-
1
-
-
53849111617
-
Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens
-
M. Achtman Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens Annu. Rev. Microbiol. 62 2008 53 70
-
(2008)
Annu. Rev. Microbiol.
, vol.62
, pp. 53-70
-
-
Achtman, M.1
-
2
-
-
0033598784
-
Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis
-
M. Achtman, K. Zurth, G. Morelli, G. Torrea, A. Guiyoule, and E. Carniel Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis Proc. Natl. Acad. Sci. USA 96 1999 14043 14048
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 14043-14048
-
-
Achtman, M.1
Zurth, K.2
Morelli, G.3
Torrea, G.4
Guiyoule, A.5
Carniel, E.6
-
3
-
-
84864059917
-
Multilocus sequence typing as a replacement for serotyping in Salmonella enterica
-
M. Achtman, J. Wain, F.X. Weill, S. Nair, Z. Zhou, V. Sangal, M.G. Krauland, J.L. Hale, H. Harbottle, A. Uesbeck, et al. S. Enterica MLST Study Group Multilocus sequence typing as a replacement for serotyping in Salmonella enterica PLoS Pathog. 8 2012 e1002776
-
(2012)
PLoS Pathog.
, vol.8
, pp. e1002776
-
-
Achtman, M.1
Wain, J.2
Weill, F.X.3
Nair, S.4
Zhou, Z.5
Sangal, V.6
Krauland, M.G.7
Hale, J.L.8
Harbottle, H.9
Uesbeck, A.10
-
4
-
-
84902986168
-
Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association
-
M.T. Alam, R.A. Petit 3rd, E.K. Crispell, T.A. Thornton, K.N. Conneely, Y. Jiang, S.W. Satola, and T.D. Read Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association Genome Biol. Evol. 6 2014 1174 1185
-
(2014)
Genome Biol. Evol.
, vol.6
, pp. 1174-1185
-
-
Alam, M.T.1
Petit, R.A.2
Crispell, E.K.3
Thornton, T.A.4
Conneely, K.N.5
Jiang, Y.6
Satola, S.W.7
Read, T.D.8
-
5
-
-
84954389558
-
International cooperation to improve access to and sustain effectiveness of antimicrobials
-
C. Årdal, K. Outterson, S.J. Hoffman, A. Ghafur, M. Sharland, N. Ranganathan, R. Smith, A. Zorzet, J. Cohn, D. Pittet, and et al. International cooperation to improve access to and sustain effectiveness of antimicrobials Lancet 387 2016 296 307
-
(2016)
Lancet
, vol.387
, pp. 296-307
-
-
Årdal, C.1
Outterson, K.2
Hoffman, S.J.3
Ghafur, A.4
Sharland, M.5
Ranganathan, N.6
Smith, R.7
Zorzet, A.8
Cohn, J.9
Pittet, D.10
-
6
-
-
34249747813
-
A novel linear plasmid mediates flagellar variation in Salmonella Typhi
-
S. Baker, J. Hardy, K.E. Sanderson, M. Quail, I. Goodhead, R.A. Kingsley, J. Parkhill, B. Stocker, and G. Dougan A novel linear plasmid mediates flagellar variation in Salmonella Typhi PLoS Pathog. 3 2007 e59
-
(2007)
PLoS Pathog.
, vol.3
, pp. e59
-
-
Baker, S.1
Hardy, J.2
Sanderson, K.E.3
Quail, M.4
Goodhead, I.5
Kingsley, R.A.6
Parkhill, J.7
Stocker, B.8
Dougan, G.9
-
7
-
-
37349058158
-
Vaccine escape recombinants emerge after pneumococcal vaccination in the United States
-
A.B. Brueggemann, R. Pai, D.W. Crook, and B. Beall Vaccine escape recombinants emerge after pneumococcal vaccination in the United States PLoS Pathog. 3 2007 e168
-
(2007)
PLoS Pathog.
, vol.3
, pp. e168
-
-
Brueggemann, A.B.1
Pai, R.2
Crook, D.W.3
Beall, B.4
-
8
-
-
84895895475
-
Evolution and transmission of drug-resistant tuberculosis in a Russian population
-
N. Casali, V. Nikolayevskyy, Y. Balabanova, S.R. Harris, O. Ignatyeva, I. Kontsevaya, J. Corander, J. Bryant, J. Parkhill, S. Nejentsev, and et al. Evolution and transmission of drug-resistant tuberculosis in a Russian population Nat. Genet. 46 2014 279 286
-
(2014)
Nat. Genet.
, vol.46
, pp. 279-286
-
-
Casali, N.1
Nikolayevskyy, V.2
Balabanova, Y.3
Harris, S.R.4
Ignatyeva, O.5
Kontsevaya, I.6
Corander, J.7
Bryant, J.8
Parkhill, J.9
Nejentsev, S.10
-
9
-
-
4644293305
-
Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis
-
P.S. Chain, E. Carniel, F.W. Larimer, J. Lamerdin, P.O. Stoutland, W.M. Regala, A.M. Georgescu, L.M. Vergez, M.L. Land, V.L. Motin, and et al. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis Proc. Natl. Acad. Sci. USA 101 2004 13826 13831
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 13826-13831
-
-
Chain, P.S.1
Carniel, E.2
Larimer, F.W.3
Lamerdin, J.4
Stoutland, P.O.5
Regala, W.M.6
Georgescu, A.M.7
Vergez, L.M.8
Land, M.L.9
Motin, V.L.10
-
10
-
-
84872457224
-
Next-generation phylogenomics
-
C.X. Chan, and M.A. Ragan Next-generation phylogenomics Biol. Direct 8 2013 3
-
(2013)
Biol. Direct
, vol.8
, pp. 3
-
-
Chan, C.X.1
Ragan, M.A.2
-
11
-
-
84857190262
-
Human genetic susceptibility to infectious disease
-
S.J. Chapman, and A.V. Hill Human genetic susceptibility to infectious disease Nat. Rev. Genet. 13 2012 175 188
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 175-188
-
-
Chapman, S.J.1
Hill, A.V.2
-
12
-
-
36749055696
-
Antimicrobial drug resistance of Salmonella enterica serovar typhi in Asia and molecular mechanism of reduced susceptibility to the fluoroquinolones
-
T.T. Chau, J.I. Campbell, C.M. Galindo, N. Van Minh Hoang, T.S. Diep, T.T. Nga, N. Van Vinh Chau, P.Q. Tuan, A.L. Page, R.L. Ochiai, and et al. Antimicrobial drug resistance of Salmonella enterica serovar typhi in asia and molecular mechanism of reduced susceptibility to the fluoroquinolones Antimicrob. Agents Chemother. 51 2007 4315 4323
-
(2007)
Antimicrob. Agents Chemother.
, vol.51
, pp. 4315-4323
-
-
Chau, T.T.1
Campbell, J.I.2
Galindo, C.M.3
Van Minh Hoang, N.4
Diep, T.S.5
Nga, T.T.6
Van Vinh Chau, N.7
Tuan, P.Q.8
Page, A.L.9
Ochiai, R.L.10
-
13
-
-
84925631043
-
The advent of genome-wide association studies for bacteria
-
P.E. Chen, and B.J. Shapiro The advent of genome-wide association studies for bacteria Curr. Opin. Microbiol. 25 2015 17 24
-
(2015)
Curr. Opin. Microbiol.
, vol.25
, pp. 17-24
-
-
Chen, P.E.1
Shapiro, B.J.2
-
14
-
-
84895858474
-
Dense genomic sampling identifies highways of pneumococcal recombination
-
C. Chewapreecha, S.R. Harris, N.J. Croucher, C. Turner, P. Marttinen, L. Cheng, A. Pessia, D.M. Aanensen, A.E. Mather, A.J. Page, and et al. Dense genomic sampling identifies highways of pneumococcal recombination Nat. Genet. 46 2014 305 309
-
(2014)
Nat. Genet.
