Acinetobacter Baumannii As Nosocomial Pathogenic Bacteria
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Insight Into the Resistome and Quorum Sensing System of a Divergent Acinetobacter Pittii Isolate from an Untouched Site of the Lechuguilla Cave
bioRxiv preprint doi: https://doi.org/10.1101/745182; this version posted August 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Insight into the resistome and quorum sensing system of a divergent Acinetobacter pittii isolate from an untouched site of the Lechuguilla Cave Han Ming Gan1,2,3*, Peter Wengert4 ,Trevor Penix4, Hazel A. Barton5, André O. Hudson4 and Michael A. Savka4 1 Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong 3220 ,Victoria, Australia 2 Deakin Genomics Centre, Deakin University, Geelong 3220 ,Victoria, Australia 3 School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia 4 Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA 5 Department of Biology, University of Akron, Akron, Ohio, USA *Corresponding author Name: Han Ming Gan Email: [email protected] Key words Acinetobacter, quorum sensing, antibiotic resistance Abstract Acinetobacter are Gram-negative bacteria belonging to the sub-phyla Gammaproteobacteria, commonly associated with soils, animal feeds and water. Some members of the Acinetobacter have been implicated in hospital-acquired infections, with broad-spectrum antibiotic resistance. Here we report the whole genome sequence of LC510, an Acinetobacter species isolated from deep within a pristine location of the Lechuguilla Cave. Pairwise nucleotide comparison to three type strains within Acinetobacter assigned LC510 as an Acinetobacter pittii isolate. Scanning of the LC510 genome identified two genes coding for β-lactamase resistance, despite the fact that LC510 was isolated from a portion of the cave not previously visited by humans and protected from anthropogenic input. -
Insight Into the Resistome and Quorum Sensing System of a Divergent Acinetobacter Pittii Isolate from 1 an Untouched Site Of
bioRxiv preprint doi: https://doi.org/10.1101/745182; this version posted November 27, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Insight into the resistome and quorum sensing system of a divergent Acinetobacter pittii isolate from 2 an untouched site of the Lechuguilla Cave 3 4 Han Ming Gan1,2,3*, Peter Wengert4 , Hazel A. Barton5, André O. Hudson4 and Michael A. Savka4 5 1 Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong 6 3220 ,Victoria, Australia 7 2 Deakin Genomics Centre, Deakin University, Geelong 3220 ,Victoria, Australia 8 3 School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Selangor, 9 Malaysia 10 4 Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA 11 5 Department of Biology, University of Akron, Akron, Ohio, USA 12 *Corresponding author 13 Name: Han Ming Gan 14 Email: [email protected] 15 Key words 16 Acinetobacter, quorum sensing, antibiotic resistance 17 18 Abstract 19 Acinetobacter are Gram-negative bacteria belonging to the sub-phyla Gammaproteobacteria, commonly 20 associated with soils, animal feeds and water. Some members of the Acinetobacter have been 21 implicated in hospital-acquired infections, with broad-spectrum antibiotic resistance. Here we report the 22 whole genome sequence of LC510, an Acinetobacter species isolated from deep within a pristine 23 location of the Lechuguilla Cave. -
Evolutionary Genomics of Conjugative Elements and Integrons
Université Paris Descartes École doctorale Interdisciplinaire Européenne 474 Frontières du Vivant Microbial Evolutionary Genomic, Pasteur Institute Evolutionary genomics of conjugative elements and integrons Thèse de doctorat en Biologie Interdisciplinaire Présentée par Jean Cury Pour obtenir le grade de Docteur de l’Université Paris Descartes Sous la direction de Eduardo Rocha Soutenue publiquement le 17 Novembre 2017, devant un jury composé de: Claudine MÉDIGUE Rapporteure CNRS, Genoscope, Évry Marie-Cécile PLOY Rapporteure Université de Limoges Érick DENAMUR Examinateur Université Paris Diderot, Paris Philippe LOPEZ Examinateur Université Pierre et Marie Curie, Paris Alan GROSSMAN Examinateur MIT, Cambdridge, USA Eduardo ROCHA Directeur de thèse CNRS, Institut Pasteur, Paris ِ عمحمود ُبدرويش َالنرد َم ْن انا ِٔ َقول ُلك ْم ما ا ُقول ُلك ْم ؟ وانا لم أ ُك ْن َ َج ًرا َص َق َل ْت ُه ُالمياه َفأ ْص َب َح ِوهاً و َق َصباً َثق َب ْت ُه ُالرياح َفأ ْص َب َح ًنايا ... انا ِع ُب َالن ْرد ، ا َرب ُح يناً وا َس ُر يناً انا ِم ُثل ُك ْم ا وا قل قليً ... The dice player Mahmoud Darwish Who am I to say to you what I am saying to you? I was not a stone polished by water and became a face nor was I a cane punctured by the wind and became a lute… I am a dice player, Sometimes I win and sometimes I lose I am like you or slightly less… Contents Acknowledgments 7 Preamble 9 I Introduction 11 1 Background for friends and family . 13 2 Horizontal Gene Transfer (HGT) . 16 2.1 Mechanisms of horizontal gene transfer . -
