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Felipe-López A, Hansmeier N, Hensel M. Destruction of the brush border by Salmonella enterica sv. Typhimurium subverts resorption by polarized epithelial cells. Front Microbiol 2024; 15:1329798. [PMID: 38894970 PMCID: PMC11183102 DOI: 10.3389/fmicb.2024.1329798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 05/06/2024] [Indexed: 06/21/2024] Open
Abstract
Salmonella enterica serovar Typhimurium is an invasive, facultative intracellular gastrointestinal pathogen that destroys the brush border of polarized epithelial cells (PEC). The brush border is critical for the functions of PEC because it resorbs nutrients from the intestinal lumen and builds a physical barrier to infecting pathogens. The manipuation of PEC during infection by Salmonella was investigated by live-cell imaging and ultrastructural analysed of the brush border. We demonstrate that the destruction of the brush border by Salmonella significantly reduces the resorption surface of PEC along with the abrogation of endocytosis at the apical side of PEC. Both these changes in the physiology of PEC were associated with the translocation of type III secretion system effector protein SopE. Additionally, the F-actin polymerization rate at the apical side of PEC was highly altered by SopE, indicating that reduced endocytosis observed in infected PEC is related to the manipulation of F-actin polymerization mediated by SopE and, to a lesser extent, by effectors SopE2 or SipA. We further observed that in the absence of SopE, Salmonella effaced microvilli and induced reticular F-actin by bacterial accumulation during prolonged infection periods. In contrast to strains translocating SopE, strains lacking SopE did not alter resorption by PEC. Finally, we observed that after engulfment of Salmonella, ezrin was lost from the apical side of PEC and found later in early endosomes containing Salmonella. Our observations suggest that the destruction of the brush border by Salmonella may contribute to the pathogenesis of diarrhea.
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Affiliation(s)
| | | | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- CellNanOs—Center of Cellular Nanoanalytics Osnabrück, Universität Osnabrück, Osnabrück, Germany
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2
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Li D, Liang W, Huang Z, Ma W, Liu Q. The spontaneously produced lysogenic prophage phi456 promotes bacterial resistance to adverse environments and enhances the colonization ability of avian pathogenic Escherichia coli strain DE456. Vet Res 2024; 55:37. [PMID: 38532498 DOI: 10.1186/s13567-024-01292-z] [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: 01/18/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
In the last decade, prophages that possess the ability of lysogenic transformation have become increasingly significant. Their transfer and subsequent activity in the host have a significant impact on the evolution of bacteria. Here, we investigate the role of prophage phi456 with high spontaneous induction in the bacterial genome of Avian pathogenic Escherichia coli (APEC) DE456. The phage particles, phi456, that were released from DE456 were isolated, purified, and sequenced. Additionally, phage particles were no longer observed either during normal growth or induced by nalidixic acid in DE456Δphi456. This indicated that the released phage particles from DE456 were only phi456. We demonstrated that phi456 contributed to biofilm formation through spontaneous induction of the accompanying increase in the eDNA content. The survival ability of DE456Δphi456 was decreased in avian macrophage HD11 under oxidative stress and acidic conditions. This is likely due to a decrease in the transcription levels of three crucial genes-rpoS, katE, and oxyR-which are needed to help the bacteria adapt to and survive in adverse environments. It has been observed through animal experiments that the presence of phi456 in the DE456 genome enhances colonization ability in vivo. Additionally, the number of type I fimbriae in DE456Δphi456 was observed to be reduced under transmission electron microscopy when compared to the wild-type strain. The qRT-PCR results indicated that the expression levels of the subunit of I fimbriae (fimA) and its apical adhesin (fimH) were significantly lower in DE456Δphi456. Therefore, it can be concluded that phi456 plays a crucial role in helping bacterial hosts survive in unfavorable conditions and enhancing the colonization ability in DE456.
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Affiliation(s)
- Dezhi Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wei Liang
- The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Zhiqiang Huang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wenwen Ma
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qing Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China.
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3
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Gül E, Huuskonen J, Abi Younes A, Maurer L, Enz U, Zimmermann J, Sellin ME, Bakkeren E, Hardt WD. Salmonella T3SS-2 virulence enhances gut-luminal colonization by enabling chemotaxis-dependent exploitation of intestinal inflammation. Cell Rep 2024; 43:113925. [PMID: 38460128 DOI: 10.1016/j.celrep.2024.113925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/12/2024] [Accepted: 02/20/2024] [Indexed: 03/11/2024] Open
Abstract
Salmonella Typhimurium (S.Tm) utilizes the chemotaxis receptor Tsr to exploit gut inflammation. However, the characteristics of this exploitation and the mechanism(s) employed by the pathogen to circumvent antimicrobial effects of inflammation are poorly defined. Here, using different naturally occurring S.Tm strains (SL1344 and 14028) and competitive infection experiments, we demonstrate that type-three secretion system (T3SS)-2 virulence is indispensable for the beneficial effects of Tsr-directed chemotaxis. The removal of the 14028-specific prophage Gifsy3, encoding virulence effectors, results in the loss of the Tsr-mediated fitness advantage in that strain. Surprisingly, without T3SS-2 effector secretion, chemotaxis toward the gut epithelium using Tsr becomes disadvantageous for either strain. Our findings reveal that luminal neutrophils recruited as a result of NLRC4 inflammasome activation locally counteract S.Tm cells exploiting the byproducts of the host immune response. This work highlights a mechanism by which S.Tm exploitation of gut inflammation for colonization relies on the coordinated effects of chemotaxis and T3SS activities.
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Affiliation(s)
- Ersin Gül
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Jemina Huuskonen
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Andrew Abi Younes
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Luca Maurer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ursina Enz
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jakob Zimmermann
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Mikael E Sellin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala, Sweden
| | - Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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4
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Gaviria-Cantin T, Fernández-Coll L, Vargas AF, Jiménez CJ, Madrid C, Balsalobre C. Expression of accessory genes in Salmonella requires the presence of the Gre factors. Genomics 2024; 116:110777. [PMID: 38163572 DOI: 10.1016/j.ygeno.2023.110777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Genomic studies with Salmonella enterica serovar Typhimurium reveal a crucial role of horizontal gene transfer (HGT) in the acquisition of accessory cellular functions involved in host-interaction. Many virulence genes are located in genomic islands, plasmids and prophages. GreA and GreB proteins, Gre factors, interact transiently with the RNA polymerase alleviating backtracked complexes during transcription elongation. The overall effect of Gre factors depletion in Salmonella expression profile was studied. Both proteins are functionally redundant since only when both Gre factors were depleted a major effect in gene expression was detected. Remarkably, the accessory gene pool is particularly sensitive to the lack of Gre factors, with 18.6% of accessory genes stimulated by the Gre factors versus 4.4% of core genome genes. Gre factors involvement is particularly relevant for the expression of genes located in genomic islands. Our data reveal that Gre factors are required for the expression of accessory genes.
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Affiliation(s)
- Tania Gaviria-Cantin
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Llorenç Fernández-Coll
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Andrés Felipe Vargas
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Carlos Jonay Jiménez
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Cristina Madrid
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain
| | - Carlos Balsalobre
- Department of Genetics, Microbiology and Statistics, School of Biology, Universitat de Barcelona, Avda. Diagonal 643, Barcelona 08028, Spain.
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5
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Gabana ADA, Núncio ASP, Lopes BC, de Oliveira JA, da Silva Monteiro L, de Menezes Coppola M, Furian TQ, Borges KA, Rodrigues LB, Mayer FQ. Different Multidrug-Resistant Salmonella spp. Serovars Isolated from Slaughter Calves in Southern Brazil. Curr Microbiol 2022; 80:11. [PMID: 36459239 DOI: 10.1007/s00284-022-03136-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
Bovines are carriers of Salmonella spp., a relevant foodborne pathogen, acting as contamination sources in slaughterhouses. Calves are prone to infection, and antimicrobial resistance may occur in such bacteria. This study aimed to determine the prevalence and virulence determinants of Salmonella spp. recovered from calves in the Rio Grande do Sul state, Brazil. Eighty-five calves' carcasses were evaluated (leather and veal meat). Thirteen Salmonella spp. isolates (8%) from 11 animals (13%) were obtained only from leather, indicating that contamination occurred before slaughter and that the meat was safe regarding this aspect. The serotypes S. Minnesota, S. Abony, S. Cerro, and S. Gafsa were identified, and all isolates were multidrug-resistant. The isolates had at least 19 virulence-related genes, and the blaOXA-48 resistance gene was detected in three (23%). The data suggest that treating infections caused by these bacteria may be difficult in animals from these farms and can also be an extended human health problem.
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Affiliation(s)
- Alex Dall Agnol Gabana
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Adriana Souto Pereira Núncio
- Faculdade de Agronomia e Medicina Veterinária, Programa de Pós-Graduação em Bioexperimentação, Universidade de Passo Fundo, BR 285, Campus I, São José, Passo Fundo, RS, 99052-900, Brazil
| | - Bruna Correa Lopes
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Júlia Alves de Oliveira
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Luana da Silva Monteiro
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Mario de Menezes Coppola
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Thales Quedi Furian
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9090, Agronomia, Porto Alegre, RS, 91540-000, Brazil
| | - Karen Apellanis Borges
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9090, Agronomia, Porto Alegre, RS, 91540-000, Brazil
| | - Laura Beatriz Rodrigues
- Faculdade de Agronomia e Medicina Veterinária, Programa de Pós-Graduação em Bioexperimentação, Universidade de Passo Fundo, BR 285, Campus I, São José, Passo Fundo, RS, 99052-900, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil. .,Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500 - Agronomia, Porto Alegre, RS, 91501-970, Brazil.
