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Wheeler J, Rosengart A, Jiang Z, Tan K, Treutle N, Ionides EL. Informing policy via dynamic models: Cholera in Haiti. PLoS Comput Biol 2024; 20:e1012032. [PMID: 38683863 PMCID: PMC11081515 DOI: 10.1371/journal.pcbi.1012032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 05/09/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
Public health decisions must be made about when and how to implement interventions to control an infectious disease epidemic. These decisions should be informed by data on the epidemic as well as current understanding about the transmission dynamics. Such decisions can be posed as statistical questions about scientifically motivated dynamic models. Thus, we encounter the methodological task of building credible, data-informed decisions based on stochastic, partially observed, nonlinear dynamic models. This necessitates addressing the tradeoff between biological fidelity and model simplicity, and the reality of misspecification for models at all levels of complexity. We assess current methodological approaches to these issues via a case study of the 2010-2019 cholera epidemic in Haiti. We consider three dynamic models developed by expert teams to advise on vaccination policies. We evaluate previous methods used for fitting these models, and we demonstrate modified data analysis strategies leading to improved statistical fit. Specifically, we present approaches for diagnosing model misspecification and the consequent development of improved models. Additionally, we demonstrate the utility of recent advances in likelihood maximization for high-dimensional nonlinear dynamic models, enabling likelihood-based inference for spatiotemporal incidence data using this class of models. Our workflow is reproducible and extendable, facilitating future investigations of this disease system.
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Affiliation(s)
- Jesse Wheeler
- Statistics Department, University of Michigan, Ann Arbor, Michigan, United States of America
| | - AnnaElaine Rosengart
- Statistics and Data Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Zhuoxun Jiang
- Statistics Department, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kevin Tan
- Wharton Statistics and Data Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Noah Treutle
- Statistics Department, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Edward L. Ionides
- Statistics Department, University of Michigan, Ann Arbor, Michigan, United States of America
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2
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Mittal M, Tripathi S, Saini A, Mani I. Phage for treatment of Vibrio cholerae infection. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:21-39. [PMID: 37770173 DOI: 10.1016/bs.pmbts.2023.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Bacteriophages (or "phages") are ubiquitous and the amplest biological entities on our planet. It is a natural enemy of bacteria. Cholera is one of the most known diseases to cause multiple pandemics around the world, killing millions of people. The pathogen of cholera is Vibrio species. Up until the emergence of multidrug resistance, preventive therapeutics like antibiotics were the most effective means of battling bacteria. Globally, one of the most significant challenges in treating microbial infections is the development of drug-resistant strains. Based on their antibacterial properties and unique characteristics, phages are being comprehensively evaluated taxonomically. Moreover, phage-based vaccination is evolving as one of the most encouraging preventive approaches. Due to this, its related research got remarkable recognition. However, due to the rapid emergence of bacterial resistance to antibiotics, the use of phages (phage therapy) could be a major motive for research because the most promising solution lies in bacteriophages. This chapter briefly highlights the promising use of bacteriophages to combat Vibrio-related infectious diseases.
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Affiliation(s)
- Milky Mittal
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, New Delhi, India
| | - Surbhi Tripathi
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, New Delhi, India
| | - Ashok Saini
- Department of Microbiology, Institute of Home Economics, University of Delhi, New Delhi, India.
| | - Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
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3
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Sun H, Zhu C, Fu X, Khattak S, Wang J, Liu Z, Kong Q, Mou H, Secundo F. Effects of intestinal microbiota on physiological metabolism and pathogenicity of Vibrio. Front Microbiol 2022; 13:947767. [PMID: 36081796 PMCID: PMC9445811 DOI: 10.3389/fmicb.2022.947767] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Vibrio species are disseminated broadly in the marine environment. Some of them can cause severe gastroenteritis by contaminating seafood and drinking water, such as Vibrio parahaemolyticus, Vibrio cholerae, and Vibrio vulnificus. However, their pathogenic mechanism still needs to be revealed to prevent and reduce morbidity. This review comprehensively introduces and discusses the common pathogenic process of Vibrio including adhesion, cell colonization and proliferation, and resistance to host immunity. Vibrio usually produces pathogenic factors including hemolysin, type-III secretion system, and adhesion proteins. Quorum sensing, a cell molecular communication system between the bacterial cells, plays an important role in Vibrio intestinal invasion and colonization. The human immune system can limit the virulence of Vibrio or even kill the bacteria through different responses. The intestinal microbiota is a key component of the immune system, but information on its effects on physiological metabolism and pathogenicity of Vibrio is seldom available. In this review, the effects of intestinal microorganisms and their metabolites on the invasion and colonization of common pathogenic Vibrio and VBNC status cells are discussed, which is conducive to finding the next-generation prebiotics. The strategy of dietary intervention is discussed for food safety control. Finally, future perspectives are proposed to prevent Vibrio infection in aquaculture.
