PMC:7152911 / 117648-118661 JSONTXT

Annnotations TAB JSON ListView MergeView

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7152911","sourcedb":"PMC","sourceid":"7152911","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7152911","text":"Several comprehensive reviews have been provided on the detection of environmental pathogens (Baeumner, 2003; Justino et al. 2017). Here, we describe the most common environmental pathogens found both in and outside of clinical settings. Common environmental pathogens in a non-clinical setting include Legionella spp., which cause Legionnellosis, Mycobacterium tuberculosis, which causes tuberculosis, and Naegleria fowleri, which causes amoebic meningitis. In addition to bacteria and protozoa, fungi, nematodes, and insects are also environmental pathogens. Common environmental pathogens in clinical settings associated with healthcare-acquired infections include drug-resistant and multi-drug resistant (MDR) pathogens, such as Clostridium difficile (CD) (Hookman and Barkin, 2009), which causes CD-associated diarrhea and antibiotic-induced colitis, and methicillin-resistant S. aureus (MRSA), which causes severe infections in various parts of the body, including the urinary tract (Gordon and Lowy, 2008).","tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"1859","span":{"begin":348,"end":374},"obj":"Species"},{"id":"1860","span":{"begin":407,"end":424},"obj":"Species"},{"id":"1861","span":{"begin":733,"end":754},"obj":"Species"},{"id":"1862","span":{"begin":882,"end":891},"obj":"Species"},{"id":"1863","span":{"begin":303,"end":313},"obj":"Species"},{"id":"1864","span":{"begin":756,"end":758},"obj":"Species"},{"id":"1865","span":{"begin":801,"end":803},"obj":"Species"},{"id":"1866","span":{"begin":860,"end":871},"obj":"Chemical"},{"id":"1867","span":{"begin":332,"end":346},"obj":"Disease"},{"id":"1868","span":{"begin":389,"end":401},"obj":"Disease"},{"id":"1869","span":{"begin":439,"end":457},"obj":"Disease"},{"id":"1870","span":{"begin":649,"end":659},"obj":"Disease"},{"id":"1871","span":{"begin":815,"end":823},"obj":"Disease"},{"id":"1872","span":{"begin":847,"end":854},"obj":"Disease"},{"id":"1873","span":{"begin":920,"end":930},"obj":"Disease"}],"attributes":[{"id":"A1859","pred":"tao:has_database_id","subj":"1859","obj":"Tax:1773"},{"id":"A1860","pred":"tao:has_database_id","subj":"1860","obj":"Tax:5763"},{"id":"A1861","pred":"tao:has_database_id","subj":"1861","obj":"Tax:1496"},{"id":"A1862","pred":"tao:has_database_id","subj":"1862","obj":"Tax:1280"},{"id":"A1863","pred":"tao:has_database_id","subj":"1863","obj":"Tax:446"},{"id":"A1864","pred":"tao:has_database_id","subj":"1864","obj":"Tax:1496"},{"id":"A1865","pred":"tao:has_database_id","subj":"1865","obj":"Tax:1496"},{"id":"A1866","pred":"tao:has_database_id","subj":"1866","obj":"MESH:D008712"},{"id":"A1868","pred":"tao:has_database_id","subj":"1868","obj":"MESH:D014376"},{"id":"A1869","pred":"tao:has_database_id","subj":"1869","obj":"MESH:D004404"},{"id":"A1870","pred":"tao:has_database_id","subj":"1870","obj":"MESH:D007239"},{"id":"A1871","pred":"tao:has_database_id","subj":"1871","obj":"MESH:D003967"},{"id":"A1872","pred":"tao:has_database_id","subj":"1872","obj":"MESH:D003092"},{"id":"A1873","pred":"tao:has_database_id","subj":"1873","obj":"MESH:D007239"},{"subj":"1859","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1860","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1861","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1862","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1863","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1864","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1865","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1866","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1867","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1868","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1869","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1870","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1871","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1872","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1873","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]},{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T17","span":{"begin":955,"end":959},"obj":"Body_part"},{"id":"T18","span":{"begin":975,"end":988},"obj":"Body_part"}],"attributes":[{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma256135"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma0326482"},{"subj":"T17","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T18","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T90","span":{"begin":303,"end":313},"obj":"Disease"},{"id":"T91","span":{"begin":362,"end":374},"obj":"Disease"},{"id":"T92","span":{"begin":389,"end":401},"obj":"Disease"},{"id":"T93","span":{"begin":447,"end":457},"obj":"Disease"},{"id":"T95","span":{"begin":649,"end":659},"obj":"Disease"},{"id":"T96","span":{"begin":815,"end":823},"obj":"Disease"},{"id":"T97","span":{"begin":847,"end":854},"obj":"Disease"},{"id":"T98","span":{"begin":893,"end":897},"obj":"Disease"},{"id":"T99","span":{"begin":920,"end":933},"obj":"Disease"}],"attributes":[{"id":"A90","pred":"mondo_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/MONDO_0005824"},{"id":"A91","pred":"mondo_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/MONDO_0018076"},{"id":"A92","pred":"mondo_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/MONDO_0018076"},{"id":"A93","pred":"mondo_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/MONDO_0004796"},{"id":"A94","pred":"mondo_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/MONDO_0021108"},{"id":"A95","pred":"mondo_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A96","pred":"mondo_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/MONDO_0001673"},{"id