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An in vivo expression technology screen for Vibrio cholerae genes expressed in human volunteers. Proc Natl Acad Sci U S A 2007; 104:18229-34. [PMID: 17986616 DOI: 10.1073/pnas.0705636104] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In vivo expression technology (IVET) has been widely used to study gene expression of human bacterial pathogens in animal models, but has heretofore not been used in humans to our knowledge. As part of ongoing efforts to understand Vibrio cholerae pathogenesis and develop improved V. cholerae vaccines, we have performed an IVET screen in humans for genes that are preferentially expressed by V. cholerae during infection. A library of 8,734 nontoxigenic V. cholerae strains carrying transcriptional fusions of genomic DNA to a resolvase gene was ingested by five healthy adult volunteers. Transcription of the fusion leads to resolvase-dependent excision of a sacB-containing cassette and thus the selectable phenotype of sucrose resistance (Suc(R)). A total of approximately 20,000 Suc(R) isolates, those carrying putative in vivo-induced fusions, were recovered from volunteer stool samples. Analysis of the fusion junctions from >7,000 Suc(R) isolates from multiple samples from multiple volunteers identified 217 candidate genes for preferential expression during human infection. Of genes or operons induced in three or more volunteers, the majority of those tested (65%) were induced in an infant mouse model. VC0201 (fhuC), which encodes the ATPase of a ferrichrome ABC transporter, is one of the identified in vivo-induced genes and is required for virulence in the mouse model.
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202
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Fournier PE, Drancourt M, Raoult D. Bacterial genome sequencing and its use in infectious diseases. THE LANCET. INFECTIOUS DISEASES 2007; 7:711-23. [DOI: 10.1016/s1473-3099(07)70260-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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203
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Association of Vibrio cholerae O1 El Tor and O139 Bengal with the Copepods Acartia tonsa and Eurytemora affinis. Appl Environ Microbiol 2007; 73:7926-33. [PMID: 17951440 DOI: 10.1128/aem.01238-07] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The association of Vibrio cholerae with zooplankton has been suggested as an important factor in transmission of human epidemic cholera, and the ability to colonize zooplankton surfaces may play a role in the temporal variation and predominance of the two different serogroups (V. cholerae O1 El Tor and O139) in the aquatic environment. To date, interactions between specific serogroups and species of plankton remain poorly understood. Laboratory microcosm experiments were carried out to compare quantitatively the colonization of two copepod species, Acartia tonsa and Eurytemora affinis, by each of the epidemic serogroups. V. cholerae O1 consistently achieved higher abundances than V. cholerae O139 in colonizing adults of each copepod species as well as the multiple life stages of E. affinis. This difference in colonization may be significant in the general predominance of V. cholerae O1 in cholera epidemics in rural Bangladesh where water supplies are taken directly from the environment.
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204
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Blokesch M, Schoolnik GK. Serogroup conversion of Vibrio cholerae in aquatic reservoirs. PLoS Pathog 2007; 3:e81. [PMID: 17559304 PMCID: PMC1891326 DOI: 10.1371/journal.ppat.0030081] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 04/19/2007] [Indexed: 11/18/2022] Open
Abstract
The environmental reservoirs for Vibrio cholerae are natural aquatic habitats, where it colonizes the chitinous exoskeletons of copepod molts. Growth of V. cholerae on a chitin surface induces competence for natural transformation, a mechanism for intra-species gene exchange. The antigenically diverse O-serogroup determinants of V. cholerae are encoded by a genetically variable biosynthetic cluster of genes that is flanked on either side by chromosomal regions that are conserved between different serogroups. To determine whether this genomic motif and chitin-induced natural transformation might enable the exchange of serogroup-specific gene clusters between different O serogroups of V. cholerae, a strain of V. cholerae O1 El Tor was co-cultured with a strain of V. cholerae O139 Bengal within a biofilm on the same chitin surface immersed in seawater, and O1-to-O139 transformants were obtained. Serogroup conversion of the O1 recipient by the O139 donor was demonstrated by comparative genomic hybridization, biochemical and serological characterization of the O-antigenic determinant, and resistance of O1-to-O139 transformants to bacteriolysis by a virulent O1-specific phage. Serogroup conversion was shown to have occurred as a single-step exchange of large fragments of DNA. Crossovers were localized to regions of homology common to other V. cholerae serogroups that flank serogroup-specific encoding sequences. This result and the successful serogroup conversion of an O1 strain by O37 genomic DNA indicate that chitin-induced natural transformation might be a common mechanism for serogroup conversion in aquatic habitats and for the emergence of V. cholerae variants that are better adapted for survival in environmental niches or more pathogenic for humans. The reservoirs of Vibrio cholerae are aquatic environments, where it attaches to the chitin-containing shells of small crustaceans. Chitin serves as a nutrient for V. cholerae and it induces natural transformation, a process by which it acquires new genes from other microbes in the same habitat. The most compelling consequence of a V. cholerae gene acquisition event occurred in 1992 when a vast cholera epidemic erupted in India and Bangladesh and spread through Asia. Genetic analysis showed that this outbreak was due to the acquisition of a gene cluster that converted the ancestral V. cholerae O1 El Tor serogroup to an entirely new serogroup, designated O139 Bengal. This report shows that acquisition of the O139 gene cluster by an O1 El Tor strain can be mediated by natural transformation and that this can occur within a community of bacteria living on a chitin surface. The O139 derivatives of this transformation event were not killed by bacteriophages that attack O1 strains, explaining in part why O139 strains have replaced O1 strains in some Asian water sources. These results also illustrate how a combination of genetic and ecological factors can lead to the emergence of new pathogenic microbes in environmental reservoirs.
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Affiliation(s)
- Melanie Blokesch
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gary K Schoolnik
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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205
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Pukatzki S, Ma AT, Revel AT, Sturtevant D, Mekalanos JJ. Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. Proc Natl Acad Sci U S A 2007; 104:15508-13. [PMID: 17873062 PMCID: PMC2000545 DOI: 10.1073/pnas.0706532104] [Citation(s) in RCA: 550] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. Protein structure search algorithms predict that VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. VgrG-1 was shown to interact with itself, VgrG-2, and VgrG-3, suggesting that such a complex does form. Because the phage tail spike protein complex acts as a membrane-penetrating structure as well as a conduit for the passage of DNA into phage-infected cells, we propose that the VgrG components of the T6SS apparatus may assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells.
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Affiliation(s)
- Stefan Pukatzki
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - Amy T. Ma
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - Andrew T. Revel
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - Derek Sturtevant
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - John J. Mekalanos
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
- *To whom correspondence should be addressed. E-mail:
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206
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Jayapal KP, Lian W, Glod F, Sherman DH, Hu WS. Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans. BMC Genomics 2007; 8:229. [PMID: 17623098 PMCID: PMC1934918 DOI: 10.1186/1471-2164-8-229] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Accepted: 07/10/2007] [Indexed: 11/20/2022] Open
Abstract
Background The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of synteny. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle differences between these two chromosomes. Results We identified five large S. coelicolor genomic islands (larger than 25 kb) and 18 smaller islets absent in S. lividans chromosome. Many of these regions show anomalous GC bias and codon usage patterns. Six of them are in close vicinity of tRNA genes while nine are flanked with near perfect repeat sequences indicating that these are probable recent evolutionary acquisitions into S. coelicolor. Embedded within these segments are at least four DNA methylases and two probable methyl-sensing restriction endonucleases. Comparison with S. coelicolor transcriptome and proteome data revealed that some of the missing genes are active during the course of growth and differentiation in S. coelicolor. In particular, a pair of methylmalonyl CoA mutase (mcm) genes involved in polyketide precursor biosynthesis, an acyl-CoA dehydrogenase implicated in timing of actinorhodin synthesis and bldB, a developmentally significant regulator whose mutation causes complete abrogation of antibiotic synthesis belong to this category. Conclusion Our findings provide tangible hints for elucidating the genetic basis of important phenotypic differences between these two streptomycetes. Importantly, absence of certain genes in S. lividans identified here could potentially explain the relative ease of DNA transformations and the conditional lack of actinorhodin synthesis in S. lividans.
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Affiliation(s)
- Karthik P Jayapal
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE., Minneapolis, MN 55455, USA
| | - Wei Lian
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE., Minneapolis, MN 55455, USA
- Abbott Bioresearch Center, 100 Research Drive, Worcester, MA 01605, USA
| | - Frank Glod
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, USA
- Fonds National de la Recherche, 6 rue Antoine de Saint-Exupéry, L-1017 Kirchberg, Luxembourg
| | - David H Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE., Minneapolis, MN 55455, USA
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207
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Makri S, Purdy AE, Bartlett D, Fierer J. Pathogenicity of environmental isolates of V. cholerae in mice. Microbes Infect 2007; 9:1351-8. [PMID: 17890125 DOI: 10.1016/j.micinf.2007.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 06/20/2007] [Accepted: 06/22/2007] [Indexed: 11/24/2022]
Abstract
Environmental V. cholerae (Vc) have the potential for virulence in people and they may also be a reservoir of accessory virulence genes. We infected mice with two non-O1, non-O139 Vc (TP and SIO) that were isolated in San Diego County and compared them to Vc O1 El Tor N16961 using a model of pneumonia in adult mice. Live but not heat killed Vc El Tor and TP caused fatal hemorrhagic pneumonia despite a >90% decrease in CFU in 24h suggesting the disease was toxin mediated. SIO did not cause pneumonia in normal mice but neutropenic, gp91phox and complement (C3) mice were more susceptible to all three strains. TP and SIO lack ctx but have rtxA, hlyA, and hapA, genes that encode virulence factors in Vc El Tor. The explanation for the enhanced virulence of TP remains to be determined.