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Affiliation(s)
- Han Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changliang Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xiaodan Fu
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi, Nanchang University, Nanchang, China
| | - Shakir Khattak
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jingyu Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zhihao Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Qing Kong
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Haijin Mou
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
- *Correspondence: Haijin Mou
| | - Francesco Secundo
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR, Milan, Italy
- Francesco Secundo
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Conrad JW, Harwood VJ. Sewage Promotes Vibrio vulnificus Growth and Alters Gene Transcription in Vibrio vulnificus CMCP6. Microbiol Spectr 2022; 10:e0191321. [PMID: 35171011 PMCID: PMC8849060 DOI: 10.1128/spectrum.01913-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 11/20/2022] Open
Abstract
Vibrio vulnificus is a naturally occurring, potentially lethal pathogen found in coastal waters, fish, and shellfish. Sewage spills in coastal waters occur when infrastructure fails due to severe storms or age, and may affect bacterial populations by altering nutrient levels. This study investigated effects of sewage on clonal and natural V. vulnificus populations in microcosms. Addition of 1% sewage to estuarine water caused the density of a pure culture of V. vulnificus CMCP6 and a natural V. vulnificus population to increase significantly, by two to three orders of magnitude, whether measured by quantitative PCR (qPCR) or culture and in batch and continuous cultures. Changes in the transcription of six virulence- and survival-associated genes in response to sewage were assessed using continuous culture. Exposure to sewage affected transcription of genes that may be associated with virulence, i.e., it modulated the oxidative stress response by altering superoxide dismutase transcription, significantly increasing sodB transcription while repressing sodA. Sewage also repressed transcription of nptA, which encodes a sodium-phosphate cotransporter. Sewage had no effect on sodC transcription or the putative virulence-associated genes hupA or wza. The effects of environmentally relevant levels of sewage on V. vulnificus populations and gene transcription suggest that sewage spills that impact warm coastal waters could lead to an increased risk of V. vulnificus infections. IMPORTANCE Vibrio vulnificus infections have profound impacts such as limb amputation and death for individuals with predisposing conditions. The warming climate is contributing to rising V. vulnificus prevalence in waters that were previously too cold to support high levels of the pathogen. Climate change is also expected to increase precipitation in many regions, which puts more pressure on wastewater infrastructure and will result in more frequent sewage spills. The finding that 1% wastewater in estuarine water leads to 100 to over 1,000-fold greater V. vulnificus concentrations suggests that human exposure to oysters and estuarine water could have greater health impacts in the future. Further, wastewater had a significant effect on gene transcription and has the potential to affect virulence during the initial environment-to-host transition.
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Affiliation(s)
- James W. Conrad
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
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5
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Modulation of quorum sensing-associated virulence in bacteria: carbohydrate as a key factor. Arch Microbiol 2021; 203:1881-1890. [PMID: 33641039 DOI: 10.1007/s00203-021-02235-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/11/2020] [Accepted: 02/11/2021] [Indexed: 01/21/2023]
Abstract
Quorum sensing (QS) is a method of inter-cellular communication that permits bacteria to dispense information about cell density and to synchronize the gene expression accordingly. Gram-positive and Gram-negative bacteria utilize distinct quorum sensing mechanisms for effective pathogenesis. Virulence factor production by pathogenic bacteria is one of the important traits that is under the control of QS. A growing body of evidence has indicated the role of the nutritional environment notably by carbohydrates in dictating the QS-associated virulence gene regulation. The modulation of QS by carbohydrates mitigates the survival and establishment of the pathogen within its host which in turn leads to an increase in morbidity and mortality. This mini-review throws light on the predilection of pathogenic bacteria to rapidly regulate its QS-linked virulence gene expression based on the changing nutrient levels that assist them in prospering within diverse niches.
