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Yamasaki Y, Singh P, Vimonish R, Ueti M, Bankhead T. Development and Application of an In Vitro Tick Feeding System to Identify Ixodes Tick Environment-Induced Genes of the Lyme Disease Agent, Borrelia burgdorferi. Pathogens 2024; 13:487. [PMID: 38921785 PMCID: PMC11207009 DOI: 10.3390/pathogens13060487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
The bacterial agent of Lyme disease, Borrelia burgdorferi, exists in an enzootic cycle by adapting to dissimilar mammalian and tick environments. The genetic elements necessary for host and vector adaptation are spread across a bacterial genome comprised of a linear chromosome and essential linear and circular plasmids. The promoter trap system, In Vivo Expression Technology (IVET), has been used to identify promoters of B. burgdorferi that are transcriptionally active specifically during infection of a murine host. However, an observed infection bottleneck effect in mice prevented the application of this system to study promoters induced in a tick environment. In this study, we adapted a membrane-based in vitro feeding system as a novel method to infect the Ixodes spp. vector with B. burgdorferi. Once adapted, we performed IVET screens as a proof of principle via an infected bloodmeal on the system. The screen yielded B. burgdorferi promoters that are induced during tick infection and verified relative expression levels using qRT-PCR. The results of our study demonstrate the potential of our developed in vitro tick feeding system and IVET systems to gain insight into the adaptive gene expression of the Lyme disease bacteria to the tick vector.
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Affiliation(s)
- Youki Yamasaki
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA; (Y.Y.); (P.S.); (R.V.)
| | - Preeti Singh
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA; (Y.Y.); (P.S.); (R.V.)
| | - Rubikah Vimonish
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA; (Y.Y.); (P.S.); (R.V.)
| | - Massaro Ueti
- Animal Disease Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Pullman, WA 99164, USA;
| | - Troy Bankhead
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA; (Y.Y.); (P.S.); (R.V.)
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Nishikawa S, Ogawa Y, Shiraiwa K, Nozawa R, Nakayama M, Eguchi M, Shimoji Y. Rational Design of Live-Attenuated Vaccines against Genome-Reduced Pathogens. Microbiol Spectr 2022; 10:e0377622. [PMID: 36453908 PMCID: PMC9769512 DOI: 10.1128/spectrum.03776-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022] Open
Abstract
To develop safe and highly effective live vaccines, rational vaccine design is necessary. Here, we sought a simple approach to rationally develop a safe attenuated vaccine against the genome-reduced pathogen Erysipelothrix rhusiopathiae. We examined the mRNA expression of all conserved amino acid biosynthetic genes remaining in the genome after the reductive evolution of E. rhusiopathiae. Reverse transcription-quantitative PCR (qRT-PCR) analysis revealed that half of the 14 genes examined were upregulated during the infection of murine J774A.1 macrophages. Gene deletion was possible only for three proline biosynthesis genes, proB, proA, and proC, the last of which was upregulated 29-fold during infection. Five mutants bearing an in-frame deletion of one (ΔproB, ΔproA, or ΔproC mutant), two (ΔproBA mutant), or three (ΔproBAC mutant) genes exhibited attenuated growth during J774A.1 infection, and the attenuation and vaccine efficacy of these mutants were confirmed in mice and pigs. Thus, for the rational design of live vaccines against genome-reduced bacteria, the selective targeting of genes that escaped chromosomal deletions during evolution may be a simple approach for identifying genes which are specifically upregulated during infection. IMPORTANCE Identification of bacterial genes that are specifically upregulated during infection can lead to the rational construction of live vaccines. For this purpose, genome-based approaches, including DNA microarray analysis and IVET (in vivo expression technology), have been used so far; however, these methods can become laborious and time-consuming. In this study, we used a simple in silico approach and showed that in genome-reduced bacteria, the genes which evolutionarily remained conserved for metabolic adaptations during infection may be the best targets for the deletion and construction of live vaccines.
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Affiliation(s)
- Sayaka Nishikawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yohsuke Ogawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Kazumasa Shiraiwa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Rieko Nozawa
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Momoko Nakayama
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahiro Eguchi
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yoshihiro Shimoji
- National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
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Ngassam-Tchamba C, Duprez JN, Fergestad M, De Visscher A, L'Abee-Lund T, De Vliegher S, Wasteson Y, Touzain F, Blanchard Y, Lavigne R, Chanishvili N, Cassart D, Mainil J, Thiry D. In vitro and in vivo assessment of phage therapy against Staphylococcus aureus causing bovine mastitis. J Glob Antimicrob Resist 2020; 22:762-770. [PMID: 32645442 DOI: 10.1016/j.jgar.2020.06.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/01/2020] [Accepted: 06/04/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVE The aim of this study was to assess the efficacy of lytic bacteriophages on Staphylococcus aureus causing bovine mastitis, by in vitro and in vivo assays using Galleria mellonella and murine mastitis models. METHODS Between May and December 2016, ten S. aureus (five methicillin-resistant and five methicillin-sensitive) isolates were isolated from milk samples of cattle with mastitis in Belgium and Norway. The isolates were assessed in vitro for their susceptibility to four lytic bacteriophages (Romulus, Remus, ISP and DSM105264) and subsequently in vivo in G. mellonella larvae and in murine mastitis model. RESULTS Romulus, Remus and ISP showed a lytic activity against the S. aureus isolates in vitro. A larvae survival rate below 50% was observed at 4 days post-inoculation (DPI) in the groups infected with a methicillin-sensitive S. aureus isolate and treated with these three phages in vivo. An incomplete recovery of the mouse mastitis was observed at 48h post-inoculation (HPI) in the groups infected and treated with the ISP phage in vivo. CONCLUSIONS: The observations are much more pronounced statistically between the infected- phosphate buffered saline (PBS)-treated and infected-phage-treated groups in G. mellonella and the murine mastitis model demonstrating an effect of the phages against S. aureus associated with bovine mastitis.
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Affiliation(s)
- C Ngassam-Tchamba
- Bacteriology, Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine and Institute for Fundamental and Applied Research in Animals and Health (FARAH), University of Liège, Quartier Vallée 2, Avenue Cureghem 6, B-4000 Liège, Belgium
| | - J N Duprez
- Bacteriology, Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine and Institute for Fundamental and Applied Research in Animals and Health (FARAH), University of Liège, Quartier Vallée 2, Avenue Cureghem 6, B-4000 Liège, Belgium
| | - M Fergestad
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - A De Visscher
- M-team & Mastitis and Milk Quality Research Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - T L'Abee-Lund
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - S De Vliegher
- M-team & Mastitis and Milk Quality Research Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Y Wasteson
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - F Touzain
- Viral Genetics and Bio-security Unit, ANSES, Ploufragan-Plouzané laboratory, Rue des Fusillés, 22 440 Ploufragan, France
| | - Y Blanchard
- Viral Genetics and Bio-security Unit, ANSES, Ploufragan-Plouzané laboratory, Rue des Fusillés, 22 440 Ploufragan, France
| | - R Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - N Chanishvili
- R & D Department, Eliava Institute of Bacteriophages, 3 Levan Gotua St, T'bilisi, Georgia
| | - D Cassart
- Department of Morphology and Pathology, Faculty of Veterinary Medicine and Institute for Fundamental and Applied Research in Animals and Health (FARAH), University of Liège, Quartier Vallée 2, Avenue Cureghem 6, B-4000 Liège, Belgium
| | - J Mainil
- Bacteriology, Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine and Institute for Fundamental and Applied Research in Animals and Health (FARAH), University of Liège, Quartier Vallée 2, Avenue Cureghem 6, B-4000 Liège, Belgium
| | - D Thiry
- Bacteriology, Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine and Institute for Fundamental and Applied Research in Animals and Health (FARAH), University of Liège, Quartier Vallée 2, Avenue Cureghem 6, B-4000 Liège, Belgium.
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Kida Y, Yamamoto T, Kuwano K. SdsA1, a secreted sulfatase, contributes to the in vivo virulence of Pseudomonas aeruginosa in mice. Microbiol Immunol 2020; 64:280-295. [PMID: 31907968 DOI: 10.1111/1348-0421.12772] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/10/2019] [Accepted: 01/05/2020] [Indexed: 01/08/2023]
Abstract
Mucin is a glycoprotein that is the primary component of the mucus overlaying the epithelial tissues. Because mucin functions as a first line of the innate immune system, Pseudomonas aeruginosa appears to require interaction with mucin to establish infection in the host. However, the interactions between P. aeruginosa and mucin have been poorly understood. In this study, using in vivo expression technology (IVET), we attempted to identify mucin-inducible promoters that are likely to be involved in the establishment of P. aeruginosa infection. The IVET analysis revealed that the genes encoding glycosidases, sulfatases, and peptidases that are thought to be required for the utilization of mucin as a nutrient are present in 13 genes downstream of the identified promoters. Our results indicated that, among them, sdsA1 encoding a secreted sulfatase plays a central role in the degradation of mucin. It was then demonstrated that disruption of sdsA1 leads to a decreased release of sulfate from mucin and sulfated sugars. Furthermore, the sdsA1 mutant showed a reduction in the ability of mucin gel penetration and an attenuation of virulence in leukopenic mice compared with the wild-type strain. Collectively, these results suggest that SdsA1 plays an important role as a virulence factor of P. aeruginosa.
