@article {38566,
	title = {Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico},
	journal = {Journal of Clinical MicrobiologyJ. Clin. Microbiol.Journal of Clinical MicrobiologyJ. Clin. Microbiol.},
	year = {2012},
	type = {10.1128/JCM.00189-12},
	abstract = {Vibrio cholerae O1 Classical (CL) biotype caused the 5th and 6th, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the 7th pandemic in Asia in the 1970{\textquoteright}s by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia, and it had never been reported from Latin America, V. cholerae CL and ET biotypes, including hybrid ET were found associated with endemic cholera in Mexico between 1991 and 1997. In this study, CL biotype strains isolated from endemic cholera in Mexico, between 1983 and 1997 were characterized in terms of major phenotypic and genetic traits, and compared with CL biotype strains isolated in Bangladesh between 1962 and 1989. According to sero- and bio-typing data, all V. cholerae strains tested had the major phenotypic and genotypic characteristics specific for the CL biotype. Antibiograms revealed the majority of the Bangladeshi strains to be resistant to trimethoprim/sulfamethoxazole, furazolidone, ampicillin, and gentamycin, while the Mexican strains were sensitive to all of these drugs, as well as to ciprofloxacin, erythromycin, and tetracycline. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA revealed characteristic banding patterns for all the CL biotype strains, although the Mexican strains differed with the Bangladeshi strains in 1-2 DNA bands. The difference may be subtle, but consistent, as confirmed by the sub-clustering patterns in the PFGE-based dendrogram, and can serve as regional signature, suggesting pre-1991 existence and evolution of the CL biotype strains in the Americas, independent from that of Asia.},
	isbn = {0095-1137, 1098-660X},
	author = {Alam, Munirul and Islam, M. Tarequl and Rashed, Shah Manzur and Johura, Fatema-Tuz and Bhuiyan, Nurul A. and Delgado, Gabriela and Morales, Rosario and Mendez, Jose Luis and Navarro, Armando and Watanabe, Haruo and Hasan, Nur- A. and Rita R. Colwell and Cravioto, Alejandro}
}
@article {38568,
	title = {Vibrio Cholerae O1 Detection in Estuarine and Coastal Zooplankton},
	journal = {Journal of Plankton ResearchJ. Plankton Res.Journal of Plankton ResearchJ. Plankton Res.},
	volume = {33},
	year = {2011},
	type = {10.1093/plankt/fbq093},
	abstract = {Vibrio cholerae is an autochthonous marine bacterium, and its association with diverse planktonic crustaceans has been extensively investigated; however, the presence of V. cholerae on individuals of most phyla of planktonic animals is still incompletely understood. The objective of this study was to analyze the distribution of V. cholerae serogroup O1 associated with specific zooplankton taxa in an estuary and the adjacent continental shelf of the southeastern Brazilian coast. The occurrence of the bacterium was assessed in zooplankton samples, specifically on the most abundant taxa, using direct fluorescence assay (DFA) and direct viable count{\textendash}direct fluorescence assay (DVC{\textendash}DFA) methods. Vibrio cholerae O1 was detected in 88\% of samples collected from the Santos-Bertioga estuary and in 67\% of samples from the shelf. The salinity of the estuarine water ranged from 21.8 to 34.6, significantly lower than the shelf water which was 32.1{\textendash}36.1. Salinity was the only environmental variable measured that displayed a significant correlation with the presence of V. cholerae (P< 0.05). Vibrio cholerae O1 was detected in chaetognaths, pluteus larvae of echinoderms and planktonic fish eggs (Engraulidae), all new sites for this bacterium.},
	keywords = {DFA, estuary, plankton, Southwest Atlantic},
	isbn = {0142-7873, 1464-3774},
	author = {Martinelli Filho, Jos{\'e} E. and Lopes, Rubens M. and Rivera, Irma N. G. and Rita R. Colwell}
}
@article {38561,
	title = {Validating the systematic position of {\i}t Plationus Segers, Murugan \& Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase},
	journal = {HydrobiologiaHydrobiologia},
