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Clonality, recombination, and hybridization in the plumbing-inhabiting human pathogen Fusarium keratoplasticum

Dylan P G Short¹, Kerry O'Donnell, David M Geiser

¹Department of Plant Pathology, University of California, Davis, 1636 E Alisal St,, Salinas, CA 93905, USA. DGeiser@PSU.edu.

BMC Evolutionary Biology

|April 29, 2014

Abstract

Background:

Recent work has shown that Fusarium species and genotypes most commonly associated with human infections, particularly of the cornea (mycotic keratitis), are the same as those most commonly isolated from plumbing systems. The species most dominant in plumbing biofilms is Fusarium keratoplasticum, a cosmopolitan fungus known almost exclusively from animal infections and biofilms. To better understand its diversity and population dynamics, we developed and utilized a nine-locus sequence-based typing system to make inferences about clonality, recombination, population structure, species boundaries and hybridization.

Results:

High levels of genetic diversity and evidence for recombination and clonality were detected among 75 clinical and 156 environmental isolates of Fusarium keratoplasticum. The multilocus sequence typing system (MLST) resolved 111 unique nine-locus sequence types (STs). The single locus bifactorial determinants of mating compatibility (mating types MAT1-1 and MAT1-2), were found in a ratio of 70:30. All but one of the 49 isolates of the most common ST (FSSC 2d-2) came from human infections, mostly of the cornea, and from biofilms associated with contact lenses and plumbing surfaces. Significant levels of phylogenetic incongruence were found among loci. Putative clonal relationships among genotypes were estimated, showing a mixture of large clonal complexes and unrelated singletons. Discordance between the nuclear ribosomal rRNA and other gene genealogies is consistent with introgression of ribosomal RNA alleles of phylogenetic species FSSC 9 into F. keratoplasticum. No significant population subdivision based on clinical versus non-clinical sources was found.

Conclusions:

Incongruent phylogenetic trees and the presence of both mating types within otherwise identical STs were observed, providing evidence for sexuality in F. keratoplasticum. Cryptic speciation suggested in a published three-locus MLST system was not supported with the addition of new loci, but evidence of introgression of ribosomal RNA genes from another strongly supported phylogenetic species (FSSC 9), also known from plumbing systems and human infections, was detected in two isolates. Overall, F. keratoplasticum is a diverse and geographically unstructured species with a mixed clonal and recombinant life history.

Insights

Fusarium keratoplasticum, a fungus found in plumbing and human infections, shows high genetic diversity and evidence of sexual reproduction. This study reveals its complex population dynamics and potential for gene flow between environmental and clinical strains.

Area of Science:

Medical Mycology
Population Genetics
Environmental Microbiology

Background:

Fusarium species, particularly Fusarium keratoplasticum, are frequently isolated from both plumbing systems and human infections, especially mycotic keratitis.
F. keratoplasticum is a cosmopolitan fungus predominantly found in biofilms and animal infections.

Purpose of the Study:

To investigate the genetic diversity, population structure, and reproductive strategies of Fusarium keratoplasticum.
To understand the relationships between environmental and clinical isolates of F. keratoplasticum.

Main Methods:

Development and application of a nine-locus sequence-based typing system (multilocus sequence typing - MLST).
Analysis of 75 clinical and 156 environmental isolates.
Inference of clonality, recombination, population structure, species boundaries, and hybridization.

Main Results:

High genetic diversity and evidence of both clonality and recombination were detected in F. keratoplasticum.
The MLST system identified 111 unique sequence types (STs), with a common ST predominantly found in human infections and biofilms.
Phylogenetic incongruence among loci and evidence of ribosomal RNA gene introgression from another species (FSSC 9) were observed.

Conclusions:

The study provides evidence for sexual reproduction in F. keratoplasticum, challenging previous notions of cryptic speciation.
F. keratoplasticum exhibits a mixed clonal and recombinant life history, is genetically diverse, and lacks significant population subdivision based on source.
The findings highlight the interconnectedness of environmental and clinical fungal populations.

Read full analysis

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