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Affiliation(s)
- Yutaka Kida
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Takeshi Yamamoto
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Koichi Kuwano
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka, Japan
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Response of the Biocontrol Agent Pseudomonas pseudoalcaligenes AVO110 to Rosellinia necatrix Exudate. Appl Environ Microbiol 2019; 85:AEM.01741-18. [PMID: 30478234 PMCID: PMC6344628 DOI: 10.1128/aem.01741-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/17/2018] [Indexed: 01/08/2023] Open
Abstract
Diseases associated with fungal root invasion cause a significant loss of fruit tree production worldwide. The bacterium Pseudomonas pseudoalcaligenes AVO110 controls avocado white root rot disease caused by Rosellinia necatrix by using mechanisms involving competition for nutrients and niches. Here, a functional genomics approach was conducted to identify the bacterial traits involved in the interaction with this fungal pathogen. Our results contribute to a better understanding of the multitrophic interactions established among bacterial biocontrol agents, the plant rhizosphere, and the mycelia of soilborne pathogens. The rhizobacterium Pseudomonas pseudoalcaligenes AVO110, isolated by the enrichment of competitive avocado root tip colonizers, controls avocado white root rot disease caused by Rosellinia necatrix. Here, we applied signature-tagged mutagenesis (STM) during the growth and survival of AVO110 in fungal exudate-containing medium with the goal of identifying the molecular mechanisms linked to the interaction of this bacterium with R. necatrix. A total of 26 STM mutants outcompeted by the parental strain in fungal exudate, but not in rich medium, were selected and named growth-attenuated mutants (GAMs). Twenty-one genes were identified as being required for this bacterial-fungal interaction, including membrane transporters, transcriptional regulators, and genes related to the metabolism of hydrocarbons, amino acids, fatty acids, and aromatic compounds. The bacterial traits identified here that are involved in the colonization of fungal hyphae include proteins involved in membrane maintenance (a dynamin-like protein and ColS) or cyclic-di-GMP signaling and chemotaxis. In addition, genes encoding a DNA helicase (recB) and a regulator of alginate production (algQ) were identified as being required for efficient colonization of the avocado rhizosphere. IMPORTANCE Diseases associated with fungal root invasion cause a significant loss of fruit tree production worldwide. The bacterium Pseudomonas pseudoalcaligenes AVO110 controls avocado white root rot disease caused by Rosellinia necatrix by using mechanisms involving competition for nutrients and niches. Here, a functional genomics approach was conducted to identify the bacterial traits involved in the interaction with this fungal pathogen. Our results contribute to a better understanding of the multitrophic interactions established among bacterial biocontrol agents, the plant rhizosphere, and the mycelia of soilborne pathogens.
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Identification of a two-component Class IIb bacteriocin in Streptococcus pyogenes by recombinase-based in vivo expression technology. Sci Rep 2016; 6:36233. [PMID: 27808235 PMCID: PMC5093712 DOI: 10.1038/srep36233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 10/10/2016] [Indexed: 12/30/2022] Open
Abstract
Streptococcus pyogenes is a globally prominent bacterial pathogen that exhibits strict tropism for the human host, yet bacterial factors responsible for the ability of S. pyogenes to compete within this limited biological niche are not well understood. Using an engineered recombinase-based in vivo expression technology (RIVET) system, we identified an in vivo-induced promoter region upstream of a predicted Class IIb bacteriocin system in the M18 serotype S. pyogenes strain MGAS8232. This promoter element was not active under in vitro laboratory conditions, but was highly induced within the mouse nasopharynx. Recombinant expression of the predicted mature S. pyogenes bacteriocin peptides (designated SpbM and SpbN) revealed that both peptides were required for antimicrobial activity. Using a gain of function experiment in Lactococcus lactis, we further demonstrated S. pyogenes immunity function is encoded downstream of spbN. These data highlight the importance of bacterial gene regulation within appropriate environments to help understand mechanisms of niche adaptation by bacterial pathogens.
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Singh A, Blaskovic D, Joo J, Yang Z, Jackson SH, Coleman WG, Yan M. Investigating the Role of Helicobacter pylori PriA Protein. Helicobacter 2016; 21:295-304. [PMID: 26817518 PMCID: PMC8483055 DOI: 10.1111/hel.12283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND In bacteria, PriA protein, a conserved DEXH-type DNA helicase, plays a central role in replication restart at stalled replication forks. Its unique DNA binding property allows it to recognize and stabilize stalled forks and the structures derived from them. PriA plays a very critical role in replication fork stabilization and DNA repair in E. coli and N. gonorrhoeae. In our in vivo expression technology screen, priA gene was induced in vivo when Helicobacter pylori infects mouse stomach. MATERIALS AND METHODS We decided to elucidate the role of H. pylori PriA protein in survival in mouse stomach, survival in gastric epithelial cells and macrophage cells, DNA repair, acid stress, and oxidative stress. RESULTS The priA null mutant strain was unable to colonize mice stomach mucosa after long-term infections. Mouse colonization was observed after 1 week of infection, but the levels were much lower than the wild-type HpSS1 strain. PriA protein was found to be important for intracellular survival of epithelial cell-/macrophage cell-ingested H. pylori. Also, a priA null mutant was more sensitive to DNA-damaging agents and was much more sensitive to acid and oxidative stress as compared to the wild-type strain. CONCLUSIONS These data suggest that the PriA protein is needed for survival and persistence of H. pylori in mice stomach mucosa.
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Affiliation(s)
- Aparna Singh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Dusan Blaskovic
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Jungsoo Joo
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Zhen Yang
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Sharon H. Jackson
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD
| | - William G. Coleman
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD,National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD
| | - Ming Yan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
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A Modular, Tn7-Based System for Making Bioluminescent or Fluorescent Salmonella and Escherichia coli Strains. Appl Environ Microbiol 2016; 82:4931-43. [PMID: 27260360 DOI: 10.1128/aem.01346-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 05/31/2016] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Our goal was to develop a robust tagging method that can be used to track bacterial strains in vivo To address this challenge, we adapted two existing systems: a modular plasmid-based reporter system (pCS26) that has been used for high-throughput gene expression studies in Salmonella and Escherichia coli and Tn7 transposition. We generated kanamycin- and chloramphenicol-resistant versions of pCS26 with bacterial luciferase, green fluorescent protein (GFP), and mCherry reporters under the control of σ(70)-dependent promoters to provide three different levels of constitutive expression. We improved upon the existing Tn7 system by modifying the delivery vector to accept pCS26 constructs and moving the transposase genes from a nonreplicating helper plasmid into a temperature-sensitive plasmid that can be conditionally maintained. This resulted in a 10- to 30-fold boost in transposase gene expression and transposition efficiencies of 10(-8) to 10(-10) in Salmonella enterica serovar Typhimurium and E. coli APEC O1, whereas the existing Tn7 system yielded no successful transposition events. The new reporter strains displayed reproducible signaling in microwell plate assays, confocal microscopy, and in vivo animal infections. We have combined two flexible and complementary tools that can be used for a multitude of molecular biology applications within the Enterobacteriaceae This system can accommodate new promoter-reporter combinations as they become available and can help to bridge the gap between modern, high-throughput technologies and classical molecular genetics. IMPORTANCE This article describes a flexible and efficient system for tagging bacterial strains. Using our modular plasmid system, a researcher can easily change the reporter type or the promoter driving expression and test the parameters of these new constructs in vitro Selected constructs can then be stably integrated into the chromosomes of desired strains in two simple steps. We demonstrate the use of this system in Salmonella and E. coli, and we predict that it will be widely applicable to other bacterial strains within the Enterobacteriaceae This technology will allow for improved in vivo analysis of bacterial pathogens.
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Roberfroid S, Vanderleyden J, Steenackers H. Gene expression variability in clonal populations: Causes and consequences. Crit Rev Microbiol 2016; 42:969-84. [PMID: 26731119 DOI: 10.3109/1040841x.2015.1122571] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
During the last decade it has been shown that among cell variation in gene expression plays an important role within clonal populations. Here, we provide an overview of the different mechanisms contributing to gene expression variability in clonal populations. These are ranging from inherent variations in the biochemical process of gene expression itself, such as intrinsic noise, extrinsic noise and bistability to individual responses to variations in the local micro-environment, a phenomenon called phenotypic plasticity. Also genotypic variations caused by clonal evolution and phase variation can contribute to gene expression variability. Consequently, gene expression studies need to take these fluctuations in expression into account. However, frequently used techniques for expression quantification, such as microarrays, RNA sequencing, quantitative PCR and gene reporter fusions classically determine the population average of gene expression. Here, we discuss how these techniques can be adapted towards single cell analysis by integration with single cell isolation, RNA amplification and microscopy. Alternatively more qualitative selection-based techniques, such as mutant screenings, in vivo expression technology (IVET) and recombination-based IVET (RIVET) can be applied for detection of genes expressed only within a subpopulation. Finally, differential fluorescence induction (DFI), a protocol specially designed for single cell expression is discussed.
