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Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism. Infect Immun 2021; 89:IAI.00606-20. [PMID: 33361201 DOI: 10.1128/iai.00606-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/10/2020] [Indexed: 11/20/2022] Open
Abstract
The Enteritidis and Dublin serovars of Salmonella enterica are phylogenetically closely related yet differ significantly in host range and virulence. S Enteritidis is a broad-host-range serovar that commonly causes self-limited gastroenteritis in humans, whereas S Dublin is a cattle-adapted serovar that can infect humans, often resulting in invasive extraintestinal disease. The mechanism underlying the higher invasiveness of S Dublin remains undetermined. In this work, we quantitatively compared the proteomes of clinical isolates of each serovar grown under gut-mimicking conditions. Compared to S Enteritidis, the S Dublin proteome was enriched in proteins linked to response to several stress conditions, such as those encountered during host infection, as well as to virulence. The S Enteritidis proteome contained several proteins related to central anaerobic metabolism pathways that were undetected in S Dublin. In contrast to what has been observed in other extraintestinal serovars, most of the coding genes for these pathways are not degraded in S Dublin. Thus, we provide evidence that S Dublin metabolic functions may be much more affected than previously reported based on genomic studies. Single and double null mutants in stress response proteins Dps, YciF, and YgaU demonstrate their relevance to S Dublin invasiveness in a murine model of invasive salmonellosis. All in all, this work provides a basis for understanding interserovar differences in invasiveness and niche adaptation, underscoring the relevance of using proteomic approaches to complement genomic studies.
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Petersen E, Miller SI. The cellular microbiology of Salmonellae interactions with macrophages. Cell Microbiol 2019; 21:e13116. [PMID: 31509644 DOI: 10.1111/cmi.13116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/27/2022]
Abstract
Salmonellae are important enteric pathogens that cause gastroenteritis and systemic illnesses. Macrophages are important components of both the innate and acquired immune system, acting as phagocytes with significant antimicrobial killing activities that present antigen to the adaptive immune system. Macrophages can also be cultured from a variety of sites as primary cells, and the study of the survival and interactions of Salmonellae with these cells is a very early model of infection and cellular microbiology. This review traces the history of discoveries made using Salmonellae infection of macrophages and addresses the possibility of future research in this area, in particular with regards to understanding the complexity of individual bacteria and macrophage cell variability and how such heterogeneity may alter the outcome of infection.
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Affiliation(s)
- Erik Petersen
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Samuel I Miller
- Department of Microbiology, University of Washington, Seattle, WA, USA.,Department of Immunology, University of Washington, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
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Kröger C, Colgan A, Srikumar S, Händler K, Sivasankaran SK, Hammarlöf DL, Canals R, Grissom JE, Conway T, Hokamp K, Hinton JCD. An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. Cell Host Microbe 2014; 14:683-95. [PMID: 24331466 DOI: 10.1016/j.chom.2013.11.010] [Citation(s) in RCA: 344] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/13/2013] [Accepted: 11/21/2013] [Indexed: 11/15/2022]
Abstract
Bacterial transcriptional networks consist of hundreds of transcription factors and thousands of promoters. However, the true complexity of transcription in a bacterial pathogen and the effect of the environments encountered during infection remain to be established. We present a simplified approach for global promoter identification in bacteria using RNA-seq-based transcriptomic analyses of 22 distinct infection-relevant environmental conditions. Individual RNA samples were combined to identify most of the 3,838 Salmonella enterica serovar Typhimurium promoters in just two RNA-seq runs. Individual in vitro conditions stimulated characteristic transcriptional signatures, and the suite of 22 conditions induced transcription of 86% of all S. Typhimurium genes. We highlight the environmental conditions that induce the Salmonella pathogenicity islands and present a small RNA expression landscape of 280 sRNAs. This publicly available compendium of environmentally controlled expression of every transcriptional feature of S. Typhimurium constitutes a useful resource for the bacterial research community.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Aoife Colgan
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Shabarinath Srikumar
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Kristian Händler
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Sathesh K Sivasankaran
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Disa L Hammarlöf
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rocío Canals
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Joe E Grissom
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Tyrrell Conway
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Karsten Hokamp
- Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jay C D Hinton
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland; Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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Mastroeni P, Grant A. Dynamics of spread of Salmonella enterica in the systemic compartment. Microbes Infect 2013; 15:849-57. [PMID: 24183878 DOI: 10.1016/j.micinf.2013.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/09/2013] [Indexed: 12/21/2022]
Abstract
Traditional microbiological and immunological tools, combined with modern imaging, and molecular and mathematical approaches, have revealed the dispersive nature of Salmonella infections. Bacterial escape from infected cells, spread in the tissues and attempts to restrain this process by the host give rise to fascinating scenarios that underpin the pathogenesis of salmonelloses.
