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Kalalah AA, Koenig SSK, Feng P, Bosilevac JM, Bono JL, Eppinger M. Pathogenomes of Shiga Toxin Positive and Negative Escherichia coli O157:H7 Strains TT12A and TT12B: Comprehensive Phylogenomic Analysis Using Closed Genomes. Microorganisms 2024; 12:699. [PMID: 38674643 PMCID: PMC11052207 DOI: 10.3390/microorganisms12040699] [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: 03/02/2024] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Shiga toxin-producing Escherichia coli are zoonotic pathogens that cause food-borne human disease. Among these, the O157:H7 serotype has evolved from an enteropathogenic O55:H7 ancestor through the displacement of the somatic gene cluster and recurrent toxigenic conversion by Shiga toxin-converting bacteriophages. However, atypical strains that lack the Shiga toxin, the characteristic virulence hallmark, are circulating in this lineage. For this study, we analyzed the pathogenome and virulence inventories of the stx+ strain, TT12A, isolated from a patient with hemorrhagic colitis, and its respective co-isolated stx- strain, TT12B. Sequencing the genomes to closure proved critical to the cataloguing of subtle strain differentiating sequence and structural polymorphisms at a high-level of phylogenetic accuracy and resolution. Phylogenomic profiling revealed SNP and MLST profiles similar to the near clonal outbreak isolates. Their prophage inventories, however, were notably different. The attenuated atypical non-shigatoxigenic status of TT12B is explained by the absence of both the ΦStx1a- and ΦStx2a-prophages carried by TT12A, and we also recorded further alterations in the non-Stx prophage complement. Phenotypic characterization indicated that culture growth was directly impacted by the strains' distinct lytic phage complement. Altogether, our phylogenomic and phenotypic analyses show that these intimately related isogenic strains are on divergent Stx(+/stx-) evolutionary paths.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Peter Feng
- U.S. Food and Drug Administration (FDA), College Park, MD 20740, USA
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
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Kalalah AA, Koenig SSK, Bono JL, Bosilevac JM, Eppinger M. Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli. Front Microbiol 2024; 15:1364026. [PMID: 38562479 PMCID: PMC10982417 DOI: 10.3389/fmicb.2024.1364026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) of non-O157:H7 serotypes are responsible for global and widespread human food-borne disease. Among these serogroups, O26, O45, O103, O111, O121, and O145 account for the majority of clinical infections and are colloquially referred to as the "Big Six." The "Big Six" strain panel we sequenced and analyzed in this study are reference type cultures comprised of six strains representing each of the non-O157 STEC serogroups curated and distributed by the American Type Culture Collection (ATCC) as a resource to the research community under panel number ATCC MP-9. The application of long- and short-read hybrid sequencing yielded closed chromosomes and a total of 14 plasmids of diverse functions. Through high-resolution comparative phylogenomics, we cataloged the shared and strain-specific virulence and resistance gene content and established the close relationship of serogroup O26 and O103 strains featuring flagellar H-type 11. Virulence phenotyping revealed statistically significant differences in the Stx-production capabilities that we found to be correlated to the strain's individual stx-status. Among the carried Stx1a, Stx2a, and Stx2d phages, the Stx2a phage is by far the most responsive upon RecA-mediated phage mobilization, and in consequence, stx2a + isolates produced the highest-level of toxin in this panel. The availability of high-quality closed genomes for this "Big Six" reference set, including carried plasmids, along with the recorded genomic virulence profiles and Stx-production phenotypes will provide a valuable foundation to further explore the plasticity in evolutionary trajectories in these emerging non-O157 STEC lineages, which are major culprits of human food-borne disease.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
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3
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Pascal SB, Lorenzo R, Farías MVN, Rossen JW, Lucchesi PMA, Krüger A. Characterization of the flanking region of the Shiga toxin operon in Stx2a bacteriophages reveals a diversity of the NanS-p sialate O-acetylesterase gene. AIMS Microbiol 2023; 9:570-590. [PMID: 37649799 PMCID: PMC10462455 DOI: 10.3934/microbiol.2023030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 09/01/2023] Open
Abstract
Shiga toxin-producing E. coli (STEC) are diarrheagenic strains that can cause bloody diarrhea and hemolytic-uremic syndrome. Their main virulence factor, the Shiga toxin (Stx), is encoded by phages integrated into the bacterial chromosome. Stx phages are widely diverse and carry many genes with limited or unknown function. As the toxin subtype Stx2a is associated with highly pathogenic strains, this study was mainly focused on the characterization of the stx flanking region of Stx2a phages. Of particular interest was a sialate O-acetylesterase (NanS-p), which has been described previously to be encoded downstream stx in some phage genomes and may confer a growth advantage for STEC. Complete DNA sequences of Stx2a phages and prophages were retrieved from the GenBank database, and the genomic regions from anti-terminator Q to holin S genes were bioinformatically analyzed. Predicted NanSp sequences from phages encoding other Stx subtypes were also studied. Additionally, expression of nanS-p was quantified by qPCR in strains selected from our laboratory collection. The analysis of Stx2a phage genomes showed that all carried the Q, stx2a, nanS-p and S genes, but with allele diversity and other sequence differences. In particular, sequence differences were detected in each of the three domains of NanS-p esterases encoded by Stx2a phages and other Stx phages; however, nanS-p was not identified in the Stx2e, Stx2f and Stx2g phages analyzed. The expression of nanS-p increased in most stx2a-positive strains under phage inducing conditions, as was previously shown for stx2a. As the present work showed diversity at the Q-S region among Stx phages, and particularly in the encoded NanS-p enzyme, future studies will be necessary to evaluate if NanS-p variants differ in their activity and to assess the impact of the absence of nanS-p in certain Stx phages.
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Affiliation(s)
- Stefanía B. Pascal
- Universidad Nacional del Centro de la Provincia de Buenos Aires (UNCPBA), Facultad de Ciencias Veterinarias, CISAPA, Tandil, Buenos Aires, Argentina
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CICPBA-CONICET, Tandil, Buenos Aires, Argentina
| | - Ramiro Lorenzo
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CICPBA-CONICET, Tandil, Buenos Aires, Argentina
- Laboratory of Neurophysiology, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - María Victoria Nieto Farías
- Universidad Nacional del Centro de la Provincia de Buenos Aires (UNCPBA), Facultad de Ciencias Veterinarias, CISAPA, Tandil, Buenos Aires, Argentina
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CICPBA-CONICET, Tandil, Buenos Aires, Argentina
| | - John W.A. Rossen
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Hospital, Zwolle, The Netherlands
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Paula M. A. Lucchesi
- Universidad Nacional del Centro de la Provincia de Buenos Aires (UNCPBA), Facultad de Ciencias Veterinarias, CISAPA, Tandil, Buenos Aires, Argentina
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CICPBA-CONICET, Tandil, Buenos Aires, Argentina
| | - Alejandra Krüger
- Universidad Nacional del Centro de la Provincia de Buenos Aires (UNCPBA), Facultad de Ciencias Veterinarias, CISAPA, Tandil, Buenos Aires, Argentina
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CICPBA-CONICET, Tandil, Buenos Aires, Argentina
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Frazão N, Gordo I. Ecotype formation and prophage domestication during gut bacterial evolution. Bioessays 2023; 45:e2300063. [PMID: 37353919 DOI: 10.1002/bies.202300063] [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: 04/12/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/25/2023]
Abstract
How much bacterial evolution occurs in our intestines and which factors control it are currently burning questions. The formation of new ecotypes, some of which capable of coexisting for long periods of time, is highly likely in our guts. Horizontal gene transfer driven by temperate phages that can perform lysogeny is also widespread in mammalian intestines. Yet, the roles of mutation and especially lysogeny as key drivers of gut bacterial adaptation remain poorly understood. The mammalian gut contains hundreds of bacterial species, each with many strains and ecotypes, whose abundance varies along the lifetime of a host. A continuous high input of mutations and horizontal gene transfer events mediated by temperate phages drives that diversity. Future experiments to study the interaction between mutations that cause adaptation in microbiomes and lysogenic events with different costs and benefits will be key to understand the dynamic microbiomes of mammals. Also see the video abstract here: https://youtu.be/Zjqsiyb5Pk0.
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Affiliation(s)
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Shah SA, Deng L, Thorsen J, Pedersen AG, Dion MB, Castro-Mejía JL, Silins R, Romme FO, Sausset R, Jessen LE, Ndela EO, Hjelmsø M, Rasmussen MA, Redgwell TA, Leal Rodríguez C, Vestergaard G, Zhang Y, Chawes B, Bønnelykke K, Sørensen SJ, Bisgaard H, Enault F, Stokholm J, Moineau S, Petit MA, Nielsen DS. Expanding known viral diversity in the healthy infant gut. Nat Microbiol 2023; 8:986-998. [PMID: 37037943 PMCID: PMC10159846 DOI: 10.1038/s41564-023-01345-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/17/2023] [Indexed: 04/12/2023]
Abstract
The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.
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Affiliation(s)
- Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders G Pedersen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
| | | | - Ronalds Silins
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Fie O Romme
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Romain Sausset
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Leon E Jessen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Eric Olo Ndela
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mathis Hjelmsø
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Morten A Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Tamsin A Redgwell
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Cristina Leal Rodríguez
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Yichang Zhang
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Francois Enault
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Quebec, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
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Henrot C, Petit M. Signals triggering prophage induction in the gut microbiota. Mol Microbiol 2022; 118:494-502. [PMID: 36164818 PMCID: PMC9827884 DOI: 10.1111/mmi.14983] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/15/2022] [Accepted: 09/18/2022] [Indexed: 01/12/2023]
Abstract
Compared to bacteria of the gut microbiota, bacteriophages are still poorly characterised, and their physiological importance is far less known. Temperate phages are probably a major actor in the gut, as it is estimated that 80% of intestinal bacteria are lysogens, meaning that they are carrying prophages. In addition, prophage induction rates are higher in the gut than in vitro. However, studies on the signals leading to prophage induction have essentially focused on genotoxic agents with poor relevance for this environment. In this review, we sum up recent findings about signals able to trigger prophage induction in the gut. Three categories of signals are at play: those originating from interactions between intestinal microbes, those from the human or animal host physiology and those from external intakes. These recent results highlight the diversity of factors influencing prophage induction in the gut, and start to unveil ways by which microbiota composition may be modulated.
