Investigation of nosocomial pneumocystis infections: usefulness of longitudinal screening of epidemic and post-epidemic pneumocystis genotypes.

BACKGROUND: Twenty-five patients, of whom 22 were renal transplant recipients, developed Pneumocystis jirovecii infections at the nephrology department of Reims University Hospital (France) from September 2008 to October 2009, whereas only four sporadic cases had been diagnosed in this department over the 14 previous years. AIM: This outbreak was investigated by analysing patient encounters and P. jirovecii types. METHODS: A transmission map was drawn up. P. jirovecii typing at DHPS, ITS and mtLSU rRNA sequences was performed in the patients of the cluster (18 patients with Pneumocystis pneumonia (PCP) and seven colonized patients), 10 unlinked control patients (six PCP patients and four colonized patients), as well as 23 other patients diagnosed with P. jirovecii (nine PCP patients and 14 colonized patients) in the same department over a three-year post-epidemic period. FINDINGS: Eleven encounters between patients harbouring the same types were observed. Three PCP patients and one colonized patient were considered as possible index cases. The most frequent types in the cluster group and the control group were identical. However, their frequency was significantly higher in the first than in the second group (P < 0.01). Identical types were also identified in the post-epidemic group, suggesting a second outbreak due to the same strain, contemporary to a disruption in prevention measures. CONCLUSIONS: These results provide additional data on the role of both PCP and colonized patients as infectious sources. Longitudinal screening of P. jirovecii types in infected patients, including colonized patients, is required in the investigation of the fungus's circulation within hospitals.

Early diagnosis and monitoring of mucormycosis by detection of circulating DNA in serum: retrospective analysis of 44 cases collected through the French Surveillance Network of Invasive Fungal Infections (RESSIF).

The main objective of this study was to assess the diagnostic performance of a set of three Mucorales quantitative PCR assays in a retrospective multicentre study. Mucormycosis cases were recorded thanks to the French prospective surveillance programme (RESSIF network). The day of sampling of the first histological or mycological positive specimen was defined as day 0 (D0). Detection of circulating DNA was performed on frozen serum samples collected from D-30 to D30, using quantitative PCR assays targeting Rhizomucor, Lichtheimia, Mucor/Rhizopus. Forty-four patients diagnosed with probable (n = 19) or proven (n = 25) mucormycosis were included. Thirty-six of the 44 patients (81%) had at least one PCR-positive serum. The first PCR-positive sample was observed 9 days (range 0-28 days) before diagnosis was made using mycological criteria and at least 2 days (range 0-24 days) before imaging. The identifications provided with the quantitative PCR assays were all concordant with culture and/or PCR-based identification of the causal species. Survival rate at D84 was significantly higher for patients with an initially positive PCR that became negative after treatment initiation than for patients whose PCR remained positive (48% and 4%, respectively; p <10-6). The median time for complete negativity of PCR was 7 days (range 3-19 days) after initiation of l-AmB treatment. Despite some limitations due to the retrospective design of the study, we showed that Mucorales quantitative PCR could not only confirm the mucormycosis diagnosis when other mycological arguments were present but could also anticipate this diagnosis. Quantification of DNA loads may also be a useful adjunct to treatment monitoring.

Scedosporium apiospermum Otitis Complicated by a Temporomandibular Arthritis: A Case Report and Mini-Review.

Scedosporium apiospermum is an ubiquitous fungus responsible for various infections in immunocompromised and immunocompetent patients. Ear infections are infrequent. We report an exceptional case of S. apiospermum external otitis complicated by temporomandibular joint arthritis. After 6 months of antibiotherapy, diagnosis was established by mycological analysis of external auditory canal and infratemporal fossae needle sampling. A satisfactory outcome was obtained after 2 months of voriconazole alone. We have reviewed 15 cases of S. apiospermum otitis. Seven of these patients were immunocompromised. Most common clinical presentation included a chronic external otitis lasting months or years before complication stage. Most common clinical features included recurrent unilateral otalgia (11/15) and purulent otorrhea (13/15). Diagnosis was often made at later stage (12/15) with local extension to bones and/or soft tissues (9/15) or cerebral lethal dissemination (3/15).The extremely low incidence of S. apiospermum otomycosis and its non-specific presentation results in a frequent diagnosis delay. A mycological investigation should be performed in case of persistent external otitis and/or osteolysis despite prolonged antibiotic treatment to prevent further extension of the disease.

Implementation of an FTIR spectral library of 486 filamentous fungi strains for rapid identification of molds.