, vol.46
, pp. 305-309
-
-
Chewapreecha, C.1
Harris, S.R.2
Croucher, N.J.3
Turner, C.4
Marttinen, P.5
Cheng, L.6
Pessia, A.7
Aanensen, D.M.8
Mather, A.E.9
Page, A.J.10
-
15
-
-
84908135412
-
Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes
-
C. Chewapreecha, P. Marttinen, N.J. Croucher, S.J. Salter, S.R. Harris, A.E. Mather, W.P. Hanage, D. Goldblatt, F.H. Nosten, C. Turner, and et al. Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes PLoS Genet. 10 2014 e1004547
-
(2014)
PLoS Genet.
, vol.10
, pp. e1004547
-
-
Chewapreecha, C.1
Marttinen, P.2
Croucher, N.J.3
Salter, S.J.4
Harris, S.R.5
Mather, A.E.6
Hanage, W.P.7
Goldblatt, D.8
Nosten, F.H.9
Turner, C.10
-
16
-
-
70349304423
-
Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae
-
J. Chun, C.J. Grim, N.A. Hasan, J.H. Lee, S.Y. Choi, B.J. Haley, E. Taviani, Y.S. Jeon, D.W. Kim, J.H. Lee, and et al. Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae Proc. Natl. Acad. Sci. USA 106 2009 15442 15447
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 15442-15447
-
-
Chun, J.1
Grim, C.J.2
Hasan, N.A.3
Lee, J.H.4
Choi, S.Y.5
Haley, B.J.6
Taviani, E.7
Jeon, Y.S.8
Kim, D.W.9
Lee, J.H.10
-
17
-
-
84907371489
-
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
-
F. Coll, R. McNerney, J.A. Guerra-Assunção, J.R. Glynn, J. Perdigão, M. Viveiros, I. Portugal, A. Pain, N. Martin, and T.G. Clark A robust SNP barcode for typing Mycobacterium tuberculosis complex strains Nat. Commun. 5 2014 4812
-
(2014)
Nat. Commun.
, vol.5
, pp. 4812
-
-
Coll, F.1
McNerney, R.2
Guerra-Assunção, J.A.3
Glynn, J.R.4
Perdigão, J.5
Viveiros, M.6
Portugal, I.7
Pain, A.8
Martin, N.9
Clark, T.G.10
-
18
-
-
77952841173
-
Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved
-
I. Comas, J. Chakravartti, P.M. Small, J. Galagan, S. Niemann, K. Kremer, J.D. Ernst, and S. Gagneux Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved Nat. Genet. 42 2010 498 503
-
(2010)
Nat. Genet.
, vol.42
, pp. 498-503
-
-
Comas, I.1
Chakravartti, J.2
Small, P.M.3
Galagan, J.4
Niemann, S.5
Kremer, K.6
Ernst, J.D.7
Gagneux, S.8
-
19
-
-
84884995578
-
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans
-
I. Comas, M. Coscolla, T. Luo, S. Borrell, K.E. Holt, M. Kato-Maeda, J. Parkhill, B. Malla, S. Berg, G. Thwaites, and et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans Nat. Genet. 45 2013 1176 1182
-
(2013)
Nat. Genet.
, vol.45
, pp. 1176-1182
-
-
Comas, I.1
Coscolla, M.2
Luo, T.3
Borrell, S.4
Holt, K.E.5
Kato-Maeda, M.6
Parkhill, J.7
Malla, B.8
Berg, S.9
Thwaites, G.10
-
20
-
-
84947417802
-
M. Tuberculosis T Cell Epitope Analysis Reveals Paucity of Antigenic Variation and Identifies Rare Variable TB Antigens
-
M. Coscolla, R. Copin, J. Sutherland, F. Gehre, B. de Jong, O. Owolabi, G. Mbayo, F. Giardina, J.D. Ernst, and S. Gagneux M. tuberculosis T Cell Epitope Analysis Reveals Paucity of Antigenic Variation and Identifies Rare Variable TB Antigens Cell Host Microbe 18 2015 538 548
-
(2015)
Cell Host Microbe
, vol.18
, pp. 538-548
-
-
Coscolla, M.1
Copin, R.2
Sutherland, J.3
Gehre, F.4
De Jong, B.5
Owolabi, O.6
Mbayo, G.7
Giardina, F.8
Ernst, J.D.9
Gagneux, S.10
-
21
-
-
84960145647
-
Helicobacter pylori Diversity and Gastric Cancer Risk
-
T.L. Cover Helicobacter pylori Diversity and Gastric Cancer Risk MBio 7 2016 7
-
(2016)
MBio
, vol.7
, pp. 7
-
-
Cover, T.L.1
-
22
-
-
84919359586
-
The application of genomics to tracing bacterial pathogen transmission
-
N.J. Croucher, and X. Didelot The application of genomics to tracing bacterial pathogen transmission Curr. Opin. Microbiol. 23 2015 62 67
-
(2015)
Curr. Opin. Microbiol.
, vol.23
, pp. 62-67
-
-
Croucher, N.J.1
Didelot, X.2
-
23
-
-
79251544864
-
Rapid pneumococcal evolution in response to clinical interventions
-
N.J. Croucher, S.R. Harris, C. Fraser, M.A. Quail, J. Burton, M. van der Linden, L. McGee, A. von Gottberg, J.H. Song, K.S. Ko, and et al. Rapid pneumococcal evolution in response to clinical interventions Science 331 2011 430 434
-
(2011)
Science
, vol.331
, pp. 430-434
-
-
Croucher, N.J.1
Harris, S.R.2
Fraser, C.3
Quail, M.A.4
Burton, J.5
Van Der Linden, M.6
McGee, L.7
Von Gottberg, A.8
Song, J.H.9
Ko, K.S.10
-
24
-
-
84878735463
-
Population genomics of post-vaccine changes in pneumococcal epidemiology
-
N.J. Croucher, J.A. Finkelstein, S.I. Pelton, P.K. Mitchell, G.M. Lee, J. Parkhill, S.D. Bentley, W.P. Hanage, and M. Lipsitch Population genomics of post-vaccine changes in pneumococcal epidemiology Nat. Genet. 45 2013 656 663
-
(2013)
Nat. Genet.
, vol.45
, pp. 656-663
-
-
Croucher, N.J.1
Finkelstein, J.A.2
Pelton, S.I.3
Mitchell, P.K.4
Lee, G.M.5
Parkhill, J.6
Bentley, S.D.7
Hanage, W.P.8
Lipsitch, M.9
-
26
-
-
84933069206
-
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
-
N.J. Croucher, A.J. Page, T.R. Connor, A.J. Delaney, J.A. Keane, S.D. Bentley, J. Parkhill, and S.R. Harris Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins Nucleic Acids Res. 43 2015 e15
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e15
-
-
Croucher, N.J.1
Page, A.J.2
Connor, T.R.3
Delaney, A.J.4
Keane, J.A.5
Bentley, S.D.6
Parkhill, J.7
Harris, S.R.8
-
27
-
-
84859754930
-
Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. Cholerae virulence
-
B.W. Davies, R.W. Bogard, T.S. Young, and J.J. Mekalanos Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence Cell 149 2012 358 370
-
(2012)
Cell
, vol.149
, pp. 358-370
-
-
Davies, B.W.1
Bogard, R.W.2
Young, T.S.3
Mekalanos, J.J.4
-
28
-
-
33846032295
-
A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?
-
X. Didelot, M. Achtman, J. Parkhill, N.R. Thomson, and D. Falush A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination? Genome Res. 17 2007 61 68
-
(2007)
Genome Res.
, vol.17
, pp. 61-68
-
-
Didelot, X.1
Achtman, M.2
Parkhill, J.3
Thomson, N.R.4
Falush, D.5
-
29
-
-
84871366407
-
Microevolutionary analysis of Clostridium difficile genomes to investigate transmission
-
X. Didelot, D.W. Eyre, M. Cule, C.L. Ip, M.A. Ansari, D. Griffiths, A. Vaughan, L. O'Connor, T. Golubchik, E.M. Batty, and et al. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission Genome Biol. 13 2012 R118
-
(2012)
Genome Biol.