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Affiliation(s)
- Caroline Henrot
- Université Paris‐Saclay, INRAEAgroParisTech, Micalis InstituteJouy‐en‐JosasFrance,Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1Université de LyonLyonFrance
| | - Marie‐Agnès Petit
- Université Paris‐Saclay, INRAEAgroParisTech, Micalis InstituteJouy‐en‐JosasFrance
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7
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Lange ME, Uwiera RRE, Inglis GD. Enteric Escherichia coli O157:H7 in Cattle, and the Use of Mice as a Model to Elucidate Key Aspects of the Host-Pathogen-Microbiota Interaction: A Review. Front Vet Sci 2022; 9:937866. [PMID: 35898542 PMCID: PMC9310005 DOI: 10.3389/fvets.2022.937866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/02/2022] [Indexed: 11/24/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 is responsible for foodborne disease outbreaks, typically associated with the consumption of undercooked foods contaminated with cattle manure containing the bacterium. At present, effective mitigations do not exist. Many of the factors regulating enteric colonization by E. coli O157:H7 in cattle, and how cattle respond to the bacterium are unknown. In this regard, intestinal colonization locations, shedding patterns, interactions with the enteric microbiota, and host immune responses to infection are current knowledge gaps. As disturbances to host homeostasis are believed to play an important role in the enteric survival of the bacterium, it is important to consider the potential importance of stress during cattle production. Husbandry logistics, cost, and the high genetic, physiological, and microbial heterogeneity in cattle has greatly hampered the ability of researchers to elucidate key aspects of the host-pathogen-microbiota interaction. Although mice have not been extensively used as a cattle model, the utilization of murine models has the potential to identify mechanisms to facilitate hypothesis formulation and efficacy testing in cattle. Murine models have been effectively used to mechanistically examine colonization of the intestine, host responses to infection, and to interactively ascertain how host physiological status (e.g., due to physiological stress) and the enteric microbiota influences colonization and disease. In addition to reviewing the relevant literature on intestinal colonization and pathogenesis, including existing knowledge gaps, the review provides information on how murine models can be used to elucidate mechanisms toward the development of rationale-based mitigations for E. coli O157:H7 in cattle.
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Affiliation(s)
- Maximo E. Lange
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Richard R. E. Uwiera
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - G. Douglas Inglis
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
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Tiamani K, Luo S, Schulz S, Xue J, Costa R, Khan Mirzaei M, Deng L. The role of virome in the gastrointestinal tract and beyond. FEMS Microbiol Rev 2022; 46:6608358. [PMID: 35700129 PMCID: PMC9629487 DOI: 10.1093/femsre/fuac027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 01/11/2023] Open
Abstract
The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In addition, these viruses interact with the immune cells, trigger a broad range of immune responses, and influence different metabolic pathways. Besides its key role in regulating the human gut homeostasis, the intestinal virome contributes to disease development in distant organs, both directly and indirectly. In this review, we will describe the changes in the gut virome through life, health, and disease, followed by discussing the interactions between the virome, the microbiome, and the human host as well as providing an overview of their contribution to gut disease and disease of distant organs.
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Affiliation(s)
| | | | - Sarah Schulz
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rita Costa
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Li Deng
- Corresponding author: Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany; Chair of Prevention of Microbial Diseases, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany. E-mail:
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9
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Allué-Guardia A, Koenig SSK, Martinez RA, Rodriguez AL, Bosilevac JM, Feng† P, Eppinger M. Pathogenomes and variations in Shiga toxin production among geographically distinct clones of Escherichia coli O113:H21. Microb Genom 2022; 8. [PMID: 35394418 PMCID: PMC9453080 DOI: 10.1099/mgen.0.000796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Infections with globally disseminated Shiga toxin-producing Escherichia coli (STEC) of the O113:H21 serotype can progress to severe clinical complications, such as hemolytic uremic syndrome (HUS). Two phylogeographically distinct clonal complexes have been established by multi locus sequence typing (MLST). Infections with ST-820 isolates circulating exclusively in Australia have caused severe human disease, such as HUS. Conversely, ST-223 isolates prevalent in the US and outside Australia seem to rarely cause severe human disease but are frequent contaminants. Following a genomic epidemiology approach, we wanted to gain insights into the underlying cause for this disparity. We examined the plasticity in the genome make-up and Shiga toxin production in a collection of 20 ST-820 and ST-223 strains isolated from produce, the bovine reservoir, and clinical cases. STEC are notorious for assembly into fragmented draft sequences when using short-read sequencing technologies due to the extensive and partly homologous phage complement. The application of long-read technology (LRT) sequencing yielded closed reference chromosomes and plasmids for two representative ST-820 and ST-223 strains. The established high-resolution framework, based on whole genome alignments, single nucleotide polymorphism (SNP)-typing and MLST, includes the chromosomes and plasmids of other publicly available O113:H21 sequences and allowed us to refine the phylogeographical boundaries of ST-820 and ST-223 complex isolates and to further identify a historic non-shigatoxigenic strain from Mexico as a quasi-intermediate. Plasmid comparison revealed strong correlations between the strains' featured pO113 plasmid genotypes and chromosomally inferred ST, which suggests coevolution of the chromosome and virulence plasmids. Our pathogenicity assessment revealed statistically significant differences in the Stx2a-production capabilities of ST-820 as compared to ST-223 strains under RecA-induced Stx phage mobilization, a condition that mimics Stx-phage induction. These observations suggest that ST-820 strains may confer an increased pathogenic potential in line with the strain-associated epidemiological metadata. Still, some of the tested ST-223 cultures sourced from contaminated produce or the bovine reservoir also produced Stx at levels comparable to those of ST-820 isolates, which calls for awareness and for continued surveillance of this lineage.
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Affiliation(s)
- Anna Allué-Guardia
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Ricardo A. Martinez
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Armando L. Rodriguez
- University of Texas at San Antonio, Research Computing Support Group, San Antonio, TX, USA
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Peter Feng†
- U.S. Food and Drug Administration (FDA), College Park, MD, USA
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
- *Correspondence: Mark Eppinger,
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10
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Lodato PB. The effect of two ribonucleases on the production of Shiga toxin and stx-bearing bacteriophages in Enterohaemorrhagic Escherichia coli. Sci Rep 2021; 11:18372. [PMID: 34526533 PMCID: PMC8443680 DOI: 10.1038/s41598-021-97736-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/27/2021] [Indexed: 11/20/2022] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) comprise a group of intestinal pathogens responsible for a range of illnesses, including kidney failure and neurological compromise. EHEC produce critical virulence factors, Shiga toxin (Stx) 1 or 2, and the synthesis of Stx2 is associated with worse disease manifestations. Infected patients only receive supportive treatment because some conventional antibiotics enable toxin production. Shiga toxin 2 genes (stx2) are carried in λ-like bacteriophages (stx2-phages) inserted into the EHEC genome as prophages. Factors that cause DNA damage induce the lytic cycle of stx2-phages, leading to Stx2 production. The phage Q protein is critical for transcription antitermination of stx2 and phage lytic genes. This study reports that deficiency of two endoribonucleases (RNases), E and G, significantly delayed cell lysis and impaired production of both Stx2 and stx2-phages, unlike deficiency of either enzyme alone. Moreover, scarcity of both enzymes reduced the concentrations of Q and stx2 transcripts and slowed cell growth.
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Affiliation(s)
- Patricia B Lodato
- Department of Microbiology and Immunology, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO, 63501, USA.
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11
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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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12
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Marongiu L, Burkard M, Venturelli S, Allgayer H. Dietary Modulation of Bacteriophages as an Additional Player in Inflammation and Cancer. Cancers (Basel) 2021; 13:cancers13092036. [PMID: 33922485 PMCID: PMC8122878 DOI: 10.3390/cancers13092036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 01/06/2023] Open
Abstract
Natural compounds such as essential oils and tea have been used successfully in naturopathy and folk medicine for hundreds of years. Current research is unveiling the molecular role of their antibacterial, anti-inflammatory, and anticancer properties. Nevertheless, the effect of these compounds on bacteriophages is still poorly understood. The application of bacteriophages against bacteria has gained a particular interest in recent years due to, e.g., the constant rise of antimicrobial resistance to antibiotics, or an increasing awareness of different types of microbiota and their potential contribution to gastrointestinal diseases, including inflammatory and malignant conditions. Thus, a better knowledge of how dietary products can affect bacteriophages and, in turn, the whole gut microbiome can help maintain healthy homeostasis, reducing the risk of developing diseases such as diverse types of gastroenteritis, inflammatory bowel disease, or even cancer. The present review summarizes the effect of dietary compounds on the physiology of bacteriophages. In a majority of works, the substance class of polyphenols showed a particular activity against bacteriophages, and the primary mechanism of action involved structural damage of the capsid, inhibiting bacteriophage activity and infectivity. Some further dietary compounds such as caffeine, salt or oregano have been shown to induce or suppress prophages, whereas others, such as the natural sweeter stevia, promoted species-specific phage responses. A better understanding of how dietary compounds could selectively, and specifically, modulate the activity of individual phages opens the possibility to reorganize the microbial network as an additional strategy to support in the combat, or in prevention, of gastrointestinal diseases, including inflammation and cancer.
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Affiliation(s)
- Luigi Marongiu
- Department of Experimental Surgery—Cancer Metastasis, Medical Faculty Mannheim, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany;
| | - Markus Burkard
- Department of Biochemistry of Nutrition, University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany;
| | - Sascha Venturelli
- Department of Biochemistry of Nutrition, University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany;
- Department of Vegetative and Clinical Physiology, University Hospital of Tuebingen, Otfried-Müllerstr. 27, 72076 Tuebingen, Germany
- Correspondence: (S.V.); (H.A.); Tel.: +49-(0)711-459-24113 (ext. 24195) (S.V.); +49-(0)621-383-71630 (ext. 71635) (H.A.); Fax: +49-(0)-711-459-23822 (S.V.); +49-(0)-621-383-71631 (H.A.)
| | - Heike Allgayer
- Department of Experimental Surgery—Cancer Metastasis, Medical Faculty Mannheim, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Str. 13-17, 68167 Mannheim, Germany;
- Correspondence: (S.V.); (H.A.); Tel.: +49-(0)711-459-24113 (ext. 24195) (S.V.); +49-(0)621-383-71630 (ext. 71635) (H.A.); Fax: +49-(0)-711-459-23822 (S.V.); +49-(0)-621-383-71631 (H.A.)
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13
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Flowers LJ, Hu S, Shrestha A, Martinot AJ, Leong JM, Osburne MS. Citrobacter rodentium Lysogenized with a Shiga Toxin-Producing Phage: A Murine Model for Shiga Toxin-Producing E. coli Infection. Methods Mol Biol 2021; 2291:381-397. [PMID: 33704765 DOI: 10.1007/978-1-0716-1339-9_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Shiga toxin-producing E. coli (STEC) is a common foodborne pathogen in developed countries. STEC generates "attaching and effacing" (AE) lesions on colonic epithelium, characterized by effacement of microvilli and the formation of actin "pedestals" beneath intimately attached bacteria. In addition, STEC are lysogenized with a phage that, upon induction, can produce potent Shiga toxins (Stx), potentially leading to both hemorrhagic colitis and hemolytic uremic syndrome. Investigation of the pathogenesis of this disease has been challenging because STEC does not readily colonize conventional mice.Citrobacter rodentium (CR) is a related mouse pathogen that also generates AE lesions. Whereas CR does not produce Stx, a murine model for STEC utilizes CR lysogenized with an E. coli-derived Stx phage, generating CR(Φstx), which both colonizes conventional mice and readily gives rise to systemic disease. We present here key methods for the use of CR(Φstx) infection as a highly predictable murine model for infection and disease by STEC. Importantly, we detail CR(Φstx) inoculation by feeding, determination of pathogen colonization, production of phage and toxin, and assessment of intestinal and renal pathology. These methods provide a framework for studying STEC-mediated systemic disease that may aid in the development of efficacious therapeutics.