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6
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Demeter A, Jacomin AC, Gul L, Lister A, Lipscombe J, Invernizzi R, Branchu P, Macaulay I, Nezis IP, Kingsley RA, Korcsmaros T, Hautefort I. Computational prediction and experimental validation of Salmonella Typhimurium SopE-mediated fine-tuning of autophagy in intestinal epithelial cells. Front Cell Infect Microbiol 2022; 12:834895. [PMID: 36061866 PMCID: PMC9428466 DOI: 10.3389/fcimb.2022.834895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Macroautophagy is a ubiquitous homeostasis and health-promoting recycling process of eukaryotic cells, targeting misfolded proteins, damaged organelles and intracellular infectious agents. Some intracellular pathogens such as Salmonella enterica serovar Typhimurium hijack this process during pathogenesis. Here we investigate potential protein-protein interactions between host transcription factors and secreted effector proteins of Salmonella and their effect on host gene transcription. A systems-level analysis identified Salmonella effector proteins that had the potential to affect core autophagy gene regulation. The effect of a SPI-1 effector protein, SopE, that was predicted to interact with regulatory proteins of the autophagy process, was investigated to validate our approach. We then confirmed experimentally that SopE can directly bind to SP1, a host transcription factor, which modulates the expression of the autophagy gene MAP1LC3B. We also revealed that SopE might have a double role in the modulation of autophagy: Following initial increase of MAP1LC3B transcription triggered by Salmonella infection, subsequent decrease in MAP1LC3B transcription at 6h post-infection was SopE-dependent. SopE also played a role in modulation of the autophagy flux machinery, in particular MAP1LC3B and p62 autophagy proteins, depending on the level of autophagy already taking place. Upon typical infection of epithelial cells, the autophagic flux is increased. However, when autophagy was chemically induced prior to infection, SopE dampened the autophagic flux. The same was also observed when most of the intracellular Salmonella cells were not associated with the SCV (strain lacking sifA) regardless of the autophagy induction status before infection. We demonstrated how regulatory network analysis can be used to better characterise the impact of pathogenic effector proteins, in this case, Salmonella. This study complements previous work in which we had demonstrated that specific pathogen effectors can affect the autophagy process through direct interaction with autophagy proteins. Here we show that effector proteins can also influence the upstream regulation of the process. Such interdisciplinary studies can increase our understanding of the infection process and point out targets important in intestinal epithelial cell defense.
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Affiliation(s)
- Amanda Demeter
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | | | - Lejla Gul
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ashleigh Lister
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - James Lipscombe
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Rachele Invernizzi
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Priscilla Branchu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Iain Macaulay
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- *Correspondence: Tamas Korcsmaros,
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7
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Chen Q, Dharmaraj T, Cai PC, Burgener EB, Haddock NL, Spakowitz AJ, Bollyky PL. Bacteriophage and Bacterial Susceptibility, Resistance, and Tolerance to Antibiotics. Pharmaceutics 2022; 14:1425. [PMID: 35890320 PMCID: PMC9318951 DOI: 10.3390/pharmaceutics14071425] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages, viruses that infect and replicate within bacteria, impact bacterial responses to antibiotics in complex ways. Recent studies using lytic bacteriophages to treat bacterial infections (phage therapy) demonstrate that phages can promote susceptibility to chemical antibiotics and that phage/antibiotic synergy is possible. However, both lytic and lysogenic bacteriophages can contribute to antimicrobial resistance. In particular, some phages mediate the horizontal transfer of antibiotic resistance genes between bacteria via transduction and other mechanisms. In addition, chronic infection filamentous phages can promote antimicrobial tolerance, the ability of bacteria to persist in the face of antibiotics. In particular, filamentous phages serve as structural elements in bacterial biofilms and prevent the penetration of antibiotics. Over time, these contributions to antibiotic tolerance favor the selection of resistance clones. Here, we review recent insights into bacteriophage contributions to antibiotic susceptibility, resistance, and tolerance. We discuss the mechanisms involved in these effects and address their impact on bacterial fitness.
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Affiliation(s)
- Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Tejas Dharmaraj
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Pamela C. Cai
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA;
| | - Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; (E.B.B.); (A.J.S.)
| | - Naomi L. Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Andy J. Spakowitz
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; (E.B.B.); (A.J.S.)
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
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8
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Cornuault JK, Moineau S. Induction and Elimination of Prophages Using CRISPR Interference. CRISPR J 2021; 4:549-557. [PMID: 34406037 DOI: 10.1089/crispr.2021.0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Prophages are widely spread among bacterial genomes, and they can have positive or negative effects on their hosts. A key aspect in the study of prophages is the discovery of their induction signals. Prophage induction can occur by inactivating a phage transcriptional repressor, which is responsible for maintaining the lysogenic state. This repressor can be inactivated through the bacterial SOS response. However, the induction signals for numerous prophages do not involve the SOS system, and therefore significant efforts are needed to identify these conditions. Similarly, curing bacterial strains of inducible prophages is a tedious process, requiring the screening of several colonies. Here, we investigated whether transcriptional silencing of a prophage repressor using CRISPR interference (CRISPRi) would lead to prophage induction. Using Escherichia coli phages λ and P2 as models, we demonstrated the efficiency of CRISPRi for prophage induction and for curing lysogenic strains of their prophages.
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Affiliation(s)
- Jeffrey K Cornuault
- Département de Biochimie, de Mmicrobiologie, et de Bio-informatique, Faculté des sciences et de Génie, Université Laval, Québec City, Canada; Université Laval, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, Canada; and Université Laval, Québec City, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Mmicrobiologie, et de Bio-informatique, Faculté des sciences et de Génie, Université Laval, Québec City, Canada; Université Laval, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, Canada; and Université Laval, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada
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9
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Schroven K, Aertsen A, Lavigne R. Bacteriophages as drivers of bacterial virulence and their potential for biotechnological exploitation. FEMS Microbiol Rev 2021; 45:5902850. [PMID: 32897318 DOI: 10.1093/femsre/fuaa041] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteria-infecting viruses (phages) and their hosts maintain an ancient and complex relationship. Bacterial predation by lytic phages drives an ongoing phage-host arms race, whereas temperate phages initiate mutualistic relationships with their hosts upon lysogenization as prophages. In human pathogens, these prophages impact bacterial virulence in distinct ways: by secretion of phage-encoded toxins, modulation of the bacterial envelope, mediation of bacterial infectivity and the control of bacterial cell regulation. This review builds the argument that virulence-influencing prophages hold extensive, unexplored potential for biotechnology. More specifically, it highlights the development potential of novel therapies against infectious diseases, to address the current antibiotic resistance crisis. First, designer bacteriophages may serve to deliver genes encoding cargo proteins which repress bacterial virulence. Secondly, one may develop small molecules mimicking phage-derived proteins targeting central regulators of bacterial virulence. Thirdly, bacteria equipped with phage-derived synthetic circuits which modulate key virulence factors could serve as vaccine candidates to prevent bacterial infections. The development and exploitation of such antibacterial strategies will depend on the discovery of other prophage-derived, virulence control mechanisms and, more generally, on the dissection of the mutualistic relationship between temperate phages and bacteria, as well as on continuing developments in the synthetic biology field.
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Affiliation(s)
- Kaat Schroven
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Kasteelpark Arenberg 23, 3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
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10
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Koeppel MB, Glaser J, Baumgartner T, Spriewald S, Gerlach RG, von Armansperg B, Leong JM, Stecher B. Scalable Reporter Assays to Analyze the Regulation of stx2 Expression in Shiga Toxin-Producing Enteropathogens. Toxins (Basel) 2021; 13:toxins13080534. [PMID: 34437405 PMCID: PMC8402550 DOI: 10.3390/toxins13080534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022] Open
Abstract
Stx2 is the major virulence factor of EHEC and is associated with an increased risk for HUS in infected patients. The conditions influencing its expression in the intestinal tract are largely unknown. For optimal management and treatment of infected patients, the identification of environmental conditions modulating Stx2 levels in the human gut is of central importance. In this study, we established a set of chromosomal stx2 reporter assays. One system is based on superfolder GFP (sfGFP) using a T7 polymerase/T7 promoter-based amplification loop. This reporter can be used to analyze stx2 expression at the single-cell level using FACSs and fluorescence microscopy. The other system is based on the cytosolic release of the Gaussia princeps luciferase (gluc). This latter reporter proves to be a highly sensitive and scalable reporter assay that can be used to quantify reporter protein in the culture supernatant. We envision that this new set of reporter tools will be highly useful to comprehensively analyze the influence of environmental and host factors, including drugs, small metabolites and the microbiota, on Stx2 release and thereby serve the identification of risk factors and new therapies in Stx-mediated pathologies.
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Affiliation(s)
- Martin B. Koeppel
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; (J.G.); (T.B.); (S.S.); (B.v.A.)
- German Center for Infection Research (DZIF), Partner Site LMU Munich, 80336 Munich, Germany
- Correspondence: (M.B.K.); (B.S.)
| | - Jana Glaser
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; (J.G.); (T.B.); (S.S.); (B.v.A.)
- German Center for Infection Research (DZIF), Partner Site LMU Munich, 80336 Munich, Germany
| | - Tobias Baumgartner
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; (J.G.); (T.B.); (S.S.); (B.v.A.)
- German Center for Infection Research (DZIF), Partner Site LMU Munich, 80336 Munich, Germany
| | - Stefanie Spriewald
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; (J.G.); (T.B.); (S.S.); (B.v.A.)
- German Center for Infection Research (DZIF), Partner Site LMU Munich, 80336 Munich, Germany
| | - Roman G. Gerlach
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Wasserturmstraße 3/5, 91054 Erlangen, Germany;
| | - Benedikt von Armansperg
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; (J.G.); (T.B.); (S.S.); (B.v.A.)
- German Center for Infection Research (DZIF), Partner Site LMU Munich, 80336 Munich, Germany
| | - John M. Leong
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA;
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany; (J.G.); (T.B.); (S.S.); (B.v.A.)
- German Center for Infection Research (DZIF), Partner Site LMU Munich, 80336 Munich, Germany
- Correspondence: (M.B.K.); (B.S.)
