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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Multilevel population genetic analysis of vanA and vanB Enterococcus faecium causing nosocomial outbreaks in 27
Ana R Freitas1,2, Ana P Tedim2,3,4, Maria V Francia5
1UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.
Objectives:
Vancomycin-resistant Enterococcus faecium (VREfm) have been increasingly reported since the 1980s. Despite the high number of published studies about VRE epidemiology, the dynamics and evolvability of these microorganisms are still not fully understood. A multilevel population genetic analysis of VREfm outbreak strains since 1986, representing the first comprehensive characterization of plasmid content in E. faecium, was performed to provide a detailed view of potential transmissible units.
Methods:
From a comprehensive MeSH search, we identified VREfm strains causing hospital outbreaks (1986-2012). In total, 53 VanA and 18 VanB isolates (27 countries, 5 continents) were analysed and 82 vancomycin-susceptible E. faecium (VSEfm) were included for comparison. Clonal relatedness was established by PFGE and MLST (goeBURST/Bayesian Analysis of Population Structure, BAPS). Characterization of van transposons (PCR mapping, RFLP, sequencing), plasmids (transfer, ClaI-RFLP, PCR typing of relaxases, replication-initiation proteins and toxin-antitoxin systems, hybridization, sequencing), bacteriocins and virulence determinants (PCR, hybridization, sequencing) was performed.
Results:
VREfm were mainly associated with major human lineages ST17, ST18 and ST78. VREfm and VSEfm harboured plasmids of different families [RCR, small theta plasmids, RepA_N (pRUM/pLG1) and Inc18] able to yield mosaic elements. Tn1546-vanA was mainly located on pRUM/Axe-Txe (USA) and Inc18-pIP186 (Europe) plasmids. The VanB2 type (Tn5382/Tn1549) was predominant among VanB strains (chromosome and plasmids).
Conclusions:
Both strains and plasmids contributed to the spread and persistence of vancomycin resistance among E. faecium. Horizontal gene transfer events among genetic elements from different clonal lineages (same or different species) result in chimeras with different stability and host range, complicating the surveillance of epidemic plasmids.
Insights
Vancomycin-resistant Enterococcus faecium (VREfm) spread through both bacterial strains and plasmids. Horizontal gene transfer creates complex, evolving resistance elements that challenge surveillance efforts.
Area of Science:
- Microbiology
- Genetics
- Epidemiology
Background:
- Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a significant nosocomial pathogen since the 1980s.
- Understanding the population dynamics and evolvability of VREfm is crucial for effective control strategies.
- Previous studies have focused on epidemiology, but a comprehensive analysis of plasmid content and its role in VREfm evolution is lacking.
Purpose of the Study:
- To perform a multilevel population genetic analysis of VREfm outbreak strains from 1986 to 2012.
- To comprehensively characterize the plasmid content and its contribution to the spread and persistence of vancomycin resistance in E. faecium.
- To investigate the dynamics of transmissible genetic elements in VREfm.
Main Methods:
- Analysis of 53 VanA and 18 VanB VREfm isolates from 27 countries, alongside 82 vancomycin-susceptible E. faecium (VSEfm) controls.
- Determination of clonal relatedness using Pulsed-Field Gel Electrophoresis (PFGE) and Multilocus Sequence Typing (MLST).
- Comprehensive characterization of vancomycin transposons and plasmids, including PCR mapping, sequencing, and transfer experiments.
Main Results:
- VREfm strains were predominantly associated with major human lineages ST17, ST18, and ST78.
- Both VREfm and VSEfm harbored diverse plasmid families, forming mosaic elements.
- Specific plasmids (pRUM/Axe-Txe and Inc18-pIP186) were identified as key carriers of the Tn1546-vanA transposon in different geographical regions.
Conclusions:
- Both bacterial strains and plasmids play a significant role in the dissemination and maintenance of vancomycin resistance in E. faecium.
- Horizontal gene transfer between different genetic elements leads to the formation of chimeric plasmids with variable stability and host range.
- The complexity arising from these genetic exchanges complicates the surveillance of epidemic plasmids and VREfm spread.
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