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Affiliation(s)
- Laurice J Flowers
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Tufts University Graduate School in Biomedical Sciences, Boston, MA, USA.,Department of Dermatology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shenglan Hu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding, Guangzhou, China
| | - Anishma Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Amanda J Martinot
- Department of Infectious Diseases and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - John M Leong
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Marcia S Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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14
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Naïli I, Gardette M, Garrivier A, Daniel J, Desvaux M, Pizza M, Gobert A, Marchal T, Loukiadis E, Jubelin G. Interplay between enterohaemorrhagic Escherichia coli and nitric oxide during the infectious process. Emerg Microbes Infect 2021; 9:1065-1076. [PMID: 32459575 PMCID: PMC7336997 DOI: 10.1080/22221751.2020.1768804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) are bacterial pathogens responsible for life-threatening diseases in humans such as bloody diarrhoea and the hemolytic and uremic syndrome. To date, no specific therapy is available and treatments remain essentially symptomatic. In recent years, we demonstrated in vitro that nitric oxide (NO), a major mediator of the intestinal immune response, strongly represses the synthesis of the two cardinal virulence factors in EHEC, namely Shiga toxins (Stx) and the type III secretion system, suggesting NO has a great potential to protect against EHEC infection. In this study, we investigated the interplay between NO and EHEC in vivo using mouse models of infection. Using a NO-sensing reporter strain, we determined that EHEC sense NO in the gut of infected mice. Treatment of infected mice with a specific NOS inhibitor increased EHEC adhesion to the colonic mucosa but unexpectedly decreased Stx activity in the gastrointestinal tract, protecting mice from renal failure. Taken together, our data indicate that NO can have both beneficial and detrimental consequences on the outcome of an EHEC infection, and underline the importance of in vivo studies to increase our knowledge in host–pathogen interactions.
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Affiliation(s)
- Ilham Naïli
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,GSK, Siena, Italy
| | - Marion Gardette
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,Université de Lyon, CNRS, INRAE, Université Claude Bernard Lyon 1, VetAgro Sup, Laboratoire d'Ecologie Microbienne, F-63280 Marcy l'Etoile, France
| | - Annie Garrivier
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Julien Daniel
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | | | - Alain Gobert
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Thierry Marchal
- VetAgro Sup, Laboratoire vétérinaire d'histopathologie, F-63280 Marcy-l'Etoile, France
| | - Estelle Loukiadis
- Université de Lyon, CNRS, INRAE, Université Claude Bernard Lyon 1, VetAgro Sup, Laboratoire d'Ecologie Microbienne, F-63280 Marcy l'Etoile, France.,VetAgro Sup, Laboratoire national de référence des E. coli, F-63280 Marcy-l'Etoile, France
| | - Grégory Jubelin
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
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15
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A Toxic Environment: a Growing Understanding of How Microbial Communities Affect Escherichia coli O157:H7 Shiga Toxin Expression. Appl Environ Microbiol 2020; 86:AEM.00509-20. [PMID: 32358004 DOI: 10.1128/aem.00509-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) strains, including E. coli O157:H7, cause severe illness in humans due to the production of Shiga toxin (Stx) and other virulence factors. Because Stx is coregulated with lambdoid prophage induction, its expression is especially susceptible to environmental cues. Infections with Stx-producing E. coli can be difficult to model due to the wide range of disease outcomes: some infections are relatively mild, while others have serious complications. Probiotic organisms, members of the gut microbiome, and organic acids can depress Stx production, in many cases by inhibiting the growth of EHEC strains. On the other hand, the factors currently known to amplify Stx act via their effect on the stx-converting phage. Here, we characterize two interactive mechanisms that increase Stx production by O157:H7 strains: first, direct interactions with phage-susceptible E. coli, and second, indirect amplification by secreted factors. Infection of susceptible strains by the stx-converting phage can expand the Stx-producing population in a human or animal host, and phage infection has been shown to modulate virulence in vitro and in vivo Acellular factors, particularly colicins and microcins, can kill O157:H7 cells but may also trigger Stx expression in the process. Colicins, microcins, and other bacteriocins have diverse cellular targets, and many such molecules remain uncharacterized. The identification of additional Stx-amplifying microbial interactions will improve our understanding of E. coli O157:H7 infections and help elucidate the intricate regulation of pathogenicity in EHEC strains.
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16
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Hauser JR, Atitkar RR, Petro CD, Lindsey RL, Strockbine N, O'Brien AD, Melton-Celsa AR. The Virulence of Escherichia coli O157:H7 Isolates in Mice Depends on Shiga Toxin Type 2a (Stx2a)-Induction and High Levels of Stx2a in Stool. Front Cell Infect Microbiol 2020; 10:62. [PMID: 32175286 PMCID: PMC7054288 DOI: 10.3389/fcimb.2020.00062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/07/2020] [Indexed: 12/28/2022] Open
Abstract
In this study we compared nine Shiga toxin (Stx)-producing Escherichia coli O157:H7 patient isolates for Stx levels, stx-phage insertion site(s), and pathogenicity in a streptomycin (Str)-treated mouse model. The strains encoded stx2a, stx1a and stx2a, or stx2a and stx2c. All of the strains elaborated 105-106 cytotoxic doses 50% (CD50) into the supernatant after growth in vitro as measured on Vero cells, and showed variable levels of increased toxin production after growth with sub-inhibitory levels of ciprofloxacin (Cip). The stx2a+stx2c+ isolates were 90–100% lethal for Str-treated BALB/c mice, though one isolate, JH2013, had a delayed time-to-death. The stx2a+ isolate was avirulent. Both an stx2a and a recA deletion mutant of one of the stx2a+stx2c+ strains, JH2010, exhibited at least a three-log decrease in cytotoxicity in vitro and both were avirulent in the mice. Stool from Str-treated mice infected with the highly virulent isolates were 10- to 100-fold more cytotoxic than feces from mice infected with the clinical isolate, JH2012, that made only Stx2a. Taken together these findings demonstrate that the stx2a-phage from JH2010 induces to higher levels in vivo than does the phage from JH2012. The stx1a+stx2a+ clinical isolates were avirulent and neutralization of Stx1 in stool from mice infected with those strains indicated that the toxin produced in vivo was primarily Stx1a. Treatment of mice infected with Stx1a+Stx2a+ isolates with Cip resulted in an increase in Stx2a production in vivo and lethality in the mice. Our data suggest that high levels of Stx2a in stool are predictive of virulence in mice.
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Affiliation(s)
- Jocelyn R Hauser
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Rama R Atitkar
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Courtney D Petro
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Rebecca L Lindsey
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Nancy Strockbine
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Alison D O'Brien
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Angela R Melton-Celsa
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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17
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Filipiak M, Łoś JM, Łoś M. Efficiency of induction of Shiga-toxin lambdoid prophages in Escherichia coli due to oxidative and antibiotic stress depends on the combination of prophage and the bacterial strain. J Appl Genet 2019; 61:131-140. [PMID: 31808108 PMCID: PMC6968986 DOI: 10.1007/s13353-019-00525-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/19/2019] [Accepted: 09/26/2019] [Indexed: 11/30/2022]
Abstract
In the study presented here, we tested, how large a fraction of lysogenic culture was undergoing filamentation, which could indicate triggering of the SOS response or SOS-independent prophage induction that is also known to cause cell filamentation. Here, antibiotic stress was triggered by adding mitomycin C and oxidative stress was induced by hydrogen peroxide. Observation of bacterial cells under an optical microscope revealed more filamenting cells for lysogenic Escherichia coli than for strains not carrying a prophage. Moreover, the amount of filamenting cells depended not only on the stress agents used and the type of the prophage, but also on the host. During induction of the 933W prophage, the resulting phage titer and the amount of elongating cells were different when using E. coli O157:H7 EDL933 clinical isolate and the E. coli MG1655 laboratory strain. The amount of filamenting cells correlates well with the observed phage titers.
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Affiliation(s)
- Michalina Filipiak
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza Street 59, 80-308, Gdansk, Poland
| | - Joanna M Łoś
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza Street 59, 80-308, Gdansk, Poland.
- Phage Consultants, Partyzantow Street 10/18, 80-254, Gdansk, Poland.
| | - Marcin Łoś
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza Street 59, 80-308, Gdansk, Poland
- Phage Consultants, Partyzantow Street 10/18, 80-254, Gdansk, Poland
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18
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Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens. Appl Environ Microbiol 2019; 85:AEM.00853-19. [PMID: 31253674 PMCID: PMC6696956 DOI: 10.1128/aem.00853-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/19/2019] [Indexed: 12/16/2022] Open
Abstract
The fast-growing marine bacterium Vibrio natriegens represents an emerging strain for molecular biology and biotechnology. Genome sequencing and quantitative PCR analysis revealed that the first chromosome of V. natriegens ATCC 14048 contains two prophage regions (VNP1 and VNP2) that are both inducible by the DNA-damaging agent mitomycin C and exhibit spontaneous activation under standard cultivation conditions. Their activation was also confirmed by live cell imaging of an mCherry fusion to the major capsid proteins of VNP1 and VNP2. Transmission electron microscopy visualized the release of phage particles belonging to the Siphoviridae family into the culture supernatant. Freeing V. natriegens from its proviral load, followed by phenotypic characterization, revealed an improved robustness of the prophage-free variant toward DNA-damaging conditions, reduced cell lysis under hypo-osmotic conditions, and an increased pyruvate production compared to wild-type levels. Remarkably, the prophage-free strain outcompeted the wild type in a competitive growth experiment, emphasizing that this strain is a promising platform for future metabolic engineering approaches.IMPORTANCE The fast-growing marine bacterium Vibrio natriegens represents an emerging model host for molecular biology and biotechnology, featuring a reported doubling time of less than 10 minutes. In many bacterial species, viral DNA (prophage elements) may constitute a considerable fraction of the whole genome and may have detrimental effects on the growth and fitness of industrial strains. Genome analysis revealed the presence of two prophage regions in the V. natriegens genome that were shown to undergo spontaneous induction under standard cultivation conditions. In this study, we generated a prophage-free variant of V. natriegens Remarkably, the prophage-free strain exhibited a higher tolerance toward DNA damage and hypo-osmotic stress. Moreover, it was shown to outcompete the wild-type strain in a competitive growth experiment. In conclusion, our study presents the prophage-free variant of V. natriegens as a promising platform strain for future biotechnological applications.
