Minireview the Ecology, Biology and Pathogenesis of Acinetobacter Spp
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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 . -
Acinetobacter Baumannii – a Neglected Pathogen in Veterinary and Environmental Health in Germany
Veterinary Research Communications (2019) 43:1–6 https://doi.org/10.1007/s11259-018-9742-0 REVIEW ARTICLE Acinetobacter baumannii – a neglected pathogen in veterinary and environmental health in Germany Gamal Wareth1 & Heinrich Neubauer1 & Lisa D. Sprague1 Received: 25 October 2018 /Accepted: 6 December 2018 /Published online: 27 December 2018 # The Author(s) 2018 Abstract The emergence and global spread of drug resistant Acinetobacter (A.) baumannii is a cause of great concern. The current knowledge on antibiotic resistance in A. baumannii from animal origin is mostly based on few internationally published case reports, investigations of strain collections and several whole genome analyses. This lack of data results in a somewhat sketchy picture on how to assess the possible impact of drug resistant A. baumannii strains on veterinary and public health in Germany. Consequently, there is an urgent need to intensify the surveillance of A. baumannii in pet animals, the farm animal population and wildlife. Keywords Acinetobacter baumannii . Review . Antibiotic resistance . Germany Introduction limited number of widespread clones appear to be responsible for hospital outbreaks in many countries (Diancourt et al. Acinetobacter (A.) baumannii is a gram-negative opportunis- 2010). Eight international clonal lineages have been described tic nosocomial pathogen belonging to the genus Acinetobacter so far and comparative typing of outbreak strains obtained all and a member of the family Moraxellaceae. Acinetobacter over Europe revealed the dominance of three clones, original- spp. are non-motile, non-fastidious Gram-negative, non- ly named European clones I-III (Dijkshoorn et al. 1996; Karah fermenting, catalase positive, oxidase negative, strictly aero- et al. -
Linking the Resistome and Plasmidome to the Microbiome
The ISME Journal (2019) 13:2437–2446 https://doi.org/10.1038/s41396-019-0446-4 ARTICLE Linking the resistome and plasmidome to the microbiome 1,2 3 3 3 1,2 Thibault Stalder ● Maximilian O. Press ● Shawn Sullivan ● Ivan Liachko ● Eva M. Top Received: 15 February 2019 / Revised: 2 May 2019 / Accepted: 10 May 2019 / Published online: 30 May 2019 © The Author(s) 2019. This article is published with open access Abstract The rapid spread of antibiotic resistance among bacterial pathogens is a serious human health threat. While a range of environments have been identified as reservoirs of antibiotic resistance genes (ARGs), we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to our inability to identify the natural bacterial hosts of ARGs and the mobile genetic elements that mediate this spread, such as plasmids and integrons. Here we demonstrate that the in vivo proximity-ligation method Hi-C can reconstruct a known plasmid-host association from a wastewater community, and identify the in situ host range of ARGs, plasmids, and integrons by physically linking them to their host chromosomes. Hi-C detected both previously known and novel associations between ARGs, mobile genetic elements and host genomes, thus validating this method. We showed that IncQ plasmids and class 1 integrons had the broadest host range in this wastewater, and identified bacteria belonging to Moraxellaceae, Bacteroides,andPrevotella, and 1234567890();,: 1234567890();,: especially Aeromonadaceae as the most likely reservoirs of ARGs in this community. A better identification of the natural carriers of ARGs will aid the development of strategies to limit resistance spread to pathogens. -
Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment
antibiotics Article Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment Alicia Sorgen 1, James Johnson 2, Kevin Lambirth 2, Sandra M. Clinton 3 , Molly Redmond 1 , Anthony Fodor 2 and Cynthia Gibas 2,* 1 Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (A.S.); [email protected] (M.R.) 2 Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (J.J.); [email protected] (K.L.); [email protected] (A.F.) 3 Department of Geography & Earth Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-704-687-8378 Abstract: Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify Citation: Sorgen, A.; Johnson, J.; phenotypically resistant cultivable portions of these bacterial communities and characterized the Lambirth, K.; Clinton, -
Moraxella Species: Infectious Microbes Identified by Use of Time-Of
Japanese Journal of Ophthalmology (2019) 63:328–336 https://doi.org/10.1007/s10384-019-00669-4 CLINICAL INVESTIGATION Moraxella species: infectious microbes identifed by use of time‑of‑fight mass spectrometry Shunsuke Takahashi1 · Kazuhiro Murata1 · Kenji Ozawa1 · Hiroki Yamada2 · Hideaki Kawakami3 · Asami Nakayama4 · Yuko Asano5 · Kiyofumi Mochizuki1 · Hiroshige Mikamo6 Received: 14 August 2018 / Accepted: 2 April 2019 / Published online: 4 July 2019 © Japanese Ophthalmological Society 2019 Abstract Purpose To report the clinical manifestations, identifcation, antimicrobial susceptibilities, and treatment outcomes of ocular infections caused by Moraxella species. Study design Retrospective study. Patients and methods The medical records of all patients treated at the Departments of Ophthalmology of the Ogaki Munici- pal Hospital and the Gifu University Graduate School of Medicine for ocular infections caused by Moraxella species between January 2011 and June 2017 were examined. The stored Moraxella species isolated from ocular samples were identifed by matrix-assisted laser desorption/ionization time-of-fight mass spectrometry (MALDI-TOF MS), molecular identifcation, and the biochemical properties. Results Sixteen eyes of 16 patients were treated for Moraxella ocular infections. The patients’ median age was 72 years. A predisposing systemic or ocular condition was identifed in 15 of the patients. Nine of the patients developed keratitis; four, conjunctivitis; and three, blebitis. M lacunata (6 eyes), M catarrhalis (6), M nonliquefaciens (3), and M osloensis (1) were identifed by MALDI-TOF MS. All isolates were sensitive to levofoxacin, tobramycin, ceftazidime, ceftriaxone, and cefa- zolin. Twelve patients with keratitis or blebitis were treated with various topical antimicrobial combinations, and systemic antibiotics were used in 10 of the 12 patients. -
Characterization of Bacterial Communities Associated
www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5. -
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. -
Download Article (PDF)
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