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Abstract
Vibrio cholerae remains a challenge in the developing world and incidence of the disease it causes, cholera, is anticipated to increase with rising global temperatures and with emergent, highly infectious strains. At present, the underlying metabolic processes that support V. cholerae growth during infection are less well understood than specific virulence traits, such as production of a toxin or pilus. In this study, we determined that oxidative metabolism of host substrates such as mucin contribute significantly to V. cholerae population expansion in vivo. Identifying metabolic pathways critical for growth can provide avenues for controlling V. cholerae infection and the knowledge may be translatable to other pathogens of the gastrointestinal tract. Vibrio cholerae replicates to high cell density in the human small intestine, leading to the diarrheal disease cholera. During infection, V. cholerae senses and responds to environmental signals that govern cellular responses. Spatial localization of V. cholerae within the intestine affects nutrient availability and metabolic pathways required for replicative success. Metabolic processes used by V. cholerae to reach such high cell densities are not fully known. We sought to better define the metabolic traits that contribute to high levels of V. cholerae during infection. By disrupting the pyruvate dehydrogenase (PDH) complex and pyruvate formate-lyase (PFL), we could differentiate aerobic and anaerobic metabolic pathway involvement in V. cholerae proliferation. We demonstrate that oxidative metabolism is a key contributor to the replicative success of V. choleraein vivo using an infant mouse model in which PDH mutants were attenuated 100-fold relative to the wild type for colonization. Additionally, metabolism of host substrates, including mucin, was determined to support V. cholerae growth in vitro as a sole carbon source, primarily under aerobic growth conditions. Mucin likely contributes to population expansion during human infection as it is a ubiquitous source of carbohydrates. These data highlight oxidative metabolism as important in the intestinal environment and warrant further investigation of how oxygen and other host substrates shape the intestinal landscape that ultimately influences bacterial disease. We conclude from our results that oxidative metabolism of host substrates is a key driver of V. cholerae proliferation during infection, leading to the substantial bacterial burden exhibited in cholera patients.
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7
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A MARTX Toxin rtxA Gene Is Controlled by Host Environmental Signals through a CRP-Coordinated Regulatory Network in Vibrio vulnificus. mBio 2020; 11:mBio.00723-20. [PMID: 32723914 PMCID: PMC7387792 DOI: 10.1128/mbio.00723-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A MARTX toxin, RtxA, is an essential virulence factor of many pathogens, including Vibrio species. H-NS and HlyU repress and derepress, respectively, rtxA expression of a life-threatening pathogen, Vibrio vulnificus. We found that Lrp directly activates rtxA independently of H-NS and HlyU, and leucine inhibits the Lrp-mediated activation of rtxA. Furthermore, we demonstrated that CRP represses rtxA but derepresses in the presence of exogenous glucose. CRP represses rtxA not only directly by binding to upstream of rtxA but also indirectly by repressing lrp and hlyU. This is the first report of a regulatory network comprising CRP, Lrp, H-NS, and HlyU, which coordinates the rtxA expression in response to environmental signals such as leucine and glucose during infection. This elaborate regulatory network will enhance the fitness of V. vulnificus and contribute to its successful infection within the host. A multifunctional autoprocessing repeats-in-toxin (MARTX) toxin plays an essential role in the virulence of many pathogens, including a fulminating human pathogen Vibrio vulnificus. H-NS and HlyU repress and derepress expression of the MARTX toxin gene rtxA in V. vulnificus, respectively. However, little is known about other regulatory proteins and environmental signals involved in rtxA regulation. In this study, we found that a leucine-responsive regulatory protein (Lrp) activates rtxA by binding directly and specifically to the rtxA promoter, PrtxA. Phased hypersensitivity resulting from DNase I cleavage of the PrtxA regulatory region suggests that Lrp probably induces DNA bending in PrtxA. Lrp activates PrtxA independently of H-NS and HlyU, and leucine inhibits Lrp binding to PrtxA and reduces the Lrp-mediated activation. Furthermore, a cyclic AMP receptor protein (CRP) represses PrtxA, and exogenous glucose relieves the CRP-mediated repression. Biochemical and mutational analyses demonstrated that CRP binds directly and specifically to the upstream region of PrtxA, which presumably alters the DNA conformation in PrtxA and thus represses rtxA. Moreover, CRP represses expression of lrp and hlyU by binding directly to their upstream regions, forming coherent feed-forward loops with Lrp and HlyU. In conclusion, expression of rtxA is controlled by a regulatory network comprising CRP, Lrp, H-NS, and HlyU in response to changes in host environmental signals such as leucine and glucose. This collaborative regulation enables the elaborate expression of rtxA, thereby enhancing the fitness and pathogenesis of V. vulnificus during the course of infection.
