, S.M.5    Mitchell, H.M.6
  • 29
    • 84955496277 scopus 로고    scopus 로고
    • Design and investigation of PolyFermS in vitro continuous fermentation models inoculated with immobilized fecal microbiota mimicking the elderly colon
    • Fehlbaum S, Chassard C, Haug MC, Fourmestraux C, Derrien M, Lacroix C. 2015. Design and investigation of PolyFermS in vitro continuous fermentation models inoculated with immobilized fecal microbiota mimicking the elderly colon. PLoS One 10:e0142793. https://doi.org/10.1371/journal.pone.0142793.
    • (2015) Plos One , vol.10
    • Fehlbaum, S.1    Chassard, C.2    Haug, M.C.3    Fourmestraux, C.4    Derrien, M.5    Lacroix, C.6
  • 31
    • 84896696508 scopus 로고    scopus 로고
    • Highly variable microbiota development in the chicken gastrointestinal tract
    • Stanley D, Geier MS, Hughes RJ, Denman SE, Moore RJ. 2013. Highly variable microbiota development in the chicken gastrointestinal tract. PLoS One 8:e84290. https://doi.org/10.1371/journal.pone.0084290.
    • (2013) Plos One , vol.8
    • Stanley, D.1    Geier, M.S.2    Hughes, R.J.3    Denman, S.E.4    Moore, R.J.5
  • 32
    • 84866146940 scopus 로고    scopus 로고
    • Diversity, stability and resilience of the human gut microbiota
    • Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220-230. https://doi.org/10.1038/nature11550.
    • (2012) Nature , vol.489 , pp. 220-230
    • Lozupone, C.A.1    Stombaugh, J.I.2    Gordon, J.I.3    Jansson, J.K.4    Knight, R.5
  • 33
    • 84880097532 scopus 로고    scopus 로고
    • Influence of Salmonella enterica serovar Enteritidis infection on the composition of chicken cecal microbiota
    • Videnska P, Sisak F, Havlickova H, Faldynova M, Rychlik I. 2013. Influence of Salmonella enterica serovar Enteritidis infection on the composition of chicken cecal microbiota. BMC Vet Res 9:140. https://doi.org/10.1186/1746-6148-9-140.
    • (2013) BMC Vet Res , vol.9 , pp. 140
    • Videnska, P.1    Sisak, F.2    Havlickova, H.3    Faldynova, M.4    Rychlik, I.5
  • 34
    • 84871905995 scopus 로고    scopus 로고
    • Influence of Salmonella enterica serovar enteritidis infection on the development of the cecum microbiota in newly hatched chicks
    • Juricova H, Videnska P, Lukac M, Faldynova M, Babak V, Havlickova H, Sisak F, Rychlik I. 2013. Influence of Salmonella enterica serovar enteritidis infection on the development of the cecum microbiota in newly hatched chicks. Appl Environ Microbiol 79:745–747. https://doi.org/10.1128/AEM.02628-12.
    • (2013) Appl Environ Microbiol , vol.79 , pp. 745-747
    • Juricova, H.1    Videnska, P.2    Lukac, M.3    Faldynova, M.4    Babak, V.5    Havlickova, H.6    Sisak, F.7    Rychlik, I.8
  • 35
    • 80051856129 scopus 로고    scopus 로고
    • The influence of the cage system and colonisation of Salmonella Enteritidis on the microbial gut flora of laying hens studied by T-RFLP and 454 pyrosequencing
    • Nordentoft S, Mølbak L, Bjerrum L, De Vylder J, Van Immerseel F, Pedersen K. 2011. The influence of the cage system and colonisation of Salmonella Enteritidis on the microbial gut flora of laying hens studied by T-RFLP and 454 pyrosequencing. BMC Microbiol 11:187. https://doi.org/10.1186/1471-2180-11-187.
    • (2011) BMC Microbiol , vol.11 , pp. 187
    • Nordentoft, S.1    Mølbak, L.2    Bjerrum, L.3    De Vylder, J.4    Van Immerseel, F.5    Pedersen, K.6
  • 36
    • 85006452530 scopus 로고    scopus 로고
    • Salmonella enterica serovars Enteritidis infection alters the indigenous microbiota diversity in young layer chicks
    • Mon KK, Saelao P, Halstead MM, Chanthavixay G, Chang HC, Garas L, Maga EA, Zhou H. 2015. Salmonella enterica serovars Enteritidis infection alters the indigenous microbiota diversity in young layer chicks. Front Vet Sci 2:61. https://doi.org/10.3389/fvets.2015.00061.
