Genomic Epidemiology of Elizabethkingia Infections

Elizabethkingia species are emerging opportunistic pathogens responsible for severe nosocomial and community-acquired infections, notably neonatal meningitis, pneumonia and bloodstream infections. Genomic epidemiology has revealed extensive diversity within the genus, with whole-genome sequencing enabling precise species identification beyond classical biochemical tests. Population studies have uncovered multiple phylogenetic lineages of Elizabethkingia anophelis, E. meningoseptica and E. miricola, each associated with distinct resistance gene profiles and mobile genetic elements. Analyses of core and accessory genomes have demonstrated a large open pan-genome, reflecting frequent horizontal gene transfer events that shape antimicrobial resistance and virulence. High-resolution molecular typing schemes, such as core genome multilocus sequence typing, have delineated outbreak subclusters and traced transmission pathways within healthcare environments. Moreover, unusual mutator phenotypes arising from disrupted DNA repair genes have been linked to accelerated evolutionary rates, raising concerns over the rapid emergence of multidrug-resistant strains. Together, these insights underscore the global significance of genomic surveillance in guiding infection control, informing targeted therapy and anticipating future outbreak dynamics.

Research from Nature Portfolio

Evolutionary analyses of a large Elizabethkingia anophelis outbreak in the United States have revealed an unusually high mutation rate driven by a disrupted DNA repair gene, resulting in multiple phylogenetic subclusters with distinct temporal and geographic patterns. This study highlighted how a naturally occurring mutator phenotype can accelerate adaptation and influence outbreak dynamics. Foundational work on global diversity employed comparative genomics of E. anophelis isolates from Africa, Asia and other regions to define core and accessory genome components, establish a public multilocus sequence typing scheme and map the distribution of antimicrobial resistance determinants. These efforts provided a framework for standardised molecular surveillance and demonstrated the power of genomics in resolving species boundaries and transmission networks.

Genomic Epidemiology of Elizabethkingia Infections publication trend

The graph below shows the total number of articles in genomic epidemiology of elizabethkingia infections across all publications each year (not limited to Nature Index journals).

Technical terms

Whole-genome sequencing: Determination of the complete DNA sequence of an organism’s genome at a single time.

Phylogenetic analysis: Inference of evolutionary relationships among isolates based on comparative genomic data.

Pan-genome: The total set of genes present within all strains of a species, encompassing core and accessory genomes.

Core genome multilocus sequence typing (cgMLST): A high-resolution typing method that compares allelic profiles across a defined set of conserved genes.

Mutator phenotype: Increased mutation rate in a bacterial population due to defects in DNA repair systems.

Mobile genetic element: DNA segments such as plasmids, transposons or integrative conjugative elements that can move within or between genomes.

Antimicrobial resistance determinant: Genetic feature that confers reduced susceptibility to one or more antimicrobial agents.

Metallo-β-lactamase: Enzyme requiring metal ions to hydrolyse β-lactam antibiotics, often mediating high-level resistance.

References

1. Neonatal Elizabethkingia anophelis meningitis originating from the water reservoir of an automated infant milk dispenser, the Netherlands, February 2024. Eurosurveillance (2024).
2. Opportunistic Elizabethkingia miricola Infections in Intensive Care Unit, Spain - Volume 30, Number 4—April 2024 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases (2024).
3. Review on infection control strategies to minimize outbreaks of the emerging pathogen Elizabethkingia anophelis. Antimicrobial Resistance & Infection Control (2023).
4. Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. Nature Communications (2017).
5. Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis. Scientific Reports (2016).