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A genomic overview of the population structure of Salmonella.

Alikhan NF, Zhou Z, Sergeant MJ, Achtman M.

PLoS Genet. 2018 Apr 5;14(4):e1007261. doi: 10.1371/journal.pgen.1007261. eCollection 2018 Apr. Review.


What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.

Connor TR, Owen SV, Langridge G, Connell S, Nair S, Reuter S, Dallman TJ, Corander J, Tabing KC, Le Hello S, Fookes M, Doublet B, Zhou Z, Feltwell T, Ellington MJ, Herrera S, Gilmour M, Cloeckaert A, Achtman M, Parkhill J, Wain J, De Pinna E, Weill FX, Peters T, Thomson N.

MBio. 2016 Aug 23;7(4). pii: e00527-16. doi: 10.1128/mBio.00527-16.


How old are bacterial pathogens?

Achtman M.

Proc Biol Sci. 2016 Aug 17;283(1836). pii: 20160990. doi: 10.1098/rspb.2016.0990. Review.


Formal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence.

Achtman M, Zhou Z, Didelot X.

PLoS One. 2015 Aug 14;10(8):e0134435. doi: 10.1371/journal.pone.0134435. eCollection 2015.


Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe.

Kay GL, Sergeant MJ, Zhou Z, Chan JZ, Millard A, Quick J, Szikossy I, Pap I, Spigelman M, Loman NJ, Achtman M, Donoghue HD, Pallen MJ.

Nat Commun. 2015 Apr 7;6:6717. doi: 10.1038/ncomms7717.


The role of China in the global spread of the current cholera pandemic.

Didelot X, Pang B, Zhou Z, McCann A, Ni P, Li D, Achtman M, Kan B.

PLoS Genet. 2015 Mar 13;11(3):e1005072. doi: 10.1371/journal.pgen.1005072. eCollection 2015 Mar.


Distinct genealogies for plasmids and chromosome.

Achtman M, Zhou Z.

PLoS Genet. 2014 Dec 18;10(12):e1004874. doi: 10.1371/journal.pgen.1004874. eCollection 2014 Dec. No abstract available.


Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.

Zhou Z, McCann A, Weill FX, Blin C, Nair S, Wain J, Dougan G, Achtman M.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12199-204. doi: 10.1073/pnas.1411012111. Epub 2014 Aug 4.


Genetic variations of live attenuated plague vaccine strains (Yersinia pestis EV76 lineage) during laboratory passages in different countries.

Cui Y, Yang X, Xiao X, Anisimov AP, Li D, Yan Y, Zhou D, Rajerison M, Carniel E, Achtman M, Yang R, Song Y.

Infect Genet Evol. 2014 Aug;26:172-9. doi: 10.1016/j.meegid.2014.05.023. Epub 2014 Jun 4.


Parallel independent evolution of pathogenicity within the genus Yersinia.

Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, Corander J, Dufour M, Ringwood T, Savin C, Bouchier C, Martin L, Miettinen M, Shubin M, Riehm JM, Laukkanen-Ninios R, Sihvonen LM, Siitonen A, Skurnik M, Falcão JP, Fukushima H, Scholz HC, Prentice MB, Wren BW, Parkhill J, Carniel E, Achtman M, McNally A, Thomson NR.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6768-73. doi: 10.1073/pnas.1317161111. Epub 2014 Apr 21.


The ubiquitous nature of Listeria monocytogenes clones: a large-scale Multilocus Sequence Typing study.

Haase JK, Didelot X, Lecuit M, Korkeala H; L. monocytogenes MLST Study Group, Achtman M.

Environ Microbiol. 2014 Feb;16(2):405-16. doi: 10.1111/1462-2920.12342. Epub 2013 Dec 16.


Recent acquisition of Helicobacter pylori by Baka pygmies.

Nell S, Eibach D, Montano V, Maady A, Nkwescheu A, Siri J, Elamin WF, Falush D, Linz B, Achtman M, Moodley Y, Suerbaum S.

PLoS Genet. 2013;9(9):e1003775. doi: 10.1371/journal.pgen.1003775. Epub 2013 Sep 19.


Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona.

Zhou Z, McCann A, Litrup E, Murphy R, Cormican M, Fanning S, Brown D, Guttman DS, Brisse S, Achtman M.

PLoS Genet. 2013 Apr;9(4):e1003471. doi: 10.1371/journal.pgen.1003471. Epub 2013 Apr 18.