Filamentous fungi may cause food and feed spoilage and produce harmful metabolites to human and animal health such as mycotoxins. Identification of fungi using conventional phenotypic methods is time-consuming and molecular methods are still quite expensive and require specific laboratory skills. In the last two decades, it has been shown that Fourier transform infrared (FTIR) spectroscopy was an efficient tool for microorganism identification. The aims of this study were to use a simple protocol for the identification of filamentous fungi using FTIR spectroscopy coupled with a partial least squares discriminant analysis (PLS-DA), to implement a procedure to validate the obtained results, and to assess the transferability of the method and database. FTIR spectra of 486 strains (43 genera and 140 species) were recorded. An IR spectral database built with 288 strains was used to identify 105 different strains. It was found that 99.17% and 92.3% of spectra derived from these strains were correctly assigned at the genus and species levels, respectively. The establishment of a score and a threshold permitted to validate 80.79% of the results obtained. A standardization function (SF) was also implemented and tested on FTIR data from another instrument on a different site and permitted to increase the percentage of well predicted spectra for this set from 72.15% to 89.13%. This study confirms the good performance of high throughput FTIR spectroscopy for fungal identification using a spectral library of molds of industrial relevance.

[Post-traumatic mucormycosis due to Lichtheimia corymbifera: three case reports]. / Mucormycoses post-traumatiques à Lichtheimia corymbifera: à propos de 3 cas.

We report 3 cases of post-traumatic cutaneous mucormycosis caused by Lichtheimia corymbifera, two of them occurring after a farm working accident. Management of post-traumatic mucormycoses consists of a wide excision of the infected tissue, combined with immediate antifungal therapy. Liposomal amphotericin B is the recommended first line treatment. Few studies have evaluated the efficacy of posaconazole. All 3 patients received a surgical debridement and liposomal amphotericin B, which was followed by posaconazole in 2 cases. The duration of the antifungal treatment is not yet well defined. All three patients received a treatment of five weeks with a favorable outcome.

Differentiation and identification of filamentous fungi by high-throughput FTIR spectroscopic analysis of mycelia.

Routine identification of fungi based on phenotypic and genotypic methods can be fastidious and time-consuming. In this context, there is a constant need for new approaches allowing the rapid identification of molds. Fourier-transform infrared (FTIR) spectroscopy appears as such an indicated method. The objective of this work was to evaluate the potential of FTIR spectroscopy for an early differentiation and identification of filamentous fungi. One hundred and thirty-one strains identified using DNA sequencing, were analyzed using FTIR spectroscopy of the mycelia obtained after a reduced culture time of 48 h compared to current conventional methods. Partial least square discriminant analysis was used as a chemometric method to analyze the spectral data and for identification of the fungal strains from the phylum to the species level. Calibration models were constructed using 106 strains pertaining to 14 different genera and 32 species and were used to identify 25 fungal strains in a blind manner. Identification levels of 98.97% and 98.77% achieved were correctly assigned to the genus and species levels respectively. FTIR spectroscopy with its high discriminating power and rapidity therefore shows strong promise for routine fungal identification. Upgrading of our database is ongoing to test the technique's robustness.

Usefulness of matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry for identifying clinical Trichosporon isolates.

Trichosporon spp. have recently emerged as significant human pathogens. Identification of these species is important, both for epidemiological purposes and for therapeutic management, but conventional identification based on biochemical traits is hindered by the lack of updates to the species databases provided by the different commercial systems. In this study, 93 strains, or isolates, belonging to 16 Trichosporon species were subjected to both molecular identification using IGS1 gene sequencing and matrix-assisted laser desorption ionisation-time-of-flight (MALDI-TOF) analysis. Our results confirmed the limits of biochemical systems for identifying Trichosporon species, because only 27 (36%) of the isolates were correctly identified using them. Different protein extraction procedures were evaluated, revealing that incubation for 30 min with 70% formic acid yields the spectra with the highest scores. Among the six different reference spectra databases that were tested, a specific one composed of 18 reference strains plus seven clinical isolates allowed the correct identification of 67 of the 68 clinical isolates (98.5%). Although until recently it has been less widely applied to the basidiomycetous fungi, MALDI-TOF appears to be a valuable tool for identifying clinical Trichosporon isolates at the species level.

Reactivity of (1→3)-ß-d-glucan assay in bacterial bloodstream infections.