, vol.13
, pp. R118
-
-
Didelot, X.1
Eyre, D.W.2
Cule, M.3
Ip, C.L.4
Ansari, M.A.5
Griffiths, D.6
Vaughan, A.7
O'Connor, L.8
Golubchik, T.9
Batty, E.M.10
-
30
-
-
84926204537
-
The role of China in the global spread of the current cholera pandemic
-
X. Didelot, B. Pang, Z. Zhou, A. McCann, P. Ni, D. Li, M. Achtman, and B. Kan The role of China in the global spread of the current cholera pandemic PLoS Genet. 11 2015 e1005072
-
(2015)
PLoS Genet.
, vol.11
, pp. e1005072
-
-
Didelot, X.1
Pang, B.2
Zhou, Z.3
McCann, A.4
Ni, P.5
Li, D.6
Achtman, M.7
Kan, B.8
-
31
-
-
84958178396
-
Within-host evolution of bacterial pathogens
-
X. Didelot, A.S. Walker, T.E. Peto, D.W. Crook, and D.J. Wilson Within-host evolution of bacterial pathogens Nat. Rev. Microbiol. 14 2016 150 162
-
(2016)
Nat. Rev. Microbiol.
, vol.14
, pp. 150-162
-
-
Didelot, X.1
Walker, A.S.2
Peto, T.E.3
Crook, D.W.4
Wilson, D.J.5
-
32
-
-
84907518951
-
Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever
-
G. Dougan, and S. Baker Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever Annu. Rev. Microbiol. 68 2014 317 336
-
(2014)
Annu. Rev. Microbiol.
, vol.68
, pp. 317-336
-
-
Dougan, G.1
Baker, S.2
-
33
-
-
84906732045
-
Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions
-
B.E. Dutilh, C.C. Thompson, A.C. Vicente, M.A. Marin, C. Lee, G.G. Silva, R. Schmieder, B.G. Andrade, L. Chimetto, D. Cuevas, and et al. Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions BMC Genomics 15 2014 654
-
(2014)
BMC Genomics
, vol.15
, pp. 654
-
-
Dutilh, B.E.1
Thompson, C.C.2
Vicente, A.C.3
Marin, M.A.4
Lee, C.5
Silva, G.G.6
Schmieder, R.7
Andrade, B.G.8
Chimetto, L.9
Cuevas, D.10
-
34
-
-
0037022337
-
Comparative genomic analysis of Vibrio cholerae: Genes that correlate with cholera endemic and pandemic disease
-
M. Dziejman, E. Balon, D. Boyd, C.M. Fraser, J.F. Heidelberg, and J.J. Mekalanos Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease Proc. Natl. Acad. Sci. USA 99 2002 1556 1561
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 1556-1561
-
-
Dziejman, M.1
Balon, E.2
Boyd, D.3
Fraser, C.M.4
Heidelberg, J.F.5
Mekalanos, J.J.6
-
35
-
-
84969526136
-
-
arXiv, arXiv:1510.06863
-
Earle, S.G., Wu, C.-H., Charlesworth, J., Stoesser, N., Gordon, N.C., Walker, T.M., Spencer, C.C.A., Iqbal, Z., Clifton, D.A., Hopkins, K.L., et al. (2016). Identifying lineage effects when controlling for population structure improves power in bacterial association studies. arXiv, arXiv:1510.06863, http://arxiv.org/abs/1510.06863.
-
(2016)
Identifying Lineage Effects When Controlling for Population Structure Improves Power in Bacterial Association Studies
-
-
Earle, S.G.1
Wu, C.-H.2
Charlesworth, J.3
Stoesser, N.4
Gordon, N.C.5
Walker, T.M.6
Spencer, C.C.A.7
Iqbal, Z.8
Clifton, D.A.9
Hopkins, K.L.10
-
36
-
-
84965189781
-
Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient
-
V. Eldholm, G. Norheim, B. von der Lippe, W. Kinander, U.R. Dahle, D.A. Caugant, T. Mannsåker, A.T. Mengshoel, A.M. Dyrhol-Riise, and F. Balloux Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient Genome Biol. 15 2014 490
-
(2014)
Genome Biol.
, vol.15
, pp. 490
-
-
Eldholm, V.1
Norheim, G.2
Von Der Lippe, B.3
Kinander, W.4
Dahle, U.R.5
Caugant, D.A.6
Mannsåker, T.7
Mengshoel, A.T.8
Dyrhol-Riise, A.M.9
Balloux, F.10
-
37
-
-
84920901628
-
Genomic epidemiology of the Haitian cholera outbreak: A single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic
-
M. Eppinger, T. Pearson, S.S. Koenig, O. Pearson, N. Hicks, S. Agrawal, F. Sanjar, K. Galens, S. Daugherty, J. Crabtree, and et al. Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic MBio 5 2014 e01721
-
(2014)
MBio
, vol.5
, pp. e01721
-
-
Eppinger, M.1
Pearson, T.2
Koenig, S.S.3
Pearson, O.4
Hicks, N.5
Agrawal, S.6
Sanjar, F.7
Galens, K.8
Daugherty, S.9
Crabtree, J.10
-
38
-
-
33646591556
-
Beijing/W genotype Mycobacterium tuberculosis and drug resistance
-
European Concerted Action on New Generation Genetic Markers and Techniques for the Epidemiology and Control of Tuberculosis Beijing/W genotype Mycobacterium tuberculosis and drug resistance Emerg. Infect. Dis. 12 2006 736 743
-
(2006)
Emerg. Infect. Dis.
, vol.12
, pp. 736-743
-
-
-
39
-
-
84884510020
-
Diverse sources of C. Difficile infection identified on whole-genome sequencing
-
D.W. Eyre, M.L. Cule, D.J. Wilson, D. Griffiths, A. Vaughan, L. O'Connor, C.L. Ip, T. Golubchik, E.M. Batty, J.M. Finney, and et al. Diverse sources of C. difficile infection identified on whole-genome sequencing N. Engl. J. Med. 369 2013 1195 1205
-
(2013)
N. Engl. J. Med.
, vol.369
, pp. 1195-1205
-
-
Eyre, D.W.1
Cule, M.L.2
Wilson, D.J.3
Griffiths, D.4
Vaughan, A.5
O'Connor, L.6
Ip, C.L.7
Golubchik, T.8
Batty, E.M.9
Finney, J.M.10
-
40
-
-
33746556194
-
Genome-wide association mapping in bacteria?
-
D. Falush, and R. Bowden Genome-wide association mapping in bacteria? Trends Microbiol. 14 2006 353 355
-
(2006)
Trends Microbiol.
, vol.14
, pp. 353-355
-
-
Falush, D.1
Bowden, R.2
-
41
-
-
0037423837
-
Traces of human migrations in Helicobacter pylori populations
-
D. Falush, T. Wirth, B. Linz, J.K. Pritchard, M. Stephens, M. Kidd, M.J. Blaser, D.Y. Graham, S. Vacher, G.I. Perez-Perez, and et al. Traces of human migrations in Helicobacter pylori populations Science 299 2003 1582 1585
-
(2003)
Science
, vol.299
, pp. 1582-1585
-
-
Falush, D.1
Wirth, T.2
Linz, B.3
Pritchard, J.K.4
Stephens, M.5
Kidd, M.6
Blaser, M.J.7
Graham, D.Y.8
Vacher, S.9
Perez-Perez, G.I.10
-
42
-
-
84884992001
-
Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
-
M.R. Farhat, B.J. Shapiro, K.J. Kieser, R. Sultana, K.R. Jacobson, T.C. Victor, R.M. Warren, E.M. Streicher, A. Calver, A. Sloutsky, and et al. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis Nat. Genet. 45 2013 1183 1189
-
(2013)
Nat. Genet.
