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Supplementary of: Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam

Citation

Vu Thi Ngoc, Bich (2021), Supplementary of: Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam, Dryad, Dataset, https://doi.org/10.5061/dryad.h44j0zpjv

Abstract

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.

Methods

The data contains the results of experiments which were designed to identify the K serotypes of Klebsiella pneumoniae 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 

 

Usage Notes

1. Title of Dataset: 
Data set of "Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam"
2. Author Information
    A. Principal Investigator Contact Information
        Name: Vu Thi Ngoc Bich
        Institution: Oxford University Clinical Research Unit and Welcome Trust Major Asia Programme, Vietnam 
        Address: The 6th floor, National Hospital of Tropical Disease, 78 Giai Phong, Dong Da, Ha Noi. Vietnam
        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: 
Data are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication)
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
6. Recommended citation for this dataset: 
Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam. (https://doi:10.5061/dryad.h44j0zpjv)

DATA & FILE OVERVIEW

1. File List: 
- Serotype_Clinical isolates.rar: 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 Klebsiella penumoniae isolates from clinical specimens of origin. The electrophoresis_map.xlsx file describes the position of PCR products on each plate of electrophoresis gels. 
- Serotype_community isolates.rar: 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 Klebsiella penumoniae isolates from clinical specimens of origin. The file's names and the position of samples on electrophoresis gels were described in the electrophoresis_map.xlsx. The number in the image file's name indicate the Well ID variables in the electrophoresis_map file.
- Supplementary.xlsx: This file contains the results of K serotyping identification in relation to their Sequence type and antibiotic susceptibility of assessed Klebsiella pneumoniae isolates.
2. Relationship between files, if important: 
- Supplementary.xlsx is a summary result, which was interpreted from the files in Serotype_Clinical isolates.rar and Serotype_community isolates.rar folders.
3. Additional related data collected that was not included in the current data package: 
No
4. Are there multiple versions of the dataset? No
    METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 
The data contains the results of experiments which were designed to identify the k serotypes of Klebsiella pneumoniae 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 
2. Methods for processing the data: 
Serotype_Clinical isolates.rar and Serotype_community isolates.rar folders are the raw data
3. Instrument- or software-specific information needed to interpret the data: 
No need
4. Standards and calibration information, if appropriate: 
No
5. Environmental/experimental conditions: 
The experimental conditions have been described to produce an MS accepted for publication in F1000Research
6. Describe any quality-assurance procedures performed on the data: Not apply

7. People involved with sample collection, processing, analysis and/or submission: 
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: [Serotype_Clinical isolates.rar/electrophoresis_map.xlsx]
1. Number of variables: 
18 variables
2. Number of cases/rows: 
39 rows: indicates for 39 maps of each electrophoresis gels plate 
3. Variable List: 
- Plate name
- Description
- Well 1 to Well 16
4. Missing data codes: 
No
5. Specialized formats or other abbreviations used: 
K1, K2, K5, K20, K56, K57 and K64 indicates for K serotypes of Klebsiella pneumoniae isolates

DATA-SPECIFIC INFORMATION FOR: [Serotype_Community isolates.rar/electrophoresis_map.xlsx]
1. Number of variables: 
14 variables
2. Number of cases/rows: 
110 rows: indicates for Well ID of 110 Klebsiella pneumoniae isolates on electrophoresis gels plates 
3. Variable List: 
Well ID: indicates for Well ID of 110 Klebsiella pneumoniae isolates on electrophoresis gels plates
K1, K2, K5, K20, K56, K57 and K64: indicates for K serotypes of Klebsiella pneumoniae isolates
4. Missing data codes: 
No
5. Specialized formats or other abbreviations used: 
K1, K2, K5, K20, K56, K57 and K64 indicates for K serotypes of Klebsiella pneumoniae isolates

DATA-SPECIFIC INFORMATION FOR: [Supplementary.xlsx/Kp_All_AST]
1. Number of variables: 
25 variables
2. Number of cases/rows: 
203 rows: indicates for Well ID of 110 Klebsiella pneumoniae isolates on electrophoresis gels plates 
3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
Well_ID (Electrophoresis): indicates for Well ID of 203 Klebsiella pneumoniae isolates on electrophoresis gels plates
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. 
Year of collection: indicates the year that samples were taken
Site: indicates type of specimens
Site-Group: indicates type of specimens where they belong (commensal or invasive)
Identification-API test: indicates the name of bacteria that were identified by API method
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.
ESBL: indicates Extended-spectrum beta-lactamases positive isolates or Extended-spectrum beta-lactamases negative isolates.
K_Serotype: Serotype of Klebsiella pneumoniae isolates (K1, K2, K5, K20, K56, K57 and K64). Value (-) indicates undetected serotype.
Sequence type: was the results of multilocus sequence type (MLST)
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 Klesiella pneumoniae isolates. Link: (https://pubmlst.org/bigsdb?db=pubmlst_mlst_seqdef&page=schemeInfo&scheme_id=13)
Clonal complex: indicates the group of sequence types. 
4. Missing data codes: 
No
5. Specialized formats or other abbreviations used: 
None