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11
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Hussain S, Ouyang P, Zhu Y, Khalique A, He C, Liang X, Shu G, Yin L. Type 3 secretion system 1 of Salmonella typhimurium and its inhibitors: a novel strategy to combat salmonellosis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:34154-34166. [PMID: 33966165 DOI: 10.1007/s11356-021-13986-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
Unsuccessful vaccination against Salmonella due to a large number of serovars, and antibiotic resistance, necessitates the development of novel therapeutics to treat salmonellosis. The development of anti-virulence agents against multi-drug-resistant bacteria is a novel strategy because of its non-bacterial feature. Hence, a thorough study of the type three secretion system (T3SS) of Salmonella would help us better understand its role in bacterial pathogenesis and development of anti-virulence agents. However, T3SS can be inhibited by different chemicals at different stages of infection and sequenced delivery of effectors can be blocked to restrict the progression of disease. This review highlights the role of T3SS-1 in the internalization, survival, and replication of Salmonella within the intestinal epithelium and T3SS inhibitors. We concluded that the better we understand the structures and functions of T3SS, the more we have chances to develop anti-virulence agents. Furthermore, greater insights into the T3SS inhibitors of Salmonella would help in the mitigation of the antibiotic resistance problem and would lead us to the era of new therapeutics against salmonellosis.
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Affiliation(s)
- Sajjad Hussain
- College of Veterinary Medicine, Sichuan Agriculture University, Huimin Road 211, Wenjiang, Chengdu, China
| | - Ping Ouyang
- College of Veterinary Medicine, Sichuan Agriculture University, Huimin Road 211, Wenjiang, Chengdu, China
| | - Yingkun Zhu
- College of Veterinary Medicine, Sichuan Agriculture University, Huimin Road 211, Wenjiang, Chengdu, China
| | - Abdul Khalique
- College of Veterinary Medicine, Sichuan Agriculture University, Huimin Road 211, Wenjiang, Chengdu, China
| | - Changliang He
- College of Veterinary Medicine, Sichuan Agriculture University, Huimin Road 211, Wenjiang, Chengdu, China
| | - Xiaoxia Liang
- College of Veterinary Medicine, Sichuan Agriculture University, Huimin Road 211, Wenjiang, Chengdu, China
| | - Gang Shu
- College of Veterinary Medicine, Sichuan Agriculture University, Huimin Road 211, Wenjiang, Chengdu, China
| | - Lizi Yin
- College of Veterinary Medicine, Sichuan Agriculture University, Huimin Road 211, Wenjiang, Chengdu, China.
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12
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Cadel-Six S, Cherchame E, Douarre PE, Tang Y, Felten A, Barbet P, Litrup E, Banerji S, Simon S, Pasquali F, Gourmelon M, Mensah N, Borowiak M, Mistou MY, Petrovska L. The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe. Front Microbiol 2021; 12:651124. [PMID: 34093465 PMCID: PMC8175864 DOI: 10.3389/fmicb.2021.651124] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/16/2021] [Indexed: 01/23/2023] Open
Abstract
The European epidemic monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) characterized by the multi locus sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this Salmonella in Europe. The epidemic S. 1,4,[5],12:i:- ST34 emerged in the 1980s by an acquisition of the Salmonella Genomic Island (SGI)-4 at the 3' end of the phenylalanine phe tRNA locus conferring resistance to copper and arsenic toxicity. Subsequent integration of the Tn21 transposon into the fljAB locus gave resistance to mercury toxicity and several classes of antibiotics used in food-producing animals (ASSuT profile). The second step of the evolution occurred in the 1990s, with the integration of mTmV and mTmV-like prophages carrying the perC and/or sopE genes involved in the ability to reduce nitrates in intestinal contents and facilitate the disruption of the junctions of the host intestinal epithelial cells. Heavy metals are largely used as food supplements or pesticide for cultivation of seeds intended for animal feed so the expansion of the epidemic S. 1,4,[5],12:i:- ST34 was strongly related to the multiple-heavy metal resistance acquired by transposons, integrative and conjugative elements and facilitated by the escape until 2011 from the regulatory actions applied in the control of S. Typhimurium in Europe. The genomic plasticity of the epidemic S. 1,4,[5],12:i:- was demonstrated in our study by the analysis of the plasmidome. We were able to identify plasmids harboring genes mediating resistance to phenicols, colistin, and fluoroquinolone and also describe for the first time in six of the analyzed genomes the presence of two plasmids (pERR1744967-1 and pERR2174855-2) previously described only in strains of enterotoxigenic Escherichia coli and E. fergusonii.
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Affiliation(s)
- Sabrina Cadel-Six
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Emeline Cherchame
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | | | - Yue Tang
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Arnaud Felten
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Pauline Barbet
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sangeeta Banerji
- Robert Koch-Institute, Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Sandra Simon
- Robert Koch-Institute, Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Federique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Michèle Gourmelon
- Ifremer, RBE, SGMM, Health, Environment and Microbiology Laboratory, Plouzané, France
| | - Nana Mensah
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Michel-Yves Mistou
- Université Paris-Saclay, INRAE, Centre International de Ressource Microbienne (CIRM) MaIAGE, Jouy-en-Josas, France
| | - Liljana Petrovska
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
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13
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Tassinari E, Bawn M, Thilliez G, Charity O, Acton L, Kirkwood M, Petrovska L, Dallman T, Burgess CM, Hall N, Duffy G, Kingsley RA. Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone. Microb Genom 2020; 6:mgen000456. [PMID: 33112226 PMCID: PMC7725340 DOI: 10.1099/mgen.0.000456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/01/2020] [Indexed: 01/10/2023] Open
Abstract
Epidemic and pandemic clones of bacterial pathogens with distinct characteristics continually emerge, replacing those previously dominant through mechanisms that remain poorly characterized. Here, whole-genome-sequencing-powered epidemiology linked horizontal transfer of a virulence gene, sopE, to the emergence and clonal expansion of a new epidemic Salmonella enterica serovar Typhimurium (S. Typhimurium) clone. The sopE gene is sporadically distributed within the genus Salmonella and rare in S. enterica Typhimurium lineages, but was acquired multiple times during clonal expansion of the currently dominant pandemic monophasic S. Typhimurium sequence type (ST) 34 clone. Ancestral state reconstruction and time-scaled phylogenetic analysis indicated that sopE was not present in the common ancestor of the epidemic clade, but later acquisition resulted in increased clonal expansion of sopE-containing clones that was temporally associated with emergence of the epidemic, consistent with increased fitness. The sopE gene was mainly associated with a temperate bacteriophage mTmV, but recombination with other bacteriophage and apparent horizontal gene transfer of the sopE gene cassette resulted in distribution among at least four mobile genetic elements within the monophasic S. enterica Typhimurium ST34 epidemic clade. The mTmV prophage lysogenic transfer to other S. enterica serovars in vitro was limited, but included the common pig-associated S. enterica Derby (S. Derby). This may explain mTmV in S. Derby co-circulating on farms with monophasic S. Typhimurium ST34, highlighting the potential for further transfer of the sopE virulence gene in nature. We conclude that whole-genome epidemiology pinpoints potential drivers of evolutionary and epidemiological dynamics during pathogen emergence, and identifies targets for subsequent research in epidemiology and bacterial pathogenesis.
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Affiliation(s)
- Eleonora Tassinari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Gaetan Thilliez
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Oliver Charity
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Luke Acton
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mark Kirkwood
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Timothy Dallman
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, London, UK
| | | | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
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14
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Marônek M, Link R, Monteleone G, Gardlík R, Stolfi C. Viruses in Cancers of the Digestive System: Active Contributors or Idle Bystanders? Int J Mol Sci 2020; 21:ijms21218133. [PMID: 33143318 PMCID: PMC7663754 DOI: 10.3390/ijms21218133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
The human virome, which is a collection of all the viruses that are present in the human body, is increasingly being recognized as an essential part of the human microbiota. The human gastrointestinal tract and related organs (e.g., liver, pancreas, and gallbladder)-composing the gastrointestinal (or digestive) system-contain a huge number of viral particles which contribute to maintaining tissue homeostasis and keeping our body healthy. However, perturbations of the virome steady-state may, both directly and indirectly, ignite/sustain oncogenic mechanisms contributing to the initiation of a dysplastic process and/or cancer progression. In this review, we summarize and discuss the available evidence on the association and role of viruses in the development of cancers of the digestive system.
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Affiliation(s)
- Martin Marônek
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (M.M.); (R.G.)
| | - René Link
- Institute of Experimental Medicine, Faculty of Medicine, University of Pavol Jozef Šafárik, 040 11 Košice, Slovakia;
| | - Giovanni Monteleone
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Roman Gardlík
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (M.M.); (R.G.)
| | - Carmine Stolfi
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy;
- Division of Clinical Biochemistry and Clinical Molecular Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-06-72596163
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15
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Fattinger SA, Böck D, Di Martino ML, Deuring S, Samperio Ventayol P, Ek V, Furter M, Kreibich S, Bosia F, Müller-Hauser AA, Nguyen BD, Rohde M, Pilhofer M, Hardt WD, Sellin ME. Salmonella Typhimurium discreet-invasion of the murine gut absorptive epithelium. PLoS Pathog 2020; 16:e1008503. [PMID: 32365138 PMCID: PMC7224572 DOI: 10.1371/journal.ppat.1008503] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/14/2020] [Accepted: 03/26/2020] [Indexed: 01/15/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S.Tm) infections of cultured cell lines have given rise to the ruffle model for epithelial cell invasion. According to this model, the Type-Three-Secretion-System-1 (TTSS-1) effectors SopB, SopE and SopE2 drive an explosive actin nucleation cascade, resulting in large lamellipodia- and filopodia-containing ruffles and cooperative S.Tm uptake. However, cell line experiments poorly recapitulate many of the cell and tissue features encountered in the host’s gut mucosa. Here, we employed bacterial genetics and multiple imaging modalities to compare S.Tm invasion of cultured epithelial cell lines and the gut absorptive epithelium in vivo in mice. In contrast to the prevailing ruffle-model, we find that absorptive epithelial cell entry in the mouse gut occurs through “discreet-invasion”. This distinct entry mode requires the conserved TTSS-1 effector SipA, involves modest elongation of local microvilli in the absence of expansive ruffles, and does not favor cooperative invasion. Discreet-invasion preferentially targets apicolateral hot spots at cell–cell junctions and shows strong dependence on local cell neighborhood. This proof-of-principle evidence challenges the current model for how S.Tm can enter gut absorptive epithelial cells in their intact in vivo context. Bacterial pathogens can use secreted effector molecules to drive entry into host cells. Studies of the intestinal pathogen S.Tm have been central to uncover the mechanistic basis for the entry process. More than two decades of research have resulted in a detailed model for how S.Tm invades gut epithelial cells through effector triggering of large Rho-GTPase-dependent actin ruffles. However, the evidence for this model comes predominantly from studies in cultured cell lines. These experimental systems lack many of the architectural and signaling features of the intact gut epithelium. Our study surprisingly reveals that in the intact mouse gut, S.Tm invades absorptive epithelial cells through a process that does not require the Rho-GTPase-activating effectors and can proceed in the absence of the prototypical ruffling response. Instead, S.Tm exploits another effector, SipA, to sneak in through discreet entry structures close to cell–cell junctions. Our results challenge the current model for S.Tm epithelial cell entry and emphasizes the need of taking a physiological host cell context into account when studying bacterium–host cell interactions.
