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Crone S, Vives-Flórez M, Kvich L, Saunders AM, Malone M, Nicolaisen MH, Martínez-García E, Rojas-Acosta C, Catalina Gomez-Puerto M, Calum H, Whiteley M, Kolter R, Bjarnsholt T. The environmental occurrence of Pseudomonas aeruginosa. APMIS 2019; 128:220-231. [PMID: 31709616 DOI: 10.1111/apm.13010] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/06/2019] [Indexed: 01/08/2023]
Abstract
Pseudomonas aeruginosa is generally described as ubiquitous in natural settings, such as soil and water. However, because anecdotal observations and published reports have questioned whether or not this description is true, we undertook a rigorous study using three methods to investigate the occurrence of P. aeruginosa: We investigated environmental samples, analyzed 16S rRNA data, and undertook a systematic review and meta-analysis of published data. The environmental sample screening identified P. aeruginosa as significantly associated with hydrocarbon and pesticide-contaminated environments and feces, as compared to uncontaminated environments in which its prevalence was relatively low. The 16S rRNA data analysis showed that P. aeruginosa sequences were present in all habitats but were most abundant in samples from human and animals. Similarly, the meta-analysis revealed that samples obtained from environments with intense human contact had a higher prevalence of P. aeruginosa compared to those with less human contact. Thus, we found a clear tendency of P. aeruginosa to be present in places closely linked with human activity. Although P. aeruginosa may be ubiquitous in nature, it is usually scarce in pristine environments. Thus, we suggest that P. aeruginosa should be described as a bacterium largely found in locations associated with human activity.
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Affiliation(s)
- Stephanie Crone
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martha Vives-Flórez
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Lasse Kvich
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Aaron M Saunders
- Department of Laboratory, Food and Environmental Science, Business Academy Aarhus, Viby J, Denmark
| | - Matthew Malone
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, Australia.,South West Sydney Limb Preservation and Wound Research, South Western Sydney Local Health District, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - Mette H Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Esteban Martínez-García
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Systems Biology Program, National Center of Biotechnology CSIC, Madrid, Spain
| | | | | | - Henrik Calum
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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Olender T, Keydar I, Pinto JM, Tatarskyy P, Alkelai A, Chien MS, Fishilevich S, Restrepo D, Matsunami H, Gilad Y, Lancet D. The human olfactory transcriptome. BMC Genomics 2016; 17:619. [PMID: 27515280 PMCID: PMC4982115 DOI: 10.1186/s12864-016-2960-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 07/21/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-characterized human olfactory epithelial samples and compared the results to novel and published mouse olfactory epithelium as well as 16 human control tissues. RESULTS We identified 194 non-olfactory receptor (OR) genes that are overexpressed in human olfactory tissues vs. CONTROLS The highest overexpression is seen for lipocalins and bactericidal/permeability-increasing (BPI)-fold proteins, which in other species include secreted odorant carriers. Mouse-human discordance in orthologous lipocalin expression suggests different mammalian evolutionary paths in this family. Of the overexpressed genes 36 have documented olfactory function while for 158 there is little or no previous such functional evidence. The latter group includes GPCRs, neuropeptides, solute carriers, transcription factors and biotransformation enzymes. Many of them may be indirectly implicated in sensory function, and ~70 % are over expressed also in mouse olfactory epithelium, corroborating their olfactory role. Nearly 90 % of the intact OR repertoire, and ~60 % of the OR pseudogenes are expressed in the olfactory epithelium, with the latter showing a 3-fold lower expression. ORs transcription levels show a 1000-fold inter-paralog variation, as well as significant inter-individual differences. We assembled 160 transcripts representing 100 intact OR genes. These include 1-4 short 5' non-coding exons with considerable alternative splicing and long last exons that contain the coding region and 3' untranslated region of highly variable length. Notably, we identified 10 ORs with an intact open reading frame but with seemingly non-functional transcripts, suggesting a yet unreported OR pseudogenization mechanism. Analysis of the OR upstream regions indicated an enrichment of the homeobox family transcription factor binding sites and a consensus localization of a specific transcription factor binding site subfamily (Olf/EBF). CONCLUSIONS We provide an overview of expression levels of ORs and auxiliary genes in human olfactory epithelium. This forms a transcriptomic view of the entire OR repertoire, and reveals a large number of over-expressed uncharacterized human non-receptor genes, providing a platform for future discovery.
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Affiliation(s)
- Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Ifat Keydar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jayant M Pinto
- Section of Otolaryngology-Head and Neck Surgery, University of Chicago, Chicago, IL, USA
| | - Pavlo Tatarskyy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Alkelai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ming-Shan Chien
- Department of Molecular Genetics and Microbiology, Department of Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Diego Restrepo
- Department of Cell and Developmental Biology, Neuroscience Program, and Rocky Mountain Taste and Smell Center, University of Colorado School of Medicine, Aurora, CO, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Department of Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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The epidemiological characteristics and genetic diversity of dengue virus during the third largest historical outbreak of dengue in Guangdong, China, in 2014. J Infect 2015; 72:80-90. [PMID: 26546854 DOI: 10.1016/j.jinf.2015.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 10/13/2015] [Accepted: 10/18/2015] [Indexed: 11/20/2022]
Abstract
OBJECTIVES The third largest historical outbreak of dengue occurred during July to December 2014, in 20 of 21 cities of Guangdong, China. The epidemiological and molecular characteristics of the introduction, expansion and phylogeny of the DENV isolates involved in this outbreak were investigated. METHODS A combination analyses of epidemiological characteristics and genetic diversity of dengue virus was performed in this study. RESULTS In total, 45,236 cases and 6 fatalities were reported. Unemployed individuals, retirees and retailers were the most affected populations. A total of 6024 cases were verified to have DENV infections by nucleic acid detection, of which 5947, 74 and 3 were confirmed to have DENV-1, -2, and -3 infections, respectively. Phylogenetic analyses of DENV-1 isolates were assigned into three genotypes (I, IV, and V). Genotype V was the predominant genotype that likely originated from Singapore. The DENV-2 isolates were assigned to the Cosmopolitan and Asian I genotypes. A unique DENV-3 isolate (genotype III) shared high similarity with isolates obtained from Guangdong in 2013. CONCLUSIONS A combination analyses demonstrated the multiple geographical origins of this outbreak, and highlight the importance of early detection, the case management and vector surveillance for preventing further dengue epidemics in Guangdong.
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