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Affiliation(s)
- Stamatoula Makri
- Division of Infectious Diseases, VA Medical Center, San Diego, CA, USA
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208
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Hsiao NH, Kirby R. Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system. Antonie van Leeuwenhoek 2007; 93:1-25. [PMID: 17588127 PMCID: PMC2140096 DOI: 10.1007/s10482-007-9175-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2007] [Accepted: 05/11/2007] [Indexed: 11/30/2022]
Abstract
DNA/DNA microarray hybridization was used to compare the genome content of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens with that of Streptomyces coelicolor A3(2). The array data showed an about 93% agreement with the genome sequence data available for S. avermitilis and also showed a number of trends in the genome structure for Streptomyces and closely related Kitasatospora. A core central region was well conserved, which might be predicted from previous research and this was linked to a low degree of gene conservation in the terminal regions of the linear chromosome across all four species. Between these regions there are two areas of intermediate gene conservation by microarray analysis where gene synteny is still detectable in S. avermitilis. Nonetheless, a range of conserved genes could be identified within the terminal regions. Variation in the genes involved in differentiation, transcription, DNA replication, etc. provides interesting insights into which genes in these categories are generally conserved and which are not. The results also provide target priorities for possible gene knockouts in a group of bacteria with a very large numbers of genes with unknown functions compared to most bacterial species.
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Affiliation(s)
- Nai-hua Hsiao
- Microbial Physiology, University of Groningen, Kerklaan 30, NL-9751 NN Haren, Groningen, The Netherlands
| | - Ralph Kirby
- Department of Life Science, National Yang-Ming University, Beitou, Taipei, 114 Taiwan
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209
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Feten G, Almøy T, Snipen L, Aakra A, Nyquist OL, Aastveit AH. Mixture models as a method to find present and divergent genes in comparative genomic hybridization studies on bacteria. Biom J 2007; 49:242-58. [PMID: 17476947 DOI: 10.1002/bimj.200510286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Comparative genomic hybridization (CGH) using microarrays is performed on bacteria in order to test for genomic diversity within various bacterial species. The microarrays used for CGH are based on the genome of a fully sequenced bacterium strain, denoted reference strain. Labelled DNA fragments from a sample strain of interest and from the reference strain are hybridized to the array. Based on the obtained ratio intensities and the total intensities of the signals, each gene is classified as either present (one copy or multiple copies) or divergent (zero copies). In this paper mixture models with different number of components are tted on different combinations of variables and compared with each other. The study shows that mixture models fitted on both the ratio intensities and the total intensities including the replicates for each gene improve, compared to previously published methods, the results for several of the data sets tested. Some summaries of the data sets are proposed as a guide for the choice of model and the choice of number of components. The models are applied on data from CGH experiments with the bacteria Staphylococcus aureus and
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Affiliation(s)
- Guri Feten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 As, Norway.
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210
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Pang B, Yan M, Cui Z, Ye X, Diao B, Ren Y, Gao S, Zhang L, Kan B. Genetic diversity of toxigenic and nontoxigenic Vibrio cholerae serogroups O1 and O139 revealed by array-based comparative genomic hybridization. J Bacteriol 2007; 189:4837-49. [PMID: 17468246 PMCID: PMC1913441 DOI: 10.1128/jb.01959-06] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Toxigenic serogroups O1 and O139 of Vibrio cholerae may cause cholera epidemics or pandemics. Nontoxigenic strains within these serogroups also exist in the environment, and also some may cause sporadic cases of disease. Herein, we investigate the genomic diversity among toxigenic and nontoxigenic O1 and O139 strains by comparative genomic microarray hybridization with the genome of El Tor strain N16961 as a base. Conservation of the toxigenic O1 El Tor and O139 strains is found as previously reported, whereas accumulation of genome changes was documented in toxigenic El Tor strains isolated within the 40 years of the seventh pandemic. High phylogenetic diversity in nontoxigenic O1 and O139 strains is observed, and most of the genes absent from nontoxigenic strains are clustered together in the N16961 genome. By comparing these toxigenic and nontoxigenic strains, we observed that the small chromosome of V. cholerae is quite conservative and stable, outside of the superintegron region. In contrast to the general stability of the genome, the superintegron demonstrates pronounced divergence among toxigenic and nontoxigenic strains. Additionally, sequence variation in virulence-related genes is found in nontoxigenic El Tor strains, and we speculate that these intermediate strains may have pathogenic potential should they acquire CTX prophage alleles and other gene clusters. This genome-wide comparison of toxigenic and nontoxigenic V. cholerae strains may promote understanding of clonal differentiation of V. cholerae and contribute to an understanding of the origins and clonal selection of epidemic strains.
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Affiliation(s)
- Bo Pang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, P.O. Box 5, Changping, Beijing 102206, People's Republic of China
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211
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Keymer DP, Miller MC, Schoolnik GK, Boehm AB. Genomic and phenotypic diversity of coastal Vibrio cholerae strains is linked to environmental factors. Appl Environ Microbiol 2007; 73:3705-14. [PMID: 17449702 PMCID: PMC1932678 DOI: 10.1128/aem.02736-06] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studies of Vibrio cholerae diversity have focused primarily on pathogenic isolates of the O1 and O139 serotypes. However, autochthonous environmental isolates of this species routinely display more extensive genetic diversity than the primarily clonal pathogenic strains. In this study, genomic and metabolic profiles of 41 non-O1/O139 environmental isolates from central California coastal waters and four clinical strains are used to characterize the core genome and metabolome of V. cholerae. Comparative genome hybridization using microarrays constructed from the fully sequenced V. cholerae O1 El Tor N16961 genome identified 2,787 core genes that approximated the projected species core genome within 1.6%. Core genes are almost universally present in strains with widely different niches, suggesting that these genes are essential for persistence in diverse aquatic environments. In contrast, the dispensable genes and phenotypic traits identified in this study should provide increased fitness for certain niche environments. Environmental parameters, measured in situ during sample collection, are correlated to the presence of specific dispensable genes and metabolic capabilities, including utilization of mannose, sialic acid, citrate, and chitosan oligosaccharides. These results identify gene content and metabolic pathways that are likely selected for in certain coastal environments and may influence V. cholerae population structure in aquatic environments.
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Affiliation(s)
- Daniel P Keymer
- Department of Civil Engineering, Stanford University School of Medicine, CA 94305, USA.
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212
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Miller MC, Keymer DP, Avelar A, Boehm AB, Schoolnik GK. Detection and transformation of genome segments that differ within a coastal population of Vibrio cholerae strains. Appl Environ Microbiol 2007; 73:3695-704. [PMID: 17449699 PMCID: PMC1932674 DOI: 10.1128/aem.02735-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is an autochthonous member of diverse aquatic ecosystems around the globe. Collectively, the genomes of environmental V. cholerae strains comprise a large repository of encoded functions which can be acquired by individual V. cholerae lineages through uptake and recombination. To characterize the genomic diversity of environmental V. cholerae, we used comparative genome hybridization to study 41 environmental strains isolated from diverse habitats along the central California coast, a region free of endemic cholera. These data were used to classify genes of the epidemic V. cholerae O1 sequenced strain N16961 as conserved, variably present, or absent from the isolates. For the most part, absent genes were restricted to large mobile elements and have known functions in pathogenesis. Conversely, genes present in some, but not all, California isolates were in smaller contiguous clusters and were less likely to be near genes with functions in DNA mobility. Two such clusters of variable genes encoding different selectable metabolic phenotypes (mannose and diglucosamine utilization) were transformed into the genomes of environmental isolates by chitin-dependent competence, indicating that this mechanism of general genetic exchange is conserved among V. cholerae. The transformed DNA had an average size of 22.7 kbp, demonstrating that natural competence can mediate the movement of large chromosome fragments. Thus, whether variable genes arise through the acquisition of new sequences by horizontal gene transfer or by the loss of preexisting DNA though deletion, natural transformation provides a mechanism by which V. cholerae clones can gain access to the V. cholerae pan-genome.
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Affiliation(s)
- Michael C Miller
- Department of Medicine, Stanford University School of Medicine, CA 94305, USA.
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213
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Faruque SM, Tam VC, Chowdhury N, Diraphat P, Dziejman M, Heidelberg JF, Clemens JD, Mekalanos JJ, Nair GB. Genomic analysis of the Mozambique strain of Vibrio cholerae O1 reveals the origin of El Tor strains carrying classical CTX prophage. Proc Natl Acad Sci U S A 2007; 104:5151-6. [PMID: 17360342 PMCID: PMC1829278 DOI: 10.1073/pnas.0700365104] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cholera outbreaks in subSaharan African countries are caused by strains of the El Tor biotype of toxigenic Vibrio cholerae O1. The El Tor biotype is the causative agent of the current seventh cholera pandemic, whereas the classical biotype, which was associated with the sixth pandemic, is now extinct. Besides other genetic differences the CTX prophages encoding cholera toxin in the two biotypes of V. cholerae O1 have distinct repressor (rstR) genes. However, recent incidences of cholera in Mozambique were caused by an El Tor biotype V. cholerae O1 strain that, unusually, carries a classical type (CTX(class)) prophage. We conducted genomic analysis of the Mozambique strain and its CTX prophage together with chromosomal phage integration sites to understand the origin of this atypical strain and its evolutionary relationship with the true seventh pandemic strain. These analyses showed that the Mozambique strain carries two copies of CTX(class) prophage located on the small chromosome in a tandem array that allows excision of the prophage, but the excised phage genome was deficient in replication and did not produce CTX(class) virion. Comparative genomic microarray analysis revealed that the strain shares most of its genes with the typical El Tor strain N16961 but did not carry the TLC gene cluster, and RS1 sequence, adjacent to the CTX prophage. Our data are consistent with the Mozambique strain's having evolved from a progenitor similar to the seventh pandemic strain, involving multiple recombination events and suggest a model for origination of El Tor strains carrying the classical CTX prophage.
