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Ventola E, Bogaerts B, De Keersmaecker SCJ, Vanneste K, Roosens NHC, Mattheus W, Ceyssens PJ. Shifting national surveillance of Shigella infections toward geno-serotyping by the development of a tailored Luminex assay and NGS workflow. Microbiologyopen 2019; 8:e00807. [PMID: 30924299 PMCID: PMC6692546 DOI: 10.1002/mbo3.807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 02/01/2023] Open
Abstract
The phylogenetically closely related Shigella species and enteroinvasive Escherichia coli (EIEC) are responsible for millions of episodes of bacterial dysenteriae worldwide. Given its distinct epidemiology and public health relevance, only Shigellae are subject to mandatory reporting and follow‐up by public health authorities. However, many clinical laboratories struggle to differentiate non‐EIEC, EIEC, and Shigella in their current workflows, leading to inaccuracies in surveillance and rising numbers of misidentified E. coli samples at the National Reference Centre (NRC). In this paper, we describe two novel tools to enhance Shigella surveillance. First, we developed a low‐cost Luminex‐based multiplex assay combining five genetic markers for species identification with 11 markers for serotype prediction for S. sonnei and S. flexneri isolates. Using a test panel of 254 clinical samples, this assay has a sensitivity of 100% in differentiation of EIEC/Shigella pathotype from non‐EIEC strains, and 68.7% success rate in distinction of Shigella and EIEC. A novel, and particularly successful marker was a Shigella‐specific deletion in the spermidine acetyltransferase gene speG, reflecting its metabolic decay. For Shigella serotype prediction, the multiplex assay scored a sensitivity and specificity of 96.6% and 98.4%, respectively. All discrepancies were analyzed with whole‐genome sequencing and shown to be related to causative mutations (stop codons, indels, and promoter mutations) in glycosyltransferase genes. This observation spurred the development of an in silico workflow which extracts the Shigella serotype from Next‐Generation Sequencing (NGS) data, taking into account gene functionality. Both tools will be implemented in the workflow of the NRC, and will play a major role in the shift from phenotypic to genotyping‐based surveillance of shigellosis in Belgium.
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Affiliation(s)
- Eleonora Ventola
- National Reference Centre of Salmonella and Shigella, Brussels, Belgium.,Department of Biology and Biotechnology "C. Darwin", "Sapienza" Università di Roma, Rome, Italy
| | - Bert Bogaerts
- Transversal activities in Applied Genomics, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Brussels, Belgium
| | | | - Wesley Mattheus
- National Reference Centre of Salmonella and Shigella, Brussels, Belgium
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Pasqua M, Michelacci V, Di Martino ML, Tozzoli R, Grossi M, Colonna B, Morabito S, Prosseda G. The Intriguing Evolutionary Journey of Enteroinvasive E. coli (EIEC) toward Pathogenicity. Front Microbiol 2017; 8:2390. [PMID: 29259590 PMCID: PMC5723341 DOI: 10.3389/fmicb.2017.02390] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/20/2017] [Indexed: 01/01/2023] Open
Abstract
Among the intestinal pathogenic Escherichia coli, enteroinvasive E. coli (EIEC) are a group of intracellular pathogens able to enter epithelial cells of colon, multiplicate within them, and move between adjacent cells with a mechanism similar to Shigella, the ethiological agent of bacillary dysentery. Despite EIEC belong to the same pathotype of Shigella, they neither have the full set of traits that define Shigella nor have undergone the extensive gene decay observed in Shigella. Molecular analysis confirms that EIEC are widely distributed among E. coli phylogenetic groups and correspond to bioserotypes found in many E. coli serogroups. Like Shigella, also in EIEC the critical event toward a pathogenic life-style consisted in the acquisition by horizontal gene transfer of a large F-type plasmid (pINV) containing the genes required for invasion, intracellular survival, and spreading through the intestinal mucosa. In Shigella, the ample gain in virulence determinants has been counteracted by a substantial loss of functions that, although important for the survival in the environment, are redundant or deleterious for the life inside the host. The pathoadaptation process that has led Shigella to modify its metabolic profile and increase its pathogenic potential is still in infancy in EIEC, although maintenance of some features typical of E. coli might favor their emerging relevance as intestinal pathogens worldwide, as documented by recent outbreaks in industrialized countries. In this review, we will discuss the evolution of EIEC toward Shigella-like invasive forms going through the epidemiology, including the emergence of new virulent strains, their genome organization, and the complex interactions they establish with the host.
