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Strict anaerobes are undeniably important residents of the cystic fibrosis (CF) lung but are still unknowns. The main objectives of this study were to describe anaerobic bacteria diversity in CF airway microbiota and to evaluate the association with lung function. An observational study was conducted during eight months. A hundred and one patients were enrolled in the study, and 150 sputum samples were collected using a sterile sample kit designed to preserve anaerobic conditions. An extended-culture approach on 112 sputa and a molecular approach (quantitative PCR targeting three of the main anaerobic genera in CF lung: Prevotella, Veillonella, and Fusobacterium ) on 141 sputa were developed. On culture, 91.1% of sputa were positive for at least one anaerobic bacterial species, with an average of six anaerobic species detected per sputum. Thirty-one anaerobic genera and 69 species were found, which is the largest anaerobe diversity ever reported in CF lungs. Better lung function (defined as Forced Expiratory Volume in one second > 70%) was significantly associated with higher quantification of Veillonella . These results raise the question of the potential impact of anaerobes on lung function.

COVID-19 is characterized by respiratory symptoms of various severities, ranging from mild upper respiratory signs to acute respiratory failure/acute respiratory distress syndrome associated with a high mortality rate. However, the pathophysiology of the disease is largely unknown. Shotgun metagenomics from nasopharyngeal swabs were used to characterize the genomic, metagenomic and transcriptomic features of patients from the first pandemic wave with various forms of COVID-19, including outpatients, patients hospitalized not requiring intensive care, and patients in the intensive care unit, to identify viral and/or host factors associated with the most severe forms of the disease. Neither the genetic characteristics of SARS-CoV-2, nor the detection of bacteria, viruses, fungi or parasites were associated with the severity of pulmonary disease. Severe pneumonia was associated with overexpression of cytokine transcripts activating the CXCR2 pathway, whereas patients with benign disease presented with a T helper “Th1-Th17” profile. The latter profile was associated with female gender and a lower mortality rate. Our findings indicate that the most severe cases of COVID-19 are characterized by the presence of overactive immune cells resulting in neutrophil pulmonary infiltration which, in turn, could enhance the inflammatory response and prolong tissue damage. These findings make CXCR2 antagonists, in particular IL-8 antagonists, promising candidates for the treatment of patients with severe COVID-19.

Shotgun metagenomics (SMg) usefulness for brain abscess diagnosis is not known. We describe a case of brain abscess diagnosed with SMg and provide a review of the literature. A 70-year-old woman was diagnosed with multiple brain abscesses. Standard culture techniques and 16S rRNA gene sequencing of abscess samples remained negative. SMg finally revealed the presence of sequences from Streptococcus anginosus and Fusobacterium nucleatum, leading to antimicrobial treatment adaptation and corticosteroids initiation. The patient finally recovered. A literature review retrieved fifteen other cases of brain abscesses diagnosed with SMg. SMg results led to changes in patient management in most cases. The existing literature about the performances of SMg, its advantages, future evolutions, and limitations is then discussed. SMg place in routine should be evaluated and defined through prospective studies.

Diagnosis of prosthetic Joint Infections (PJI) remains challenging at the microbiological level. Despite the implementation and adoption of new methods, an heterogeniety of microbiological practices is still observed. These CRIOGO recommendations (Centre de Référence des Infections Ostéo-articulaires du Grand Ouest) aim to set out some basic principles for the diagnosis of PJI in microbiology laboratories. The CRIOGO microbiologists’ team who have been working together for 15 years were invited to provide regional recommendations for microbiology diagnosis based on their practical expertise. These recommendations were developed through a systematic review of the literature and discussion amongst experts. The proposed CRIOGO recommendations were voted on upon by a 10 local panelists via the Delphi process. Total consensus was reached on all 27 recommendations that received 100% agreement. The CRIOGO microbiologists’ team proposed practical guidelines in response to the most frequently asked questions received at our laboratory reference centres. A short, comprehensive answer supported by literature backs up the argument. Out of the 27 detailed CRIOGO recommendations, 22 achieved 100% consensus. This work was initiated to harmonise our daily practices for managing PJI diagnosis within the CRIOGO network in line with the literature.

The sex gap is well-documented in respiratory diseases such as cystic fibrosis and chronic obstructive pulmonary disease. While the differences between males and females in prevalence, severity and prognosis are well-established, the pathophysiology of the sex difference has been poorly characterized to date. Over the past 10 years, metagenomics-based studies have revealed the presence of a resident microbiome in the respiratory tract and its central role in respiratory disease. The lung microbiome is associated with host immune response and health outcomes in both animal models and patient cohorts. The study of the lung microbiome is therefore an interesting new avenue to explore in order to understand the sex gap observed in respiratory diseases. Another important parameter to consider is the gut-lung axis, since the gut microbiome plays a crucial role in distant immune modulation in respiratory diseases, and an intestinal “microgenderome” has been reported: i.e., sexual dimorphism in the gut microbiome. The microgenderome provides new pathophysiological clues, as it defines the interactions between microbiome, sex hormones, immunity and disease susceptibility. As research on the microbiome is increasing in volume and scope, the objective of this review was to describe the state-of-the-art on the sex gap in respiratory medicine (acute pulmonary infection and chronic lung disease) in the light of the microbiome, including evidence of local (lung) or distant (gut) contributions to the pathophysiology of these diseases.

