ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Antimicrobials, Resistance and Chemotherapy
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1582121
This article is part of the Research TopicMultidrug Resistant Gram-negative Bacteria in Fragile HostsView all 6 articles
Molecular characterization, comparative genome analysis and resistance determinants of three clinical Elizabethkingia miricola strains isolated from Michigan
Provisionally accepted
- 1College of Health and Human Sciences, Northern Illinois University, DeKalb, IL 60015, Northern Illinois University, DeKalb, United States
- 2Department of Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, University of Giessen, Giessen, Germany
- 3Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI 48824, United States
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Elizabethkingia miricola is a gram-negative bacterium that causes life-threatening infections in vulnerable populations. Unlike other species in the Elizabethkingia genus, E. miricola also leads to meningitis-like diseases in aquatic invertebrates such as frogs, raising concerns about its zoonotic transmission potential. Management of its infection is complicated by unclear transmission pathways and multi-drug resistance. In this study, we analyzed three clinical strains (E. miricola Mich-1, Mich-2, and Mich-3) isolated from patients in Michigan using morphology observations, biochemical tests, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF/MS), and genome sequencing. Average Nucleotide Identity (ANI) analysis revealed that the Michigan strains were nearly identical and shared 96.52% identity with the type strain E. miricola DSM 14571, confirming their classification as E. miricola. Comprehensive comparative genomic analyses were conducted across 28 strains, including human isolates and strains from invertebrates like frogs. The strains exhibited open pan-genome characteristics. Mich-1 shared 3,199 genes (83.2%) with human isolates but fewer genes with frog-derived isolates (ranging from 3,319 to 3,375). This phylogenetic analysis highlights regional variation and the global diversity of E. miricola isolates, revealing connections between clinical and environmental strains. Antibiotic susceptibility testing revealed that the three clinical strains were resistant to 13 out of 16 tested drugs, with susceptibility only to trimethoprim/sulfamethoxazole and ciprofloxacin. The strains carried five β-lactamase-encoding genes (BlaB-10, BlaB-39, CME-1, , conferring resistance to penams, cephalosporins, and carbapenems. Several virulence-associated genes were conserved across clinical and frog isolates. These genes contribute to stress adaptation, adherence, and immune modulation. This study underscores the evolutionary adaptability of E. miricola genomes, highlighting their capacity to acquire genetic traits that enable survival in diverse niches. This adaptability facilitates the emergence of more resistant and virulent strains, posing significant threats to both human and animal health.
Keywords: Elizabethkingia miricola, genome analysis, antimicrobial resistance, molecular identification, Pangenomes
Received: 24 Feb 2025; Accepted: 24 Jun 2025.
Copyright: © 2025 Chen, Agah, Blom and Walker. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Shicheng Chen, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL 60015, Northern Illinois University, DeKalb, United States
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