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19
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To CZ, Bhunia AK. Three Dimensional Vero Cell-Platform for Rapid and Sensitive Screening of Shiga-Toxin Producing Escherichia coli. Front Microbiol 2019; 10:949. [PMID: 31134009 PMCID: PMC6514307 DOI: 10.3389/fmicb.2019.00949] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 04/15/2019] [Indexed: 01/27/2023] Open
Abstract
Shiga-toxin producing Escherichia coli (STEC) is a serious public health concern. Current Vero cell assay, although sensitive, is lengthy and requires 48-72 h to assess STEC presence in a sample. In this study, we investigated if Vero cells in a three-dimensional (3D) platform would provide improved sensitivity for rapid screening of STEC. Vero cells (epithelial kidney cell line) were grown as a monolayer (2D) or in a collagen-matrix (3D) and exposed to Shiga-toxin (Stx) preparation or STEC cells that were pre-exposed to antibiotics (mitomycin C, ciprofloxacin, or polymyxin B) for toxin induction. Lactate dehydrogenase (LDH) release from Vero cells was used as a biomarker for cytotoxicity. Modified tryptic soy broth (mTSB) as enrichment broth containing mitomycin C (2 μg/ml) or ciprofloxacin (100 ng/ml) significantly induced Stx production, which was further confirmed by the dot-immunoblot assay. The 3D Vero platform detected STEC after 6 h post-infection with cytotoxicity values ranging from 33 to 79%, which is considerably faster than the traditional 2D platform, when tested with STEC. The cytotoxicity for non-Stx producing bacteria, Salmonella, Listeria, Citrobacter, Serratia, and Hafnia was found to be below the cytotoxicity cutoff value of 15%. The detection limit for the 3D Vero cell assay was estimated to be 107 CFU/ml for bacteria and about 32 ng/ml for Stx in 6 h. STEC-inoculated ground beef samples (n = 27) resulted in 38-46% cytotoxicity, and the bacterial isolates (n = 42) from ground beef samples were further confirmed to be stx1 and stx2 positive in a multiplex PCR yielding a very low false-positive result. This 3D cell-based screening assay relies on mammalian cell pathogen interaction that can complement other molecular techniques for the detection of cell-free Stx or STEC cells from food samples for early detection and prevention.
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Affiliation(s)
- Celina Z. To
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States
| | - Arun K. Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, United States
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20
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Magaziner SJ, Zeng Z, Chen B, Salmond GPC. The Prophages of Citrobacter rodentium Represent a Conserved Family of Horizontally Acquired Mobile Genetic Elements Associated with Enteric Evolution towards Pathogenicity. J Bacteriol 2019; 201:e00638-18. [PMID: 30782635 PMCID: PMC6456863 DOI: 10.1128/jb.00638-18] [Citation(s) in RCA: 15] [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: 10/25/2018] [Accepted: 01/23/2019] [Indexed: 01/08/2023] Open
Abstract
Prophage-mediated horizontal gene transfer (HGT) plays a key role in the evolution of bacteria, enabling access to new environmental niches, including pathogenicity. Citrobacter rodentium is a host-adapted intestinal mouse pathogen and important model organism for attaching and effacing (A/E) pathogens, including the clinically significant enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC, respectively). Even though C. rodentium contains 10 prophage genomic regions, including an active temperate phage, ΦNP, little was known regarding the nature of C. rodentium prophages in the bacterium's evolution toward pathogenicity. In this study, our characterization of ΦNP led to the discovery of a second, fully functional temperate phage, named ΦSM. We identify the bacterial host receptor for both phages as lipopolysaccharide (LPS). ΦNP and ΦSM are likely important mediators of HGT in C. rodentium Bioinformatic analysis of the 10 prophage regions reveals cargo genes encoding known virulence factors, including several type III secretion system (T3SS) effectors. C. rodentium prophages are conserved across a wide range of pathogenic enteric bacteria, including EPEC and EHEC as well as pathogenic strains of Salmonella enterica, Shigella boydii, and Klebsiella pneumoniae Phylogenetic analysis of core enteric backbone genes compared against prophage evolutionary models suggests that these prophages represent an important, conserved family of horizontally acquired enteric-bacterium-associated pathogenicity determinants. In addition to highlighting the transformative role of bacteriophage-mediated HGT in C. rodentium's evolution toward pathogenicity, these data suggest that the examination of conserved families of prophages in other pathogenic bacteria and disease outbreaks might provide deeper evolutionary and pathological insights otherwise obscured by more classical analysis.IMPORTANCE Bacteriophages are obligate intracellular parasites of bacteria. Some bacteriophages can confer novel bacterial phenotypes, including pathogenicity, through horizontal gene transfer (HGT). The pathogenic bacterium Citrobacter rodentium infects mice using mechanisms similar to those employed by human gastrointestinal pathogens, making it an important model organism. Here, we examined the 10 prophages of C. rodentium, investigating their roles in its evolution toward virulence. We characterized ΦNP and ΦSM, two endogenous active temperate bacteriophages likely important for HGT. We showed that the 10 prophages encode predicted virulence factors and are conserved within other intestinal pathogens. Phylogenetic analysis suggested that they represent a conserved family of horizontally acquired enteric-bacterium-associated pathogenic determinants. Consequently, similar analysis of prophage elements in other pathogens might further understanding of their evolution and pathology.
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Affiliation(s)
- Samuel J Magaziner
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ziyue Zeng
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Bihe Chen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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21
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Response to Questions Posed by the Food and Drug Administration Regarding Virulence Factors and Attributes that Define Foodborne Shiga Toxin-Producing Escherichia coli (STEC) as Severe Human Pathogens †. J Food Prot 2019; 82:724-767. [PMID: 30969806 DOI: 10.4315/0362-028x.jfp-18-479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
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- NACMCF Executive Secretariat, * U.S. Department of Agriculture, Food Safety and Inspection Service, Office of Public Health Science, PP3, 9-178, 1400 Independence Avenue S.W., Washington, D.C. 20250-3700, USA
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22
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The SOS Response Mediates Sustained Colonization of the Mammalian Gut. Infect Immun 2019; 87:IAI.00711-18. [PMID: 30510108 DOI: 10.1128/iai.00711-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022] Open
Abstract
Bacteria have a remarkable ability to survive, persist, and ultimately adapt to environmental challenges. A ubiquitous environmental hazard is DNA damage, and most bacteria have evolved a network of genes to combat genotoxic stress. This network is known as the SOS response and aids in bacterial survival by regulating genes involved in DNA repair and damage tolerance. Recently, the SOS response has been shown to play an important role in bacterial pathogenesis, and yet the role of the SOS response in nonpathogenic organisms and in physiological settings remains underexplored. Using a commensal Escherichia coli strain, MP1, we showed that the SOS response plays a vital role during colonization of the murine gut. In an unperturbed environment, the SOS-off mutant is impaired for stable colonization relative to a wild-type strain, suggesting the presence of genotoxic stress in the mouse gut. We evaluated the possible origins of genotoxic stress in the mouse gut by examining factors associated with the host versus the competing commensal organisms. In a dextran sulfate sodium (DSS) colitis model, the SOS-off colonization defect persisted but was not exacerbated. In contrast, in a germ-free model, the SOS-off mutant colonized with efficiency equal to that seen with the wild-type strain, suggesting that competing commensal organisms might be a significant source of genotoxic stress. This report extends our understanding of the importance of a functional SOS response for bacterial fitness in the context of a complex physiological environment and highlights the SOS response as a possible mechanism that contributes to ongoing genomic changes, including potential antibiotic resistance, in the microbiome of healthy hosts.
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23
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Lange ME, Uwiera RRE, Inglis GD. Housing Gnotobiotic Mice in Conventional Animal Facilities. ACTA ACUST UNITED AC 2019; 9:e59. [DOI: 10.1002/cpmo.59] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Máximo E. Lange
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre; Lethbridge Alberta Canada
- Department of Agricultural, Food, and Nutritional Science, University of Alberta; Edmonton Alberta Canada
| | - Richard R. E. Uwiera
- Department of Agricultural, Food, and Nutritional Science, University of Alberta; Edmonton Alberta Canada
| | - G. Douglas Inglis
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre; Lethbridge Alberta Canada
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24
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Balasubramanian S, Osburne MS, BrinJones H, Tai AK, Leong JM. Prophage induction, but not production of phage particles, is required for lethal disease in a microbiome-replete murine model of enterohemorrhagic E. coli infection. PLoS Pathog 2019; 15:e1007494. [PMID: 30629725 PMCID: PMC6328086 DOI: 10.1371/journal.ppat.1007494] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/01/2018] [Indexed: 12/12/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) colonize intestinal epithelium by generating characteristic attaching and effacing (AE) lesions. They are lysogenized by prophage that encode Shiga toxin 2 (Stx2), which is responsible for severe clinical manifestations. As a lysogen, prophage genes leading to lytic growth and stx2 expression are repressed, whereas induction of the bacterial SOS response in response to DNA damage leads to lytic phage growth and Stx2 production both in vitro and in germ-free or streptomycin-treated mice. Some commensal bacteria diminish prophage induction and concomitant Stx2 production in vitro, whereas it has been proposed that phage-susceptible commensals may amplify Stx2 production by facilitating successive cycles of infection in vivo. We tested the role of phage induction in both Stx production and lethal disease in microbiome-replete mice, using our mouse model encompassing the murine pathogen Citrobacter rodentium lysogenized with the Stx2-encoding phage Φstx2dact. This strain generates EHEC-like AE lesions on the murine intestine and causes lethal Stx-mediated disease. We found that lethal mouse infection did not require that Φstx2dact infect or lysogenize commensal bacteria. In addition, we detected circularized phage genomes, potentially in the early stage of replication, in feces of infected mice, confirming that prophage induction occurs during infection of microbiota-replete mice. Further, C. rodentium (Φstx2dact) mutants that do not respond to DNA damage or express stx produced neither high levels of Stx2 in vitro or lethal infection in vivo, confirming that SOS induction and concomitant expression of phage-encoded stx genes are required for disease. In contrast, C. rodentium (Φstx2dact) mutants incapable of prophage genome excision or of packaging phage genomes retained the ability to produce Stx in vitro, as well as to cause lethal disease in mice. Thus, in a microbiome-replete EHEC infection model, lytic induction of Stx-encoding prophage is essential for lethal disease, but actual phage production is not.
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Affiliation(s)
- Sowmya Balasubramanian
- Department of Molecular Biology and Microbiology at Tufts University School of Medicine, Boston, MA, United States of America
| | - Marcia S. Osburne
- Department of Molecular Biology and Microbiology at Tufts University School of Medicine, Boston, MA, United States of America
| | - Haley BrinJones
- Department of Molecular Biology and Microbiology at Tufts University School of Medicine, Boston, MA, United States of America
| | - Albert K. Tai
- Department of Immunology at Tufts University School of Medicine, Boston, MA, United States of America
| | - John M. Leong
- Department of Molecular Biology and Microbiology at Tufts University School of Medicine, Boston, MA, United States of America
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25
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Abstract
The highly conserved catabolic process of autophagy delivers unwanted proteins or damaged organelles to vacuoles for degradation and recycling. This is essential for the regulation of cellular homeostasis, stress adaptation, and programmed cell death in eukaryotes. In particular, emerging evidence indicates that autophagy plays a multifunctional regulatory role in plant innate immunity during plant-pathogen interactions. In this review, we highlight existing knowledge regarding the involvement of autophagy in plant immunity, mechanisms functioning in the induction of autophagy upon pathogen infection, and possible directions for future research.
