Clonality, recombination, and hybridization in the plumbing-inhabiting human pathogen Fusarium keratoplasticuminferred from multilocus sequence typing
© Short et al.; licensee BioMed Central Ltd. 2014
Received: 3 February 2014
Accepted: 16 April 2014
Published: 26 April 2014
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.
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.
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.
Fusarium is a large cosmopolitan genus of filamentous fungi best-known for causing a plethora of economically important plant diseases and mycotoxicoses . Fusaria also cause human infections ranging from sinusitis, pneumonia, and localized skin lesions to life-threatening disseminated mycoses in immune-compromised and immune-suppressed individuals . Along with Aspergillus, it is a frequent cause of trauma-associated mycotic keratitis in the tropics  and it is a predominant cause of contact-lens associated mycotic keratitis worldwide [4–9]. Fusarium is noted for its resistance to the broad-spectrum of antifungal drugs currently available . Multilocus sequence typing (MLST) is a common and powerful tool for elucidating the diversity and population biology of microbial pathogens [11–13]. Several MLST systems have been developed for studying the genetic diversity and population biology of fungal human pathogens including, among others, Aspergillus , Blastomyces , Candida , Coccidioides , Cryptococcus , Histoplasma , and Pneumocystis . Several studies utilizing MLST and genealogical concordance phylogenetic species recognition in Fusarium have revealed strongly supported species boundaries and have elucidated the spectrum of fusaria associated with human pathogenicity [4, 9, 12, 21–27]. The application of MLST to mycotic pathogens has identified epidemic clones , uncovered signatures of linkage equilibrium associated with sexual recombination [28–30], and revealed cryptic speciation [15, 31, 32]. Typing systems are also valuable for epidemiological inference and for providing a framework for understanding the distribution of important phenotypes within species such as antimicrobial drug resistance .
Knowledge of species boundaries is a prerequisite for studying intraspecific population dynamics , and through several molecular systematics studies, the phylogenetic diversity of clinical fusaria has been elucidated [22–24]. Molecular markers useful for phylogenetics tend to utilize coding and intron sequences of various genes and have proved useful for distinguishing not only species, but also common intraspecific sequence types (STs) [26, 34–36]. A three-locus MLST system developed for clinically relevant members of the species-rich Fusarium solani species complex (FSSC), which are all nested with Clade 3, utilizes an intron-rich portion of the translation elongation factor 1-alpha gene (TEF), a portion of the nuclear ribosomal RNA gene repeat that includes the internal transcribed spacer (ITS) regions and D1-D2 region of the nuclear large ribosomal RNA subunit gene (rDNA), and the gene encoding RNA polymerase II second largest subunit (RPB2) . This system resolves ~60 phylogenetic species within the FSSC and distinguishes over 300 genetically distinct STs within Clade 3 of the FSSC .
Fusarium continues to be a nosocomial problem and MLST studies have highlighted the prevalence of certain widespread STs in hospital environments . Members of the F. oxysporum species complex (e.g., FOSC ST 33) [25, 37] and the FSSC , specifically F. petroliphilum (e.g., FSSC 1-a) and F. keratoplasticum (e.g., FSSC 2-d) , are the fusaria most commonly identified in hospital water systems employing MLST. Clinically important STs within F. keratoplasticum and other fusaria appear to be ubiquitous in indoor plumbing [40, 41]. Moreover, multiple STs that are associated with cases of contact lens-associated mycotic keratitis  may also be found in this environment [4, 42]. In fact, based on current analyses [39, 41], F. keratoplasticum is the single most common Fusarium species associated with human infections.
Although its monophyly is well-supported [9, 21, 24, 43], F. keratoplasticum (FSSC 2) does not possess any distinctive morphological characters and is highly variable in culture , so morphological identification is impossible. Therefore, a three-locus MLST system was developed, which resolved 55 unique STs within F. keratoplasticum primarily from clinical sources . In a subsequent expanded analysis, nearly half (107/231) of the isolates from clinical and environmental sources belonged to a single ST, FSSC 2-d . In addition to supporting its monophyly, the combined three-locus phylogeny showed a moderately supported partition within F. keratoplasticum, suggesting that further genetic subdivision may exist within this species . Also, evidence suggesting introgressive hybridization between F. keratoplasticum and a second FSSC species (FSSC 9) was reported .
To better understand the population biology of F. keratoplasticum, the three-locus MLST system was expanded to include six novel sequence-based markers, developed using the complete genome sequence of a related species, FSSC 11 (F. solani f. sp pisi) . In addition, a PCR assay for mating-type determination  was utilized as a tenth locus to discriminate STs and investigate the potential for sexual reproduction. These markers were used to screen environmental and clinical isolates to infer the intraspecific diversity and relative roles of recombination, clonality, and hybridization in F. keratoplasticum.