, vol.45
, pp. 1183-1189
-
-
Farhat, M.R.1
Shapiro, B.J.2
Kieser, K.J.3
Sultana, R.4
Jacobson, K.R.5
Victor, T.C.6
Warren, R.M.7
Streicher, E.M.8
Calver, A.9
Sloutsky, A.10
-
43
-
-
84862886432
-
Invasive non-typhoidal salmonella disease: An emerging and neglected tropical disease in Africa
-
N.A. Feasey, G. Dougan, R.A. Kingsley, R.S. Heyderman, and M.A. Gordon Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa Lancet 379 2012 2489 2499
-
(2012)
Lancet
, vol.379
, pp. 2489-2499
-
-
Feasey, N.A.1
Dougan, G.2
Kingsley, R.A.3
Heyderman, R.S.4
Gordon, M.A.5
-
44
-
-
81155131410
-
Gene decay in Shigella as an incipient stage of host-adaptation
-
Y. Feng, Z. Chen, and S.L. Liu Gene decay in Shigella as an incipient stage of host-adaptation PLoS ONE 6 2011 e27754
-
(2011)
PLoS ONE
, vol.6
, pp. e27754
-
-
Feng, Y.1
Chen, Z.2
Liu, S.L.3
-
45
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
R.D. Fleischmann, M.D. Adams, O. White, R.A. Clayton, E.F. Kirkness, A.R. Kerlavage, C.J. Bult, J.F. Tomb, B.A. Dougherty, J.M. Merrick, and et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd Science 269 1995 496 512
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
Clayton, R.A.4
Kirkness, E.F.5
Kerlavage, A.R.6
Bult, C.J.7
Tomb, J.F.8
Dougherty, B.A.9
Merrick, J.M.10
-
46
-
-
84879682699
-
Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
-
C.B. Ford, R.R. Shah, M.K. Maeda, S. Gagneux, M.B. Murray, T. Cohen, J.C. Johnston, J. Gardy, M. Lipsitch, and S.M. Fortune Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis Nat. Genet. 45 2013 784 790
-
(2013)
Nat. Genet.
, vol.45
, pp. 784-790
-
-
Ford, C.B.1
Shah, R.R.2
Maeda, M.K.3
Gagneux, S.4
Murray, M.B.5
Cohen, T.6
Johnston, J.C.7
Gardy, J.8
Lipsitch, M.9
Fortune, S.M.10
-
49
-
-
1842585488
-
Salmonella typhi encodes a functional cytolethal distending toxin that is delivered into host cells by a bacterial-internalization pathway
-
E. Haghjoo, and J.E. Galán Salmonella typhi encodes a functional cytolethal distending toxin that is delivered into host cells by a bacterial-internalization pathway Proc. Natl. Acad. Sci. USA 101 2004 4614 4619
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 4614-4619
-
-
Haghjoo, E.1
Galán, J.E.2
-
50
-
-
79955666433
-
New flagellin gene for Salmonella enterica serovar Typhi from the East Indonesian archipelago
-
M. Hatta, A.R. Sultan, R. Pastoor, and H.L. Smits New flagellin gene for Salmonella enterica serovar Typhi from the East Indonesian archipelago Am. J. Trop. Med. Hyg. 84 2011 429 434
-
(2011)
Am. J. Trop. Med. Hyg.
, vol.84
, pp. 429-434
-
-
Hatta, M.1
Sultan, A.R.2
Pastoor, R.3
Smits, H.L.4
-
51
-
-
84871990888
-
Emergence and global spread of epidemic healthcare-associated Clostridium difficile
-
M. He, F. Miyajima, P. Roberts, L. Ellison, D.J. Pickard, M.J. Martin, T.R. Connor, S.R. Harris, D. Fairley, K.B. Bamford, and et al. Emergence and global spread of epidemic healthcare-associated Clostridium difficile Nat. Genet. 45 2013 109 113
-
(2013)
Nat. Genet.
, vol.45
, pp. 109-113
-
-
He, M.1
Miyajima, F.2
Roberts, P.3
Ellison, L.4
Pickard, D.J.5
Martin, M.J.6
Connor, T.R.7
Harris, S.R.8
Fairley, D.9
Bamford, K.B.10
-
52
-
-
58149174244
-
High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography
-
R. Hershberg, M. Lipatov, P.M. Small, H. Sheffer, S. Niemann, S. Homolka, J.C. Roach, K. Kremer, D.A. Petrov, M.W. Feldman, and S. Gagneux High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography PLoS Biol. 6 2008 e311
-
(2008)
PLoS Biol.
, vol.6
, pp. e311
-
-
Hershberg, R.1
Lipatov, M.2
Small, P.M.3
Sheffer, H.4
Niemann, S.5
Homolka, S.6
Roach, J.C.7
Kremer, K.8
Petrov, D.A.9
Feldman, M.W.10
Gagneux, S.11
-
53
-
-
48349124258
-
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
-
K.E. Holt, J. Parkhill, C.J. Mazzoni, P. Roumagnac, F.X. Weill, I. Goodhead, R. Rance, S. Baker, D.J. Maskell, J. Wain, and et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi Nat. Genet. 40 2008 987 993
-
(2008)
Nat. Genet.
, vol.40
, pp. 987-993
-
-
Holt, K.E.1
Parkhill, J.2
Mazzoni, C.J.3
Roumagnac, P.4
Weill, F.X.5
Goodhead, I.6
Rance, R.7
Baker, S.8
Maskell, D.J.9
Wain, J.10
-
54
-
-
84856587343
-
High-resolution genotyping of the endemic Salmonella Typhi population during a VI (typhoid) vaccination trial in Kolkata
-
K.E. Holt, S. Dutta, B. Manna, S.K. Bhattacharya, B. Bhaduri, D.J. Pickard, R.L. Ochiai, M. Ali, J.D. Clemens, and G. Dougan High-resolution genotyping of the endemic Salmonella Typhi population during a Vi (typhoid) vaccination trial in Kolkata PLoS Negl. Trop. Dis. 6 2012 e1490
-
(2012)
PLoS Negl. Trop. Dis.
, vol.6
, pp. e1490
-
-
Holt, K.E.1
Dutta, S.2
Manna, B.3
Bhattacharya, S.K.4
Bhaduri, B.5
Pickard, D.J.6
Ochiai, R.L.7
Ali, M.8
Clemens, J.D.9
Dougan, G.10
-
55
-
-
84955557346
-
Toward Complete Bacterial Genome Sequencing Through the Combined Use of Multiple Next-Generation Sequencing Platforms
-
H. Jeong, D.H. Lee, C.M. Ryu, and S.H. Park Toward Complete Bacterial Genome Sequencing Through the Combined Use of Multiple Next-Generation Sequencing Platforms J. Microbiol. Biotechnol. 26 2016 207 212
-
(2016)
J. Microbiol. Biotechnol.
, vol.26
, pp. 207-212
-
-
Jeong, H.1
Lee, D.H.2
Ryu, C.M.3
Park, S.H.4
-
56
-
-
18644378721
-
Genome sequence of Shigella flexneri 2a: Insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157
-
Q. Jin, Z. Yuan, J. Xu, Y. Wang, Y. Shen, W. Lu, J. Wang, H. Liu, J. Yang, F. Yang, and et al. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157 Nucleic Acids Res. 30 2002 4432 4441
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4432-4441
-
-
Jin, Q.1
Yuan, Z.2
Xu, J.3
Wang, Y.4
Shen, Y.5
Lu, W.6
Wang, J.7
Liu, H.8
Yang, J.9
Yang, F.10
-
57
-
-
33646236087
-
Invasive multidrug-resistant non-typhoidal Salmonella infections in Africa: Zoonotic or anthroponotic transmission?
