Gregory C. Booton

WHAT MOLECULES CAN TELL US ABOUT POPULATIONS: CHOOSING ANDUSING A MOLECULAR MARKER

The rapid development of molecular techniques offers a palette of technical approaches for population biologists interested in a wide range of questions. For example, these tools can be used to determine individual reproductive success or to measure rates of genetic divergence among populations. Which technique is most appropriate for a par- ticular question depends upon (1) the extent of genetic polymorphism required to best answer the question, (2) the analytical or statistical approaches available for the techniques application, and (3) the pragmatics of time and costs of materials. Here we evaluate the application of several major techniques (protein electrophoresis, nuclear and mitochondrial RFLPs (restriction fragment length polymorphisms), minisatellite and microsatellite VNTRs (variable number tandem repeats), RAPDs (random amplified polymorphic DNA), and DNA sequencing) to an array of questions regarding individual identification, exclusion and assignment of parentage, and various levels of population structure. In our evaluation, we briefly explain the technical components of each molecular approach and assess whether the typical outcomes expected from each approach will provide useful information as applied to each level of inquiry. For studies of population genetic structure, protein electrophoresis remains a powerful tool for most taxa, although techniques based on nucleic acids (par- ticularly DNA sequencing and mitochondrial DNA RFLPs) are useful here as well. Recently developed nucleic acid techniques (e.g., VNTRs) can often identify enough genetic vari- ability to address questions of self-identification or parentage. Some of the newest tech- niques (RAPDs and microsatellites) are potentially useful across a number of levels of inquiry, although procedures for adopting them are still developing.

Use of Subgenic 18S Ribosomal DNA PCR and Sequencing for Genus and Genotype Identification of Acanthamoebae from Humans with Keratitis and from Sewage Sludge

ABSTRACT This study identified subgenic PCR amplimers from 18S rDNA that were (i) highly specific for the genus Acanthamoeba, (ii) obtainable from all known genotypes, and (iii) useful for identification of individual genotypes. A 423- to 551-bpAcanthamoeba-specific amplimer ASA.S1 obtained with primers JDP1 and JDP2 was the most reliable for purposes i and ii. A variable region within this amplimer also identified genotype clusters, but purpose iii was best achieved with sequencing of the genotype-specific amplimer GTSA.B1. Because this amplimer could be obtained from any eukaryote, axenic Acanthamoeba cultures were required for its study. GTSA.B1, produced with primers CRN5 and 1137, extended between reference bp 1 and 1475. Genotypic identification relied on three segments: bp 178 to 355, 705 to 926, and 1175 to 1379. ASA.S1 was obtained from single amoeba, from cultures of all known 18S rDNA genotypes, and from corneal scrapings of Scottish patients with suspected Acanthamoeba keratitis (AK). The AK PCR findings were consistent with culture results for 11 of 15 culture-positive specimens and detected Acanthamoeba in one of nine culture-negative specimens. ASA.S1 sequences were examined for 6 of the 11 culture-positive isolates and were most closely associated with genotypic cluster T3-T4-T11. A similar distance analysis using GTSA.B1 sequences identified nine South African AK-associated isolates as genotype T4 and three isolates from sewage sludge as genotype T5. Our results demonstrate the usefulness of 18S ribosomal DNA PCR amplimers ASA.S1 and GTSA.B1 for Acanthamoeba-specific detection and reliable genotyping, respectively, and provide further evidence that T4 is the predominant genotype in AK.

Identification and Distribution of Acanthamoeba Species Genotypes Associated with Nonkeratitis Infections

ABSTRACT Acanthamoeba is a free-living protozoan genus found in a wide variety of natural habitats, including water, soil, and air. Pathogenic isolates of Acanthamoeba are medically relevant as the causative agent of sight- threatening Acanthamoeba keratitis (AK), serious infections of other organs, and fatal granulomatous amebic encephalitis. Previous work employing DNA sequences of nuclear and mitochondrial small-subunit rRNA genes (SSU rRNA genes) determined the genotypic diversity of Acanthamoeba and found that many named species of Acanthamoeba are associated with particular genotypes. These studies also concluded that nearly all AK infections result from a single molecular genotype: T4. Here, we asked whether Acanthamoeba clinical isolates from non-AK infections are also associated with particular genotypes. DNA sequence determination of nuclear SSU rRNA genes was employed for genotypic identification of 29 isolates of Acanthamoeba from non-AK infections. Sequence analysis demonstrates that T4 is the predominant genotype in non-AK infections, including those in brain, cerebrospinal fluid, nasal passages, skin, and lung. Rare genotypes (T1, T10, and T12) have been isolated from brain infections. We conclude that genotype T4 is the primary genotype in non-AK Acanthamoeba infections, as was the case in AK infections. However, the genotypes that were isolated from brains have not been observed in environmental isolates of Acanthamoeba, and their natural ecological niche is unknown.

