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Hollender M, Sałek M, Karlicki M, Karnkowska A. Single-cell genomics revealed Candidatus Grellia alia sp. nov. as an endosymbiont of Eutreptiella sp. (Euglenophyceae). Protist 2024; 175:126018. [PMID: 38325049 DOI: 10.1016/j.protis.2024.126018] [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: 09/12/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/09/2024]
Abstract
Though endosymbioses between protists and prokaryotes are widespread, certain host lineages have received disproportionate attention what may indicate either a predisposition to such interactions or limited studies on certain protist groups due to lack of cultures. The euglenids represent one such group in spite of microscopic observations showing intracellular bacteria in some strains. Here, we perform a comprehensive molecular analysis of a previously identified endosymbiont in the Eutreptiella sp. CCMP3347 using a single cell approach and bulk culture sequencing. The genome reconstruction of this endosymbiont allowed the description of a new endosymbiont Candidatus Grellia alia sp. nov. from the family Midichloriaceae. Comparative genomics revealed a remarkably complete conjugative type IV secretion system present in three copies on the plasmid sequences of the studied endosymbiont, a feature missing in the closely related Grellia incantans. This study addresses the challenge of limited host cultures with endosymbionts by showing that the genomes of endosymbionts reconstructed from single host cells have the completeness and contiguity that matches or exceeds those coming from bulk cultures. This paves the way for further studies of endosymbionts in euglenids and other protist groups. The research also provides the opportunity to study the diversity of endosymbionts in natural populations.
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Affiliation(s)
- Metody Hollender
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Marta Sałek
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Michał Karlicki
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland.
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2
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Rayamajhee B, Willcox MDP, Henriquez FL, Petsoglou C, Subedi D, Carnt N. Acanthamoeba, an environmental phagocyte enhancing survival and transmission of human pathogens. Trends Parasitol 2022; 38:975-990. [PMID: 36109313 DOI: 10.1016/j.pt.2022.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 01/13/2023]
Abstract
The opportunistic protist Acanthamoeba, which interacts with other microbes such as bacteria, fungi, and viruses, shows significant similarity in cellular and functional aspects to human macrophages. Intracellular survival of microbes in this microbivorous amoebal host may be a crucial step for initiation of infection in higher eukaryotic cells. Therefore, Acanthamoeba-microbe adaptations are considered an evolutionary model of macrophage-pathogen interactions. This paper reviews Acanthamoeba as an emerging human pathogen and different ecological interactions between Acanthamoeba and microbes that may serve as environmental training grounds and a genetic melting pot for the evolution, persistence, and transmission of potential human pathogens.
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Affiliation(s)
- Binod Rayamajhee
- School of Optometry and Vision Science, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia.
| | - Mark D P Willcox
- School of Optometry and Vision Science, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia.
| | - Fiona L Henriquez
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Blantyre, South Lanarkshire, G72 0LH, UK
| | - Constantinos Petsoglou
- Sydney and Sydney Eye Hospital, Southeastern Sydney Local Health District, Sydney, Australia; Save Sight Institute, University of Sydney, Sydney, Australia
| | - Dinesh Subedi
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Nicole Carnt
- School of Optometry and Vision Science, Faculty of Medicine and Health, University of New South Wales (UNSW), Sydney, Australia
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3
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Martyn JE, Gomez-Valero L, Buchrieser C. The evolution and role of eukaryotic-like domains in environmental intracellular bacteria: the battle with a eukaryotic cell. FEMS Microbiol Rev 2022; 46:6529235. [DOI: 10.1093/femsre/fuac012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Intracellular pathogens that are able to thrive in different environments, such as Legionella spp. which preferentially live in protozoa in aquatic environments or environmental Chlamydiae which replicate either within protozoa or a range of animals, possess a plethora of cellular biology tools to influence their eukaryotic host. The host manipulation tools that evolved in the interaction with protozoa, confer these bacteria the capacity to also infect phylogenetically distinct eukaryotic cells, such as macrophages and thus they can also be human pathogens. To manipulate the host cell, bacteria use protein secretion systems and molecular effectors. Although these molecular effectors are encoded in bacteria, they are expressed and function in a eukaryotic context often mimicking or inhibiting eukaryotic proteins. Indeed, many of these effectors have eukaryotic-like domains. In this review we propose that the main pathways environmental intracellular bacteria need to subvert in order to establish the host eukaryotic cell as a replication niche are chromatin remodelling, ubiquitination signalling, and modulation of protein-protein interactions via tandem repeat domains. We then provide mechanistic insight into how these proteins might have evolved as molecular weapons. Finally, we highlight that in environmental intracellular bacteria the number of eukaryotic-like domains and proteins is considerably higher than in intracellular bacteria specialised to an isolated niche, such as obligate intracellular human pathogens. As mimics of eukaryotic proteins are critical components of host pathogen interactions, this distribution of eukaryotic-like domains suggests that the environment has selected them.