Population structures in the SARA and SARB reference collections of Salmonella enterica according to MLST, MLEE and microarray hybridization.

Achtman M, Hale J, Murphy RA, Boyd EF, Porwollik S.

Infect Genet Evol. 2013 Jun;16:314-25. doi: 10.1016/j.meegid.2013.03.003. Epub 2013 Mar 16.


A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic.

Holden MT, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H, Skov R, Westh H, Zemlicková H, Coombs G, Kearns AM, Hill RL, Edgeworth J, Gould I, Gant V, Cooke J, Edwards GF, McAdam PR, Templeton KE, McCann A, Zhou Z, Castillo-Ramírez S, Feil EJ, Hudson LO, Enright MC, Balloux F, Aanensen DM, Spratt BG, Fitzgerald JR, Parkhill J, Achtman M, Bentley SD, Nübel U.

Genome Res. 2013 Apr;23(4):653-64. doi: 10.1101/gr.147710.112. Epub 2013 Jan 8.


Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis.

Cui Y, Yu C, Yan Y, Li D, Li Y, Jombart T, Weinert LA, Wang Z, Guo Z, Xu L, Zhang Y, Zheng H, Qin N, Xiao X, Wu M, Wang X, Zhou D, Qi Z, Du Z, Wu H, Yang X, Cao H, Wang H, Wang J, Yao S, Rakin A, Li Y, Falush D, Balloux F, Achtman M, Song Y, Wang J, Yang R.

Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):577-82. doi: 10.1073/pnas.1205750110. Epub 2012 Dec 27.


Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

O'Farrell B, Haase JK, Velayudhan V, Murphy RA, Achtman M.

PLoS One. 2012;7(10):e48022. doi: 10.1371/journal.pone.0048022. Epub 2012 Oct 29.


Population genetic structure of 4,12:a:- Salmonella enterica strains from harbor porpoises.

Haase JK, Brown DJ, Weill FX, Mather H, Foster G, Brisse S, Wain J, Achtman M.

Appl Environ Microbiol. 2012 Dec;78(24):8829-33. doi: 10.1128/AEM.02310-12. Epub 2012 Oct 5.


Multilocus sequence typing as a replacement for serotyping in Salmonella enterica.

Achtman M, Wain J, Weill FX, Nair S, Zhou Z, Sangal V, Krauland MG, Hale JL, Harbottle H, Uesbeck A, Dougan G, Harrison LH, Brisse S; S. Enterica MLST Study Group.

PLoS Pathog. 2012;8(6):e1002776. doi: 10.1371/journal.ppat.1002776. Epub 2012 Jun 21.


CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections.

Fabre L, Zhang J, Guigon G, Le Hello S, Guibert V, Accou-Demartin M, de Romans S, Lim C, Roux C, Passet V, Diancourt L, Guibourdenche M, Issenhuth-Jeanjean S, Achtman M, Brisse S, Sola C, Weill FX.

PLoS One. 2012;7(5):e36995. doi: 10.1371/journal.pone.0036995. Epub 2012 May 18.


Age of the association between Helicobacter pylori and man.

Moodley Y, Linz B, Bond RP, Nieuwoudt M, Soodyall H, Schlebusch CM, Bernhöft S, Hale J, Suerbaum S, Mugisha L, van der Merwe SW, Achtman M.

PLoS Pathog. 2012;8(5):e1002693. doi: 10.1371/journal.ppat.1002693. Epub 2012 May 10.


Insights from genomic comparisons of genetically monomorphic bacterial pathogens.

Achtman M.

Philos Trans R Soc Lond B Biol Sci. 2012 Mar 19;367(1590):860-7. doi: 10.1098/rstb.2011.0303. Review.


Genomic analysis uncovers a phenotypically diverse but genetically homogeneous Escherichia coli ST131 clone circulating in unrelated urinary tract infections.

Clark G, Paszkiewicz K, Hale J, Weston V, Constantinidou C, Penn C, Achtman M, McNally A.

J Antimicrob Chemother. 2012 Apr;67(4):868-77. doi: 10.1093/jac/dkr585. Epub 2012 Jan 18.


Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli.

Shepard SM, Danzeisen JL, Isaacson RE, Seemann T, Achtman M, Johnson TJ.

J Bacteriol. 2012 Jan;194(2):395-405. doi: 10.1128/JB.06225-11. Epub 2011 Nov 11.