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Affiliation(s)
- Stefanie Roberfroid
- a Department of Microbial and Molecular Systems , Centre of Microbial and Plant Genetics, KU Leuven , Leuven , Belgium
| | - Jos Vanderleyden
- a Department of Microbial and Molecular Systems , Centre of Microbial and Plant Genetics, KU Leuven , Leuven , Belgium
| | - Hans Steenackers
- a Department of Microbial and Molecular Systems , Centre of Microbial and Plant Genetics, KU Leuven , Leuven , Belgium
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Influence of Salmonella enterica Serovar Typhimurium ssrB on Colonization of Eastern Oysters (Crassostrea virginica) as Revealed by a Promoter Probe Screen. Appl Environ Microbiol 2015; 82:328-39. [PMID: 26497459 DOI: 10.1128/aem.02870-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/20/2015] [Indexed: 12/14/2022] Open
Abstract
Although Salmonella has been isolated from 7.4 to 8.6% of domestic raw oysters, representing a significant risk for food-borne illness, little is known about the factors that influence their initial colonization by Salmonella. This study tested the hypothesis that specific regulatory changes enable a portion of the invading Salmonella population to colonize oysters. An in vivo promoter probe library screen identified 19 unique regions as regulated during colonization. The mutants in the nearest corresponding downstream genes were tested for colonization defects in oysters. Only one mutation, in ssrB, resulted in a significantly reduced ability to colonize oysters compared to that of wild-type Salmonella. Because ssrB regulates Salmonella pathogenicity island 2 (SPI-2)-dependent infections in vertebrate macrophages, the possibility that ssrB mediated colonization of oyster hemocytes in a similar manner was examined. However, no difference in hemocyte colonization was observed. The complementary hypothesis that signal exchange between Salmonella and the oyster's native microbial community aids colonization was also tested. Signals that triggered responses in quorum sensing (QS) reporters were shown to be produced by oyster-associated bacteria and present in oyster tissue. However, no evidence for signal exchange was observed in vivo. The sdiA reporter responded to salinity, suggesting that SdiA may also have a role in environmental sensing. Overall, this study suggests the initial colonization of live oysters by Salmonella is controlled by a limited number of regulators, including ssrB.
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Casselli T, Bankhead T. Use of in vivo Expression Technology for the Identification of Putative Host Adaptation Factors of the Lyme Disease Spirochete. J Mol Microbiol Biotechnol 2015; 25:349-61. [PMID: 26488479 DOI: 10.1159/000439305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The causative agent of Lyme disease, Borrelia burgdorferi, is an obligate parasite that requires either a tick vector or a mammalian host for survival. Identification of the bacterial genes that are specifically expressed during infection of the mammalian host could provide targets for novel therapeutics and vaccines. In vivo expression technology (IVET) is a reporter-based promoter trap system that utilizes selectable markers to identify promoters of bacterial host-specific genes. Using previously characterized genes for in vivo and in vitro selection, this study utilized an IVET system that allows for selection of B. burgdorferi sequences that act as active promoters only during murine infection. This promoter trap system was able to successfully distinguish active promoter sequences both in vivo and in vitro from control sequences and a library of cloned B. burgdorferi genomic fragments. However, a bottleneck effect during the experimental mouse infection limited the utility for genome-wide promoter screening. Overall, IVET was demonstrated as a tool for the identification of in vivo-induced promoter elements of B. burgdorferi, and the observed infection bottleneck apparent using a polyclonal infection pool provides insight into the dynamics of experimental infection with B. burgdorferi.
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Affiliation(s)
- Timothy Casselli
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Wash., USA
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Lee SW, Shet UK, Park SW, Lim HP, Yun KD, Kang SS, Kim SE. Identification of Enterococcus faecalis antigens specifically expressed in vivo. Restor Dent Endod 2015; 40:306-11. [PMID: 26587417 PMCID: PMC4650527 DOI: 10.5395/rde.2015.40.4.306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/10/2015] [Indexed: 01/05/2023] Open
Abstract
Objectives Molecular mechanism of the pathogenicity of Enterococcus faecalis (E. faecalis), a suspected endodontic pathogen, has not yet been adequately elucidated due to limited information on its virulence factors. Here we report the identification of in vivo expressed antigens of E. faecalis by using a novel immunoscreening technique called change-mediated antigen technology (CMAT) and an experimental animal model of endodontic infection. Materials and Methods Among 4,500 E. coli recombinant clones screened, 19 positive clones reacted reproducibly with hyperimmune sera obtained from rabbits immunized with E. faecalis cells isolated from an experimental endodontic infection. DNA sequences from 16 of these in vivo-induced (IVI) genes were determined. Results Identified protein antigens of E. faecalis included enzymes involved in housekeeping functions, copper resistance protein, putative outer membrane proteins, and proteins of unknown function. Conclusions In vivo expressed antigens of E. faecalis could be identified by using a novel immune-screening technique CMAT and an experimental animal model of endodontic infection. Detailed analysis of these IVI genes will lead to a better understanding of the molecular mechanisms involved in the endodontic infection of E. faecalis.
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Affiliation(s)
- Seok-Woo Lee
- Department of Dental Education, Dental Science Research Institute and BK21 Project, School of Dentistry, Gwangju, Korea. ; Department of Periodontology, Dental Science Research Institute and BK21 Project, School of Dentistry, Gwangju, Korea
| | - Uttom K Shet
- Department of Maxillofacial Surgery, Dental Science Research Institute and BK21 Project, School of Dentistry, Gwangju, Korea
| | - Sang-Won Park
- Department of Prosthodontics, Dental Science Research Institute and BK21 Project, School of Dentistry, Gwangju, Korea
| | - Hyun-Pil Lim
- Department of Prosthodontics, Dental Science Research Institute and BK21 Project, School of Dentistry, Gwangju, Korea
| | - Kwi-Dug Yun
- Department of Prosthodontics, Dental Science Research Institute and BK21 Project, School of Dentistry, Gwangju, Korea
| | - Seong Soo Kang
- Department of Veterinary Medicine, Chonnam National University, Gwangju, Korea
| | - Se Eun Kim
- Department of Veterinary Medicine, Chonnam National University, Gwangju, Korea
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Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis. PLoS Pathog 2015; 11:e1004600. [PMID: 25590628 PMCID: PMC4295882 DOI: 10.1371/journal.ppat.1004600] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/03/2014] [Indexed: 11/19/2022] Open
Abstract
We recently found that Yersinia pseudotuberculosis can be used as a model of persistent bacterial infections. We performed in vivo RNA-seq of bacteria in small cecal tissue biopsies at early and persistent stages of infection to determine strategies associated with persistence. Comprehensive analysis of mixed RNA populations from infected tissues revealed that Y. pseudotuberculosis undergoes transcriptional reprogramming with drastic down-regulation of T3SS virulence genes during persistence when the pathogen resides within the cecum. At the persistent stage, the expression pattern in many respects resembles the pattern seen in vitro at 26oC, with for example, up-regulation of flagellar genes and invA. These findings are expected to have impact on future rationales to identify suitable bacterial targets for new antibiotics. Other genes that are up-regulated during persistence are genes involved in anaerobiosis, chemotaxis, and protection against oxidative and acidic stress, which indicates the influence of different environmental cues. We found that the Crp/CsrA/RovA regulatory cascades influence the pattern of bacterial gene expression during persistence. Furthermore, arcA, fnr, frdA, and wrbA play critical roles in persistence. Our findings suggest a model for the life cycle of this enteropathogen with reprogramming from a virulent to an adapted phenotype capable of persisting and spreading by fecal shedding. To establish infection and colonize within a host, infecting pathogens have to cope with a variety of destructive surroundings. The food-borne pathogen Y. pseudotuberculosis can cause persistent infection in mice. Upon infection, Y. pseudotuberculosis passes the anti-microbial gastrointestinal milieu and finally remains associated with lymphoid follicles in cecal tissue surrounded by polymorphonuclear leukocytes, indicating that the bacteria are exposed to multiple environmental cues. We performed complex RNA-seq of small cecal biopsies of infected mice to reveal Y. pseudotuberculosis gene expression in vivo. We found that Y. pseudotuberculosis underwent reprogramming from a virulent phenotype, expressing virulence genes during early infection, to an adapted phenotype capable of persisting in the harsh cecal environment. Persistence was characterized by a novel expression pattern with down-regulation of virulence genes and up-regulation of genes involved in anaerobiosis, chemotaxis, and protection against oxidative and acidic stress. Mutagenesis of selected genes revealed that the regulator rovA was critical for the establishment of infection, and that arcA, fnr, frdA, and wrbA play critical roles in maintaining infection for long periods of time. Our study shows the power of RNA deep sequencing, which can be used to reveal the in vivo expression patterns of small amounts of bacteria in complex intestinal environments.