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Affiliation(s)
- Jessica E Martyn
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires and CNRS UMR 3525, Paris, France
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4
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Amaro F, Martín-González A. Microbial warfare in the wild-the impact of protists on the evolution and virulence of bacterial pathogens. Int Microbiol 2021; 24:559-571. [PMID: 34365574 DOI: 10.1007/s10123-021-00192-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/03/2021] [Accepted: 06/28/2021] [Indexed: 01/01/2023]
Abstract
During the long history of co-evolution with protists, bacteria have evolved defense strategies to avoid grazing and survive phagocytosis. These mechanisms allow bacteria to exploit phagocytic cells as a protective niche in which to escape from environmental stress and even replicate. Importantly, these anti-grazing mechanisms can function as virulence factors when bacteria infect humans. Here, we discuss how protozoan predation exerts a selective pressure driving bacterial virulence and shaping their genomes, and how bacteria-protist interactions might contribute to the spread of antibiotic resistance as well. We provide examples to demonstrate that besides being voracious bacterial predators, protozoa can serve as melting pots where intracellular organisms exchange genetic information, or even "training grounds" where some pathogens become hypervirulent after passing through. In this special issue, we would like to emphasize the tremendous impact of bacteria-protist interactions on human health and the potential of amoebae as model systems to study biology and evolution of a variety of pathogens. Besides, a better understanding of bacteria-protist relationships will help us expand our current understanding of bacterial virulence and, likely, how pathogens emerge.
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Affiliation(s)
- Francisco Amaro
- Department of Genetics, Physiology and Microbiology, School of Biology, Complutense University of Madrid, 28040, Madrid, Spain.
| | - Ana Martín-González
- Department of Genetics, Physiology and Microbiology, School of Biology, Complutense University of Madrid, 28040, Madrid, Spain
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5
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Abstract
Amoebae are protists that have complicated relationships with bacteria, covering the whole spectrum of symbiosis. Amoeba-bacterium interactions contribute to the study of predation, symbiosis, pathogenesis, and human health. Given the complexity of their relationships, it is necessary to understand the ecology and evolution of their interactions. In this paper, we provide an updated review of the current understanding of amoeba-bacterium interactions. We start by discussing the diversity of amoebae and their bacterial partners. We also define three types of ecological interactions between amoebae and bacteria and discuss their different outcomes. Finally, we focus on the implications of amoeba-bacterium interactions on human health, horizontal gene transfer, drinking water safety, and the evolution of symbiosis. In conclusion, amoeba-bacterium interactions are excellent model systems to investigate a wide range of scientific questions. Future studies should utilize advanced techniques to address research gaps, such as detecting hidden diversity, lack of amoeba genomes, and the impacts of amoeba predation on the microbiome.
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Gutiérrez R, Shalit T, Markus B, Yuan C, Nachum-Biala Y, Elad D, Harrus S. Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov., two novel species closely related to the zoonotic Bartonella elizabethae, isolated from black rats and wild desert rodent-fleas. Int J Syst Evol Microbiol 2020; 70:1656-1665. [PMID: 32100689 DOI: 10.1099/ijsem.0.003952] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The genus Bartonella (Family: Bartonellaceae; Order: Rhizobiales; Class: Alphaproteobacteria) comprises facultative intracellular Gram-negative, haemotropic, slow-growing, vector-borne bacteria. Wild rodents and their fleas harbor a great diversity of species and strains of the genus Bartonella, including several zoonotic ones. This genetic diversity coupled with a fastidious nature of the organism results in a taxonomic challenge that has led to a massive collection of uncharacterized strains. Here, we report the genomic and phenotypic characterization of two strains, members of the genus Bartonella (namely Tel Aviv and OE 1-1), isolated from Rattus rattus rats and Synosternus cleopatrae fleas, respectively. Scanning electron microscopy revealed rod-shaped bacteria with polar pili, lengths ranging from 1.0 to 2.0 µm and widths ranging from 0.3 to 0.6 µm. OE 1-1 and Tel Aviv strains contained one single chromosome of 2.16 and 2.23 Mbp and one plasmid of 29.0 and 41.5 Kbp, with average DNA G+C contents of 38.16 and 38.47 mol%, respectively. These strains presented an average nucleotide identity (ANI) of 89.9 %. Bartonella elizabethae was found to be the closest phylogenetic relative of both strains (ANI=90.9-93.6 %). The major fatty acids identified in both strains were C18:1ω7c, C18 : 0 and C16 : 0. They differ from B. elizabethae in their C17 : 0 and C15 : 0 compositions. Both strains are strictly capnophilic and their biochemical profiles resembled those of species of the genus Bartonella with validly published names, whereas differences in arylamidase activities partially assisted in their speciation. Genomic and phenotypic differences demonstrate that OE 1-1 and Tel Aviv strains represent novel individual species, closely related to B. elizabethae, for which we propose the names Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov.