Revival of Seeliger's historical 'Special Listeria Culture Collection'.

Haase JK, Murphy RA, Choudhury KR, Achtman M.

Environ Microbiol. 2011 Dec;13(12):3163-71. doi: 10.1111/j.1462-2920.2011.02610.x. Epub 2011 Oct 18.


Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing.

Laukkanen-Ninios R, Didelot X, Jolley KA, Morelli G, Sangal V, Kristo P, Brehony C, Imori PF, Fukushima H, Siitonen A, Tseneva G, Voskressenskaya E, Falcao JP, Korkeala H, Maiden MC, Mazzoni C, Carniel E, Skurnik M, Achtman M.

Environ Microbiol. 2011 Dec;13(12):3114-27. doi: 10.1111/j.1462-2920.2011.02588.x. Epub 2011 Sep 27.


Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar.

Vogler AJ, Chan F, Wagner DM, Roumagnac P, Lee J, Nera R, Eppinger M, Ravel J, Rahalison L, Rasoamanana BW, Beckstrom-Sternberg SM, Achtman M, Chanteau S, Keim P.

PLoS Negl Trop Dis. 2011 Sep;5(9):e1319. doi: 10.1371/journal.pntd.0001319. Epub 2011 Sep 13.


A broad brush, global overview of bacterial sexuality.

Achtman M.

PLoS Genet. 2011 Aug;7(8):e1002255. doi: 10.1371/journal.pgen.1002255. Epub 2011 Aug 18. No abstract available.


Molecular epidemiology of extraintestinal pathogenic Escherichia coli isolates from a regional cohort of elderly patients highlights the prevalence of ST131 strains with increased antimicrobial resistance in both community and hospital care settings.

Croxall G, Hale J, Weston V, Manning G, Cheetham P, Achtman M, McNally A.

J Antimicrob Chemother. 2011 Nov;66(11):2501-8. doi: 10.1093/jac/dkr349. Epub 2011 Aug 22.


Recombination and population structure in Salmonella enterica.

Didelot X, Bowden R, Street T, Golubchik T, Spencer C, McVean G, Sangal V, Anjum MF, Achtman M, Falush D, Donnelly P.

PLoS Genet. 2011 Jul;7(7):e1002191. doi: 10.1371/journal.pgen.1002191. Epub 2011 Jul 28.


Salmonella enterica Serotype Typhi with nonclassical quinolone resistance phenotype.

Accou-Demartin M, Gaborieau V, Song Y, Roumagnac P, Marchou B, Achtman M, Weill FX.

Emerg Infect Dis. 2011 Jun;17(6):1091-4. doi: 10.3201/eid/1706.101242.


Population Genetics.

Suerbaum S, Achtman M.

In: Mobley HLT, Mendz GL, Hazell SL, editors. Helicobacter pylori: Physiology and Genetics. Washington (DC): ASM Press; 2001. Chapter 32.


Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.

Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, Achtman M.

Nat Genet. 2010 Dec;42(12):1140-3. doi: 10.1038/ng.705. Epub 2010 Oct 31.


Distinct clones of Yersinia pestis caused the black death.

Haensch S, Bianucci R, Signoli M, Rajerison M, Schultz M, Kacki S, Vermunt M, Weston DA, Hurst D, Achtman M, Carniel E, Bramanti B.

PLoS Pathog. 2010 Oct 7;6(10):e1001134. doi: 10.1371/journal.ppat.1001134.


Evolution and population structure of Salmonella enterica serovar Newport.

Sangal V, Harbottle H, Mazzoni CJ, Helmuth R, Guerra B, Didelot X, Paglietti B, Rabsch W, Brisse S, Weill FX, Roumagnac P, Achtman M.

J Bacteriol. 2010 Dec;192(24):6465-76. doi: 10.1128/JB.00969-10. Epub 2010 Oct 8.


A global overview of the genetic and functional diversity in the Helicobacter pylori cag pathogenicity island.

Olbermann P, Josenhans C, Moodley Y, Uhr M, Stamer C, Vauterin M, Suerbaum S, Achtman M, Linz B.

PLoS Genet. 2010 Aug 19;6(8):e1001069. doi: 10.1371/journal.pgen.1001069.


Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families.

Morelli G, Didelot X, Kusecek B, Schwarz S, Bahlawane C, Falush D, Suerbaum S, Achtman M.

PLoS Genet. 2010 Jul 22;6(7):e1001036. doi: 10.1371/journal.pgen.1001036.