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Lactobacillus reuteri 100-23 modulates urea hydrolysis in the murine stomach. Appl Environ Microbiol 2014; 80:6104-13. [PMID: 25063664 DOI: 10.1128/aem.01876-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Comparisons of in vivo (mouse stomach) and in vitro (laboratory culture) transcriptomes of Lactobacillus reuteri strain 100-23 were made by microarray analysis. These comparisons revealed the upregulation of genes associated with acid tolerance, including urease production, in the mouse stomach. Inactivation of the ureC gene reduced the acid tolerance of strain 100-23 in vitro, and the mutant was outcompeted by the wild type in the gut of ex-Lactobacillus-free mice. Urine analysis showed that stable isotope-labeled urea, administered by gavage, was metabolized to a greater extent in Lactobacillus-free mice than animals colonized by strain 100-23. This surprising observation was associated with higher levels of urease activity and fecal-type bacteria in the stomach digesta of Lactobacillus-free mice. Despite the modulation of urea hydrolysis in the stomach, recycling of urea nitrogen in the murine host was not affected since the essential amino acid isoleucine, labeled with a stable isotope, was detected in the livers of both Lactobacillus-free and 100-23-colonized animals. Therefore, our experiments reveal a new and unexpected impact of Lactobacillus colonization on urea hydrolysis in the murine gut.
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Marvasi M, Noel JT, George AS, Farias MA, Jenkins KT, Hochmuth G, Xu Y, Giovanonni JJ, Teplitski M. Ethylene signalling affects susceptibility of tomatoes to Salmonella. Microb Biotechnol 2014; 7:545-55. [PMID: 24888884 PMCID: PMC4265073 DOI: 10.1111/1751-7915.12130] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/07/2014] [Accepted: 04/19/2014] [Indexed: 12/03/2022] Open
Abstract
Fresh fruits and vegetables are increasingly recognized as important reservoirs of human pathogens, and therefore, significant attention has been directed recently to understanding mechanisms of the interactions between plants and enterics, like Salmonella. A screen of tomato cultivars for their susceptibility to Salmonella revealed significant differences in the ability of this human pathogen to multiply within fruits; expression of the Salmonella genes (cysB, agfB, fadH) involved in the interactions with tomatoes depended on the tomato genotype and maturity stage. Proliferation of Salmonella was strongly reduced in the tomato mutants with defects in ethylene synthesis, perception and signal transduction. While mutation in the ripening-related ethylene receptor Nr resulted only in a modest reduction in Salmonella numbers within tomatoes, strong inhibition of the Salmonella proliferation was observed in rin and nor tomato mutants. RIN and NOR are regulators of ethylene synthesis and ripening. A commercial tomato variety heterozygous for rin was less susceptible to Salmonella under the greenhouse conditions but not when tested in the field over three production seasons.
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Affiliation(s)
- Massimiliano Marvasi
- Soil and Water Science Department, Genetics Institute, University of Florida-IFAS, Gainesville, FL, 32611, USA
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LaRocque RC, Harris JB, Ryan ET, Qadri F, Calderwood SB. Postgenomic approaches to cholera vaccine development. Expert Rev Vaccines 2014; 5:337-46. [PMID: 16827618 DOI: 10.1586/14760584.5.3.337] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cholera remains an important public health threat. A cholera vaccine that provides durable protection at the mucosal surface, especially among children in endemic settings, is urgently needed. The availability of the complete genome sequence of a clinical isolate of Vibrio cholerae O1 El Tor has allowed for comparative and functional genomic approaches in the study of cholera. This work holds promise for the identification of bacterial targets of protective human immune responses and may contribute to the development of a new generation of cholera vaccines.
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Affiliation(s)
- Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, GRJ 504, 55 Fruit Street, Boston, MA 02114, USA.
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Junjua M, Galia W, Gaci N, Uriot O, Genay M, Bachmann H, Kleerebezem M, Dary A, Roussel Y. Development of the recombinase-based in vivo expression technology in Streptococcus thermophilus and validation using the lactose operon promoter. J Appl Microbiol 2013; 116:620-31. [PMID: 24279757 DOI: 10.1111/jam.12376] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/15/2013] [Accepted: 10/24/2013] [Indexed: 11/27/2022]
Abstract
AIMS To construct and validate the recombinase-based in vivo expression technology (R-IVET) tool in Streptococcus thermophilus (ST). METHODS AND RESULTS The R-IVET system we constructed in the LMD-9 strain includes the plasmid pULNcreB allowing transcriptional fusion with the gene of the site-specific recombinase Cre and the chromosomal cassette containing a spectinomycin resistance gene flanked by two loxP sites. When tested in M17 medium, promoters of the genes encoding the protease PrtS, the heat-shock protein Hsp16 and of the lactose operon triggered deletion of the cassette, indicating promoter activity in these conditions. The lactose operon promoter was also found to be activated during the transit in the murine gastrointestinal tract. CONCLUSIONS The R-IVET system developed in ST is relatively stable, functional, very sensitive and can be used to assay activity of promoters, which are specifically active in in vivo conditions. SIGNIFICANCE AND IMPACT OF THE STUDY This first adaptation of R-IVET to ST provides a highly valuable tool allowing an exploration of the physiological state of ST in the GIT of mammals, fermentation processes or dairy products.
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Affiliation(s)
- M Junjua
- Unité de Recherche, 'Animal & Fonctionnalités des Produits Animaux', Équipe 'Protéolyse et Biofonctionnalités des Protéines et des Peptides', UC INRA 340, Université de Lorraine, Vandœuvre-lès-Nancy, France
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18
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Tsonos J, Vandenheuvel D, Briers Y, De Greve H, Hernalsteens JP, Lavigne R. Hurdles in bacteriophage therapy: deconstructing the parameters. Vet Microbiol 2013; 171:460-9. [PMID: 24315040 DOI: 10.1016/j.vetmic.2013.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 10/30/2013] [Accepted: 11/01/2013] [Indexed: 10/26/2022]
Abstract
Bacterial infections in animals impact our food production, leading to economic losses due to food rejection and the need for preventive and curative measures. Since the onset of the antibiotic era, the rise of antibiotic-resistant pathogens is causing scares in health care and food producing facilities worldwide. In the search of new therapeutics, re-evaluation of bacteriophage (phage) therapy, using naturally occurring bacterial viruses to tackle infections, is gaining interest. Many studies report about phage therapy success, showing the value and power of these natural viruses. Although phages carry some interesting traits and their basic biology is now well understood, this review argues that phage therapy has not revealed all of its secrets and many parameters remain understudied, making the outcome of phage therapy highly variable depending on the disease incidence. These difficulties include poorly understood mechanisms of phage penetration and distribution throughout the body, the variable expression and accessibility of phage receptors on the bacterial host in in vivo conditions and the unusual (non-linear) phage pharmacokinetics. These parameters are not easily measured in realistic in vivo settings, but are nevertheless important hurdles to overcome the high variability of phage therapy trials. This critical approach is in accordance with Goethe's statement; "Difficulties increase the nearer we get to the goal". However, since the importance of the goal itself also rises, both difficulties and goal justify the need for additional in depth research in this domain.
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Affiliation(s)
- Jessica Tsonos
- Viral Genetics Research Group, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Department Structural Biology, VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium.
| | - Dieter Vandenheuvel
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium.
| | - Yves Briers
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium.
| | - Henri De Greve
- Structural and Molecular Microbiology, VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Department Structural Biology, VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | | | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium.
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Hu Y, Shang Y, Huang J, Wang Y, Ren F, Jiao Y, Pan Z, Jiao XA. A novel immunoproteomics method for identifying in vivo-induced Campylobacter jejuni antigens using pre-adsorbed sera from infected patients. Biochim Biophys Acta Gen Subj 2013; 1830:5229-35. [DOI: 10.1016/j.bbagen.2013.06.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 04/30/2013] [Accepted: 06/29/2013] [Indexed: 02/01/2023]
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Li S, Song J, Huang H, Chen W, Li M, Zhao Y, Cong Y, Zhu J, Rao X, Hu X, Hu F. Identification of in-vivo induced genes of Streptococcus suis serotype 2 specially expressed in infected human. Microb Pathog 2013; 63:8-15. [DOI: 10.1016/j.micpath.2013.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 05/15/2013] [Accepted: 05/22/2013] [Indexed: 10/26/2022]
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Marvasi M, Cox CE, Xu Y, Noel JT, Giovannoni JJ, Teplitski M. Differential regulation of Salmonella typhimurium genes involved in O-antigen capsule production and their role in persistence within tomato fruit. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:793-800. [PMID: 23489058 DOI: 10.1094/mpmi-09-12-0208-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Enteric pathogens, including non-typhoidal Salmonella spp. and enterovirulent Escherichia coli, are capable of persisting and multiplying within plants. Yet, little is still known about the mechanisms of these interactions. This study identified the Salmonella yihT gene (involved in synthesis of the O-antigen capsule) as contributing to persistence in immature tomato fruit. Deletion of yihT reduced competitive fitness of S. enterica sv. Typhimurium in green (but not ripe, regardless of color) tomato fruit by approximately 3 logs. The yihT recombinase-based in vivo expression technology (RIVET) reporter was strongly activated in unripe tomato fruit, and fitness of the mutant inversely correlated with the level of the yihT gene expression. Expression of yihT in mature tomato fruit was low, and yihT did not affect competitive fitness within mature fruit. To better understand the molecular basis of the phenotype, behaviors of the yihT RIVET reporter and the yihT mutant were tested in tomato fruit defective in ethylene signaling. These experiments suggest a role for functional ethylene-mediated signaling in the persistence of Salmonella spp. within tomato fruit. Furthermore, jasmonic acid and its precursors strongly reduced expression of yihT.