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Affiliation(s)
- Martina Pasqua
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Valeria Michelacci
- European Union Reference Laboratory for Escherichia coli, Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Letizia Di Martino
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Rosangela Tozzoli
- European Union Reference Laboratory for Escherichia coli, Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Milena Grossi
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Bianca Colonna
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Stefano Morabito
- European Union Reference Laboratory for Escherichia coli, Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Gianni Prosseda
- Istituto Pasteur Italia, Department of Biology and Biotechnology "C. Darwin", Sapienza Università di Roma, Rome, Italy
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Campilongo R, Di Martino ML, Marcocci L, Pietrangeli P, Leuzzi A, Grossi M, Casalino M, Nicoletti M, Micheli G, Colonna B, Prosseda G. Molecular and functional profiling of the polyamine content in enteroinvasive E. coli : looking into the gap between commensal E. coli and harmful Shigella. PLoS One 2014; 9:e106589. [PMID: 25192335 PMCID: PMC4156367 DOI: 10.1371/journal.pone.0106589] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/31/2014] [Indexed: 11/19/2022] Open
Abstract
Polyamines are small molecules associated with a wide variety of physiological functions. Bacterial pathogens have developed subtle strategies to exploit polyamines or manipulate polyamine-related processes to optimize fitness within the host. During the transition from its innocuous E. coli ancestor, Shigella, the aetiological agent of bacillary dysentery, has undergone drastic genomic rearrangements affecting the polyamine profile. A pathoadaptation process involving the speG gene and the cad operon has led to spermidine accumulation and loss of cadaverine. While a higher spermidine content promotes the survival of Shigella within infected macrophages, the lack of cadaverine boosts the pathogenic potential of the bacterium in host tissues. Enteroinvasive E. coli (EIEC) display the same pathogenicity process as Shigella, but have a higher infectious dose and a higher metabolic activity. Pathoadaption events affecting the cad locus have occurred also in EIEC, silencing cadaverine production. Since EIEC are commonly regarded as evolutionary intermediates between E. coli and Shigella, we investigated on their polyamine profile in order to better understand which changes have occurred along the path to pathogenicity. By functional and molecular analyses carried out in EIEC strains belonging to different serotypes, we show that speG has been silenced in one strain only, favouring resistance to oxidative stress conditions and survival within macrophages. At the same time, we observe that the content of spermidine and putrescine, a relevant intermediate in the synthesis of spermidine, is higher in all strains as compared to E. coli. This may represent an evolutionary response to the lack of cadaverine. Indeed, restoring cadaverine synthesis decreases the expression of the speC gene, whose product affects putrescine production. In the light of these results, we discuss the possible impact of pathoadaptation events on the evolutionary emergence of a polyamine profile favouring to the pathogenic lifestyle of Shigella and EIEC.
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Affiliation(s)
- Rosaria Campilongo
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Maria Letizia Di Martino
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Roma, Italy
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy
| | - Lucia Marcocci
- Dipartimento di Biochimica, Sapienza Università di Roma, Roma, Italy
| | - Paola Pietrangeli
- Dipartimento di Biochimica, Sapienza Università di Roma, Roma, Italy
| | - Adriano Leuzzi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Milena Grossi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Roma, Italy
| | | | - Mauro Nicoletti
- Dipartimento di Scienze Sperimentali e Cliniche, Università G. D'Annunzio, Chieti, Italy
| | - Gioacchino Micheli
- Istituto di Biologia, Medicina Molecolare e NanoBiotecnologie, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Bianca Colonna
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Gianni Prosseda
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Roma, Italy
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The global response regulator ExpA controls virulence gene expression through RsmA-mediated and RsmA-independent pathways in Pectobacterium wasabiae SCC3193. Appl Environ Microbiol 2014; 80:1972-84. [PMID: 24441162 DOI: 10.1128/aem.03829-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
ExpA (GacA) is a global response regulator that controls the expression of major virulence genes, such as those encoding plant cell wall-degrading enzymes (PCWDEs) in the model soft rot phytopathogen Pectobacterium wasabiae SCC3193. Several studies with pectobacteria as well as related phytopathogenic gammaproteobacteria, such as Dickeya and Pseudomonas, suggest that the control of virulence by ExpA and its homologues is executed partly by modulating the activity of RsmA, an RNA-binding posttranscriptional regulator. To elucidate the extent of the overlap between the ExpA and RsmA regulons in P. wasabiae, we characterized both regulons by microarray analysis. To do this, we compared the transcriptomes of the wild-type strain, an expA mutant, an rsmA mutant, and an expA rsmA double mutant. The microarray data for selected virulence-related genes were confirmed through quantitative reverse transcription (qRT-PCR). Subsequently, assays were performed to link the observed transcriptome differences to changes in bacterial phenotypes such as growth, motility, PCWDE production, and virulence in planta. An extensive overlap between the ExpA and RsmA regulons was observed, suggesting that a substantial portion of ExpA regulation appears to be mediated through RsmA. However, a number of genes involved in the electron transport chain and oligogalacturonide metabolism, among other processes, were identified as being regulated by ExpA independently of RsmA. These results suggest that ExpA may only partially impact fitness and virulence via RsmA.
