Patterns of genome evolution that have accompanied host adaptation in Salmonella

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 3, 2015, Pages 863-868

  Langridge, Gemma C ^a   Fookesa, Maria ^a   Connora, Thomas R ^a,h   Feltwella, Theresa ^a   Feaseya, Nicholas ^a   Parsonsb, Bryony N ^b   Seth Smitha, Helena M B ^a,i   Barquista, Lars ^a   Stedmana, Anna ^a   Humphreyd, Tom ^c   Wigleyb, Paul ^b   Petersf, Sarah E ^d   Maskellf, Duncan J ^d   Coranderg, Jukka ^e   Chabalgoityh, Jose A ^f   Barrowi, Paul ^g   Parkhilla, Julian ^a   Dougana, Gordon ^a   Thomsona, Nicholas R ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF LIVERPOOL   (United Kingdom)

^c SWANSEA UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e UNIVERSITY OF HELSINKI   (Finland)

^f Universidad de la Republica Instituto de Higiene   (Uruguay)

^g UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^h CARDIFF UNIVERSITY   (United Kingdom)

ⁱ UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Host adaptation; Metabolism; Pseudogene; Salmonella

Indexed keywords

ARTICLE; BACTERIOPHAGE TYPING; CLADISTICS; CONTROLLED STUDY; DEGRADATION; DISEASE SEVERITY; EVOLUTIONARY ADAPTATION; GENE LOSS; GENOME; HOST; HOST RANGE; HUMAN; METABOLIC CAPACITY; METABOLISM; NONHUMAN; PATHOGENICITY; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; PSEUDOGENE; SALMONELLA ENTERICA; SEROTYPE; ADAPTATION; BACTERIAL CHROMOSOME; BACTERIAL GENOME; GENETICS; MOLECULAR EVOLUTION; SALMONELLA;

ANIMALIA; AVES; BACTERIA (MICROORGANISMS); BOS; SALMONELLA; SALMONELLA ENTERICA; SALMONELLA ENTERITIDIS;

ADAPTATION, PHYSIOLOGICAL; CHROMOSOMES, BACTERIAL; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; PSEUDOGENES; SALMONELLA;

EID: 84921327912     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1416707112     Document Type: Article

References (30)

1. Parkhill J, et al. (2003) Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet 35(1): 32-40.
2. Rohmer L, et al. (2007) Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains. Genome Biol 8(6):R102.
3. Cole ST, et al. (2001) Massive gene decay in the leprosy bacillus. Nature 409(6823): 1007-1011.
4. Moran NA, Plague GR (2004) Genomic changes following host restriction in bacteria. Curr Opin Genet Dev 14(6):627-633.
5. Majowicz SE, et al.; International Collaboration on Enteric Disease "Burden of Illness" Studies (2010) The global burden of nontyphoidal Salmonella gastroenteritis. Clin Infect Dis 50(6):882-889.
6. Boyd EF, et al. (1993) Salmonella reference collection B (SARB): Strains of 37 serovars of subspecies I. J Gen Microbiol 139(Pt 6):1125-1132.
7. Porwollik S, et al. (2005) Differences in gene content between Salmonella enterica serovar Enteritidis isolates and comparison to closely related serovars Gallinarum and Dublin. J Bacteriol 187(18):6545-6555.
8. Thomson NR, et al. (2008) Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res 18(10):1624-1637.
9. Achtman M, et al.; S. Enterica MLST Study Group (2012) Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. PLoS Pathog 8(6):e1002776.
10. Selander RK, et al. (1992) Molecular evolutionary genetics of the cattle-adapted serovar Salmonella dublin. J Bacteriol 174(11):3587-3592.
11. Olsen JE, Skov M (1994) Genomic lineage of Salmonella enterica serovar Dublin. Vet Microbiol 40(3-4):271-282.
12. Corander J, Marttinen P, Sirén J, Tang J (2008) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9(1):539.
13. Nauerby B, Pedersen K, Dietz HH, Madsen M (2000) Comparison of Danish isolates of Salmonella enterica serovar enteritidis PT9a and PT11 from hedgehogs (Erinaceus europaeus) and humans by plasmid profiling and pulsed-field gel electrophoresis. J Clin Microbiol 38(10):3631-3635.
14. Fookes M, et al. (2011) Salmonella bongori provides insights into the evolution of the Salmonellae. PLoS Pathog 7(8):e1002191.
15. Blondel CJ, et al. (2010) Contribution of the type VI secretion system encoded in SPI-19 to chicken colonization by Salmonella enterica serotypes Gallinarum and Enteritidis. PLoS One 5(7):e11724.
16. Blondel CJ, et al. (2013) The type VI secretion system encoded in Salmonella pathogenicity island 19 is required for Salmonella enterica serotype Gallinarum survival within infected macrophages. Infect Immun 81(4):1207-1220.
17. Parkhill J, et al. (2001) Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413(6858):848-852.
18. Rodríguez-Peña JM, Buisan M, Ibáñez M, Rotger R (1997) Genetic map of the virulence plasmid of Salmonella enteritidis and nucleotide sequence of its replicons. Gene 188(1):53-61.
19. Rychlik I, Lovell MA, Barrow PA (1998) The presence of genes homologous to the K88 genes faeH and faeI on the virulence plasmid of Salmonella gallinarum. FEMS Microbiol Lett 159(2):255-260.
20. Chiu C-H, et al. (2005) The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res 33(5): 1690-1698.
21. Nuccio S-P, Bäumler AJ (2014) Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut. MBio 5(2):e00929-14.
22. Pollack JR, Ames BN, Neilands JB (1970) Iron transport in Salmonella typhimurium: Mutants blocked in the biosynthesis of enterobactin. J Bacteriol 104(2):635-639.
23. Skaar EP (2010) The battle for iron between bacterial pathogens and their vertebrate hosts. PLoS Pathog 6(8):e1000949.
24. Barquist L, et al. (2013) A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Res 41(8):4549-4564.
25. Dhawi AA, et al. (2011) Adaptation to the chicken intestine in Salmonella Enteritidis PT4 studied by transcriptional analysis. Vet Microbiol 153(1-2):198-204.
26. Kingsley RA, et al. (2009) Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res 19(12):2279-2287.
27. Price-Carter M, Tingey J, Bobik TA, Roth JR (2001) The alternative electron acceptor tetrathionate supports B12-dependent anaerobic growth of Salmonella enterica serovar typhimurium on ethanolamine or 1,2-propanediol. J Bacteriol 183(8):2463-2475.
28. Winter SE, et al. (2010) Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467(7314):426-429.
29. Tang J, Hanage WP, Fraser C, Corander J (2009) Identifying currents in the gene pool for bacterial populations using an integrative approach. PLOS Comput Biol 5(8): e1000455.
30. Marttinen P, et al. (2012) Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res 40(1):e6.