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8
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Mari L, Casagrandi R, Bertuzzo E, Rinaldo A, Gatto M. Conditions for transient epidemics of waterborne disease in spatially explicit systems. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181517. [PMID: 31218018 PMCID: PMC6549988 DOI: 10.1098/rsos.181517] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/12/2019] [Indexed: 05/06/2023]
Abstract
Waterborne diseases are a diverse family of infections transmitted through ingestion of-or contact with-water infested with pathogens. Outbreaks of waterborne infections often show well-defined spatial signatures that are typically linked to local eco-epidemiological conditions, water-mediated pathogen transport and human mobility. In this work, we apply a spatially explicit network model describing the transmission cycle of waterborne pathogens to determine invasion conditions in metacommunities endowed with a realistic spatial structure. Specifically, we aim to define conditions under which pathogens can temporarily colonize a set of human communities, thus triggering a transient epidemic outbreak. To that end, we apply generalized reactivity analysis, a recently developed methodological framework for the study of transient dynamics in ecological systems subject to external perturbations. The study of pathogen invasion is complemented by the detection of the spatial signatures associated with the perturbations to a disease-free system that are expected to be amplified the most over different time scales. Understanding the drivers of waterborne disease dynamics over time scales that are relevant to epidemic and/or endemic transmission is a crucial, cross-disciplinary challenge, as large portions of the developing world still struggle to cope with the burden of these infections.
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Affiliation(s)
- Lorenzo Mari
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
- Author for correspondence: Lorenzo Mari e-mail:
| | - Renato Casagrandi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
| | - Enrico Bertuzzo
- Dipartimento di Scienze Ambientali, Informatica e Statistica, Università Ca’ Foscari Venezia, 30170 Venezia Mestre, Italy
| | - Andrea Rinaldo
- Laboratory of Ecohydrology, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Dipartimento ICEA, Università di Padova, 35131 Padova, Italy
| | - Marino Gatto
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
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9
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Abstract
Cholera infections caused by the gamma-proteobacterium Vibrio cholerae have ravaged human populations for centuries, and cholera pandemics have afflicted every corner of the globe. Fortunately, interventions such as oral rehydration therapy, antibiotics/antimicrobials, and vaccines have saved countless people afflicted with cholera, and new interventions such as probiotics and phage therapy are being developed as promising approaches to treat even more cholera infections. Although current therapies are mostly effective and can reduce disease transmission, cholera outbreaks remain deadly, as was seen during recent outbreaks in Haiti, Ethiopia, and Yemen. This is due to significant underlying political and socioeconomic complications, including shortages of vaccines and clean food and water and a lack of health surveillance. In this review, we highlight the strengths and weaknesses of current cholera therapies, discuss emerging technologies, and argue that a multi-pronged, flexible approach is needed to continue to reduce the worldwide burden of cholera.
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Affiliation(s)
- Brian Y Hsueh
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Christopher M Waters
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
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10
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Metzger LC, Matthey N, Stoudmann C, Collas EJ, Blokesch M. Ecological implications of gene regulation by TfoX and TfoY among diverse Vibrio species. Environ Microbiol 2019; 21:2231-2247. [PMID: 30761714 PMCID: PMC6618264 DOI: 10.1111/1462-2920.14562] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/16/2019] [Accepted: 02/10/2019] [Indexed: 01/26/2023]
Abstract
Bacteria of the genus Vibrio are common members of aquatic environments where they compete with other prokaryotes and defend themselves against grazing predators. A macromolecular protein complex called the type VI secretion system (T6SS) is used for both purposes. Previous research showed that the sole T6SS of the human pathogen V. cholerae is induced by extracellular (chitin) or intracellular (low c‐di‐GMP levels) cues and that these cues lead to distinctive signalling pathways for which the proteins TfoX and TfoY serve as master regulators. In this study, we tested whether the TfoX‐ and TfoY‐mediated regulation of T6SS, concomitantly with natural competence or motility, was conserved in non‐cholera Vibrio species, and if so, how these regulators affected the production of individual T6SSs in double‐armed vibrios. We show that, alongside representative competence genes, TfoX regulates at least one T6SS in all tested Vibrio species. TfoY, on the other hand, fostered motility in all vibrios but had a more versatile T6SS response in that it did not foster T6SS‐mediated killing in all tested vibrios. Collectively, our data provide evidence that the TfoX‐ and TfoY‐mediated signalling pathways are mostly conserved in diverse Vibrio species and important for signal‐specific T6SS induction.