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Affiliation(s)
- Ricardo Gutiérrez
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Tali Shalit
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 7610000, Israel
| | - Barak Markus
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 7610000, Israel
| | - Congli Yuan
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, PR China
| | - Yaarit Nachum-Biala
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
| | - Daniel Elad
- The Kimron Veterinary Institute, Bet Dagan, 50250, Israel
| | - Shimon Harrus
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, 7610000, Israel
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Flores-Ríos R, Moya-Beltrán A, Pareja-Barrueto C, Arenas-Salinas M, Valenzuela S, Orellana O, Quatrini R. The Type IV Secretion System of ICE Afe1: Formation of a Conjugative Pilus in Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:30. [PMID: 30804894 PMCID: PMC6370655 DOI: 10.3389/fmicb.2019.00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/09/2019] [Indexed: 01/10/2023] Open
Abstract
The dispersal of mobile genetic elements and their gene cargo relies on type IV secretion systems (T4SS). In this work the ICEAfe1 Tra-type T4SS nanomachine, encoded in the publicly available genome of Acidithiobacillus ferrooxidans ATCC 23270TY, was characterized in terms of its organization, conservation, expression and mating bridge formation. Twenty-one conjugative genes grouped in four genetic clusters encode the ICEAfe1 T4SS, containing all the indispensable functions for the formation and stabilization of the pili and for DNA processing. The clusters' organization resembles that of other mobile genetic elements (such as plasmids and integrative and conjugative elements-ICEs). Sequence conservation, genetic organization and distribution of the tra system in the genomes of other sequenced Acidithiobacillus spp. suggests that the ICEAfe1 T4SS could mediate the lateral gene transfer between related bacteria. All ICEAfe1 T4SS genes are transcriptionally active and expressed from four independent operons. The transcriptional levels of selected marker genes increase in response to Mitomycin C treatment, a DNA damage elicitor that has acknowledged stimulatory effects on excision rates and gene expression of other ICEs, including ICEAfe1. Using a tailor-made pilin-antiserum against ICEAfe1 T4SS TraA pilin and epifluorescence microscopy, the presence of the conjugative pili on the cell surface of A. ferrooxidans could be demonstrated. Additionally, immunodetection assays, by immunogold, allowed the identification of pili-like extracellular structures. Together, the results obtained in this work demonstrate that the ICEAfe1 T4SS is phylogenetically conserved within the taxon, is expressed at mRNA and protein levels in vivo in the A. ferrooxidans type strain, and produces a pili-like structure of extracellular and intercellular localization in this model acidophile, supporting its functionality. Additional efforts will be required to prove conjugation of the ICEAfe1 or parts of this element through the cognate T4SS.
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Affiliation(s)
- Rodrigo Flores-Ríos
- Fundación Ciencia y Vida, Santiago, Chile.,Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Ana Moya-Beltrán
- Fundación Ciencia y Vida, Santiago, Chile.,Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | | | - Mauricio Arenas-Salinas
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | | | - Omar Orellana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia y Vida, Santiago, Chile.,Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
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Park CH, Lee A, Lee Y, Eun CS, Lee SK, Han DS. Evaluation of gastric microbiome and metagenomic function in patients with intestinal metaplasia using 16S rRNA gene sequencing. Helicobacter 2019; 24:e12547. [PMID: 30440093 PMCID: PMC6587566 DOI: 10.1111/hel.12547] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Despite recent advances in studies on the gastric microbiome, the role of the non-Helicobacter pylori gastric microbiome in gastric carcinogenesis remains unclear. We evaluated the characteristics of the gastric microbiome and metagenomic functions in patients with IM. METHODS Participants were classified into six groups according to disease status (chronic superficial gastritis [CSG], intestinal metaplasia [IM], and cancer) and H. pylori- infection status (H. pylori-positive and H. pylori-negative). The gastric microbiome was analyzed in mucosal tissues at the gastric antrum by 16S rRNA gene sequencing. Moreover, we assessed the metagenome including the type IV secretion system (T4SS) gene, as T4SS proteins are essential for transferring CagA from H. pylori- into the human gastric epithelium. RESULTS Among the 138 included patients, 48, 9, 23, 14, 12, and 32 were classified into the H. pylori-negative CSG, H. pylori-negative IM, H. pylori-negative cancer, H. pylori-positive CSG, H. pylori-positive IM, and H. pylori-positive cancer groups, respectively. Cyanobacteria were predominant in the H. pylori-negative CSG group compared to in the H. pylori-negative IM and H. pylori-negative cancer groups (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 14.0% vs 4.2% vs 0.04%, P < 0.001). In contrast, Rhizobiales were commonly observed in the H. pylori-negative IM group (H. pylori-negative CSG vs H. pylori-negative IM vs H. pylori-negative cancer: 1.9% vs 15.4% vs 2.8%, P < 0.001). The relative abundance of Rhizobiales increased as H. pylori-infected stomachs progressed from gastritis to IM. In the H. pylori-negative IM group, genes encoding T4SS were prevalent among the metagenome. Additionally, after H. pylori- eradication therapy, the gastric microbiome was similar to the microbiome observed after spontaneous clearance of H. pylori-. CONCLUSIONS The relative abundance of Rhizobiales was higher in patients with H. pylori-negative IM than in those with H. pylori-negative CSG or cancer. Additionally, T4SS genes were highly observed in the metagenome of patients with IM. Highly abundant T4SS proteins in these patients may promote gastric carcinogenesis.