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Affiliation(s)
- Shah M. Faruque
- *Molecular Genetics Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
- To whom correspondence may be addressed. E-mail: or
| | - Vincent C. Tam
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - Nityananda Chowdhury
- *Molecular Genetics Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Pornphan Diraphat
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 73170, Thailand
| | - Michelle Dziejman
- School of Medicine and Dentistry, University of Rochester, 601 Elmwood Avenue, Box 672, Rochester, NY 14642
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - John F. Heidelberg
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850
| | - John D. Clemens
- **International Vaccine Institute, Kwanak, P.O. Box 14, Seoul 151-600, Korea; and
| | - John J. Mekalanos
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - G. Balakrish Nair
- *Molecular Genetics Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
- To whom correspondence may be addressed. E-mail: or
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214
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Lloyd AL, Rasko DA, Mobley HLT. Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli. J Bacteriol 2007; 189:3532-46. [PMID: 17351047 PMCID: PMC1855899 DOI: 10.1128/jb.01744-06] [Citation(s) in RCA: 179] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) strains are responsible for the majority of uncomplicated urinary tract infections, which can present clinically as cystitis or pyelonephritis. UPEC strain CFT073, isolated from the blood of a patient with acute pyelonephritis, was most cytotoxic and most virulent in mice among our strain collection. Based on the genome sequence of CFT073, microarrays were utilized in comparative genomic hybridization (CGH) analysis of a panel of uropathogenic and fecal/commensal E. coli isolates. Genomic DNA from seven UPEC (three pyelonephritis and four cystitis) isolates and three fecal/commensal strains, including K-12 MG1655, was hybridized to the CFT073 microarray. The CFT073 genome contains 5,379 genes; CGH analysis revealed that 2,820 (52.4%) of these genes were common to all 11 E. coli strains, yet only 173 UPEC-specific genes were found by CGH to be present in all UPEC strains but in none of the fecal/commensal strains. When the sequences of three additional sequenced UPEC strains (UTI89, 536, and F11) and a commensal strain (HS) were added to the analysis, 131 genes present in all UPEC strains but in no fecal/commensal strains were identified. Seven previously unrecognized genomic islands (>30 kb) were delineated by CGH in addition to the three known pathogenicity islands. These genomic islands comprise 672 kb of the 5,231-kb (12.8%) genome, demonstrating the importance of horizontal transfer for UPEC and the mosaic structure of the genome. UPEC strains contain a greater number of iron acquisition systems than do fecal/commensal strains, which is reflective of the adaptation to the iron-limiting urinary tract environment. Each strain displayed distinct differences in the number and type of known virulence factors. The large number of hypothetical genes in the CFT073 genome, especially those shown to be UPEC specific, strongly suggests that many urovirulence factors remain uncharacterized.
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Affiliation(s)
- Amanda L Lloyd
- Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Bldg. II, 1150 West Medical Center Dr., Ann Arbor, MI 48109-0620, USA
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Raskin DM, Judson N, Mekalanos JJ. Regulation of the stringent response is the essential function of the conserved bacterial G protein CgtA in Vibrio cholerae. Proc Natl Acad Sci U S A 2007; 104:4636-41. [PMID: 17360576 PMCID: PMC1838653 DOI: 10.1073/pnas.0611650104] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gene encoding the conserved bacterial G protein CgtA (Obg) is essential for viability in every organism in which it has been studied. CgtA has been reported to be involved in several diverse bacterial functions, including ribosome assembly, DNA repair, sporulation, and morphological development. However, none of these functions have been identified as essential. Here we show that depletion of CgtA in Vibrio cholerae causes global changes in gene expression that are consistent with induction of a classical low nutrient stress response or "stringent" response. We show that depletion of CgtA leads to increased ppGpp levels that correlate with induction of the global stress response and cessation of growth. The enzyme RelA is responsible for synthesis of the alarmone ppGpp during the stringent response. We show that CgtA is no longer essential in a relA deletion mutant and thus conclude that the essentiality of CgtA is directly linked to its ability to affect ppGpp levels. The enzyme SpoT degrades ppGpp, and here we show that SpoT is essential in a RelA+ CgtA+ background but not in a relA deletion mutant. We also confirmed that CgtA interacts with SpoT in a two-hybrid assay. We suggest that the essential function of CgtA is as a repressor of the stringent response that acts by regulating SpoT activity to maintain low ppGpp levels when bacteria are growing in a nutrient-rich environment.
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Affiliation(s)
- David M. Raskin
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - Nicholas Judson
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
| | - John J. Mekalanos
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115
- To whom correspondence should be addressed. E-mail:
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216
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Newton R, Hinds J, Wernisch L. A Hidden Markov model web application for analysing bacterial genomotyping DNA microarray experiments. ACTA ACUST UNITED AC 2007; 5:211-8. [PMID: 17140267 DOI: 10.2165/00822942-200605040-00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Whole genome DNA microarray genomotyping experiments compare the gene content of different species or strains of bacteria. A statistical approach to analysing the results of these experiments was developed, based on a Hidden Markov model (HMM), which takes adjacency of genes along the genome into account when calling genes present or absent. The model was implemented in the statistical language R and applied to three datasets. The method is numerically stable with good convergence properties. Error rates are reduced compared with approaches that ignore spatial information. Moreover, the HMM circumvents a problem encountered in a conventional analysis: determining the cut-off value to use to classify a gene as absent. An Apache Struts web interface for the R script was created for the benefit of users unfamiliar with R. The application may be found at http://hmmgd.cryst.bbk.ac.uk/hmmgd. The source code illustrating how to run R scripts from an Apache Struts-based web application is available from the corresponding author on request. The application is also available for local installation if required.
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Affiliation(s)
- Richard Newton
- School of Crystallography, Birkbeck College, University of London, London, UK.
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217
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Aakra A, Nyquist OL, Snipen L, Reiersen TS, Nes IF. Survey of genomic diversity among Enterococcus faecalis strains by microarray-based comparative genomic hybridization. Appl Environ Microbiol 2007; 73:2207-17. [PMID: 17220255 PMCID: PMC1855650 DOI: 10.1128/aem.01599-06] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We have compared nine Enterococcus faecalis strains with E. faecalis V583 by comparative genomic hybridization using microarrays (CGH). The strains used in this study (the "test" strains) originated from various environments. CGH is a powerful and promising tool for obtaining novel information on genome diversity in bacteria. By CGH, one obtains clues about which genes are present or divergent in the strains, compared to a reference strain (here, V583). The information obtained by CGH is important from both ecological and systematic points of view. CGH of E. faecalis showed considerable diversity in gene content: Compared to V583, the percentage of divergent genes in the test strains varied from 15% to 23%, and 154 genes were divergent in all strains. The main variation was found in regions corresponding to exogenously acquired or mobile DNA in V583. Antibiotic resistance genes, virulence factors, and integrated plasmid genes dominated among the divergent genes. The strains examined showed various contents of genes corresponding to the pTEF1, pTEF2, and pTEF3 genes in V583. The extensive transport and metabolic capabilities of V583 appeared similar in the test strains; CGH indicated that the ability to transport and metabolize various carbohydrates was similar in the test strains (verified by API 50 CH assays). The contents of genes related to stress tolerance appeared similar in V583 and the nine test strains, supporting the view of E. faecalis as an organism able to resist harsh conditions.
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Affiliation(s)
- Agot Aakra
- Laboratory of Microbial Gene Technology, Department of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, P.O. Box 5003, N-1432 As, Norway.
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218
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Taboada EN, Luebbert CC, Nash JHE. Studying bacterial genome dynamics using microarray-based comparative genomic hybridization. Methods Mol Biol 2007; 396:223-53. [PMID: 18025696 DOI: 10.1007/978-1-59745-515-2_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genome sequencing has revealed the remarkable amount of genetic diversity that can be encountered in bacterial genomes. In particular, the comparison of genome sequences from closely related strains has uncovered significant differences in gene content, hinting at the dynamic nature of bacterial genomes. The study of these genome dynamics is crucial to leveraging genomic information because the genome sequence of a single bacterial strain may not accurately represent the genome of the species. The dynamic nature of bacterial genome content has required us to apply the concepts of comparative genomics (CG) at the species level. Although direct genome sequence comparisons are an ideal method of performing CG, one current constraint is the limited availability of multiple genome sequences from a given bacterial species. DNA microarray-based comparative genomic hybridization (MCGH), which can be used to determine the presence or absence of thousands of genes in a single hybridization experiment, provides a powerful alternative for determining genome content and has been successfully used to investigate the genome dynamics of a wide number of bacterial species. Although MCGH-based studies have already provided a new vista on bacterial genome diversity, original methods for MCGH have been limited by the absence of novel gene sequences included in the microarray. New applications of the MCGH platform not only promise to accelerate the pace of novel gene discovery but will also help provide an integrated microarray-based approach to the study of bacterial CG.