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Affiliation(s)
- Lisa C Metzger
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Noémie Matthey
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Candice Stoudmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Esther J Collas
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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11
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Qi X, Tester RF. Starch containing formulations for diarrhoea therapy. Clin Nutr ESPEN 2018; 28:36-40. [PMID: 30390891 DOI: 10.1016/j.clnesp.2018.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/09/2018] [Indexed: 12/18/2022]
Abstract
Diarrhoea therapies in general include a number of approaches (depending on local practise and the cause of the diarrhoea) aimed at: (i) removing the cause (e.g. lactose in the diet); (ii) treating the cause of infection if present (e.g. antibiotics); (iii) reducing the effect of the cause (e.g. adsorbent); (iv) depressing gastric motility and secretions (e.g. various drugs); (v) probiotic bacteria with perhaps prebiotic energy sources and most importantly of all (vi) rehydration using rehydration salt solutions (oral rehydration therapy, ORT, using oral rehydration solutions, ORS). Glucose has been included in ORS formats for rapidly available energy since ORS formats were developed initially- but has the disadvantage of a high osmotic pressure. It is used in modern ORS formats to promote sodium absorption, however. The use of α-glucans (glucose containing oligo- or polysaccharides) in ORS formats is gaining ground in terms of utilisation for diarrhoea - a fairly recent approach to therapy in the western world. The use of different α-glucans in ORS formulations is discussed and strategies for the development further of therapies is investigated. This review is aimed at the scientific and medical communities.
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Affiliation(s)
- Xin Qi
- Glycologic Limited, 70 Cowcaddens Road, Glasgow, G4 0BA, UK.
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12
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Kieser S, Sarker SA, Sakwinska O, Foata F, Sultana S, Khan Z, Islam S, Porta N, Combremont S, Betrisey B, Fournier C, Charpagne A, Descombes P, Mercenier A, Berger B, Brüssow H. Bangladeshi children with acute diarrhoea show faecal microbiomes with increased Streptococcus abundance, irrespective of diarrhoea aetiology. Environ Microbiol 2018; 20:2256-2269. [PMID: 29786169 DOI: 10.1111/1462-2920.14274] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 12/22/2022]
Abstract
We report streptococcal dysbiosis in acute diarrhoea irrespective of aetiology. Compared with 20 healthy local controls, 71 Bangladeshi children hospitalized with acute diarrhoea (AD) of viral, mixed viral/bacterial, bacterial and unknown aetiology showed a significantly decreased bacterial diversity with loss of pathways characteristic for the healthy distal colon microbiome (mannan degradation, methylerythritol phosphate and thiamin biosynthesis), an increased proportion of faecal streptococci belonging to the Streptococcus bovis and Streptococcus salivarius species complexes, and an increased level of E. coli-associated virulence genes. No enteropathogens could be attributed to a subgroup of patients. Elevated lytic coliphage DNA was detected in 2 out of 5 investigated enteroaggregative E. coli (EAEC)-infected patients. Streptococcal outgrowth in AD is discussed as a potential nutrient-driven consequence of glucose provided with oral rehydration solution.
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Affiliation(s)
- Silas Kieser
- Gut Ecosystem Department, Institute of Nutritional Science, Nestlé Research Centre, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
| | - Shafiqul A Sarker
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Nutrition and Clinical Services Division, 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Olga Sakwinska
- Gut Ecosystem Department, Institute of Nutritional Science, Nestlé Research Centre, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
| | - Francis Foata
- Gut Ecosystem Department, Institute of Nutritional Science, Nestlé Research Centre, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
| | - Shamima Sultana
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Nutrition and Clinical Services Division, 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Zeenat Khan
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Nutrition and Clinical Services Division, 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Shoheb Islam
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Nutrition and Clinical Services Division, 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212, Bangladesh
| | - Nadine Porta
- Gut Ecosystem Department, Institute of Nutritional Science, Nestlé Research Centre, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
| | - Séverine Combremont
- Gut Ecosystem Department, Institute of Nutritional Science, Nestlé Research Centre, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
| | - Bertrand Betrisey
- Nestlé Institute of Health Sciences, EPFL Innovation Park, CH-1015, Lausanne, Switzerland
| | - Coralie Fournier
- Nestlé Institute of Health Sciences, EPFL Innovation Park, CH-1015, Lausanne, Switzerland
| | - Aline Charpagne
- Nestlé Institute of Health Sciences, EPFL Innovation Park, CH-1015, Lausanne, Switzerland
| | - Patrick Descombes
- Nestlé Institute of Health Sciences, EPFL Innovation Park, CH-1015, Lausanne, Switzerland
| | - Annick Mercenier
- Gut Ecosystem Department, Institute of Nutritional Science, Nestlé Research Centre, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
| | - Bernard Berger
- Gut Ecosystem Department, Institute of Nutritional Science, Nestlé Research Centre, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
| | - Harald Brüssow