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Di Martino ML, Fioravanti R, Barbabella G, Prosseda G, Colonna B, Casalino M. Molecular evolution of the nicotinic acid requirement within the Shigella/EIEC pathotype. Int J Med Microbiol 2013; 303:651-61. [DOI: 10.1016/j.ijmm.2013.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/05/2013] [Accepted: 09/08/2013] [Indexed: 11/27/2022] Open
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Di Martino ML, Campilongo R, Casalino M, Micheli G, Colonna B, Prosseda G. Polyamines: emerging players in bacteria-host interactions. Int J Med Microbiol 2013; 303:484-91. [PMID: 23871215 DOI: 10.1016/j.ijmm.2013.06.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/13/2013] [Accepted: 06/16/2013] [Indexed: 12/17/2022] Open
Abstract
Polyamines are small polycationic molecules found in almost all cells and associated with a wide variety of physiological processes. In recent years it has become increasingly clear that, in addition to core physiological functions, polyamines play a crucial role in bacterial pathogenesis. Considerable evidence has built up that bacteria have evolved mechanisms to turn these molecules to their own advantage and a novel standpoint to look at host-bacterium interactions emerges from the interplay among polyamines, host cells and infecting bacteria. In this review, we highlight how human bacterial pathogens have developed their own resourceful strategies to exploit polyamines or manipulate polyamine-related processes to optimize their fitness within the host. Besides contributing to a better understanding of the complex relationship between a pathogen and its host, acquisitions in this field have a significant potential towards the development of novel antibacterial therapeutic approaches.
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Affiliation(s)
- Maria Letizia Di Martino
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Via dei Sardi 70, 00185 Roma, Italy; Dipartimento di Biologia, Università Roma Tre, Viale G. Marconi 446, 00146 Roma, Italy
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Prosseda G, Di Martino ML, Campilongo R, Fioravanti R, Micheli G, Casalino M, Colonna B. Shedding of genes that interfere with the pathogenic lifestyle: the Shigella model. Res Microbiol 2012; 163:399-406. [DOI: 10.1016/j.resmic.2012.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 07/08/2012] [Indexed: 12/31/2022]
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A new piece of the Shigella Pathogenicity puzzle: spermidine accumulation by silencing of the speG gene [corrected]. PLoS One 2011; 6:e27226. [PMID: 22102881 PMCID: PMC3213128 DOI: 10.1371/journal.pone.0027226] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/12/2011] [Indexed: 11/19/2022] Open
Abstract
The genome of Shigella, a gram negative bacterium which is the causative agent of bacillary dysentery, shares strong homologies with that of its commensal ancestor, Escherichia coli. The acquisition, by lateral gene transfer, of a large plasmid carrying virulence determinants has been a crucial event in the evolution towards the pathogenic lifestyle and has been paralleled by the occurrence of mutations affecting genes, which negatively interfere with the expression of virulence factors. In this context, we have analysed to what extent the presence of the plasmid-encoded virF gene, the major activator of the Shigella regulon for invasive phenotype, has modified the transcriptional profile of E. coli. Combining results from transcriptome assays and comparative genome analyses we show that in E. coli VirF, besides being able to up-regulate several chromosomal genes, which potentially influence bacterial fitness within the host, also activates genes which have been lost by Shigella. We have focused our attention on the speG gene, which encodes spermidine acetyltransferase, an enzyme catalysing the conversion of spermidine into the physiologically inert acetylspermidine, since recent evidence stresses the involvement of polyamines in microbial pathogenesis. Through identification of diverse mutations, which prevent expression of a functional SpeG protein, we show that the speG gene has been silenced by convergent evolution and that its inactivation causes the marked increase of intracellular spermidine in all Shigella spp. This enhances the survival of Shigella under oxidative stress and allows it to better face the adverse conditions it encounters inside macrophage. This is supported by the outcome of infection assays performed in mouse peritoneal macrophages and of a competitive-infection assay on J774 macrophage cell culture. Our observations fully support the pathoadaptive nature of speG inactivation in Shigella and reveal that the accumulation of spermidine is a key determinant in the pathogenicity strategy adopted by this microrganism.
