Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River

Microbial Ecology

Volumn 73, Issue 3, 2017, Pages 734-738

  Vezzulli, L ^a   Grande, C ^a   Tassistro, G ^a   Brettar, I ^b   Hofle M G ^b   Pereira, R P A ^b   Mushi, D ^b   Pallavicini, A ^c   Vassallo, P ^a   Pruzzo, C ^a  

^a UNIVERSITY OF GENOA   (Italy)

^b HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^c UNIVERSITY OF TRIESTE   (Italy)

Author keywords

Africa; Next generation sequencing; Vibrio cholerae; Whole genome enrichment

Indexed keywords

BACTERIAL DNA;

DNA SEQUENCE; GENETICS; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; METAGENOMICS; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; PROCEDURES; RIVER; TANZANIA; VIBRIO CHOLERAE;

BASE SEQUENCE; DNA, BACTERIAL; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; RIVERS; SEQUENCE ANALYSIS, DNA; TANZANIA; VIBRIO CHOLERAE;

EID: 84997522709     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-016-0902-x     Document Type: Article

References (13)

1. Colwell RR (1996) Global climate and infectious disease: the cholera paradigm. Science 274:2031–2025
2. Xu HS, Roberts N, Singleton FL, Attwell RW, Grimes DJ, Colwell RR (1982) Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb Ecol 8:313–323
3. Vezzulli L, Stauder M, Grande C, Pezzati E, Verheye HM, Owens NJP et al (2015) gbpA as a novel qPCR target for the species-specific detection of Vibrio cholerae O1, O139, non-O1/non-O139 in environmental, stool, and historical continuous plankton recorder samples. PLoS ONE 10:e0123983. doi:10.1371/journal.pone.0123983
4. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W et al (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27(2):182–189
5. Chen LH, Xiong ZH, Sun LL, Yang J, Jin Q (2012) VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 40:D641–D645
6. Liu B, Pop M (2009) ARDB-antibiotic resistance genes database. Nucleic Acids Res 37:D443–7
7. Burrus V, Quezada-Calvillo R, Marrero J, Waldor MK (2006) SXT-related integrating conjugative element in new world Vibrio cholerae. Appl Environ Microbiol 72(4):3054–3057
8. Acosta CJ, Galindo CM, Kimario J, Senkoro K, Urassa H, Casals C et al (2001) Cholera outbreak in Southern Tanzania: risk factors and patterns of transmission. Emerg Infect Dis 7:583–7
9. Naha A, Chowdhury G, Ghosh-Banerjee J, Senoh M, Takahashi T, Ley B et al (2013) Molecular characterization of high-level-cholera-toxin-producing El Tor variant Vibrio cholerae strains in the Zanzibar Archipelago of Tanzania. J Clin Microbiol 51:1040–1045
10. Crecchio C, Stotzky G (1998) Binding of DNA on humic acids: effect on transformation of Bacillus subtilis and resistance to DNase. Soil Biol Biochem 30:1061–1067
11. Vlassov VV, Laktionov PP, Rykova EY (2007) Extracellular nucleic acids. Bioessays 29(7):654–67
12. Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D (2007) Release and persistence of extracellular DNA in the environment. Environ Biosaf Res 6:37–53
13. Blokesch M, Schoolnik GK (2007) Serogroup conversion of Vibrio cholerae in aquatic reservoirs. PLoS Pathog 3:733–742