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Affiliation(s)
- Stefan A. Fattinger
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Desirée Böck
- Institute of Molecular Biology & Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Maria Letizia Di Martino
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sabrina Deuring
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Pilar Samperio Ventayol
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Viktor Ek
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Markus Furter
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Saskia Kreibich
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Francesco Bosia
- Institute of Molecular Biology & Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | | | - Bidong D. Nguyen
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Martin Pilhofer
- Institute of Molecular Biology & Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland
- * E-mail: (MP); (WDH); (MES)
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
- * E-mail: (MP); (WDH); (MES)
| | - Mikael E. Sellin
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail: (MP); (WDH); (MES)
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16
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Maronek M, Link R, Ambro L, Gardlik R. Phages and Their Role in Gastrointestinal Disease: Focus on Inflammatory Bowel Disease. Cells 2020; 9:E1013. [PMID: 32325706 PMCID: PMC7226564 DOI: 10.3390/cells9041013] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic autoinflammatory diseases including Crohn's disease and ulcerative colitis. Although the molecular mechanisms governing the pathogenesis of gastrointestinal inflammation are not completely clear, the main factors are presumed to be genetic predisposition, environmental exposure, and the intestinal microbiome. Hitherto, most of the studies focusing on the role of the microbiome studied the action and effect of bacteria. However, the intestinal microbiome comprises other members of the microbial community as well, namely, fungi, protozoa, and viruses. We believe that bacteriophages are among the main orchestrators of the effect of microbiota on the gut mucosa. Therefore, this review aims to summarize the knowledge of the role of intestinal phageome in IBD and to discuss the concept of phage therapy and its future applications.
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Affiliation(s)
- Martin Maronek
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Rene Link
- Institute of Experimental Medicine, Faculty of Medicine, University of Pavol Jozef Šafárik, 040 11 Košice, Slovakia; (R.L.); (L.A.)
| | - Lubos Ambro
- Institute of Experimental Medicine, Faculty of Medicine, University of Pavol Jozef Šafárik, 040 11 Košice, Slovakia; (R.L.); (L.A.)
| | - Roman Gardlik
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
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17
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Miller EA, Elnekave E, Flores-Figueroa C, Johnson A, Kearney A, Munoz-Aguayo J, Tagg KA, Tschetter L, Weber BP, Nadon CA, Boxrud D, Singer RS, Folster JP, Johnson TJ. Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America. mSphere 2020; 5:e00056-20. [PMID: 32295868 PMCID: PMC7160679 DOI: 10.1128/msphere.00056-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/26/2020] [Indexed: 01/09/2023] Open
Abstract
Two separate human outbreaks of Salmonella enterica serotype Reading occurred between 2017 and 2019 in the United States and Canada, and both outbreaks were linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys and to determine the genomic context of outbreaks involving this infrequently isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole-genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade, isolates clustered into three subclades, including an "emergent" clade that contained only isolates dated 2016 or later, with many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades, suggesting that the apparent success of currently circulating subclades is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source.IMPORTANCE Increasingly, outbreak investigations involving foodborne pathogens are difficult due to the interconnectedness of food animal production and distribution, and homogeneous nature of industry integration, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole-genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincided with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in commercial turkeys and ability to cause illness in humans.
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Affiliation(s)
- Elizabeth A Miller
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Ehud Elnekave
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | | | - Abigail Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Ashley Kearney
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Jeannette Munoz-Aguayo
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
| | | | - Lorelee Tschetter
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Bonnie P Weber
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Celine A Nadon
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Dave Boxrud
- Minnesota Department of Health, Saint Paul, Minnesota, USA
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Jason P Folster
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
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18
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Gilbert RA, Townsend EM, Crew KS, Hitch TCA, Friedersdorff JCA, Creevey CJ, Pope PB, Ouwerkerk D, Jameson E. Rumen Virus Populations: Technological Advances Enhancing Current Understanding. Front Microbiol 2020; 11:450. [PMID: 32273870 PMCID: PMC7113391 DOI: 10.3389/fmicb.2020.00450] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/02/2020] [Indexed: 01/07/2023] Open
Abstract
The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often out-numbering the microbial populations that they both predate on and co-exist with. To date the research effort devoted to understanding rumen-associated viral populations has been considerably less than that given to the other microbial populations, yet their contribution to maintaining microbial population balance, intra-ruminal microbial lysis, fiber breakdown, nutrient cycling and genetic transfer may be highly significant. This review follows the technological advances which have contributed to our current understanding of rumen viruses and drawing on knowledge from other environmental and animal-associated microbiomes, describes the known and potential roles and impacts viruses have on rumen function and speculates on the future directions of rumen viral research.
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Affiliation(s)
- Rosalind A. Gilbert
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor M. Townsend
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kathleen S. Crew
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
| | - Thomas C. A. Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Jessica C. A. Friedersdorff
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Christopher J. Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Phillip B. Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Diane Ouwerkerk
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor Jameson
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
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19
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Röder J, Hensel M. Presence of SopE and mode of infection result in increased
Salmonella
‐containing vacuole damage and cytosolic release during host cell infection by
Salmonella enterica. Cell Microbiol 2020; 22:e13155. [DOI: 10.1111/cmi.13155] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Jennifer Röder
- Abteilung MikrobiologieUniversitat Osnabruck Osnabrück Germany
| | - Michael Hensel
- Abteilung MikrobiologieUniversitat Osnabruck Osnabrück Germany
- CellNanOs – Center for Cellular Nanoanalytics, Fachbereich Biologie/ChemieUniversität Osnabrück Osnabrück Germany
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Gymoese P, Kiil K, Torpdahl M, Østerlund MT, Sørensen G, Olsen JE, Nielsen EM, Litrup E. WGS based study of the population structure of Salmonella enterica serovar Infantis. BMC Genomics 2019; 20:870. [PMID: 31730461 PMCID: PMC6858691 DOI: 10.1186/s12864-019-6260-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar. RESULTS We sequenced a global collection of 100 S. Infantis strains. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a long branch. The remaining strains, all in eBG31, were divided into three lineages that were estimated to have separated approximately 150 years ago. One lineage contained the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a clone with preference for these sources. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. Another lineage contained three genetic clusters with more rarely isolated strains of mainly animal origin, possibly less sampled or less infectious clones. Conserved prophages were identified in all strains, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S. Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed. CONCLUSIONS This study analysed a global S. Infantis population and described its genetic structure. We hypothesize that the population has evolved in three separate lineages, with one more successfully emerging lineage. We furthermore detected conserved prophages present in the entire population and cluster specific prophages, which probably shaped the population structure.
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Affiliation(s)
- Pernille Gymoese
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mia Torpdahl
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mark T. Østerlund
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Gitte Sørensen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C, Denmark
| | - Eva M. Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
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Rezaei Javan R, Ramos-Sevillano E, Akter A, Brown J, Brueggemann AB. Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis. Nat Commun 2019; 10:4852. [PMID: 31649284 PMCID: PMC6813308 DOI: 10.1038/s41467-019-12825-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023] Open
Abstract
Prophages (viral genomes integrated within a host bacterial genome) can confer various phenotypic traits to their hosts, such as enhanced pathogenicity. Here we analyse >1300 genomes of 70 different Streptococcus species and identify nearly 800 prophages and satellite prophages (prophages that do not encode their own structural components but rely on the bacterial host and another helper prophage for survival). We show that prophages and satellite prophages are widely distributed among streptococci in a structured manner, and constitute two distinct entities with little effective genetic exchange between them. Cross-species transmission of prophages is not uncommon. Furthermore, a satellite prophage is associated with virulence in a mouse model of Streptococcus pneumoniae infection. Our findings highlight the potential importance of prophages in streptococcal biology and pathogenesis. Prophages are viral genomes integrated within bacterial genomes. Here, Rezaei Javan et al. identify nearly 800 prophages and satellite prophages in > 1300 Streptococcus genomes, and show that a satellite prophage is associated with virulence in a mouse model of pneumococcal infection.
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Affiliation(s)
| | | | - Asma Akter
- Department of Medicine, Imperial College London, London, UK
| | - Jeremy Brown
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Angela B Brueggemann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,Department of Medicine, Imperial College London, London, UK. .,Nuffield Department of Population Health, University of Oxford, Oxford, UK.
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Sinha A, Maurice CF. Bacteriophages: Uncharacterized and Dynamic Regulators of the Immune System. Mediators Inflamm 2019; 2019:3730519. [PMID: 31582898 PMCID: PMC6754933 DOI: 10.1155/2019/3730519] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022] Open
Abstract
The human gut is an extremely active immunological site interfacing with the densest microbial community known to colonize the human body, the gut microbiota. Despite tremendous advances in our comprehension of how the gut microbiota is involved in human health and interacts with the mammalian immune system, most studies are incomplete as they typically do not consider bacteriophages. These bacterial viruses are estimated to be as numerous as their bacterial hosts, with tremendous and mostly uncharacterized genetic diversity. In addition, bacteriophages are not passive members of the gut microbiota, as highlighted by the recent evidence for their active involvement in human health. Yet, how bacteriophages interact with their bacterial hosts and the immune system in the human gut remains poorly described. Here, we aim to fill this gap by providing an overview of bacteriophage communities in the gut during human development, detailing recent findings for their bacterial-mediated effects on the immune response and summarizing the latest evidence for direct interactions between them and the immune system. The dramatic increase in antibiotic-resistant bacterial pathogens has spurred a renewed interest in using bacteriophages for therapy, despite the many unknowns about bacteriophages in the human body. Going forward, more studies encompassing the communities of bacteria, bacteriophages, and the immune system in diverse health and disease settings will provide invaluable insight into this dynamic trio essential for human health.