-
S. Kariuki, G. Revathi, N. Kariuki, J. Kiiru, J. Mwituria, J. Muyodi, J.W. Githinji, D. Kagendo, A. Munyalo, and C.A. Hart Invasive multidrug-resistant non-typhoidal Salmonella infections in Africa: zoonotic or anthroponotic transmission? J. Med. Microbiol. 55 2006 585 591
-
(2006)
J. Med. Microbiol.
, vol.55
, pp. 585-591
-
-
Kariuki, S.1
Revathi, G.2
Kariuki, N.3
Kiiru, J.4
Mwituria, J.5
Muyodi, J.6
Githinji, J.W.7
Kagendo, D.8
Munyalo, A.9
Hart, C.A.10
-
58
-
-
73249140740
-
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype
-
R.A. Kingsley, C.L. Msefula, N.R. Thomson, S. Kariuki, K.E. Holt, M.A. Gordon, D. Harris, L. Clarke, S. Whitehead, V. Sangal, and et al. Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype Genome Res. 19 2009 2279 2287
-
(2009)
Genome Res.
, vol.19
, pp. 2279-2287
-
-
Kingsley, R.A.1
Msefula, C.L.2
Thomson, N.R.3
Kariuki, S.4
Holt, K.E.5
Gordon, M.A.6
Harris, D.7
Clarke, L.8
Whitehead, S.9
Sangal, V.10
-
59
-
-
84958186684
-
Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host
-
E.J. Klemm, E. Gkrania-Klotsas, J. Hadfield, J.L. Forbester, S.R. Harris, C. Hale, J.N. Heath, T. Wileman, S. Clare, L. Kane, and et al. Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host Nature Microbiology 1 2016 15023
-
(2016)
Nature Microbiology
, vol.1
, pp. 15023
-
-
Klemm, E.J.1
Gkrania-Klotsas, E.2
Hadfield, J.3
Forbester, J.L.4
Harris, S.R.5
Hale, C.6
Heath, J.N.7
Wileman, T.8
Clare, S.9
Kane, L.10
-
60
-
-
84883407838
-
Understanding human variation in infectious disease susceptibility through clinical and cellular GWAS
-
D.C. Ko, and T.J. Urban Understanding human variation in infectious disease susceptibility through clinical and cellular GWAS PLoS Pathog. 9 2013 e1003424
-
(2013)
PLoS Pathog.
, vol.9
, pp. e1003424
-
-
Ko, D.C.1
Urban, T.J.2
-
61
-
-
84893416584
-
Human and Helicobacter pylori coevolution shapes the risk of gastric disease
-
N. Kodaman, A. Pazos, B.G. Schneider, M.B. Piazuelo, R. Mera, R.S. Sobota, L.A. Sicinschi, C.L. Shaffer, J. Romero-Gallo, T. de Sablet, and et al. Human and Helicobacter pylori coevolution shapes the risk of gastric disease Proc. Natl. Acad. Sci. USA 111 2014 1455 1460
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 1455-1460
-
-
Kodaman, N.1
Pazos, A.2
Schneider, B.G.3
Piazuelo, M.B.4
Mera, R.5
Sobota, R.S.6
Sicinschi, L.A.7
Shaffer, C.L.8
Romero-Gallo, J.9
De Sablet, T.10
-
62
-
-
84899830343
-
Predicting the virulence of MRSA from its genome sequence
-
M. Laabei, M. Recker, J.K. Rudkin, M. Aldeljawi, Z. Gulay, T.J. Sloan, P. Williams, J.L. Endres, K.W. Bayles, P.D. Fey, and et al. Predicting the virulence of MRSA from its genome sequence Genome Res. 24 2014 839 849
-
(2014)
Genome Res.
, vol.24
, pp. 839-849
-
-
Laabei, M.1
Recker, M.2
Rudkin, J.K.3
Aldeljawi, M.4
Gulay, Z.5
Sloan, T.J.6
Williams, P.7
Endres, J.L.8
Bayles, K.W.9
Fey, P.D.10
-
63
-
-
84943144528
-
Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus
-
M. Laabei, A.C. Uhlemann, F.D. Lowy, E.D. Austin, M. Yokoyama, K. Ouadi, E. Feil, H.A. Thorpe, B. Williams, M. Perkins, and et al. Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus PLoS Biol. 13 2015 e1002229
-
(2015)
PLoS Biol.
, vol.13
, pp. e1002229
-
-
Laabei, M.1
Uhlemann, A.C.2
Lowy, F.D.3
Austin, E.D.4
Yokoyama, M.5
Ouadi, K.6
Feil, E.7
Thorpe, H.A.8
Williams, B.9
Perkins, M.10
-
64
-
-
84908406609
-
Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: High-resolution picture of genomic changes that mediate immune evasion
-
e01974-e14
-
A. Lamelas, S.R. Harris, K. Röltgen, J.P. Dangy, J. Hauser, R.A. Kingsley, T.R. Connor, A. Sie, A. Hodgson, G. Dougan, and et al. Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion MBio 5 2014 e01974-e14
-
(2014)
MBio
, vol.5
-
-
Lamelas, A.1
Harris, S.R.2
Röltgen, K.3
Dangy, J.P.4
Hauser, J.5
Kingsley, R.A.6
Connor, T.R.7
Sie, A.8
Hodgson, A.9
Dougan, G.10
-
65
-
-
84868158515
-
Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice
-
T.D. Lawley, S. Clare, A.W. Walker, M.D. Stares, T.R. Connor, C. Raisen, D. Goulding, R. Rad, F. Schreiber, C. Brandt, and et al. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice PLoS Pathog. 8 2012 e1002995
-
(2012)
PLoS Pathog.
, vol.8
, pp. e1002995
-
-
Lawley, T.D.1
Clare, S.2
Walker, A.W.3
Stares, M.D.4
Connor, T.R.5
Raisen, C.6
Goulding, D.7
Rad, R.8
Schreiber, F.9
Brandt, C.10
-
66
-
-
84878802119
-
SnpTree - A web-server to identify and construct SNP trees from whole genome sequence data
-
P. Leekitcharoenphon, R.S. Kaas, M.C. Thomsen, C. Friis, S. Rasmussen, and F.M. Aarestrup snpTree - a web-server to identify and construct SNP trees from whole genome sequence data BMC Genomics 13 Suppl 7 2012 S6
-
(2012)
BMC Genomics
, vol.13
, pp. S6
-
-
Leekitcharoenphon, P.1
Kaas, R.S.2
Thomsen, M.C.3
Friis, C.4
Rasmussen, S.5
Aarestrup, F.M.6
-
67
-
-
82255186689
-
Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes
-
T.D. Lieberman, J.B. Michel, M. Aingaran, G. Potter-Bynoe, D. Roux, M.R. Davis Jr., D. Skurnik, N. Leiby, J.J. LiPuma, J.B. Goldberg, and et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes Nat. Genet. 43 2011 1275 1280
-
(2011)
Nat. Genet.
, vol.43
, pp. 1275-1280
-
-
Lieberman, T.D.1
Michel, J.B.2
Aingaran, M.3
Potter-Bynoe, G.4
Roux, D.5
Davis, M.R.6
Skurnik, D.7
Leiby, N.8
LiPuma, J.J.9
Goldberg, J.B.10
-
68
-
-
33847201150
-
An African origin for the intimate association between humans and Helicobacter pylori
-
B. Linz, F. Balloux, Y. Moodley, A. Manica, H. Liu, P. Roumagnac, D. Falush, C. Stamer, F. Prugnolle, S.W. van der Merwe, and et al. An African origin for the intimate association between humans and Helicobacter pylori Nature 445 2007 915 918
-
(2007)
Nature
, vol.445
, pp. 915-918
-
-
Linz, B.1
Balloux, F.2
Moodley, Y.3
Manica, A.4
Liu, H.5
Roumagnac, P.6
Falush, D.7
Stamer, C.8
Prugnolle, F.9
Van Der Merwe, S.W.10
-
69
-
-
13144252236
-
Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
-
M.C. Maiden, J.A. Bygraves, E. Feil, G. Morelli, J.E. Russell, R. Urwin, Q. Zhang, J. Zhou, K. Zurth, D.A. Caugant, and et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms Proc. Natl. Acad. Sci. USA 95 1998 3140 3145
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 3140-3145
-
-
Maiden, M.C.1
Bygraves, J.A.2
Feil, E.3
Morelli, G.4
Russell, J.E.5
Urwin, R.6
Zhang, Q.7
Zhou, J.8
Zurth, K.9
Caugant, D.A.10
-
70
-
-
84884290186
-
MLST revisited: The gene-by-gene approach to bacterial genomics
-
M.C. Maiden, M.J. Jansen van Rensburg, J.E. Bray, S.G. Earle, S.A. Ford, K.A. Jolley, and N.D. McCarthy MLST revisited: the gene-by-gene approach to bacterial genomics Nat. Rev. Microbiol. 11 2013 728 736
-
(2013)
Nat. Rev. Microbiol.