Point-of-care syndromic PCR (POC SPCR) assays are useful tools for the rapid detection of the most common causative agents of community-acquired infections responsible for meningitis and encephalitis infections. We evaluated the performance characteristics of the new QIAstat-Dx® Meningitis/Encephalitis panel (QS) compared to the laboratory reference methods and the POC SPCR Biofire® FilmArray® Meningitis Encephalitis Panel (FA). Viral (Enterovirus, Parechovirus, HSV-1, HSV-2, HHV-6, VZV) and bacterial (E. coli K1, H. influenzae, L. monocytogenes, encapsulated N. meningitidis, M. pneumoniae, S. agalactiae, S. pneumoniae, S. pyogenes) pathogens were suspended at low concentrations and tested with the POC SPCR systems. The reproducibility, analytical specificity, carryover contamination, interferences and clinical samples were evaluated. All samples tested positive with both QS and FA except for those containing the lowest concentrations of Enterovirus-D68-B3, Echovirus-30 and S. agalactiae which were only detected by FA. In terms of analytical specificity, we observed 3 false positive results out of 48 QS tests versus 1 out of 37 FA tests. For the other studied criteria, both QS and FA performed as expected. Our results suggest that the performance characteristics of QS are close to those of FA. A prospective multicenter study would be useful to complete the performances evaluation of QS.

Bacteria belonging to the genus Achromobacter are increasingly isolated from respiratory samples of people with cystic fibrosis (PWCF). The management of this multidrug-resistant genus is challenging and characterised by a lack of international recommendations, therapeutic guidelines and data concerning antibiotic susceptibility, especially concerning the newer antibiotics. The objective of this study was to describe the antibiotic susceptibility of Achromobacter isolates from PWCF, including susceptibility to new antibiotics. The minimum inhibitory concentrations (MICs) of 22 antibiotics were determined for a panel of 23 Achromobacter isolates from 19 respiratory samples of PWCF. Two microdilution MIC plates were used: EUMDROXF® plate (Sensititre) and Micronaut-S Pseudomonas MIC® plate (Merlin) and completed by a third method if necessary (E-test® or UMIC®). Among usual antimicrobial agents, the most active was imipenem (70% susceptibility). Trimethoprim-sulfamethoxazole, piperacillin and tigecycline (65%, 56% and 52% susceptibility, respectively) were still useful for the treatment of Achromobacter infections. Among new therapeutic options, β-lactams combined with a β-lactamase-inhibitor did not bring benefits compared to β-lactam alone. On the other hand, cefiderocol appeared as a promising therapeutic alternative for managing Achromobacter infections in PWCF. This study provides the first results on the susceptibility of clinical Achromobacter isolates concerning new antibiotics. More microbiological and clinical data are required to establish the optimal treatment of Achromobacter infections.

The importance and abundance of strict anaerobic bacteria in the respiratory microbiota of people with cystic fibrosis (PWCF) is now established through studies based on high-throughput sequencing or extended-culture methods. In CF respiratory niche, one of the most prevalent anaerobic genera is Prevotella, and particularly the species Prevotella melaninogenica. The objective of this study was to evaluate the antibiotic susceptibility of this anaerobic species. Fifty isolates of P. melaninogenica cultured from sputum of 50 PWCF have been included. Antibiotic susceptibility testing was performed using the agar diffusion method. All isolates were susceptible to the following antibiotics: amoxicillin/clavulanic acid, piperacillin/tazobactam, imipenem and metronidazole. A total of 96% of the isolates (48/50) were resistant to amoxicillin (indicating beta-lactamase production), 34% to clindamycin (17/50) and 24% to moxifloxacin (12/50). Moreover, 10% (5/50) were multidrug-resistant. A significant and positive correlation was found between clindamycin resistance and chronic azithromycin administration. This preliminary study on a predominant species of the lung “anaerobiome” shows high percentages of resistance, potentially exacerbated by the initiation of long-term antibiotic therapy in PWCF. The anaerobic resistome characterization, focusing on species rather than genera, is needed in the future to better prevent the emergence of resistance within lung microbiota.

