Virulence related sequences; insights provided by comparative genomics of Streptococcus uberis of differing virulence

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Hossain, Maqsud ^a   Egan, Sharon A ^a   Coffey, Tracey ^a   Ward, Philip N ^b   Wilson, Ray ^c   Leigh, James A ^a   Emes, Richard D ^a,c  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Comparative genomics; CRISPRs; de novo assembly; Mastitis; Streptococcus uberis; vru

Indexed keywords

BACTERIOCIN;

ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BACTERIAL VIRULENCE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; GENE LOSS; GENE SEQUENCE; MASTITIS; NONHUMAN; PROPHAGE; STREPTOCOCCUS UBERIS; ANIMAL; BACTERIAL GENOME; BOVINE; BOVINE MASTITIS; CLASSIFICATION; DNA SEQUENCE; FEMALE; GENETICS; METABOLISM; MICROBIOLOGY; MILK; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PATHOLOGY; PHYLOGENY; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; STREPTOCOCCUS; VIRULENCE;

BOVINAE; POSIBACTERIA; STREPTOCOCCACEAE; STREPTOCOCCUS UBERIS;

ANIMALS; BACTERIOCINS; BASE SEQUENCE; CATTLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; COMPARATIVE GENOMIC HYBRIDIZATION; FEMALE; GENOME, BACTERIAL; MASTITIS, BOVINE; MILK; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; STREPTOCOCCUS; VIRULENCE;

EID: 84929150523     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1512-6     Document Type: Article

References (40)

1. Bramley AJ, Dodd FH. Reviews of the progress of dairy science: mastitis control-progress and prospects. J Dairy Res. 1984;51(3):481-512.
2. Bradley AJ, Leach KA, Breen JE, Green LE, Green MJ. Survey of the incidence and aetiology of mastitis on dairy farms in England and Wales. Vet Rec. 2007;160(8):253-7.
3. Bradley AJ, Barkema H, Biggs A, Green MJ, Lam T. Control of mastitis and enhancement of milk quality. In: Green MJ, editor. Dairy Herd Health. Oxfordshire, UK: CABI; 2012.
4. Bradley AB H, Biggs A, Green M, Lam T. Control of mastitis and enhancement of milk quality. In: Green M, editor. Dairy herd health. UK: CPI Group (UK) Ltd; 2012.
5. Leigh JA. Streptococcus uberis: a permanent barrier to the control of bovine mastitis? Vet J. 1999;157(3):225-38.
6. Ward PN, Holden MT, Leigh JA, Lennard N, Bignell A, Barron A, et al. Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis. BMC Genomics. 2009;10:54.
7. Leigh JA, Egan SA, Ward PN, Field TR, Coffey TJ. Sortase anchored proteins of Streptococcus uberis play major roles in the pathogenesis of bovine mastitis in dairy cattle. Vet Res. 2010;41(5):63.
8. Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics. 2010;11:11-5.
9. Galardini M, Biondi EG, Bazzicalupo M, Mengoni A. CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med. 2011;6:11.
10. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
11. Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. PGAP: Pan-Genomes Analysis Pipeline. Bioinformatics. 2011;28(3):416-8.
12. Edgar RC. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics. 2007;8:18.
13. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:W52-7.
14. Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007;8:172.
15. Grissa I, Vergnaud G, Pourcel C. CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2008;36:W145-8.
16. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res. 2011;39:W347-52.
17. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-7.
18. Leekitcharoenphon P, Kaas RS, Thomsen MC, Friis C, Rasmussen S, Aarestrup FM. snpTree--a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics. 2012;13(7):S6.
19. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52(5):696-704.
20. Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carrico JA. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics. 2012;13:87.
21. Field TR, Ward PN, Pedersen LH, Leigh JA. The hyaluronic acid capsule of Streptococcus uberis is not required for the development of infection and clinical mastitis. Infect Immun. 2003;71(1):132-9.
22. Smith AJ, Ward PN, Field TR, Jones CL, Lincoln RA, Leigh JA. MtuA, a lipoprotein receptor antigen from Streptococcus uberis, is responsible for acquisition of manganese during growth in milk and is essential for infection of the lactating bovine mammary gland. Infect Immun. 2003;71(9):4842-9.
23. Hill AW. Pathogenicity of two strains of Streptococcus uberis infused into lactating and non-lactating bovine mammary glands. Res Vet Sci. 1988;45(3):400-4.
24. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome". Proc Natl Acad Sci. 2005;102(39):13950-5.
25. Bruen T, Phillipe H, Bryant D. A quick and robust statistical test to detect the presence of recombination. Genetics. 2006;17:2665-81.
26. Martin PR, Hoiby EA. Streptococcal serogroup A epidemic in Norway 1987-1988. Scand J Infect Dis. 1990;22(4):421-9.
27. Cho KH, Caparon MG. Patterns of virulence gene expression differ between biofilm and tissue communities of Streptococcus pyogenes. Mol Microbiol. 2005;57(6):1545-56.
28. Ward PN, Field TR, Ditcham WG, Maguin E, Leigh JA. Identification and disruption of two discrete loci encoding hyaluronic acid capsule biosynthesis genes hasA, hasB, and hasC in Streptococcus uberis. Infect Immun. 2001;69(1):392-9.
29. Ashbaugh CD, Alberti S, Wessels MR. Molecular analysis of the capsule gene region of group A Streptococcus: the hasAB genes are sufficient for capsule expression. J Bacteriol. 1998;180(18):4955-9.
30. Egan SA, Ward PN, Watson M, Field TR, Leigh JA. Vru (Sub0144) controls expression of proven and putative virulence determinants and alters the ability of Streptococcus uberis to cause disease in dairy cattle. Microbiology. 2012;158(Pt 6):1581-92.
31. Flores AR, Olsen RJ, Wunsche A, Kumaraswami M, Shelburne 3rd SA, Carroll RK, et al. Natural variation in the promoter of the gene encoding the Mga regulator alters host-pathogen interactions in group a Streptococcus carrier strains. Infect Immun. 2013;81(11):4128-38.
32. Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol. 2010;64:475-93.
33. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010;327(5962):167-70.
34. Karginov FV, Hannon GJ. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell. 2010;37(1):7-19.
35. Koonin EV, Makarova KS. CRISPR-Cas: an adaptive immunity system in prokaryotes. F1000 Biol Rep. 2009;1:95.
36. Sorek R, Kunin V, Hugenholtz P. CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol. 2008;6(3):181-6.
37. van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci. 2009;34(8):401-7.
38. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 2011;9(6):467-77.
39. Brussow H, Canchaya C, Hardt WD. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev. 2004;68(3):560-602.
40. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:402.