":"A97","pred":"mondo_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/MONDO_0005292"},{"id":"A98","pred":"mondo_id","subj":"T98","obj":"http://purl.obolibrary.org/obo/MONDO_0100073"},{"id":"A99","pred":"mondo_id","subj":"T99","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"subj":"T90","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T91","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T92","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T93","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T95","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T96","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T97","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T98","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T99","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T114","span":{"begin":272,"end":273},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T115","span":{"begin":474,"end":482},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_2"},{"id":"T116","span":{"begin":975,"end":988},"obj":"http://purl.obolibrary.org/obo/UBERON_0001008"}],"attributes":[{"subj":"T114","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T115","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T116","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T37111","span":{"begin":668,"end":672},"obj":"Chemical"},{"id":"T33883","span":{"begin":693,"end":697},"obj":"Chemical"},{"id":"T9618","span":{"begin":709,"end":712},"obj":"Chemical"},{"id":"T89888","span":{"begin":756,"end":758},"obj":"Chemical"},{"id":"T97800","span":{"begin":801,"end":803},"obj":"Chemical"},{"id":"T69352","span":{"begin":828,"end":838},"obj":"Chemical"},{"id":"T94262","span":{"begin":860,"end":871},"obj":"Chemical"}],"attributes":[{"id":"A33846","pred":"chebi_id","subj":"T37111","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"},{"id":"A92887","pred":"chebi_id","subj":"T33883","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"},{"id":"A36998","pred":"chebi_id","subj":"T9618","obj":"http://purl.obolibrary.org/obo/CHEBI_53218"},{"id":"A39555","pred":"chebi_id","subj":"T89888","obj":"http://purl.obolibrary.org/obo/CHEBI_8673"},{"id":"A39798","pred":"chebi_id","subj":"T97800","obj":"http://purl.obolibrary.org/obo/CHEBI_8673"},{"id":"A1114","pred":"chebi_id","subj":"T69352","obj":"http://purl.obolibrary.org/obo/CHEBI_33281"},{"id":"A23444","pred":"chebi_id","subj":"T94262","obj":"http://purl.obolibrary.org/obo/CHEBI_6827"},{"subj":"T37111","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T33883","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T9618","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T89888","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T97800","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T69352","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T94262","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T5","span":{"begin":693,"end":707},"obj":"http://purl.obolibrary.org/obo/GO_0042493"}],"attributes":[{"subj":"T5","pred":"source","obj":"LitCovid-PD-GO-BP"}]},{"project":"LitCovid-PD-HP","denotations":[{"id":"T11","span":{"begin":447,"end":457},"obj":"Phenotype"},{"id":"T12","span":{"begin":693,"end":707},"obj":"Phenotype"},{"id":"T13","span":{"begin":815,"end":823},"obj":"Phenotype"},{"id":"T14","span":{"begin":847,"end":854},"obj":"Phenotype"},{"id":"T15","span":{"begin":913,"end":930},"obj":"Phenotype"}],"attributes":[{"id":"A11","pred":"hp_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/HP_0001287"},{"id":"A12","pred":"hp_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/HP_0020174"},{"id":"A13","pred":"hp_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/HP_0002014"},{"id":"A14","pred":"hp_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/HP_0002583"},{"id":"A15","pred":"hp_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/HP_0032169"},{"subj":"T11","pred":"source","obj":"LitCovid-PD-HP"},{"subj":"T12","pred":"source","obj":"LitCovid-PD-HP"},{"subj":"T13","pred":"source","obj":"LitCovid-PD-HP"},{"subj":"T14","pred":"source","obj":"LitCovid-PD-HP"},{"subj":"T15","pred":"source","obj":"LitCovid-PD-HP"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T954","span":{"begin":0,"end":124},"obj":"Sentence"},{"id":"T955","span":{"begin":125,"end":131},"obj":"Sentence"},{"id":"T956","span":{"begin":132,"end":237},"obj":"Sentence"},{"id":"T957","span":{"begin":238,"end":458},"obj":"Sentence"},{"id":"T958","span":{"begin":459,"end":560},"obj":"Sentence"},{"id":"T959","span":{"begin":561,"end":1013},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T954","pred":"source","obj":"LitCovid-sentences"},{"subj":"T955","pred":"source","obj":"LitCovid-sentences"},{"subj":"T956","pred":"source","obj":"LitCovid-sentences"},{"subj":"T957","pred":"source","obj":"LitCovid-sentences"},{"subj":"T958","pred":"source","obj":"LitCovid-sentences"},{"subj":"T959","pred":"source","obj":"LitCovid-sentences"}]},{"project":"2_test","denotations":[{"id":"32364936-12920503-7713160","span":{"begin":104,"end":108},"obj":"12920503"},{"id":"32364936-19340897-7713161","span":{"begin":781,"end":785},"obj":"19340897"},{"id":"32364936-18462090-7713162","span":{"begin":1007,"end":1011},"obj":"18462090"}],"attributes":[{"subj":"32364936-12920503-7713160","pred":"source","obj":"2_test"},{"subj":"32364936-19340897-7713161","pred":"source","obj":"2_test"},{"subj":"32364936-18462090-7713162","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#d9ec93","default":true},{"id":"LitCovid-PD-FMA-UBERON","color":"#e593ec"},{"id":"LitCovid-PD-MONDO","color":"#93eccb"},{"id":"LitCovid-PD-CLO","color":"#ecb193"},{"id":"LitCovid-PD-CHEBI","color":"#9693ec"},{"id":"LitCovid-PD-GO-BP","color":"#a9ec93"},{"id":"LitCovid-PD-HP","color":"#ec93c3"},{"id":"LitCovid-sentences","color":"#93ddec"},{"id":"2_test","color":"#ece193"}]}]}}