Epidemiological and Molecular Analysis of Virulence and Antibiotic Resistance in Acinetobacter Baumannii
UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE VETERINARIA DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR IV TESIS DOCTORAL Epidemiological and Molecular Analysis of Virulence and Antibiotic Resistance in Acinetobacter baumannii Análisis Epidemiológico y Molecular de la Virulencia y la Antibiorresistencia en Acinetobacter baumannii MEMORIA PARA OPTAR AL GRADO DE DOCTOR PRESENTADA POR Elias Dahdouh DIRECTORA Mónica Suárez Rodríguez Madrid, 2017 © Elias Dahdouh, 2016 UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE VETERINARIA DEPARTAMENTO DE BIOQUIMICA Y BIOLOGIA MOLECULAR IV TESIS DOCTORAL Análisis Epidemiológico y Molecular de la Virulencia y la Antibiorresistencia en Acinetobacter baumannii Epidemiological and Molecular Analysis of Virulence and Antibiotic Resistance in Acinetobacter baumannii MEMORIA PARA OPTAR AL GRADO DE DOCTOR PRESENTADA POR Elias Dahdouh Directora Mónica Suárez Rodríguez Madrid, 2016 UNIVERSIDAD COMPLUTENSE DE MADRID FACULTAD DE VETERINARIA Departamento de Bioquímica y Biología Molecular IV ANALYSIS EPIDEMIOLOGICO Y MOLECULAR DE LA VIRULENCIA Y LA ANTIBIORRESISTENCIA EN Acinetobacter baumannii EPIDEMIOLOGICAL AND MOLECULAR ANALYSIS OF VIRULENCE AND ANTIBIOTIC RESISTANCE IN Acinetobacter baumannii MEMORIA PARA OPTAR AL GRADO DE DOCTOR PRESENTADA POR Elias Dahdouh Bajo la dirección de la doctora Mónica Suárez Rodríguez Madrid, Diciembre de 2016 First and foremost, I would like to thank God for the continued strength and determination that He has given me. I would also like to thank my father Abdo, my brother Charbel, my fiancée, Marisa, and all my friends for their endless support and for standing by me at all times. Moreover, I would like to thank Dra. Monica Suarez Rodriguez and Dr. Ziad Daoud for giving me the opportunity to complete this doctoral study and for their guidance, encouragement, and friendship. -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 2 Microalgae
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley, -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 1 Microalgae 2 Richard G. Do
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley, -
The Microbiota Continuum Along the Female Reproductive Tract and Its Relation to Uterine-Related Diseases
ARTICLE DOI: 10.1038/s41467-017-00901-0 OPEN The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases Chen Chen1,2, Xiaolei Song1,3, Weixia Wei4,5, Huanzi Zhong 1,2,6, Juanjuan Dai4,5, Zhou Lan1, Fei Li1,2,3, Xinlei Yu1,2, Qiang Feng1,7, Zirong Wang1, Hailiang Xie1, Xiaomin Chen1, Chunwei Zeng1, Bo Wen1,2, Liping Zeng4,5, Hui Du4,5, Huiru Tang4,5, Changlu Xu1,8, Yan Xia1,3, Huihua Xia1,2,9, Huanming Yang1,10, Jian Wang1,10, Jun Wang1,11, Lise Madsen 1,6,12, Susanne Brix 13, Karsten Kristiansen1,6, Xun Xu1,2, Junhua Li 1,2,9,14, Ruifang Wu4,5 & Huijue Jia 1,2,9,11 Reports on bacteria detected in maternal fluids during pregnancy are typically associated with adverse consequences, and whether the female reproductive tract harbours distinct microbial communities beyond the vagina has been a matter of debate. Here we systematically sample the microbiota within the female reproductive tract in 110 women of reproductive age, and examine the nature of colonisation by 16S rRNA gene amplicon sequencing and cultivation. We find distinct microbial communities in cervical canal, uterus, fallopian tubes and perito- neal fluid, differing from that of the vagina. The results reflect a microbiota continuum along the female reproductive tract, indicative of a non-sterile environment. We also identify microbial taxa and potential functions that correlate with the menstrual cycle or are over- represented in subjects with adenomyosis or infertility due to endometriosis. The study provides insight into the nature of the vagino-uterine microbiome, and suggests that sur- veying the vaginal or cervical microbiota might be useful for detection of common diseases in the upper reproductive tract. -
