The impact of antibiotic induction on virulence and antibiotic resistance in Klebsiella pneumoniae
Data files
Nov 06, 2024 version files 55.47 KB
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data_1498779.xlsx
51.09 KB
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README.md
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Abstract
Background: Klebsiella pneumoniae is an opportunistic pathogen causing nosocomial infections, classified into carbapenem-sensitive and carbapenem-resistant strains. Understanding the virulence factors and antibiotic resistance of these strains is essential for effective clinical management.
Objective: This study compared the virulence genes and antibiotic resistance profiles of 50 carbapenem-sensitive Klebsiella pneumoniae (CSKP) strains and 50 carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, examining their expression under antibiotic pressure and the mechanisms contributing to their pathogenicity.
Methods: Virulence genes (rmpA, rmpA2, iucA, iutA, Peg-344, ybts, iroB) were detected in both strains using polymerase chain reaction (PCR). Antibiotic susceptibility testing established minimum inhibitory concentrations (MICs) for key antibiotics. Gene expression analysis was performed with quantitative reverse transcription PCR (qRT-PCR) after 10 days of antibiotic exposure.
Results: CSKP strains exhibited significantly higher positivity rates for virulence genes compared to CRKP strains. CRKP strains predominantly expressed resistance genes KPC, SHV, and CTX-M3, whereas no resistance genes were found in CSKP. Antibiotic susceptibility tests showed increased MICs, particularly for ciprofloxacin and imipenem, following antibiotic induction. CSKP demonstrated elevated expression of rmpA and rmpA2, while CRKP showed increased expression of SHV, and KPC after antibiotic exposure.
Conclusion: This study highlights the intricate relationship between virulence and resistance in Klebsiella pneumoniae. CSKP strains show strong virulence factor expression, while CRKP strains adapt to antibiotic pressure through altered gene expression patterns. These findings underscore the urgent need for continuous surveillance and innovative therapeutic strategies to combat multidrug-resistant Klebsiella pneumoniae infections
README: The impact of antibiotic induction on virulence and antibiotic resistance in Klebsiella pneumoniae
https://doi.org/10.5061/dryad.4qrfj6qks
Description of the data and file structure
1. Introduction
This README provides essential information about the data uploaded to Dryad. The data presented here is related to "a study on bacterial gene expression under antibiotic exposure".
2. Data Overview
2.1 Data Sources
- Bacterial Strains: The data was obtained from the strains were retrieved from a preserved culture collection at the microbiology laboratory.
- Experimental Procedures: Multiple experimental procedures were carried out, including conventional PCR, antibiotic induction experiments, and real - time quantitative PCR (qPCR).
2.2 Data Types
Genetic Data:
- DNA sequences related to virulence and antimicrobial resistance genes were analyzed. The results of conventional PCR for detecting these genes are included in the dataset.
- RNA data was also collected for qPCR analysis. After RNA extraction and reverse transcription to cDNA, the expression levels of virulence and resistance genes were measured.
- Descriptions of data in each column are below:
ROX: Roxithromycin
ROXA: Roxithromycin acetylsalicylate
AKN: Amikacin
AMC: Amoxicillin - Clavulanic Acid
CAZ: Ceftazidime
CFP: Cefoperazone
CRO: Ceftriaxone
CXT: Cefuroxime Axetil
FEP: Cefepime
IMI: Imipenem
LVX: Levofloxacin
TSU: Tosufloxacin
TZP: Piperacillin - Tazobactam
ESBL_NM: Extended Spectrum Beta - Lactamase - Non - Metallic
ETP: Ertapenem
* Day 4 CIP: The strains induced by Ciprofloxacin for 4 days
* Day 4 IPM: The strains induced by Imipenem for 4 days
* Day 4 PB: The strains induced by Polymyxin B for 4 days
* Day 4 CAZ-AVP: The strains induced by Ceftazidime - Avibactam for 4 days
* Day 7 CIP: The strains induced by Ciprofloxacin for 7 days
* Day 7 IPM: The strains induced by Imipenem for 7 days
* Day 7 PB: The strains induced by Polymyxin B for 7 days
* Day 7 CAZ-AVP: The strains induced by Ceftazidime - Avibactam for 7 days
* Day 10 CIP: The strains induced by Ciprofloxacin for 10 days
* Day 10 IPM: The strains induced by Imipenem for 10 days
* Day 10 PB: The strains induced by Polymyxin B for 10 days
* Day 10 CAZ-AVP: The strains induced by Ceftazidime - Avibactam for 10 daysExperimental Metadata:
- Information about the bacterial strains, such as whether they are carbapenem - sensitive or - resistant, and their growth phases.
- The experimental data include the presence or absence of virulence gene and drug resistance gene detection, the minimum inhibitory concentration (MIC, with the unit of μg/ml) values of bacteria at each stage, and the qPCR expression values of representative virulence genes and drug resistance genes at each stage.
3. File Structure
Antibiotic_inductionDirectory:- Files here document the data from the antibiotic induction experiment.
qPCR_dataDirectory:- Holds data related to qPCR analysis. This includes files with the Ct values for each gene analyzed in triplicate, as well as the calculated expression levels using the 2 - ΔΔCT method. The "+" and "-" simply represent whether the gene was detected or not.
4. Data Quality Assurance
- Experimental Repetition: All key experiments (PCR, antibiotic induction, and qPCR) were repeated multiple times to ensure the reliability of the results. For example, each gene was analyzed in triplicate during qPCR.
- Quality Control in Experimental Procedures:
- In DNA extraction, the concentration of the obtained DNA was measured and verified to be approximately 100 ng/µL.
- For PCR and qPCR, standard protocols were followed, and positive and negative controls were included in each experiment to check for false - positive and false - negative results.
5. Contact Information
If you have any questions or need further clarification regarding the data, please contact keda419@163.com.
Files and variables
File: data_1498779.xlsx
Description: PCR MIC qPCR
Code/software
Excel can be used to view the file.
Methods
Eight carbapenem-resistant Klebsiella pneumoniae (CRKP) strains (with resistance and virulence genes) and eight carbapenem-sensitive Klebsiella pneumoniae (CSKP) strains (same virulence genes) strains were chosen. Strains were inoculated into LB broth and incubated at 37°C to logarithmic phase. The antibiotic - induction protocol was adjusted (Wistrand - Yuen et al., 2018). Induction: Day 1, 1/2 MIC; Day 2, 1 MIC; Day 3, 2 MIC, increasing for 10 days to 512 MIC or 64 μg/mL (if initial MIC > 64 μg/mL). Daily treatment with antibiotics to assess susceptibility and resistance changes.
Three time points (baseline, Day 4, Day 7, Day 10) were selected after antibiotic - induction (Gaudin et al., 2013; Viers et al., 2014). Total RNA was isolated using a kit (Bioteke, Shanghai).