A case of tinea incognita and differential diagnosis of figurate erythema

A patient with tinea incognita is presented together with a review of the literature of figurate erythema. Figurate lesions are emblematic for dermatology and perhaps the most picturesque efflorescences. The differential diagnosis can be broad and sometimes challenging. Many clinical entities with resembling primary and secondary efflorescences have to be considered as differentials and can be due to anti-infectious, paraneoplastic, allergic, autoimmune or other immune reactions.

Diagnostik von Pilzinfektionen

Zusammenfassung. Die klinischen Zeichen einer Pilzinfektion sind häufig unspezifisch und es gibt meist viele mögliche Differentialdiagnosen. Laboruntersuchungen sind für die Diagnose deshalb essentiell. Für eine optimale Untersuchung ist die Präanalytik wichtig, es braucht eine korrekte Probenentnahme und genügend Informationen auf dem Laborauftrag. Die Methoden umfassen Mikroskopie, Kultur, Serologie (Biomarker) und Molekularbiologie. Je nach Mykose und je nach Infektionsort werden andere Methoden gewählt. In den letzten Jahren haben neue Entwicklungen bei serologischen und molekularbiologischen Methoden die Diagnostik erheblich verbessert und erlauben z. T. die Diagnosestellung, wo dies früher nicht möglich gewesen wäre.

EAACI Molecular Allergology User's Guide

The availability of allergen molecules ('components') from several protein families has advanced our understanding of immunoglobulin E (IgE)-mediated responses and enabled 'component-resolved diagnosis' (CRD). The European Academy of Allergy and Clinical Immunology (EAACI) Molecular Allergology User's Guide (MAUG) provides comprehensive information on important allergens and describes the diagnostic options using CRD. Part A of the EAACI MAUG introduces allergen molecules, families, composition of extracts, databases, and diagnostic IgE, skin, and basophil tests. Singleplex and multiplex IgE assays with components improve both sensitivity for low-abundance allergens and analytical specificity; IgE to individual allergens can yield information on clinical risks and distinguish cross-reactivity from true primary sensitization. Part B discusses the clinical and molecular aspects of IgE-mediated allergies to foods (including nuts, seeds, legumes, fruits, vegetables, cereal grains, milk, egg, meat, fish, and shellfish), inhalants (pollen, mold spores, mites, and animal dander), and Hymenoptera venom. Diagnostic algorithms and short case histories provide useful information for the clinical workup of allergic individuals targeted for CRD. Part C covers protein families containing ubiquitous, highly cross-reactive panallergens from plant (lipid transfer proteins, polcalcins, PR-10, profilins) and animal sources (lipocalins, parvalbumins, serum albumins, tropomyosins) and explains their diagnostic and clinical utility. Part D lists 100 important allergen molecules. In conclusion, IgE-mediated reactions and allergic diseases, including allergic rhinoconjunctivitis, asthma, food reactions, and insect sting reactions, are discussed from a novel molecular perspective. The EAACI MAUG documents the rapid progression of molecular allergology from basic research to its integration into clinical practice, a quantum leap in the management of allergic patients.

The Role of Malassezia spp. in Atopic Dermatitis

Malassezia spp. is a genus of lipophilic yeasts and comprises the most common fungi on healthy human skin. Despite its role as a commensal on healthy human skin, Malassezia spp. is attributed a pathogenic role in atopic dermatitis. The mechanisms by which Malassezia spp. may contribute to the pathogenesis of atopic dermatitis are not fully understood. Here, we review the latest findings on the pathogenetic role of Malassezia spp. in atopic dermatitis (AD). For example, Malassezia spp. produces a variety of immunogenic proteins that elicit the production of specific IgE antibodies and may induce the release of pro-inflammatory cytokines. In addition, Malassezia spp. induces auto-reactive T cells that cross-react between fungal proteins and their human counterparts. These mechanisms contribute to skin inflammation in atopic dermatitis and therefore influence the course of this disorder. Finally, we discuss the possible benefit of an anti-Malassezia spp. treatment in patients with atopic dermatitis.

Tinea capitis and tinea faciei in the Zurich area - an 8-year survey of trends in the epidemiology and treatment patterns

BACKGROUND

Tinea capitis and tinea faciei are dermatophyte infections of the scalp and glabrous skin of the face affecting mainly prepubertal children. During the past 30 years, a significant increase and a change in the pattern of infectious agents has been noted for tinea capitis.