A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A.

Song Y, Roumagnac P, Weill FX, Wain J, Dolecek C, Mazzoni CJ, Holt KE, Achtman M.

J Antimicrob Chemother. 2010 Aug;65(8):1631-41. doi: 10.1093/jac/dkq175. Epub 2010 May 28.


Ethnic and geographic differentiation of Helicobacter pylori within Iran.

Latifi-Navid S, Ghorashi SA, Siavoshi F, Linz B, Massarrat S, Khegay T, Salmanian AH, Shayesteh AA, Masoodi M, Ghanadi K, Ganji A, Suerbaum S, Achtman M, Malekzadeh R, Falush D.

PLoS One. 2010 Mar 22;5(3):e9645. doi: 10.1371/journal.pone.0009645.


Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium.

Eppinger M, Worsham PL, Nikolich MP, Riley DR, Sebastian Y, Mou S, Achtman M, Lindler LE, Ravel J.

J Bacteriol. 2010 Mar;192(6):1685-99. doi: 10.1128/JB.01518-09. Epub 2010 Jan 8.


Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype.

Kingsley RA, Msefula CL, Thomson NR, Kariuki S, Holt KE, Gordon MA, Harris D, Clarke L, Whitehead S, Sangal V, Marsh K, Achtman M, Molyneux ME, Cormican M, Parkhill J, MacLennan CA, Heyderman RS, Dougan G.

Genome Res. 2009 Dec;19(12):2279-87. doi: 10.1101/gr.091017.109. Epub 2009 Nov 9.


Fate of the H-NS-repressed bgl operon in evolution of Escherichia coli.

Sankar TS, Neelakanta G, Sangal V, Plum G, Achtman M, Schnetz K.

PLoS Genet. 2009 Mar;5(3):e1000405. doi: 10.1371/journal.pgen.1000405. Epub 2009 Mar 6.


The peopling of the Pacific from a bacterial perspective.

Moodley Y, Linz B, Yamaoka Y, Windsor HM, Breurec S, Wu JY, Maady A, Bernhöft S, Thiberge JM, Phuanukoonnon S, Jobb G, Siba P, Graham DY, Marshall BJ, Achtman M.

Science. 2009 Jan 23;323(5913):527-30. doi: 10.1126/science.1166083.


Horizontal versus familial transmission of Helicobacter pylori.

Schwarz S, Morelli G, Kusecek B, Manica A, Balloux F, Owen RJ, Graham DY, van der Merwe S, Achtman M, Suerbaum S.

PLoS Pathog. 2008 Oct;4(10):e1000180. doi: 10.1371/journal.ppat.1000180. Epub 2008 Oct 24.


Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens.

Achtman M.

Annu Rev Microbiol. 2008;62:53-70. doi: 10.1146/annurev.micro.62.081307.162832. Review.


Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus.

Nübel U, Roumagnac P, Feldkamp M, Song JH, Ko KS, Huang YC, Coombs G, Ip M, Westh H, Skov R, Struelens MJ, Goering RV, Strommenger B, Weller A, Witte W, Achtman M.

Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):14130-5. doi: 10.1073/pnas.0804178105. Epub 2008 Sep 4.


High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G.

Nat Genet. 2008 Aug;40(8):987-93. doi: 10.1038/ng.195. Epub 2008 Jul 27.


Ceftriaxone-resistant salmonella enterica serotype Newport, France.

Egorova S, Timinouni M, Demartin M, Granier SA, Whichard JM, Sangal V, Fabre L, Delauné A, Pardos M, Millemann Y, Espié E, Achtman M, Grimont PA, Weill FX.

Emerg Infect Dis. 2008 Jun;14(6):954-7. doi: 10.3201/eid1406.071168.


Microbial diversity and the genetic nature of microbial species.

Achtman M, Wagner M.

Nat Rev Microbiol. 2008 Jun;6(6):431-40. doi: 10.1038/nrmicro1872. Epub 2008 May 7. Review.


High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia.

Baker S, Holt K, van de Vosse E, Roumagnac P, Whitehead S, King E, Ewels P, Keniry A, Weill FX, Lightfoot D, van Dissel JT, Sanderson KE, Farrar J, Achtman M, Deloukas P, Dougan G.

J Clin Microbiol. 2008 May;46(5):1741-6. doi: 10.1128/JCM.02249-07. Epub 2008 Mar 5.

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