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Affiliation(s)
- Anshul Sinha
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Corinne F. Maurice
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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Yildirim Z, Sakin T, Akçelik M, Akçelik N. Characterization of SE-P3, P16, P37, and P47 bacteriophages infectingSalmonellaEnteritidis. J Basic Microbiol 2019; 59:1049-1062. [DOI: 10.1002/jobm.201900102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/30/2019] [Accepted: 06/22/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Zeliha Yildirim
- Department of Food Engineering, Faculty of Engineering; Niğde Ömer Halisdemir University; Niğde Turkey
| | - Tuba Sakin
- Department of Food Engineering, Faculty of Engineering; Niğde Ömer Halisdemir University; Niğde Turkey
| | - Mustafa Akçelik
- Department of Biology, Faculty of Science; Ankara University; Ankara Turkey
| | - Nesife Akçelik
- Department of Biotecnology, Institute of Biotechnology; Ankara University; Ankara Turkey
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Müller J, Spriewald S, Stecher B, Stadler E, Fuchs TM. Evolutionary Stability of Salmonella Competition with the Gut Microbiota: How the Environment Fosters Heterogeneity in Exploitative and Interference Competition. J Mol Biol 2019; 431:4732-4748. [PMID: 31260689 DOI: 10.1016/j.jmb.2019.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/19/2019] [Accepted: 06/19/2019] [Indexed: 11/27/2022]
Abstract
Following ingestion, gastrointestinal pathogens compete against the gastrointestinal microbiota and overcome host immune defenses in order to cause infections. Besides employing direct killing mechanisms, the commensal microbiota occupies metabolic niches to outcompete invading pathogens. Salmonella enterica serovar Typhimurium (S. Typhimurium) uses several strategies to successfully colonize the gut and establish infection, of which an increasing number is based on phenotypic heterogeneity within the S. Typhimurium population. The utilization of myo-inositol (MI) and the production of colicin confer a selective advantage over the microbiota in terms of exploitative and interference competition, respectively. In this review, we summarize the genetic basis underlying bistability of MI catabolism and colicin production. As demonstrated by single-cell analyses, a stochastic switch in the expression of the genes responsible for colicin production and MI degradation constitutes the heterogeneity of the two phenotypes. Both genetic systems are tightly regulated to avoid their expression under non-appropriate conditions and possible detrimental effects on bacterial fitness. Moreover, evolutionary mechanisms underlying formation and stability of these phenotypes in S. Typhimurium are discussed. We propose that both MI catabolism and colicin production create a bet-hedging strategy, which provides an adaptive benefit for S. Typhimurium in the fluctuating environment of the mammalian gut.
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Affiliation(s)
- Johannes Müller
- Technische Universität München, Centre for Mathematical Sciences, Boltzmannstr. 3, 85747 Garching, Germany; Institute for Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Stefanie Spriewald
- Max von Pettenkofer-Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer-Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Eva Stadler
- Technische Universität München, Centre for Mathematical Sciences, Boltzmannstr. 3, 85747 Garching, Germany
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institut für Molekulare Pathogenese, Naumburger Str. 96a, 07743 Jena, Germany.
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Jariah ROA, Hakim MS. Interaction of phages, bacteria, and the human immune system: Evolutionary changes in phage therapy. Rev Med Virol 2019; 29:e2055. [PMID: 31145517 DOI: 10.1002/rmv.2055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/01/2019] [Accepted: 05/02/2019] [Indexed: 12/26/2022]
Abstract
Phages and bacteria are known to undergo dynamic and co-evolutionary arms race interactions in order to survive. Recent advances from in vitro and in vivo studies have improved our understanding of the complex interactions between phages, bacteria, and the human immune system. This insight is essential for the development of phage therapy to battle the growing problems of antibiotic resistance. It is also pivotal to prevent the development of phage-resistance during the implementation of phage therapy in the clinic. In this review, we discuss recent progress of the interactions between phages, bacteria, and the human immune system and its clinical application for phage therapy. Proper phage therapy design will ideally produce large burst sizes, short latent periods, broad host ranges, and a low tendency to select resistance.
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Affiliation(s)
- Rizka O A Jariah
- Department of Health Science, Faculty of Vocational Studies, Universitas Airlangga, Surabaya, Indonesia
| | - Mohamad S Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Characterization of Salmonella Typhimurium and its monophasic variant 1,4, [5],12:i:- isolated from different sources. Folia Microbiol (Praha) 2019; 64:711-718. [PMID: 30721446 DOI: 10.1007/s12223-019-00683-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 01/21/2019] [Indexed: 01/19/2023]
Abstract
In order to characterize the most commonly detected Salmonella serotypes, we tested 124 isolates of S. Typhimurium and 89 isolates of the monophasic variant of S. Typhimurium (S. 1,4, [5],12:i:-) for their antimicrobial susceptibility by means of the Kirby-Bauer disk-diffusion method, and for the detection of 19 genes (four Phage Markers (g13, Sieb, eat, g8), ten prophage-related virulence genes (gipA, gtgB, nanH, gogB, grvA, sopE, sspH1, sspH2, sodC1, gtgE), and five plasmid-borne virulence genes (spvC, pefA, mig5, rcK, srgA)) by means of PCR-based assays. A total of 213 strains were analyzed from, humans (n = 122), animals (n = 25), food (n = 46), and irrigation water (n = 20). S. Typhimurium isolates showed higher variability, in both their resistance profiles and molecular typing, than S. 1,4, [5],12:i:-. Strains from irrigation water displayed significantly higher susceptibility to antibiotics than those from the other sources. Resistance to ampicillin, streptomycin, sulfonamide, and tetracycline was the most commonly detected resistance profile (R-type), being in serovar S. 1,4, [5],12:i:-, frequently associated to resistance to other antimicrobials. Significant differences in genetic profiles in the two abovementioned Salmonella serotypes were found. None of the plasmid-borne virulence genes investigated were detected in S. 1,4, [5],12:i:- isolates, while those genes, characterized 37.9% of the S. Typhimurium strains. Differences in the prevalence of some molecular targets between the two Salmonella serotypes deserve further study. Importantly, the grvA gene was found exclusively in S. Typhimurium strains, whereas sopE, sodC, gtgB, and gipA were mainly detected, with a statistically significant difference, in S. 1,4, [5],12:i:- isolates.
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Borges KA, Furian TQ, Souza SN, Salle CTP, Moraes HLS, Nascimento VP. Antimicrobial Resistance and Molecular Characterization of Salmonella Enterica Serotypes Isolated from Poultry Sources in Brazil. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2019. [DOI: 10.1590/1806-9061-2018-0827] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- KA Borges
- Universidade Federal do Rio Grande do Sul, Brazil
| | - TQ Furian
- Universidade Federal do Rio Grande do Sul, Brazil
| | - SN Souza
- Universidade Federal do Rio Grande do Sul, Brazil
| | - CTP Salle
- Universidade Federal do Rio Grande do Sul, Brazil
| | - HLS Moraes
- Universidade Federal do Rio Grande do Sul, Brazil
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28
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Branchu P, Bawn M, Kingsley RA. Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants. Infect Immun 2018; 86:e00079-18. [PMID: 29784861 PMCID: PMC6056856 DOI: 10.1128/iai.00079-18] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is one of approximately 2,500 distinct serovars of the genus Salmonella but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of nontyphoidal Salmonella (NTS) infections, accounting for a quarter of infections, second only to S. enterica serovar Enteritidis in incidence. S Typhimurium was once considered the archetypal broad-host-range Salmonella serovar due to its wide distribution in livestock and wild animals, and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, and ATCC 14028). But it has become clear that these strains do not reflect the genotypic or phenotypic diversity of S Typhimurium. Here, we review the epidemiological record of S Typhimurium and studies of the host-pathogen interactions of diverse strains of S Typhimurium. We present the concept of distinct pathovariants of S Typhimurium that exhibit diversity of host range, distribution in the environment, pathogenicity, and risk to food safety. We review recent evidence from whole-genome sequencing that has revealed the extent of genomic diversity of S Typhimurium pathovariants, the genomic basis of differences in the level of risk to human and animal health, and the molecular epidemiology of prominent strains. An improved understanding of the impact of genome variation of bacterial pathogens on pathogen-host and pathogen-environment interactions has the potential to improve quantitative risk assessment and reveal how new pathogens evolve.
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Affiliation(s)
- Priscilla Branchu
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
- Earlham Institute, Norwich Research Park, Colney, Norwich, United Kingdom
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
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CRP-cAMP mediates silencing of Salmonella virulence at the post-transcriptional level. PLoS Genet 2018; 14:e1007401. [PMID: 29879120 PMCID: PMC5991649 DOI: 10.1371/journal.pgen.1007401] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/09/2018] [Indexed: 12/14/2022] Open
Abstract
Invasion of epithelial cells by Salmonella enterica requires expression of genes located in the pathogenicity island I (SPI-1). The expression of SPI-1 genes is very tightly regulated and activated only under specific conditions. Most studies have focused on the regulatory pathways that induce SPI-1 expression. Here, we describe a new regulatory circuit involving CRP-cAMP, a widely established metabolic regulator, in silencing of SPI-1 genes under non-permissive conditions. In CRP-cAMP-deficient strains we detected a strong upregulation of SPI-1 genes in the mid-logarithmic growth phase. Genetic analyses revealed that CRP-cAMP modulates the level of HilD, the master regulator of Salmonella invasion. This regulation occurs at the post-transcriptional level and requires the presence of a newly identified regulatory motif within the hilD 3'UTR. We further demonstrate that in Salmonella the Hfq-dependent sRNA Spot 42 is under the transcriptional repression of CRP-cAMP and, when this transcriptional repression is relieved, Spot 42 exerts a positive effect on hilD expression. In vivo and in vitro assays indicate that Spot 42 targets, through its unstructured region III, the 3'UTR of the hilD transcript. Together, our results highlight the biological relevance of the hilD 3'UTR as a hub for post-transcriptional control of Salmonella invasion gene expression.