, vol.11
, pp. 728-736
-
-
Maiden, M.C.1
Jansen Van Rensburg, M.J.2
Bray, J.E.3
Earle, S.G.4
Ford, S.A.5
Jolley, K.A.6
McCarthy, N.D.7
-
71
-
-
84955119180
-
The 5300-year-old Helicobacter pylori genome of the Iceman
-
F. Maixner, B. Krause-Kyora, D. Turaev, A. Herbig, M.R. Hoopmann, J.L. Hallows, U. Kusebauch, E.E. Vigl, P. Malfertheiner, F. Megraud, and et al. The 5300-year-old Helicobacter pylori genome of the Iceman Science 351 2016 162 165
-
(2016)
Science
, vol.351
, pp. 162-165
-
-
Maixner, F.1
Krause-Kyora, B.2
Turaev, D.3
Herbig, A.4
Hoopmann, M.R.5
Hallows, J.L.6
Kusebauch, U.7
Vigl, E.E.8
Malfertheiner, P.9
Megraud, F.10
-
72
-
-
84942465718
-
Worldwide occurrence of integrative conjugative element encoding multidrug resistance determinants in epidemic Vibrio cholerae O1
-
M.A. Marin, E.L. Fonseca, B.N. Andrade, A.C. Cabral, and A.C. Vicente Worldwide occurrence of integrative conjugative element encoding multidrug resistance determinants in epidemic Vibrio cholerae O1 PLoS ONE 9 2014 e108728
-
(2014)
PLoS ONE
, vol.9
, pp. e108728
-
-
Marin, M.A.1
Fonseca, E.L.2
Andrade, B.N.3
Cabral, A.C.4
Vicente, A.C.5
-
73
-
-
84908425385
-
Environmental heterogeneity drives within-host diversification and evolution of Pseudomonas aeruginosa
-
e01592-e14
-
T. Markussen, R.L. Marvig, M. Gómez-Lozano, K. Aanæs, A.E. Burleigh, N. Høiby, H.K. Johansen, S. Molin, and L. Jelsbak Environmental heterogeneity drives within-host diversification and evolution of Pseudomonas aeruginosa MBio 5 2014 e01592-e14
-
(2014)
MBio
, vol.5
-
-
Markussen, T.1
Marvig, R.L.2
Gómez-Lozano, M.3
Aanæs, K.4
Burleigh, A.E.5
Høiby, N.6
Johansen, H.K.7
Molin, S.8
Jelsbak, L.9
-
74
-
-
84855261123
-
Detection of recombination events in bacterial genomes from large population samples
-
P. Marttinen, W.P. Hanage, N.J. Croucher, T.R. Connor, S.R. Harris, S.D. Bentley, and J. Corander Detection of recombination events in bacterial genomes from large population samples Nucleic Acids Res. 40 2012 e6
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e6
-
-
Marttinen, P.1
Hanage, W.P.2
Croucher, N.J.3
Connor, T.R.4
Harris, S.R.5
Bentley, S.D.6
Corander, J.7
-
75
-
-
85028139131
-
Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis
-
R.L. Marvig, L.M. Sommer, S. Molin, and H.K. Johansen Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis Nat. Genet. 47 2015 57 64
-
(2015)
Nat. Genet.
, vol.47
, pp. 57-64
-
-
Marvig, R.L.1
Sommer, L.M.2
Molin, S.3
Johansen, H.K.4
-
76
-
-
9644254192
-
Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid
-
M. McClelland, K.E. Sanderson, S.W. Clifton, P. Latreille, S. Porwollik, A. Sabo, R. Meyer, T. Bieri, P. Ozersky, M. McLellan, and et al. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid Nat. Genet. 36 2004 1268 1274
-
(2004)
Nat. Genet.
, vol.36
, pp. 1268-1274
-
-
McClelland, M.1
Sanderson, K.E.2
Clifton, S.W.3
Latreille, P.4
Porwollik, S.5
Sabo, A.6
Meyer, R.7
Bieri, T.8
Ozersky, P.9
McLellan, M.10
-
77
-
-
84958234886
-
'Add, stir and reduce': Yersinia spp. As model bacteria for pathogen evolution
-
A. McNally, N.R. Thomson, S. Reuter, and B.W. Wren 'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution Nat. Rev. Microbiol. 14 2016 177 190
-
(2016)
Nat. Rev. Microbiol.
, vol.14
, pp. 177-190
-
-
McNally, A.1
Thomson, N.R.2
Reuter, S.3
Wren, B.W.4
-
78
-
-
27444438599
-
The microbial pan-genome
-
D. Medini, C. Donati, H. Tettelin, V. Masignani, and R. Rappuoli The microbial pan-genome Curr. Opin. Genet. Dev. 15 2005 589 594
-
(2005)
Curr. Opin. Genet. Dev.
, vol.15
, pp. 589-594
-
-
Medini, D.1
Donati, C.2
Tettelin, H.3
Masignani, V.4
Rappuoli, R.5
-
79
-
-
84928483773
-
Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage
-
M. Merker, C. Blin, S. Mona, N. Duforet-Frebourg, S. Lecher, E. Willery, M.G. Blum, S. Rüsch-Gerdes, I. Mokrousov, E. Aleksic, and et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage Nat. Genet. 47 2015 242 249
-
(2015)
Nat. Genet.
, vol.47
, pp. 242-249
-
-
Merker, M.1
Blin, C.2
Mona, S.3
Duforet-Frebourg, N.4
Lecher, S.5
Willery, E.6
Blum, M.G.7
Rüsch-Gerdes, S.8
Mokrousov, I.9
Aleksic, E.10
-
80
-
-
58849086252
-
The peopling of the Pacific from a bacterial perspective
-
Y. Moodley, B. Linz, Y. Yamaoka, H.M. Windsor, S. Breurec, J.Y. Wu, A. Maady, S. Bernhöft, J.M. Thiberge, S. Phuanukoonnon, and et al. The peopling of the Pacific from a bacterial perspective Science 323 2009 527 530
-
(2009)
Science
, vol.323
, pp. 527-530
-
-
Moodley, Y.1
Linz, B.2
Yamaoka, Y.3
Windsor, H.M.4
Breurec, S.5
Wu, J.Y.6
Maady, A.7
Bernhöft, S.8
Thiberge, J.M.9
Phuanukoonnon, S.10
-
81
-
-
84863692086
-
Age of the association between Helicobacter pylori and man
-
Y. Moodley, B. Linz, R.P. Bond, M. Nieuwoudt, H. Soodyall, C.M. Schlebusch, S. Bernhöft, J. Hale, S. Suerbaum, L. Mugisha, and et al. Age of the association between Helicobacter pylori and man PLoS Pathog. 8 2012 e1002693
-
(2012)
PLoS Pathog.
, vol.8
, pp. e1002693
-
-
Moodley, Y.1
Linz, B.2
Bond, R.P.3
Nieuwoudt, M.4
Soodyall, H.5
Schlebusch, C.M.6
Bernhöft, S.7
Hale, J.8
Suerbaum, S.9
Mugisha, L.10
-
82
-
-
80053133499
-
Evidence for several waves of global transmission in the seventh cholera pandemic
-
A. Mutreja, D.W. Kim, N.R. Thomson, T.R. Connor, J.H. Lee, S. Kariuki, N.J. Croucher, S.Y. Choi, S.R. Harris, M. Lebens, and et al. Evidence for several waves of global transmission in the seventh cholera pandemic Nature 477 2011 462 465
-
(2011)
Nature
, vol.477
, pp. 462-465
-
-
Mutreja, A.1
Kim, D.W.2
Thomson, N.R.3
Connor, T.R.4
Lee, J.H.5
Kariuki, S.6
Croucher, N.J.7
Choi, S.Y.8
Harris, S.R.9
Lebens, M.10
-
83
-
-
84868201561
-
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa
-
C.K. Okoro, R.A. Kingsley, T.R. Connor, S.R. Harris, C.M. Parry, M.N. Al-Mashhadani, S. Kariuki, C.L. Msefula, M.A. Gordon, E. de Pinna, and et al. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa Nat. Genet. 44 2012 1215 1221
-
(2012)
Nat. Genet.