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26
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Del Cogliano ME, Pinto A, Goldstein J, Zotta E, Ochoa F, Fernández-Brando RJ, Muniesa M, Ghiringhelli PD, Palermo MS, Bentancor LV. Relevance of Bacteriophage 933W in the Development of Hemolytic Uremic Syndrome (HUS). Front Microbiol 2018; 9:3104. [PMID: 30619183 PMCID: PMC6300567 DOI: 10.3389/fmicb.2018.03104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/30/2018] [Indexed: 11/13/2022] Open
Abstract
Hemolytic uremic syndrome (HUS), principally caused by shiga toxins (Stxs), is associated with Shiga toxin-producing Escherichia coli (STEC) infections. We previously reported Stx2 expression by host cells in vitro and in vivo. As the genes encoding the two Stx subunits are located in bacteriophage genomes, the aim of the current study was to evaluate the role of bacteriophage induction in HUS development in absence of an E. coli O157:H7 genomic background. Mice were inoculated with a non-pathogenic E. coli strain carrying the lysogenic bacteriophage 933W (C600Φ933W), and bacteriophage excision was induced by an antibiotic. The mice died 72 h after inoculation, having developed pathogenic damage typical of STEC infection. As well as renal and intestinal damage, markers of central nervous system (CNS) injury were observed, including aberrant immunolocalization of neuronal nuclei (NeuN) and increased expression of glial fibrillary acidic protein (GFAP). These results show that bacteriophage 933W without an E. coli O157:H7 background is capable of inducing the pathogenic damage associated with STEC infection. In addition, a novel mouse model was developed to evaluate therapeutic approaches focused on the bacteriophage as a new target.
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Affiliation(s)
- Manuel E Del Cogliano
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Alipio Pinto
- Laboratorio de Neurofisiopatología, Departamento de Fisiología, Facultad de Medicina, Instituto de Fisiología y Biofísica Bernardo Houssay (CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jorge Goldstein
- Laboratorio de Neurofisiopatología, Departamento de Fisiología, Facultad de Medicina, Instituto de Fisiología y Biofísica Bernardo Houssay (CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Elsa Zotta
- Laboratorio de Fisiopatogenia, Departamento de Fisiología, Facultad de Medicina, Instituto de Fisiología y Biofísica Bernardo Houssay (CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Ochoa
- Laboratorio de Fisiopatogenia, Departamento de Fisiología, Facultad de Medicina, Instituto de Fisiología y Biofísica Bernardo Houssay (CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Romina Jimena Fernández-Brando
- Laboratorio de Patogénesis e Inmunología de Procesos Infecciones, Instituto de Medicina Experimental (CONICET), Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Maite Muniesa
- Microbiology Section, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Pablo D Ghiringhelli
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Marina S Palermo
- Laboratorio de Patogénesis e Inmunología de Procesos Infecciones, Instituto de Medicina Experimental (CONICET), Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Leticia V Bentancor
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Universidad Nacional de Quilmes, Buenos Aires, Argentina
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27
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Howard-Varona C, Vik DR, Solonenko NE, Li YF, Gazitua MC, Chittick L, Samiec JK, Jensen AE, Anderson P, Howard-Varona A, Kinkhabwala AA, Abedon ST, Sullivan MB. Fighting Fire with Fire: Phage Potential for the Treatment of E. coli O157 Infection. Antibiotics (Basel) 2018; 7:E101. [PMID: 30453470 PMCID: PMC6315980 DOI: 10.3390/antibiotics7040101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023] Open
Abstract
Hemolytic⁻uremic syndrome is a life-threating disease most often associated with Shiga toxin-producing microorganisms like Escherichia coli (STEC), including E. coli O157:H7. Shiga toxin is encoded by resident prophages present within this bacterium, and both its production and release depend on the induction of Shiga toxin-encoding prophages. Consequently, treatment of STEC infections tend to be largely supportive rather than antibacterial, in part due to concerns about exacerbating such prophage induction. Here we explore STEC O157:H7 prophage induction in vitro as it pertains to phage therapy-the application of bacteriophages as antibacterial agents to treat bacterial infections-to curtail prophage induction events, while also reducing STEC O157:H7 presence. We observed that cultures treated with strictly lytic phages, despite being lysed, produce substantially fewer Shiga toxin-encoding temperate-phage virions than untreated STEC controls. We therefore suggest that phage therapy could have utility as a prophylactic treatment of individuals suspected of having been recently exposed to STEC, especially if prophage induction and by extension Shiga toxin production is not exacerbated.
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Affiliation(s)
| | - Dean R Vik
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - M Consuelo Gazitua
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Lauren Chittick
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Jennifer K Samiec
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Aubrey E Jensen
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Paige Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | | | | | - Stephen T Abedon
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA.
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28
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Keen EC, Dantas G. Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity. Trends Microbiol 2018; 26:943-954. [PMID: 29909042 PMCID: PMC6436384 DOI: 10.1016/j.tim.2018.05.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022]
Abstract
Recent years have witnessed an explosion of interest in the human microbiota. Although commensal bacteria have dominated research efforts to date, mounting evidence suggests that endogenous viral populations (the 'virome') play key roles in basic human physiology. The most numerous constituents of the human virome are not eukaryotic viruses but rather bacteriophages, viruses that infect bacteria. Here, we review phages' interactions with their immediate (prokaryotic) and extended (eukaryotic) hosts and with each other, with a particular emphasis on the temperate phages and prophages which dominate the human virome. We also discuss key outstanding questions in this emerging field and emphasize the urgent need for functional studies in animal models to complement previous in vitro work and current computational approaches.
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Affiliation(s)
- Eric C Keen
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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29
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Hernandez-Doria JD, Sperandio V. Bacteriophage Transcription Factor Cro Regulates Virulence Gene Expression in Enterohemorrhagic Escherichia coli. Cell Host Microbe 2018; 23:607-617.e6. [PMID: 29746832 DOI: 10.1016/j.chom.2018.04.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/15/2018] [Accepted: 04/16/2018] [Indexed: 10/16/2022]
Abstract
Bacteriophage-encoded genetic elements control bacterial biological functions. Enterohemorrhagic Escherichia coli (EHEC) strains harbor lambda-phages encoding the Shiga-toxin (Stx), which is expressed during the phage lytic cycle and associated with exacerbated disease. Phages also reside dormant within bacterial chromosomes through their lysogenic cycle, but how this impacts EHEC virulence remains unknown. We find that during lysogeny the phage transcription factor Cro activates the EHEC type III secretion system (T3SS). EHEC lambdoid phages are lysogenic under anaerobic conditions when Cro binds to and activates the promoters of T3SS genes. Interestingly, the Cro sequence varies among phages carried by different EHEC outbreak strains, and these changes affect Cro-dependent T3SS regulation. Additionally, infecting mice with the related pathogen C. rodentium harboring the bacteriophage cro from EHEC results in greater T3SS gene expression and enhanced virulence. Collectively, these findings reveal the role of phages in impacting EHEC virulence and their potential to affect outbreak strains.
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Affiliation(s)
- Juan D Hernandez-Doria
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA.
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30
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Torres AG, Amaral MM, Bentancor L, Galli L, Goldstein J, Krüger A, Rojas-Lopez M. Recent Advances in Shiga Toxin-Producing Escherichia coli Research in Latin America. Microorganisms 2018; 6:microorganisms6040100. [PMID: 30274180 PMCID: PMC6313304 DOI: 10.3390/microorganisms6040100] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/01/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022] Open
Abstract
Pathogenic Escherichia coli are known to be a common cause of diarrheal disease and a frequently occurring bacterial infection in children and adults in Latin America. Despite the effort to combat diarrheal infections, the south of the American continent remains a hot spot for infections and sequelae associated with the acquisition of one category of pathogenic E. coli, the Shiga toxin-producing E. coli (STEC). This review will focus on an overview of the prevalence of different STEC serotypes in human, animals and food products, focusing on recent reports from Latin America outlining the recent research progress achieved in this region to combat disease and endemicity in affected countries and to improve understanding on emerging serotypes and their virulence factors. Furthermore, this review will highlight the progress done in vaccine development and treatment and will also discuss the effort of the Latin American investigators to respond to the thread of STEC infections by establishing a multidisciplinary network of experts that are addressing STEC-associated animal, human and environmental health issues, while trying to reduce human disease. Regardless of the significant scientific contributions to understand and combat STEC infections worldwide, many significant challenges still exist and this review has focus in the Latin American efforts as an example of what can be accomplished when multiple groups have a common goal.
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Affiliation(s)
- Alfredo G Torres
- Department of Microbiology and Immunology, Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Maria M Amaral
- Laboratorio de Fisiopatogenia, Departamento de Fisiología, Instituto de Fisiología y Biofísica Bernardo Houssay, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina.
| | - Leticia Bentancor
- Laboratory of Genetic Engineering and Molecular Biology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Buenos Aires 1876, Argentina.
| | - Lucia Galli
- Instituto de Genética Veterinaria Ing. Fernando N. Dulout (UNLP-CONICET, La Plata), Facultad de Ciencias Veterinarias, La Plata 1900, Argentina.
| | - Jorge Goldstein
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Fisiología y Biofísica Houssay, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina.
| | - Alejandra Krüger
- Centro de Investigación Veterinaria de Tandil (CONICET-CIC-UNCPBA), Facultad de Ciencias Veterinarias, Tandil 7000, Argentina.
| | - Maricarmen Rojas-Lopez
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.
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31
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Górski A, Jończyk-Matysiak E, Międzybrodzki R, Weber-Dąbrowska B, Łusiak-Szelachowska M, Bagińska N, Borysowski J, Łobocka MB, Węgrzyn A, Węgrzyn G. Phage Therapy: Beyond Antibacterial Action. Front Med (Lausanne) 2018; 5:146. [PMID: 29876350 PMCID: PMC5974148 DOI: 10.3389/fmed.2018.00146] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
Until recently, phages were considered as mere “bacteria eaters” with potential for use in combating antimicrobial resistance. The real value of phage therapy assessed according to the standards of evidence-based medicine awaits confirmation by clinical trials. However, the progress in research on phage biology has shed more light on the significance of phages. Accumulating data indicate that phages may also interact with eukaryotic cells. How such interactions could be translated into advances in medicine (especially novel means of therapy) is discussed herein.