	volume = {644},
	year = {2010},
	type = {DOI 10.1007/s10750-010-0203-1},
	abstract = {Members of the family Brachionidae are free-living organisms that range in size from 170 to 250 microns. They comprise part of the zooplankton in freshwater and marine systems worldwide. Morphologically, members of the family are characterized by a single piece loricated body without furrows, grooves, sulci or dorsal head shields, and a malleate trophi. Differences in these structures have been traditionally used to recognize 217 species that are classified into seven genera. However, the validity of the species, Plationus patulus, P. patulus macracanthus P. polyacanthus, and P. felicitas have been confused because they were alternatively assigned in Brachionus or Platyias, when considering only morphological and ecological characters. Based on scanning electron microscope (SEM) images of the trophi, these taxa were assigned in a new genus, Plationus. In this study, we examined the systematic position of P. patulus and P. patulus macracanthus using DNA sequences of two genes: the cytochrome oxidase subunit 1 (cox1) and domains D2 and D3 of the large subunit of the nuclear ribosomal RNA (LSU). In addition, the cox1 and LSU sequences representing five genera of Brachionidae (Anuraeopsis, Brachionus, Keratella, Plationus, and Platyias) plus four species of three families from the order Ploima were used as the outgroup. The maximum likelihood (ML) analyses were conducted for each individual gene as well as for the combined (cox1 + LSU) data set. The ML tree from the combined data set yielded the family Brachionidae as a monophyletic group with weak bootstrap support (< 50\%). Five main clades in this tree had high (> 85\%) bootstrap support. The first clade was composed of three populations of P. patulus + P. patulus macracanthus. The second clade was composed of a single species of Platyias. The third clade was composed of six species of Brachionus. The fourth clade included a single species of the genus Anuraeopsis, and the fifth clade was composed of three species of the genus Keratella. The genetic divergence between Plationus and Platyias ranged from 18.4 to 19.2\% for cox1, and from 4.5 to 4.9\% for LSU, and between Brachionus and Plationus, it ranged from 16.9 to 23.1\% (cox1), and from 7.3 to 9.1\% (LSU). Morphological evidence, the amount of genetic divergence, the systematic position of Plationus within the family Brachionidae, and the position of Plationus as a sister group of Brachionus and Platyias support the validity of Plationus patulus and P. patulus macracanthus into the genus Plationus.},
	keywords = {Cox1, likelihood, LSU, maximum, Phylogeny, Plationus},
	author = {Reyna-Fabian, M. E. and Laclette, J. P. and Michael P. Cummings and Garc{\'\i}a-Varela, M.}
}
@article {38565,
	title = {Viable but not cultivable bacteria},
	journal = {Uncultivated MicroorganismsUncultivated Microorganisms},
	year = {2009},
	type = {10.1007/978-3-540-85465-4_1},
	abstract = {A well-studied, long-term survival mechanism employed by Gram-positive bacteria is formation of endospores. For Gram-negative bacteria, the assumption has been that a survival state does not exist. However, a dormancy state has been described for Gram-negative bacteria and designated as the viable but nonculturable (VBNC) strategy of nonspore-forming cells. A variety of environmental factors are involved in induction of the viable but nonculturable state and Vibrio cholerae provides a useful paradigm for the VBNC phenomenon. It is now accepted that plate counts cannot be relied upon to enumerate or detect VBNC cells. Therefore, direct methods employing fluorescent staining, molecular genetic probes, and other molecular methods have proven both useful and reliable in detecting and enumerating both culturable and nonculturable cells. A predictive model for cholera has been developed, based on ground truth data gathered using these molecular methods and combining them with data obtained by remote sensing, employing satellites. It is clear that microbiology in the twenty-first century has been enhanced by these new tools and paradigms.},