- Gut Ecosystem Department, Institute of Nutritional Science, Nestlé Research Centre, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
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13
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Manneh-Roussel J, Haycocks JRJ, Magán A, Perez-Soto N, Voelz K, Camilli A, Krachler AM, Grainger DC. cAMP Receptor Protein Controls Vibrio cholerae Gene Expression in Response to Host Colonization. mBio 2018; 9:e00966-18. [PMID: 29991587 PMCID: PMC6050953 DOI: 10.1128/mbio.00966-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/14/2018] [Indexed: 11/20/2022] Open
Abstract
The bacterium Vibrio cholerae is native to aquatic environments and can switch lifestyles to cause disease in humans. Lifestyle switching requires modulation of genetic systems for quorum sensing, intestinal colonization, and toxin production. Much of this regulation occurs at the level of gene expression and is controlled by transcription factors. In this work, we have mapped the binding of cAMP receptor protein (CRP) and RNA polymerase across the V. cholerae genome. We show that CRP is an integral component of the regulatory network that controls lifestyle switching. Focusing on a locus necessary for toxin transport, we demonstrate CRP-dependent regulation of gene expression in response to host colonization. Examination of further CRP-targeted genes reveals that this behavior is commonplace. Hence, CRP is a key regulator of many V. cholerae genes in response to lifestyle changes.IMPORTANCE Cholera is an infectious disease that is caused by the bacterium Vibrio cholerae Best known for causing disease in humans, the bacterium is most commonly found in aquatic ecosystems. Hence, humans acquire cholera following ingestion of food or water contaminated with V. cholerae Transition between an aquatic environment and a human host triggers a lifestyle switch that involves reprogramming of V. cholerae gene expression patterns. This process is controlled by a network of transcription factors. In this paper, we show that the cAMP receptor protein (CRP) is a key regulator of V. cholerae gene expression in response to lifestyle changes.
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Affiliation(s)
- Jainaba Manneh-Roussel
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - James R J Haycocks
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Andrés Magán
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Nicolas Perez-Soto
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Kerstin Voelz
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Tufts University, Boston, Massachusetts, USA
| | - Anne-Marie Krachler
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, Texas, USA
| | - David C Grainger
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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14
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Glucose-Specific Enzyme IIA of the Phosphoenolpyruvate:Carbohydrate Phosphotransferase System Modulates Chitin Signaling Pathways in Vibrio cholerae. J Bacteriol 2017; 199:JB.00127-17. [PMID: 28461445 DOI: 10.1128/jb.00127-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/21/2017] [Indexed: 12/13/2022] Open
Abstract
In Vibrio cholerae, the genes required for chitin utilization and natural competence are governed by the chitin-responsive two-component system (TCS) sensor kinase ChiS. In the classical TCS paradigm, a sensor kinase specifically phosphorylates a cognate response regulator to activate gene expression. However, our previous genetic study suggested that ChiS stimulates the non-TCS transcriptional regulator TfoS by using mechanisms distinct from classical phosphorylation reactions (S. Yamamoto, J. Mitobe, T. Ishikawa, S. N. Wai, M. Ohnishi, H. Watanabe, and H. Izumiya, Mol Microbiol 91:326-347, 2014, https://doi.org/10.1111/mmi.12462). TfoS specifically activates the transcription of tfoR, encoding a small regulatory RNA essential for competence gene expression. Whether ChiS and TfoS interact directly remains unknown. To determine if other factors mediate the communication between ChiS and TfoS, we isolated transposon mutants that turned off tfoR::lacZ expression but possessed intact chiS and tfoS genes. We demonstrated an unexpected association of chitin-induced signaling pathways with the glucose-specific enzyme IIA (EIIAglc) of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) for carbohydrate uptake and catabolite control of gene expression. Genetic and physiological analyses revealed that dephosphorylated EIIAglc inactivated natural competence and tfoR transcription. Chitin-induced expression of the chb operon, which is required for chitin transport and catabolism, was also repressed by dephosphorylated EIIAglc Furthermore, the regulation of tfoR and chb expression by EIIAglc was dependent on ChiS and intracellular levels of ChiS were not affected by disruption of the gene encoding EIIAglc These results define a previously unknown connection between the PTS and chitin signaling pathways in V. cholerae and suggest a strategy whereby this bacterium can physiologically adapt to the existing nutrient status.IMPORTANCE The EIIAglc protein of the PTS coordinates a wide variety of physiological functions with carbon availability. In this report, we describe an unexpected association of chitin-activated signaling pathways in V. cholerae with EIIAglc The signaling pathways are governed by the chitin-responsive TCS sensor kinase ChiS and lead to the induction of chitin utilization and natural competence. We show that dephosphorylated EIIAglc inhibits both signaling pathways in a ChiS-dependent manner. This inhibition is different from classical catabolite repression that is caused by lowered levels of cyclic AMP. This work represents a newly identified connection between the PTS and chitin signaling pathways in V. cholerae and suggests a strategy whereby this bacterium can physiologically adapt to the existing nutrient status.