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Affiliation(s)
- Chan Hyuk Park
- Department of Internal MedicineHanyang University Guri Hospital, Hanyang University College of MedicineGuriKorea,Department of Medicine, The Graduate SchoolYonsei UniversitySeoulKorea
| | - A‐reum Lee
- Department of Internal MedicineHanyang University Guri Hospital, Hanyang University College of MedicineGuriKorea
| | - Yu‐ra Lee
- Department of Internal MedicineHanyang University Guri Hospital, Hanyang University College of MedicineGuriKorea
| | - Chang Soo Eun
- Department of Internal MedicineHanyang University Guri Hospital, Hanyang University College of MedicineGuriKorea
| | - Sang Kil Lee
- Division of Gastroenterology, Department of Internal MedicineSeverance Hospital, Yonsei University College of MedicineSeoulKorea
| | - Dong Soo Han
- Department of Internal MedicineHanyang University Guri Hospital, Hanyang University College of MedicineGuriKorea
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Frank HK, Boyd SD, Hadly EA. Global fingerprint of humans on the distribution of Bartonella bacteria in mammals. PLoS Negl Trop Dis 2018; 12:e0006865. [PMID: 30439961 PMCID: PMC6237287 DOI: 10.1371/journal.pntd.0006865] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/21/2018] [Indexed: 12/11/2022] Open
Abstract
As humans move and alter habitats, they change the disease risk for themselves, their commensal animals and wildlife. Bartonella bacteria are prevalent in mammals and cause numerous human infections. Understanding how this genus has evolved and switched hosts in the past can reveal how current patterns were established and identify potential mechanisms for future cross-species transmission. We analyzed patterns of Bartonella transmission and likely sources of spillover using the largest collection of Bartonella gltA genotypes assembled, including 67 new genotypes. This pathogenic genus likely originated as an environmental bacterium and insect commensal before infecting mammals. Rodents and domestic animals serve as the reservoirs or at least key proximate host for most Bartonella genotypes in humans. We also find evidence of exchange of Bartonella between phylogenetically distant domestic animals and wildlife, likely due to increased contact. Care should be taken to avoid contact between humans, domestic animals and wildlife to protect the health of all. As humans move around the globe they contact new environments, potentially introducing novel diseases to wildlife, domestic animals and humans. Understanding how current infection patterns were established and how humans have likely altered them can help protect human, animal and environmental health. We traced the evolution of and distribution of globally distributed, pathogenic Bartonella, a common and well-studied bacterial genus in wildlife and humans that can cause cat scratch disease, trench fever and other diseases. We showed that humans are likely changing disease risk for themselves and the animals in their environment by moving themselves and domestic animals, as evidenced by large geographic movements of infections or shared infections in distantly related species. Not only does this increase our knowledge about Bartonella, an important emerging pathogen, but our investigation can serve as a model for elucidating the driving role of humans in changing disease landscapes.
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Affiliation(s)
- Hannah K. Frank
- Department of Biology, Stanford University, Stanford, California, United States of America
- Department of Pathology, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Elizabeth A. Hadly
- Department of Biology, Stanford University, Stanford, California, United States of America
- Stanford Woods Institute for the Environment, Stanford University, Stanford, California, United States of America
- Center for Innovation in Global Health, Stanford University, Stanford, California, United States of America
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10
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Abstract
Carrion's disease (CD) is a neglected biphasic vector-borne illness related to Bartonella bacilliformis. It is found in the Andean valleys and is transmitted mainly by members of the Lutzomyia genus but also by blood transfusions and from mother to child. The acute phase, Oroya fever, presents severe anemia and fever. The lethality is high in the absence of adequate treatment, despite the organism being susceptible to most antibiotics. Partial immunity is developed after infection by B. bacilliformis, resulting in high numbers of asymptomatic carriers. Following infection there is the chronic phase, Peruvian warts, involving abnormal proliferation of the endothelial cells. Despite potentially being eradicable, CD has been expanded due to human migration and geographical expansion of the vector. Moreover, in vitro studies have demonstrated the risk of the development of antimicrobial resistance. These findings, together with the description of new Bartonella species producing CD-like infections, the presence of undescribed potential vectors in new areas, the lack of adequate diagnostic tools and knowledge of the immunology and bacterial pathogenesis of CD, and poor international visibility, have led to the risk of increasing the potential expansion of resistant strains which will challenge current treatment schemes as well as the possible appearance of CD in areas where it is not endemic.
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Affiliation(s)
- Cláudia Gomes
- Institute for Global Health, Barcelona Centre for International Health Research, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Joaquim Ruiz
- Institute for Global Health, Barcelona Centre for International Health Research, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
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11
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Muchesa P, Leifels M, Jurzik L, Hoorzook KB, Barnard TG, Bartie C. Coexistence of free-living amoebae and bacteria in selected South African hospital water distribution systems. Parasitol Res 2016; 116:155-165. [PMID: 27730363 PMCID: PMC7088035 DOI: 10.1007/s00436-016-5271-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/21/2016] [Indexed: 12/13/2022]
Abstract
Pathogenic free-living amoebae (FLA), such as Naegleria fowleri, Balamuthia mandrillaris and Acanthamoeba species isolated from aquatic environments have been implicated in central nervous system, eye and skin human infections. They also allow the survival, growth and transmission of bacteria such as Legionella, Mycobacteria and Vibrio species in water systems. The purpose of this study was to investigate the co-occurrence of potentially pathogenic FLA and their associated bacteria in hospital water networks in Johannesburg, South Africa. A total of 178 water (n = 95) and swab (n = 83) samples were collected from two hospital water distribution systems. FLA were isolated using the amoebal enrichment technique and identified using PCR and 18S rDNA sequencing. Amoebae potentially containing intra-amoebal bacteria were lysed and cultured on blood agar plates. Bacterial isolates were characterized using the VITEK®2 compact System. Free-living amoebae were isolated from 77 (43.3 %) of the samples. Using microscopy, PCR and 18S rRNA sequencing, Acanthamoeba spp. (T3 and T20 genotypes), Vermamoeba vermiformis and Naegleria gruberi specie were identified. The Acanthamoeba T3 and T20 genotypes have been implicated in eye and central nervous system infections. The most commonly detected bacterial species were Serratia marcescens, Stenotrophomonas maltophilia, Delftia acidovorans, Sphingomonas paucimobilis and Comamonas testosteroni. These nosocomial pathogenic bacteria are associated with systematic blood, respiratory tract, the urinary tract, surgical wounds and soft tissues infections. The detection of FLA and their associated opportunistic bacteria in the hospital water systems point out to a potential health risk to immune-compromised individuals.