	author = {Rita R. Colwell}
}
@article {38567,
	title = {Vibrio cholerae non-O1, non-O139 strains isolated before 1992 from Varanasi, India are multiple drug resistant, contain intSXT, dfr18 and aadA5 genes},
	journal = {Environmental MicrobiologyEnvironmental Microbiology},
	volume = {10},
	year = {2008},
	type = {10.1111/j.1462-2920.2007.01502.x},
	abstract = {In this study, we report the presence of the SXT element and Class I integron in Vibrio cholerae non-O1, non-O139 strains isolated from Varanasi, India. Isolates were resistant to cotrimoxazole, trimethoprim and/or streptomycin, furazolidone and ampicillin. None contained plasmids. Polymerase chain reaction (PCR) and DNA sequencing revealed the presence of antibiotic resistance gene cassettes, aadA1, aadA2, aadA5 and dfrA15, in the Class I integron and SXT, an integrative conjugative element containing dfr18, sulII and strAB, in three and six of the isolates respectively. Conjugation experiments, followed by PCR analysis of transconjugants, provided evidence for the transferable nature of intSXT and associated antibiotic resistance gene cassettes. This is the first report of the occurrence of SXT ICE, dfr18, sulII, strAB and aadA5 genes in environmental V.~cholerae non-O1, non-O139 strains from Varanasi, India, that had been isolated before 1992.},
	isbn = {1462-2920},
	author = {Mohapatra, Harapriya and Mohapatra, Saswat S. and Mantri, Chinmay K. and Rita R. Colwell and Singh, Durg V.}
}
@article {38563,
	title = {Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes},
	journal = {VirologyVirology},
	volume = {365},
	year = {2007},
	type = {16/j.virol.2007.02.037},
	abstract = {Topoisomerase enzymes regulate superhelical tension in DNA resulting from transcription, replication, repair, and other molecular transactions. Poxviruses encode an unusual type IB topoisomerase that acts only at conserved DNA sequences containing the core pentanucleotide 5{\textquoteright}-(T/C)CCTT-3{\textquoteright}. In X-ray structures of the variola virus topoisomerase bound to DNA, protein-DNA contacts were found to extend beyond the core pentanucleotide, indicating that the full recognition site has not yet been fully defined in functional studies. Here we report quantitation of DNA cleavage rates for an optimized 13~bp site and for all possible single base substitutions (40 total sites), with the goals of understanding the molecular mechanism of recognition and mapping topoisomerase sites in poxvirus genome sequences. The data allow a precise definition of enzyme-DNA interactions and the energetic contributions of each. We then used the resulting "action matrix" to show that favorable topoisomerase sites are distributed all along the length of poxvirus DNA sequences, consistent with a requirement for local release of superhelical tension in constrained topological domains. In orthopox genomes, an additional central cluster of sites was also evident. A negative correlation of predicted topoisomerase sites was seen relative to early terminators, but no correlation was seen with early or late promoters. These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo.},
	keywords = {Annotation of topoisomerase sites, Sequence specific recognition, Topoisomerase IB, Variola virus},
	isbn = {0042-6822},
	author = {Minkah, Nana and Hwang, Young and Perry, Kay and Van Duyne, Gregory D. and Hendrickson, Robert and Lefkowitz, Elliot J. and Sridhar Hannenhalli and Bushman, Frederic D.}
}
@article {38564,
	title = {Viable but nonculturable Vibrio cholerae O1 in biofilms in the aquatic environment and their role in cholera transmission},
	journal = {Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences},
	volume = {104},
	year = {2007},
	type = {10.1073/pnas.0705599104},