To diagnose invasive fungal infections, the detection of (1 → 3)-ß-d-glucan in serum has shown variable specificity, depending on the targeted population. Several circumstances for false-positive results of beta-glucan tests have been identified, among which are severe bacterial infections. In this study, we measured (1 → 3)-ß-d-glucan by the Fungitell test in the serum of 62 patients (one serum sample tested per patient) for whom invasive fungal infection was not suspected: 19 control subjects and 43 patients with bacteraemia. The test was interpretable for 58 sera: all 19 control subjects had negative beta-glucan test; among the 39 bacteraemic patients, we report 16 false-positive results. For the 22 patients undergoing bacteraemia due to Gram-negative bacilli, we observed 13 false-positive results (59%). Among the 17 patients with bloodstream infection involving Gram-positive cocci, three false-positive tests were recorded, but none in the eight cases of Streptococcus pneumoniae bacteraemia. Statistical analysis showed that beta-glucan levels were significantly higher in patients with Gram-negative bacilli bloodstream infection in comparison to those with bacteraemia due to Gram-positive cocci. These results were independent from other previously described causes for false-positive beta-glucan tests. These data might help physicians to interpret positive beta-glucan detection when an invasive fungal infection is suspected, especially for patients with bacterial infections.

In vitro susceptibility testing of Candida and Aspergillus spp. to voriconazole and other antifungal agents using Etest: results of a French multicentre study.

Minimum inhibitory concentrations (MICs) of the antifungal agent voriconazole were determined using the Etest and compared with those of amphotericin B, itraconazole and fluconazole using 1986 clinical isolates of Candida spp. Voriconazole MICs were also compared with those of amphotericin B and itraconazole using 391 clinical isolates of Aspergillus spp. Voriconazole was found to have more potent activity and lower MIC values than amphotericin B, itraconazole and fluconazole against C. albicans, C. tropicalis, C. parapsilosis and C. kefyr. Against C. glabrata and C. krusei, voriconazole was more active than either of the other two azole antifungals but had similar activity to amphotericin B. For species of Aspergillus, MIC values of voriconazole were lower than those of amphotericin B and itraconazole against A. fumigatus and A. flavus, and were similar to those of amphotericin B against A. niger. Against A. terreus, MIC values for voriconazole and itraconazole were similar. A. terreus is known to be resistant to amphotericin B, and this was reflected in higher MIC values compared with those of voriconazole and itraconazole. Voriconazole therefore compares very favourably with other antifungal agents against a large number of clinical isolates of Candida and Aspergillus spp.

Respiratory diseases in French cork workers.

A cross-sectional study on suberosis was conducted in the Champagne-Ardenne County, France, to determine the prevalence of respiratory symptoms, the level of pulmonary function, and the presence of precipitins against Penicillium frequentans. Thirteen of the 33 workers exposed to cork dust had respiratory symptoms excluding hypersensitivity pneumonitis. The respiratory symptoms were not correlated with tobacco habits or duration of exposure. The levels of pulmonary function were not significantly impaired. No precipitin arc against Penicillium frequentans was found in the sera of exposed workers. The varied symptomatology of suberosis may point to several different diseases, each with its own determining factor. In the present study, exposure to weak humidity and low level of cork dust were related to asthma and chronic bronchitis only, excluding hypersensitivity pneumonitis.

Use of Fourier-transform infrared spectroscopy for typing of Candida albicans strains isolated in intensive care units.

Comparative studies of Candida albicans strains are essential for proving cross-infections in epidemiological investigations. Typing of C. albicans strains is mainly based on genotypic methods. Fourier-transform infrared (FTIR) spectroscopy is described in this study as a novel phenotypic approach to the typing of C. albicans. The first step in the approach was the standardization of sample preparation (culture conditions and sampling parameters) and acquisition and classification parameters (spectral acquisition, spectral window selection, classification algorithm, and heterogeneity threshold). The second step consisted of validating the established parameters with a set of 79 strains of C. albicans isolated over 4 months from nine patients hospitalized in two intensive care units. Strains were isolated from multiple anatomical sites with repeated sampling. FTIR spectroscopy results were compared to randomly amplified polymorphic DNA (RAPD) results; this analysis showed that the amplification patterns of strains isolated from a given patient were identical and that different patients had different profiles. FTIR spectroscopy data were analyzed by hierarchical clustering performed with the second-derivative spectra. This classification revealed nine groups, one per patient. Only one spectrum out of 79 was misclassified by the FTIR spectroscopy method. RAPD and FTIR spectroscopy results were in good agreement, showing that, when nosocomial candidiasis transmission is suspected and urgent information is needed, this technique may be useful as a quick identification tool to give solid clues before confirmation by a genotypic method.

Evaluation of the fungitest kit by using strains from human immunodeficiency virus-infected patients: study of azole drug susceptibility.