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219
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Nair GB, Safa A, Bhuiyan NA, Nusrin S, Murphy D, Nicol C, Valcanis M, Iddings S, Kubuabola I, Vally H. Isolation of Vibrio cholerae O1 strains similar to pre-seventh pandemic El Tor strains during an outbreak of gastrointestinal disease in an island resort in Fiji. J Med Microbiol 2006; 55:1559-1562. [PMID: 17030916 DOI: 10.1099/jmm.0.46734-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five strains of Vibrio cholerae O1, one each from an Australian and a New Zealand tourist with gastrointestinal illness returning from an island resort in Fiji and the remaining three from water sources located in the same resort, were extensively characterized. Conventional phenotypic traits that are used for biotyping of O1 V. cholerae categorized all five strains as belonging to the El Tor biotype. Genetic screening of 11 regions that are associated with virulence in V. cholerae showed variable results. The absence of genes comprising Vibrio seventh pandemic island-I (VSP-I) and VSP-II in all the strains indicated that these strains were very similar to the pre-seventh pandemic V. cholerae O1 El Tor strains. The ctxAB genes were absent in all strains whereas orfU and zot were present in four strains, indicating that the strains were non-toxigenic. Four strains carried a truncated CTX prophage. Although epidemiological and molecular studies suggested that these strains did not cause cholera amongst tourists at the resort, their similarity to pre-seventh pandemic strains, their prior association with gastrointestinal illness and their presence in the island resort setting warrant more attention.
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Affiliation(s)
- G Balakrish Nair
- International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B) Dhaka, Bangladesh
| | - Ashrafus Safa
- International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B) Dhaka, Bangladesh
| | - N A Bhuiyan
- International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B) Dhaka, Bangladesh
| | - Suraia Nusrin
- International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B) Dhaka, Bangladesh
| | - Denise Murphy
- Public Health Microbiology, Queensland Health Scientific Services, Coopers Plains, Queensland, Australia
| | - Carolyn Nicol
- Institute of Environmental Science and Research Limited (ESR), Kenepuru Science Centre, Poriru, New Zealand
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory (MDUPHL), Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Steven Iddings
- World Health Organization (WHO), South Pacific Office, Suva, Fiji
| | - Ili Kubuabola
- Fiji Centre for Communicable Disease Control, Mataika House, Suva, Fiji
| | - Hassan Vally
- National Centre for Epidemiology and Population Health, ANU College of Medicine and Health Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
- World Health Organization (WHO), South Pacific Office, Suva, Fiji
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220
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Abstract
Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.
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Affiliation(s)
- Ashlee M Earl
- Department of Microbiology & Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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221
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Safa A, Bhuyian NA, Nusrin S, Ansaruzzaman M, Alam M, Hamabata T, Takeda Y, Sack DA, Nair GB. Genetic characteristics of Matlab variants of Vibrio cholerae O1 that are hybrids between classical and El Tor biotypes. J Med Microbiol 2006; 55:1563-1569. [PMID: 17030917 DOI: 10.1099/jmm.0.46689-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Matlab variants of Vibrio cholerae O1, defined as hybrids between the classical and El Tor biotypes, were first isolated from hospitalized patients with acute secretory diarrhoea in Matlab, a rural area of Bangladesh. These variants could not be categorized as classical or El Tor biotypes by phenotypic and genotypic tests, and had representative traits of both the biotypes. A number of virulence-associated genes and/or gene clusters were screened by PCR and DNA sequencing. El Tor-specific gene clusters, Vibrio seventh-pandemic islands (VSP)-I and -II and repeat toxin (RTX) were present in the genome of these variants, indicating their El Tor lineage, whereas the nucleotide-sequence-derived CtxB amino acid sequence of these strains grouped them under the classical biotype. Matlab variants possessed all the necessary genes to initiate pandemics. The genetic relatedness of Matlab variants to the V. cholerae strains recently isolated in Mozambique is another important observation of this study, which underscores the epidemiological significance of Matlab variants.
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Affiliation(s)
- Ashrafus Safa
- Laboratory Sciences Division, Enteric Microbiology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Centre for Health and Population Research, GPO Box 128, Dhaka 1000, Bangladesh
| | - N A Bhuyian
- Laboratory Sciences Division, Enteric Microbiology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Centre for Health and Population Research, GPO Box 128, Dhaka 1000, Bangladesh
| | - Suraia Nusrin
- Laboratory Sciences Division, Enteric Microbiology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Centre for Health and Population Research, GPO Box 128, Dhaka 1000, Bangladesh
| | - M Ansaruzzaman
- Laboratory Sciences Division, Enteric Microbiology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Centre for Health and Population Research, GPO Box 128, Dhaka 1000, Bangladesh
| | - Munirul Alam
- Laboratory Sciences Division, Enteric Microbiology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Centre for Health and Population Research, GPO Box 128, Dhaka 1000, Bangladesh
| | - T Hamabata
- International Medical Research Center of Japan, Toyama, Tokyo, Japan
| | | | - David A Sack
- Laboratory Sciences Division, Enteric Microbiology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Centre for Health and Population Research, GPO Box 128, Dhaka 1000, Bangladesh
| | - G Balakrish Nair
- Laboratory Sciences Division, Enteric Microbiology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Centre for Health and Population Research, GPO Box 128, Dhaka 1000, Bangladesh
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222
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Nair GB, Qadri F, Holmgren J, Svennerholm AM, Safa A, Bhuiyan NA, Ahmad QS, Faruque SM, Faruque ASG, Takeda Y, Sack DA. Cholera due to altered El Tor strains of Vibrio cholerae O1 in Bangladesh. J Clin Microbiol 2006; 44:4211-3. [PMID: 16957040 PMCID: PMC1698305 DOI: 10.1128/jcm.01304-06] [Citation(s) in RCA: 192] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Revised: 08/01/2006] [Accepted: 08/14/2006] [Indexed: 11/20/2022] Open
Abstract
We determined the types of cholera toxin (CT) produced by a collection of 185 Vibrio cholerae O1 strains isolated in Bangladesh over the past 45 years. All of the El Tor strains of V. cholerae O1 isolated since 2001 produced CT of the classical biotype, while those isolated before 2001 produced CT of the El Tor biotype.
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Affiliation(s)
- G Balakrish Nair
- Laboratory Sciences Division, ICDDR,B: Centre for Health and Population Research, Mohakhali, Dhaka 1212, Bangladesh.
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223
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Lepage E, Brinster S, Caron C, Ducroix-Crepy C, Rigottier-Gois L, Dunny G, Hennequet-Antier C, Serror P. Comparative genomic hybridization analysis of Enterococcus faecalis: identification of genes absent from food strains. J Bacteriol 2006; 188:6858-68. [PMID: 16980489 PMCID: PMC1595521 DOI: 10.1128/jb.00421-06] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Enterococcus faecalis, a member of the natural microbiota of animal and human intestinal tracts, is also present as a natural contaminant in a variety of fermented foods. Over the last decade, E. faecalis has emerged as a major cause of nosocomial infections. We investigated the genetic diversity in 30 clinical and food isolates, including strains V583 and MMH594, in order to determine whether clinical and food isolates could be distinguished. Data were obtained using comparative genomic hybridization and specific PCR with a total of 202 probes of E. faecalis, selected using the available V583 genome sequence and part of the MMH594 pathogenicity island. The cognate genes encoded mainly exported proteins. Hybridization data were analyzed by a two-component mixture model that estimates the probability of any given gene to be either present or absent in the strains. A total of 78 genes were found to be variable, as they were absent in at least one isolate. Most of the variable genes were clustered in regions that, in the published V583 sequence, related to prophages or mobile genetic elements. The variable genes were distributed in three main groups: (i) genes equally distributed between clinical and dairy food isolates, (ii) genes absent from dairy food-related isolates, and (iii) genes present in MMH594 and V583 strains only. Further analysis of the distribution of the last gene group in 70 other isolates confirmed that six of the probed genes were always absent in dairy food-related isolates, whereas they were detected in clinical and/or commensal isolates. Two of them corresponded to prophages that were not detected in the cognate isolates, thus possibly extending the number of genes absent from dairy food isolates. Genes specifically detected in clinical isolates may prove valuable for the development of new risk assessment markers for food safety studies and for identification of new factors that may contribute to host colonization or infection.
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Affiliation(s)
- E Lepage
- Unité des Bactéries Lactiques et pathogènes Opportunistes, INRA, Jouy-en-Josas, France
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224
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Terekhova D, Iyer R, Wormser GP, Schwartz I. Comparative genome hybridization reveals substantial variation among clinical isolates of Borrelia burgdorferi sensu stricto with different pathogenic properties. J Bacteriol 2006; 188:6124-34. [PMID: 16923879 PMCID: PMC1595389 DOI: 10.1128/jb.00459-06] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clinical and murine studies suggest that there is a differential pathogenicity of different genotypes of Borrelia burgdorferi, the spirochetal agent of Lyme disease. Comparative genome hybridization was used to explore the relationship between different genotypes. The chromosomes of all studied isolates were highly conserved (>93%) with respect to both sequence and gene order. Plasmid sequences were substantially more diverse. Plasmids lp54, cp26, and cp32 were present in all tested isolates, and their sequences and gene order were conserved. The majority of linear plasmids showed variation both in terms of presence among different isolates and in terms of sequence and gene order. The data strongly imply that all B. burgdorferi clinical isolates contain linear plasmids related to each other, but the structure of these replicons may vary substantially from isolate to isolate. These alterations include deletions and presumed rearrangements that are likely to result in unique plasmid elements in many isolates. There is a strong correlation between complete genome hybridization profiles and other typing methods, which, in turn, also correlate to differences in pathogenicity. Because there is substantially less variation in the chromosomal and circular plasmid portions of the genome, the major differences in open reading frame content and genomic diversity among isolates are linear plasmid driven.