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Affiliation(s)
- P Muchesa
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa.
| | - M Leifels
- Department of Hygiene, Social and Environmental Medicine, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - L Jurzik
- Department of Hygiene, Social and Environmental Medicine, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - K B Hoorzook
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - T G Barnard
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - C Bartie
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
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12
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Delafont V, Bouchon D, Héchard Y, Moulin L. Environmental factors shaping cultured free-living amoebae and their associated bacterial community within drinking water network. WATER RESEARCH 2016; 100:382-392. [PMID: 27219048 DOI: 10.1016/j.watres.2016.05.044] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/10/2016] [Accepted: 05/13/2016] [Indexed: 05/08/2023]
Abstract
Free-living amoebae (FLA) constitute an important part of eukaryotic populations colonising drinking water networks. However, little is known about the factors influencing their ecology in such environments. Because of their status as reservoir of potentially pathogenic bacteria, understanding environmental factors impacting FLA populations and their associated bacterial community is crucial. Through sampling of a large drinking water network, the diversity of cultivable FLA and their bacterial community were investigated by an amplicon sequencing approach, and their correlation with physicochemical parameters was studied. While FLA ubiquitously colonised the water network all year long, significant changes in population composition were observed. These changes were partially explained by several environmental parameters, namely water origin, temperature, pH and chlorine concentration. The characterisation of FLA associated bacterial community reflected a diverse but rather stable consortium composed of nearly 1400 OTUs. The definition of a core community highlighted the predominance of only few genera, majorly dominated by Pseudomonas and Stenotrophomonas. Co-occurrence analysis also showed significant patterns of FLA-bacteria association, and allowed uncovering potentially new FLA - bacteria interactions. From our knowledge, this study is the first that combines a large sampling scheme with high-throughput identification of FLA together with associated bacteria, along with their influencing environmental parameters. Our results demonstrate the importance of physicochemical parameters in the ecology of FLA and their bacterial community in water networks.
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Affiliation(s)
- Vincent Delafont
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipes Microbiologie de l'Eau & Ecologie, Evolution, Symbiose, France; Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, 33, Avenue Jean Jaurès, 94200 Ivry sur Seine, France
| | - Didier Bouchon
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipes Microbiologie de l'Eau & Ecologie, Evolution, Symbiose, France
| | - Yann Héchard
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipes Microbiologie de l'Eau & Ecologie, Evolution, Symbiose, France
| | - Laurent Moulin
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, 33, Avenue Jean Jaurès, 94200 Ivry sur Seine, France.
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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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14
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Current and past strategies for bacterial culture in clinical microbiology. Clin Microbiol Rev 2015; 28:208-36. [PMID: 25567228 DOI: 10.1128/cmr.00110-14] [Citation(s) in RCA: 281] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome.
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15
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Zhu Q, Kosoy M, Olival KJ, Dittmar K. Horizontal transfers and gene losses in the phospholipid pathway of bartonella reveal clues about early ecological niches. Genome Biol Evol 2014; 6:2156-69. [PMID: 25106622 PMCID: PMC4159011 DOI: 10.1093/gbe/evu169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bartonellae are mammalian pathogens vectored by blood-feeding arthropods. Although of increasing medical importance, little is known about their ecological past, and host associations are underexplored. Previous studies suggest an influence of horizontal gene transfers in ecological niche colonization by acquisition of host pathogenicity genes. We here expand these analyses to metabolic pathways of 28 Bartonella genomes, and experimentally explore the distribution of bartonellae in 21 species of blood-feeding arthropods. Across genomes, repeated gene losses and horizontal gains in the phospholipid pathway were found. The evolutionary timing of these patterns suggests functional consequences likely leading to an early intracellular lifestyle for stem bartonellae. Comparative phylogenomic analyses discover three independent lineage-specific reacquisitions of a core metabolic gene—NAD(P)H-dependent glycerol-3-phosphate dehydrogenase (gpsA)—from Gammaproteobacteria and Epsilonproteobacteria. Transferred genes are significantly closely related to invertebrate Arsenophonus-, and Serratia-like endosymbionts, and mammalian Helicobacter-like pathogens, supporting a cellular association with arthropods and mammals at the base of extant Bartonella spp. Our studies suggest that the horizontal reacquisitions had a key impact on bartonellae lineage specific ecological and functional evolution.
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Affiliation(s)
- Qiyun Zhu
- Department of Biological Sciences, University at Buffalo, State University of New York
| | - Michael Kosoy
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Foothills Research Campus, Fort Collins, Colorado
| | | | - Katharina Dittmar
- Department of Biological Sciences, University at Buffalo, State University of New York Graduate Program of Evolution, Ecology, and Behavior, University at Buffalo, State University of New York
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16
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Kebbi-Beghdadi C, Greub G. Importance of amoebae as a tool to isolate amoeba-resisting microorganisms and for their ecology and evolution: the Chlamydia paradigm. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:309-24. [PMID: 24992529 DOI: 10.1111/1758-2229.12155] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/14/2014] [Accepted: 02/16/2014] [Indexed: 05/23/2023]
Abstract
Free-living amoebae are distributed worldwide and are frequently in contact with humans and animals. As cysts, they can survive in very harsh conditions and resist biocides and most disinfection procedures. Several microorganisms, called amoeba-resisting microorganisms (ARMs), have evolved to survive and multiply within these protozoa. Among them are many important pathogens, such as Legionella and Mycobacteria, and also several newly discovered Chlamydia-related bacteria, such as Parachlamydia acanthamoebae, Estrella lausannensis, Simkania negevensis or Waddlia chondrophila whose pathogenic role towards human or animal is strongly suspected. Amoebae represent an evolutionary crib for their resistant microorganisms since they can exchange genetic material with other ARMs and develop virulence traits that will be further used to infect other professional phagocytes. Moreover, amoebae constitute an ideal tool to isolate strict intracellular microorganisms from complex microbiota, since they will feed on other fast-growing bacteria, such as coliforms potentially present in the investigated samples. The paradigm that ARMs are likely resistant to macrophages, another phagocytic cell, and that they are likely virulent towards humans and animals is only partially true. Indeed, we provide examples of the Chlamydiales order that challenge this assumption and suggest that the ability to multiply in protozoa does not strictly correlate with pathogenicity and that we should rather use the ability to replicate in multiple and diverse eukaryotic cells as an indirect marker of virulence towards mammals. Thus, cell-culture-based microbial culturomics should be used in the future to try to discover new pathogenic bacterial species.