OBJECTIVES

The aim of this study was to determine trends in the current epidemiological situation of tinea capitis and tinea faciei in the Zurich area, Switzerland and adjacent Central and Eastern Switzerland.

METHODS

Consecutive cases diagnosed between 2006 and 2013 were studied retrospectively.

RESULTS

A total of 90 tinea capitis and 40 tinea faciei cases were observed. Anthropophilic isolates (primarily Trichophyton violaceum and Microsporum audouinii) accounted for 76% of tinea capitis cases. In contrast, zoophilic isolates (primarily T. interdigitale) were responsible for 73% of tinea faciei cases. The peak incidence in both conditions was in 4-8 year-old children. While the annual number of tinea faciei cases remained stable over the past 8 years, a trend for an increase in T. violaceum-positive tinea capitis has been observed. This was mainly due to patients of African ethnicity.

CONCLUSIONS

Anthropophilic isolates accounted for three quarters of tinea capitis and one quarter of tinea faciei cases. T. violaceum-positive tinea capitis was primarily linked to patients of African ethnicity. Tinea capitis caused by Microsporum spp. was more refractory to therapy and needed longer treatment than Trichophyton spp.-induced infection.

Nodular secondary syphilis in a woman

We report the case of a 21-year-old woman with symmetrically distributed, ulcerated nodules and plaques on the face, neck and arms. Initial differential diagnoses included pyoderma or sarcoidosis based on the clinical presentation and histopathology with non-caseating granulomas. After inefficient treatment with topical and systemic fusidic acid and steroids, we diagnosed nodular secondary syphilis owing to positive serology and immunohistochemical staining of Treponema pallidum in lesional skin. After treatment with benzathine penicillin, skin lesions improved and antibody titres declined significantly within 3 months. Nodular skin lesions in secondary syphilis are rare with 15 reported cases within the last 20 years. Furthermore, the granulomatous histology is often misleading. Our patient's case suggests that the physicians should be aware of syphilis as a possible differential diagnosis also in patients outside a high-risk population for sexually transmitted diseases and with an unusual clinical presentation.

Usefulness of IgM-specific enzyme immunoassays for serodiagnosis of syphilis: comparative evaluation of three different assays

OBJECTIVES

IgM antibodies are usually the first to be produced during treponemal infection. Three commercially available enzyme immunoassays (EIA) for detection of IgM antibodies against Treponema pallidum were evaluated.

METHODS

Results of the Anti-Treponema-pallidum-ELISA (IgM; Euroimmun), Pathozyme Syphilis M Capture (Omega Diagnostics) and recomWell Treponema IgM (Mikrogen) were compared with those of the T. pallidum particle agglutination (TPPA) and the Venereal Disease Research Laboratory (VDRL) tests for 307 serum samples.

RESULTS

The overall sensitivity (95% confidence interval [CI]) of the TPPA was 100% (97.7-100%) compared to 83.3% (76.5-88.8%) of the VDRL, 88.5% (82.4-93.0%) of the Pathozyme, 84.6% (78.0-89.9) of the Euroimmun, and 73.6% (66.1-80.4%) of a modified recomWell test procedure. Specificities were in the range of 91.4-100%. In primary syphilis, sensitivities of the Pathozyme (89.8%; 95% CI, 79.2-96.2%) and Euroimmun tests (81.4%; 95% CI, 69.1-90.3%) were significantly higher (p < 0.05) than the sensitivity of the VDRL test (61%; 95% CI, 47.4-73.5%). IgM EIAs even were positive in some cases of suspected very early infection where the VDRL was non-reactive and the TPPA was indeterminate.

CONCLUSIONS

In cases of suspected early infection specific IgM EIAs should be used in addition to other screening tests. The VDRL is not recommended for screening.