One hundred eighteen Candida clinical isolates from human immunodeficiency virus-infected patients were tested for their susceptibilities to fluconazole and itraconazole by Fungitest and the National Committee for Clinical Laboratory Standards MIC method. Fungitest results depended on both yeast species and antifungal agents. This test is able to detect sensitive strains (97% agreement with results of the MIC method in tests with fluconazole and 84% agreement in tests with itraconazole) but has a poor capacity to detect resistant strains (26% agreement in tests with fluconazole and 5% agreement in tests with itraconazole).

[Characterization of specific IgG, IgM, IgA and IgE isotypes in profound candidiasis]. / Caractérisation des isotypes spécifiques IgG, IgM, IgA et IgE dans les candidoses profondes.

Enzyme-linked immunofiltration assay technique (Elisa) has been applied to the characterization of G, M, A and E anti-Candida antibodies isotypes specific to cell wall mannans in 201 sera from 126 patients. These sera were studied at the same time using Co-immunoelectrodiffusion and indirect immunofluorescence. In 18 of 21 patients with systemic candidiasis, Elisa demonstrated the presence of antimannan IgG antibodies in sera contemporary of Candida positive blood culture. These IgG were associated with antimannan IgM, A and E in 15 patients. In 37 patients colonized with Candida, used as negative controls, antimannan IgG were detected in 3 cases, and in 2 were associated with specific IgMs. The sensitivity and specificity of Elisa IgM and IgA in the diagnosis of systemic Candidiasis were 85.7% and 81%, respectively. The kinetic study shows that the different isotypes appeared most of the time simultaneously. The evolution of the 4 isotypes beyond the acute episode was variable and without correlation with the clinical status. The decrease of IgG was slower than the one of IgM, IgA or IgE. The systematic research, in at risk patients, of antimannan antibodies using Elisa required simple technology. A simple method should allow to aim at other functional antigens which could be used in a quantitative manner to determine the efficacy of the medical treatment.

Accelerated detection of DNA on membranes by automated enzyme-linked immunofiltration assay.

Methods used to detect DNA after transfer to nitro-cellulose or nylon membranes are all based on slow incubation with agitation. We describe an application of the ELIFA technique (enzyme-linked immunofiltration assay) for rapid detection of DNA immobilized on a membrane by active filtration of the reagents across the membrane. The different steps (saturation, hybridization to a nonisotopically labeled probe, washing, and immunoenzymatic revelation) are automated and controlled by a microcomputer that determines the direction of flow and flow rates of the solutions through the membrane. We applied this method to the detection of Toxoplasma gondii DNA in 108 samples of amniotic fluid during antenatal tests for toxoplasmosis and compared the results with those obtained by the conventional method. In addition to a major time saving (2 h against almost 15 h), automation improves reproducibility and avoids manipulation of the membranes between the different steps, while keeping the same sensitivity and specificity as the standard method.

Characterization of specific anti-Candida IgM, IgA and IgE: diagnostic value in deep-seated infections.

The proposed serological diagnosis of systemic Candida infections is based on a microplate immunocapture technique detecting IgM, IgA and IgE anti-Candida antibodies. Activity is revealed with a suspension of human erythrocytes sensitized with somatic antigen of Candida albicans, and is quantified on an automated plate reader. The sera were obtained from patients with deep-seated (n = 56) and superficial (n = 193) candidosis. We compared this immunological method with a combination of indirect immunofluorescence and co-immunoelectrodiffusion. The immunocapture method was more sensitive (80.4% vs. 48.2% with indirect immunofluorescence and 58.9% with co-immunoelectrodiffusion), and often provided the diagnosis at an earlier stage, with clear therapeutic advantages. The IgA isotype was a particularly valuable marker of deep-seated Candida infections.

Genotyping human and bovine isolates of Cryptosporidium parvum by polymerase chain reaction-restriction fragment length polymorphism analysis of a repetitive DNA sequence.

In order to define transmission routes of cryptosporidiosis and develop markers that distinguish Cryptosporidium parvum isolates, we have identified 2 polymorphic restriction enzyme sites in a C. parvum repetitive DNA sequence. The target sequence was amplified by polymerase chain reaction from 100 to 500 oocysts and the amplified product was subjected to restriction enzyme digestion. Typing of 23 isolates showed that 10/10 calf isolates had the same profile. In contrast, 2 patterns were observed among human isolates: 7/13 displayed the calf profile, and 6/13 presented another pattern. The PCR-RFLP assay described here is a sensitive tool to distinguish C. parvum isolates.

Early neonatal diagnosis of congenital toxoplasmosis: value of comparative enzyme-linked immunofiltration assay immunological profiles and anti-Toxoplasma gondii immunoglobulin M (IgM) or IgA immunocapture and implications for postnatal therapeutic strategies.