Environmental Biodiversity, Human Microbiota, and Allergy Are Interrelated
Environmental biodiversity, human microbiota, and allergy are interrelated Ilkka Hanskia,1, Leena von Hertzenb, Nanna Fyhrquistc, Kaisa Koskinend, Kaisa Torppaa, Tiina Laatikainene, Piia Karisolac, Petri Auvinend, Lars Paulind, Mika J. Mäkeläb, Erkki Vartiainene, Timo U. Kosunenf, Harri Aleniusc, and Tari Haahtelab,1 aDepartment of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland; bSkin and Allergy Hospital, Helsinki University Central Hospital, FI-00029 Helsinki, Finland; cFinnish Institute of Occupational Health, FI-00250 Helsinki, Finland; dInstitute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; eNational Institute for Health and Welfare, FI-00271 Helsinki, Finland; and fDepartment of Bacteriology and Immunology, Haartman Institute, University of Helsinki, FI-00014 Helsinki, Finland Contributed by Ilkka Hanski, April 4, 2012 (sent for review March 14, 2012) Rapidly declining biodiversity may be a contributing factor to environmental biodiversity influences the composition of the another global megatrend—the rapidly increasing prevalence of commensal microbiota of the study subjects. Environmental bio- allergies and other chronic inflammatory diseases among urban diversity was characterized at two spatial scales, the vegetation populations worldwide. According to the “biodiversity hypothesis,” cover of the yards and the major land use types within 3 km of the reduced contact of people with natural environmental features and homes of the study subjects. Commensal microbiota sampling biodiversity may adversely affect the human commensal microbiota evaluated the skin bacterial flora, identified to the genus level from and its immunomodulatory capacity. Analyzing atopic sensitization DNA samples obtained from the volar surface of the forearm. (i.e., allergic disposition) in a random sample of adolescents living in Second, we investigate whether atopy is related to environmental a heterogeneous region of 100 × 150 km, we show that environ- biodiversity in the surroundings of the study subjects’ homes. -
Acinetobacter Baylyi Long-Term Stationary-Phase Protein Stip Is a Protease Required for Normal Cell Morphology and Resistance to Tellurite Blake Reichert, Amber J
726 ARTICLE Acinetobacter baylyi long-term stationary-phase protein StiP is a protease required for normal cell morphology and resistance to tellurite Blake Reichert, Amber J. Dornbusch, Joshua Arguello, Sarah E. Stanley, Kristine M. Lang, C. Phoebe Lostroh, and Margaret A. Daugherty Abstract: We investigated the Acinetobacter baylyi gene ACIAD1960, known from previous work to be expressed during long-term stationary phase. The protein encoded by this gene had been annotated as a Conserved Hypothetical Protein, surrounded by putative tellurite resistance (“Ter”) proteins. Sequence analysis suggested that the protein belongs to the DUF1796 putative papain-like protease family. Here, we show that the purified protein, subsequently named StiP, has cysteine protease activity. Deletion of stiP causes hypersensitivity to tellurite, altered population dynamics during long-term batch culture, and most strikingly, dramatic alteration of normal cell morphology. StiP and associated Ter proteins (the StiP–Ter cluster) are therefore important for regulating cell morphology, likely in response to oxidative damage or depletion of intracellular thiol pools, triggered artificially by tellurite exposure. Our finding has broad significance because while tellurite is an extremely rare compound in nature, oxidative damage, the need to maintain a particular balance of intracellular thiols, and the need to regulate cell morphology are ubiquitous. Key words: long-term stationary phase, tellurite resistance, DUF1796, Ter domain, cell division. Résumé : Nous avons fait l’étude du gène ACIAD1960 d’Acinetobacter baylyi, qui selon des travaux antérieurs serait exprimé au cours de la phase stationnaire prolongée. La protéine codée par ce gène a été libellée « protéine hypothétique conservée » et est entourée de protéines putatives de résistance a` la tellurite (« Ter »). -
Update on the Epidemiology, Treatment, and Outcomes of Carbapenem-Resistant Acinetobacter Infections