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Affiliation(s)
- Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria (CRIB), Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
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17
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Merhej V, Angelakis E, Socolovschi C, Raoult D. Genotyping, evolution and epidemiological findings of Rickettsia species. INFECTION GENETICS AND EVOLUTION 2014; 25:122-37. [DOI: 10.1016/j.meegid.2014.03.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/12/2023]
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18
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Minnick MF, Anderson BE, Lima A, Battisti JM, Lawyer PG, Birtles RJ. Oroya fever and verruga peruana: bartonelloses unique to South America. PLoS Negl Trop Dis 2014; 8:e2919. [PMID: 25032975 PMCID: PMC4102455 DOI: 10.1371/journal.pntd.0002919] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bartonella bacilliformis is the bacterial agent of Carrión's disease and is presumed to be transmitted between humans by phlebotomine sand flies. Carrión's disease is endemic to high-altitude valleys of the South American Andes, and the first reported outbreak (1871) resulted in over 4,000 casualties. Since then, numerous outbreaks have been documented in endemic regions, and over the last two decades, outbreaks have occurred at atypical elevations, strongly suggesting that the area of endemicity is expanding. Approximately 1.7 million South Americans are estimated to be at risk in an area covering roughly 145,000 km2 of Ecuador, Colombia, and Peru. Although disease manifestations vary, two disparate syndromes can occur independently or sequentially. The first, Oroya fever, occurs approximately 60 days following the bite of an infected sand fly, in which infection of nearly all erythrocytes results in an acute hemolytic anemia with attendant symptoms of fever, jaundice, and myalgia. This phase of Carrión's disease often includes secondary infections and is fatal in up to 88% of patients without antimicrobial intervention. The second syndrome, referred to as verruga peruana, describes the endothelial cell-derived, blood-filled tumors that develop on the surface of the skin. Verrugae are rarely fatal, but can bleed and scar the patient. Moreover, these persistently infected humans provide a reservoir for infecting sand flies and thus maintaining B. bacilliformis in nature. Here, we discuss the current state of knowledge regarding this life-threatening, neglected bacterial pathogen and review its host-cell parasitism, molecular pathogenesis, phylogeny, sand fly vectors, diagnostics, and prospects for control.
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Affiliation(s)
- Michael F. Minnick
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Burt E. Anderson
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Amorce Lima
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - James M. Battisti
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Phillip G. Lawyer
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard J. Birtles
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
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Abstract
Discoveries in cytogenetics, molecular biology, and genomics have revealed that genome change is an active cell-mediated physiological process. This is distinctly at variance with the pre-DNA assumption that genetic changes arise accidentally and sporadically. The discovery that DNA changes arise as the result of regulated cell biochemistry means that the genome is best modelled as a read-write (RW) data storage system rather than a read-only memory (ROM). The evidence behind this change in thinking and a consideration of some of its implications are the subjects of this article. Specific points include the following: cells protect themselves from accidental genome change with proofreading and DNA damage repair systems; localized point mutations result from the action of specialized trans-lesion mutator DNA polymerases; cells can join broken chromosomes and generate genome rearrangements by non-homologous end-joining (NHEJ) processes in specialized subnuclear repair centres; cells have a broad variety of natural genetic engineering (NGE) functions for transporting, diversifying and reorganizing DNA sequences in ways that generate many classes of genomic novelties; natural genetic engineering functions are regulated and subject to activation by a range of challenging life history events; cells can target the action of natural genetic engineering functions to particular genome locations by a range of well-established molecular interactions, including protein binding with regulatory factors and linkage to transcription; and genome changes in cancer can usefully be considered as consequences of the loss of homeostatic control over natural genetic engineering functions.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
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20
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Alphaproteobacteria species as a source and target of lateral sequence transfers. Trends Microbiol 2014; 22:147-56. [DOI: 10.1016/j.tim.2013.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/05/2013] [Accepted: 12/17/2013] [Indexed: 11/22/2022]
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Abstract
The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology; University of Chicago; Chicago, IL USA
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22
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Socolovschi C, Audoly G, Raoult D. Connection of toxin-antitoxin modules to inoculation eschar and arthropod vertical transmission in Rickettsiales. Comp Immunol Microbiol Infect Dis 2013; 36:199-209. [PMID: 23414774 DOI: 10.1016/j.cimid.2013.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 01/10/2013] [Accepted: 01/18/2013] [Indexed: 12/01/2022]
Abstract
The biological role of toxin-antitoxin systems (TAS) in pathogenicity and cell addiction of Rickettsia was recently reported. We realized a comparative genomic analysis onto 33 rickettsial genomes and correlated the presence of TAS encoding genes with vertical transmission (VT) in arthropod hosts, the presence of inoculation eschar in humans and experimental animals, and the mortality in humans. There is a significant statistical link between TAS and the presence of an eschar (p≤0.0001). The presence of TAS is also significantly inversely correlated with mortality. The toxic effect of TAS may increase the local reaction, thus inhibiting the spread of rickettsiae associated with fatal outcome of the disease. The TAS were also linked to VT (p≤0.0001). Together with our previous findings we speculate that this is the first addiction system evidenced in intracellular bacteria. Thus, the TAS, as selfish genetic elements, might be essential to the evolutionary strategy of intracellular bacteria.