Diagnostic strategies for congenital toxoplasmosis have changed profoundly in recent years. Immunological diagnostic methods, long considered disappointing, can now be used at a very early stage. Over a 3-year period, 1,050 infants at risk of congenital toxoplasmosis (born to 1,048 mothers infected during pregnancy) were monitored for a minimum of 12 months and a maximum of 7 years. More than 6,000 serum specimens were analyzed by comparative mother-infant immunological profiles (CIPs) based on an enzyme-linked immunofiltration assay (ELIFA) and an immunocapture method for the detection of specific immunoglobulin M (IgM) and IgA. IgG antibodies were also titrated. One hundred three cases of congenital toxoplasmosis were demonstrated. The CIP-ELIFA method had a better diagnostic yield (sensitivity, 90%) than specific IgM and/or IgA detection by immunocapture assay (sensitivity, 77%). By using a combination of these tests, congenital infection was diagnosed in the first month and the first 3 months of life in 90 and 94% of infants with toxoplasmosis, respectively, with a specificity of 99.8% and a positive predictive value of 99% at 8 months of age. This dual diagnostic approach (ELIFA and IgM-IgA immunocapture) is highly efficient and has important implications for therapy. Indeed, early postnatal diagnosis based on objective evidence enables therapy with pyrimethamine-sulfadoxine to be started immediately for 24 months, while spiramycin (which used to be given preventively for 9 to 12 months to all infants at risk) can be stopped after the first 3 months of life.

Detection of Toxoplasma gondii in immunodeficient subjects by gene amplification: influence of therapeutics.

Polymerase chain reaction (PCR) technology was used to detect Toxoplasma gondii DNA in 253 immunodeficient subjects, 179 of whom were infected with the human immunodeficiency virus (HIV). The incidence of toxoplasmosis was 12.3% (22/179) in the HIV-infected subjects and 2.7% (2/74) in the remainder. The sensitivity of the PCR during episodes of toxoplasmosis in HIV-infected subjects not on antiparasitic treatment was 86.6% on peripheral blood and 60% on cerebrospinal fluid (CSF), but was only 25% and 16.7%, respectively, in subjects receiving specific treatment or prophylaxis against Pneumocystis carinii. Among the HIV-seronegative population, six patients undergoing anticancer chemotherapy were PCR positive on bronchoalveolar lavage fluid but did not develop pulmonary toxoplasmosis, suggesting transient carriage.

[Extrinsic allergic alveolitis of occupational origin]. / Les alvéolites allergiques extrinsèques d'origine professionnelle.

Occupational factors encountered in farming and other agricultural activities produce a particular risk for respiratory diseases. For some, such as extrinsic allergic alveolitis, diagnosis depends upon a range of epidemiological, clinical, radiological and immunological arguments. Farmer's lung is one of the most common form of extrinsic allergic alveolitis. Bird breeder's lung is another, the list is long. The environmental allergens likely to affect alveoli and interstitial tissues have been identified, but simple detection of antibodies does not constitute a pathognomonic criterion of extrinsic allergic alveolitis. Co-immuno-electrodiffusion is a rapid and sensitive technique for the demonstration of remarkable precipitating systems of extrinsic allergic alveolitis. This investigation enables subjects who really have the disease to be distinguished from contact subjects. Diagnosis is important to prevent development of a disabling and irreversible pulmonary fibrosis.

[Value and limitations of anti-mannan antibodies research by co-immunoelectrodiffusion in the diagnosis of deep candidiasis]. / Intérêt et limites de la recherche des anticorps anti-mannane par co-immunoélectrodiffusion dans le diagnostic des candidoses profondes.

Several groups have evaluated detection of antibodies against Candida, with somewhat conflicting results. In this study, co-counterimmunoelectrodiffusion was used to detect antimannan antibodies specific of components of the Candida membrane. Study patients were divided into two groups according to whether their history for Candida infection was negative (population A, n = 102) or positive (population B). Different antigen levels were used in order to differentiate low and high antimannan antibody levels. Among the 102 sera in population A, 42 were positive for antimannan antibodies; the antimannan antibody titer was low in 40 cases and high in 2 cases. In population B (53 patients), antimannan antibodies were found in 97 of the 98 sera studied; titers were high in 95 cases. Use of an antigen level that detects only high titers of antimannan antibodies thus provides a sensitive and specific tool for the diagnosis of deep candidiasis. The simplicity and rapidity of this test are particularly valuable in situations where emergency treatment is needed.