Review Article www.cmj.ac.kr Update on the Epidemiology, Treatment, and Outcomes of Carbapenem-resistant Acinetobacter infections Uh Jin Kim, Hee Kyung Kim, Joon Hwan An, Soo Kyung Cho, Kyung-Hwa Park and Hee-Chang Jang* Department of Infectious Diseases, Chonnam National University Medical School, Gwangju, Korea Carbapenem-resistant Acinetobacter species are increasingly recognized as major no- Article History: socomial pathogens, especially in patients with critical illnesses or in intensive care. received 18 July, 2014 18 July, 2014 The ability of these organisms to accumulate diverse mechanisms of resistance limits revised accepted 28 July, 2014 the available therapeutic agents, makes the infection difficult to treat, and is associated with a greater risk of death. In this review, we provide an update on the epidemiology, Corresponding Author: resistance mechanisms, infection control measures, treatment, and outcomes of carba- Hee-Chang Jang penem-resistant Acinetobacter infections. Department of Infectious Diseases, Chonnam National University Medical Key Words: Acinetobacter baumannii; Colistin; Drug therapy School, 160, Baekseo-ro, Dong-gu, Gwangju 501-746, Korea This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial TEL: +82-62-220-6296 License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, FAX: +82-62-225-8578 distribution, and reproduction in any medium, provided the original work is properly cited. E-mail: [email protected] INTRODUCTION species by their phenotypic traits is difficult, and identi- fication of individual species by use of current automated Acinetobacter species are aerobic gram-negative bacilli or manual commercial systems will require further con- that are ubiquitous in natural environments such as soil firmation testing. -
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Biologia 66/2: 288—293, 2011 Section Cellular and Molecular Biology DOI: 10.2478/s11756-011-0021-6 The first investigation of the diversity of bacteria associated with Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) Hacer Muratoglu, Zihni Demirbag &KazimSezen* Karadeniz Technical University, Faculty of Arts and Sciences, Department of Biology, 61080 Trabzon, Turkey; e-mail: [email protected] Abstract: Colorado potato beetle, Leptinotarsa decemlineata (Say), is a devastating pest of potatoes in North America and Europe. L. decemlineata has developed resistance to insecticides used for its control. In this study, in order to find a more effective potential biological control agent against L. decemlineata, we investigated its microbiota and tested their insecticidal effects. According to morphological, physiological and biochemical tests as well as 16S rDNA sequences, microbiota was identified as Leclercia adecarboxylata (Ld1), Acinetobacter sp. (Ld2), Acinetobacter sp. (Ld3), Pseudomonas putida (Ld4), Acinetobacter sp. (Ld5) and Acinetobacter haemolyticus (Ld6). The insecticidal activities of isolates at 1.8×109 bacteria/mL dose within five days were 100%, 100%, 35%, 100%, 47% and 100%, respectively, against the L. decemlineata larvae. The results indicate that Leclercia adecarboxylata (Ld1) and Pseudomonas putida (Ld4) isolates may be valuable potential biological control agents for biological control of L. decemlineata. Key words: Leptinotarsa decemlineata; 16S rDNA; microbiota; insecticidal activity; microbial control. Abbreviations: ANOVA, one-way analysis of variance; LSD, least significant difference; PBS, phosphate buffer solution. Introduction used because of marketing concerns and limited num- ber of transgenic varieties available. Also, recombinant Potato is an important crop with ∼4.3 million tons defence molecules in plants may affect parasitoids or of production on 192,000 hectares of growing area predators indirectly (Bouchard et al. -
Mapping the Diversity of Microbial Lignin Catabolism: Experiences from the Elignin Database
Applied Microbiology and Biotechnology (2019) 103:3979–4002 https://doi.org/10.1007/s00253-019-09692-4 MINI-REVIEW Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database Daniel P. Brink1 & Krithika Ravi2 & Gunnar Lidén2 & Marie F Gorwa-Grauslund1 Received: 22 December 2018 /Revised: 6 February 2019 /Accepted: 9 February 2019 /Published online: 8 April 2019 # The Author(s) 2019 Abstract Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database (www.elignindatabase.com), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings. Keywords Lignin . Database . Aromatic metabolism . Catabolic pathways