Identification of dermatophytes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In this study we evaluated the suitability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of dermatophytes in diagnostic laboratories. First, a spectral database was built with 108 reference strains belonging to 18 species of the anamorphic genera Epidermophyton, Microsporum and Trichophyton. All strains were well characterized by morphological criteria and ITS sequencing (gold standard). The dendrogram resulting from MALDI-TOF mass spectra was almost identical with the phylogenetic tree based on ITS sequencing. Subsequently, MALDI-TOF MS SuperSpectra were created for the identification of Epidermophyton floccosum, Microsporium audouinii, M. canis, M. gypseum (teleomorph: Arthroderma gypseum), M. gypseum (teleomorph: A. incurvatum), M. persicolor, A. benhamiae (Tax. Entity 3 and Am-Eur. race), T. erinacei, T. interdigitale (anthropophilic and zoophilic populations), T. rubrum/T. violaceum, T. tonsurans and T. terrestre. Because T. rubrum and T. violaceum did not present enough mismatches, a SuperSpectrum covering both species was created, and differentiation between them was done by comparison of eight specific peptide masses. In the second part of this study, MALDI-TOF MS with the newly created SuperSpectra was tested using 141 clinical isolates representing nine species. Analyses were done with 3-day-old cultures. Results were compared to morphological identification and ITS sequencing; 135/141 (95.8%) strains were correctly identified by MALDI-TOF MS compared to 128/141 (90.8%) by morphology. Therefore, MALDI-TOF MS has proven to be a useful and rapid identification method for dermatophytes.

Serological response to treatment of syphilis according to disease stage and HIV status

The serological response to treatment was studied in 264 syphilis patients; it was influenced by syphilis stage but not by human immunodeficiency virus infection and reinfection. Some of the recommendations of current guidelines are critically discussed, and amendments are proposed.

Background. Serology is the mainstay for syphilis diagnosis and treatment monitoring. We investigated serological response to treatment of syphilis according to disease stage and HIV status.

Methods. A retrospective cohort study of 264 patients with syphilis was conducted, including 90 primary, 133 secondary, 33 latent, and 8 tertiary syphilis cases. Response to treatment as measured by the Venereal Disease Research Laboratory (VDRL) test and a specific IgM (immunoglobulin M) capture enzyme-linked immunosorbent assay (ELISA; Pathozyme-IgM) was assessed by Cox regression analysis.

Results. Forty-two percent of primary syphilis patients had a negative VDRL test at their diagnosis. Three months after treatment, 85%–100% of primary syphilis patients had reached the VDRL endpoint, compared with 76%–89% of patients with secondary syphilis and 44%–79% with latent syphilis. In the overall multivariate Cox regression analysis, serological response to treatment was not influenced by human immunodeficiency virus (HIV) infection and reinfection. However, within primary syphilis, HIV patients with a CD4 count of <500 cells/μL had a slower treatment response (P = .012). Compared with primary syphilis, secondary and latent syphilis showed a slower serological response of VDRL (P = .092 and P < .001) and Pathozyme-IgM tests (P < .001 and P = .012).

Conclusions. The VDRL should not be recommended as a screening test owing to lack of sensitivity. The syphilis disease stage significantly influences treatment response whereas HIV coinfection only within primary syphilis has an impact. VDRL test titers should decline at least 4-fold within 3–6 months after therapy for primary or secondary syphilis, and within 12–24 months for latent syphilis. IgM ELISA might be a supplement for diagnosis and treatment monitoring.

Congenital syphilis in Switzerland: gone, forgotten, on the return

INTRODUCTION

Acquired syphilis has re-emerged in many Western European countries. In contrast to international guidelines, screening for syphilis in pregnancy is not generally recommended in Switzerland. There has been an increase in the incidence of laboratory syphilis notifications in recent years, regardless of gender and age.

METHODS

We conducted a retrospective study, evaluating the total numbers of pregnant women with positive syphilis serology (Treponema pallidum Particle Agglutination assay, TPPA) from 2000 to 2009, and evaluated the clinical management and outcome of their offspring. In addition, we sought to determine cases of infectious syphilis (primary, secondary, and early latent syphilis) reported to the Swiss Federal Office of Public Health in women of childbearing age, which has previously been shown to precede changes in the incidence of congenital syphilis within a population.

RESULTS

Out of 13,833 women who gave birth at our institution, positive syphilis serology was found in 9 pregnant women during the 10 years studied. A total of 6 pregnant women were diagnosed having syphilis infection during pregnancy. Regarding their offspring, 8 of the 9 newborns were tested serologically. One neonate experienced congenital syphilis because the adequately treated mother developed re-infection after treatment. Within the Swiss population, infectious syphilis cases in women of childbearing age increased substantially from 2006 to 2009.