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Affiliation(s)
- Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Ryszard Międzybrodzki
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Marzanna Łusiak-Szelachowska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Natalia Bagińska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata B Łobocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
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32
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Krüger A, Burgán J, Friedrich AW, Rossen JWA, Lucchesi PMA. ArgO145, a Stx2a prophage of a bovine O145:H- STEC strain, is closely related to phages of virulent human strains. INFECTION GENETICS AND EVOLUTION 2018; 60:126-132. [PMID: 29476813 DOI: 10.1016/j.meegid.2018.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/18/2018] [Accepted: 02/17/2018] [Indexed: 01/08/2023]
Abstract
Shiga toxins (Stx) are the main virulence factor of a pathogroup of Escherichia coli strains that cause severe human diseases. These toxins are encoded in prophages (Stx prophages), and generally their expression depends on prophage induction. Several studies have reported high diversity among both Stx prophages and Stx. In particular, the toxin subtype Stx2a is associated with high virulence and HUS. Here, we report the genome of ArgO145, an inducible Stx2a prophage identified in a bovine O145:H- strain which produced high levels of Shiga toxin and Stx phage particles. The ArgO145 genome shared lambda phage organization, with recombination, regulation, replication, lysis, and head and tail structural gene regions, although some lambda genes encoding regulatory proteins could not be identified. Remarkably, some Stx2a phages of strains isolated from patients in other countries showed high similarity to ArgO145.
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Affiliation(s)
- A Krüger
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CONICET-CIC, Laboratorio de Inmunoquímica y Biotecnología, Argentina.
| | - J Burgán
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CONICET-CIC, Laboratorio de Inmunoquímica y Biotecnología, Argentina
| | - A W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands
| | - J W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands
| | - P M A Lucchesi
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CONICET-CIC, Laboratorio de Inmunoquímica y Biotecnología, Argentina
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Del Cogliano ME, Hollmann A, Martinez M, Semorile L, Ghiringhelli PD, Maffía PC, Bentancor LV. Cationic Antimicrobial Peptides Inactivate Shiga Toxin-Encoding Bacteriophages. Front Chem 2017; 5:122. [PMID: 29312928 PMCID: PMC5742231 DOI: 10.3389/fchem.2017.00122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/08/2017] [Indexed: 12/20/2022] Open
Abstract
Shiga toxin (Stx) is the principal virulence factor during Shiga toxin-producing Escherichia coli (STEC) infections. We have previously reported the inactivation of bacteriophage encoding Stx after treatment with chitosan, a linear polysaccharide polymer with cationic properties. Cationic antimicrobial peptides (cAMPs) are short linear aminoacidic sequences, with a positive net charge, which display bactericidal or bacteriostatic activity against a wide range of bacterial species. They are promising novel antibiotics since they have shown bactericidal effects against multiresistant bacteria. To evaluate whether cationic properties are responsible for bacteriophage inactivation, we tested seven cationic peptides with proven antimicrobial activity as anti-bacteriophage agents, and one random sequence cationic peptide with no antimicrobial activity as a control. We observed bacteriophage inactivation after incubation with five cAMPs, but no inactivating activity was observed with the random sequence cationic peptide or with the non-alpha helical cAMP Omiganan. Finally, to confirm peptide-bacteriophage interaction, zeta potential was analyzed by following changes on bacteriophage surface charges after peptide incubation. According to our results we could propose that: (1) direct interaction of peptides with phage is a necessary step for bacteriophage inactivation, (2) cationic properties are necessary but not sufficient for bacteriophage inactivation, and (3) inactivation by cationic peptides could be sequence (or structure) specific. Overall our data suggest that these peptides could be considered a new family of molecules potentially useful to decrease bacteriophage replication and Stx expression.
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Affiliation(s)
- Manuel E Del Cogliano
- Laboratory of Genetic Engineering and Molecular Biology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Axel Hollmann
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Laboratory of Biointerfaces and Biomimetic Systems, CITSE, National University of Santiago del Estero, Santiago del Estero, Argentina.,Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina
| | - Melina Martinez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina
| | - Liliana Semorile
- Laboratory of Genetic Engineering and Molecular Biology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina.,Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina
| | - Pablo D Ghiringhelli
- Laboratory of Genetic Engineering and Molecular Biology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina
| | - Paulo C Maffía
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina
| | - Leticia V Bentancor
- Laboratory of Genetic Engineering and Molecular Biology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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Bacterial Chat: Intestinal Metabolites and Signals in Host-Microbiota-Pathogen Interactions. Infect Immun 2017; 85:IAI.00476-17. [PMID: 28947641 DOI: 10.1128/iai.00476-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Intestinal bacteria employ microbial metabolites from the microbiota and chemical signaling during cell-to-cell communication to regulate several cellular functions. Pathogenic bacteria are extremely efficient in orchestrating their response to these signals through complex signaling transduction systems. Precise coordination and interpretation of these multiple chemical cues is important within the gastrointestinal (GI) tract. Enteric foodborne pathogens, such as enterohemorrhagic Escherichia coli (EHEC) and Salmonella enterica serovar Typhimurium, or the surrogate murine infection model for EHEC, Citrobacter rodentium, are all examples of microorganisms that modulate the expression of their virulence repertoire in response to signals from the microbiota or the host, such as autoinducer-3 (AI-3), epinephrine (Epi), and norepinephrine (NE). The QseBC and QseEF two-component systems, shared by these pathogens, are involved in sensing these signals. We review how these signaling systems sense and relay these signals to drive bacterial gene expression; specifically, to modulate virulence. We also review how bacteria chat via chemical signals integrated with metabolite recognition and utilization to promote successful associations among enteric pathogens, the microbiota, and the host.
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35
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Aijaz I, Koudelka GB. Tetrahymena phagocytic vesicles as ecological micro-niches of phage transfer. FEMS Microbiol Ecol 2017; 93:3061358. [PMID: 28334205 DOI: 10.1093/femsec/fix030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/01/2017] [Indexed: 11/14/2022] Open
Abstract
The microbial communities in natural environments such as soil, pond water, or animal rumens are composed of a diverse mixture of bacteria and protozoa including ciliates or flagellates. In such microbiomes, a major source of bacterial mortality is grazing by phagocytic protists. Many protists are omnivorous heterotrophs, feeding on a range of different bacterial species. Due to this indiscriminate feeding, different bacterial species can assemble together in the same phagocytic vesicles where they can potentially exchange genetic material. Here we show that Tetrahymena thermophila imports and accumulates phage donor and recipient bacterial strains in its phagocytic vesicles and that under laboratory conditions the ingested bacteria remain viable for ≥2 h. Prophages in the ingested bacteria induce immediately after ingestion, and the released phages are concentrated in the phagocytic vesicles of the ciliate. These phages retain their ability to infect phage-susceptible bacterial strains. As a consequence of being confined within the phagosome, the frequency of lysogen formation in these vesicles increases 6-fold as compared with the bulk solution. Collectively, these observations suggest that T. thermophila aids in dissemination of bacteriophages by accumulating susceptible bacteria and phages in their phagocytic vesicles.
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36
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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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Eaton KA, Fontaine C, Friedman DI, Conti N, Alteri CJ. Pathogenesis of Colitis in Germ-Free Mice Infected With EHEC O157:H7. Vet Pathol 2017; 54:710-719. [PMID: 28178427 DOI: 10.1177/0300985817691582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Enterohemorrhagic Escherichia coli (EHEC) are strains of E. coli that express Shiga toxins (Stx) and cause hemorrhagic colitis. In some cases, disease can progress to hemolytic uremic syndrome, a potentially fatal form of kidney disease. Both enteric and renal disease are associated with the expression of stx genes, which are often carried on lysogenic phage. Toxin is expressed following induction and conversion of the phage to lytic growth. The authors previously used a germ-free mouse model to demonstrate that toxin gene expression is enhanced during growth in vivo and that renal disease is dependent on both prophage induction and expression of Stx2. In the current study, the authors document and quantify necrotizing colitis, examine the progression of enteric and renal disease, and determine the role of Stx2, phage genes, and the type 3 secretion system (T3SS) in bacterial colonization and colitis and systemic disease. By 1 day after inoculation, EHEC-monocolonized mice developed colitis, which decreased in severity thereafter. Systemic disease developed subsequently. Infection with EHEC mutant strains revealed that renal failure and splenic necrosis were absolutely dependent on the expression of Stx2 but that T3SS function and prophage excision were not necessary for systemic disease. In contrast, colitis was only partly dependent on Stx2. This study demonstrates that in germ-free mice, like in human patients, EHEC causes early colitis followed by renal failure and that systemic disease but not colitis is Stx2 dependent.
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Affiliation(s)
- K A Eaton
- 1 University of Michigan Medical School, Ann Arbor, MI, USA
| | - C Fontaine
- 1 University of Michigan Medical School, Ann Arbor, MI, USA
| | - D I Friedman
- 1 University of Michigan Medical School, Ann Arbor, MI, USA
| | - N Conti
- 1 University of Michigan Medical School, Ann Arbor, MI, USA
| | - C J Alteri
- 1 University of Michigan Medical School, Ann Arbor, MI, USA
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Shaaban S, Cowley LA, McAteer SP, Jenkins C, Dallman TJ, Bono JL, Gally DL. Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing. Microb Genom 2016; 2:e000096. [PMID: 28348836 PMCID: PMC5359411 DOI: 10.1099/mgen.0.000096] [Citation(s) in RCA: 24] [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: 07/28/2016] [Accepted: 10/31/2016] [Indexed: 11/18/2022] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) O157 is a zoonotic pathogen for which colonization of cattle and virulence in humans is associated with multiple horizontally acquired genes, the majority present in active or cryptic prophages. Our understanding of the evolution and phylogeny of EHEC O157 continues to develop primarily based on core genome analyses; however, such short-read sequences have limited value for the analysis of prophage content and its chromosomal location. In this study, we applied Single Molecule Real Time (SMRT) sequencing, using the Pacific Biosciences long-read sequencing platform, to isolates selected from the main sub-clusters of this clonal group. Prophage regions were extracted from these sequences and from published reference strains. Genome position and prophage diversity were analysed along with genetic content. Prophages could be assigned to clusters, with smaller prophages generally exhibiting less diversity and preferential loss of structural genes. Prophages encoding Shiga toxin (Stx) 2a and Stx1a were the most diverse, and more variable compared to prophages encoding Stx2c, further supporting the hypothesis that Stx2c-prophage integration was ancestral to acquisition of other Stx types. The concept that phage type (PT) 21/28 (Stx2a+, Stx2c+) strains evolved from PT32 (Stx2c+) was supported by analysis of strains with excised Stx-encoding prophages. Insertion sequence elements were over-represented in prophage sequences compared to the rest of the genome, showing integration in key genes such as stx and an excisionase, the latter potentially acting to capture the bacteriophage into the genome. Prophage profiling should allow more accurate prediction of the pathogenic potential of isolates.