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Affiliation(s)
- Pietro Mastroeni
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom.
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Morales EH, Collao B, Desai PT, Calderón IL, Gil F, Luraschi R, Porwollik S, McClelland M, Saavedra CP. Probing the ArcA regulon under aerobic/ROS conditions in Salmonella enterica serovar Typhimurium. BMC Genomics 2013; 14:626. [PMID: 24044554 PMCID: PMC3848847 DOI: 10.1186/1471-2164-14-626] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 09/16/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Hydrogen peroxide (H₂O₂) is a reactive oxygen species (ROS), which is part of the oxidative burst encountered upon internalization of Salmonella enterica serovar Typhimurium (S. Typhimurium) by phagocytic cells. It has previously been established that, the ArcAB two-component system plays a critical role in ROS resistance, but the genes regulated by the system remained undetermined to date. We therefore investigated the ArcA regulon in aerobically growing S. Typhimurium before and after exposure to H₂O₂ by querying gene expression and other physiological changes in wild type and ΔarcA strains. RESULTS In the ΔarcA strain, expression of 292 genes showed direct or indirect regulation by ArcA in response to H₂O₂, of which 141were also regulated in aerobiosis, but in the opposite direction. Gene set enrichment analysis (GSEA) of the expression data from WT and ΔarcA strains, revealed that, in response to H₂O₂ challenge in aerobically grown cells, ArcA down regulated multiple PEP-PTS and ABC transporters, while up regulating genes involved in glutathione and glycerolipid metabolism and nucleotide transport. Further biochemical analysis guided by GSEA results showed that deletion of arcA during aerobic growth lead to increased reactive oxygen species (ROS) production which was concomitant with an increased NADH/NAD+ ratio. In absence of ArcA under aerobic conditions, H₂O₂ exposure resulted in lower levels of glutathione reductase activity, leading to a decreased GSH (reduced glutathione)/GSSG (oxidized glutathione) ratio. CONCLUSION The ArcA regulon was defined in 2 conditions, aerobic growth and the combination of peroxide treatment and aerobic growth in S. Typhimurium. ArcA coordinates a response that involves multiple aspects of the carbon flux through central metabolism, which ultimately modulates the reducing potential of the cell.
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Affiliation(s)
- Eduardo H Morales
- Laboratorio de Microbiología Molecular, Facultad Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.
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Hammarlöf DL, Canals R, Hinton JCD. The FUN of identifying gene function in bacterial pathogens; insights from Salmonella functional genomics. Curr Opin Microbiol 2013; 16:643-51. [PMID: 24021902 DOI: 10.1016/j.mib.2013.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/12/2013] [Indexed: 02/01/2023]
Abstract
The availability of thousands of genome sequences of bacterial pathogens poses a particular challenge because each genome contains hundreds of genes of unknown function (FUN). How can we easily discover which FUN genes encode important virulence factors? One solution is to combine two different functional genomic approaches. First, transcriptomics identifies bacterial FUN genes that show differential expression during the process of mammalian infection. Second, global mutagenesis identifies individual FUN genes that the pathogen requires to cause disease. The intersection of these datasets can reveal a small set of candidate genes most likely to encode novel virulence attributes. We demonstrate this approach with the Salmonella infection model, and propose that a similar strategy could be used for other bacterial pathogens.
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Affiliation(s)
- Disa L Hammarlöf
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
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Frederiksen RF, Paspaliari DK, Larsen T, Storgaard BG, Larsen MH, Ingmer H, Palcic MM, Leisner JJ. Bacterial chitinases and chitin-binding proteins as virulence factors. MICROBIOLOGY (READING, ENGLAND) 2013; 159:833-847. [PMID: 23519157 DOI: 10.1099/mic.0.051839-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacterial chitinases (EC 3.2.1.14) and chitin-binding proteins (CBPs) play a fundamental role in the degradation of the ubiquitous biopolymer chitin, and the degradation products serve as an important nutrient source for marine- and soil-dwelling bacteria. However, it has recently become clear that representatives of both Gram-positive and Gram-negative bacterial pathogens encode chitinases and CBPs that support infection of non-chitinous mammalian hosts. This review addresses this biological role of bacterial chitinases and CBPs in terms of substrate specificities, regulation, secretion and involvement in cellular and animal infection.