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Affiliation(s)
- Massimiliano Marvasi
- Soil and Water Science Department, Genetics Institute Rm330E, 2033 Mowry Rd, University of Florida-IFAS, Gainesville 32611, USA
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Amerizadeh A, Khoo BY, Teh AY, Golkar M, Abdul Karim IZ, Osman S, Yunus MH, Noordin R. Identification and real-time expression analysis of selected Toxoplasma gondii in-vivo induced antigens recognized by IgG and IgM in sera of acute toxoplasmosis patients. BMC Infect Dis 2013; 13:287. [PMID: 23800344 PMCID: PMC3695809 DOI: 10.1186/1471-2334-13-287] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/13/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Toxoplasma gondii is an obligate intracellular zoonotic parasite of the phylum Apicomplexa which infects a wide range of warm-blooded animals, including humans. In this study in-vivo induced antigens of this parasite was investigated using in-vivo induced antigen technology (IVIAT) and pooled sera from patients with serological evidence of acute infection. METHODS The pooled sera was first pre-absorbed against three different preparations of antigens from in-vitro-grown cells of each T. gondii and E. coli XL1-Blue MRF', subsequently it was used to screen T. gondii cDNA phage expression library. Positive clones from each group were subjected to quantitative real-time PCR expression analysis on mRNA of in-vivo and in-vitro grown parasites. RESULTS A total of 29 reactive clones from each IgM and IgG immunoscreenings were found to have high homology to T. gondii genes. Quantitative real-time PCR expression analysis showed that 20 IgM-detected genes and 11 IgG-detected genes were up-regulated in-vivo relative to their expression levels in-vitro. These included genes encoding micronemes, sterol-regulatory element binding protein site, SRS34A, MIC2-associated protein M2AP, nucleoredoxin, protein phosphatase 2C and several hypothetical proteins. A hypothetical protein (GenBank accession no. 7899266) detected by IgG had the highest in-vivo over in-vitro fold change of 499.86; while another up-regulated hypothetical protein (GenBank accession no. 7898829) recognized by IgM showed high sensitivity (90%) and moderate specificity (70%) in detecting T. gondii antibodies when tested with 20 individual serum samples. CONCLUSION The highly up-regulated genes and the corresponding proteins, in particular the hypothetical proteins, may be useful in further studies on understanding the disease pathogenesis and as potential vaccine candidates.
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Affiliation(s)
- Atefeh Amerizadeh
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia
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Identification of Toxoplasma gondii in-vivo induced antigens by cDNA library immunoscreening with chronic toxoplasmosis sera. Microb Pathog 2012; 54:60-6. [PMID: 23044055 DOI: 10.1016/j.micpath.2012.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/01/2012] [Accepted: 09/16/2012] [Indexed: 11/22/2022]
Abstract
Toxoplasmosis is an infection caused by the parasite Toxoplasma gondii. Chronically-infected individuals with a compromised immune system are at risk for reactivation of the disease. In-vivo induced antigen technology (IVIAT) is a promising method for the identification of antigens expressed in-vivo. The aim of the present study was to apply IVIAT to identify antigens which are expressed in-vivo during T. gondii infection using sera from individuals with chronic toxoplasmosis. Forty serum samples were pooled, pre-adsorped against three different preparations of antigens, from each in-vitro grown T. gondii and Escherichia coli XLBlue MRF', and then used to screen a T. gondii cDNA expression library. Sequencing of DNA inserts from positive clones showed eight open reading frames with high homology to T. gondii genes. Expression analysis using quantitative real-time PCR showed that SAG1-related sequence 3 (SRS3) and two hypothetical genes were up-regulated in-vivo relative to their expression levels in-vitro. These three proteins also showed high sensitivity and specificity when tested with individual serum samples. Five other proteins namely M16 domain peptidase, microneme protein, elongation factor 1-alpha, pre-mRNA-splicing factor and small nuclear ribonucleoprotein F had lower RNA expression in-vivo as compared to in-vitro. SRS3 and the two hypothetical proteins warrant further investigation into their roles in the pathogenesis of toxoplasmosis.
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Kroj A, Schmidt H. Selection of in vivo expressed genes of Escherichia coli O157:H7 strain EDL933 in ground meat under elevated temperature conditions. J Food Prot 2012; 75:1743-50. [PMID: 23043821 DOI: 10.4315/0362-028x.jfp-11-453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Enterohemorrhagic Escherichia coli O157:H7 strains are important foodborne pathogens that are often transmitted to humans by the ingestion of raw or undercooked meat of bovine origin. To investigate adaptation of this pathogen during persistence and growth in ground meat, we established an in vivo expression technology model to identify genes that are expressed during growth in this food matrix under elevated temperatures (42°C). To improve on the antibiotic-based selection method, we constructed the promoter trap vector pAK-1, containing a promoterless kanamycin resistance gene. A genomic library of E. coli O157:H7 strain EDL933 was constructed in pAK-1 and used for promoter selection in ground meat. The 20 in vivo expressed genes identified were associated with transport processes, metabolism, macromolecule synthesis, and stress response. For most of the identified genes, only hypothetical functions could be assigned. The results of our study provide the first insights into the complex response of E. coli O157:H7 to a ground meat environment under elevated temperatures and establish a suitable vector for promoter studies or selection of in vivo induced promoters in foods such as ground meat.
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Affiliation(s)
- Andrea Kroj
- Department of Food Microbiology, Institute of Food Science and Biotechnology, Garbenstraße 28, University of Hohenheim, 70599 Stuttgart, Germany
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25
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Singh A, Hodgson N, Yan M, Joo J, Gu L, Sang H, Gregory-Bryson E, Wood WG, Ni Y, Smith K, Jackson SH, Coleman WG. Screening Helicobacter pylori genes induced during infection of mouse stomachs. World J Gastroenterol 2012; 18:4323-34. [PMID: 22969195 PMCID: PMC3436047 DOI: 10.3748/wjg.v18.i32.4323] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 07/30/2012] [Accepted: 08/03/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the effect of in vivo environment on gene expression in Helicobacter pylori (H. pylori) as it relates to its survival in the host.
METHODS: In vivo expression technology (IVET) systems are used to identify microbial virulence genes. We modified the IVET-transcriptional fusion vector, pIVET8, which uses antibiotic resistance as the basis for selection of candidate genes in host tissues to develop two unique IVET-promoter-screening vectors, pIVET11 and pIVET12. Our novel IVET systems were developed by the fusion of random Sau3A DNA fragments of H. pylori and a tandem-reporter system of chloramphenicol acetyltransferase and beta-galactosidase. Additionally, each vector contains a kanamycin resistance gene. We used a mouse macrophage cell line, RAW 264.7 and mice, as selective media to identify specific genes that H. pylori expresses in vivo. Gene expression studies were conducted by infecting RAW 264.7 cells with H. pylori. This was followed by real time polymerase chain reaction (PCR) analysis to determine the relative expression levels of in vivo induced genes.
RESULTS: In this study, we have identified 31 in vivo induced (ivi) genes in the initial screens. These 31 genes belong to several functional gene families, including several well-known virulence factors that are expressed by the bacterium in infected mouse stomachs. Virulence factors, vacA and cagA, were found in this screen and are known to play important roles in H. pylori infection, colonization and pathogenesis. Their detection validates the efficacy of these screening systems. Some of the identified ivi genes have already been implicated to play an important role in the pathogenesis of H. pylori and other bacterial pathogens such as Escherichia coli and Vibrio cholerae. Transcription profiles of all ivi genes were confirmed by real time PCR analysis of H. pylori RNA isolated from H. pylori infected RAW 264.7 macrophages. We compared the expression profile of H. pylori and RAW 264.7 coculture with that of H. pylori only. Some genes such as cagA, vacA, lpxC, murI, tlpC, trxB, sodB, tnpB, pgi, rbfA and infB showed a 2-20 fold upregulation. Statistically significant upregulation was obtained for all the above mentioned genes (P < 0.05). tlpC, cagA, vacA, sodB, rbfA, infB, tnpB, lpxC and murI were also significantly upregulated (P < 0.01). These data suggest a strong correlation between results obtained in vitro in the macrophage cell line and in the intact animal.
CONCLUSION: The positive identification of these genes demonstrates that our IVET systems are powerful tools for studying H. pylori gene expression in the host environment.