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Zhang K, Riba A, Nietschke M, Torow N, Repnik U, Pütz A, Fulde M, Dupont A, Hensel M, Hornef M. Minimal SPI1-T3SS effector requirement for Salmonella enterocyte invasion and intracellular proliferation in vivo. PLoS Pathog 2018. [PMID: 29522566 PMCID: PMC5862521 DOI: 10.1371/journal.ppat.1006925] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Effector molecules translocated by the Salmonella pathogenicity island (SPI)1-encoded type 3 secretion system (T3SS) critically contribute to the pathogenesis of human Salmonella infection. They facilitate internalization by non-phagocytic enterocytes rendering the intestinal epithelium an entry site for infection. Their function in vivo has remained ill-defined due to the lack of a suitable animal model that allows visualization of intraepithelial Salmonella. Here, we took advantage of our novel neonatal mouse model and analyzed various bacterial mutants and reporter strains as well as gene deficient mice. Our results demonstrate the critical but redundant role of SopE2 and SipA for enterocyte invasion, prerequisite for transcriptional stimulation and mucosal translocation in vivo. In contrast, the generation of a replicative intraepithelial endosomal compartment required the cooperative action of SipA and SopE2 or SipA and SopB but was independent of SopA or host MyD88 signaling. Intraepithelial growth had no critical influence on systemic spread. Our results define the role of SPI1-T3SS effector molecules during enterocyte invasion and intraepithelial proliferation in vivo providing novel insight in the early course of Salmonella infection. Non-typhoidal Salmonella represent a major causative agent of gastroenteritis worldwide. Hallmark of the pathogenesis is their ability to actively invade the intestinal epithelium by virtue of their type 3 secretion system that delivers bacterial virulence factors directly into the host cell cytosol. The role of these virulence factors during enterocyte entry and intraepithelial growth has only been investigated in vitro since the previously established in vivo models in small animals did not allow visualization of intraepithelial Salmonella. However, immortalized cell lines lack the overlaying mucus layer, final cell lineage differentiation, apical-basolateral polarization as well as continuous migration along the crypt villus axis and thus the role of virulence factors during the Salmonella infection in vivo has remained largely undefined. Here, we took advantage of our novel neonatal mouse infection model and for the first time systematically analyzed the importance of Salmonella virulence factors for enterocyte invasion and intraepithelial growth.
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Affiliation(s)
- Kaiyi Zhang
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Ambre Riba
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Monika Nietschke
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Natalia Torow
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Urska Repnik
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Andreas Pütz
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Aline Dupont
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Michael Hensel
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Mathias Hornef
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
- * E-mail:
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Phage-mediated dissemination of virulence factors in pathogenic bacteria facilitated by antibiotic growth promoters in animals: a perspective. Anim Health Res Rev 2017; 18:160-166. [DOI: 10.1017/s1466252317000147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AbstractAddition of sub-therapeutic antibiotics to the feed of food-producing animals for growth promotion and disease prevention has become a common agricultural practice in many countries. The emergence of antibiotic-resistant pathogens is a looming concern associated with the use of antibiotic growth promoters (AGPs) around the world. In addition, some studies have shown that AGPs may not only affect antibiotic resistance but may also stimulate the dissemination of virulence factors via bacteriophages. Although only a few studies are currently available in the literature regarding this topic, in this article we endeavor to provide a perspective about how AGPs would impact the transmission of virulence factors by horizontal gene transfer via phages in a few pathogenic bacterial species significant to livestock production.
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Zárate S, Taboada B, Yocupicio-Monroy M, Arias CF. Human Virome. Arch Med Res 2017; 48:701-716. [DOI: 10.1016/j.arcmed.2018.01.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/22/2018] [Indexed: 12/16/2022]
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Zhang K, Griffiths G, Repnik U, Hornef M. Seeing is understanding: Salmonella's way to penetrate the intestinal epithelium. Int J Med Microbiol 2017; 308:97-106. [PMID: 28939439 DOI: 10.1016/j.ijmm.2017.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
The molecular processes that govern host-microbial interaction illustrate not only the sophisticated and multifaceted mechanisms that protect the host from infection, but also the elaborated features of microbial pathogens that have evolved to overcome or evade the host's immune system. Here we focus on Salmonella that like other enteric pathogens must overcome the intestinal mucosal immune system, a surface constantly on alert and evolved to restrict the enteric microbiota. We discuss the initial step of Salmonella infection, the penetration of the intestinal epithelial barrier and the models used to study this fascinating aspect of microbial pathogenesis.
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Affiliation(s)
- Kaiyi Zhang
- Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany
| | | | - Urska Repnik
- Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Mathias Hornef
- Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany.
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Hume PJ, Singh V, Davidson AC, Koronakis V. Swiss Army Pathogen: The Salmonella Entry Toolkit. Front Cell Infect Microbiol 2017; 7:348. [PMID: 28848711 PMCID: PMC5552672 DOI: 10.3389/fcimb.2017.00348] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/21/2017] [Indexed: 02/04/2023] Open
Abstract
Salmonella causes disease in humans and animals ranging from mild self-limiting gastroenteritis to potentially life-threatening typhoid fever. Salmonellosis remains a considerable cause of morbidity and mortality globally, and hence imposes a huge socio-economic burden worldwide. A key property of all pathogenic Salmonella strains is the ability to invade non-phagocytic host cells. The major determinant of this invasiveness is a Type 3 Secretion System (T3SS), a molecular syringe that injects virulence effector proteins directly into target host cells. These effectors cooperatively manipulate multiple host cell signaling pathways to drive pathogen internalization. Salmonella does not only rely on these injected effectors, but also uses several other T3SS-independent mechanisms to gain entry into host cells. This review summarizes our current understanding of the methods used by Salmonella for cell invasion, with a focus on the host signaling networks that must be coordinately exploited for the pathogen to achieve its goal.
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Affiliation(s)
- Peter J Hume
- Department of Pathology, University of CambridgeCambridge, United Kingdom
| | - Vikash Singh
- Department of Pathology, University of CambridgeCambridge, United Kingdom
| | - Anthony C Davidson
- Department of Pathology, University of CambridgeCambridge, United Kingdom
| | - Vassilis Koronakis
- Department of Pathology, University of CambridgeCambridge, United Kingdom
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Wotzka SY, Nguyen BD, Hardt WD. Salmonella Typhimurium Diarrhea Reveals Basic Principles of Enteropathogen Infection and Disease-Promoted DNA Exchange. Cell Host Microbe 2017; 21:443-454. [PMID: 28407482 DOI: 10.1016/j.chom.2017.03.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/17/2017] [Accepted: 03/24/2017] [Indexed: 12/18/2022]
Abstract
Despite decades of research, efficient therapies for most enteropathogenic bacteria are still lacking. In this review, we focus on Salmonella enterica Typhimurium (S. Typhimurium), a frequent cause of acute, self-limiting food-borne diarrhea and a model that has revealed key principles of enteropathogen infection. We review the steps of gut infection and the mucosal innate-immune defenses limiting pathogen burdens, and we discuss how inflammation boosts gut luminal S. Typhimurium growth. We also discuss how S. Typhimurium-induced inflammation accelerates the transfer of plasmids and phages, which may promote the transmission of antibiotic resistance and facilitate emergence of pathobionts and pathogens with enhanced virulence. The targeted manipulation of the microbiota and vaccination might offer strategies to prevent this evolution. As gut luminal microbes impact various aspects of the host's physiology, improved strategies for preventing enteropathogen infection and disease-inflicted DNA exchange may be of broad interest well beyond the acute infection.
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Affiliation(s)
- Sandra Y Wotzka
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bidong D Nguyen
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
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36
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Gaviria-Cantin T, El Mouali Y, Le Guyon S, Römling U, Balsalobre C. Gre factors-mediated control of hilD transcription is essential for the invasion of epithelial cells by Salmonella enterica serovar Typhimurium. PLoS Pathog 2017; 13:e1006312. [PMID: 28426789 PMCID: PMC5398713 DOI: 10.1371/journal.ppat.1006312] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/23/2017] [Indexed: 11/19/2022] Open
Abstract
The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated process. Signaling cascades triggered by different environmental and physiological signals converge to control HilD, an AraC regulator that coordinates the expression of several virulence factors. The expression of hilD is modulated at several steps of the expression process. Here, we report that the invasion of epithelial cells by S. Typhimurium strains lacking the Gre factors, GreA and GreB, is impaired. By interacting with the RNA polymerase secondary channel, the Gre factors prevent backtracking of paused complexes to avoid arrest during transcriptional elongation. Our results indicate that the Gre factors are required for the expression of the bacterial factors needed for epithelial cell invasion by modulating expression of HilD. This regulation does not occur at transcription initiation and depends on the capacity of the Gre factors to prevent backtracking of the RNA polymerase. Remarkably, genetic analyses indicate that the 3’-untranslated region (UTR) of hilD is required for Gre-mediated regulation of hilD expression. Our data provide new insight into the complex regulation of S. Typhimurium virulence and highlight the role of the hilD 3’-UTR as a regulatory motif. Salmonella enterica serovar Typhimurium is a foodborne pathogen that causes gastroenteritis in humans. To successfully trigger infection, S. Typhimurium invades epithelial cells, a process that requires the coordinated expression of a set of genes. HilD is a pivotal regulator of S. Typhimurium pathogenicity, as it activates the expression of the genes required for invasion of intestinal epithelium. Expression and activity of HilD are tightly regulated and respond to several environmental and physiological conditions. In this report, we introduce the transcription elongation as a novel level of regulation of hilD. We describe that the Gre factors, proteins that prevent backtracking of paused RNA polymerase complexes during transcription elongation, are required for the expression of HilD and the subsequent expression of genes involved in the invasion of epithelial cells.