Environmental Isolation of Balamuthia mandrillaris Associated with a Case of Amebic Encephalitis

ABSTRACT This report describes the first isolation of the ameba Balamuthia mandrillaris from an environmental soil sample associated with a fatal case of amebic encephalitis in a northern California child. Isolation of the ameba into culture from autopsied brain tissue confirmed the presence of Balamuthia. In trying to locate a possible source of infection, soil and water samples from the childs home and play areas were examined for the presence of Balamuthia. The environmental samples (plated onto nonnutrient agar with Escherichia coli as a food source) contained, in addition to the ameba, a variety of soil organisms, including other amebas, ciliates, fungi, and nematodes, as contaminants. Presumptive Balamuthia amebas were recognized only after cultures had been kept for several weeks, after they had burrowed into the agar. These were transferred through a succession of nonnutrient agar plates to eliminate fungal and other contaminants. In subsequent transfers, axenic Naegleria amebas and, later, tissue cultures (monkey kidney cells) served as the food source. Finally, the amebas were transferred to cell-free axenic medium. In vitro, the Balamuthia isolate is a slow-growing organism with a generation time of ∼30 h and produces populations of ∼2 × 105 amebas per ml. It was confirmed as Balamuthia by indirect immunofluorescence staining with rabbit anti-Balamuthia serum and human anti-Balamuthia antibody-containing serum from the amebic encephalitis patient. The environmental isolate is similar in its antimicrobial sensitivities and identical in its 16S ribosomal DNA sequences to the Balamuthia isolate from the deceased patient.

The relative value of confocal microscopy and superficial corneal scrapings in the diagnosis of Acanthamoeba keratitis.

Purpose: To compare the relative diagnostic value of confocal microscopy and superficial corneal cultures in the diagnosis of Acanthamoeba keratitis by using clinical and microbiologic definitions of disease. Methods: Results of confocal microscopy, superficial corneal smear, and superficial corneal culture were analyzed for validity against 2 different microbiologic and a clinical composite standard for Acanthamoeba keratitis. Results: In patients with both clinical characteristics and objective evidence of Acanthamoeba keratitis, confocal microscopy exhibited a sensitivity of 90.6% (95% confidence interval [CI]: 79.3%-96.9%) and a specificity of 100% (95% CI: 95.0%-100%). In patients with either positive culture or smear evidence of Acanthamoeba keratitis, confocal microscopy showed a sensitivity of 90.9% (95% CI: 78.3%-97.5%) and specificity of 90.1% (95% CI: 81.5%-95.6%). In strictly culture-positive patients, confocal microscopy showed a sensitivity of 92.9% (95% CI: 76.5%-99.1%) and a specificity of 77.3% (95% CI: 67.7%-85.2%). Of the 53 patients with Acanthamoeba keratitis, confocal microscopy was positive in 48 patients, whereas corneal smears and cultures were positive in 30 of 41 and 23 of 42 patients, respectively. Sensitivity of Acanthamoeba culture was 52.8% (95% CI: 38.6%-66.7%) in patients with a clinical diagnosis of Acanthamoeba keratitis. Simultaneous testing of smear and superficial corneal scraping resulted in a sensitivity of 83.0% (95% CI: 70.2%-91.9%), independent of the results of confocal microscopy. Conclusions: As confocal microscopy comes into wider clinical use, it remains in need of clinical and pathologic correlation. When performed and interpreted by an experienced operator, confocal microscopy is both sensitive and specific in the diagnosis of Acanthamoeba keratitis. Contemporaneous corneal scrapings are independently sensitive in the detection of Acanthamoeba keratitis, and a combination of both diagnostic modalities offers the highest likelihood of rapidly and accurately diagnosing Acanthamoeba keratitis in patients with atypical keratitis.

Identification of Balamuthia mandrillaris by PCR Assay Using the Mitochondrial 16S rRNA Gene as a Target

ABSTRACT Balamuthia mandrillaris is an opportunistic pathogen that causes granulomatous amebic meningoencephalitis in animals, including humans. Based on sequence analysis of mitochondrial small-subunit-rRNA genes, we developed primers that amplify a Balamuthia-specific PCR product. These primers will be useful for retrospective analyses of fixed tissues and possible identification of Balamuthia in vivo.