Data on the genomics of Porphyromonas species other than Porphyromonas gingivalis (POTG), particularly within pulmonary environments, are scarce. In this study, we conducted whole genome sequencing (WGS) on pulmonary isolates of POTG, specifically P. catoniae (n=3), P. pasteri (n=1), and P. uenonis (n=2), from people with cystic fibrosis. These genomic analyses were complemented with antimicrobial susceptibility tests for these strains. We compared the genomic sequences of these pulmonary isolates with those of previously characterized Porphyromonas species. Our study revealed a distinct clade differentiation between non-pigmented and pigmented Porphyromonas species. Interestingly, unlike P. gingivalis, the pulmonary POTG strains lacked known virulence genes, except a putative hemolysin gene. Regarding antibiotic resistance, notable resistances were limited to vancomycin in P. catoniae and clindamycin in P. uenonis. These findings support the hypothesis that POTG species may predominantly behave as commensals in the lung environment rather than as pathogens. Porphyromonas constitutes a prevalent genus of anaerobic bacteria within the respiratory tract. Despite its ubiquity, the precise taxonomic delineation of Porphyromonas species implicated in respiratory conditions needs to be better defined, as most microbiome analyses report results only at the genus level. Consequently, data about these pulmonary species often default to associations with Porphyromonas gingivalis, a well-characterized oral pathogen. In this study, we sequenced the complete genomes of six Porphyromonas strains isolated from the airway microbiota of people with cystic fibrosis (CF) to enhance the representation and identification of Porphyromonas other than gingivalis (POTG) species. Our phylogenomic analysis aimed to elucidate the diversity within pulmonary POTG. Notably, genomes of the commensal species Porphyromonas catoniae isolated from CF patients did not harbor virulence genes typically associated with P. gingivalis. Additionally, phenotypic resistance profiling against nine clinically relevant antibiotics revealed low resistance levels, notwithstanding the frequent antibiotic treatments administered to CF patients. Our findings provide compelling evidence for the non-pathogenic role of these POTG species in the pulmonary environment. Six Porphyromonas genomes generated in this study are available in the Sequence Read Archive and GenBank databases under BioProject accession PRJEB75658. The raw data set generated during the current study is available in the European Nucleotide Archive (repository with the project accession number. The authors confirm that all supporting data, code, and protocols have been provided within the article or through supplementary data files.

Plain English summary Patient-oriented research (POR) has received increasing attention in recent years. In this approach, patients’ experiential knowledge, derived from their experiences of living with a condition or illness and of interacting with the healthcare system, is recognized, valued, and seen as complementary to scientific knowledge. Early career researchers (ECRs) are the next generation of researchers, but little is known about how they perceive POR. In this study, ECRs were invited to reflect on what POR is, how patients can best contribute to research, and ECRs’ own role in developing POR. Using a technique designed to collect expert opinions and find consensus—the Delphi method—a panel of 16 ECRs responded, in three rounds, to three questionnaires, with the second and third being built on responses to the preceding ones. Based on their understanding, the panelists agreed that the most important element in defining POR would be valuing, mobilizing, and legitimizing the experiential knowledge of patients who live with a particular health condition. Panelists considered patients to be integral members of the research team, but were less convinced that they should be considered co-researchers. The panelists saw themselves as taking part in developing POR by sharing information, teaching, and encouraging POR among their peers, as well as by participating actively in organizations interested in POR. This is the first study to examine the perspectives of ECRs, who, along with many others, have an important role in supporting the on-going development of POR so that it becomes more widely adopted. Background Literature on patient-oriented research (POR) is growing rapidly. This field is increasingly encouraged by funders and structured by new research networks. POR involves moving away from considering patients as ‘subjects’, towards perceiving them as experts with experience-based knowledge. However, little is known about how early-career researchers (ECRs) perceive POR and their roles in developing it. This study examined how ECRs perceive POR, patients’ roles, the future of POR, and their own role in developing this approach. Methods A three-round Delphi study was conducted with Quebec’s Strategy for People and Patient-Oriented Research and Trials (SUPPORT) Unit awardees, composed of graduate students and clinicians, all ECRs. Of the 25 invited, 18 agreed to participate (72%), with a three-round retention rate of 89% ( n  = 16 on 18). Panelists answered open-ended questions, selected the most salient statements, and rated their (dis)agreement with proposals using a 7-point scale. Results Five main themes emerged: 1) ECRs’ knowledge of and experience with POR; 2) the POR definition; 3) patients’ roles and contributions; 4) the future of POR; and 5) ECRs’ roles in POR development. This study revealed that the ECRs were not so familiar with POR, even given their opportunities for networking within a scholarship program. Panelists agreed on the main components of a POR definition: valuing, mobilizing, and legitimizing the experiential knowledge of patients living with a health condition; conducting research that focuses on patients’ concerns, participation, and outcomes; and integrating active partnership among a variety of actors. Panelists considered patients to be integral members of the research team (M = 5.31 ± 1.66), but were less convinced they should be considered co-researchers (M = 4.50 ± 1.75). Panelists saw themselves as playing many roles in developing POR, such as becoming well-informed about it and acting as knowledge brokers, motivators, doers, delegators, and activists. Conclusion The ECRs’ perspectives are informative on how the next generation of researchers envision POR, its future and how they might contribute to developing this approach. There is a clear need for a coherent and concerted strategy for POR capacity development, in which ECRs’ perspectives and their specific needs are taken into account.