DOI: 10.5061/dryad.h44j0zpjv
title: Supplementary of: Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam

description: Introduction: Recent reports indicate the emergence of community-acquired
 pneumonia associated with K64-Klebsiella pneumoniae. Here, we identify the
 capsular types and sequence type of invasive and commensal K. pneumoniae
 isolates from Vietnam. Methods: We included 93 K. pneumoniae isolates from
 patients hospitalized at the National Hospital for Tropical Diseases,
 Hanoi between 2007 and 2011; and 110 commensal isolates from throat swabs
 from healthy volunteers living in rural and urban Hanoi in 2012. We
 determined sequence types by multi-locus sequence typing (MLST) and
 capsule typing for seven K types by PCR. Antibiotic susceptibility testing
 was performed using disk diffusion. Results: The most common detected
 capsule types were K1 (39/203, 19.2%, mainly ST23) and K2 (31/203, 15.3%,
 multiple STs: ST65, ST86, ST380). We found significantly more K2 isolates
 among invasive in comparison to commensal isolates (22.6% vs 9%, p = 0.01)
 but no significant difference was observed between invasive and commensal
 K1 isolates (14.5% vs 24.7%, p = 0.075). K64 with varying sequence types
 were predominantly seen among invasive K. pneumoniae (8 vs. 3) and were
 isolated from sepsis and meningitis patients. Among K64 isolates, one was
 carbapenem-resistant with ST799. Conclusion: Our study confirms that
 capsule type K64 K. pneumoniae is associated with community-acquired
 invasive infections in Vietnam. Research is needed to unravel the
 mechanisms of virulence of capsule typeK64 in both community and hospital
 setting.
description: The data contains the results of experiments which were designed
 to identify the K serotypes of <em>Klebsiella pneumoniae</em>
 and the procedure was followed the protocols in the publication in the
 links: https://pubmed.ncbi.nlm.nih.gov/19785524 and
 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080670   
description: 1. Title of Dataset: <br> Data set of
 "<em>Klebsiella pneumoniae</em> with capsule type K64 is
 overrepresented among invasive disease in Vietnam"<br> 2.
 Author Information<br>     A. Principal Investigator Contact
 Information<br>         Name: Vu Thi Ngoc Bich<br>       
  Institution: Oxford University Clinical Research Unit and Welcome Trust
 Major Asia Programme, Vietnam <br>         Address: The 6th floor,
 National Hospital of Tropical Disease, 78 Giai Phong, Dong Da, Ha Noi.
 Vietnam<br>         Email: bichvtn@oucru.org   
  3. Date of data collection (single date, range, approximate date): from
 2013-01 to 2017-01 4. Geographic location of data
 collection: Ha Noi - Vietnam 5. Information about
 funding sources that supported the collection of the data: Wellcome Trust,
 Oxtrec 49-12 SHARING/ACCESS INFORMATION
 1. Licenses/restrictions placed on the data: <br> Data are
 available under the terms of the Creative Commons Zero “No rights
 reserved” data waiver (CC0 1.0 Public domain dedication)<br> 2.
 Links to publications that cite or use the data:  3.
 Links to other publicly accessible locations of the data: 
 4. Links/relationships to ancillary data sets: 
 5. Was data derived from another source?  No<br> 6.
 Recommended citation for this dataset: <br> <em>Klebsiella
 pneumoniae</em> with capsule type K64 is overrepresented among
 invasive disease in Vietnam.
 (https://doi:10.5061/dryad.h44j0zpjv) DATA &
 FILE OVERVIEW 1. File List: <br> -
 <strong>Serotype_Clinical isolates.rar:</strong> The folder
 contains 34 pictural files in .jpg format(from plate1_Clinic.jpg to
 plate47_Clinic.jpg). Each file contains images of PCR products on
 electrophoresis gels. The PCR products were amplified to identify
 serotypes (K1, K2, K5, K20, K56, K57 and K64) of <em>Klebsiella
 penumoniae</em> isolates from clinical specimens of origin. The
 <strong>electrophoresis_map.xlsx</strong> file describes the
 position of PCR products on each plate of electrophoresis gels. <br>
 - <strong>Serotype_community isolates.rar:</strong> The folder
 contains 21 files of geldoc.jpg format. Each file contains images of PCR
 products on electrophoresis gels. The PCR products were amplified to
 identify serotypes (K1, K2, K5, K20, K56, K57 and K64) of
 <em>Klebsiella penumoniae</em> isolates from clinical
 specimens of origin. The file's names and the position of samples on
 electrophoresis gels were described in the
 <strong>electrophoresis_map.xlsx</strong>. The number in the
 image file's name indicate the Well ID variables in the
 electrophoresis_map file.<br> -
 <strong>Supplementary.xlsx:</strong> This file contains the
 results of K serotyping identification in relation to their Sequence type
 and antibiotic susceptibility of assessed <em>Klebsiella
 pneumoniae</em> isolates.<br> 2. Relationship between files,
 if important: <br> - Supplementary.xlsx is a summary result, which
 was interpreted from the files in Serotype_Clinical isolates.rar and
 Serotype_community isolates.rar folders.<br> 3. Additional related
 data collected that was not included in the current data
 package: <br> No<br> 4. Are there multiple versions of the
 dataset? No<br>     METHODOLOGICAL INFORMATION 1.