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Affiliation(s)
- Tania Gaviria-Cantin
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Youssef El Mouali
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Soazig Le Guyon
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Carlos Balsalobre
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
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37
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Diard M, Bakkeren E, Cornuault JK, Moor K, Hausmann A, Sellin ME, Loverdo C, Aertsen A, Ackermann M, De Paepe M, Slack E, Hardt WD. Inflammation boosts bacteriophage transfer between Salmonella spp. Science 2017; 355:1211-1215. [PMID: 28302859 DOI: 10.1126/science.aaf8451] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 12/19/2016] [Accepted: 02/22/2017] [Indexed: 12/12/2022]
Abstract
Bacteriophage transfer (lysogenic conversion) promotes bacterial virulence evolution. There is limited understanding of the factors that determine lysogenic conversion dynamics within infected hosts. A murine Salmonella Typhimurium (STm) diarrhea model was used to study the transfer of SopEΦ, a prophage from STm SL1344, to STm ATCC14028S. Gut inflammation and enteric disease triggered >55% lysogenic conversion of ATCC14028S within 3 days. Without inflammation, SopEΦ transfer was reduced by up to 105-fold. This was because inflammation (e.g., reactive oxygen species, reactive nitrogen species, hypochlorite) triggers the bacterial SOS response, boosts expression of the phage antirepressor Tum, and thereby promotes free phage production and subsequent transfer. Mucosal vaccination prevented a dense intestinal STm population from inducing inflammation and consequently abolished SopEΦ transfer. Vaccination may be a general strategy for blocking pathogen evolution that requires disease-driven transfer of temperate bacteriophages.
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Affiliation(s)
| | | | - Jeffrey K Cornuault
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy en Josas, France
| | - Kathrin Moor
- Institute of Microbiology, ETH Zurich, Switzerland
| | | | - Mikael E Sellin
- Institute of Microbiology, ETH Zurich, Switzerland.,Present address: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
| | - Claude Loverdo
- Laboratoire Jean Perrin (UMR 8237), CNRS-UPMC, 75005 Paris, France
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, KU Leuven, Belgium
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zurich, and Department of Environmental Microbiology, Eawag, Switzerland
| | - Marianne De Paepe
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy en Josas, France
| | - Emma Slack
- Institute of Microbiology, ETH Zurich, Switzerland
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Byndloss MX, Rivera-Chávez F, Tsolis RM, Bäumler AJ. How bacterial pathogens use type III and type IV secretion systems to facilitate their transmission. Curr Opin Microbiol 2017; 35:1-7. [DOI: 10.1016/j.mib.2016.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 10/21/2022]
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Christie GE, Calendar R. Bacteriophage P2. BACTERIOPHAGE 2016; 6:e1145782. [PMID: 27144088 DOI: 10.1080/21597081.2016.1145782] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 10/22/2022]
Abstract
P2 is the original member of a highly successful family of temperate phages that are frequently found in the genomes of gram-negative bacteria. This article focuses on the organization of the P2 genome and reviews current knowledge about the function of each open reading frame.
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Affiliation(s)
- Gail E Christie
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine , Richmond, VA, USA
| | - Richard Calendar
- Department of Molecular and Cell Biology, University of California , Berkeley, CA, USA
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40
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Bartoli C, Roux F, Lamichhane JR. Molecular mechanisms underlying the emergence of bacterial pathogens: an ecological perspective. MOLECULAR PLANT PATHOLOGY 2016; 17:303-10. [PMID: 26062772 PMCID: PMC6638374 DOI: 10.1111/mpp.12284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rapid emergence of new bacterial diseases negatively affects both human health and agricultural productivity. Although the molecular mechanisms underlying these disease emergences are shared between human- and plant-pathogenic bacteria, not much effort has been made to date to understand disease emergences caused by plant-pathogenic bacteria. In particular, there is a paucity of information in the literature on the role of environmental habitats in which plant-pathogenic bacteria evolve and on the stress factors to which these microbes are unceasingly exposed. In this microreview, we focus on three molecular mechanisms underlying pathogenicity in bacteria, namely mutations, genomic rearrangements and the acquisition of new DNA sequences through horizontal gene transfer (HGT). We briefly discuss the role of these mechanisms in bacterial disease emergence and elucidate how the environment can influence the occurrence and regulation of these molecular mechanisms by directly impacting disease emergence. The understanding of such molecular evolutionary mechanisms and their environmental drivers will represent an important step towards predicting bacterial disease emergence and developing sustainable management strategies for crops.
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Affiliation(s)
- Claudia Bartoli
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, F-31326, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, F-31326, Castanet-Tolosan, France
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41
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Davies EV, Winstanley C, Fothergill JL, James CE. The role of temperate bacteriophages in bacterial infection. FEMS Microbiol Lett 2016; 363:fnw015. [PMID: 26825679 DOI: 10.1093/femsle/fnw015] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2016] [Indexed: 12/17/2022] Open
Abstract
Bacteriophages are viruses that infect bacteria. There are an estimated 10(31) phage on the planet, making them the most abundant form of life. We are rapidly approaching the centenary of their identification, and yet still have only a limited understanding of their role in the ecology and evolution of bacterial populations. Temperate prophage carriage is often associated with increased bacterial virulence. The rise in use of technologies, such as genome sequencing and transcriptomics, has highlighted more subtle ways in which prophages contribute to pathogenicity. This review discusses the current knowledge of the multifaceted effects that phage can exert on their hosts and how this may contribute to bacterial adaptation during infection.
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Affiliation(s)
- Emily V Davies
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool L69 7BE, UK
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool L69 7BE, UK
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool L69 7BE, UK
| | - Chloe E James
- Biomedical Research Centre and Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
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Feiner R, Argov T, Rabinovich L, Sigal N, Borovok I, Herskovits AA. A new perspective on lysogeny: prophages as active regulatory switches of bacteria. Nat Rev Microbiol 2016; 13:641-50. [PMID: 26373372 DOI: 10.1038/nrmicro3527] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Unlike lytic phages, temperate phages that enter lysogeny maintain a long-term association with their bacterial host. In this context, mutually beneficial interactions can evolve that support efficient reproduction of both phages and bacteria. Temperate phages are integrated into the bacterial chromosome as large DNA insertions that can disrupt gene expression, and they may pose a fitness burden on the cell. However, they have also been shown to benefit their bacterial hosts by providing new functions in a bacterium-phage symbiotic interaction termed lysogenic conversion. In this Opinion article, we discuss another type of bacterium-phage interaction, active lysogeny, in which phages or phage-like elements are integrated into the bacterial chromosome within critical genes or operons and serve as switches that regulate bacterial genes via genome excision.
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Affiliation(s)
- Ron Feiner
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Argov
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Lev Rabinovich
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nadejda Sigal
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anat A Herskovits
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
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43
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Ben Salem R, Abbassi M, García V, García-Fierro R, Njoud C, Messadi L, Rodicio MR. Detection and Molecular Characterization ofSalmonella entericaSerovar Eppendorf Circulating in Chicken Farms in Tunisia. Zoonoses Public Health 2015; 63:320-7. [DOI: 10.1111/zph.12234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Indexed: 11/30/2022]
Affiliation(s)
- R. Ben Salem
- Veterinary Research Institute of Tunisia; Tunis Tunisia
- Faculty of Sciences of Bizert; University of Carthage; Bizert Tunisia
| | - M.S. Abbassi
- Veterinary Research Institute of Tunisia; Tunis Tunisia
| | - V. García
- Departamento de Biología Funcional; Área de Microbiología; Universidad de Oviedo; Oviedo Spain
| | - R. García-Fierro
- Departamento de Biología Funcional; Área de Microbiología; Universidad de Oviedo; Oviedo Spain
| | - C. Njoud
- Regional Center of Veterinary Research; Sousse Tunisia
| | - L. Messadi
- National School of Veterinary Medicine; Department of Microbiology and Immunology; University of La Manouba; Sidi Thabet Tunisia
| | - M. R. Rodicio
- Departamento de Biología Funcional; Área de Microbiología; Universidad de Oviedo; Oviedo Spain
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44
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Abeles SR, Ly M, Santiago-Rodriguez TM, Pride DT. Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes. PLoS One 2015; 10:e0134941. [PMID: 26309137 PMCID: PMC4550281 DOI: 10.1371/journal.pone.0134941] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/15/2015] [Indexed: 12/23/2022] Open
Abstract
Viruses are integral members of the human microbiome. Many of the viruses comprising the human virome have been identified as bacteriophage, and little is known about how they respond to perturbations within the human ecosystem. The intimate association of phage with their cellular hosts suggests their communities may change in response to shifts in bacterial community membership. Alterations to human bacterial biota can result in human disease including a reduction in the host's resilience to pathogens. Here we report the ecology of oral and fecal viral communities and their responses to long-term antibiotic therapy in a cohort of human subjects. We found significant differences between the viral communities of each body site with a more heterogeneous fecal virus community compared with viruses in saliva. We measured the relative diversity of viruses, and found that the oral viromes were significantly more diverse than fecal viromes. There were characteristic changes in the membership of oral and fecal bacterial communities in response to antibiotics, but changes in fecal viral communities were less distinguishing. In the oral cavity, an abundance of papillomaviruses found in subjects on antibiotics suggests an association between antibiotics and papillomavirus production. Despite the abundance of papillomaviruses identified, in neither the oral nor the fecal viromes did antibiotic therapy have any significant impact upon overall viral diversity. There was, however, an apparent expansion of the reservoir of genes putatively involved in resistance to numerous classes of antibiotics in fecal viromes that was not paralleled in oral viromes. The emergence of antibiotic resistance in fecal viromes in response to long-term antibiotic therapy in humans suggests that viruses play an important role in the resilience of human microbial communities to antibiotic disturbances.