Isolates of F. keratoplasticum
We analyzed 231 F. keratoplasticum isolates collected from a variety of sources and geographic origins in this study. Sources included human infections (N = 76), plumbing drains (N = 110), as well as veterinary infections, soil and various anthropogenic substrates (Additional file 1: Table S1). The human isolates presented in this paper have come from many sources over decades and were collected in a clinical setting. The isolates were sent from clinics for identification. We do not request or maintain personal information about the patients, and only keep data on the body part/disease associated with the isolate, and its general geographic source. Although isolations from six continents are represented, 84% of the isolates were from North America.
Locus development and primer design
Characteristics of loci employed
Genome position in MPVI2
P. I. chars.3
No. of indels/Msats: no. of alleles for each5
4 : 3,3,2,2s
2 : 2s, 2
5 : 2,5,2s,2s,2s
2 : 2s, 2s
4 : 2s,2,2s,2s
2 : 11,2
Primer pairs used for PCR amplification and Sanger sequencing
Annealing temp. (°C)
Seq. composition (bp)2
256 intronic; 411 exonic
705 coding; 324 ITS
213 exonic, 331 intergenic
MAT1-S-1 F: ATGGCTTTCCGCAGTAAGGA
MAT2-S-1 F: GGGAATCTGAGAAAGATACGTAC
Nucleic acid manipulation
Isolates were grown in 5 mL of potato dextrose broth (PDB) in test tubes for 14 days. Mycelium was then collected, rinsed with sterile distilled water, dried with paper towels, and transferred to 2 mL tubes for lyophilization. Mycelium was ground to a fine powder using plastic pestles and total genomic DNA was isolated using a DNeasy Plant Minikit protocol (Qiagen, Valencia, CA, USA) and suspended in a 100 μl volume of elution buffer. PCR and sequencing was performed using GoTaq PCR Kits (Promega, Madison, WI, USA) in 50 μl volumes following the manufacturer’s instructions, with reactions subjected to 2 minutes at 94°C, 35 cycles of 1 minute at 94°C, 1 minute at the appropriate annealing temperature (Table 2), and 1 minute at 72°C, followed by 10 minutes at 72°C. PCR products were sequenced at the Penn State Nucleic Acid Facility, Huck Institute of Life Sciences, University Park, PA. A multiplex PCR for identifying MAT idiomorph was performed as previously described . PCR products were visualized using a 1.5% w/v agarose gel and scored as MAT1-1 or MAT1-2 based on amplicon size (~200 and 800 bp, respectively). Portions of the nuclear ribosomal intergenic spacer region (IGS) were also amplified and sequenced in two putative hybrid isolates as previously described  using Invitrogen PlatinumTaq kits (Life Technologies, Carlsbad, CA USA) following the manufacturer’s instructions.
Sequence type (ST) diversity
NCBI GenBank accessions for DNA sequence data for six loci developed for F. keratoplasticum
GenBank accession numbers
Estimation of clonal relationships
To generate population snapshots and to estimate clonal relationships among genotypes, the set of 111 unique digitized nine-locus STs was used as input into an MLST analysis  implemented using the web application eBURST , at the single locus variant (SLV) level. The total set of 231 digitized nine-locus STs was also analyzed at the triple locus variant (TLV) level utilizing the goEBURST algorithm  implemented in PHYLOVIZ . STs that were not part of any TLV group were added manually as standalone data points. Mating-type data and source information were manually superimposed upon the resulting display of the TLV analysis with high-level edges (connections between STs identical at 7/8 and 6/8 loci) displayed as dashed and dotted lines, respectively. STs of isolates previously reported as producing cyclosporins in vitro [39, 59] were indicated on the population snapshots in order to visualize those associated with this phenotype.
Multilocus tests for linkage disequilibrium
To test for the non-random association of alleles, a clone corrected, digitized nine-locus ST dataset was used to calculate the Index of Association (I A )  together with rBarD, an alternative measure of IA adjusted for the number of loci, using MULTILOCUS ver. 1.3b . The observed I A and rBarD values were calculated for the nine-locus dataset and compared to 1000 randomized datasets. In addition, a standardized I A was calculated using LIAN . Additionally, to account for potential effects due to physical linkage, I A and rBarD were recalculated on clone corrected datasets with each of the nine loci removed separately.
