Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing
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{"title"=>"Bacterial landscape of bloodstream infections in neutropenic patients via high throughput sequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Peter", "last_name"=>"Gyarmati", "scopus_author_id"=>"16642394200"}, {"first_name"=>"Christian", "last_name"=>"Kjellander", "scopus_author_id"=>"55088191300"}, {"first_name"=>"Carl", "last_name"=>"Aust", "scopus_author_id"=>"55000735800"}, {"first_name"=>"Mats", "last_name"=>"Kalin", "scopus_author_id"=>"36904591200"}, {"first_name"=>"Lars", "last_name"=>"Öhrmalm", "scopus_author_id"=>"36025581600"}, {"first_name"=>"Christian G.", "last_name"=>"Giske", "scopus_author_id"=>"8533832000"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"606195807", "pmid"=>"26270467", "doi"=>"10.1371/journal.pone.0135756", "issn"=>"19326203", "scopus"=>"2-s2.0-84942893153", "sgr"=>"84942893153", "isbn"=>"10.1371/journal.pone.0135756"}, "id"=>"23194356-1555-3671-9ccb-5f230dbaaae0", "abstract"=>"BACKGROUND: Bloodstream infection (BSI) is a common and potentially life-threatening complication in patients with hematological malignancies and therapy-induced neutropenia. Administration of broad spectrum antibiotics has substantially decreased the mortality rate in febrile neutropenia, but bacterial infection is documented in only one-third or fewer of the cases. BSI is typically diagnosed by blood culture; however, this method can detect only culturable pathogens.\\n\\nMETHODS: In the present study, a total of 130 blood samples from hematological patients receiving dose-intensive antitumoural treatment were subjected to 16S rRNA PCR and 62 of them were cultured. PCR positive samples were processed to high throughput sequencing by amplifying the V1-V3 regions of the 16S rRNA gene to obtain a full spectrum of bacteria present in BSI.\\n\\nRESULTS: Five phyla and 30 genera were identified with sequencing compared to 2 phyla and 4 genera with culture. The largest proportion of bacteria detected by sequencing belonged to Proteobacteria (55.2%), Firmicutes (33.4%) and Actinobacteria (8.6%), while Fusobacteria (0.4%) and Bacteroidetes (0.1%) were also detected. Ninety-eight percent of the bacteria identified by sequencing were opportunistic human pathogens and 65% belonged to the normal human microbiota.\\n\\nCONCLUSIONS: The present study indicates that BSIs in neutropenic hosts contain a much broader diversity of bacteria, likely with host origin, than previously realized. The elevated ratio of Proteobacteria in BSI corroborates the results found in other systemic inflammatory diseases, such as inflammatory bowel disease or mucosal infections. This knowledge may become of value for tailoring antimicrobial drug administration.", "link"=>"http://www.mendeley.com/research/bacterial-landscape-bloodstream-infections-neutropenic-patients-via-high-throughput-sequencing-1", "reader_count"=>17, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Agricultural and Biological Sciences"=>5, "Medicine and Dentistry"=>7, "Chemistry"=>1, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>7}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Denmark"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2212181"], "description"=>"<p>The graph was reconstructed based on the data from [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135756#pone.0135756.ref044\" target=\"_blank\">44</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135756#pone.0135756.ref045\" target=\"_blank\">45</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135756#pone.0135756.ref051\" target=\"_blank\">51</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135756#pone.0135756.ref053\" target=\"_blank\">53</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135756#pone.0135756.ref055\" target=\"_blank\">55</a>]. Axes show percentages.</p>", "links"=>[], "tags"=>["BSI.ResultsFive phyla", "hematological malignancies", "throughput sequencing", "Bacterial Landscape", "mortality rate", "blood culture", "neutropenic patients", "culturable pathogens.MethodsIn", "bacteria", "hematological patients", "16 S rRNA gene", "host origin", "130 blood samples", "30 genera", "16 S rRNA PCR", "neutropenic hosts", "4 genera", "proteobacteria", "mucosal infections", "spectrum antibiotics", "antimicrobial drug administration", "High Throughput Sequencing BackgroundBloodstream infection", "BSI corroborates", "neutropenia", "bloodstream infections", "2 phyla", "bowel disease"], "article_id"=>1510769, "categories"=>["Biological Sciences"], "users"=>["Peter Gyarmati", "Christian Kjellander", "Carl Aust", "Mats Kalin", "Lars Öhrmalm", "Christian G. Giske"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135756.g005", "stats"=>{"downloads"=>6, "page_views"=>42, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Composition_of_microbiota_from_different_parts_of_the_body_classified_by_four_major_bacterial_phyla_/1510769", "title"=>"Composition of microbiota from different parts of the body classified by four major bacterial phyla.