Type 2-high asthma is associated with a specific indoor mycobiome and microbiome.

BACKGROUND: The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters. OBJECTIVE: The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA). METHODS: A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during "stable" or pulmonary "exacerbation" periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes. RESULTS: Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The ß-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation. CONCLUSION: These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma.

Toward the Standardization of Mycological Examination of Sputum Samples in Cystic Fibrosis: Results from a French Multicenter Prospective Study.

Fungal respiratory colonization of cystic fibrosis (CF) patients emerges as a new concern; however, the heterogeneity of mycological protocols limits investigations. We first aimed at setting up an efficient standardized protocol for mycological analysis of CF sputa that was assessed during a prospective, multicenter study: "MucoFong" program (PHRC-06/1902). Sputa from 243 CF patients from seven centers in France were collected over a 15-month period and submitted to a standardized protocol based on 6 semi-selective media. After mucolytic pretreatment, sputa were plated in parallel on cycloheximide-enriched (ACT37), erythritol-enriched (ERY37), benomyl dichloran-rose bengal (BENO37) and chromogenic (CAN37) media incubated at 37 °C and on Sabouraud-chloramphenicol (SAB27) and erythritol-enriched (ERY27) media incubated at 20-27 °C. Each plate was checked twice a week during 3 weeks. Fungi were conventionally identified; time for detection of fungal growth was noted for each species. Fungal prevalences and media performances were assessed; an optimal combination of media was determined using the Chi-squared automatic interaction detector method. At least one fungal species was isolated from 81% of sputa. Candida albicans was the most prevalent species (58.8%), followed by Aspergillus fumigatus (35.4%). Cultivation on CAN37, SAB27, ACT37 and ERY27 during 16 days provided an optimal combination, detecting C. albicans, A. fumigatus, Scedosporium apiospermum complex and Exophiala spp. with sensitivities of 96.5, 98.8, 100 and 100%. Combination of these four culture media is recommended to ensure the growth of key fungal pathogens in CF respiratory specimens. The use of such consensual protocol is of major interest for merging results from future epidemiological studies.

A summary of cryptosporidiosis outbreaks reported in France and overseas departments, 2017-2020.

Cryptosporidium is a known foodborne pathogen, ranked fifth out of 24 among foodborne parasites in terms of importance and a cause of many cryptosporidiosis outbreaks worldwide. In France, very few outbreaks were reported before 2017, and data recently obtained by the Expert Laboratory of the Cryptosporidiosis National Reference Center (CNR-LE-Cryptosporidiosis) have shown that outbreaks are in fact common and frequently underreported. In this work, we aim to report the characteristics of outbreaks detected in France during the period 2017-2020 and present a summary of investigations carried out by the CNR-LE-Cryptosporidiosis. During the study period, there were eleven cryptosporidiosis outbreaks, including three with no identified origin. Among the eight identified outbreaks: six were due to water contamination (five tap water and one recreational water), one was due to direct contact with infected calves, and one was due to consumption of contaminated curd cheese. Among these outbreaks, five of them exceeded one hundred cases. Recent results obtained by the CNR-LE-Cryptosporidiosis revealed the multiannual occurrence of Cryptosporidium outbreaks in France. Waterborne outbreaks were more frequently detected, while foodborne outbreaks which are more difficult to detect were likely underreported.

Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis.

Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. CF respiratory tract is now considered to be a polymicrobial niche and advances in high-throughput sequencing allowed to analyze its microbiota and mycobiota. However, no NGS studies until now have characterized both communities during CF pulmonary exacerbation (CFPE). Thirty-three sputa isolated from patients with and without CFPE were used for metagenomic high-throughput sequencing targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to highlight correlations in compositional data. The decline in respiratory function was associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida, and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as relevantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by the correlation network. For the first time, we included documented mycobiome data into a version of the ecological Climax/Attack model that opens new lines of thoughts about the physiopathology of CF lung disease and future perspectives to improve its therapeutic management.

The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis.

In recent years, the gut microbiota has been considered as a full-fledged actor of the gut-brain axis, making it possible to take a new step in understanding the pathophysiology of both neurological and psychiatric diseases. However, most of the studies have been devoted to gut bacterial microbiota, forgetting the non-negligible fungal flora. In this review, we expose how the role of the fungal component in the microbiota-gut-brain axis is legitimate, through its interactions with both the host, especially with the immune system, and the gut bacteria. We also discuss published data that already attest to a role of the mycobiome in the microbiota-gut-brain axis, and the impact of fungi on clinical and therapeutic research.

Mouse model of colonization of the digestive tract with Acinetobacter baumannii and subsequent pneumonia.

AIM: Implementing a mouse model of Acinetobacter baumannii (AB) digestive colonization and studying the propensity of an intestinal reservoir of AB to be at the origin of pneumonia. MATERIALS & METHODS: After a disruption of the digestive flora by piperacillin-tazobactam, two multidrug-resistant AB strains were intranasally inoculated to two cohorts of ten mice daily. For each strain, five mice were rendered transiently neutropenic. RESULTS & CONCLUSION: One strain persisted several weeks in the digestive tract, even after stopping piperacillin-tazobactam injections, leading to the hypothesis that some AB strains can authentically colonize the gut. Most of the immunocompromised mice experienced clinical signs and positive lung cultures, which were associated with positive spleen cultures, an argument in favor of bacterial translocation.

Early Detection of Schistosoma Egg-Induced Pulmonary Granulomas in a Returning Traveler.

We report the case of a French traveler who developed acute pulmonary schistosomiasis 2 months after visiting Benin. He presented with a 1-month history of fever, cough, and thoracic pain. Initial investigations revealed hypereosinophilia and multiple nodular lesions on chest computed tomography scan. Lung biopsies were performed 2 months later because of migrating chest infiltrates and increasing eosinophilia. Histological examination showed schistosomal egg-induced pulmonary granulomas with ova exhibiting a prominent terminal spine, resembling Schistosoma haematobium. However, egg shells were Ziehl-Neelsen positive, raising the possibility of a Schistosoma intercalatum or a Schistosoma guineensis infection. Moreover, involvement of highly infectious hybrid species cannot be excluded considering the atypical early pulmonary oviposition. This case is remarkable because of the rarity of pulmonary schistosomiasis, its peculiar clinical presentation and difficulties in making species identification. It also emphasizes the need to consider schistosomiasis diagnosis in all potentially exposed travelers with compatible symptoms.

The impact of performing bacterial identification and antimicrobial susceptibility testing on bronchoalveolar fluid cultures 24 h a day in a microbiology laboratory.

We previously demonstrated the positive impact of performing bacterial identification and antimicrobial susceptibility testing (AST) after day hours (night service [NS]) for certain clinical samples on the treatment of infected patients. Our objective was to evaluate the impact of including positive bronchoalveolar lavage (BAL) cultures in our NS. Two major positive consequences were recorded: initiation of earlier appropriate treatment and earlier change to a reduced-spectrum but still effective regimen. Reductions in delay were defined as the differences between the hours actually spent and hours estimated as though laboratory tests had been performed in the absence of NS. Fifty BALs were included. The NS led to the implementation of earlier appropriate therapy in 10 cases (20%), to earlier de-escalation in 15 cases (30%), and to earlier appropriate therapy and de-escalation in 4 cases (8%). In conclusion, performing bacterial identification and AST for positive BAL after laboratory opening hours could be relevant.