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Affiliation(s)
- Shira R. Abeles
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, United States of America
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, La Jolla, CA, 92093, United States of America
| | | | - David T. Pride
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, United States of America
- Department of Pathology, University of California, San Diego, La Jolla, CA, 92093, United States of America
- * E-mail:
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45
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Switt AIM, Sulakvelidze A, Wiedmann M, Kropinski AM, Wishart DS, Poppe C, Liang Y. Salmonella phages and prophages: genomics, taxonomy, and applied aspects. Methods Mol Biol 2015; 1225:237-87. [PMID: 25253259 DOI: 10.1007/978-1-4939-1625-2_15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Since this book was originally published in 2007 there has been a significant increase in the number of Salmonella bacteriophages, particularly lytic virus, and Salmonella strains which have been fully sequenced. In addition, new insights into phage taxonomy have resulted in new phage genera, some of which have been recognized by the International Committee of Taxonomy of Viruses (ICTV). The properties of each of these genera are discussed, along with the role of phage as agents of genetic exchange, as therapeutic agents, and their involvement in phage typing.
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Affiliation(s)
- Andrea I Moreno Switt
- Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Escuela de Medicina Veterinaria, Republica 440, 8370251, Santiago, Chile
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46
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Carden S, Okoro C, Dougan G, Monack D. Non-typhoidal Salmonella Typhimurium ST313 isolates that cause bacteremia in humans stimulate less inflammasome activation than ST19 isolates associated with gastroenteritis. Pathog Dis 2014; 73:ftu023. [PMID: 25808600 PMCID: PMC4399442 DOI: 10.1093/femspd/ftu023] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2014] [Indexed: 02/07/2023] Open
Abstract
Salmonella is an enteric pathogen that causes a range of diseases in humans. Non-typhoidal Salmonella (NTS) serovars such as Salmonella enterica serovar Typhimurium generally cause a self-limiting gastroenteritis whereas typhoidal serovars cause a systemic disease, typhoid fever. However, S. Typhimurium isolates within the multi-locus sequence type ST313 have emerged in sub-Saharan Africa as a major cause of bacteremia in humans. The S. Typhimurium ST313 lineage is phylogenetically distinct from classical S. Typhimurium lineages, such as ST19, that cause zoonotic gastroenteritis worldwide. Previous studies have shown that the ST313 lineage has undergone genome degradation when compared to the ST19 lineage, similar to that observed for typhoidal serovars. Currently, little is known about phenotypic differences between ST313 isolates and other NTS isolates. We find that representative ST313 isolates invade non-phagocytic cells less efficiently than the classical ST19 isolates that are more commonly associated with gastroenteritis. In addition, ST313 isolates induce less Caspase-1-dependent macrophage death and IL-1β release than ST19 isolates. ST313 isolates also express relatively lower levels of mRNA of the genes encoding the SPI-1 effector sopE2 and the flagellin, fliC, providing possible explanations for the decrease in invasion and inflammasome activation. The ST313 isolates have invasion and inflammatory phenotypes that are intermediate; more invasive and inflammatory than Salmonella enterica serovar Typhi and less than ST19 isolates associated with gastroenteritis. This suggests that both phenotypically and at the genomic level ST313 isolates are evolving signatures that facilitate a systemic lifestyle in humans.
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Affiliation(s)
- Sarah Carden
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chinyere Okoro
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Denise Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Abstract
Prophage-encoded genes can provide a variety of benefits for their bacterial hosts. These beneficial genes are often contained within “moron” elements. Morons, thus termed as the insertion of the DNA encoding them adds “more on” the genome in which they are found, are independent transcriptional units disseminated among phage genomes through horizontal gene transfer. Morons have been identified in the majority of phage genomes and they have been found to play diverse roles in bacterial physiology. At present, we are only beginning to ascribe functions to the many proteins encoded within these ubiquitous genetic elements. Recently, we discovered that the first described moron-encoded protein, gp15 of phage HK97, is expressed from the HK97 prophage and functions as a superinfection exclusion protein, protecting its host from genome injection by other phages. This work and the growing body of data pertaining to other morons challenges the traditional view of phages as purely parasites of bacteria and emphasizes the symbiotic relationship between bacteria and prophages.
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Affiliation(s)
- Nichole Cumby
- Department of Molecular Genetics; University of Toronto; Toronto, ON Canada
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48
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Maier L, Barthel M, Stecher B, Maier RJ, Gunn JS, Hardt WD. Salmonella Typhimurium strain ATCC14028 requires H2-hydrogenases for growth in the gut, but not at systemic sites. PLoS One 2014; 9:e110187. [PMID: 25303479 PMCID: PMC4193879 DOI: 10.1371/journal.pone.0110187] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/11/2014] [Indexed: 11/23/2022] Open
Abstract
Salmonella enterica is a common cause of diarrhea. For eliciting disease, the pathogen has to colonize the gut lumen, a site colonized by the microbiota. This process/initial stage is incompletely understood. Recent work established that one particular strain, Salmonella enterica subspecies 1 serovar Typhimurium strain SL1344, employs the hyb H2-hydrogenase for consuming microbiota-derived H2 to support gut luminal pathogen growth: Protons from the H2-splitting reaction contribute to the proton gradient across the outer bacterial membrane which can be harvested for ATP production or for import of carbon sources. However, it remained unclear, if other Salmonella strains would use the same strategy. In particular, earlier work had left unanswered if strain ATCC14028 might use H2 for growth at systemic sites. To clarify the role of the hydrogenases, it seems important to establish if H2 is used at systemic sites or in the gut and if Salmonella strains may differ with respect to the host sites where they require H2 in vivo. In order to resolve this, we constructed a strain lacking all three H2-hydrogenases of ATCC14028 (14028hyd3) and performed competitive infection experiments. Upon intragastric inoculation, 14028hyd3 was present at 100-fold lower numbers than 14028WT in the stool and at systemic sites. In contrast, i.v. inoculation led to equivalent systemic loads of 14028hyd3 and the wild type strain. However, the pathogen population spreading to the gut lumen featured again up to 100-fold attenuation of 14028hyd3. Therefore, ATCC14028 requires H2-hydrogenases for growth in the gut lumen and not at systemic sites. This extends previous work on ATCC14028 and supports the notion that H2-utilization might be a general feature of S. Typhimurium gut colonization.
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Affiliation(s)
- Lisa Maier
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Manja Barthel
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Bärbel Stecher
- Max von Pettenkofer-Institut, München, Germany
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Robert J. Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - John S. Gunn
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, Biomedical Research Tower, The Ohio State University, Columbus, Ohio, United States of America
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49
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Abeles SR, Pride DT. Molecular bases and role of viruses in the human microbiome. J Mol Biol 2014; 426:3892-906. [PMID: 25020228 PMCID: PMC7172398 DOI: 10.1016/j.jmb.2014.07.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/30/2014] [Accepted: 07/04/2014] [Indexed: 12/24/2022]
Abstract
Viruses are dependent biological entities that interact with the genetic material of most cells on the planet, including the trillions within the human microbiome. Their tremendous diversity renders analysis of human viral communities ("viromes") to be highly complex. Because many of the viruses in humans are bacteriophage, their dynamic interactions with their cellular hosts add greatly to the complexities observed in examining human microbial ecosystems. We are only beginning to be able to study human viral communities on a large scale, mostly as a result of recent and continued advancements in sequencing and bioinformatic technologies. Bacteriophage community diversity in humans not only is inexorably linked to the diversity of their cellular hosts but also is due to their rapid evolution, horizontal gene transfers, and intimate interactions with host nucleic acids. There are vast numbers of observed viral genotypes on many body surfaces studied, including the oral, gastrointestinal, and respiratory tracts, and even in the human bloodstream, which previously was considered a purely sterile environment. The presence of viruses in blood suggests that virome members can traverse mucosal barriers, as indeed these communities are substantially altered when mucosal defenses are weakened. Perhaps the most interesting aspect of human viral communities is the extent to which they can carry gene functions involved in the pathogenesis of their hosts, particularly antibiotic resistance. Persons in close contact with each other have been shown to share a fraction of oral virobiota, which could potentially have important implications for the spread of antibiotic resistance to healthy individuals. Because viruses can have a large impact on ecosystem dynamics through mechanisms such as the transfers of beneficial gene functions or the lysis of certain populations of cellular hosts, they may have both beneficial and detrimental roles that affect human health, including improvements in microbial resilience to disturbances, immune evasion, maintenance of physiologic processes, and altering the microbial community in ways that promote or prevent pathogen colonization.
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Affiliation(s)
- Shira R Abeles
- Department of Medicine, University of California, San Diego, CA 92093, USA
| | - David T Pride
- Department of Medicine, University of California, San Diego, CA 92093, USA; Department of Pathology, University of California, San Diego, CA 92093, USA.
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50
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The Dynamic Interactions between Salmonella and the Microbiota, within the Challenging Niche of the Gastrointestinal Tract. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:846049. [PMID: 27437481 PMCID: PMC4897363 DOI: 10.1155/2014/846049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/14/2014] [Indexed: 12/25/2022]
Abstract
Understanding how Salmonella species establish successful infections remains a foremost research priority. This gastrointestinal pathogen not only faces the hostile defenses of the host's immune system, but also faces fierce competition from the large and diverse community of microbiota for space and nutrients. Salmonella have solved these challenges ingeniously. To jump-start growth, Salmonella steal hydrogen produced by the gastrointestinal microbiota. Type 3 effector proteins are subsequently secreted by Salmonella to trigger potent inflammatory responses, which generate the alternative terminal electron acceptors tetrathionate and nitrate. Salmonella exclusively utilize these electron acceptors for anaerobic respiration, permitting metabolic access to abundant substrates such as ethanolamine to power growth blooms. Chemotaxis and flagella-mediated motility enable the identification of nutritionally beneficial niches. The resulting growth blooms also promote horizontal gene transfer amongst the resident microbes. Within the gastrointestinal tract there are opportunities for chemical signaling between host cells, the microbiota, and Salmonella. Host produced catecholamines and bacterial autoinducers form components of this chemical dialogue leading to dynamic interactions. Thus, Salmonella have developed remarkable strategies to initially shield against host defenses and to transiently compete against the intestinal microbiota leading to successful infections. However, the immunocompetent host is subsequently able to reestablish control and clear the infection.
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