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Affiliation(s)
- Darya Terekhova
- Department of Microbiology and Immunology, New York Medical College, BSB Room 308, Valhalla, NY 10595, USA
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225
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Yoon SS, Mekalanos JJ. 2,3-butanediol synthesis and the emergence of the Vibrio cholerae El Tor biotype. Infect Immun 2006; 74:6547-56. [PMID: 17015461 PMCID: PMC1698044 DOI: 10.1128/iai.00695-06] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is an aquatic bacterium that causes the severe diarrheal disease cholera. V. cholerae strains of the O1 serogroup exist as two biotypes, classical and El Tor. Toxigenic strains of the El Tor biotype emerged to cause the seventh pandemic of cholera in 1961 and subsequently displaced strains of the classical biotype both in the environment and as a cause of cholera within a decade. The factors that drove emergence of the El Tor biotype and the displacement of the classical biotype are unknown. Here, we show a unique difference in carbohydrate metabolism between these two biotypes. When grown with added carbohydrates, classical biotype strains generated a sharp decrease in medium pH, resulting in loss of viability. However, growth of El Tor biotype strain N16961 was enhanced due to its ability to produce 2,3-butanediol, a neutral fermentation end product, and suppress the accumulation of organic acids. An N16961 mutant (SSY01) defective in 2,3-butanediol synthesis showed the same defect in growth that classical biotype strains show in media rich in carbohydrates. Importantly, the SSY01 mutant was attenuated in its ability to colonize the intestines of infant mice, suggesting that host carbohydrates may be available to V. cholerae within the intestinal environment. Similarly, the SSY01 mutant failed to develop biofilms when utilizing N-acetyl-D-glucosamine as a carbon source. Because growth on N-acetyl-D-glucosamine likely reflects the ability of a strain to grow on chitin in certain aquatic environments, we conclude that the strains of classical biotype are likely defective compared to those of El Tor in growth in any environmental niche that is rich in chitin and/or other metabolizable carbohydrates. We propose that the ability to metabolize sugars without production of acid by-products might account for the improved evolutionary fitness of the V. cholerae El Tor biotype compared to that of the classical biotype both as a global cause of cholera and as an environmental organism.
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Affiliation(s)
- Sang Sun Yoon
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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226
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W. On SL, Dorrell N, Petersen L, Bang DD, Morris S, Forsythe SJ, Wren BW. Numerical analysis of DNA microarray data of Campylobacter jejuni strains correlated with survival, cytolethal distending toxin and haemolysin analyses. Int J Med Microbiol 2006; 296:353-63. [DOI: 10.1016/j.ijmm.2006.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2005] [Revised: 03/13/2006] [Accepted: 03/13/2006] [Indexed: 10/24/2022] Open
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227
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Halatsi K, Oikonomou I, Lambiri M, Mandilara G, Vatopoulos A, Kyriacou A. PCR detection of Salmonella spp. using primers targeting the quorum sensing gene sdiA. FEMS Microbiol Lett 2006; 259:201-7. [PMID: 16734780 DOI: 10.1111/j.1574-6968.2006.00266.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Bacteria communicate with one another and with their host using chemical signalling molecules. This phenomenon is generally described as quorum sensing. A set of primers for PCR detection of Salmonella spp. has been designed using as target the sdiA gene which encodes a signal receptor of the LuxR family. The PCR product (274 bp) was confirmed by sequencing. A number of 81 non-Salmonella strains (representing 24 different species) were tested and gave negative results, while a total of 101 different serotypes of Salmonella (155 strains) tested positive for the presence of the sdiA gene. The sensitivity and specificity of the sdiA-based PCR assay were also checked in artificially contaminated human faecal samples. In this study, we demonstrate that quorum sensing genes can be successfully exploited as diagnostic markers.
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Affiliation(s)
- Konstantia Halatsi
- Department of Dietetics and Nutritional Science, Harokopio University, Athens, Greece
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228
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Reen FJ, Almagro-Moreno S, Ussery D, Boyd EF. The genomic code: inferring Vibrionaceae niche specialization. Nat Rev Microbiol 2006; 4:697-704. [PMID: 16894340 DOI: 10.1038/nrmicro1476] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Vibrionaceae show a wide range of niche specialization, from free-living forms to those attached to biotic and abiotic surfaces, from symbionts to pathogens and from estuarine inhabitants to deep-sea piezophiles. The existence of complete genome sequences for closely related species from varied aquatic niches makes this group an excellent case study for genome comparison.
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Affiliation(s)
- F Jerry Reen
- F. Jerry Reen and Salvador Almagro Moreno are at the Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
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229
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Gentry TJ, Wickham GS, Schadt CW, He Z, Zhou J. Microarray applications in microbial ecology research. MICROBIAL ECOLOGY 2006; 52:159-75. [PMID: 16897303 DOI: 10.1007/s00248-006-9072-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Accepted: 04/07/2006] [Indexed: 05/11/2023]
Abstract
Microarray technology has the unparalleled potential to simultaneously determine the dynamics and/or activities of most, if not all, of the microbial populations in complex environments such as soils and sediments. Researchers have developed several types of arrays that characterize the microbial populations in these samples based on their phylogenetic relatedness or functional genomic content. Several recent studies have used these microarrays to investigate ecological issues; however, most have only analyzed a limited number of samples with relatively few experiments utilizing the full high-throughput potential of microarray analysis. This is due in part to the unique analytical challenges that these samples present with regard to sensitivity, specificity, quantitation, and data analysis. This review discusses specific applications of microarrays to microbial ecology research along with some of the latest studies addressing the difficulties encountered during analysis of complex microbial communities within environmental samples. With continued development, microarray technology may ultimately achieve its potential for comprehensive, high-throughput characterization of microbial populations in near real time.
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Affiliation(s)
- T J Gentry
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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230
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Garaizar J, Rementeria A, Porwollik S. DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens? ACTA ACUST UNITED AC 2006; 47:178-89. [PMID: 16831204 DOI: 10.1111/j.1574-695x.2006.00081.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Genomic hybridization on whole genome arrays detects the presence or absence of similar DNA regions in sufficiently related microorganisms, allowing genome-wide comparison of their genetic contents. A whole genome array is based on a sequenced bacterial isolate, and is a collection of DNA probes fixed on a solid support. In a single hybridization experiment, the absence/presence status of all genes of the sequenced microbe in the queried isolate can be examined. The objective of this minireview is to summarize the past usage of DNA microarray technology for microbial strain characterizations, and to estimate its future utilization in epidemiological studies and molecular typing of bacterial pathogens. The studies reviewed here confirm the usefulness of microarray technology for the detection of genetic polymorphisms. However, the construction or purchase of DNA microarrays and the performance of strain to strain hybridization experiments are still prohibitively expensive for routine application. Future use of arrays in epidemiology is likely to depend on the development of more cost-effective protocols, more robust and simplified formats, and the adequate evaluation of their performance (efficacy) and convenience (efficiency) compared with other genotyping methods. It seems more likely that a more focused assay, concentrating on genomic regions of variability previously detected by genome-wide microarrays, will find broad application in routine bacterial epidemiology.
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Affiliation(s)
- Javier Garaizar
- Department of Immunology, Microbiology, and Parasitology, Faculty of Pharmacy, University of the Basque Country, Vitoria-Gasteiz, Spain.
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231
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Howard SL, Gaunt MW, Hinds J, Witney AA, Stabler R, Wren BW. Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity. J Bacteriol 2006; 188:3645-53. [PMID: 16672618 PMCID: PMC1482848 DOI: 10.1128/jb.188.10.3645-3653.2006] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yersinia enterocolitica, an important cause of human gastroenteritis generally caused by the consumption of livestock, has traditionally been categorized into three groups with respect to pathogenicity, i.e., nonpathogenic (biotype 1A), low pathogenicity (biotypes 2 to 5), and highly pathogenic (biotype 1B). However, genetic differences that explain variation in pathogenesis and whether different biotypes are associated with specific nonhuman hosts are largely unknown. In this study, we applied comparative phylogenomics (whole-genome comparisons of microbes with DNA microarrays combined with Bayesian phylogenies) to investigate a diverse collection of 94 strains of Y. enterocolitica consisting of 35 human, 35 pig, 15 sheep, and 9 cattle isolates from nonpathogenic, low-pathogenicity, and highly pathogenic biotypes. Analysis confirmed three distinct statistically supported clusters composed of a nonpathogenic clade, a low-pathogenicity clade, and a highly pathogenic clade. Genetic differences revealed 125 predicted coding sequences (CDSs) present in all highly pathogenic strains but absent from the other clades. These included several previously uncharacterized CDSs that may encode novel virulence determinants including a hemolysin, a metalloprotease, and a type III secretion effector protein. Additionally, 27 CDSs were identified which were present in all 47 low-pathogenicity strains and Y. enterocolitica 8081 but absent from all nonpathogenic 1A isolates. Analysis of the core gene set for Y. enterocolitica revealed that 20.8% of the genes were shared by all of the strains, confirming this species as highly heterogeneous, adding to the case for the existence of three subspecies of Y. enterocolitica. Further analysis revealed that Y. enterocolitica does not cluster according to source (host).