    • (2015) Front Vet Sci , vol.2 , pp. 61
    • Mon, K.K.1    Saelao, P.2    Halstead, M.M.3    Chanthavixay, G.4    Chang, H.C.5    Garas, L.6    Maga, E.A.7    Zhou, H.8
  • 37
    • 84868294096 scopus 로고    scopus 로고
    • Intrinsic and acquired resistance mechanisms in enterococcus
    • Hollenbeck BL, Rice LB. 2012. Intrinsic and acquired resistance mechanisms in enterococcus. Virulence 3:421-433. https://doi.org/10.4161/viru.21282.
    • (2012) Virulence , vol.3 , pp. 421-433
    • Hollenbeck, B.L.1    Rice, L.B.2
  • 38
    • 0032879213 scopus 로고    scopus 로고
    • Plasmid transfer in the animal intestine and other dynamic bacterial populations: The role of community structure and environment
    • Licht TR, Christensen BB, Krogfelt KA, Molin S. 1999. Plasmid transfer in the animal intestine and other dynamic bacterial populations: the role of community structure and environment. Microbiology 145:2615–2622. https://doi.org/10.1099/00221287-145-9-2615.
    • (1999) Microbiology , vol.145 , pp. 2615-2622
    • Licht, T.R.1    Christensen, B.B.2    Krogfelt, K.A.3    Molin, S.4
  • 39
    • 0036961416 scopus 로고    scopus 로고
    • Plasmids spread very fast in heterogeneous bacterial communities
    • Dionisio F, Matic I, Radman M, Rodrigues OR, Taddei F. 2002. Plasmids spread very fast in heterogeneous bacterial communities. Genetics 162: 1525–1532.
    • (2002) Genetics , vol.162 , pp. 1525-1532
    • Dionisio, F.1    Matic, I.2    Radman, M.3    Rodrigues, O.R.4    Taddei, F.5
  • 40
    • 73849092448 scopus 로고    scopus 로고
    • Transfer of plasmid-mediated CTX-M-9 from Salmonella enterica serotype Virchow to Enterobacteriaceae in human flora-associated rats treated with cefixime
    • Faure S, Perrin-Guyomard A, Delmas JM, Chatre P, Laurentie M. 2010. Transfer of plasmid-mediated CTX-M-9 from Salmonella enterica serotype Virchow to Enterobacteriaceae in human flora-associated rats treated with cefixime. Antimicrob Agents Chemother 54:164-169. https://doi.org/10.1128/AAC.00310-09.
    • (2010) Antimicrob Agents Chemother , vol.54 , pp. 164-169
    • Faure, S.1    Perrin-Guyomard, A.2    Delmas, J.M.3    Chatre, P.4    Laurentie, M.5
  • 41
    • 0041922546 scopus 로고    scopus 로고
    • Multiple antibiotic resistance gene transfer from animal to human enterococci in the digestive tract of gnotobiotic mice
    • Moubareck C, Bourgeois N, Courvalin P, Doucet-Populaire F. 2003. Multiple antibiotic resistance gene transfer from animal to human enterococci in the digestive tract of gnotobiotic mice. Antimicrob Agents Chemother 47:2993–2996. https://doi.org/10.1128/AAC.47.9.2993-2996.2003.
    • (2003) Antimicrob Agents Chemother , vol.47 , pp. 2993-2996
    • Moubareck, C.1    Bourgeois, N.2    Courvalin, P.3    Doucet-Populaire, F.4
  • 43
    • 84903539426 scopus 로고    scopus 로고
    • Human intestinal cells modulate conjugational transfer of multidrug resistance plasmids between clinical Escherichia coli isolates
    • Machado AM, Sommer MO. 2014. Human intestinal cells modulate conjugational transfer of multidrug resistance plasmids between clinical Escherichia coli isolates. PLoS One 9:e100739. https://doi.org/10.1371/journal.pone.0100739.
    • (2014) Plos One , vol.9
    • Machado, A.M.1    Sommer, M.O.2
  • 44
    • 84862207235 scopus 로고    scopus 로고
    • Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow
    • Kim HJ, Huh D, Hamilton G, Ingber DE. 2012. Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow. Lab Chip 12:2165–2174. https://doi.org/10.1039/c2lc40074j.
    • (2012) Lab Chip , vol.12 , pp. 2165-2174
    • Kim, H.J.1    Huh, D.2    Hamilton, G.3    Ingber, D.E.4
  • 46
    • 84980378920 scopus 로고    scopus 로고
    • Curing vector for IncI1 plasmids and its use to provide evidence for a metabolic burden of IncI1 CTX-M-1 plasmid pIFM3791 on Klebsiella pneumoniae
    • Freire Martín I, Thomas CM, Laing E, AbuOun M, La Ragione RM, Woodward MJ. 2016. Curing vector for IncI1 plasmids and its use to provide evidence for a metabolic burden of IncI1 CTX-M-1 plasmid pIFM3791 on Klebsiella pneumoniae. J Med Microbiol 65:611-618. https://doi.org/10.1099/jmm.0.000271.