Detection of recombination
A clone corrected, concatenated NEXUS data file with constant characters removed was used to generate a NeighborNet in SPLITSTREE4 , and to calculate the dataset’s δ score (a measure of treelikeness, where higher δ values may reflect higher levels of recombination)  and phylogenetic diversity, a measure of diversity based on branch lengths . A clone corrected, concatenated dataset including all nucleotide characters was used to perform the PHI test for recombination  implemented in SPLITSTREE4. Incompatibility among all 9 individual gene trees was assessed using COMPAT.PY, a program to detect topological conflict between supported clades in phylogenetic trees . For each of the nine loci, one of 200 MP trees generated using PAUPRAT  with branch lengths included was used as input in a test for topological conflict.
Detection of interspecific introgression
Based on the discovery of two putative hybrids of F. keratoplasticum (FRC S-2406 and FRC S-2509) that possess identical rDNA sequences to those of FSSC 9 , sequence data from the nine-locus MLST system were generated for three members of FSSC 9 (FRC S-2485, FRC S-2530, FRC S-2540). For comparative purposes, portions of the nine loci were also sequenced for FSSC 5 (FRC S-2519), F. petroliphilum (FSSC 1, FRC S-2550), and F. solani f. sp pisi (FSSC 11) (http://genome.jgi.doe.gov/Necha2/Necha2.home.html). Individual unrooted MP gene trees were generated as described previously to assess whether other loci of the two putative hybrid isolates showed affiliation to FSSC 9. Finally, a portion of the intergenic spacer region of the nuclear ribosomal RNA gene repeat (IGS) was sequenced for the two putative hybrids, three FSSC 9 isolates, and one F. keratoplasticum isolate (NRRL 32710) and analyzed to determine whether this portion of the rRNA repeat was also introgressed.
F. keratoplasticumshows high levels of ST diversity
Inferred relationships among clones and clonal complexes
Evidence for non-random association of alleles
Summary statistics for the F. keratoplasticum data set
No. nine-locus STs
MAT1-1:MAT1-2 (without 2-d types)
Average genetic diversity of loci2
NeighborNet δ score3
Index of Association5
Standardized I A 7
No. of eBURST SLV groups (clonal complexes)
No. STs connected at SLV level
No. isolates in SLV level STs
No. singletons at SLV level
Evidence for recombination
Introgression between phylogenetic species
The primary goal of this study was to apply novel sequence based markers to understand the diversity and population biology of F. keratoplasticum, the most common clinically relevant Fusarium [21, 24]. In addition to their utility in addressing questions related to their basic ecology and epidemiology, MLST in F. keratoplasticum provides a framework for the study of biologically relevant phenotypes. For example, F. keratoplasticum STs vary in the types of secondary metabolites produced, including cyclosporins [39, 59] (Figure 2). Sexual fertility also appears to be a variable phenotype within F. keratoplasticum. Perithecium formation was previously reported as very rare in crosses of opposite mating types, although a cross between STs 2-ss1 and 2-ll1 produced recombinant ascospores under laboratory conditions . Finally, biofilm formation in F. keratoplasticum is another variable trait with practical significance. Although NRRL 22641 (=ATCC 36031) was recommended by the International Organization for Standardization guidelines for testing disinfectants, it does not form biofilms in in vitro models  and this singleton (ST 2-c1) appears to be quite divergent (Figure 2) and aberrant morphologically , casting further doubt on its choice for testing the efficacy of antimicrobials. It is unknown whether this isolate’s failure to form biofilms can be attributed to mutation, perhaps post-isolation, or phenotypes segregating in natural populations. In addition to those reported here, further tests of ATCC 36031 in comparison to other clinical isolates has led to the recommendation that multiple clinical isolates be utilized in disinfectant testing .
High levels of sequence type diversity in F. keratoplasticum
Polymorphisms within the nine loci employed in this study ranged from 6–33 alleles per locus. The six new markers developed in this study were originally targeted because they harbored microsatellite repeats in the F. solani f. sp pisi genome. Sequencing these regions in F. keratoplasticum revealed high levels of nucleotide polymorphisms in addition to polymorphic repeats, motivating us to utilize them more fully as sequence-based markers and also to avoid issues of convergence that can be problematic in interpreting alleles based on variable numbers of tandem repeats . SNPs were the most common polymorphisms observed within F. keratoplasticum (163 out of ~7650 characters). Polymorphism per region sequenced was higher than observed in MLST systems of other fungi pathogenic to humans such as Aspergillus fumigatus , but lower than the dimorphic mycotic pathogens C. albicans, C. tropicalis and C. glabrata (6). Testing the primers designed in this study against other FSSC species indicated utility of these markers broadly in the complex (Figure 4), as they successfully amplified DNA from F. petroliphilum (FSSC 1), F. falciforme (FSSC 3 + 4), and FSSC phylogenetic species 5, 9, 18, 22 and 24. Many polymorphisms were found in other FSSC species, especially in the microsatellite repeats, which were extremely variable between species, though the same repeats motifs were often monomorphic within F. keratoplasticum. Although the six new loci developed in this study consisted almost entirely of non-coding sequence residing in intergenic regions, the level of genetic diversity observed at these loci within F. keratoplasticum were surprisingly similar to that of the protein-coding genes (Table 2).
