Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants

BMC Microbiology

Volumn 12, Issue , 2012, Pages

  Power, Peter M ^a   Bentley, Stephen D ^b   Parkhill, Julian ^b   Moxon, E Richard ^a   Hood, Derek W ^a,c  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Genome sequence; Haemophilus influenzae; Population structure; Transformation

Indexed keywords

GENOMIC DNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIUM ISOLATE; BACTERIUM TRANSFORMATION; CONTROLLED STUDY; DNA SEQUENCE; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHICAL VARIATION (SPECIES); HAEMOPHILUS INFLUENZAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATTERN RECOGNITION; PHENOTYPE; SEROTYPE;

CLUSTER ANALYSIS; GENE TRANSFER, HORIZONTAL; GENETIC VARIATION; GENOME, BACTERIAL; GENOTYPE; HAEMOPHILUS INFECTIONS; HAEMOPHILUS INFLUENZAE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PHYLOGENY;

HAEMOPHILUS INFLUENZAE;

EID: 84869877463     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-12-273     Document Type: Article

References (24)

1. Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model. Boissy R, Ahmed A, Janto B, Earl J, Hall BG, Hogg JS, Pusch GD, Hiller LN, Powell E, Hayes J, et al. BMC Genomics 12 187
2. The microbial pan-genome. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R, Curr Opin Genet Dev 2005 15 6 589 594 10.1016/j.gde.2005.09.006 16185861
3. Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Hogg J, Hu F, Janto B, Boissy R, Hayes J, Keefe R, Post J, Ehrlich G, Genome Biol 2007 8 6 103 10.1186/gb-2007-8-6-r103 17550610
4. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Science 1995 269 5223 496 512 10.1126/science.7542800 7542800
5. A taxonomic study of the genus Haemophilus, with the proposal of a new species. Kilian M, J Gen Microbiol 1976 93 1 9 62 10.1099/00221287-93-1-9 772168
6. Clonal population structure of encapsulated Haemophilus influenzae. Musser JM, Kroll JS, Moxon ER, Selander RK, Infect Immun 1988 56 8 1837 1845 2899551
7. Subtyping isolates of Haemophilus influenzae type b by outer-membrane protein profiles. Barenkamp SJ, Munson RS, Granoff DM, J Infect Dis 1981 143 5 668 676 10.1093/infdis/143.5.668 6972422
8. Outer membrane protein and biotype analysis of pathogenic nontypable Haemophilus influenzae. Barenkamp SJ, Munson RS, Granoff DM, Infect Immun 1982 36 2 535 540 6979511
9. High level of sequence diversity in the 16S rRNA genes of Haemophilus influenzae isolates is useful for molecular subtyping. Sacchi CT, Alber D, Dull P, Mothershed EA, Whitney AM, Barnett GA, Popovic T, Mayer LW, J Clin Microbiol 2005 43 8 3734 3742 10.1128/JCM.43.8.3734-3742.2005 16081903
10. Determination of the epidemiology and transmission of nontypable Haemophilus influenzae in children with otitis media by comparison of total genomic DNA restriction fingerprints. Loos BG, Bernstein JM, Dryja DM, Murphy TF, Dickinson DP, Infect Immun 1989 57 9 2751 2757 2788138
11. Development of a ribotyping scheme forHaemophilus influenzae type b. Leaves NI, Jordens JZ, European Journal of Clinical Microbiology & Infectious 1994 13 12 1038 1045 10.1007/BF02111824 14757004
12. Molecular Genetic Basis of Ribotyping. Bouchet V, Huot H, Goldstein R, Clin Microbiol Rev 2008 21 2 262 10.1128/CMR.00026-07 18400796
13. Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing. Meats E, Feil E, Stringer S, Cody A, Goldstein R, Kroll J, Popovic T, Spratt B, J Clin Microbiol 2003 41 4 1623 1636 10.1128/JCM.41.4.1623-1636.2003 12682154
14. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Zerbino DR, Birney E, Genome Res 2008 18 5 821 829 10.1101/gr.074492.107 18349386
15. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Li H, Ruan J, Durbin R, Genome Res 2008 18 11 1851 1858 10.1101/gr.078212.108 18714091
16. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Darling AC, Mau B, Blattner FR, Perna NT, Genome Res 2004 14 7 1394 1403 10.1101/gr.2289704 15231754
17. Transformation of natural genetic variation into Haemophilus influenzae genomes. Mell JC, Shumilina S, Hall IM, Redfield RJ, PLoS Pathog 2011 7 7 1002151 10.1371/journal.ppat.1002151 21829353
18. Quantification of rare allelic variants from pooled genomic DNA. Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, et al. Nat Methods 2009 6 4 263 265 10.1038/nmeth.1307 19252504
19. The complete genome sequence of Escherichia coli K-12. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, et al. Science 1997 277 5331 1453 1462 10.1126/science.277.5331.1453 9278503
20. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, et al. Mol Syst Biol 2006 2 2006 0007 16738553
21. Rapid pneumococcal evolution in response to clinical interventions. Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, et al. Science 2011 331 6016 430 434 10.1126/science.1198545 21273480
22. Genomic islands: tools of bacterial horizontal gene transfer and evolution. Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW, Crook DW, FEMS Microbiol Rev 2009 33 2 376 393 10.1111/j.1574-6976.2008.00136.x 19178566
23. Methods for serotyping nasopharyngeal isolates of Haemophilus influenzae: slide agglutination, Quellung reaction, countercurrent immunoelectrophoresis, latex agglutination, and antiserum agar. Ingram DL, Collier AM, Pendergrass E, King SH, J Clin Microbiol 1979 9 5 570 574 383743
24. Defined nongrowth media for stage II development of competence in Haemophilus influenzae. Herriott RM, Meyer EM, Vogt M, J Bacteriol 1970 101 2 517 524 5308771