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Tamir-Ariel D, Rosenberg T, Navon N, Burdman S. A secreted lipolytic enzyme from Xanthomonas campestris pv. vesicatoria is expressed in planta and contributes to its virulence. MOLECULAR PLANT PATHOLOGY 2012; 13:556-67. [PMID: 22176521 PMCID: PMC6638646 DOI: 10.1111/j.1364-3703.2011.00771.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A recombinase-based in vivo expression technology (RIVET) approach with Xanthomonas campestris pv. vesicatoria (Xcv) revealed that lipA, annotated as putative secreted lipase, is expressed during the interaction between this pathogen and tomato. Here, the tnpR and uidA reporter genes were used to show that lipA is strongly induced in XVM2 minimal medium and during the early stages of tomato infection by Xcv. A mutant strain impaired in lipA was generated by insertional mutagenesis. This mutant grew in a similar manner to the wild-type in rich medium, but its growth was significantly compromised in a medium containing olive oil as a single carbon source. The lipolytic activity of the extracellular fraction of the lipA mutant was reduced significantly relative to that of the wild-type strain, thus confirming that lipA indeed encodes a functional secreted enzyme with lipolytic activity. A plasmid carrying a wild-type copy of lipA complemented the lipA mutant for extracellular lipolytic activity. Dip inoculation experiments with tomato lines Hawaii 7998 (H7998) and Micro Tom showed that the lipA mutant grew to a lesser extent than the wild-type in tomato leaves. Following leaf syringe infiltrations, the mutant strain induced disease symptoms that were less severe than those induced by the wild-type strain, supporting a significant role of lipA in the pathogenicity of Xcv.
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Affiliation(s)
- Dafna Tamir-Ariel
- Department of Plant Pathology and Microbiology and The Otto Warburg Minerva Center for Agricultural Biotechnology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel
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Selective Capture of Transcribed Sequences: A Promising Approach for Investigating Bacterium-Insect Interactions. INSECTS 2012; 3:295-306. [PMID: 26467961 PMCID: PMC4553629 DOI: 10.3390/insects3010295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/17/2012] [Accepted: 02/21/2012] [Indexed: 12/20/2022]
Abstract
Bacterial interactions with eukaryotic hosts are complex processes which vary from pathogenic to mutualistic. Identification of bacterial genes differentially expressed in the host, promises to unravel molecular mechanisms driving and maintaining such interactions. Several techniques have been developed in the past 20 years to investigate bacterial gene expression within their hosts. The most commonly used techniques include in-vivo expression technology, signature-tagged mutagenesis, differential fluorescence induction, and cDNA microarrays. However, the limitations of these techniques in analyzing bacterial in-vivo gene expression indicate the need to develop alternative tools. With many advantages over the other methods for analyzing bacterial in-vivo gene expression, selective capture of transcribed sequences (SCOTS) technique has the prospect of becoming an elegant tool for discovery of genes involved in the bacterium-host interaction. Here, we summarize the advances in SCOTS technique, including its current and potential applications in bacterial gene expression studies under a variety of conditions from in-vitro to in-vivo and from mammals to insects.
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An R, Grewal PS. Comparative study of differential gene expression in closely related bacterial species by comparative hybridization. Methods Mol Biol 2012; 815:103-119. [PMID: 22130987 DOI: 10.1007/978-1-61779-424-7_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The ability to profile bacterial gene expression has markedly advanced the capacity to understand the molecular mechanisms of pathogenesis, epidemiology, and therapeutics. This advance has been coupled with the development of techniques that enable investigators to identify bacterial specifically expressed genes and promise to open new avenues of functional genomics by allowing researchers to focus on the identified differentially expressed genes. During the past two decades, a number of approaches have been developed to investigate bacterial genes differentially expressed in response to the changing environment, particularly during interaction with their hosts. The most commonly used techniques include in vivo expression technology, signature-tagged mutagenesis, differential fluorescence induction, and cDNA microarrays, which fall into two broad classes: mutagenesis-based technologies and hybridization-based technologies. Selective capture of transcribed sequences, a recently emerging method, is a hybridization-based technique. This technique is powerful in analyzing differential gene expression of the bacteria, with the superb ability to investigate the bacterial species with unknown genomic information. Herein, we describe the application of this technique in a comparative study of the gene expression between two closely related bacteria induced or repressed under a variety of conditions.
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Affiliation(s)
- Ruisheng An
- Department of Entomology, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691, USA.
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Gomez JE, Clatworthy A, Hung DT. Probing bacterial pathogenesis with genetics, genomics, and chemical biology: past, present, and future approaches. Crit Rev Biochem Mol Biol 2011; 46:41-66. [PMID: 21250782 DOI: 10.3109/10409238.2010.538663] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Classical genetic approaches for studying bacterial pathogenesis have provided a solid foundation for our current understanding of microbial physiology and the interactions between pathogen and host. During the past decade however, advances in several arenas have expanded the ways in which the biology of pathogens can be studied. This review discussed the impact of these advances on bacterial genetics, including the application of genomics and chemical biology to the study of pathogenesis.
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Affiliation(s)
- James E Gomez
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Beatty KE. Chemical strategies for tagging and imaging the proteome. MOLECULAR BIOSYSTEMS 2011; 7:2360-7. [DOI: 10.1039/c1mb05040k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tamir-Ariel D, Rosenberg T, Burdman S. The Xanthomonas campestris pv. vesicatoria citH gene is expressed early in the infection process of tomato and is positively regulated by the TctDE two-component regulatory system. MOLECULAR PLANT PATHOLOGY 2011; 12:57-71. [PMID: 21118349 PMCID: PMC6640381 DOI: 10.1111/j.1364-3703.2010.00652.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Xanthomonas campestris pv. vesicatoria (Xcv) is the causal agent of bacterial spot disease of tomato and pepper. Previously, we have reported the adaptation of a recombinase- or resolvase-based in vivo expression technology (RIVET) approach to identify Xcv genes that are specifically induced during its interaction with tomato. Analysis of some of these genes revealed that a citH (citrate transporter) homologous gene contributes to Xcv virulence on tomato. Here, we demonstrate that the citH product indeed facilitates citrate uptake by showing the following: citH is specifically needed for Xcv growth in citrate, but not in other carbon sources; the citH promoter is specifically induced by citrate; and the concentration of citrate from tomato leaf apoplast is considerably reduced following growth of the wild-type and a citH-complemented strain, but not the citH mutant. We also show that, in the Xcv-tomato interaction, the promoter activity of the citH gene is induced as early as 2.5h after Xcv is syringe infiltrated into tomato leaves, and continues to be active for at least 96h after inoculation. We identified an operon containing a two-component regulatory system homologous to tctD/tctE influencing citH expression in Xcv, as well as its heterologous expression in Escherichia coli. The expression of hrp genes does not seem to be affected in the citH mutant, and this mutant cannot be complemented for growth in planta when co-inoculated with the wild-type strain, indicating that citrate uptake in the apoplast is important for the virulence of Xcv.
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Affiliation(s)
- Dafna Tamir-Ariel
- Department of Plant Pathology and Microbiology and The Otto Warburg Minerva Center for Agricultural Biotechnology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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In Vivo Studies of Clostridium perfringens in Mouse Gas Gangrene Model. Curr Microbiol 2010; 62:999-1008. [DOI: 10.1007/s00284-010-9821-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 11/05/2010] [Indexed: 10/18/2022]
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Hanin A, Sava I, Bao Y, Huebner J, Hartke A, Auffray Y, Sauvageot N. Screening of in vivo activated genes in Enterococcus faecalis during insect and mouse infections and growth in urine. PLoS One 2010; 5:e11879. [PMID: 20686694 PMCID: PMC2912369 DOI: 10.1371/journal.pone.0011879] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 07/05/2010] [Indexed: 12/15/2022] Open
Abstract
Enterococcus faecalis is part of the commensal microbiota of humans and its main habitat is the gastrointestinal tract. Although harmless in healthy individuals, E. faecalis has emerged as a major cause of nosocomial infections. In order to better understand the transformation of a harmless commensal into a life-threatening pathogen, we developed a Recombination-based In VivoExpression Technology for E. faecalis. Two R-IVET systems with different levels of sensitivity have been constructed in a E. faecalis V583 derivative strain and tested in the insect model Galleria mellonella, during growth in urine, in a mouse bacteremia and in a mouse peritonitis model. Our combined results led to the identification of 81 in vivo activated genes. Among them, the ef_3196/7 operon was shown to be strongly induced in the insect host model. Deletion of this operonic structure demonstrated that this two-component system was essential to the E. faecalis pathogenic potential in Galleria. Gene ef_0377, induced in insect and mammalian models, has also been further analyzed and it has been demonstrated that this ankyrin-encoding gene was also involved in E. faecalis virulence. Thus these R-IVET screenings led to the identification of new E. faecalis factors implied in in vivo persistence and pathogenic potential of this opportunistic pathogen.