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15
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Rinaldo A, Bertuzzo E, Blokesch M, Mari L, Gatto M. Modeling Key Drivers of Cholera Transmission Dynamics Provides New Perspectives for Parasitology. Trends Parasitol 2017; 33:587-599. [PMID: 28483382 DOI: 10.1016/j.pt.2017.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 04/01/2017] [Accepted: 04/10/2017] [Indexed: 11/15/2022]
Abstract
Hydroclimatological and anthropogenic factors are key drivers of waterborne disease transmission. Information on human settlements and host mobility on waterways along which pathogens and hosts disperse, and relevant hydroclimatological processes, can be acquired remotely and included in spatially explicit mathematical models of disease transmission. In the case of epidemic cholera, such models allowed the description of complex disease patterns and provided insight into the course of ongoing epidemics. The inclusion of spatial information in models of disease transmission can aid in emergency management and the assessment of alternative interventions. Here, we review the study of drivers of transmission via spatially explicit approaches and argue that, because many parasitic waterborne diseases share the same drivers as cholera, similar principles may apply.
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Affiliation(s)
- Andrea Rinaldo
- Laboratory of Ecohydrology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Dipartimento ICEA, Università di Padova, Padova, Italy.
| | - Enrico Bertuzzo
- Laboratory of Ecohydrology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Department of Environmental Sciences, Informatics and Statistics, University Cà Foscari Venice, Venezia Mestre, Italy
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lorenzo Mari
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy
| | - Marino Gatto
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy
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16
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Finger F, Genolet T, Mari L, de Magny GC, Manga NM, Rinaldo A, Bertuzzo E. Mobile phone data highlights the role of mass gatherings in the spreading of cholera outbreaks. Proc Natl Acad Sci U S A 2016; 113:6421-6. [PMID: 27217564 PMCID: PMC4988598 DOI: 10.1073/pnas.1522305113] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spatiotemporal evolution of human mobility and the related fluctuations of population density are known to be key drivers of the dynamics of infectious disease outbreaks. These factors are particularly relevant in the case of mass gatherings, which may act as hotspots of disease transmission and spread. Understanding these dynamics, however, is usually limited by the lack of accurate data, especially in developing countries. Mobile phone call data provide a new, first-order source of information that allows the tracking of the evolution of mobility fluxes with high resolution in space and time. Here, we analyze a dataset of mobile phone records of ∼150,000 users in Senegal to extract human mobility fluxes and directly incorporate them into a spatially explicit, dynamic epidemiological framework. Our model, which also takes into account other drivers of disease transmission such as rainfall, is applied to the 2005 cholera outbreak in Senegal, which totaled more than 30,000 reported cases. Our findings highlight the major influence that a mass gathering, which took place during the initial phase of the outbreak, had on the course of the epidemic. Such an effect could not be explained by classic, static approaches describing human mobility. Model results also show how concentrated efforts toward disease control in a transmission hotspot could have an important effect on the large-scale progression of an outbreak.