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Affiliation(s)
- Sarah L Howard
- Department of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, UK
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232
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Beyhan S, Tischler AD, Camilli A, Yildiz FH. Differences in gene expression between the classical and El Tor biotypes of Vibrio cholerae O1. Infect Immun 2006; 74:3633-42. [PMID: 16714595 PMCID: PMC1479229 DOI: 10.1128/iai.01750-05] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Differences in whole-genome expression patterns between the classical and El Tor biotypes of Vibrio cholerae O1 were determined under conditions that induce virulence gene expression in the classical biotype. A total of 524 genes (13.5% of the genome) were found to be differentially expressed in the two biotypes. The expression of genes encoding proteins required for biofilm formation, chemotaxis, and transport of amino acids, peptides, and iron was higher in the El Tor biotype. These gene expression differences may contribute to the enhanced survival capacity of the El Tor biotype in environmental reservoirs. The expression of genes encoding virulence factors was higher in the classical than in the El Tor biotype. In addition, the vieSAB genes, which were originally identified as regulators of ctxA transcription, were expressed at a fivefold higher level in the classical biotype. We determined the VieA regulon in both biotypes by transcriptome comparison of wild-type and vieA deletion mutant strains. VieA predominantly regulates gene expression in the classical biotype; 401 genes (10.3% of the genome), including those encoding proteins required for virulence, exopolysaccharide biosynthesis, and flagellum production as well as those regulated by sigmaE, are differentially expressed in the classical vieA deletion mutant. In contrast, only five genes were regulated by VieA in the El Tor biotype. A large fraction (20.8%) of the genes that are differentially expressed in the classical versus the El Tor biotype are controlled by VieA in the classical biotype. Thus, VieA is a major regulator of genes in the classical biotype under virulence gene-inducing conditions.
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Affiliation(s)
- Sinem Beyhan
- Department of Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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233
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Alam M, Hasan NA, Sadique A, Bhuiyan NA, Ahmed KU, Nusrin S, Nair GB, Siddique AK, Sack RB, Sack DA, Huq A, Colwell RR. Seasonal cholera caused by Vibrio cholerae serogroups O1 and O139 in the coastal aquatic environment of Bangladesh. Appl Environ Microbiol 2006; 72:4096-104. [PMID: 16751520 PMCID: PMC1489596 DOI: 10.1128/aem.00066-06] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 03/13/2006] [Indexed: 11/20/2022] Open
Abstract
Since Vibrio cholerae O139 first appeared in 1992, both O1 El Tor and O139 have been recognized as the epidemic serogroups, although their geographic distribution, endemicity, and reservoir are not fully understood. To address this lack of information, a study of the epidemiology and ecology of V. cholerae O1 and O139 was carried out in two coastal areas, Bakerganj and Mathbaria, Bangladesh, where cholera occurs seasonally. The results of a biweekly clinical study (January 2004 to May 2005), employing culture methods, and of an ecological study (monthly in Bakerganj and biweekly in Mathbaria from March 2004 to May 2005), employing direct and enrichment culture, colony blot hybridization, and direct fluorescent-antibody methods, showed that cholera is endemic in both Bakerganj and Mathbaria and that V. cholerae O1, O139, and non-O1/non-O139 are autochthonous to the aquatic environment. Although V. cholerae O1 and O139 were isolated from both areas, most noteworthy was the isolation of V. cholerae O139 in March, July, and September 2004 in Mathbaria, where seasonal cholera was clinically linked only to V. cholerae O1. In Mathbaria, V. cholerae O139 emerged as the sole cause of a significant outbreak of cholera in March 2005. V. cholerae O1 reemerged clinically in April 2005 and established dominance over V. cholerae O139, continuing to cause cholera in Mathbaria. In conclusion, the epidemic potential and coastal aquatic reservoir for V. cholerae O139 have been demonstrated. Based on the results of this study, the coastal ecosystem of the Bay of Bengal is concluded to be a significant reservoir for the epidemic serogroups of V. cholerae.
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Affiliation(s)
- Munirul Alam
- International Center for Diarrhoeal Disease Research, Dhaka, Bangladesh
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234
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Yao Y, Xie Y, Kim KS. Genomic comparison of Escherichia coli K1 strains isolated from the cerebrospinal fluid of patients with meningitis. Infect Immun 2006; 74:2196-206. [PMID: 16552050 PMCID: PMC1418925 DOI: 10.1128/iai.74.4.2196-2206.2006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Escherichia coli is a major cause of enteric/diarrheal diseases, urinary tract infections, and sepsis. E. coli K1 is the leading gram-negative organism causing neonatal meningitis, but the microbial basis of E. coli K1 meningitis is incompletely understood. Here we employed comparative genomic hybridization to investigate 11 strains of E. coli K1 isolated from the cerebrospinal fluid (CSF) of patients with meningitis. These 11 strains cover the majority of common O serotypes in E. coli K1 isolates from CSF. Our data demonstrated that these 11 strains of E. coli K1 can be categorized into two groups based on their profile for putative virulence factors, lipoproteins, proteases, and outer membrane proteins. Of interest, we showed that some open reading frames (ORFs) encoding the type III secretion system apparatus were found in group 2 strains but not in group 1 strains, while ORFs encoding the general secretory pathway are predominant in group 1 strains. These findings suggest that E. coli K1 strains isolated from CSF can be divided into two groups and these two groups of E. coli K1 may utilize different mechanisms to induce meningitis.
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Affiliation(s)
- Yufeng Yao
- Division of Pediatric Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
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235
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Hurley CC, Quirke A, Reen FJ, Boyd EF. Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates. BMC Genomics 2006; 7:104. [PMID: 16672049 PMCID: PMC1464126 DOI: 10.1186/1471-2164-7-104] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Accepted: 05/03/2006] [Indexed: 11/23/2022] Open
Abstract
Background Vibrio parahaemolyticus is an aquatic, halophilic, Gram-negative bacterium, first discovered in 1950 in Japan during a food-poisoning outbreak. Infections resulting from consumption of V. parahaemolyticus have increased globally in the last 10 years leading to the bacterium's classification as a newly emerging pathogen. In 1996 the first appearance of a pandemic V. parahaemolyticus clone occurred, a new O3:K6 serotype strain that has now been identified worldwide as a major cause of seafood-borne gastroenteritis. Results We examined the sequenced genome of V. parahaemolyticus RIMD2210633, an O3:K6 serotype strain isolated in Japan in 1996, by bioinformatic analyses to uncover genomic islands (GIs) that may play a role in the emergence and pathogenesis of pandemic strains. We identified 7 regions ranging in size from 10 kb to 81 kb that had the characteristics of GIs such as aberrant base composition compared to the core genome, presence of phage-like integrases, flanked by direct repeats and the absence of these regions from closely related species. Molecular analysis of worldwide clinical isolates of V. parahaemolyticus recovered over the last 33 years demonstrated that a 24 kb region named V. parahaemolyticus island-1 (VPaI-1) encompassing ORFs VP0380 to VP0403 is only present in new O3:K6 and related strains recovered after 1995. We investigated the presence of 3 additional regions, VPaI-4 (VP2131 to VP2144), VPaI-5 (VP2900 to VP2910) and VPaI-6 (VPA1254 to VPA1270) by PCR assays and Southern blot analyses among the same set of V. parahaemolyticus isolates. These 3 VPaI regions also gave similar distribution patterns amongst the 41 strains examined. Conclusion The 4 VPaI regions examined may represent DNA acquired by the pandemic group of V. parahaemolyticus isolates that increased their fitness either in the aquatic environment or in their ability to infect humans.
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Affiliation(s)
- Catherine C Hurley
- Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - AnneMarie Quirke
- Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - F Jerry Reen
- Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - E Fidelma Boyd
- Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
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236
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Wang Y, Leung PC, Qian PY, Gu JD. Antibiotic resistance and plasmid profile of environmental isolates of Vibrio species from Mai Po Nature Reserve, Hong Kong. ECOTOXICOLOGY (LONDON, ENGLAND) 2006; 15:371-8. [PMID: 16680524 DOI: 10.1007/s10646-006-0078-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/01/2006] [Indexed: 05/09/2023]
Abstract
In this study, three environmental isolates of Vibrio species were isolated from water and sediment samples of Mai Po Nature Reserve, Hong Kong SAR. They were identified to be Vibrio cholerae MP-1, Vibrio aestuarianus MP-2 and Vibrio vulnificus MP-3 by both biochemical test and subsequent full-length 16S rDNA sequencing. Both disc diffusion susceptibility test and microplate dilution technique were used to investigate the antibiotic resistance profile of these three bacteria. Results from both assays were in generally good agreement. All three isolates were strongly resistant to beta-lactam family of antibiotics while susceptible to tetracycline, chloramphenicol, nalidixic acid and streptomycin. In addition, V. cholerae MP-1 was very tolerant to high concentration of vibriostatic agent O/129 to 40 microg/ml, at which the growth of V. aestuarianus MP-2 and V. vulnificus MP-2 was completely inhibited. A small naturally occurring plasmid was found in V. cholerae MP-1 while no plasmid was detected in the other two bacteria. This study suggests that Mai Po Nature Reserve harbors bacteria of unique characteristics that warrant further investigation.