 Description of methods used for collection/generation of data: <br>
 The data contains the results of experiments which were designed to
 identify the k serotypes of <em>Klebsiella pneumoniae</em> and
 the procedure has followed the protocols in the publication in the links:
 https://pubmed.ncbi.nlm.nih.gov/19785524 and
 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080670 <br> 2. Methods for processing the data: <br> Serotype_Clinical isolates.rar and Serotype_community isolates.rar folders are the raw data<br> 3. Instrument- or software-specific information needed to interpret the data: <br> No need<br> 4. Standards and calibration information, if appropriate: <br> No<br> 5. Environmental/experimental conditions: <br> The experimental conditions have been described to produce an MS accepted for publication in F1000Research<br> 6. Describe any quality-assurance procedures performed on the data: Not apply 7. People involved with sample collection, processing, analysis and/or submission: <br> Bich Vu Thi Ngoc, Sylvain Brisse, Trinh Dao Tuyet, Dung Vu Tien Viet, Kathryn E. Holt, Trung Nguyen Vu, Huong Tran Thi Kieu, Diep Nguyen Thi Ngoc, H. Rogier van Doorn, Heiman F.L. Wertheim DATA-SPECIFIC INFORMATION FOR: [<strong>Serotype_Clinical isolates.rar/electrophoresis_map.xlsx</strong>]<br> 1. Number of variables: <br> 18 variables<br> 2. Number of cases/rows: <br> 39 rows: indicates for 39 maps of each electrophoresis gels plate <br> 3. Variable List: <br> - Plate name<br> - Description<br> - Well 1 to Well 16<br> 4. Missing data codes: <br> No<br> 5. Specialized formats or other abbreviations used: <br> K1, K2, K5, K20, K56, K57 and K64 indicates for K serotypes of <em>Klebsiella pneumoniae</em> isolates DATA-SPECIFIC INFORMATION FOR: [<strong>Serotype_Community isolates.rar/electrophoresis_map.xlsx</strong>]<br> 1. Number of variables: <br> 14 variables<br> 2. Number of cases/rows: <br> 110 rows: indicates for Well ID of 110 <em>Klebsiella pneumoniae</em> isolates on electrophoresis gels plates <br> 3. Variable List: <br> Well ID: indicates for Well ID of 110 <em>Klebsiella pneumoniae</em> isolates on electrophoresis gels plates<br> K1, K2, K5, K20, K56, K57 and K64: indicates for K serotypes of <em>Klebsiella pneumoniae</em> isolates<br> 4. Missing data codes: <br> No<br> 5. Specialized formats or other abbreviations used: <br> K1, K2, K5, K20, K56, K57 and K64 indicates for K serotypes of <em>Klebsiella pneumoniae</em> isolates DATA-SPECIFIC INFORMATION FOR: [<strong>Supplementary.xlsx/Kp_All_AST</strong>]<br> 1. Number of variables: <br> 25 variables<br> 2. Number of cases/rows: <br> 203 rows: indicates for Well ID of 110 <em>Klebsiella pneumoniae</em> isolates on electrophoresis gels plates <br> 3. Variable List: <br> &lt;list variable name(s), description(s), unit(s)and value labels as appropriate for each&gt;<br> Well_ID (Electrophoresis): indicates for Well ID of 203 <em>Klebsiella pneumoniae</em> isolates on electrophoresis gels plates<br> Sample_ID: indicates participant ID of healthy people who participate in the study (from row 1 to row 111). From row 112 to row 204, this variable indicates the ID of the microbiological laboratory of specimens. <br> Year of collection: indicates the year that samples were taken<br> Site: indicates type of specimens<br> Site-Group: indicates type of specimens where they belong (commensal or invasive)<br> Identification-API test: indicates the name of bacteria that were identified by API method<br> Amoxicillin clavulanic, Ampicillin, Cefepime, Piperacillin-tazobactam, Ciprofloxacin, Trimethoprim/sulfamethoxazole, Imipenem, Meropenem: These variables indicate the antibiotic panel to determine antibiotic susceptibility of the isolates in the study.<br> ESBL: indicates Extended-spectrum beta-lactamases positive isolates or Extended-spectrum beta-lactamases negative isolates.<br> K_Serotype: Serotype of<em> Klebsiella pneumoniae</em> isolates (K1, K2, K5, K20, K56, K57 and K64). Value (-) indicates undetected serotype.<br> Sequence type: was the results of multilocus sequence type (MLST)<br> gapA, infB, mdh, pgi, phoE, rfoB and tonB: indicates allenic numbers of seven house-keeping genes that were used to identify the sequence types of <em>Klesiella pneumoniae</em> isolates. Link: (https://pubmlst.org/bigsdb?db=pubmlst_mlst_seqdef&page=schemeInfo&scheme_id=13)<br> Clonal complex: indicates the group of sequence types. <br> 4. Missing data codes: <br> No<br> 5. Specialized formats or other abbreviations used: <br> None