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Affiliation(s)
- Aurelie Hanin
- Laboratoire de Microbiologie de l'Environnement, EA956 USC INRA2017, Université de Caen, Caen, France
| | - Irina Sava
- Division of Infection Diseases, Department of Medicine, University Medical Center, Freiburg, Germany
| | - YinYin Bao
- Division of Infection Diseases, Department of Medicine, University Medical Center, Freiburg, Germany
| | - Johannes Huebner
- Division of Infection Diseases, Department of Medicine, University Medical Center, Freiburg, Germany
| | - Axel Hartke
- Laboratoire de Microbiologie de l'Environnement, EA956 USC INRA2017, Université de Caen, Caen, France
| | - Yanick Auffray
- Laboratoire de Microbiologie de l'Environnement, EA956 USC INRA2017, Université de Caen, Caen, France
| | - Nicolas Sauvageot
- Laboratoire de Microbiologie de l'Environnement, EA956 USC INRA2017, Université de Caen, Caen, France
- * E-mail:
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Harro JM, Peters BM, O'May GA, Archer N, Kerns P, Prabhakara R, Shirtliff ME. Vaccine development in Staphylococcus aureus: taking the biofilm phenotype into consideration. ACTA ACUST UNITED AC 2010; 59:306-23. [PMID: 20602638 PMCID: PMC2936112 DOI: 10.1111/j.1574-695x.2010.00708.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Vaccine development against pathogenic bacteria is an imperative initiative as bacteria are gaining resistance to current antimicrobial therapies and few novel antibiotics are being developed. Candidate antigens for vaccine development can be identified by a multitude of high-throughput technologies that were accelerated by access to complete genomes. While considerable success has been achieved in vaccine development against bacterial pathogens, many species with multiple virulence factors and modes of infection have provided reasonable challenges in identifying protective antigens. In particular, vaccine candidates should be evaluated in the context of the complex disease properties, whether planktonic (e.g. sepsis and pneumonia) and/or biofilm associated (e.g. indwelling medical device infections). Because of the phenotypic differences between these modes of growth, those vaccine candidates chosen only for their efficacy in one disease state may fail against other infections. This review will summarize the history and types of bacterial vaccines and adjuvants as well as present an overview of modern antigen discovery and complications brought about by polymicrobial infections. Finally, we will also use one of the better studied microbial species that uses differential, multifactorial protein profiles to mediate an array of diseases, Staphylococcus aureus, to outline some of the more recently identified problematic issues in vaccine development in this biofilm-forming species.
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Affiliation(s)
- Janette M Harro
- Department of Microbial Pathogenesis, Dental School, University of Maryland, Baltimore, MD, USA
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Noel JT, Joy J, Smith JN, Fatica M, Schneider KR, Ahmer BMM, Teplitski M. Salmonella SdiA recognizes N-acyl homoserine lactone signals from Pectobacterium carotovorum in vitro, but not in a bacterial soft rot. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:273-282. [PMID: 20121449 DOI: 10.1094/mpmi-23-3-0273] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Genomes of Salmonella enterica isolates, including those linked to outbreaks of produce-associated gastroenteritis, contain sdiA, which encodes a receptor of N-acyl homoserine lactones (AHL). AHL are the quorum-sensing signals used by bacteria to coordinately regulate gene expression within -their populations. Because S. enterica does not produce its own AHL, SdiA is hypothesized to function in the interspecies cross-talk with AHL-producing bacteria. Under laboratory conditions, S. enterica responded to AHL from phytobacteria by upregulating expression of srgE. AHL-dependent expression of srgE required a functional sdiA. Essentially, no sdiA-dependent resolution of the srgE recombinase-based (RIVET) reporter was observed inside a soft rot formed on a tomato by an AHL-producing strain of Pectobacterium carotovorum. The results of the control experiments suggest that sdiA is not expressed inside tomato, pepper, green onion, or carrot affected by the soft rot, and the lack of sdiA expression in planta prevents Salmonella spp. from responding to AHL. Despite its inability to detect and respond to AHL during colonization of soft rots, S. enterica reached higher final cell numbers inside a tomato soft rot compared with its growth in intact tomato fruit. The synergistic effect was the strongest under the conditions that are typical for the Florida fall/winter production season.
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Affiliation(s)
- J T Noel
- Soil and Water Science Department, University of Florida-IFAS, Gainesville 32610 USA
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Hu Y, Cong Y, Li S, Rao X, Wang G, Hu F. Identification of in vivo induced protein antigens of Salmonella enterica serovar Typhi during human infection. ACTA ACUST UNITED AC 2009; 52:942-8. [PMID: 19911130 DOI: 10.1007/s11427-009-0127-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 07/21/2009] [Indexed: 11/29/2022]
Abstract
During infectious disease episodes, pathogens express distinct subsets of virulence factors which allow them to adapt to different environments. Hence, genes that are expressed or upregulated in vivo are implicated in pathogenesis. We used in vivo induced antigen technology (IVIAT) to identify antigens which are expressed during infection with Salmonella enterica serovar Typhi. We identified 7 in vivo induced (IVI) antigens, which included BcfD (a fimbrial structural subunit), GrxC (a glutaredoxin 3), SapB (an ABC-type transport system), T3663 (an ABC-type uncharacterized transport system), T3816 (a putative rhodanese-related sulfurtransferase), T1497 (a probable TonB-dependent receptor) and T3689 (unknown function). Of the 7 identified antigens, 5 antigens had no cross-immunoreactivity in adsorbed control sera from healthy subjects. These 5 included BcfD, GrxC, SapB, T3663 and T3689. Antigens identified in this study are potential targets for drug and vaccine development and may be utilized as diagnostic agents.
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Affiliation(s)
- Yong Hu
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
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Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium. J Comput Biol 2009; 16:169-80. [DOI: 10.1089/cmb.2008.04tt] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Beatty KE, Tirrell DA. Two-color labeling of temporally defined protein populations in mammalian cells. Bioorg Med Chem Lett 2008; 18:5995-9. [PMID: 18774715 PMCID: PMC3182832 DOI: 10.1016/j.bmcl.2008.08.046] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2008] [Revised: 08/11/2008] [Accepted: 08/12/2008] [Indexed: 10/21/2022]
Abstract
The proteome undergoes complex changes in response to disease, drug treatment, and normal cellular signaling processes. Characterization of such changes requires methods for time-resolved protein identification and imaging. Here, we describe the application of two reactive methionine (Met) analogues, azidohomoalanine (Aha) and homopropargylglycine (Hpg), to label two protein populations in fixed cells. Reactive lissamine rhodamine (LR), 7-dimethylaminocoumarin (DMAC), and bodipy-630 (BDPY) dyes were prepared and examined for use in selective dye-labeling of newly synthesized proteins in Rat-1 fibroblasts. The LR and DMAC, but not BDPY, fluorophores were found to enable selective, efficient labeling of subsets of the proteome; cells labeled with Aha and Hpg exhibited fluorescence emission three- to sevenfold more intense than that of control cells treated with Met. We also examined simultaneous and sequential pulse-labeling of cells with Aha and Hpg. After pulse-labeling, cells were treated with reactive LR and DMAC dyes, and labeled cells were imaged by fluorescence microscopy and analyzed by flow cytometry. The results of these studies demonstrate that amino acid labeling can be used to achieve selective two-color imaging of temporally defined protein populations in mammalian cells.
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Affiliation(s)
- Kimberly E. Beatty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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An in vivo gene deletion system for determining temporal requirement of bacterial virulence factors. Proc Natl Acad Sci U S A 2008; 105:9385-90. [PMID: 18599442 DOI: 10.1073/pnas.0801055105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Analysis of phenotypes associated with specific mutants has been instrumental in determining the roles of a bacterial gene in a biological process. However, this technique does not allow one to address whether a specific gene or gene set is necessary to maintain such a process once it has been established. In the study of microbial pathogenesis, it is important but difficult to determine the temporal requirement of essential pathogenic determinants in the entire infection cycle. Here we report a Cre/loxP-based genetic system that allowed inducible deletion of specific bacterial genes after the pathogen had been phagocytosed by host cells. Using this system, we have examined the temporal requirement of the Dot/Icm type IV protein transporter of Legionella pneumophila during infection. We found that deletion of single essential dot/icm genes did not prevent the internalized bacteria from completing one cycle of intracellular replication. Further analyses indicate that the observed phenotypes were due to the high stability of the examined Dot/Icm protein. However, postinfection deletion within 8 h of the gene coding for the Dot/Icm substrate, SdhA, abolishes intracellular bacterial growth. This result indicates that the Dot/Icm transporter is important for intracellular bacterial growth after the initial biogenesis of the vacuole. Our study has provided a technical concept for analyzing the temporal requirement of specific bacterial proteins or protein complexes in infection or development.
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High-throughput identification and validation of in situ-expressed genes of Lactococcus lactis. Appl Environ Microbiol 2008; 74:4727-36. [PMID: 18539793 DOI: 10.1128/aem.00297-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the functional response of bacteria to their natural environment is one of the current challenges in microbiology. Over the past decades several techniques have been developed to study gene expression in complex natural habitats. Most of these methods, however, are laborious, and validation of results under in situ conditions is cumbersome. Here we report the improvement of the recombinase-based in vivo expression technology (R-IVET) by the implementation of two additional reporter genes. The first one is an alpha-galactosidase gene (melA), which facilitates the rapid identification of in vivo-induced genes. Second, the bacterial luciferase genes (luxAB) are transcriptionally coupled to the resolvase gene, which allows rapid validation and characterization of in vivo-induced genes. The system is implemented and validated in the industrially important lactic acid bacterium Lactococcus lactis. We demonstrate the applicability of the advanced R-IVET system by the identification and validation of lactococcal promoter elements that are induced in minimal medium compared to the commonly used rich laboratory medium M17. R-IVET screening led to the identification of 19 promoters that predominantly control expression of genes involved in amino acid and nucleotide metabolism and in transport functions. Furthermore, the luciferase allows high-resolution transcription analysis and enabled the identification of complex medium constituents and specific molecules involved in promoter control. Rapid target validation exemplifies the high-throughput potential of the extended R-IVET system. The system can be applied to other bacterial species, provided that the reporter genes used are functional in the organism of interest.