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Viala JPM, Méresse S, Pocachard B, Guilhon AA, Aussel L, Barras F. Sensing and adaptation to low pH mediated by inducible amino acid decarboxylases in Salmonella. PLoS One 2011; 6:e22397. [PMID: 21799843 PMCID: PMC3143133 DOI: 10.1371/journal.pone.0022397] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 06/21/2011] [Indexed: 01/16/2023] Open
Abstract
During the course of infection, Salmonella enterica serovar Typhimurium must successively survive the harsh acid stress of the stomach and multiply into a mild acidic compartment within macrophages. Inducible amino acid decarboxylases are known to promote adaptation to acidic environments. Three low pH inducible amino acid decarboxylases were annotated in the genome of S. Typhimurium, AdiA, CadA and SpeF, which are specific for arginine, lysine and ornithine, respectively. In this study, we characterized and compared the contributions of those enzymes in response to acidic challenges. Individual mutants as well as a strain deleted for the three genes were tested for their ability (i) to survive an extreme acid shock, (ii) to grow at mild acidic pH and (iii) to infect the mouse animal model. We showed that the lysine decarboxylase CadA had the broadest range of activity since it both had the capacity to promote survival at pH 2.3 and growth at pH 4.5. The arginine decarboxylase AdiA was the most performant in protecting S. Typhimurium from a shock at pH 2.3 and the ornithine decarboxylase SpeF conferred the best growth advantage under anaerobiosis conditions at pH 4.5. We developed a GFP-based gene reporter to monitor the pH of the environment as perceived by S. Typhimurium. Results showed that activities of the lysine and ornithine decarboxylases at mild acidic pH did modify the local surrounding of S. Typhimurium both in culture medium and in macrophages. Finally, we tested the contribution of decarboxylases to virulence and found that these enzymes were dispensable for S. Typhimurium virulence during systemic infection. In the light of this result, we examined the genomes of Salmonella spp. normally responsible of systemic infection and observed that the genes encoding these enzymes were not well conserved, supporting the idea that these enzymes may be not required during systemic infection.
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Affiliation(s)
- Julie P M Viala
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS (UPR-CNRS 9043), Marseille, France.
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Casalino M, Prosseda G, Barbagallo M, Iacobino A, Ceccarini P, Carmela Latella M, Nicoletti M, Colonna B. Interference of the CadC regulator in the arginine-dependent acid resistance system of Shigella and enteroinvasive E. coli. Int J Med Microbiol 2010; 300:289-95. [DOI: 10.1016/j.ijmm.2009.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/30/2009] [Accepted: 10/01/2009] [Indexed: 10/20/2022] Open
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Díaz IBZ, Chalova VI, O'Bryan CA, Crandall PG, Ricke SC. Effect of soluble maillard reaction products on cadA expression in Salmonella typhimurium. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2010; 45:162-166. [PMID: 20390946 DOI: 10.1080/03601230903472207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The presence of Maillard reaction products (MRP) in foods and food components is due to the non-enzymatic reaction between protein and carbohydrate residues triggered by thermal steps during food processing. The objective of this study was to assess the effect of MRPs and increasing lysine concentrations on S. Typhimurium growth and the expression of cadA which may be an indirect determinant of Salmonella virulence response. Variations in lysine concentrations (from 0 to 0.5 mM) did not exert any effect either on the final optical density after 6-hour incubation or the growth rates of S. Typhimurium in media containing MRPs. In contrast to the reduced final absorbancy of the bacterial cultures grown with histidine and arginine MRPs supplementations (0.1%), growth rates, in general, remained unaltered by all MRPs at each lysine concentration when compared to the control (M9 pH 5.8, no MRPs added). The induction levels of cadA in media containing 0.1% MRPs were close to cadA induction in the reference media (M9, pH 5.8 and no MRPs) and did not exceed the corresponding values by more than approximately 30%. Although the observed negligible induction of cadA under these conditions complies with the concept of its potential "anti-virulence" function, additional studies involving various concentrations and more refined MRPs are needed.
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Affiliation(s)
- Irene B Zabala Díaz
- Department of Poultry Science, Texas A&M University, College Station, Texas, USA
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The cad locus of Enterobacteriaceae: More than just lysine decarboxylation. Anaerobe 2009; 15:1-6. [DOI: 10.1016/j.anaerobe.2008.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 03/27/2008] [Accepted: 05/08/2008] [Indexed: 11/19/2022]
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Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Nat Rev Microbiol 2008; 6:387-94. [PMID: 18392032 DOI: 10.1038/nrmicro1889] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The increasing availability of DNA-sequence information for multiple pathogenic and non-pathogenic variants of individual bacterial species has indicated that both DNA acquisition and genome reduction have important roles in genome evolution. Such genomic fluidity, which is found in human pathogens such as Escherichia coli, Helicobacter pylori and Mycobacterium tuberculosis, has important consequences for the clinical management of the diseases that are caused by these pathogens and for the development of diagnostics and new molecular epidemiological methods.
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