CONCLUSIONS

The epidemiologic data suggest that congenital syphilis could become a medical problem in Switzerland due to the rise of infectious syphilis cases in women of childbearing age that have been shown to be followed by changes in the congenital syphilis incidence. The persistence of congenital syphilis in Switzerland along with this rise of infectious syphilis in women of childbearing age suggests a potential for improvement of prenatal care and syphilis control programmes.

Incubation of fungal cultures: how long is long enough?

Fungal cultures are traditionally incubated for 4 weeks or longer to maximise the recovery of slowly growing fungi. However, the data in support of this are scarce. The objectives of this study were to determine the optimum incubation time for specimens in which moulds or yeast are suspected and to review the literature. A total of 3036 fungal cultures of 2216 dermatological and 820 non-dermatological specimens were analysed. The day on which fungal growth was first noted, was recorded. Eleven of 820 non-dermatological specimens were positive after day 14; in 10 cases, the fungus was considered clinically non-relevant and in one case, the cerebrospinal fluid of a patient receiving therapy for cryptococcosis was positive with Cryptococcus neoformans. Fourteen and three of 2216 dermatological samples showed the growth of a dermatophyte in the third week and fourth week respectively. The results indicate that for specimens sent for the detection of yeast or moulds (except dermatophytes and systemic dimorphic fungi), an incubation period of 2 weeks is sufficient, whereas for dermatophytes, a 4-week incubation period is necessary. Based on these results and previous literature, an algorithm for the incubation time of fungal cultures is proposed.

Microsporum audouinii tinea capitis in a Swiss school: assessment and management of patients and asymptomatic carriers

We report three cases involving 7- to 8-year-old children from a Swiss school who had refractory tinea capitis due to an unusual strain of Microsporum audouinii which perforates hair in vitro. The patients showed no response to modern oral antifungal drugs like terbinafine and fluconazole. After switching to oral griseofulvin, two of the patients had a complete recovery, while the third was cured after the introduction of oral itraconazole. Given the high potential for contagion of this anthropophilic dermatophyte, all family members and three entire school classes were screened using the 'toothbrush technique'. Three family members and five class-mates were found to be asymptomatic carriers of M. audouinii and were consequently treated to avoid further transmission or reinfection of the treated patients. This is the first report of an outbreak of M. audouinii in Switzerland and underlines the importance of screening all contacts of patients with M. audouinii tinea capitis. Further, the effectiveness of griseofulvin in Microsporum tinea capitis has been corroborated, while newer antimycotic drugs like fluconazole or terbinafine failed.

Identification of moulds in the diagnostic laboratory—an algorithm implementing molecular and phenotypic methods

Sequence analysis provides a valuable alternative to phenotypic identification of moulds, especially for isolates lacking characteristic morphology. In this comparative prospective study, isolates that could not be identified by standard phenotypic criteria within 5 days (n = 244) were subjected to sequence analysis and further in-depth phenotypic investigations. Comparison of sequence-based with extended phenotypic identification revealed that sequence analysis was more precise in 52.0% of the isolates; in 38.6% of the isolates, both methods gave concordant results. The construction of a database consisting of high-quality sequences allowed improvement of sequence-based identification. Based on these results, we propose a diagnostic algorithm for the effective use of both phenotypic and genetic procedures for identification of moulds in the diagnostic laboratory.

Evaluation of the colorimetric VITEK 2 card for identification of gram-negative nonfermentative rods: comparison to 16S rRNA gene sequencing

Ninety strains of a collection of well-identified clinical isolates of gram-negative nonfermentative rods collected over a period of 5 years were evaluated using the new colorimetric VITEK 2 card. The VITEK 2 colorimetric system identified 53 (59%) of the isolates to the species level and 9 (10%) to the genus level; 28 (31%) isolates were misidentified. An algorithm combining the colorimetric VITEK 2 card and 16S rRNA gene sequencing for adequate identification of gram-negative nonfermentative rods was developed. According to this algorithm, any identification by the colorimetric VITEK 2 card other than Achromobacter xylosoxidans, Acinetobacter sp., Burkholderia cepacia complex, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia should be subjected to 16S rRNA gene sequencing when accurate identification of nonfermentative rods is of concern.