, vol.44
, pp. 1215-1221
-
-
Okoro, C.K.1
Kingsley, R.A.2
Connor, T.R.3
Harris, S.R.4
Parry, C.M.5
Al-Mashhadani, M.N.6
Kariuki, S.7
Msefula, C.L.8
Gordon, M.A.9
De Pinna, E.10
-
84
-
-
84901309600
-
The 2010 cholera outbreak in Haiti: How science solved a controversy
-
F.D. Orata, P.S. Keim, and Y. Boucher The 2010 cholera outbreak in Haiti: how science solved a controversy PLoS Pathog. 10 2014 e1003967
-
(2014)
PLoS Pathog.
, vol.10
, pp. e1003967
-
-
Orata, F.D.1
Keim, P.S.2
Boucher, Y.3
-
85
-
-
84947793096
-
Roary: Rapid large-scale prokaryote pan genome analysis
-
A.J. Page, C.A. Cummins, M. Hunt, V.K. Wong, S. Reuter, M.T. Holden, M. Fookes, D. Falush, J.A. Keane, and J. Parkhill Roary: rapid large-scale prokaryote pan genome analysis Bioinformatics 31 2015 3691 3693
-
(2015)
Bioinformatics
, vol.31
, pp. 3691-3693
-
-
Page, A.J.1
Cummins, C.A.2
Hunt, M.3
Wong, V.K.4
Reuter, S.5
Holden, M.T.6
Fookes, M.7
Falush, D.8
Keane, J.A.9
Parkhill, J.10
-
86
-
-
0035950154
-
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
-
J. Parkhill, G. Dougan, K.D. James, N.R. Thomson, D. Pickard, J. Wain, C. Churcher, K.L. Mungall, S.D. Bentley, M.T.G. Holden, and et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 Nature 413 2001 848 852
-
(2001)
Nature
, vol.413
, pp. 848-852
-
-
Parkhill, J.1
Dougan, G.2
James, K.D.3
Thomson, N.R.4
Pickard, D.5
Wain, J.6
Churcher, C.7
Mungall, K.L.8
Bentley, S.D.9
Holden, M.T.G.10
-
87
-
-
0042355274
-
Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica
-
J. Parkhill, M. Sebaihia, A. Preston, L.D. Murphy, N. Thomson, D.E. Harris, M.T. Holden, C.M. Churcher, S.D. Bentley, K.L. Mungall, and et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica Nat. Genet. 35 2003 32 40
-
(2003)
Nat. Genet.
, vol.35
, pp. 32-40
-
-
Parkhill, J.1
Sebaihia, M.2
Preston, A.3
Murphy, L.D.4
Thomson, N.5
Harris, D.E.6
Holden, M.T.7
Churcher, C.M.8
Bentley, S.D.9
Mungall, K.L.10
-
88
-
-
67651149484
-
Phylogenetic understanding of clonal populations in an era of whole genome sequencing
-
T. Pearson, R.T. Okinaka, J.T. Foster, and P. Keim Phylogenetic understanding of clonal populations in an era of whole genome sequencing Infect. Genet. Evol. 9 2009 1010 1019
-
(2009)
Infect. Genet. Evol.
, vol.9
, pp. 1010-1019
-
-
Pearson, T.1
Okinaka, R.T.2
Foster, J.T.3
Keim, P.4
-
89
-
-
84962311428
-
A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure
-
D. Pham Thanh, A. Karkey, S. Dongol, N. Ho Thi, C.N. Thompson, M.A. Rabaa, A. Arjyal, K.E. Holt, V. Wong, N. Tran Vu Thieu, and et al. A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure eLife 5 2016 e14003
-
(2016)
ELife
, vol.5
, pp. e14003
-
-
Pham Thanh, D.1
Karkey, A.2
Dongol, S.3
Ho Thi, N.4
Thompson, C.N.5
Rabaa, M.A.6
Arjyal, A.7
Holt, K.E.8
Wong, V.9
Tran Vu Thieu, N.10
-
90
-
-
59749094707
-
Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever
-
M.D. Phan, C. Kidgell, S. Nair, K.E. Holt, A.K. Turner, J. Hinds, P. Butcher, F.J. Cooke, N.R. Thomson, R. Titball, and et al. Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever Antimicrob. Agents Chemother. 53 2009 716 727
-
(2009)
Antimicrob. Agents Chemother.
, vol.53
, pp. 716-727
-
-
Phan, M.D.1
Kidgell, C.2
Nair, S.3
Holt, K.E.4
Turner, A.K.5
Hinds, J.6
Butcher, P.7
Cooke, F.J.8
Thomson, N.R.9
Titball, R.10
-
91
-
-
84925624433
-
Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: A new direction for bacteriology
-
T.D. Read, and R.C. Massey Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology Genome Med. 6 2014 109
-
(2014)
Genome Med.
, vol.6
, pp. 109
-
-
Read, T.D.1
Massey, R.C.2
-
92
-
-
84883349912
-
Clade-specific virulence patterns of Mycobacterium tuberculosis complex strains in human primary macrophages and aerogenically infected mice
-
N. Reiling, S. Homolka, K. Walter, J. Brandenburg, L. Niwinski, M. Ernst, C. Herzmann, C. Lange, R. Diel, S. Ehlers, and S. Niemann Clade-specific virulence patterns of Mycobacterium tuberculosis complex strains in human primary macrophages and aerogenically infected mice MBio 4 2013 4
-
(2013)
MBio
, vol.4
, pp. 4
-
-
Reiling, N.1
Homolka, S.2
Walter, K.3
Brandenburg, J.4
Niwinski, L.5
Ernst, M.6
Herzmann, C.7
Lange, C.8
Diel, R.9
Ehlers, S.10
Niemann, S.11
-
93
-
-
84899853334
-
Parallel independent evolution of pathogenicity within the genus Yersinia
-
S. Reuter, T.R. Connor, L. Barquist, D. Walker, T. Feltwell, S.R. Harris, M. Fookes, M.E. Hall, N.K. Petty, T.M. Fuchs, and et al. Parallel independent evolution of pathogenicity within the genus Yersinia Proc. Natl. Acad. Sci. USA 111 2014 6768 6773
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 6768-6773
-
-
Reuter, S.1
Connor, T.R.2
Barquist, L.3
Walker, D.4
Feltwell, T.5
Harris, S.R.6
Fookes, M.7
Hall, M.E.8
Petty, N.K.9
Fuchs, T.M.10
-
94
-
-
84955358137
-
Effect on nasopharyngeal pneumococcal carriage of replacing PCV7 with PCV13 in the Expanded Programme of Immunization in the Gambia
-
A. Roca, A. Bojang, C. Bottomley, R.A. Gladstone, J.U. Adetifa, U. Egere, S. Burr, M. Antonio, S. Bentley, B. Kampmann, et al. Pneumo13 Study Group Effect on nasopharyngeal pneumococcal carriage of replacing PCV7 with PCV13 in the Expanded Programme of Immunization in The Gambia Vaccine 33 2015 7144 7151
-
(2015)
Vaccine
, vol.33
, pp. 7144-7151
-
-
Roca, A.1
Bojang, A.2
Bottomley, C.3
Gladstone, R.A.4
Adetifa, J.U.5
Egere, U.6
Burr, S.7
Antonio, M.8
Bentley, S.9
Kampmann, B.10
-
95
-
-
33751558792
-
Evolutionary history of Salmonella typhi
-
P. Roumagnac, F.X. Weill, C. Dolecek, S. Baker, S. Brisse, N.T. Chinh, T.A. Le, C.J. Acosta, J. Farrar, G. Dougan, and M. Achtman Evolutionary history of Salmonella typhi Science 314 2006 1301 1304
-
(2006)
Science
, vol.314
, pp. 1301-1304
-
-
Roumagnac, P.1
Weill, F.X.2
Dolecek, C.3
Baker, S.4
Brisse, S.5
Chinh, N.T.6
Le, T.A.7
Acosta, C.J.8
Farrar, J.9
Dougan, G.10
Achtman, M.11
-
96
-
-
84920650884
-
Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
-
S.J. Salipante, D.J. Roach, J.O. Kitzman, M.W. Snyder, B. Stackhouse, S.M. Butler-Wu, C. Lee, B.T. Cookson, and J. Shendure Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains Genome Res. 25 2015 119 128
-
(2015)
Genome Res.