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Affiliation(s)
- Rikki F Frederiksen
- Department of Veterinary Disease Biology, Faculty of Health Sciences, University of Copenhagen, Grønnegaardsvej 15, 1870 Frederiksberg C., Denmark
| | - Dafni K Paspaliari
- Department of Veterinary Disease Biology, Faculty of Health Sciences, University of Copenhagen, Grønnegaardsvej 15, 1870 Frederiksberg C., Denmark
| | - Tanja Larsen
- Department of Veterinary Disease Biology, Faculty of Health Sciences, University of Copenhagen, Grønnegaardsvej 15, 1870 Frederiksberg C., Denmark
| | - Birgit G Storgaard
- Carlsberg Laboratory, Gamle Carlsbergvej 10, 1799 Copenhagen V., Denmark
- Department of Veterinary Disease Biology, Faculty of Health Sciences, University of Copenhagen, Grønnegaardsvej 15, 1870 Frederiksberg C., Denmark
| | - Marianne H Larsen
- Department of Veterinary Disease Biology, Faculty of Health Sciences, University of Copenhagen, Grønnegaardsvej 15, 1870 Frederiksberg C., Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health Sciences, University of Copenhagen, Grønnegaardsvej 15, 1870 Frederiksberg C., Denmark
| | - Monica M Palcic
- Carlsberg Laboratory, Gamle Carlsbergvej 10, 1799 Copenhagen V., Denmark
| | - Jørgen J Leisner
- Department of Veterinary Disease Biology, Faculty of Health Sciences, University of Copenhagen, Grønnegaardsvej 15, 1870 Frederiksberg C., Denmark
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Lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation. J Bacteriol 2011; 194:686-701. [PMID: 22139505 DOI: 10.1128/jb.06112-11] [Citation(s) in RCA: 327] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lag phase represents the earliest and most poorly understood stage of the bacterial growth cycle. We developed a reproducible experimental system and conducted functional genomic and physiological analyses of a 2-h lag phase in Salmonella enterica serovar Typhimurium. Adaptation began within 4 min of inoculation into fresh LB medium with the transient expression of genes involved in phosphate uptake. The main lag-phase transcriptional program initiated at 20 min with the upregulation of 945 genes encoding processes such as transcription, translation, iron-sulfur protein assembly, nucleotide metabolism, LPS biosynthesis, and aerobic respiration. ChIP-chip revealed that RNA polymerase was not "poised" upstream of the bacterial genes that are rapidly induced at the beginning of lag phase, suggesting a mechanism that involves de novo partitioning of RNA polymerase to transcribe 522 bacterial genes within 4 min of leaving stationary phase. We used inductively coupled plasma mass spectrometry (ICP-MS) to discover that iron, calcium, and manganese are accumulated by S. Typhimurium during lag phase, while levels of cobalt, nickel, and sodium showed distinct growth-phase-specific patterns. The high concentration of iron during lag phase was associated with transient sensitivity to oxidative stress. The study of lag phase promises to identify the physiological and regulatory processes responsible for adaptation to new environments.
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Hébrard M, Kröger C, Sivasankaran SK, Händler K, Hinton JCD. The challenge of relating gene expression to the virulence of Salmonella enterica serovar Typhimurium. Curr Opin Biotechnol 2011; 22:200-10. [PMID: 21388802 DOI: 10.1016/j.copbio.2011.02.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 02/04/2011] [Accepted: 02/10/2011] [Indexed: 12/15/2022]
Abstract
The first decade of transcriptomic studies of Salmonella enterica serovar Typhimurium focused upon gene expression in vitro, and during the infection of mammalian cells. The published regulons and stimulons show that the three Type Three Secretion Systems of S. Typhimurium respond to a diverse range of environmental conditions, and are controlled by a hierarchy of regulatory proteins. The integration of in vitro generated transcriptomic data with global gene expression of S. Typhimurium during infection is beginning to yield valuable information. The coordinated regulation of Salmonella gene expression is a key process for survival, adaptation and virulence capacities of the pathogen.