Previous MLST studies indicated that environmental and human pathogenic fusaria are diverse, spanning multiple species complexes, species, and STs within species, but certain STs have been found to be dominant. For example, Fusarium oxysporum species complex ST 33 was identified as one such widespread clonal lineage based on analysis of TEF and the IGS region. Moreover, analysis of amplified fragment length polymorphisms (AFLPs) revealed seven distinct haplotypes within ST 33 . We observed a similar trend within F. keratoplasticum with the addition of six markers to the 3-locus MLST scheme. The majority of previously defined 3-locus STs were further resolved into multiple nine-locus STs (Table 1), some of which appeared to be quite distinct (Figures 2 and 3). Furthermore, the plot of genotypic diversity vs. number of loci sampled indicated that additional diversity in the nine-locus STs remains to be resolved (Figure 1).
F. keratoplasticumhas a mixed reproductive mode
Analyses of F. keratoplasticum isolates revealed evidence of clonality and recombination, mirroring reproductive modes observed in this species. FSSC species reproduce by clonally via asexual propagules (e.g., macroconidia, microconidia, chlamydospores) and several sexually through formation of perithecia and recombinant ascospores These potential modes of reproduction are known in F. keratoplasticum . In contrast to the hypothesis of local sexual neighborhoods, where mating is thought to occur only between isolates of similar genotypes , isolates of F. keratoplasticum that produced recombinant ascospores shared only one identical sequence (locus 5439) among the nine loci. The observed frequencies of mating-types in F. keratoplasticum in the total sample deviated significantly from the expected 1:1 ratio (162:69 MAT1-1:MAT1-2; binomial cumulative probability p < 0.0001). This aberration may be due to sampling of the most common widespread clones, because when all 2-d types were removed, a ratio of 64:60 MAT1-1:MAT1-2 (binomial cumulative probability p > 0.39) was observed.
A robust estimate of the contribution of mutation relative to recombination may be calculated as the ratio of STs that form complexes of SLVs, which are assumed to have arisen via mutation, to those that do not. In F. keratoplasticum, 50 STs resolved into 9 clonal complexes of SLVs, comprising 2–22 unique STs each (Figure 2). The remaining number of STs that did not resolve into SLV clonal complexes was 61, giving an inferred 1:1.24 ratio of mutation:recombination. Without clone correction, however, 162 isolates are connected at the SLV level compared to 69 isolates that are identical at fewer than 8/9 loci, giving an inferred mutation:recombination ratio of 2.3:1. This estimate contrasts with the situation observed in the more clonal Talaromyces marneffei, where the mutation:recombination ratio was approximately 5:1 [69, 70]. A mixed clonal/recombinant structure has also been reported in clinically relevant fungi including Aspergillus fumigatus, Cryptococcus gattii , Candida albicans [30, 71], Candida glabrata , and Paracoccidioides brasiliensis .
F. keratoplasticumST 2-d as a transcontinental epidemic clone
As previously mentioned, F. keratoplasticum 2-d is the three-locus ST most commonly associated with plumbing fixture biofilms, including hospital water systems, and human infections. It comprised 46% of the isolates in our dataset (107 isolates), and despite the incomplete resolution from nine loci, it is retained as a group of related, common and geographically widespread STs. The nine-locus MLST system divided 2-d into 18 unique types, all but one of which are connected through a series of SLVs, DLVs and TLVs (Figures 3 and 2). Based on sequence information, the dominant subtypes 2-d1 and 2-d2 appear to represent a widespread clonal lineage found in the United States, Puerto Rico, Germany, and Qatar (Table 1). Additional evidence of a strong clonal component was provided by the discovery that 94% of 2-d1 and 2-d2 isolates were MAT1-1 (Figure 2A). The remaining 6% of 2-d1 and 2-d2 isolates may represent one or multiple separate evolutionary lineages that have not been resolved, even with nine loci. The presence of haplotypes that are both extremely common and widely distributed has been observed in mycotic pathogens such as Cryptococcus gattii , in which the same common clone (C. gattii ST7) is present in Australia and the United States. In contrast, ST 2-k, previously shown to be among the six most common biofilm-associated human pathogenic fusaria , showed evidence for historical recombination (Figures 3 and 2), as 2-k2 and 2-k3 were members of an unconnected TLV group in the eBURST analysis (Figure 2). In support of this, 2-k isolates show a 9:10 MAT1-1:MAT1-2 mating-type ratio, which is similar to the 1:1 ratio expected among randomly mating populations. However, interfertility of the 2-k isolates has not been tested.