, vol.25
, pp. 119-128
-
-
Salipante, S.J.1
Roach, D.J.2
Kitzman, J.O.3
Snyder, M.W.4
Stackhouse, B.5
Butler-Wu, S.M.6
Lee, C.7
Cookson, B.T.8
Shendure, J.9
-
97
-
-
84880366261
-
Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter
-
S.K. Sheppard, X. Didelot, G. Meric, A. Torralbo, K.A. Jolley, D.J. Kelly, S.D. Bentley, M.C. Maiden, J. Parkhill, and D. Falush Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter Proc. Natl. Acad. Sci. USA 110 2013 11923 11927
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 11923-11927
-
-
Sheppard, S.K.1
Didelot, X.2
Meric, G.3
Torralbo, A.4
Jolley, K.A.5
Kelly, D.J.6
Bentley, S.D.7
Maiden, M.C.8
Parkhill, J.9
Falush, D.10
-
98
-
-
62449130191
-
Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
-
G.E. Sims, S.R. Jun, G.A. Wu, and S.H. Kim Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions Proc. Natl. Acad. Sci. USA 106 2009 2677 2682
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 2677-2682
-
-
Sims, G.E.1
Jun, S.R.2
Wu, G.A.3
Kim, S.H.4
-
99
-
-
84928787997
-
Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis
-
P. Singh, A. Benjak, V.J. Schuenemann, A. Herbig, C. Avanzi, P. Busso, K. Nieselt, J. Krause, L. Vera-Cabrera, and S.T. Cole Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis Proc. Natl. Acad. Sci. USA 112 2015 4459 4464
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 4459-4464
-
-
Singh, P.1
Benjak, A.2
Schuenemann, V.J.3
Herbig, A.4
Avanzi, C.5
Busso, P.6
Nieselt, K.7
Krause, J.8
Vera-Cabrera, L.9
Cole, S.T.10
-
100
-
-
84908287843
-
Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage
-
M. Spagnoletti, D. Ceccarelli, A. Rieux, M. Fondi, E. Taviani, R. Fani, M.M. Colombo, R.R. Colwell, and F. Balloux Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage MBio 5 2014 5
-
(2014)
MBio
, vol.5
, pp. 5
-
-
Spagnoletti, M.1
Ceccarelli, D.2
Rieux, A.3
Fondi, M.4
Taviani, E.5
Fani, R.6
Colombo, M.M.7
Colwell, R.R.8
Balloux, F.9
-
101
-
-
84875262522
-
A call for antibiotic alternatives research
-
T.B. Stanton A call for antibiotic alternatives research Trends Microbiol. 21 2013 111 113
-
(2013)
Trends Microbiol.
, vol.21
, pp. 111-113
-
-
Stanton, T.B.1
-
102
-
-
84961050701
-
The genomic signatures of Shigella evolution, adaptation and geographical spread
-
H.C. The, D.P. Thanh, K.E. Holt, N.R. Thomson, and S. Baker The genomic signatures of Shigella evolution, adaptation and geographical spread Nat. Rev. Microbiol. 14 2016 235 250
-
(2016)
Nat. Rev. Microbiol.
, vol.14
, pp. 235-250
-
-
The, H.C.1
Thanh, D.P.2
Holt, K.E.3
Thomson, N.R.4
Baker, S.5
-
105
-
-
0242416999
-
Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
-
J. Wei, M.B. Goldberg, V. Burland, M.M. Venkatesan, W. Deng, G. Fournier, G.F. Mayhew, G. Plunkett 3rd, D.J. Rose, A. Darling, and et al. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T Infect. Immun. 71 2003 2775 2786
-
(2003)
Infect. Immun.
, vol.71
, pp. 2775-2786
-
-
Wei, J.1
Goldberg, M.B.2
Burland, V.3
Venkatesan, M.M.4
Deng, W.5
Fournier, G.6
Mayhew, G.F.7
Plunkett, G.8
Rose, D.J.9
Darling, A.10
-
106
-
-
77957157893
-
Gut inflammation provides a respiratory electron acceptor for Salmonella
-
S.E. Winter, P. Thiennimitr, M.G. Winter, B.P. Butler, D.L. Huseby, R.W. Crawford, J.M. Russell, C.L. Bevins, L.G. Adams, R.M. Tsolis, and et al. Gut inflammation provides a respiratory electron acceptor for Salmonella Nature 467 2010 426 429
-
(2010)
Nature
, vol.467
, pp. 426-429
-
-
Winter, S.E.1
Thiennimitr, P.2
Winter, M.G.3
Butler, B.P.4
Huseby, D.L.5
Crawford, R.W.6
Russell, J.M.7
Bevins, C.L.8
Adams, L.G.9
Tsolis, R.M.10
-
107
-
-
84930064392
-
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events
-
V.K. Wong, S. Baker, D.J. Pickard, J. Parkhill, A.J. Page, N.A. Feasey, R.A. Kingsley, N.R. Thomson, J.A. Keane, F.X. Weill, and et al. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events Nat. Genet. 47 2015 632 639
-
(2015)
Nat. Genet.
, vol.47
, pp. 632-639
-
-
Wong, V.K.1
Baker, S.2
Pickard, D.J.3
Parkhill, J.4
Page, A.J.5
Feasey, N.A.6
Kingsley, R.A.7
Thomson, N.R.8
Keane, J.A.9
Weill, F.X.10
-
108
-
-
84964612299
-
The Landscape of Realized Homologous Recombination in Pathogenic Bacteria
-
K. Yahara, X. Didelot, K.A. Jolley, I. Kobayashi, M.C. Maiden, S.K. Sheppard, and D. Falush The Landscape of Realized Homologous Recombination in Pathogenic Bacteria Mol. Biol. Evol. 33 2016 456 471
-
(2016)
Mol. Biol. Evol.
, vol.33
, pp. 456-471
-
-
Yahara, K.1
Didelot, X.2
Jolley, K.A.3
Kobayashi, I.4
Maiden, M.C.5
Sheppard, S.K.6
Falush, D.7
-
109
-
-
28544440091
-
Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery
-
F. Yang, J. Yang, X. Zhang, L. Chen, Y. Jiang, Y. Yan, X. Tang, J. Wang, Z. Xiong, J. Dong, and et al. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery Nucleic Acids Res. 33 2005 6445 6458
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6445-6458
-
-
Yang, F.1
Yang, J.2
Zhang, X.3
Chen, L.4
Jiang, Y.5
Yan, Y.6
Tang, X.7
Wang, J.8
Xiong, Z.9
Dong, J.10
-
110
-
-
84906309033
-
Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever
-
Z. Zhou, A. McCann, F.X. Weill, C. Blin, S. Nair, J. Wain, G. Dougan, and M. Achtman Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever Proc. Natl. Acad. Sci. USA 111 2014 12199 12204
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 12199-12204
-
-
Zhou, Z.1
McCann, A.2
Weill, F.X.3
Blin, C.4
Nair, S.5
Wain, J.6
Dougan, G.7
Achtman, M.8
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