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Affiliation(s)
- Yanling Wang
- Laboratory of Environmental Toxicology, Department of Ecology & Biodiversity, The University of Hong Kong, Hong Kong SAR, PR China
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237
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Liu Z, Hsiao A, Joelsson A, Zhu J. The transcriptional regulator VqmA increases expression of the quorum-sensing activator HapR in Vibrio cholerae. J Bacteriol 2006; 188:2446-53. [PMID: 16547031 PMCID: PMC1428415 DOI: 10.1128/jb.188.7.2446-2453.2006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is the causative agent of the severe diarrheal disease cholera. A number of environmental stimuli regulate virulence gene expression in V. cholerae, including quorum-sensing signals. At high cell densities, quorum sensing in V. cholerae invokes a series of signal transduction pathways in order to activate the expression of the master regulator HapR, which then represses the virulence regulon and biofilm-related genes and activates protease production. In this study, we identified a transcriptional regulator, VqmA (VCA1078), that activates hapR expression at low cell densities. Under in vitro inducing conditions, constitutive expression of VqmA represses the virulence regulon in a HapR-dependent manner. VqmA increases hapR transcription as measured by the activity of the hapR-lacZ reporter, and it increases HapR production as measured by Western blotting. Using a heterogenous luxCDABE cosmid, we found that VqmA stimulates quorum-sensing regulation at lower cell densities and that this stimulation bypasses the known LuxO-small-RNA regulatory circuits. Furthermore, we showed that VqmA regulates hapR transcription directly by binding to its promoter region and that expression of vqmA is cell density dependent and autoregulated. The physiological role of VqmA is also discussed.
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Affiliation(s)
- Zhi Liu
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104.
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238
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Zhang R, Wang Y, Gu JD. Identification of environmental plasmid-bearing Vibrio species isolated from polluted and pristine marine reserves of Hong Kong, and resistance to antibiotics and mercury. Antonie van Leeuwenhoek 2006; 89:307-15. [PMID: 16779626 DOI: 10.1007/s10482-005-9032-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/21/2005] [Indexed: 10/24/2022]
Abstract
Fifty environmental isolates of Vibrio species were isolated from water samples of Mai Po Nature Reserve and the Cape d'Aguilar Marine Reserve in Hong Kong and screened for the presence of plasmid. Mai Po is a wastewater-impacted area while the Cape d'Aguilar Marine Reserve is pristine natural marine water. Plasmid was found in Vibrio isolates from both sites at similar frequencies and each site showed distinctive plasmid profiles. These plasmid-bearing Vibrio isolates were identified as different species of the Vibrio genus by both biochemical test and subsequently full-length 16S rRNA sequences. Antibiotic resistance test showed that all these plasmid-bearing Vibrio isolates showed multiple resistance to 21 antibiotics tested. In addition, selective isolates also showed tolerance to 10 microM Hg 2+ in culture medium and they generally harbored large plasmid(s) (>30 kb). Our results show that the high frequency of plasmid in Vibrio species of both polluted and pristine environments may be ecologically important to the survival of these bacteria in the environment. The specific functioning of the cryptic plasmids remains the focus of current investigations.
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Affiliation(s)
- Ruifu Zhang
- Laboratory of Environmental Microbiology and Toxicology, Department of Ecology & Biodiversity, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong SAR, P.R. China
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239
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Abstract
Vibrio cholerae is a Gram-negative bacterium that causes the acute diarrhoeal disease cholera. After the bacterium is ingested, it passes through the digestive tract, encountering various environmental stresses including the acidic milieu of the stomach and the toxic effects of bile in the duodenum. While these stresses serve as part of a host defence system, V. cholerae has evolved resistance mechanisms that allow it to evade these defences and establish infection. We examined the expression profiles of V. cholerae in response to bile or bile acids and found an induction of biofilm genes. We found that V. cholerae shows significantly enhanced biofilm formation in response to bile acids, and that bacteria within the biofilm are more resistant to the toxicity of bile acids compared with planktonic cells. Bile acid induction of biofilms was found to be dependent on the vps genes (Vibrio polysaccharide synthesis) and their transcriptional activator VpsR, but VpsT is not required. These results contribute to the developing picture of a complex relationship between V. cholerae and its environment within the host during infection.
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Affiliation(s)
- Deborah T Hung
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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240
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Abstract
The availability of hundreds of bacterial genome sequences has altered the study of bacterial pathogenesis, affecting both design of experiments and analysis of results. Comparative genomics and genomic tools have been used to identify virulence factors and genes involved in environmental persistence of pathogens. However, a major stumbling block in the genomics revolution has been the large number of genes with unknown function that have been identified in every organism sequenced to date.
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Affiliation(s)
- David M Raskin
- Department of Microbiology & Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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241
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Joelsson A, Liu Z, Zhu J. Genetic and phenotypic diversity of quorum-sensing systems in clinical and environmental isolates of Vibrio cholerae. Infect Immun 2006; 74:1141-7. [PMID: 16428762 PMCID: PMC1360356 DOI: 10.1128/iai.74.2.1141-1147.2006] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is the causative agent of cholera, a severe and devastating diarrheal disease. V. cholerae lives naturally in various aquatic habitats during interepidemic periods. Recent studies reveal that quorum-sensing systems, which exist in many bacteria and help them monitor their population densities and regulate various cellular functions, control V. cholerae pathogenesis, biofilm formation, and protease production. In this study we surveyed quorum-sensing systems in 16 geographically diverse V. cholerae strains from epidemic-causing O1 and O139 strains as well as non-O1/non-O139 and environmental isolates and discovered an unexpectedly high rate of dysfunctional components. We also found that a functional quorum-sensing system conferred a survival advantage on bacteria in biofilms when the bacteria were exposed to seawater, though quorum sensing was less important to survival in a planktonic state under the same conditions. These findings suggest that variations in quorum-sensing systems are due to environmental selective pressures and might be beneficial to V. cholerae's fitness under certain conditions found in its natural reservoirs.
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Affiliation(s)
- Adam Joelsson
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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242
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Quirke AM, Reen FJ, Claesson MJ, Boyd EF. Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen. ACTA ACUST UNITED AC 2006; 22:905-10. [PMID: 16443635 DOI: 10.1093/bioinformatics/btl015] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED Genomic islands (GIs) are large chromosomal regions present in a subset of bacterial strains that increase the fitness of the organism under specific conditions. We compared the complete genome sequences of two Vibrio vulnificus strains YJ016 and CMCP6 and identified 14 regions (ranging in size from 14 to 117 kb), which had the characteristics of GIs. Bioinformatic analysis of these 14 GI regions identified the presence of phage-like integrase genes, aberrant GC content and genome signature (dinucleotide frequency) within each GI compared with the core genome indicating that these regions were acquired from an anomalous source. We examined the distribution of the nine GIs from strain YJ016 among 27 V. vulnificus isolates and found that most GIs were absent from the majority of these isolates. The chromosomal insertion sites of three GIs were adjacent to tRNA sites, which contained novel horizontally acquired DNA in all six available sequenced Vibrionaceae genomes. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- A M Quirke
- Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
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243
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Pukatzki S, Ma AT, Sturtevant D, Krastins B, Sarracino D, Nelson WC, Heidelberg JF, Mekalanos JJ. Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. Proc Natl Acad Sci U S A 2006; 103:1528-33. [PMID: 16432199 PMCID: PMC1345711 DOI: 10.1073/pnas.0510322103] [Citation(s) in RCA: 840] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The bacterium Vibrio cholerae, like other human pathogens that reside in environmental reservoirs, survives predation by unicellular eukaryotes. Strains of the O1 and O139 serogroups cause cholera, whereas non-O1/non-O139 strains cause human infections through poorly defined mechanisms. Using Dictyostelium discoideum as a model host, we have identified a virulence mechanism in a non-O1/non-O139 V. cholerae strain that involves extracellular translocation of proteins that lack N-terminal hydrophobic leader sequences. Accordingly, we have named these genes "VAS" genes for virulence-associated secretion, and we propose that these genes encode a prototypic "type VI" secretion system. We show that vas genes are required for cytotoxicity of V. cholerae cells toward Dictyostelium amoebae and mammalian J774 macrophages by a contact-dependent mechanism. A large number of Gram-negative bacterial pathogens carry genes homologous to vas genes and potential effector proteins secreted by this pathway (i.e., hemolysin-coregulated protein and VgrG). Mutations in vas homologs in other bacterial species have been reported to attenuate virulence in animals and cultured macrophages. Thus, the genes encoding the VAS-related, type VI secretion system likely play an important conserved function in microbial pathogenesis and represent an additional class of targets for vaccine and antimicrobial drug-based therapies.
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Affiliation(s)
- Stefan Pukatzki
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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244
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Dorrell N, Hinchliffe SJ, Wren BW. Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol 2006; 8:620-6. [PMID: 16125441 PMCID: PMC7108221 DOI: 10.1016/j.mib.2005.08.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 08/15/2005] [Indexed: 10/31/2022]
Abstract
DNA microarrays represent a powerful technology that enables whole-scale comparison of bacterial genomes. This, coupled with new methods to model DNA microarray data, is facilitating the development of robust comparative phylogenomics analyses. Such studies have dramatically increased our ability to differentiate between bacteria, highlighting previously undetected genetic differences and population structures and providing new insight into virulence and evolution of bacterial pathogens. Recent results from such studies have generated insights into the evolution of bacterial pathogens, the levels of diversity and plasticity in the genome of a species, as well as the differences in virulence amongst pathogenic bacteria.