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Affiliation(s)
- Flavio Finger
- Laboratory of Ecohydrology, École Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Tina Genolet
- Laboratory of Ecohydrology, École Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Lorenzo Mari
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
| | - Guillaume Constantin de Magny
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institute of Research for Development, 64501 Montpellier, France
| | - Noël Magloire Manga
- Service des Maladies Infectieuses et Tropicales de l'Hôpital de la Paix, Unité de Formation et de Recherche en Sciences de la Santé, Université Assane Seck de Ziguinchor, 27000 Ziguinchor, Senegal
| | - Andrea Rinaldo
- Laboratory of Ecohydrology, École Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland; Dipartimento dell'Ingegneria Civile, Edile ed Ambientale, Università di Padova, 35131 Padova, Italy
| | - Enrico Bertuzzo
- Laboratory of Ecohydrology, École Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland;
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17
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Circulation of a Quorum-Sensing-Impaired Variant of Vibrio cholerae Strain C6706 Masks Important Phenotypes. mSphere 2016; 1:mSphere00098-16. [PMID: 27303743 PMCID: PMC4888887 DOI: 10.1128/msphere.00098-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/04/2016] [Indexed: 01/09/2023] Open
Abstract
Phenotypic diversity between laboratory-domesticated bacterial strains is a common problem and often results in the failed reproduction of published data. However, researchers rarely compare such strains to elucidate the underlying mutation(s). In this study, we tested one of the best-studied V. cholerae isolates, O1 El Tor strain C6706 (a patient isolate from Peru), with respect to two main phenotypes: natural competence for transformation and type VI secretion. We recently demonstrated that the two phenotypes are coregulated and specifically induced upon the growth of pandemic V. cholerae O1 El Tor strains on chitinous surfaces. We provide evidence that of seven C6706 strains collected from different laboratories, four were impaired in the tested phenotypes due to a mutation in a QS gene. Collectively, our data indicate that the circulation of such a mutated wild-type strain of C6706 might have had important consequences for QS-related data. Vibrio cholerae, the causative agent of cholera, is a model organism for studying virulence regulation, biofilm formation, horizontal gene transfer, and the cell-to-cell communication known as quorum sensing (QS). As in any research field, discrepancies between data from diverse laboratories are sometimes observed for V. cholerae. Such discrepancies are often caused by the use of diverse patient or environmental isolates. In this study, we investigated the inability of a few laboratories to reproduce high levels of natural transformation, a mode of horizontal gene transfer that is specifically induced on chitinous surfaces. This irreproducibility was mostly related to one specific isolate of V. cholerae: the O1 El Tor C6706 strain. C6706 was previously described as QS proficient, an important prerequisite for the induction of natural competence for transformation. To elucidate the underlying problem, we collected seven isolates of the same C6706 strain from different research laboratories in North America and Europe and compared their phenotypes. Importantly, we observed a split response with respect to QS-related gene expression, including chitin-induced natural competence and type VI secretion (T6S). While approximately half of the strains behaved as reported for several other O1 El Tor pandemic isolates that are commonly studied in the laboratory, the other half were significantly impaired in QS-related expression patterns. This impairment was caused by a mutation in a QS-related gene (luxO). We conclude that the circulation of such QS-impaired wild-type strains is responsible for masking several important phenotypes of V. cholerae, including natural competence for transformation and T6S. IMPORTANCE Phenotypic diversity between laboratory-domesticated bacterial strains is a common problem and often results in the failed reproduction of published data. However, researchers rarely compare such strains to elucidate the underlying mutation(s). In this study, we tested one of the best-studied V. cholerae isolates, O1 El Tor strain C6706 (a patient isolate from Peru), with respect to two main phenotypes: natural competence for transformation and type VI secretion. We recently demonstrated that the two phenotypes are coregulated and specifically induced upon the growth of pandemic V. cholerae O1 El Tor strains on chitinous surfaces. We provide evidence that of seven C6706 strains collected from different laboratories, four were impaired in the tested phenotypes due to a mutation in a QS gene. Collectively, our data indicate that the circulation of such a mutated wild-type strain of C6706 might have had important consequences for QS-related data.
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18
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Borgeaud S, Metzger LC, Scrignari T, Blokesch M. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science 2015; 347:63-7. [PMID: 25554784 DOI: 10.1126/science.1260064] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Natural competence for transformation is a common mode of horizontal gene transfer and contributes to bacterial evolution. Transformation occurs through the uptake of external DNA and its integration into the genome. Here we show that the type VI secretion system (T6SS), which serves as a predatory killing device, is part of the competence regulon in the naturally transformable pathogen Vibrio cholerae. The T6SS-encoding gene cluster is under the positive control of the competence regulators TfoX and QstR and is induced by growth on chitinous surfaces. Live-cell imaging revealed that deliberate killing of nonimmune cells via competence-mediated induction of T6SS releases DNA and makes it accessible for horizontal gene transfer in V. cholerae.
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Affiliation(s)
- Sandrine Borgeaud
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Lisa C Metzger
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Tiziana Scrignari
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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