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Molecular characterization and prevalence of plasmids co-harbouring mcr and ESBL genes

K M G Houkes1,2, V Weterings3, J J Verweij2

  • 1Microvida, Laboratory of Medical Microbiology, Amphia Hospital, Breda, Netherlands.

Microbial Genomics
|July 29, 2025
PubMed

Insights

Multidrug-resistant Enterobacterales carrying extended-spectrum beta-lactamases (ESBLs) and colistin resistance (mcr) genes are a major threat. This study found 5.9% of ESBL-E isolates harbored mcr genes, primarily mcr-9, on IncHI plasmids, indicating a single introduction event and widespread dissemination.

Area of Science:

  • Microbiology
  • Genetics
  • Public Health

Background:

  • Multidrug-resistant Enterobacterales, particularly those with extended-spectrum beta-lactamases (ESBLs) and mobile colistin resistance (mcr) genes, present a significant global health challenge.
  • These resistant bacteria can cause difficult-to-treat infections, necessitating a deeper understanding of their genetic elements and dissemination patterns.

Purpose of the Study:

  • To investigate the prevalence of Enterobacterales co-harboring ESBL and mcr genes in a Dutch hospital setting.
  • To characterize the plasmids carrying both ESBL and mcr genes, including their genetic relatedness and evolutionary history.

Main Methods:

  • Screening of ESBL-producing Enterobacterales (ESBL-E) isolates for mcr genes using established laboratory protocols.
  • Whole-genome sequencing (long- and short-read) to identify and characterize plasmids co-harboring resistance genes.
  • Bioinformatic analyses including AMRFinderPlus, PlasmidFinder, SNP analysis, and phylogenetic inference (BEAST) to assess plasmid diversity and evolutionary relationships.

Main Results:

  • Eleven out of 188 screened ESBL-E isolates (5.9%) harbored mcr genes, with mcr-9 being the most prevalent.
  • All identified plasmids co-harboring ESBL and mcr genes belonged to the IncHI incompatibility group and carried mcr-9 and/or mcr-4.3, along with blaCTX-M-9 and/or blaSHV-12.
  • Phylogenetic and SNP analyses indicated limited diversity among the study plasmids, suggesting a single introduction event and subsequent dissemination, with an estimated most recent common ancestor emergence between 1986 and 2008.

Conclusions:

  • The co-occurrence of ESBL and mcr genes in Enterobacterales is a tangible threat, with mcr-9 being a significant contributor in this Dutch hospital.
  • Limited plasmid diversity points to a single introduction event for these co-harboring plasmids, followed by widespread dissemination.
  • The mobility of ESBL genes appears more recent compared to mcr-9, highlighting ongoing evolutionary dynamics in antimicrobial resistance.
Keywords:
Enterobacteralesextended-spectrum beta-lactamase genesmobile colistin resistance genesphylogenetic analysesplasmids

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