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Affiliation(s)
- Cristina Socolovschi
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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23
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Bertelli C, Greub G. Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms. Front Cell Infect Microbiol 2012; 2:110. [PMID: 22919697 PMCID: PMC3423634 DOI: 10.3389/fcimb.2012.00110] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Accepted: 08/01/2012] [Indexed: 12/05/2022] Open
Abstract
Based on Darwin's concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions, and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host's factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT) that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms (ARMs).
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Affiliation(s)
- Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland
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24
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Salvucci E. Selfishness, warfare, and economics; or integration, cooperation, and biology. Front Cell Infect Microbiol 2012; 2:54. [PMID: 22919645 PMCID: PMC3417387 DOI: 10.3389/fcimb.2012.00054] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 04/06/2012] [Indexed: 12/11/2022] Open
Abstract
The acceptance of Darwin's theory of evolution by natural selection is not complete and it has been pointed out its limitation to explain the complex processes that constitute the transformation of species. It is necessary to discuss the explaining power of the dominant paradigm. It is common that new discoveries bring about contradictions that are intended to be overcome by adjusting results to the dominant reductionist paradigm using all sorts of gradations and combinations that are admitted for each case. In addition to the discussion on the validity of natural selection, modern findings represent a challenge to the interpretation of the observations with the Darwinian view of competition and struggle for life as theoretical basis. New holistic interpretations are emerging related to the Net of Life, in which the interconnection of ecosystems constitutes a dynamic and self-regulating biosphere: viruses are recognized as a macroorganism with a huge collection of genes, most unknown that constitute the major planet's gene pool. They play a fundamental role in evolution since their sequences are capable of integrating into the genomes in an “infective” way and become an essential part of multicellular organisms. They have content with “biological sense” i.e., they appear as part of normal life processes and have a serious role as carrier elements of complex genetic information. Antibiotics are cell signals with main effects on general metabolism and transcription on bacterial cells and communities. The hologenome theory considers an organism and all of its associated symbiotic microbes (parasites, mutualists, synergists, amensalists) as a result of symbiopoiesis. Microbes, helmints, that are normally understood as parasites are cohabitants and they have cohabited with their host and drive the evolution and existence of the partners. Each organism is the result of integration of complex systems. The eukaryotic organism is the result of combination of bacterial, virus, and eukaryotic DNA and it is the result of the interaction of its own genome with the genome of its microbiota, and their metabolism are intertwined (as a “superorganism”) along evolution. The darwinian paradigm had its origin in the free market theories and concepts of Malthus and Spencer. Then, nature was explained on the basis of market theories moving away from an accurate explanation of natural phenomena. It is necessary to acknowledge the limitations of the dominant dogma. These new interpretations about biological processes, molecules, roles of viruses in nature, and microbial interactions are remarkable points to be considered in order to construct a solid theory adjusted to the facts and with less speculations and tortuous semantic traps.
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Affiliation(s)
- Emiliano Salvucci
- Consejo Nacional de Investigaciones Cientificas y Técnicas Argentina.
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25
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Lamrabet O, Merhej V, Pontarotti P, Raoult D, Drancourt M. The genealogic tree of mycobacteria reveals a long-standing sympatric life into free-living protozoa. PLoS One 2012; 7:e34754. [PMID: 22511965 PMCID: PMC3325273 DOI: 10.1371/journal.pone.0034754] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 03/08/2012] [Indexed: 02/07/2023] Open
Abstract
Free-living protozoa allow horizontal gene transfer with and between the microorganisms that they host. They host mycobacteria for which the sources of transferred genes remain unknown. Using BLASTp, we searched within the genomes of 15 mycobacteria for homologous genes with 34 amoeba-resistant bacteria and the free-living protozoa Dictyostelium discoideum. Subsequent phylogenetic analysis of these sequences revealed that eight mycobacterial open-reading frames (ORFs) were probably acquired via horizontal transfer from beta- and gamma-Proteobacteria and from Firmicutes, but the transfer histories could not be reliably established in details. One further ORF encoding a pyridine nucleotide disulfide oxidoreductase (pyr-redox) placed non-tuberculous mycobacteria in a clade with Legionella spp., Francisella spp., Coxiella burnetii, the ciliate Tetrahymena thermophila and D. discoideum with a high reliability. Co-culturing Mycobacterium avium and Legionella pneumophila with the amoeba Acanthamoeba polyphaga demonstrated that these two bacteria could live together in amoebae for five days, indicating the biological relevance of intra-amoebal transfer of the pyr-redox gene. In conclusion, the results of this study support the hypothesis that protists can serve as a source and a place for gene transfer in mycobacteria.
