Plasmid profiles among some ESKAPE pathogens in a tertiary care centre in south India

Abstract

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.

Keywords: Antimicrobial resistance - β; IncF - plasmids; col-horizontal gene transfer; lactamase.

Fig. 1

Species-wise distribution of plasmids among Escherichia coli and Klebsiella pneumoniae.

Fig. 2

Distribution of plasmid replicon types identified among Escherichia coli and Klebsiella pneumoniae (n=246).

Fig. 3

Level of agreement between antimicrobial resistance genes and phenotypic resistance for Escherichia coli; genes present with no antimicrobial resistance correspond to non-expression of antimicrobial resistance genes. Full black circles represent total agreement between phenotype and genotype. Half-black circles represent lesser antimicrobial resistance genes than the phenotype. Empty circles represent even lesser antimicrobial resistance genes. Quarter black circle in aminoglycosides represents about 20 per cent non-expression of antimicrobial resistance genes, and quarter black circles in tetracyclines represent lesser genotype and phenotype compared to total numbers.

Fig. 4

Level of agreement of antimicrobial resistance genes and phenotypic resistance for Klebsiella pneumoniae; genes present with no antimicrobial resistance correspond to non-expression of antimicrobial resistance genes. Full circles in penicillins, cephalosporins, aminoglycosides and fluoroquinolones represent total agreement between phenotype and genotype. Half circle in chloramphenicol represents less number of gene positives among K. pneumoniae. Empty circles in tetracyclines and chloramphenicol represent less antimicrobial resistance genes and phenotypic resistance in K. pneumoniae.

Fig. 5

Heatmap showing association frequency of antimicrobial resistance genes and plasmids in Escherichia coli. IncFII, IncFIA and IncFIB (AP001918) had highest association with the antimicrobial resistance genes in comparison to other plasmid types. The grading numbers in color strip depicts the number of genes associated with the particular plasmid type.

Fig. 6

Heatmap showing association frequency of antimicrobial resistance genes and plasmids in Klebsiella pneumoniae. ColKP3 followed by IncFII(K), IncHl1B and IncFIA had high association with antimicrobial resistance genes in comparison to other plasmid types. The grading numbers in color strip depicts the number of genes associated with the particular plasmid type.