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Affiliation(s)
- Magali Hébrard
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics & Microbiology, Trinity College, Dublin 2, Ireland
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Amano F. SEp22, Salmonella Dps, a Key Molecule Bearing Both Pathogenicity and Resistance to Environmental Stresses in Salmonella. ACTA ACUST UNITED AC 2011. [DOI: 10.1248/jhs.57.458] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Fumio Amano
- Laboratory of Biodefense & Regulation, Osaka University of Pharmaceutical Sciences
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Liu L, Agren R, Bordel S, Nielsen J. Use of genome-scale metabolic models for understanding microbial physiology. FEBS Lett 2010; 584:2556-64. [PMID: 20420838 DOI: 10.1016/j.febslet.2010.04.052] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 04/18/2010] [Accepted: 04/20/2010] [Indexed: 11/17/2022]
Abstract
The exploitation of microorganisms in industrial, medical, food and environmental biotechnology requires a comprehensive understanding of their physiology. The availability of genome sequences and accumulation of high-throughput data allows gaining understanding of microbial physiology at the systems level, and genome-scale metabolic models represent a valuable framework for integrative analysis of metabolism of microorganisms. Genome-scale metabolic models are reconstructed based on a combination of genome sequence information and detailed biochemical information, and these reconstructed models can be used for analyzing and simulating the operation of metabolism in response to different stimuli. Here we discuss the requirement for having detailed physiological insight in order to exploit microorganisms for production of fuels, chemicals and pharmaceuticals. We further describe the reconstruction process of genome-scale metabolic models and different algorithms that can be used to apply these models to gain improved insight into microbial physiology.
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Affiliation(s)
- Liming Liu
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Hamilton S, Bongaerts RJM, Mulholland F, Cochrane B, Porter J, Lucchini S, Lappin-Scott HM, Hinton JCD. The transcriptional programme of Salmonella enterica serovar Typhimurium reveals a key role for tryptophan metabolism in biofilms. BMC Genomics 2009; 10:599. [PMID: 20003355 PMCID: PMC2805695 DOI: 10.1186/1471-2164-10-599] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 12/11/2009] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Biofilm formation enhances the capacity of pathogenic Salmonella bacteria to survive stresses that are commonly encountered within food processing and during host infection. The persistence of Salmonella within the food chain has become a major health concern, as biofilms can serve as a reservoir for the contamination of food products. While the molecular mechanisms required for the survival of bacteria on surfaces are not fully understood, transcriptional studies of other bacteria have demonstrated that biofilm growth triggers the expression of specific sets of genes, compared with planktonic cells. Until now, most gene expression studies of Salmonella have focused on the effect of infection-relevant stressors on virulence or the comparison of mutant and wild-type bacteria. However little is known about the physiological responses taking place inside a Salmonella biofilm. RESULTS We have determined the transcriptomic and proteomic profiles of biofilms of Salmonella enterica serovar Typhimurium. We discovered that 124 detectable proteins were differentially expressed in the biofilm compared with planktonic cells, and that 10% of the S. Typhimurium genome (433 genes) showed a 2-fold or more change in the biofilm compared with planktonic cells. The genes that were significantly up-regulated implicated certain cellular processes in biofilm development including amino acid metabolism, cell motility, global regulation and tolerance to stress. We found that the most highly down-regulated genes in the biofilm were located on Salmonella Pathogenicity Island 2 (SPI2), and that a functional SPI2 secretion system regulator (ssrA) was required for S. Typhimurium biofilm formation. We identified STM0341 as a gene of unknown function that was needed for biofilm growth. Genes involved in tryptophan (trp) biosynthesis and transport were up-regulated in the biofilm. Deletion of trpE led to decreased bacterial attachment and this biofilm defect was restored by exogenous tryptophan or indole. CONCLUSIONS Biofilm growth of S. Typhimurium causes distinct changes in gene and protein expression. Our results show that aromatic amino acids make an important contribution to biofilm formation and reveal a link between SPI2 expression and surface-associated growth in S. Typhimurium.
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Affiliation(s)
- Shea Hamilton
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
- Department of Biological Sciences, University of Exeter, Exeter, EX4 4PS, UK
- Shea Hamilton, Faculty of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK; Brett Cochrane, Unilever SEAC, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Roy JM Bongaerts
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Francis Mulholland
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | - Brett Cochrane
- School of Biological Sciences, University of Southampton, Southampton, SO16 7PX, UK
- Shea Hamilton, Faculty of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK; Brett Cochrane, Unilever SEAC, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Jonathan Porter
- National Laboratory Service, Starcross Laboratory, Staplake Mount, Starcross, EX6 8PE, UK
| | - Sacha Lucchini
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
| | | | - Jay CD Hinton
- Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
- Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin 2, Ireland
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In Brief. Nat Rev Microbiol 2009. [DOI: 10.1038/nrmicro2230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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