Prognostic Factors Affecting Visual Outcome in Acanthamoeba Keratitis

OBJECTIVE To identify clinical and demographic factors associated with a worse visual outcome in Acanthamoeba keratitis (AK). DESIGN Retrospective, case control study. PARTICIPANTS A total of 72 eyes of 65 patients with AK who were diagnosed at the University of Illinois Eye and Ear Infirmary between May of 2003 and May of 2007 with treatment complete by October of 2007. The first affected eye was analyzed in bilateral disease. METHODS Patient demographic, clinical characteristics, treatment methods, and final visual outcome data were collected through medical record reviews for all patients diagnosed with AK. Cases were defined as patients with AK with a visual outcome worse than 20/25 or those requiring penetrating keratoplasty (PKP). Controls were defined as patients with AK with a visual outcome of 20/25 or better. Logistic regression was used to estimate the odds ratio (OR) identifying prognostic factors associated with a worse visual outcome. MAIN OUTCOME MEASURES Final visual outcome worse than 20/25. RESULTS AK was confirmed through microbiologic evidence in 48 of 65 eyes (73.8%) or with confocal microscopy in 62 of 65 eyes (95.4%). Final visual acuity data were available in 61 of 65 eyes (93.8%); of these 61 eyes, 40 (65.6%) achieved a final visual acuity of 20/25 or better. In multivariable analysis, deep stromal involvement or the presence of a ring infiltrate at presentation was independently associated with worse visual outcomes (OR, 10.27; 95% confidence interval [CI], 2.91-36.17). Symptom duration before diagnosis was statistically predictive of disease stage at presentation (OR, 4.43; 95% CI, 0.99-19.83; multivariable analysis) but not final visual outcome (OR, 2.55; 95% CI, 0.83-7.88; univariate analysis). PKP was performed in 11 of 12 eyes with active disease. CONCLUSIONS Corneal disease staging at presentation with slit-lamp examination was highly predictive of worse outcomes, allowing the identification of patients who might benefit from more aggressive medical or surgical intervention. Unlike in previous reports, patient-reported duration of symptoms before treatment was not reliable in predicting the final visual result in our series.

ACANTHAMOEBA STRAINS ISOLATED FROM ORGANS OF FRESHWATER FISHES

Contrary to data on Acanthamoeba infections in humans, little is known about infections in fishes. The present study combines the description of strains isolated from fishes with presentation of an improved method for subgeneric classification. Acanthamoeba spp. were isolated aseptically from tissues of 14 (1.7%) of 833 asymptomatic fishes collected in rivers and streams in the Czech Republic. Acanthamoebae successfully cloned from 10 of the 14 isolated strains were examined here. Morphology of these isolates was evaluated using light optics plus scanning and transmission electron microscopy. Cyst morphology, which varied extensively within and among clones, was most like morphological group II, but species-level classification was considered impossible. A distance analysis based on 442 bases in an 18S rDNA polymerase chain reaction fragment of about 460 bp placed the isolates in a clade composed of sequence types T3, T4, and T11, the 3 subdivisions of morphological group II. Fluorescent in situ hybridization (FISH) using oligonucleotide probes indicated that all isolates belong to a single subdivision of group II, the T4 sequence type. It has been concluded that the fish isolates are most closely related to strains commonly isolated from human infections, especially Acanthamoeba keratitis. The shorter diagnostic fragment sequences have proved nearly as useful as complete 18S rDNA sequences for identification of Acanthamoeba isolates.

Survival of Acanthamoeba Cysts after Desiccation for More than 20 Years

ABSTRACT Acanthamoeba is a free-living ameba that is found throughout the world and that causes encephalitis, keratitis, and cutaneous infections in humans. It has two stages in its life cycle: a trophic stage and a resistant cyst stage. We describe here the ability of Acanthamoeba cysts to survive desiccation for more than 20 years.

Detection of Balamuthia Mitochondrial 16S rRNA Gene DNA in Clinical Specimens by PCR

ABSTRACT Balamuthia mandrillaris is a free-living ameba that causes granulomatous amebic encephalitis in both immunocompromised and immunocompetent individuals. Because of a lack of pathognomonic symptoms and the difficulty in recognizing amebas in biopsied tissues, most cases are not diagnosed or effectively treated, leading to a >95% mortality. We report here on five cases of balamuthiasis that were diagnosed by indirect immunofluorescence (IIF) staining of serum for anti-Balamuthia antibodies (titer ≥ 1:128) and confirmed by IIF of unstained brain tissue sections and/or detection of amebas in hematoxylin-eosin-stained slides. Additionally, we have used the PCR for the detection of mitochondrial 16S rRNA gene DNA from the ameba in clinical specimens such as brain tissue and cerebrospinal fluid (CSF) from individuals with Balamuthia encephalitis. Balamuthia DNA was successfully detected by the PCR in clinical samples from all five individuals. It was detected in brain tissue from three cases, in CSF from three cases, and in one of two samples of lung tissue from two individuals, but not in two samples of kidney tissue tested. One sample of unfixed brain tissue was culture positive for Balamuthia. In order to test the sensitivity of the PCR for detection of Balamuthia DNA, CSF specimens from two individuals negative for amebic infection were spiked with Balamuthia amebas. We found that it was possible to detect Balamuthia DNA in the PCR mixtures containing mitochondrial DNA from 1 to as little as 0.2 ameba per reaction mixture. A single Balamuthia ameba contains multiple mitochondrial targets; thus, 0.2 ameba represents multiple targets for amplification and is not equivalent to 0.2 of an ameba as a target.