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Plasmid profiles among some ESKAPE pathogens in a tertiary care centre in south India
Naveen Kumar Devanga Ragupathi1, Yamuna Devi Bakthavatchalam1, Purva Mathur2
1Department of Clinical Microbiology, Christian Medical College, Vellore, India.
Background & Objectives:
Plasmid has led to increase in resistant bacterial pathogens through the exchange of antimicrobial resistance (AMR) genetic determinants through horizontal gene transfer. Baseline data on the occurrence of plasmids carrying AMR genes are lacking in India. This study was aimed to identify the plasmids associated with AMR genetic determinants in ESKAPE pathogens.
Methods:
A total of 112 ESKAPE isolates including Escherichia coli (n=37), Klebsiella pneumoniae (n=48, including 7 pan-drug susceptible isolates), Acinetobacter baumannii (n=8), Pseudomonas aeruginosa (n=1) and Staphylococcus aureus (n=18) were analyzed in the study. Isolates were screened for antimicrobial susceptibility and whole genome sequencing of isolates was performed using Ion Torrent (PGM) sequencer. Downstream data analysis was done using PATRIC, ResFinder, PlasmidFinder and MLSTFinder databases. All 88 whole genome sequences (WGS) were deposited at GenBank.
Results:
Most of the study isolates showed resistant phenotypes. As analyzed from WGS, the isolates included both known and unknown sequence types. The plasmid analysis revealed the presence of single or multiple plasmids in the isolates. Plasmid types such as IncHI1B(pNDM-MAR), IncFII(pRSB107), IncFIB(Mar), IncFIB(pQil), IncFIA, IncFII(K), IncR, ColKP3 and ColpVC were present in K. pneumoniae. In E. coli, IncFIA, IncFII, IncFIB, Col(BS512), IncL1, IncX3 and IncH were present along with other types. S. aureus harboured seven different plasmid groups pMW2 (rep 5), pSAS1 (rep 7), pDLK1 (rep 10), pUB110 (rep US12), Saa6159 (rep 16), pKH12 (rep 21) and pSA1308 (rep 21). The overall incidence of IncF type plasmids was 56.5 per cent followed by Col type plasmids 18.3 per cent and IncX 5.3 per cent. Other plasmid types identified were <5 per cent.
Interpretation & Conclusions:
Results from the study may serve as a baseline data for the occurrence of AMR genes and plasmids in India. Information on the association between phenotypic and genotypic expression of AMR was deciphered from the data. Further studies on the mechanism of antibiotic resistance dissemination are essential for enhancing clinical lifetime of antibiotics.
Insights
This study identified plasmids carrying antimicrobial resistance (AMR) genes in ESKAPE pathogens in India, providing crucial baseline data. Understanding plasmid-mediated AMR is vital for combating resistant bacteria and preserving antibiotic effectiveness.
Area of Science:
- Microbiology and Infectious Diseases
- Genetics and Genomics
- Public Health
Background:
- Plasmids facilitate the exchange of antimicrobial resistance (AMR) genes among bacterial pathogens via horizontal gene transfer.
- There is a lack of baseline data on the prevalence of plasmids carrying AMR genes in India.
- ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are a major cause of hospital-acquired infections.
Purpose of the Study:
- To identify plasmids associated with AMR genetic determinants in ESKAPE pathogens.
- To establish baseline data on AMR gene-carrying plasmids in India.
- To understand the genetic basis of antimicrobial resistance in key bacterial pathogens.
Main Methods:
- Analysis of 112 ESKAPE isolates including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Staphylococcus aureus.
- Antimicrobial susceptibility testing and whole genome sequencing (WGS) using Ion Torrent (PGM) sequencer.
- Data analysis using PATRIC, ResFinder, PlasmidFinder, and MLSTFinder databases; WGS data deposited at GenBank.
Main Results:
- Most isolates exhibited resistant phenotypes.
- Plasmid analysis revealed the presence of various plasmid types, including IncF (56.5%), Col (18.3%), and IncX (5.3%), in Klebsiella pneumoniae and Escherichia coli.
- Staphylococcus aureus harbored seven distinct plasmid groups.
Conclusions:
- The study provides essential baseline data on AMR genes and plasmids in Indian ESKAPE pathogens.
- Genotypic and phenotypic correlations of AMR were elucidated.
- Further research into antibiotic resistance dissemination mechanisms is crucial for preserving antibiotic efficacy.
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