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 04:02:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/2212182", "https://ndownloader.figshare.com/files/2212183", "https://ndownloader.figshare.com/files/2212184", "https://ndownloader.figshare.com/files/2212185", "https://ndownloader.figshare.com/files/2212186", "https://ndownloader.figshare.com/files/2212187"], "description"=>"<div><p>Background</p><p>Bloodstream infection (BSI) is a common and potentially life-threatening complication in patients with hematological malignancies and therapy-induced neutropenia. Administration of broad spectrum antibiotics has substantially decreased the mortality rate in febrile neutropenia, but bacterial infection is documented in only one-third or fewer of the cases. BSI is typically diagnosed by blood culture; however, this method can detect only culturable pathogens.</p><p>Methods</p><p>In the present study, a total of 130 blood samples from hematological patients receiving dose-intensive antitumoural treatment were subjected to 16S rRNA PCR and 62 of them were cultured. PCR positive samples were processed to high throughput sequencing by amplifying the V1-V3 regions of the 16S rRNA gene to obtain a full spectrum of bacteria present in BSI.</p><p>Results</p><p>Five phyla and 30 genera were identified with sequencing compared to 2 phyla and 4 genera with culture. The largest proportion of bacteria detected by sequencing belonged to Proteobacteria (55.2%), Firmicutes (33.4%) and Actinobacteria (8.6%), while Fusobacteria (0.4%) and Bacteroidetes (0.1%) were also detected. Ninety-eight percent of the bacteria identified by sequencing were opportunistic human pathogens and 65% belonged to the normal human microbiota.</p><p>Conclusions</p><p>The present study indicates that BSIs in neutropenic hosts contain a much broader diversity of bacteria, likely with host origin, than previously realized. The elevated ratio of Proteobacteria in BSI corroborates the results found in other systemic inflammatory diseases, such as inflammatory bowel disease or mucosal infections. This knowledge may become of value for tailoring antimicrobial drug administration.</p></div>", "links"=>[], "tags"=>["BSI.ResultsFive phyla", "hematological malignancies", "throughput sequencing", "Bacterial Landscape", "mortality rate", "blood culture", "neutropenic patients", "culturable pathogens.MethodsIn", "bacteria", "hematological patients", "16 S rRNA gene", "host origin", "130 blood samples", "30 genera", "16 S rRNA PCR", "neutropenic hosts", "4 genera", "proteobacteria", "mucosal infections", "spectrum antibiotics", "antimicrobial drug administration", "High Throughput Sequencing BackgroundBloodstream infection", "BSI corroborates", "neutropenia", "bloodstream infections", "2 phyla", "bowel disease"], "article_id"=>1510770, "categories"=>["Biological Sciences"], "users"=>["Peter Gyarmati", "Christian Kjellander", "Carl Aust", "Mats Kalin", "Lars Öhrmalm", "Christian G. Giske"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0135756.s001", "https://dx.doi.org/10.1371/journal.pone.0135756.s002", "https://dx.doi.org/10.1371/journal.pone.0135756.s003", "https://dx.doi.org/10.1371/journal.pone.0135756.s004", "https://dx.doi.org/10.1371/journal.pone.0135756.s005", "https://dx.doi.org/10.1371/journal.pone.0135756.s006"], "stats"=>{"downloads"=>11, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_Landscape_of_Bloodstream_Infections_in_Neutropenic_Patients_via_High_Throughput_Sequencing_/1510770", "title"=>"Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-08-13 04:02:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/2212175"], "description"=>"<p>Representation of the distribution of phyla with sequencing in all samples (a) and in individual samples (b). Detected phyla per sample with blood culture (c).</p>", "links"=>[], "tags"=>["BSI.ResultsFive phyla", "hematological malignancies", "throughput sequencing", "Bacterial Landscape", "mortality rate", "blood culture", "neutropenic patients", "culturable pathogens.MethodsIn", "bacteria", "hematological patients", "16 S rRNA gene", "host origin", "130 blood samples", "30 genera", "16 S rRNA PCR", "neutropenic hosts", "4 genera", "proteobacteria", "mucosal infections", "spectrum antibiotics", "antimicrobial drug administration", "High Throughput Sequencing BackgroundBloodstream infection", "BSI corroborates", "neutropenia", "bloodstream infections", "2 phyla", "bowel disease"], "article_id"=>1510763, "categories"=>["Biological Sciences"], "users"=>["Peter Gyarmati", "Christian Kjellander", "Carl Aust", "Mats Kalin", "Lars Öhrmalm", "Christian G. Giske"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135756.g001", "stats"=>{"downloads"=>2, "page_views"=>54, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representation_of_the_distribution_of_phyla_with_sequencing_in_all_samples_a_and_in_individual_samples_b_Detected_phyla_per_sample_with_blood_culture_c_/1510763", "title"=>"Representation of the distribution of phyla with sequencing in all samples (a) and in individual samples (b). Detected phyla per sample with blood culture (c).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 04:02:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/2212177"], "description"=>"<p>Occurrence of genera in 19 samples identified by sequencing (a). A genus was included if it reached or exceeded 0.5% of the total number of filtered reads in at least one sample. Distribution of OTU-assigned reads per genera in all samples in percentage (b). Diagram shows the pathogenicity and natural habitat of the detected genera based on read percentages (c). Over 96% of the identified reads belonged to opportunistic human pathogens (black stripes), while 64% belonged to the normal human microbiota (grey background).