The diagnosis of schistosomiasis currently relies on microscopic detection of schistosome eggs in stool or urine samples and serological assays. The poor sensitivity of standard microscopic procedures performed in routine laboratories, makes molecular detection methods of increasing interest. The aim of the study was to evaluate two in-house real-time Schistosoma PCRs, targeting respectively S. mansoni [Sm] and S. haematobium [Sh] in excreta, biopsies and sera as potential tools to diagnose active infections and to monitor treatment efficacy. Schistosoma PCRs were performed on 412 samples (124 urine, 86 stools, 8 biopsies, 194 sera) from patients with suspected schistosomiasis, before anti-parasitic treatment. Results were compared to microscopic examination and serological assays (enzyme-linked immunosorbent assay (ELISA), indirect haemagglutination (HA) and Western Blot (WB) assay). Compared to microscopy, PCRs significantly increased the sensitivity of diagnosis, from 4% to 10.5% and from 33.7% to 48.8%, for Sh in urine and Sm in stools, respectively. The overall sensitivity of PCR on serum samples was 72.7% and reached 94.1% in patients with positive excreta (microscopy). The specificity of serum PCR was 98.9%. After treatment, serum PCR positivity rates slowly declined from 93.8% at day 30 to 8% at day 360, whereas antibody detection remained positive after 1 year. Schistosoma PCRs clearly outperform standard microscopy on stools and urine and could be part of reference methods combined with WB-based serology, which remains a gold standard for initial diagnosis. When serological assays are positive and microscopy is negative, serum PCRs provide species information to guide further clinical exploration. Biomarkers such as DNA and antibodies are of limited relevance for early treatment monitoring but serum PCR could be useful when performed at least 1 year after treatment to help confirm a cured infection. Schistosomiasis is one of the most important human parasitic neglected tropical diseases. It is a major source of morbidity and mortality in Africa but also in South America, the Caribbean, the Middle East, and Asia. It is transmitted by skin penetration of schistosome cercariae via contact with freshwater. Schistosoma mansoni and S. haematobium are the most common species and are frequent causes of infection in travelers and migrants returning from endemic areas. Chronic infections with these two species can cause irreversible damage to the liver or genitourinary tract. Diagnosis mainly relies on serological screening and microscopic procedures from urine and stool specimens that can, however, fail to detect low parasite burden and depend on operator competence. So there is a need to improve the detection of this disease. With this retrospective study, we evaluate the accuracy of a specific Schistosoma PCR assay for the diagnosis of schistosomiasis on a large cohort of migrants and travelers returning from endemic areas. Our study showed that PCR, a technique allowing Schistosoma DNA amplification and detection, greatly improved the diagnosis of both parasite species in urine, feces and biopsies. We also demonstrate that the detection of circulating Schistosoma DNA in blood by PCR is useful to confirm schistosomiasis diagnosis, to provide a species identification when the microscopy research is negative and to monitor the treatment efficacy.

(1) Background: The diagnosis of invasive aspergillosis (IA) in an intensive care unit (ICU) remains a challenge and the COVID-19 epidemic makes it even harder. Here, we evaluated Aspergillus PCR input to help classifying IA in SARS-CoV-2-infected patients. (2) Methods: 45 COVID-19 patients were prospectively monitored twice weekly for Aspergillus markers and anti-Aspergillus serology. We evaluated the concordance between (I) Aspergillus PCR and culture in respiratory samples, and (II) blood PCR and serum galactomannan. Patients were classified as putative/proven/colonized using AspICU algorithm and two other methods. (3) Results: The concordance of techniques applied on respiratory and blood samples was moderate (kappa = 0.58 and kappa = 0.63, respectively), with a higher sensitivity of PCR. According to AspICU, 9/45 patients were classified as putative IA. When incorporating PCR results, 15 were putative IA because they met all criteria, probably with a lack of specificity in the context of COVID-19. Using a modified AspICU algorithm, eight patients were classified as colonized and seven as putative IA. (4) Conclusion: An appreciation of the fungal burden using PCR and Aspergillus serology was added to propose a modified AspICU algorithm. This proof of concept seemed relevant, as it was in agreement with the outcome of patients, but will need validation in larger cohorts.