16S rRNA gene sequencing versus the API 20 NE system and the VITEK 2 ID-GNB card for identification of nonfermenting Gram-negative bacteria in the clinical laboratory

Over a period of 26 months, we have evaluated in a prospective fashion the use of 16S rRNA gene sequencing as a means of identifying clinically relevant isolates of nonfermenting gram-negative bacilli (non-Pseudomonas aeruginosa) in the microbiology laboratory. The study was designed to compare phenotypic with molecular identification. Results of molecular analyses were compared with two commercially available identification systems (API 20 NE, VITEK 2 fluorescent card; bioMérieux, Marcy l'Etoile, France). By 16S rRNA gene sequence analyses, 92% of the isolates were assigned to species level and 8% to genus level. Using API 20 NE, 54% of the isolates were assigned to species and 7% to genus level, and 39% of the isolates could not be discriminated at any taxonomic level. The respective numbers for VITEK 2 were 53%, 1%, and 46%, respectively. Fifteen percent and 43% of the isolates corresponded to species not included in the API 20 NE and VITEK 2 databases, respectively. We conclude that 16S rRNA gene sequencing is an effective means for the identification of clinically relevant nonfermenting gram-negative bacilli. Based on our experience, we propose an algorithm for proper identification of nonfermenting gram-negative bacilli in the diagnostic laboratory.

Internal transcribed spacer sequencing versus biochemical profiling for identification of medically important yeasts

In this study, we established an in-house database of yeast internal transcribed spacer (ITS) sequences. This database includes medically important as well as colonizing yeasts that frequently occur in the diagnostic laboratory. In a prospective study, we compared molecular identification with phenotypic identification by using the ID32C system (bioMérieux) for yeast strains that could not be identified by a combination of CHROMagar Candida and morphology on rice agar. In total, 113 yeast strains were included in the study. By sequence analysis, 98% of all strains were identified correctly to the species level. With the ID32C, 87% of all strains were identified correctly to the species or genus level, 7% of the isolates could not be identified, and 6% of the isolates were misidentified, most of them as Candida rugosa or Candida utilis. For a diagnostic algorithm, we suggest a three-step procedure which integrates morphological criteria, biochemical investigation, and sequence analysis of the ITS region.

Pulmonary Mycobacterium sherrisii infection in a human immunodeficiency virus type 1-infected patient

We report the first case of a pulmonary infection with Mycobacterium sherrisii in a patient with advanced human immunodeficiency virus infection. Mycobacterium sherrisii is a newly described nontuberculous mycobacterium related to Mycobacterium simiae. Sequencing of the 16S rRNA gene was used for species identification. Treatment and antibiotic susceptibilities are described.

Comparison of conventional and molecular methods for identification of aerobic catalase-negative gram-positive cocci in the clinical laboratory

Over a period of 18 months we have evaluated the use of 16S ribosomal DNA (rDNA) sequence analysis as a means of identifying aerobic catalase-negative gram-positive cocci in the clinical laboratory. A total of 171 clinically relevant strains were studied. The results of molecular analyses were compared with those obtained with a commercially available phenotypic identification system (API 20 Strep system; bioMérieux sa, Marcy l'Etoile, France). Phenotypic characterization identified 67 (39%) isolates to the species level and 32 (19%) to the genus level. Seventy-two (42%) isolates could not be discriminated at any taxonomic level. In comparison, 16S rDNA sequencing identified 138 (81%) isolates to the species level and 33 (19%) to the genus level. For 42 of 67 isolates assigned to a species with the API 20 Strep system, molecular analyses yielded discrepant results. Upon further analysis it was concluded that among the 42 isolates with discrepant results, 16S rDNA sequencing was correct for 32 isolates, the phenotypic identification was correct for 2 isolates, and the results for 8 isolates remained unresolved. We conclude that 16S rDNA sequencing is an effective means for the identification of aerobic catalase-negative gram-positive cocci. With the exception of Streptococcus pneumoniae and beta-hemolytic streptococci, we propose the use of 16S rDNA sequence analysis if adequate species identification is of concern.