</p>", "links"=>[], "tags"=>["BSI.ResultsFive phyla", "hematological malignancies", "throughput sequencing", "Bacterial Landscape", "mortality rate", "blood culture", "neutropenic patients", "culturable pathogens.MethodsIn", "bacteria", "hematological patients", "16 S rRNA gene", "host origin", "130 blood samples", "30 genera", "16 S rRNA PCR", "neutropenic hosts", "4 genera", "proteobacteria", "mucosal infections", "spectrum antibiotics", "antimicrobial drug administration", "High Throughput Sequencing BackgroundBloodstream infection", "BSI corroborates", "neutropenia", "bloodstream infections", "2 phyla", "bowel disease"], "article_id"=>1510765, "categories"=>["Biological Sciences"], "users"=>["Peter Gyarmati", "Christian Kjellander", "Carl Aust", "Mats Kalin", "Lars Öhrmalm", "Christian G. Giske"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135756.g002", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Occurrence_of_genera_in_19_samples_identified_by_sequencing_a_A_genus_was_included_if_it_reached_or_exceeded_0_5_of_the_total_number_of_filtered_reads_in_at_least_one_sample_Distribution_of_OTU_assigned_reads_per_genera_in_all_samples_in_percentage_b_Dia/1510765", "title"=>"Occurrence of genera in 19 samples identified by sequencing (a). A genus was included if it reached or exceeded 0.5% of the total number of filtered reads in at least one sample. Distribution of OTU-assigned reads per genera in all samples in percentage (b). Diagram shows the pathogenicity and natural habitat of the detected genera based on read percentages (c). Over 96% of the identified reads belonged to opportunistic human pathogens (black stripes), while 64% belonged to the normal human microbiota (grey background).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 04:02:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/2212178"], "description"=>"<p>Pink nodes represent the given genera connected to the species. Green lines indicate the most prevalent species. Color lines from Bacteria to genera indicate phyla (Proteobacteria-yellow, Firmicutes-light blue, Actinobacteria-dark blue, Bacteroidetes-purple, Fusobacterium-orange). Species nodes indicate infectious properties: yellow-normal microbiota, red-human pathogen, blue-typically occurs in immunocompromised patients and/or nosocomial infections, white: taxonomy unclear/recently changed or environmental bacteria.</p>", "links"=>[], "tags"=>["BSI.ResultsFive phyla", "hematological malignancies", "throughput sequencing", "Bacterial Landscape", "mortality rate", "blood culture", "neutropenic patients", "culturable pathogens.MethodsIn", "bacteria", "hematological patients", "16 S rRNA gene", "host origin", "130 blood samples", "30 genera", "16 S rRNA PCR", "neutropenic hosts", "4 genera", "proteobacteria", "mucosal infections", "spectrum antibiotics", "antimicrobial drug administration", "High Throughput Sequencing BackgroundBloodstream infection", "BSI corroborates", "neutropenia", "bloodstream infections", "2 phyla", "bowel disease"], "article_id"=>1510766, "categories"=>["Biological Sciences"], "users"=>["Peter Gyarmati", "Christian Kjellander", "Carl Aust", "Mats Kalin", "Lars Öhrmalm", "Christian G. Giske"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135756.g003", "stats"=>{"downloads"=>3, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_microorganisms_detected_by_sequencing_on_the_species_level_/1510766", "title"=>"Schematic representation of microorganisms detected by sequencing on the species level.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 04:02:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/2212179"], "description"=>"<p>Bacteria were detected in all cases, but in 2 pairs (48–49, 120–129), the composition of bacteria changed, while in one patient (54–55), the composition of bacteria remained the same despite of antibiotic treatment. Blue ellipses indicate culture results. N/A: not available.</p>", "links"=>[], "tags"=>["BSI.ResultsFive phyla", "hematological malignancies", "throughput sequencing", "Bacterial Landscape", "mortality rate", "blood culture", "neutropenic patients", "culturable pathogens.MethodsIn", "bacteria", "hematological patients", "16 S rRNA gene", "host origin", "130 blood samples", "30 genera", "16 S rRNA PCR", "neutropenic hosts", "4 genera", "proteobacteria", "mucosal infections", "spectrum antibiotics", "antimicrobial drug administration", "High Throughput Sequencing BackgroundBloodstream infection", "BSI corroborates", "neutropenia", "bloodstream infections", "2 phyla", "bowel disease"], "article_id"=>1510767, "categories"=>["Biological Sciences"], "users"=>["Peter Gyarmati", "Christian Kjellander", "Carl Aust", "Mats Kalin", "Lars Öhrmalm", "Christian G. Giske"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135756.g004", "stats"=>{"downloads"=>9, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heat_map_showing_3_pairs_of_samples_before_and_after_antibiotic_treatment_with_the_corresponding_clinical_characteristics_follow_up_1_day_for_samples_48_49_and_54_55_5_days_for_samples_120_129_/1510767", "title"=>"Heat map showing 3 pairs of samples before and after antibiotic treatment with the corresponding clinical characteristics (follow up: 1 day for samples 48/49 and 54/55, 5 days for samples 120/129).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 04:02:34"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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