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Kaushik DK, Sehgal D. Developing Antibacterial Vaccines in Genomics and Proteomics Era. Scand J Immunol 2008; 67:544-52. [DOI: 10.1111/j.1365-3083.2008.02107.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bron PA, Meijer M, Bongers RS, de Vos WM, Kleerebezem M. Dynamics of competitive population abundance of Lactobacillus plantarum ivi gene mutants in faecal samples after passage through the gastrointestinal tract of mice. J Appl Microbiol 2008; 103:1424-34. [PMID: 17953553 DOI: 10.1111/j.1365-2672.2007.03376.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AIM This study aims to evaluate the impact of mutation of previously identified in vivo-induced (ivi) genes on the persistence and survival of Lactobacillus plantarum WCFS1 in the gastrointestinal (GI) tract of mice. METHODS AND RESULTS Nine Lact. plantarum ivi gene replacement mutants were constructed, focussing on ivi genes that encode proteins with a predicted role in cell envelope functionality, stress response and regulation. The in vitro growth characteristics of the mutants appeared identical to those observed for the wild-type strain, which agrees with the recombination-based in vivo expression technology suggestion that these genes are not transcribed in the laboratory. Quantitative PCR experiments demonstrated differences in the relative population dynamics of the Lact. plantarum ivi mutants in faecal samples after passage through the GI tract of mice. CONCLUSIONS The in situ competition experiments revealed a 100- to 1000-fold reduction of the relative abundance of three of the ivi gene mutants, harbouring deletions of genes predicted to encode a copper transporter, an orphan IIC cellobiose PTS and a cell wall anchored extracellular protein. SIGNIFICANCE AND IMPACT OF THE STUDY These experiments clearly establish that the proteins encoded by these three genes play a key role in Lact. plantarum performance during passage of the GI tract.
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Affiliation(s)
- P A Bron
- Wageningen Centre for Food Sciences, Microbial Functionality and Safety Programme, Wageningen, The Netherlands
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Shalom G, Shaw JG, Thomas MS. In vivo expression technology identifies a type VI secretion system locus in Burkholderia pseudomallei that is induced upon invasion of macrophages. MICROBIOLOGY-SGM 2007; 153:2689-2699. [PMID: 17660433 DOI: 10.1099/mic.0.2007/006585-0] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Gram-negative proteobacterium Burkholderia pseudomallei can survive and multiply within a variety of eukaryotic cells, including macrophages. This property is believed to be important for its ability to cause the disease melioidosis in a wide range of animal species, including humans. To identify determinants that are important for the ability of B. pseudomallei to survive within macrophages, in vivo expression technology (IVET) was employed. Several putative macrophage-inducible genes were identified that are likely to contribute to the virulence of B. pseudomallei, including three genes (tssH-5, tssI-5 and tssM-5) located within the same type VI secretion system cluster (tss-5), mntH, encoding a natural resistance-associated macrophage protein (NRAMP)-like manganese ion transporter, and a haem acquisition gene, bhuT. The macrophage-inducibility of the tss-5 gene cluster was confirmed by reporter gene analysis. Construction of tssH-5 and bhuT null mutants indicated that expression of the tss-5 unit and the bhu operon were not required for intramacrophage survival. A further five tss units were identified within the B. pseudomallei genome that, together with tss-5, account for approximately 2.3 % of the total genome size. The presence of six type VI secretion systems in this organism is likely to be an important factor in making this bacterium such a versatile pathogen.
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Affiliation(s)
- Gil Shalom
- Unit of Infection and Immunity, School of Medicine and Biomedical Sciences, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - Jonathan G Shaw
- Unit of Infection and Immunity, School of Medicine and Biomedical Sciences, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
| | - Mark S Thomas
- Unit of Infection and Immunity, School of Medicine and Biomedical Sciences, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
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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: 4.1] [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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Yoo JY, Kim HC, Zhu W, Kim SM, Sabet M, Handfield M, Hillman J, Progulske-Fox A, Lee SW. Identification of Tannerella forsythia antigens specifically expressed in patients with periodontal disease. FEMS Microbiol Lett 2007; 275:344-52. [PMID: 17868359 DOI: 10.1111/j.1574-6968.2007.00906.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Molecular pathogenesis of Tannerella forsythia, a putative periodontal pathogen, has not yet been adequately elucidated due to limited information on its virulence factors. Here, identification of in vivo expressed antigens of T. forsythia is reported using in vivo-induced antigen technology (IVIAT). Among 13 000 recombinant clones screened, 16 positive clones were identified that reacted reproducibly with sera obtained from patients with periodontal disease. DNA sequences from 12 of these in vivo-induced genes were determined. IVIAT-identified protein antigens of T. forsythia include: BspA, a well-defined virulence factor of T. forsythia; enzymes involved in housekeeping functions (tRNA synthetases, glycine hydroxymethyltransferase, and glucoside glucohydrolase); enzymes implicated in tissue destruction (dipeptidyl peptidase IV); a DNA mismatch repair protein; and putative outer membrane proteins of unknown function. The in vivo gene expression of these IVIAT-identified antigens was confirmed by a quantitative real-time PCR analysis. This is, to the best of the authors' knowledge, the first report using IVIAT in T. forsythia. It is anticipated that detailed analysis of the in vivo-induced genes identified by IVIAT in this study will lead to a better understanding of the molecular mechanisms mediating periodontal infection by T. forsythia.
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Affiliation(s)
- Ji Yeon Yoo
- Division of Periodontics, College of Dental Medicine, Columbia University, NY, USA
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Hughes V, Smith S, Garcia-Sanchez A, Sales J, Stevenson K. Proteomic comparison of Mycobacterium avium subspecies paratuberculosis grown in vitro and isolated from clinical cases of ovine paratuberculosis. MICROBIOLOGY-SGM 2007; 153:196-205. [PMID: 17185548 DOI: 10.1099/mic.0.29129-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Paratuberculosis (Johne's disease) poses a significant economic problem to beef, dairy and sheep industries worldwide, and is caused by Mycobacterium avium subspecies paratuberculosis. In this study, 2D PAGE was used as a tool to investigate the virulent state of M. avium subsp. paratuberculosis, incorporating the technique of beating the organism with zirconium/silica beads to provide a comprehensive representation of its proteome. A direct comparison of the proteomes of M. avium subsp. paratuberculosis scraped from the terminal ileum of ovine paratuberculosis cases, and the identical strain grown in vitro, is presented. These analyses identified a set of 10 proteins whose expression is upregulated during natural infection: 1-pyrroline-5-carboxylate dehydrogenase (RocA), a putative acyl-CoA dehydrogenase (FadE14), 2-methylcitrate dehydratase (2-mcd), arginosuccinate synthase (ArgG), universal stress protein (usp), 30S ribosomal protein S2 (RpsB), peptidyl-prolyl cis-trans isomerase (PpiA), luciferase-like monooxygenase (lmo), thiosulfate sulfurtransferase (SseA) and ATP-dependent Clp protease (ClpB). Most of the proteins identified do not have obviously related functions; however, ArgG and RocA function in the same pathway, and may have a concerted action for energy production in vivo.
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Affiliation(s)
- Valerie Hughes
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK.
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Progress in the science of probiotics: from cellular microbiology and applied immunology to clinical nutrition. Eur J Nutr 2006. [DOI: 10.1007/s00394-006-1101-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Czelleng A, Bozso Z, Ott PG, Besenyei E, Varga GJ, Szatmari A, Kiraly L, Klement Z. Identification of virulence-associated genes of Pseudomonas viridiflava activated during infection by use of a novel IVET promoter probing plasmid. Curr Microbiol 2006; 52:282-6. [PMID: 16550466 DOI: 10.1007/s00284-005-0208-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Accepted: 09/20/2005] [Indexed: 10/24/2022]
Abstract
Analysis of virulence mechanisms of plant pathogens is often limited by the lack of genetic tools that can be used to identify genes that are preferentially expressed during their interactions with plants. In the present study, we used the newly constructed IVET (in vivo expression technique) plasmid pIviGK and the corresponding antibiotic resistance-based selection method to identify genes that encode pathogenicity factors of the soft rot-causing bacterium Pseudomonas viridiflava. These included pel, the gene encoding pectate lyase, which is responsible for the development of soft rot symptoms. We have also isolated and characterized the gene mviNpv encoding a putative novel membrane associated virulence factor of P. viridiflava. A mutation in mviNpv was shown to influence motility as well as virulence of P. viridiflava. The mviNpv gene is expressed to a moderate level in LB media and its expression increases under inducing conditions as was shown by measuring in planta expression dynamics of the fused gfp reporter gene.
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Affiliation(s)
- A Czelleng
- Plant Protection Institute, Hungarian Academy of Sciences, P.O. Box 102, 1525, Budapest, Hungary.
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Affiliation(s)
- Zhimin Feng
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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