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Affiliation(s)
- Sharif Shaaban
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Lauren A. Cowley
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, London NW9 5EQ, UK
| | - Sean P. McAteer
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, London NW9 5EQ, UK
| | - Timothy J. Dallman
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, London NW9 5EQ, UK
| | - James L. Bono
- U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, NE 68933-0166, USA
| | - David L. Gally
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
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Intracellular d-Serine Accumulation Promotes Genetic Diversity via Modulated Induction of RecA in Enterohemorrhagic Escherichia coli. J Bacteriol 2016; 198:3318-3328. [PMID: 27698085 DOI: 10.1128/jb.00548-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/27/2016] [Indexed: 01/28/2023] Open
Abstract
We recently discovered that exposure of enterohemorrhagic Escherichia coli (EHEC) to d-serine resulted in accumulation of this unusual amino acid, induction of the SOS regulon, and downregulation of the type III secretion system that is essential for efficient colonization of the host. Here, we have investigated the physiological relevance of this elevated SOS response, which is of particular interest given the presence of Stx toxin-carrying lysogenic prophages on the EHEC chromosome that are activated during the SOS response. We found that RecA elevation in response to d-serine, while being significant, was heterogeneous and not capable of activating stx expression or stx phage transduction to a nonlysogenic recipient. This "SOS-like response" was, however, capable of increasing the mutation frequency associated with low-level RecA activity, thus promoting genetic diversity. Furthermore, this response was entirely dependent on RecA and enhanced in the presence of a DNA-damaging agent, indicating a functional SOS response, but did not result in observable cleavage of the LexA repressor alone, indicating a controlled mechanism of induction. This work demonstrates that environmental factors not usually associated with DNA damage are capable of promoting an SOS-like response. We propose that this modulated induction of RecA allows EHEC to adapt to environmental insults such as d-serine while avoiding unwanted phage-induced lysis. IMPORTANCE The SOS response is a global stress network that is triggered by the presence of DNA damage due to breakage or stalled replication forks. Activation of the SOS response can trigger the replication of lytic bacteriophages and promote genetic diversification through error-prone polymerases. We have demonstrated that the host-associated metabolite d-serine contributes to Escherichia coli niche specification and accumulates inside cells that cannot catabolize it. This results in a modulated activation of the SOS antirepressor RecA that is insufficient to trigger lytic bacteriophage but capable of increasing the SOS-associated mutation frequency. These findings describe how relevant signals not normally associated with DNA damage can hijack the SOS response, promoting diversity as E. coli strains adapt while avoiding unwanted phage lysis.
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40
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Wu SY, Park GY, Kim SH, Hulme J, An SSA. Diminazene aceturate: an antibacterial agent for Shiga-toxin-producing Escherichia coli O157:H7. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:3363-3378. [PMID: 27789937 PMCID: PMC5072558 DOI: 10.2147/dddt.s114832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The aim of this study was to investigate the bacteriostatic and bactericidal effects of diminazene aceturate (DA) against five strains of pathogenic bacteria and two strains of nonpathogenic bacteria. The results showed that 5 μg/mL of DA suppressed the growth of pathogenic Escherichia coli by as much as 77% compared with the controls. Enterohemorrhagic E. coli EDL933 (an E. coli O157:H7 strain) was the most sensitive to DA with a minimum inhibitory concentration of 20 μg/mL. Additional investigations showed that DA induced the highest level of intracellular reactive oxygen species in EDL933. A positive correlation between the reactive oxygen species levels and DA concentration was demonstrated. DA (5 μg/mL) was also a potent uncoupler, inducing a stationary phase collapse (70%–75%) in both strains of E. coli O157:H7. Further investigation showed that the collapse was due to the NaCl:DA ratio in the broth and was potassium ion dependent. A protease screening assay was conducted to elucidate the underlying mechanism. It was found that at neutral pH, the hydrolysis of H-Asp-pNA increased by a factor of 2–3 in the presence of DA, implying that DA causes dysregulation of the proton motive force and a decrease in cellular pH. Finally, a commercial verotoxin test showed that DA did not significantly increase toxin production in EDL933 and was a suitable antibacterial agent for Shiga-toxin-producing E. coli.
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Affiliation(s)
- Si-Ying Wu
- Department of BioNano Technology, Gachon BioNano Research Institute, Gachon University, Seongnam-si
| | - Gil-Yong Park
- Department of BioNano Technology, Gachon BioNano Research Institute, Gachon University, Seongnam-si
| | - So-Hee Kim
- Seoul National University Bundang Hospital, Gyeonggi-do, Republic of Korea
| | - John Hulme
- Department of BioNano Technology, Gachon BioNano Research Institute, Gachon University, Seongnam-si
| | - Seong Soo A An
- Department of BioNano Technology, Gachon BioNano Research Institute, Gachon University, Seongnam-si
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41
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Colon MP, Chakraborty D, Pevzner Y, Koudelka GB. Mechanisms that Determine the Differential Stability of Stx⁺ and Stx(-) Lysogens. Toxins (Basel) 2016; 8:96. [PMID: 27043626 PMCID: PMC4848623 DOI: 10.3390/toxins8040096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/23/2016] [Accepted: 03/25/2016] [Indexed: 01/29/2023] Open
Abstract
Phages 933W, BAA2326, 434, and λ are evolutionarily-related temperate lambdoid phages that infect Escherichia coli. Although these are highly-similar phages, BAA2326 and 933W naturally encode Shiga toxin 2 (Stx+), but phage 434 and λ do not (Stx−). Previous reports suggest that the 933W Stx+ prophage forms less stable lysogens in E. coli than does the Stx− prophages λ, P22, and 434. The higher spontaneous induction frequency of the Stx+ prophage may be correlated with both virulence and dispersion of the Stx2-encoding phage. Here, we examined the hypothesis that lysogen instability is a common feature of Stx+ prophages. We found in both the absence and presence of prophage inducers (DNA damaging agents, salts), the Stx+ prophages induce at higher frequencies than do Stx− prophages. The observed instability of Stx+ prophages does not appear to be the result of any differences in phage development properties between Stx+ and Stx− phages. Our results indicate that differential stability of Stx+ and Stx− prophages results from both RecA-dependent and RecA-independent effects on the intracellular concentration of the respective cI repressors.
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Affiliation(s)
- Michael P Colon
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
| | | | - Yonatan Pevzner
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
| | - Gerald B Koudelka
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
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Abstract
The first major outbreaks caused by enterohemorrhagic Escherichia coli (EHEC) raised public and medical awareness of the risks associated with acquiring this potentially deadly infection. The widespread presence of these organisms in the environment, the severity of the clinical sequelae, and the lack of treatment options and effective preventive measures demand that we obtain a better understanding of how this group of organisms cause disease. Animal models allow study of the processes and factors that contribute to disease and, as such, form a valuable tool in the repertoire of infectious disease researchers. Yet despite more than 30 years of research, it seems that no single model host reproduces the full spectrum of clinical disease induced by EHEC in humans. In the first part of this review, a synopsis of what is known about EHEC infections is garnered from human outbreaks and biopsy specimens. The main features and limitations of EHEC infection models that are based on the three most commonly used species (pigs, rabbits, and mice) are described within a historical context. Recent advances are highlighted, and a brief overview of models based on other species is given. Finally, the impact of the host on moderating EHEC infection is considered in light of growing evidence for the need to consider the biology and virulence strategies of EHEC in the context of its niche within the intestine.
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43
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De Paepe M, Tournier L, Moncaut E, Son O, Langella P, Petit MA. Carriage of λ Latent Virus Is Costly for Its Bacterial Host due to Frequent Reactivation in Monoxenic Mouse Intestine. PLoS Genet 2016; 12:e1005861. [PMID: 26871586 PMCID: PMC4752277 DOI: 10.1371/journal.pgen.1005861] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/22/2016] [Indexed: 01/21/2023] Open
Abstract
Temperate phages, the bacterial viruses able to enter in a dormant prophage state in bacterial genomes, are present in the majority of bacterial strains for which the genome sequence is available. Although these prophages are generally considered to increase their hosts’ fitness by bringing beneficial genes, studies demonstrating such effects in ecologically relevant environments are relatively limited to few bacterial species. Here, we investigated the impact of prophage carriage in the gastrointestinal tract of monoxenic mice. Combined with mathematical modelling, these experimental results provided a quantitative estimation of key parameters governing phage-bacteria interactions within this model ecosystem. We used wild-type and mutant strains of the best known host/phage pair, Escherichia coli and phage λ. Unexpectedly, λ prophage caused a significant fitness cost for its carrier, due to an induction rate 50-fold higher than in vitro, with 1 to 2% of the prophage being induced. However, when prophage carriers were in competition with isogenic phage susceptible bacteria, the prophage indirectly benefited its carrier by killing competitors: infection of susceptible bacteria led to phage lytic development in about 80% of cases. The remaining infected bacteria were lysogenized, resulting overall in the rapid lysogenization of the susceptible lineage. Moreover, our setup enabled to demonstrate that rare events of phage gene capture by homologous recombination occurred in the intestine of monoxenic mice. To our knowledge, this study constitutes the first quantitative characterization of temperate phage-bacteria interactions in a simplified gut environment. The high prophage induction rate detected reveals DNA damage-mediated SOS response in monoxenic mouse intestine. We propose that the mammalian gut, the most densely populated bacterial ecosystem on earth, might foster bacterial evolution through high temperate phage activity. Dormant bacterial viruses, or prophages, are found in the genomes of almost all bacteria, but their impact on bacterial host fitness is largely unknown. Through experiments in mice, supported by a mathematical model, we quantified the activity of Escherichia coli prophage λ in monoxenic mouse gut, as well as its impact on its carrier bacteria. λ carriage negatively impacted its hosts due to frequent reactivation, but indirectly benefited its host by killing susceptible bacterial competitors. The high prophage activity unraveled in this study reflects a constant rate of SOS response, resulting from DNA damage in monoxenic mouse intestine. Our results should motivate researchers to take the presence of prophages into account when studying the action of specific bacteria in the gastrointestinal tract of mammals.
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Affiliation(s)
- Marianne De Paepe
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
| | | | - Elisabeth Moncaut
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Son
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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44
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Hauser E, Bruederle M, Reich C, Bruckbauer A, Funk J, Schmidt H. Subtilase contributes to the cytotoxicity of a Shiga toxin-producing Escherichia coli strain encoding three different toxins. Int J Food Microbiol 2015; 217:156-61. [PMID: 26523884 DOI: 10.1016/j.ijfoodmicro.2015.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/15/2015] [Accepted: 10/23/2015] [Indexed: 11/24/2022]
Abstract
Food-borne Shiga toxin-producing Escherichia coli (STEC) O113:H21 strain TS18/08, that has previously been isolated from mixed minced meat, harbors the Shiga toxin (Stx) encoding allele stx2a, the plasmid-located subtilase cytotoxin encoding allele subAB1 and the cytolethal distending toxin type V encoding gene cdt-V. In the current study, it could be shown that each of these toxin genes was transcribed with different transcription levels at different time points by RT real time PCR under laboratory batch conditions in LB-broth. The transcription maximum for cdt-V and subAB1 was observed after 3h while stx2a transcription was highest after 6h of incubation. During this time the mean relationship of the amount of stx2a:subAB1:cdt-V transcripts was 1:26:100. Furthermore, isogenic stx2a and cdt-V chromosomal deletion mutants were constructed to measure the contribution of SubAB1 to the overall cytotoxicity of this strain. In this context, a further copy of stx2 was detected in this strain and was also deleted. Comparing the cytotoxicity of supernatants of the resulting mutant strains TS18/08-3 (Δstx2-1Δstx2-2Δcdt-V) and TS18/08-4 (Δstx2-1Δstx2-2Δcdt-VΔsubAB1) on Vero cells demonstrated a contribution of SubAB1 to the overall cytotoxic effect while the 4-fold isogenic deletion mutant did not show any cytotoxic effect and that was comparable to the non-toxic laboratory E. coli strain C600. The cytotoxic effect could be restored by complementation with the recombinant low copy plasmid pWSK29 harboring subAB1 under the control of its own promoter. In addition, the cytotoxicity of wild type strain TS18/08 to Vero cells was in the same range as the EHEC O157:H7 strain EDL933. Therefore, food-borne STEC O113:H21 strain TS18/08 can be considered as a putative human pathogen.
