PMC:4801059 / 7242-9905
Annnotations
MyTest
{"project":"MyTest","denotations":[{"id":"26884414-23326226-29787767","span":{"begin":131,"end":133},"obj":"23326226"},{"id":"26884414-9180184-29787768","span":{"begin":721,"end":723},"obj":"9180184"},{"id":"26884414-20178591-29787769","span":{"begin":837,"end":839},"obj":"20178591"},{"id":"26884414-14998500-29787770","span":{"begin":1133,"end":1135},"obj":"14998500"},{"id":"26884414-22913260-29787771","span":{"begin":1137,"end":1139},"obj":"22913260"},{"id":"26884414-17030494-29787772","span":{"begin":1262,"end":1264},"obj":"17030494"},{"id":"26884414-17030494-29787773","span":{"begin":1628,"end":1630},"obj":"17030494"},{"id":"26884414-17030494-29787774","span":{"begin":1659,"end":1661},"obj":"17030494"},{"id":"26884414-20969800-29787775","span":{"begin":1666,"end":1668},"obj":"20969800"},{"id":"26884414-24134472-29787776","span":{"begin":1721,"end":1723},"obj":"24134472"},{"id":"26884414-22935873-29787777","span":{"begin":1725,"end":1727},"obj":"22935873"},{"id":"26884414-22282460-29787778","span":{"begin":1732,"end":1734},"obj":"22282460"},{"id":"26884414-24134472-29787779","span":{"begin":1850,"end":1852},"obj":"24134472"},{"id":"26884414-22282460-29787780","span":{"begin":1854,"end":1856},"obj":"22282460"},{"id":"26884414-18826823-29787781","span":{"begin":1858,"end":1860},"obj":"18826823"},{"id":"26884414-17030494-29787782","span":{"begin":1955,"end":1957},"obj":"17030494"},{"id":"26884414-20977542-29787783","span":{"begin":1959,"end":1961},"obj":"20977542"},{"id":"26884414-22282460-29787784","span":{"begin":1963,"end":1965},"obj":"22282460"},{"id":"26884414-20847012-29787785","span":{"begin":1967,"end":1969},"obj":"20847012"},{"id":"26884414-18826823-29787786","span":{"begin":2119,"end":2121},"obj":"18826823"},{"id":"26884414-22752171-29787787","span":{"begin":2123,"end":2125},"obj":"22752171"},{"id":"26884414-20178591-29787788","span":{"begin":2140,"end":2142},"obj":"20178591"},{"id":"26884414-19969530-29787789","span":{"begin":2144,"end":2146},"obj":"19969530"},{"id":"26884414-20977542-29787790","span":{"begin":2203,"end":2205},"obj":"20977542"},{"id":"26884414-25084351-29787791","span":{"begin":2207,"end":2209},"obj":"25084351"},{"id":"26884414-23326226-29787792","span":{"begin":2307,"end":2309},"obj":"23326226"},{"id":"26884414-24134472-29787793","span":{"begin":1721,"end":1723},"obj":"24134472"},{"id":"26884414-22935873-29787794","span":{"begin":1725,"end":1727},"obj":"22935873"},{"id":"26884414-22282460-29787795","span":{"begin":1732,"end":1734},"obj":"22282460"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"BACTERIAL SELECTION IN THE URT\nBacterial pneumonia is primarily caused by the commensal bacteria normally residing in the URT [11, 12]. The most common causes of bacterial pneumonia for children \u003c5 years of age are Streptococcus pneumoniae, followed by Haemophilus influenzae and Staphylococcus aureus [11] although this varies over time and space. From a rudimentary ecological perspective, the human respiratory tract can be defined as an ecosystem with two distinct niches: the URT, characterized by regular asymptomatic carriage of commensal bacteria, and the LRT, which is inhabited at a low abundance by bacteria in healthy individuals [13]. During the first year after birth, the nasopharynx is rapidly colonized [14] and URT carriage is established via ongoing synergistic and antagonistic interactions among commensal bacteria [15]. Although pneumonia is an infection of the lungs, microbial selection in the URT may play an important role in etiology as bacterial strains in the URT can be readily aspirated into the LRT. For example, URT carriage is believed to be a necessary precursor of pneumonia due to S. pneumoniae [16, 17].\nNumerous epidemiologic studies describe synergistic and antagonistic relationships among various commensal bacteria [18–33] and, although the exact biological mechanisms remain unclear, in vivo and in vitro experiments suggest potential mechanisms involve either direct interaction between bacterial species or indirect interactions via the host immune system (Table 1). A number of population studies suggest that S. pneumoniae carriage is positively associated with H. influenzae [18–27] and Moraxella catarrhalis [18, 23–28] carriage but negatively associated with S. aureus [19, 20, 24–27, 29–32]. Furthermore, S. aureus carriage is generally negatively associated with H. influenzae and M. catarrhalis [19, 24, 31] carriage, whereas H. influenzae and M. catarrhalis are believed to be positively associated [18, 22, 24, 33]. Nevertheless, our understanding is limited, as the dynamics of niche competition likely consist of complex relationships between multiple species [31, 34] and strains [15, 35], further influenced by host and environmental factors [22, 36]. As carriage is an important precursor of respiratory infections for certain bacterial species [12], unraveling the complex system of bacterial interactions that determine URT microbiota may be key factor for understanding the etiology of pneumonia.\nTable 1 Known interactions and potential mechanisms for observed associations between primary bacterial colonizers of the nasopharynx a Epidemiologic studies. b In vitro and in vivo experiments\n\nB"}
