Evaluation of Microbial Bacterial and Fungal Diversity in Cerebrospinal Fluid Shunt Infection
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{"title"=>"Evaluation of microbial bacterial and fungal diversity in cerebrospinal fluid shunt infection", "type"=>"journal", "authors"=>[{"first_name"=>"Tamara D.", "last_name"=>"Simon", "scopus_author_id"=>"13907519700"}, {"first_name"=>"Christopher E.", "last_name"=>"Pope", "scopus_author_id"=>"26768166100"}, {"first_name"=>"Samuel R.", "last_name"=>"Browd", "scopus_author_id"=>"6508084721"}, {"first_name"=>"Jeffrey G.", "last_name"=>"Ojemann", "scopus_author_id"=>"7003269971"}, {"first_name"=>"Jay", "last_name"=>"Riva-Cambrin", "scopus_author_id"=>"25931724400"}, {"first_name"=>"Nicole", "last_name"=>"Mayer-Hamblett", "scopus_author_id"=>"6603473496"}, {"first_name"=>"Margaret", "last_name"=>"Rosenfeld", "scopus_author_id"=>"7202949614"}, {"first_name"=>"Danielle M.", "last_name"=>"Zerr", "scopus_author_id"=>"6603914989"}, {"first_name"=>"Lucas", "last_name"=>"Hoffman", "scopus_author_id"=>"9234798200"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"372732200", "sgr"=>"84897468336", "issn"=>"19326203", "pmid"=>"24421877", "scopus"=>"2-s2.0-84897468336", "doi"=>"10.1371/journal.pone.0083229", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)"}, "id"=>"233be99b-0ed6-3c9d-8a78-24dcbb610662", "abstract"=>"BACKGROUND: Cerebrospinal fluid shunt infection can be recalcitrant. Recurrence is common despite appropriate therapy for the pathogens identified by culture. Improved diagnostic and therapeutic approaches are required, and culture-independent molecular approaches to cerebrospinal fluid shunt infections have not been described.\\n\\nOBJECTIVES: To identify the bacteria and fungi present in cerebrospinal fluid from children with cerebrospinal fluid shunt infection using a high-throughput sequencing approach, and to compare those results to those from negative controls and conventional culture.\\n\\nMETHODS: This descriptive study included eight children ≤18 years old undergoing treatment for culture-identified cerebrospinal fluid shunt infection. After routine aerobic culture of each cerebrospinal fluid sample, deoxyribonucleic acid (DNA) extraction was followed by amplification of the bacterial 16S rRNA gene and the fungal ITS DNA region tag-encoded FLX-Titanium amplicon pyrosequencing and microbial phylogenetic analysis.\\n\\nRESULTS: The microbiota analyses for the initial cerebrospinal fluid samples from all eight infections identified a variety of bacteria and fungi, many of which did not grow in conventional culture. Detection by conventional culture did not predict the relative abundance of an organism by pyrosequencing, but in all cases, at least one bacterial taxon was detected by both conventional culture and pyrosequencing. Individual bacterial species fluctuated in relative abundance but remained above the limits of detection during infection treatment.\\n\\nCONCLUSIONS: Numerous bacterial and fungal organisms were detected in these cerebrospinal fluid shunt infections, even during and after treatment, indicating diverse and recalcitrant shunt microbiota. In evaluating cerebrospinal fluid shunt infection, fungal and anaerobic bacterial cultures should be considered in addition to aerobic bacterial cultures, and culture-independent approaches offer a promising alternative diagnostic approach. More effective treatment of cerebrospinal fluid shunt infections is needed to reduce unacceptably high rates of reinfection, and this work suggests that one effective strategy may be reduction of the diverse microbiota present in infection.", "link"=>"http://www.mendeley.com/research/evaluation-microbial-bacterial-fungal-diversity-cerebrospinal-fluid-shunt-infection-4", "reader_count"=>26, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>5, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>5, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>8, "Medicine and Dentistry"=>12, "Physics and Astronomy"=>1, "Psychology"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>12}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Republic of Singapore"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1341434"], "description"=>"<p>Bacterial species identified by bTEFAP in initial CSF samples from eight children with CSF shunt infection (designated “A” through “G”) are presented as a proportion of all sequence reads in the sample. Bacterial species also identified by conventional culture of the same sample are designated with an asterisk (*). Bacteria that comprised 1% or fewer of reads for each sample are designated as “other”.</p>", "links"=>[], "tags"=>["Clinical research design", "Observational studies", "epidemiology", "Infectious disease epidemiology", "Infectious diseases", "Bacterial diseases", "Nosocomial infections", "Staphylococcal infection", "Infectious disease control", "Infectious diseases of the nervous system", "neurology", "hydrocephalus", "pediatrics", "surgery", "neurosurgery", "btefap"], "article_id"=>896424, "categories"=>["Medicine"], "users"=>["Tamara D. Simon", "Christopher E. Pope", "Samuel R. Browd", "Jeffrey G. Ojemann", "Jay Riva-Cambrin", "Nicole Mayer-Hamblett", "Margaret Rosenfeld", "Danielle M. Zerr", "Lucas Hoffman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083229.