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Affiliation(s)
- Otmane Lamrabet
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Vicky Merhej
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Pierre Pontarotti
- Equipe Evolution Biologique et Modélisation UMR 6632, IRF48, Aix-Marseille Université/CNRS, Marseille, France
| | - Didier Raoult
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
- * E-mail:
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26
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Audoly G, Vincentelli R, Edouard S, Georgiades K, Mediannikov O, Gimenez G, Socolovschi C, Mège JL, Cambillau C, Raoult D. Effect of rickettsial toxin VapC on its eukaryotic host. PLoS One 2011; 6:e26528. [PMID: 22046301 PMCID: PMC3203148 DOI: 10.1371/journal.pone.0026528] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 09/28/2011] [Indexed: 11/18/2022] Open
Abstract
Rickettsia are intracellular bacteria typically associated with arthropods that can be transmitted to humans by infected vectors. Rickettsia spp. can cause mild to severe human disease with a possible protection effect of corticosteroids when antibiotic treatments are initiated. We identified laterally transferred toxin-antitoxin (TA) genetic elements, including vapB/C, in several Rickettsia genomes and showed that they are functional in bacteria and eukaryotic cells. We also generated a plaque assay to monitor the formation of lytic plaques over time and demonstrated that chloramphenicol accelerates host cell lysis of vapB/C-containing Rickettsia. Whole-genome expression, TUNEL and FISH assays on the infected cells following exposure to the antibiotic revealed early apoptosis of host cells, which was linked to over-transcription of bacterial vapB/C operons and subsequent cytoplasmic VapC toxin release. VapC that is expressed in Escherichia coli and Saccharomyces cerevisiae or microinjected into mammalian cells is toxic through RNase activity and is prevented by dexamethasone. This study provides the first biological evidence that toxin-antitoxin elements act as pathogenic factors in bacterial host cells, confirming comparative genomic evidence of their role in bacterial pathogenicity. Our results suggest that early mortality following antibiotic treatment of some bacterial infections can be prevented by administration of dexamethasone.
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Affiliation(s)
- Gilles Audoly
- Unité des Rickettsies URMITE, UMR CNRS 6236- IRD 198, Marseille, France
| | | | - Sophie Edouard
- Unité des Rickettsies URMITE, UMR CNRS 6236- IRD 198, Marseille, France
| | | | - Oleg Mediannikov
- Unité des Rickettsies URMITE, UMR CNRS 6236- IRD 198, Marseille, France
| | - Grégory Gimenez
- Unité des Rickettsies URMITE, UMR CNRS 6236- IRD 198, Marseille, France
| | | | - Jean-Louis Mège
- Unité des Rickettsies URMITE, UMR CNRS 6236- IRD 198, Marseille, France
| | | | - Didier Raoult
- Unité des Rickettsies URMITE, UMR CNRS 6236- IRD 198, Marseille, France
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27
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Rhizobium radiobacter bacteremia in a neonate. Infection 2011; 40:437-9. [PMID: 22038113 DOI: 10.1007/s15010-011-0216-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 10/10/2011] [Indexed: 10/16/2022]
Abstract
Rhizobium radiobacter bacteremia is an infrequent cause of human infection. We report a rare manifestation of R. radiobacter infection in which bacteremia occurred in a newborn infant without other risk factors.
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28
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Renvoisé A, Merhej V, Georgiades K, Raoult D. Intracellular Rickettsiales: Insights into manipulators of eukaryotic cells. Trends Mol Med 2011; 17:573-83. [PMID: 21763202 DOI: 10.1016/j.molmed.2011.05.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/11/2011] [Accepted: 05/23/2011] [Indexed: 02/08/2023]
Abstract
The order Rickettsiales comprises obligate intracellular bacteria that are the ancestors of modern eukaryotes. These bacteria infect various vectors and hosts, with some species being pathogenic to man. Rickettsiales have small, degraded genomes and provide a paradigm for increased pathogenicity despite gene loss; significant levels of genetic exchange occur between bacteria that infect the same host and with the eukaryotic hosts themselves. Crosstalk between host and bacteria appears to be mediated by a Type IV secretion system and proteins containing eukaryotic-like repeat motifs. Rickettsiales also manipulate host reproduction and induce host resistance to viruses. Manipulation of its host by Rickettsiales has long been misunderstood because of technical difficulties, but recent advances in understanding bacterial-eukaryotes interactions have been made and are reviewed here.
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Affiliation(s)
- Aurélie Renvoisé
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes CNRS-IRD UMR6236-198, Université de la Méditerranée, Faculté de Médecine, 27 bd Jean Moulin, 13385 Marseille cedex 5, France
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29
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30
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Biswas S, Rolain JM. Bartonella infection: treatment and drug resistance. Future Microbiol 2011; 5:1719-31. [PMID: 21133691 DOI: 10.2217/fmb.10.133] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bartonella species, which belong to the α-2 subgroup of Proteobacteria, are fastidious Gram-negative bacteria that are highly adapted to their mammalian host reservoirs. Bartonella species are responsible for different clinical conditions affecting humans, including Carrion's disease, cat scratch disease, trench fever, bacillary angiomatosis, endocarditis and peliosis hepatis. While some of these diseases can resolve spontaneously without treatment, in other cases, the disease is fatal without antibiotic treatment. In this article, we discuss the antibiotic susceptibility patterns of Bartonella species, detected using several methods. We also provide an overview of Bartonella infection in humans and animals and discuss the antibiotic treatment recommendations for the different infections, treatment failure and the molecular mechanism of antibiotic resistance in these bacteria.
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Affiliation(s)
- Silpak Biswas
- CNRS-IRD, UMR 6236, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, 27 boulevard Jean-Moulin, Marseille cedex 05, France
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