Complete genome sequence of Haemophilus influenzae strain 375 from the middle ear of a pediatric patient with otitis media

Genome Announcements

Volumn 2, Issue 6, 2014, Pages

  Mell, Joshua Chang ^a,b   Sinha, Sunita ^b   Balashov, Sergey ^a   Viadas, Cristina ^c,d   Grassa, Christopher J ^b   Ehrlich, Garth D ^a,b   Nislow, Corey ^b   Redfield, Rosemary J ^b   Garmendia, Junkal ^c,d  

^a DREXEL UNIVERSITY COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c CSIC   (Spain)

^d INSTITUTO DE SALUD CARLOS III   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85006073409     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.01245-14     Document Type: Article

References (18)

1. Clementi CF, Murphy TF. 2011. Non-typeable Haemophilus influenzae invasion and persistence in the human respiratory tract. Front. Cell. Infect. Microbiol. 1:1. http://dx.doi.org/10.3389/fcimb.2011.00001.
2. Jalalvand F, Riesbeck K. 2014. Haemophilus influenzae: recent advances in the understanding of molecular pathogenesis and polymicrobial infections. Curr. Opin. Infect. Dis. 27:268-274. http://dx.doi.org/10.1097/QCO.0000000000000056.
3. Hood DW, Makepeace K, Deadman ME, Rest RF, Thibault P, Martin A, Richards JC, Moxon ER. 1999. Sialic acid in the lipopolysaccharide of Haemophilus influenzae: strain distribution, influence on serum resistance and structural characterization. Mol. Microbiol. 33:679-692. http://dx.doi.org/10.1046/j.1365-2958.1999.01509.x.
4. Bouchet V, Hood DW, Li J, Brisson JR, Randle GA, Martin A, Li Z, Goldstein R, Schweda EK, Pelton SI, Richards JC, Moxon ER. 2003. Host-derived sialic acid is incorporated into Haemophilus influenzae lipopolysaccharide and is a major virulence factor in experimental otitis media. Proc. Natl. Acad. Sci. U. S. A. 100:8898-8903. http://dx.doi.org/10.1073/pnas.1432026100.
5. Morey P, Cano V, Martí-Lliteras P, López-Gómez A, Regueiro V, Saus C, Bengoechea JA, Garmendia J. 2011. Evidence for a non-replicative intracellular stage of nontypable Haemophilus influenzae in epithelial cells. Microbiology 157:234-250. http://dx.doi.org/10.1099/mic.0.040451-0.
6. López-Gómez A, Cano V, Moranta D, Morey P, García del Portillo F, Bengoechea JA, Garmendia J. 2012. Host cell kinases, α5 and β1 integrins, and Rac1 signalling on the microtubule cytoskeleton are important for non-typable Haemophilus influenzae invasion of respiratory epithelial cells. Microbiology 158:2384-2398. http://dx.doi.org/10.1099/mic.0.059972-0.
7. Morey P, Viadas C, Euba B, Hood DW, Barberán M, Gil C, Grilló MJ, Bengoechea JA, Garmendia J. 2013. Relative contributions of lipooligosaccharide inner and outer core modifications to nontypeable Haemophilus influenzae pathogenesis. Infect. Immun. 81:4100-4111. http://dx.doi.org/10.1128/IAI.00492-13.
8. Wilson K. 2001. Preparation of genomic DNA from bacteria. Curr. Protoc. Mol. Biol. Chapter 2:Unit 2.4. http://dx.doi.org/10.1002/0471142727.mb0204s56.
9. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120. http://dx.doi.org/10.1093/bioinformatics/btu170.
10. Liu B, Yuan J, Yiu SM, Li Z, Xie Y, Chen Y, Shi Y, Zhang H, Li Y, Lam TW, Luo R. 2012. COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly. Bioinformatics 28:2870-2874. http://dx.doi.org/10.1093/bioinformatics/bts563.
11. Boisvert S, Laviolette F, Corbeil J. 2010. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J. Comput. Biol. 17:1519-1533. http://dx.doi.org/10.1089/cmb.2009.0238.
12. Garmendia J, Viadas C, Calatayud L, Mell JC, Marti-Lliteras P, Euba B, Llobet E, Gil C, Bengoechea JA, Redfield RJ, Linares J. 2014. Characterization of nontypable Haemophilus influenzae isolates recovered from adult patients with underlying chronic lung disease reveals genotypic and phenotypic traits associated with persistent infection. PLoS One 9:e97020. http://dx.doi.org/10.1371/journal.pone.0097020.
13. Lin SH, Liao YC. 2013. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One 8:e60843. http://dx.doi.org/10.1371/journal. pone.0060843.
14. De Chiara M, Hood D, Muzzi A, Pickard DJ, Perkins T, Pizza M, Dougan G, Rappuoli R, Moxon ER, Soriani M, Donati C. 2014. Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure. Proc. Natl. Acad. Sci. U. S. A. 111:5439-5444. http://dx.doi.org/10.1073/pnas.1403353111.
15. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013 Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563-569. http://dx.doi.org/10.1038/nmeth.2474.
16. Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. http://dx.doi.org/10.1371/journal.pone.0011147.
17. Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997. http://arxiv.org/abs/1303.3997.
18. Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987-2993. http://dx.doi.org/10.1093/bioinformatics/btr509.