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245
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Witney AA, Marsden GL, Holden MTG, Stabler RA, Husain SE, Vass JK, Butcher PD, Hinds J, Lindsay JA. Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics. Appl Environ Microbiol 2005; 71:7504-14. [PMID: 16269792 PMCID: PMC1287626 DOI: 10.1128/aem.71.11.7504-7514.2005] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacterial comparative genomics has been revolutionized by microarrays, but the power of any microarray is dependent on the number and diversity of gene reporters it contains. Staphylococcus aureus is an important human pathogen causing a wide range of invasive and toxin-mediated diseases, and more than 20% of the genome of any isolate consists of variable genes. Seven whole-genome sequences of S. aureus are available, and we exploited this rare opportunity to design, build, and validate a comprehensive, nonredundant PCR product microarray carrying reporters that represent every predicted open reading frame (3,623 probes). Such a comprehensive microarray necessitated a novel design strategy. Validation with the seven sequenced strains showed correct identification of 93.9% of genes present or absent/divergent but was dependent on the method of analysis chosen. Microarray data were highly reproducible, reducing the need for many replicate slides. Interpretation of microarray data was enhanced by focusing on the major areas of variation--the presence or absence of mobile genetic elements (MGEs). We compiled "composite genomes" of every individual MGE and visualized their distribution. This allowed the sensitive discrimination of related isolates, including the first clear description of how isolates of the same clone of epidemic methicillin-resistant S. aureus differ substantially in their carriage of MGEs. These MGEs carry virulence and resistance genes, suggesting differences in pathogenic potential. The novel methods of design and interpretation of data generated from this microarray will enable further studies of S. aureus evolution, epidemiology, and pathogenesis.
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Affiliation(s)
- Adam A Witney
- Department of Cellular and Molecular Medicine, St. George's Hospital Medical School, London SW17 0RE, United Kingdom
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246
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McLeod SM, Kimsey HH, Davis BM, Waldor MK. CTXphi and Vibrio cholerae: exploring a newly recognized type of phage-host cell relationship. Mol Microbiol 2005; 57:347-56. [PMID: 15978069 DOI: 10.1111/j.1365-2958.2005.04676.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The genes encoding cholera toxin, one of the principal virulence factors of the diarrhoeal pathogen Vibrio cholerae, are part of the genome of CTXphi, a filamentous bacteriophage. Thus, CTXphi has played a critical role in the evolution of the pathogenicity of V. cholerae. Unlike the well-studied F pilus-specific filamentous coliphages, CTXphi integrates site-specifically into its host chromosome and forms stable lysogens. Here we focus on the CTXphi life cycle and, in particular, on recent studies of the mechanism of CTXphi integration and the factors that govern lysogeny. These and other processes illustrate the remarkable dependence of CTXphi on host-encoded factors.
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Affiliation(s)
- Sarah M McLeod
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
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247
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Lindroos HL, Mira A, Repsilber D, Vinnere O, Näslund K, Dehio M, Dehio C, Andersson SGE. Characterization of the genome composition of Bartonella koehlerae by microarray comparative genomic hybridization profiling. J Bacteriol 2005; 187:6155-65. [PMID: 16109957 PMCID: PMC1196136 DOI: 10.1128/jb.187.17.6155-6165.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bartonella henselae is present in a wide range of wild and domestic feline hosts and causes cat-scratch disease and bacillary angiomatosis in humans. We have estimated here the gene content of Bartonella koehlerae, a novel species isolated from cats that was recently identified as an agent of human endocarditis. The investigation was accomplished by comparative genomic hybridization (CGH) to a microarray constructed from the sequenced 1.93-Mb genome of B. henselae. Control hybridizations of labeled DNA from the human pathogen Bartonella quintana with a reduced genome of 1.58 Mb were performed to evaluate the accuracy of the array for genes with known levels of sequence divergence. Genome size estimates of B. koehlerae by pulsed-field gel electrophoresis matched that calculated by the CGH, indicating a genome of 1.7 to 1.8 Mb with few unique genes. As in B. quintana, sequences in the prophage and the genomic islands were reported absent in B. koehlerae. In addition, sequence variability was recorded in the chromosome II-like region, where B. koehlerae showed an intermediate retention pattern of both coding and noncoding sequences. Although most of the genes missing in B. koehlerae are also absent from B. quintana, its phylogenetic placement near B. henselae suggests independent deletion events, indicating that host specificity is not solely attributed to genes in the genomic islands. Rather, the results underscore the instability of the genomic islands even within bacterial populations adapted to the same host-vector system, as in the case of B. henselae and B. koehlerae.
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Affiliation(s)
- Hillevi L Lindroos
- Department of Molecular Evolution, Evolutionary Biology Center, Norbyvägen 18C, 752 36 Uppsala, Sweden
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248
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Champion OL, Gaunt MW, Gundogdu O, Elmi A, Witney AA, Hinds J, Dorrell N, Wren BW. Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source. Proc Natl Acad Sci U S A 2005; 102:16043-8. [PMID: 16230626 PMCID: PMC1276044 DOI: 10.1073/pnas.0503252102] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Accepted: 09/12/2005] [Indexed: 12/19/2022] Open
Abstract
Campylobacter jejuni is the predominant cause of bacterial gastroenteritis worldwide, but traditional typing methods are unable to discriminate strains from different sources that cause disease in humans. We report the use of genomotyping (whole-genome comparisons of microbes using DNA microarrays) combined with Bayesian-based algorithms to model the phylogeny of this major food-borne pathogen. In this study 111 C. jejuni strains were examined by genomotyping isolates from humans with a spectrum of C. jejuni-associated disease (70 strains), chickens (17 strains), bovines (13 strains), ovines (5 strains), and the environment (6 strains). From these data, the Bayesian phylogeny of the isolates revealed two distinct clades unequivocally supported by Bayesian probabilities (P = 1); a livestock clade comprising 31/35 (88.6%) of the livestock isolates and a "nonlivestock" clade comprising further clades of environmental isolates. Several genes were identified as characteristic of strains in the livestock clade. The most prominent was a cluster of six genes (cj1321 to cj1326) within the flagellin glycosylation locus, which were confirmed by PCR analysis as genetic markers in six additional chicken-associated strains. Surprisingly these studies show that the majority (39/70, 55.7%) of C. jejuni human isolates were found in the nonlivestock clade, suggesting that most C. jejuni infections may be from nonlivestock (and possibly nonagricultural) sources. This study has provided insight into a previously unidentified reservoir of C. jejuni infection that may have implications in disease-control strategies. The comparative phylogenomics approach described provides a robust methodological prototype that should be applicable to other microbes.
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Affiliation(s)
- Olivia L Champion
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
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249
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Rodrigues PH, Progulske-Fox A. Gene expression profile analysis of Porphyromonas gingivalis during invasion of human coronary artery endothelial cells. Infect Immun 2005; 73:6169-73. [PMID: 16113342 PMCID: PMC1231123 DOI: 10.1128/iai.73.9.6169-6173.2005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microarrays were used to identify genes of Porphyromonas gingivalis W83 differentially expressed during invasion of primary human coronary artery endothelial cells. Analyses of microarray images indicated that 62 genes were differentially regulated. Of these, 11 genes were up-regulated and 51 were down-regulated. The differential expression of 16 selected genes was confirmed by real-time PCR.
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Affiliation(s)
- Paulo H Rodrigues
- Department of Oral Biology, University of Florida, P.O. Box 100424, Gainesville, FL 32610-0424, USA
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250
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Larocque RC, Harris JB, Dziejman M, Li X, Khan AI, Faruque ASG, Faruque SM, Nair GB, Ryan ET, Qadri F, Mekalanos JJ, Calderwood SB. Transcriptional profiling of Vibrio cholerae recovered directly from patient specimens during early and late stages of human infection. Infect Immun 2005; 73:4488-93. [PMID: 16040959 PMCID: PMC1201252 DOI: 10.1128/iai.73.8.4488-4493.2005] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Understanding gene expression by bacteria during the actual course of human infection may provide important insights into microbial pathogenesis. In this study, we evaluated the transcriptional profile of Vibrio cholerae, the causative agent of cholera, in clinical specimens from cholera patients. We collected samples of human stool and vomitus that were positive by dark-field microscopy for abundant vibrios and used a microarray to compare gene expression in organisms recovered directly from specimens collected during the early and late stages of human infection. Our results reveal that V. cholerae gene expression within the human host environment differs from patterns defined in in vitro models of pathogenesis. tcpA, the major subunit of the essential V. cholerae colonization factor, was significantly more highly expressed in early than in late stages of infection; however, the genes encoding cholera toxin were not highly expressed in either phase of human infection. Furthermore, expression of the virulence regulators toxRS and tcpPH was uncoupled. Interestingly, the pattern of gene expression indicates that the human upper intestine may be a uniquely suitable environment for the transfer of genetic elements that are important in the evolution of pathogenic strains of V. cholerae. These findings provide a more detailed assessment of the transcriptome of V. cholerae in the human host than previous studies of organisms in stool alone and have implications for cholera control and the design of improved vaccines.
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Affiliation(s)
- Regina C Larocque
- Division of Infectious Diseases, Gray-Jackson 504, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA.
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