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Affiliation(s)
- Elisabeth Hauser
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, Garbenstrasse 28, University of Hohenheim, 70599 Stuttgart, Germany
| | - Matthias Bruederle
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, Garbenstrasse 28, University of Hohenheim, 70599 Stuttgart, Germany
| | - Carolin Reich
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, Garbenstrasse 28, University of Hohenheim, 70599 Stuttgart, Germany
| | - Annette Bruckbauer
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, Garbenstrasse 28, University of Hohenheim, 70599 Stuttgart, Germany
| | - Joschua Funk
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, Garbenstrasse 28, University of Hohenheim, 70599 Stuttgart, Germany
| | - Herbert Schmidt
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, Garbenstrasse 28, University of Hohenheim, 70599 Stuttgart, Germany.
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Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. mBio 2015; 6:e01578-15. [PMID: 26489866 PMCID: PMC4620475 DOI: 10.1128/mbio.01578-15] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/23/2015] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Viruses make up a major component of the human microbiota but are poorly understood in the skin, our primary barrier to the external environment. Viral communities have the potential to modulate states of cutaneous health and disease. Bacteriophages are known to influence the structure and function of microbial communities through predation and genetic exchange. Human viruses are associated with skin cancers and a multitude of cutaneous manifestations. Despite these important roles, little is known regarding the human skin virome and its interactions with the host microbiome. Here we evaluated the human cutaneous double-stranded DNA virome by metagenomic sequencing of DNA from purified virus-like particles (VLPs). In parallel, we employed metagenomic sequencing of the total skin microbiome to assess covariation and infer interactions with the virome. Samples were collected from 16 subjects at eight body sites over 1 month. In addition to the microenviroment, which is known to partition the bacterial and fungal microbiota, natural skin occlusion was strongly associated with skin virome community composition. Viral contigs were enriched for genes indicative of a temperate phage replication style and also maintained genes encoding potential antibiotic resistance and virulence factors. CRISPR spacers identified in the bacterial DNA sequences provided a record of phage predation and suggest a mechanism to explain spatial partitioning of skin phage communities. Finally, we modeled the structure of bacterial and phage communities together to reveal a complex microbial environment with a Corynebacterium hub. These results reveal the previously underappreciated diversity, encoded functions, and viral-microbial dynamic unique to the human skin virome. IMPORTANCE To date, most cutaneous microbiome studies have focused on bacterial and fungal communities. Skin viral communities and their relationships with their hosts remain poorly understood despite their potential to modulate states of cutaneous health and disease. Previous studies employing whole-metagenome sequencing without purification for virus-like particles (VLPs) have provided some insight into the viral component of the skin microbiome but have not completely characterized these communities or analyzed interactions with the host microbiome. Here we present an optimized virus purification technique and corresponding analysis tools for gaining novel insights into the skin virome, including viral "dark matter," and its potential interactions with the host microbiome. The work presented here establishes a baseline of the healthy human skin virome and is a necessary foundation for future studies examining viral perturbations in skin health and disease.
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Affiliation(s)
- Geoffrey D Hannigan
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jacquelyn S Meisel
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Amanda S Tyldsley
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Qi Zheng
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Brendan P Hodkinson
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Adam J SanMiguel
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Samuel Minot
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Elizabeth A Grice
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Hu J, Zhu MJ. Defects in polynucleotide phosphorylase impairs virulence in Escherichia coli O157:H7. Front Microbiol 2015; 6:806. [PMID: 26347717 PMCID: PMC4538292 DOI: 10.3389/fmicb.2015.00806] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/22/2015] [Indexed: 01/31/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is reported to regulate virulence in Salmonella, Yersinia sp. and Campylobacter jejuni, yet its role in Escherichia coli O157:H7 has not been investigated. To gain insights into its roles in E. coli O157:H7 virulence, pnp deletion mutants were generated and the major virulence factors were compared to their parental wild type strains. Deletion of pnp in E. coli O157:H7 dramatically decreased stx2 mRNA expression and Stx2 protein production, and impaired lambdoid prophage activation in E. coli O157:H7. Quantitative PCR further confirmed that the Stx2 phage lytic growth was repressed by pnp deletion. Consistent with reduced Stx2 production and Stx2 phage activation, the transcriptional levels of genes involved in phage lysis and replication were down-regulated. In addition, disruption of pnp in E. coli O157:H7 decreased its adhesion to intestinal epithelial cells as well as cattle colonic explant tissues. On the other hand, PNPase inactivation in E. coli O157:H7 enhanced Tir protein content and the transcription of type three secretion system components, including genes encoding intimin, Tir, and EspB as well as locus of enterocyte and effacement positive regulator, Ler. Collectively, data indicate that PNPase has pleiotropic effects on the virulence of E. coli O157:H7.
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Affiliation(s)
- Jia Hu
- School of Food Science, Washington State University, Pullman, WA USA ; Department of Animal Science, University of Wyoming, Laramie, WY USA
| | - Mei-Jun Zhu
- School of Food Science, Washington State University, Pullman, WA USA
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Fontaine CA, Skorupski AM, Vowles CJ, Anderson NE, Poe SA, Eaton KA. How free of germs is germ-free? Detection of bacterial contamination in a germ free mouse unit. Gut Microbes 2015; 6:225-33. [PMID: 26018301 PMCID: PMC4615677 DOI: 10.1080/19490976.2015.1054596] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Management of germ free animals has changed little since the beginning of the 20th century. The current upswing in their use, however, has led to interest in improved methods of screening and housing. Traditionally, germ free colonies are screened for bacterial colonization by culture and examination of Gram stained fecal samples, but some investigators have reported using PCR-based methods of microbial detection, presumably because of perceived increased sensitivity. The accuracy and detection limit for traditional compared to PCR-based screening assays are not known. The purpose of this study was to determine the limit of detection of bacterial contamination of mouse feces by aerobic and anaerobic culture, Gram stain, and qPCR, and to compare the accuracy of these tests in the context of a working germ free mouse colony. We found that the limit of detection for qPCR (approximately 10(5) cfu/g of feces) was lower than for Gram stain (approximately 10(9) cfu/g), but that all 3 assays were of similar accuracy. Bacterial culture was the most sensitive, but the least specific, and qPCR was the least sensitive and most specific. Gram stain but not qPCR detected heat-killed bacteria, indicating that bacteria in autoclaved diet are unlikely to represent a potential confounding factor for PCR screening. We conclude that as a practical matter, bacterial culture and Gram stain are adequate for screening germ free mouse colonies for bacterial contaminants, but that should low numbers of unculturable bacteria be present, they would not be detected with any of the currently available means.
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Affiliation(s)
- Clinton A Fontaine
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor, MI USA
| | - Anna M Skorupski
- College of Veterinary Medicine; Michigan State University; East Lansing, MI USA
| | - Chriss J Vowles
- Unit for Laboratory Animal Medicine; University of Michigan Medical School; Ann Arbor, MI USA
| | - Natalie E Anderson
- Unit for Laboratory Animal Medicine; University of Michigan Medical School; Ann Arbor, MI USA
| | - Sara A Poe
- Unit for Laboratory Animal Medicine; University of Michigan Medical School; Ann Arbor, MI USA
| | - Kathryn A Eaton
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor, MI USA,Correspondence to: Kathryn A Eaton;
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Albanese A, Gerhardt E, García H, Amigo N, Cataldi A, Zotta E, Ibarra C. Inhibition of water absorption and selective damage to human colonic mucosa induced by Shiga toxin-2 are enhanced by Escherichia coli O157:H7 infection. Int J Med Microbiol 2015; 305:348-54. [DOI: 10.1016/j.ijmm.2015.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 12/22/2014] [Accepted: 02/09/2015] [Indexed: 10/23/2022] Open
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Zhu W, Wang J, Zhu Y, Tang B, Zhang Y, He P, Zhang Y, Liu B, Guo X, Zhao G, Qin J. Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors. BMC Genomics 2015; 16:90. [PMID: 25887950 PMCID: PMC4338851 DOI: 10.1186/s12864-015-1321-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 02/04/2015] [Indexed: 12/20/2022] Open
Abstract
Background The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools in these organisms. Although plasmids and prophage remnants have recently been reported in Leptospira species, their characteristics and potential applications in leptospiral genetic transformation systems have not been fully evaluated. Results Three extrachromosomal replicons designated lcp1 (65,732 bp), lcp2 (56,757 bp), and lcp3 (54,986 bp) in the L. interrogans serovar Linhai strain 56609 were identified through whole genome sequencing. All three replicons were stable outside of the bacterial chromosomes. Phage particles were observed in the culture supernatant of 56609 after mitomycin C induction, and lcp3, which contained phage-related genes, was considered to be an inducible prophage. L. interrogans–Escherichia coli shuttle vectors, constructed with the predicted replication elements of single rep or rep combined with parAB loci from the three plasmids were shown to successfully transform into both saprophytic and pathogenic Leptospira species, suggesting an essential function for rep genes in supporting auto-replication of the plasmids. Additionally, a wide distribution of homologs of the three rep genes was identified in L. interrogans isolates, and correlation tests showed that the transformability of the shuttle vectors in L. interrogans isolates depended, to certain extent, on genetic compatibility between the rep sequences of both plasmid and host. Conclusions Three extrachromosomal replicons co-exist in L. interrogans, one of which we consider to be an inducible prophage. The vectors constructed with the rep genes of the three replicons successfully transformed into saprophytic and pathogenic Leptospira species alike, but this was partly dependent on genetic compatibility between the rep sequences of both plasmid and host. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1321-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weinan Zhu
- Department of Microbiology and Immunology, Institutes of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
| | - Jin Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Yongzhang Zhu
- Department of Microbiology and Immunology, Institutes of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
| | - Biao Tang
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China.
| | - Yunyi Zhang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Ping He
- Department of Microbiology and Immunology, Institutes of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
| | - Yan Zhang
- Department of Microbiology and Immunology, Institutes of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
| | - Boyu Liu
- Department of Microbiology and Immunology, Institutes of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
| | - Xiaokui Guo
- Department of Microbiology and Immunology, Institutes of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. .,State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China.
| | - Jinhong Qin
- Department of Microbiology and Immunology, Institutes of Medical Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
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