	abstract = {Vibrio cholerae persists in aquatic environments predominantly in a nonculturable state. In this study coccoid, nonculturable V. cholerae O1 in biofilms maintained for 495 days in Mathbaria, Bangladesh, pond water became culturable upon animal passage. Culturability, biofilm formation, and the wbe, ctxA, and rstR2 genes were monitored by culture, direct fluorescent antibody (DFA), and multiplex PCR. DFA counts were not possible after formation of biofilm. Furthermore, wbe, but not ctxA, were amplifiable, even after incubation for 54 and 68 days at room temperature (≈25{\textdegree}C) and 4{\textdegree}C, respectively, when no growth was detectable. Slower biofilm formation and extended culturability were observed for cultures incubated at 4{\textdegree}C, compared with ≈25{\textdegree}C, suggesting biofilm production to be temperature dependent and linked to loss of culturability. Small colonies appearing after incubation in microcosms for 54 and 68 days at 25{\textdegree}C and 4{\textdegree}C, respectively, were wbe positive and ctxA and rstR2 negative, indicating loss of bacteriophage CTXΦ. The coccoid V. cholerae O1 observed as free cells in microcosms incubated for 495 days could not be cultured, but biofilms in the same microcosms yielded culturable cells. It is concluded that biofilms can act as a reservoir for V. cholerae O1 between epidemics because of its long-term viability in biofilms. In contrast to biofilms produced in Mathbaria pond water, V. cholerae O1 in biofilms present in cholera stools and incubated under identical conditions as the Mathbaria pond water biofilms could not be cultured after 2 months, indicating that those V. cholerae cells freshly discharged into the environment are significantly less robust than cells adapted to environmental conditions.Bangladesh bacteriophage CTXΦ DFA multiplex-PCR ctxA},
	isbn = {0027-8424, 1091-6490},
	author = {Alam, M. and Sultana, M. and Nair, G. B. and Siddique, A. K. and Hasan, N. A. and Sack, R. B. and Sack, D. A. and Ahmed, K. U. and Sadique, A. and Watanabe, H. and Rita R. Colwell}
}
@article {38562,
	title = {Variation of toxigenic Vibrio cholerae O1 in the aquatic environment of Bangladesh and its correlation with the clinical strains},
	journal = {Microbiology and immunologyMicrobiology and Immunology},
	volume = {48},
	year = {2004},
	author = {Islam, M. S. and Talukder, K. A. and Khan, N. H. and Mahmud, Z. H. and Rahman, M. Z. and Nair, G. B. and Siddique, A. K. M. and Yunus, M. and Sack, D. A. and Sack, R. B. and Rita R. Colwell}
}
@article {38096,
	title = {Viable but Nonculturable Vibrio Cholerae O1 in the Aquatic Environment of Argentina},
	journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.},
	volume = {70},
	year = {2004},
	type = {10.1128/AEM.70.12.7481-7486.2004},
	abstract = {In Argentina, as in other countries of Latin America, cholera has occurred in an epidemic pattern. Vibrio cholerae O1 is native to the aquatic environment, and it occurs in both culturable and viable but nonculturable (VNC) forms, the latter during interepidemic periods. This is the first report of the presence of VNC V. cholerae O1 in the estuarine and marine waters of the R{\'\i}o de la Plata and the Argentine shelf of the Atlantic Ocean, respectively. Employing immunofluorescence and PCR methods, we were able to detect reservoirs of V. cholerae O1 carrying the virulence-associated genes ctxA and tcpA. The VNC forms of V. cholerae O1 were identified in samples of water, phytoplankton, and zooplankton; the latter organisms were mainly the copepods Acartia tonsa, Diaptomus sp., Paracalanus crassirostris, and Paracalanus parvus. We found that under favorable conditions, the VNC form of V. cholerae can revert to the pathogenic, transmissible state. We concluded that V. cholerae O1 is a resident of Argentinean waters, as has been shown to be the case in other geographic regions of the world.},
	isbn = {0099-2240, 1098-5336},
	author = {Binsztein, Norma and Costagliola, Marcela C. and Pichel, Mariana and Jurquiza, Ver{\'o}nica and Ram{\'\i}rez, Fernando C. and Akselman, Rut and Vacchino, Marta and Huq, Anwarul and Rita R. Colwell}
}
@article {38569,
	title = {A voyage of discovery: cholera, climate and complexity},
	journal = {Environmental MicrobiologyEnvironmental Microbiology},
	volume = {4},
	year = {2002},
	type = {10.1046/j.1462-2920.2002.00270.x},
	isbn = {1462-2920},
	author = {Rita R. Colwell}
}