2_test
{"project":"2_test","denotations":[{"id":"26884414-23326226-29787767","span":{"begin":131,"end":133},"obj":"23326226"},{"id":"26884414-9180184-29787768","span":{"begin":721,"end":723},"obj":"9180184"},{"id":"26884414-20178591-29787769","span":{"begin":837,"end":839},"obj":"20178591"},{"id":"26884414-14998500-29787770","span":{"begin":1133,"end":1135},"obj":"14998500"},{"id":"26884414-22913260-29787771","span":{"begin":1137,"end":1139},"obj":"22913260"},{"id":"26884414-17030494-29787772","span":{"begin":1262,"end":1264},"obj":"17030494"},{"id":"26884414-17030494-29787773","span":{"begin":1628,"end":1630},"obj":"17030494"},{"id":"26884414-17030494-29787774","span":{"begin":1659,"end":1661},"obj":"17030494"},{"id":"26884414-20969800-29787775","span":{"begin":1666,"end":1668},"obj":"20969800"},{"id":"26884414-24134472-29787776","span":{"begin":1721,"end":1723},"obj":"24134472"},{"id":"26884414-22935873-29787777","span":{"begin":1725,"end":1727},"obj":"22935873"},{"id":"26884414-22282460-29787778","span":{"begin":1732,"end":1734},"obj":"22282460"},{"id":"26884414-24134472-29787779","span":{"begin":1850,"end":1852},"obj":"24134472"},{"id":"26884414-22282460-29787780","span":{"begin":1854,"end":1856},"obj":"22282460"},{"id":"26884414-18826823-29787781","span":{"begin":1858,"end":1860},"obj":"18826823"},{"id":"26884414-17030494-29787782","span":{"begin":1955,"end":1957},"obj":"17030494"},{"id":"26884414-20977542-29787783","span":{"begin":1959,"end":1961},"obj":"20977542"},{"id":"26884414-22282460-29787784","span":{"begin":1963,"end":1965},"obj":"22282460"},{"id":"26884414-20847012-29787785","span":{"begin":1967,"end":1969},"obj":"20847012"},{"id":"26884414-18826823-29787786","span":{"begin":2119,"end":2121},"obj":"18826823"},{"id":"26884414-22752171-29787787","span":{"begin":2123,"end":2125},"obj":"22752171"},{"id":"26884414-20178591-29787788","span":{"begin":2140,"end":2142},"obj":"20178591"},{"id":"26884414-19969530-29787789","span":{"begin":2144,"end":2146},"obj":"19969530"},{"id":"26884414-20977542-29787790","span":{"begin":2203,"end":2205},"obj":"20977542"},{"id":"26884414-25084351-29787791","span":{"begin":2207,"end":2209},"obj":"25084351"},{"id":"26884414-23326226-29787792","span":{"begin":2307,"end":2309},"obj":"23326226"}],"text":"BACTERIAL SELECTION IN THE URT\nBacterial pneumonia is primarily caused by the commensal bacteria normally residing in the URT [11, 12]. The most common causes of bacterial pneumonia for children \u003c5 years of age are Streptococcus pneumoniae, followed by Haemophilus influenzae and Staphylococcus aureus [11] although this varies over time and space. From a rudimentary ecological perspective, the human respiratory tract can be defined as an ecosystem with two distinct niches: the URT, characterized by regular asymptomatic carriage of commensal bacteria, and the LRT, which is inhabited at a low abundance by bacteria in healthy individuals [13]. During the first year after birth, the nasopharynx is rapidly colonized [14] and URT carriage is established via ongoing synergistic and antagonistic interactions among commensal bacteria [15]. Although pneumonia is an infection of the lungs, microbial selection in the URT may play an important role in etiology as bacterial strains in the URT can be readily aspirated into the LRT. For example, URT carriage is believed to be a necessary precursor of pneumonia due to S. pneumoniae [16, 17].\nNumerous epidemiologic studies describe synergistic and antagonistic relationships among various commensal bacteria [18–33] and, although the exact biological mechanisms remain unclear, in vivo and in vitro experiments suggest potential mechanisms involve either direct interaction between bacterial species or indirect interactions via the host immune system (Table 1). A number of population studies suggest that S. pneumoniae carriage is positively associated with H. influenzae [18–27] and Moraxella catarrhalis [18, 23–28] carriage but negatively associated with S. aureus [19, 20, 24–27, 29–32]. Furthermore, S. aureus carriage is generally negatively associated with H. influenzae and M. catarrhalis [19, 24, 31] carriage, whereas H. influenzae and M. catarrhalis are believed to be positively associated [18, 22, 24, 33]. Nevertheless, our understanding is limited, as the dynamics of niche competition likely consist of complex relationships between multiple species [31, 34] and strains [15, 35], further influenced by host and environmental factors [22, 36]. As carriage is an important precursor of respiratory infections for certain bacterial species [12], unraveling the complex system of bacterial interactions that determine URT microbiota may be key factor for understanding the etiology of pneumonia.\nTable 1 Known interactions and potential mechanisms for observed associations between primary bacterial colonizers of the nasopharynx a Epidemiologic studies. b In vitro and in vivo experiments\n\nB"}