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_species_identified_by_bTEFAP_at_infection_diagnosis_/896424", "title"=>"Bacterial species identified by bTEFAP at infection diagnosis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-08 03:12:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1341437"], "description"=>"<p>Only bacterial taxa that constitute over 2% of the reads from each sample on any day are shown; fungi are not presented. No bacteria or fungi were detected in either of the two concurrent negative controls (CSF and PBS). The only CSF cultures that grew organisms was that collected on day 2, which grew <i>Staphylococcus epidermidis</i>. Surgeries were performed on day 1 (abdominal exploration), day 2 (CSF shunt removal) and day 14 (CSF shunt replacement). Antibiotic treatment provided is shown above the corresponding day it was given; for instance, vancomycin and meropenem were provided on days 2 through 5.</p>", "links"=>[], "tags"=>["Clinical research design", "Observational studies", "epidemiology", "Infectious disease epidemiology", "Infectious diseases", "Bacterial diseases", "Nosocomial infections", "Staphylococcal infection", "Infectious disease control", "Infectious diseases of the nervous system", "neurology", "hydrocephalus", "pediatrics", "surgery", "neurosurgery", "bacterial", "csf", "shunt", "btefap"], "article_id"=>896427, "categories"=>["Medicine"], "users"=>["Tamara D. Simon", "Christopher E. Pope", "Samuel R. Browd", "Jeffrey G. Ojemann", "Jay Riva-Cambrin", "Nicole Mayer-Hamblett", "Margaret Rosenfeld", "Danielle M. Zerr", "Lucas Hoffman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083229.g002", "stats"=>{"downloads"=>1, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proportion_of_bacterial_species_detected_over_the_course_of_CSF_shunt_infection_treatment_by_bTEFAP_sequencing_/896427", "title"=>"Proportion of bacterial species detected over the course of CSF shunt infection treatment by bTEFAP sequencing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-08 03:12:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1341438"], "description"=>"<p>Results for 8 initial CSF samples from 8 subjects are reported. For the bTEFAP results, only bacteria comprising 2% or more of reads in a sample are presented, with exceptions noted in the comments column. Underlined font indicates an organism was detected with both testing methods.</p><p>indicates a bacterium is an anaerobe; there were no attempts to culture obligate anaerobes.</p>", "links"=>[], "tags"=>["Clinical research design", "Observational studies", "epidemiology", "Infectious disease epidemiology", "Infectious diseases", "Bacterial diseases", "Nosocomial infections", "Staphylococcal infection", "Infectious disease control", "Infectious diseases of the nervous system", "neurology", "hydrocephalus", "pediatrics", "surgery", "neurosurgery", "btefap"], "article_id"=>896428, "categories"=>["Medicine"], "users"=>["Tamara D. Simon", "Christopher E. Pope", "Samuel R. Browd", "Jeffrey G. Ojemann", "Jay Riva-Cambrin", "Nicole Mayer-Hamblett", "Margaret Rosenfeld", "Danielle M. Zerr", "Lucas Hoffman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083229.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_species_identified_by_bTEFAP_at_infection_diagnosis_/896428", "title"=>"Bacterial species identified by bTEFAP at infection diagnosis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-08 03:12:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1341439"], "description"=>"<p>Fungal taxa identified by ITS1F-ITS4R fTEFAP in the 8 initial CSF samples that comprised at least 2% or more of reads for that sample. None of the samples was cultured for fungi.</p>", "links"=>[], "tags"=>["Clinical research design", "Observational studies", "epidemiology", "Infectious disease epidemiology", "Infectious diseases", "Bacterial diseases", "Nosocomial infections", "Staphylococcal infection", "Infectious disease control", "Infectious diseases of the nervous system", "neurology", "hydrocephalus", "pediatrics", "surgery", "neurosurgery", "ftefap"], "article_id"=>896429, "categories"=>["Medicine"], "users"=>["Tamara D. Simon", "Christopher E. Pope", "Samuel R. Browd", "Jeffrey G. Ojemann", "Jay Riva-Cambrin", "Nicole Mayer-Hamblett", "Margaret Rosenfeld", "Danielle M. Zerr", "Lucas Hoffman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083229.t002", "stats"=>{"downloads"=>6, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fungal_species_identified_by_fTEFAP_at_infection_diagnosis_/896429", "title"=>"Fungal species identified by fTEFAP at infection diagnosis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-08 03:12:19"}

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