Invasive pulmonary aspergillosis (IPA) in intensive care unit patients is a major concern. Influenza-associated acute respiratory distress syndrome (ARDS) and severe COVID-19 patients are both at risk of developing invasive fungal diseases. We used the new international definitions of influenza-associated pulmonary aspergillosis (IAPA) and COVID-19-associated pulmonary aspergillosis (CAPA) to compare the demographic, clinical, biological, and radiological aspects of IAPA and CAPA in a monocentric retrospective study. A total of 120 patients were included, 71 with influenza and 49 with COVID-19-associated ARDS. Among them, 27 fulfilled the newly published criteria of IPA: 17/71 IAPA (23.9%) and 10/49 CAPA (20.4%). Kaplan–Meier curves showed significantly higher 90-day mortality for IPA patients overall (p = 0.032), whereas mortality did not differ between CAPA and IAPA patients. Radiological findings showed differences between IAPA and CAPA, with a higher proportion of features suggestive of IPA during IAPA. Lastly, a wide proportion of IPA patients had low plasma voriconazole concentrations with a higher delay to reach concentrations > 2 mg/L in CAPA vs. IAPA patients (p = 0.045). Severe COVID-19 and influenza patients appeared very similar in terms of prevalence of IPA and outcome. The dramatic consequences on the patients’ prognosis emphasize the need for a better awareness in these particular populations.

The indoor air quality of healthcare and care facilities is poorly studied. The aim of this study was to qualitatively and quantitatively describe the chemical pollution and the microbiological contaminations of the indoor environment of these facilities. Methods: A wide range of chemical compounds (39 volatile and 13 semi-volatile organic compounds, carbon dioxide, fine particulate matter) and microorganisms (fungi and bacteria) were studied. Sampling campaigns were conducted in two French cities in summer 2018 and winter 2019 in six private healthcare facilities (general practitioner’s offices, dental offices, pharmacies) and four care facilities (nursing homes). Results: The highest median concentrations of chemical compounds (μg/m³) were measured for alcohols (ethanol: 378.9 and isopropanol: 23.6), ketones (acetone: 18.8), aldehydes (formaldehyde: 11.4 and acetaldehyde: 6.5) and terpenes (limonene: 4.3). The median concentration of PM_2.5 was 9.0 µg/m³. The main bacteria of these indoor environments were Staphylococcus, Micrococcus and Bacillus genera, with median bacterial concentrations in the indoor air of 14 cfu/m³. The two major fungal genera were Cladosporium and Penicillium, with median fungal concentrations of 7 cfu/m³. Conclusions: Indoor air in healthcare and care facilities contains a complex mixture of many pollutants found in higher concentrations compared to the indoor air in French hospitals in a previous study.

Azole-resistant Aspergillus fumigatus (ARAf) has emerged worldwide during the last decades. Drug pressure after long term treatments of chronically infected patients and the propagation of environmental clones selected under the pressure of imidazoles fungicides used in agriculture and farming both account for this emergence. The objectives of this study were to determine the rate of azole resistance in Aspergillus fumigatus during a 5-year period, taking into account (i) differences between underlying diseases of the patients treated, (ii) cross-resistance between azoles, and (iii) focusing on the 5-year evolution of our center’s cystic fibrosis cohort. Overall, the rates of voriconazole (VRC)-resistant and itraconazole (ITC)-resistant A. fumigatus isolates were 4.1% (38/927) and 14.5% (95/656), respectively, corresponding to 21/426 (4.9%) and 44/308 (14.3%) patients, respectively. Regarding cross-resistance, among VRC-R isolates tested for ITC, nearly all were R (20/21;95%), compared to only 27% (20/74) of VRC-R among ITC-R isolates. The level of azole resistance remained somewhat stable over years but greatly varied according to the azole drug, patient origin, and clinical setting. Whereas azole resistance during invasive aspergillosis was very scarce, patients with cystic fibrosis were infected with multiple strains and presented the highest rate of resistance: 5% (27/539) isolates were VRC-R and 17.9% (78/436) were ITC-R. These results underline that the interpretation of the azole resistance level in Aspergilllus fumigatus in a routine setting may consider the huge variability depending on the azole drug, the clinical setting, the patient background and the type of infection.