    • (2016) J Med Microbiol , vol.65 , pp. 611-618
    • Freire Martín, I.1    Thomas, C.M.2    Laing, E.3    Abuoun, M.4    La Ragione, R.M.5    Woodward, M.J.6
  • 47
    • 34248597964 scopus 로고    scopus 로고
    • A longitudinal study of environmental Salmonella contamination in caged and freerange layer flocks
    • Wales A, Breslin M, Carter B, Sayers R, Davies R. 2007. A longitudinal study of environmental Salmonella contamination in caged and freerange layer flocks. Avian Pathol 36:187–197. https://doi.org/10.1080/03079450701338755.
    • (2007) Avian Pathol , vol.36 , pp. 187-197
    • Wales, A.1    Breslin, M.2    Carter, B.3    Sayers, R.4    Davies, R.5
  • 51
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461. https://doi.org/10.1093/bioinformatics/btq461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 52
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. 2012. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610–618. https://doi.org/10.1038/ismej.2011.139.
    • (2012) ISME J , vol.6 , pp. 610-618
    • McDonald, D.1    Price, M.N.2    Goodrich, J.3    Nawrocki, E.P.4    Desantis, T.Z.5    Probst, A.6    Ersen, G.L.7    Knight, R.8    Hugenholtz, P.9
  • 54
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267. https://doi.org/10.1128/AEM.00062-07.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 55
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2 approximately maximumlikelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP. 2010. FastTree 2 approximately maximumlikelihood trees for large alignments. PLoS One 5:e9490. https://doi.org/10.1371/journal.pone.0009490.
    • (2010) Plos One , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 56
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: A new phylogenetic method for comparing microbial communities
    • Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228–8235. https://doi.org/10.1128/AEM.71.12.8228-8235.2005.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 57
    • 84991526597 scopus 로고    scopus 로고
    • EMPeror: A tool for visualizing high-throughput microbial community data
    • Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R. 2013. EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience 2:16. https://doi.org/10.1186/2047-217X-2-16.
    • (2013) Gigascience , vol.2 , pp. 16
    • Vázquez-Baeza, Y.1    Pirrung, M.2    Gonzalez, A.3    Knight, R.4
  • 58
    • 84958442612 scopus 로고
    • The estimation of the bactericidal power of the blood
    • Miles AA, Misra SS, Irwin JO. 1938. The estimation of the bactericidal power of the blood. J Hyg (Lond) 38:732–749. https://doi.org/10.1017/S002217240001158X.
    • (1938) J Hyg (Lond) , vol.38 , pp. 732-749
    • Miles, A.A.1    Misra, S.S.2    Irwin, J.O.3
  • 59
    • 85029223398 scopus 로고    scopus 로고
    • EUCAST guidelines for detection of resistance mechanisms and specific resistances of clinical and/or epidemiological importance, version 1.0. European Committee on Antimicrobial Susceptibility Testing
    • EUCAST Subcommittee for Detection of Resistance Mechanisms and Specific Resistances of Clinical and/or Epidemiological Importance. 2013. EUCAST guidelines for detection of resistance mechanisms and specific resistances of clinical and/or epidemiological importance, version 1.0. European Committee on Antimicrobial Susceptibility Testing. http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Resistance:mechanisms/EUCAST_detection_of_resistance:mechanisms_v1.0_20131211.pdf.
    • (2013)
  • 61
    • 28944447789 scopus 로고    scopus 로고
    • Rapid and simple detection of blaCTX-M genes by multiplex PCR assay
    • Xu L, Ensor V, Gossain S, Nye K, Hawkey P. 2005. Rapid and simple detection of blaCTX-M genes by multiplex PCR assay. J Med Microbiol 54:1183–1187. https://doi.org/10.1099/jmm.0.46160-0.
    • (2005) J Med Microbiol , vol.54 , pp. 1183-1187
    • Xu, L.1    Ensor, V.2    Gossain, S.3    Nye, K.4    Hawkey, P.5
  • 62
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120. https://doi.org/10.1093/bioinformatics/btu170.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 63
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760. https://doi.org/10.1093/bioinformatics/btp324.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 64
    • 68549104404 scopus 로고    scopus 로고
    • 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. https://doi.org/10.1093/bioinformatics/btp352.
    • Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6    Marth, G.7    Abecasis, G.8    Durbin, R.9
  • 65
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033.
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1


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