Introgression and hybridization
Introgression has been observed in other medically important fungi including Candida spp. , Cryptococcus , and Coccidioides , and is hypothesized to play an important role in producing diversity. Here, strong evidence of genetic exchange between two isolates of F. keratoplasticum and the unnamed species FSSC 9 is presented. FRC isolates S-2406 and S-2509 possessed RPB2 and TEF alleles that clearly placed them in F. keratoplasticum, but their rDNA appeared to have been derived from a FSSC 9 parent (100% sequence identity to all known FSSC 9 haplotypes). F. keratoplasticum and FSSC 9 are closely related, and both occur in plumbing biofilms, so the simplest explanation for this is introgression via an interspecific hybrid cross. Analyses of these putative hybrids showed that they possessed typical F. keratoplasticum alleles at all other loci, suggesting that if the introgression of rDNA was due to a hybridization event, the isolates were likely heavily backcrossed into the F. keratoplasticum background. Hybridization between closely related, phylogenetically defined species has been inferred in Fusarium in multiple instances [77–80]. The introgressed FSSC 9 rDNA included the ITS regions, the large subunit rRNA, and IGS region, and may encompass the entire rDNA gene repeat. Genome scale analyses are needed to fully assess what portion of the hybrid genomes was derived from a FSSC 9 parent. These analyses may help elucidate whether this introgression was mediated by a sexual or parasexual process. It is also possible that other unorthodox mechanisms may be at play in generating genetic diversity in F. keratoplasticum. Species that possess small conditionally dispensible (CD) chromosomes are known to be present within the FSSC  as well as in other fusaria . The genome of F. solani f. sp pisi includes three CD chromosomes, which disproportionately harbor genes with no clear Fusarium orthologues, leading to the hypothesis that they were gained through unknown horizontal gene transfer (HGT) events . While asexual transfer of CD chromosomes has not been demonstrated in the FSSC, it has been shown experimentally in F. oxysporum .
An extensive body of literature has connected many Fusarium infections, particularly ones suspected of being acquired nosocomially, to isolates resident in the patient indoor environment [21, 38, 41]. Similar to what has been observed in other common nosocomially acquired fungal pathogens, including A. fumigatus , we found no evidence differentiating clinical isolates from those collected from other sources, including biofilms in plumbing drains (Figure 2B). Although all known isolates of F. keratoplasticum are from highly anthropogenically influenced environments, nothing is known about a potential natural reservoir for this species [21, 39, 41]. While some STs show a broad geographic distribution, this MLST system may permit epidemiological inferences connecting patient and indoor environmental STs at a local scale. Diverse genotypes with patterns indicating historical recombination were observed, though there was also strong evidence for clonal expansion of epidemic STs. This mixed reproductive strategy, which is not unusual in fungal pathogens [28, 73, 84, 85], enables the expansion of successful genotypes, at the same time allowing for adaptation to changing environments and antifungal treatment strategies. The detection of natural hybridization and introgression in this sample of isolates may be indicative of another prevalent mechanism permitting adaptation to the anthropogenic environments these fungi inhabit.
Availability of supporting data
Nucleotide sequence data for F. keratoplasticum from the six new sequence markers are available through NCBI GenBank with the following accession numbers: locus 3968: JN585993-JN586184; locus 3972: JN586185-JN586372; locus 4081: JN586373-JN586556; locus 5437: JN586557-JN586711; locus 5439: JN586712-JN586899; locus 6512: JN586900-JN587087.
We thank Jean H. Juba for excellent technical assistance. This work was supported in part by a grant from the National Science Foundation, DEB 0089474 to DMG and Gary J. Samuels, National Institute of Food and Agriculture Project PEN 04527 at the Pennsylvania State Agricultural Experiment Station, and by Bausch and Lomb, Inc. DPGS was supported by NIFA grant 2010-65110-20488, Education in Genomics-Based Microbial Forensics. The mention of firm names or trade products does not imply that they are endorsed or recommended by the US Department of Agriculture over other firms or similar products not mentioned. The USDA is an equal opportunity provider and employer.
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