Ribosomal DNA sequencing for identification of aerobic gram-positive rods in the clinical laboratory (an 18-month evaluation)

We have evaluated over a period of 18 months the use of 16S ribosomal DNA (rDNA) sequence analysis as a means of identifying aerobic gram-positive rods in the clinical laboratory. Two collections of strains were studied: (i) 37 clinical strains of gram-positive rods well identified by phenotypic tests, and (ii) 136 clinical isolates difficult to identify by standard microbiological investigations, i.e., identification at the species level was impossible. Results of molecular analyses were compared with those of conventional phenotypic identification procedures. Good overall agreement between phenotypic and molecular identification procedures was found for the collection of 37 clinical strains well identified by conventional means. For the 136 clinical strains which were difficult to identify by standard microbiological investigations, phenotypic characterization identified 71 of 136 (52.2%) isolates at the genus level; 65 of 136 (47.8%) isolates could not be discriminated at any taxonomic level. In comparison, 16S rDNA sequencing identified 89 of 136 (65.4%) isolates at the species level, 43 of 136 (31.6%) isolates at the genus level, and 4 of 136 (2.9%) isolates at the family level. We conclude that (i) rDNA sequencing is an effective means for the identification of aerobic gram-positive rods which are difficult to identify by conventional techniques, and (ii) molecular identification procedures are not required for isolates well identified by phenotypic investigations.

Paenibacillus turicensis sp. nov., a novel bacterium harbouring heterogeneities between 16S rRNA genes

A Gram-positive, facultatively anaerobic, rod-shaped, endospore-forming bacterium (strain MOL722(T)) was characterized using phenotypic and molecular methods. Fatty acid analysis and biochemical examination indicated that the isolate belongs to the Gram-positive bacteria with low DNA G+C content, probably to the genus Paenibacillus. Direct sequencing of the 16S rRNA gene showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded seven different sequences varying at 15 positions, with one being an insertion. The isolate shares 98.5% sequence similarity with Paenibacillus sp. P15-9, but less than 94% similarity with other paenibacilli and bacilli. Phylogenetic analysis with different treeing methods revealed that strain MOL722(T), together with Paenibacillus sp. P15-9, forms a novel monophyletic clade within the genus Paenibacillus. Based on phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium is classified as the novel species Paenibacillus turicensis sp. nov., the type strain of which is strain MOL722(T) (= DSM 14349(T) = NCCB 100011(T)).

Turicibacter sanguinis gen. nov., sp. nov., a novel anaerobic, Gram-positive bacterium

An unknown, strictly anaerobic, Gram-positive, rod-shaped bacterium (strain MOL361T) was isolated from a blood culture of a febrile patient with acute appendicitis and characterized using phenotypic and molecular methods. Fatty acid analysis and biochemical examination indicated that the isolate most closely resembles members of the Gram-positive bacteria with low DNA G+C content. 16S rDNA sequencing revealed a relatively high overall similarity (97%) to an uncultured bacterium, but these two strains both exhibit low (<87%) 16S rDNA similarity to other bacteria. Phylogenetic analysis with different treeing methods showed that this strain forms a novel line of descent within the Gram-positive bacteria with low G+C content. Strain MOL361T is described as the type strain of a novel species within a new genus, Turicibacter sanguinis gen. nov., sp. nov.

Quantitative detection of Streptococcus pneumoniae in nasopharyngeal secretions by real-time PCR

Streptococcus pneumoniae is an important cause of community-acquired pneumonia. However, in this setting the diagnostic sensitivity of blood cultures is below 30%. Since during such infections changes in the amounts of S. pneumoniae may also occur in the upper respiratory tract, quantification of these bacteria in nasopharnygeal secretions (NPSs) may offer a suitable diagnostic approach. Real-time PCR offers a sensitive, efficient, and routinely reproducible approach to quantification. Using primers and a fluorescent probe specific for the pneumolysin gene, we were able to detect DNA from serial dilutions of S. pneumoniae cells in which the quantities of DNA ranged from the amounts extracted from 1 to 10(6) cells. No difference was noted when the same DNA was mixed with DNA extracted from NPSs shown to be deficient of S. pneumoniae following culture, suggesting that this bacterium can be detected and accurately quantitated in clinical samples. DNAs from Haemophilus influenzae, Moraxella catarrhalis, or alpha-hemolytic streptococci other than S. pneumoniae were not amplified or were only weakly amplified when there were > or =10(6) cells per reaction mixture. When the assay was applied to NPSs from patients with respiratory tract infections, the assay performed with a sensitivity of 100% and a specificity of up to 96% compared to the culture results. The numbers of S. pneumoniae organisms detected by real-time PCR correlated with the numbers detected by semiquantitative cultures. A real-time PCR that targeted the pneumolysin gene provided a sensitive and reliable means for routine rapid detection and quantification of S. pneumoniae present in NPSs. This assay may serve as a tool to study changes in the amounts of S. pneumoniae during lower respiratory tract infections.