Dolosigranulum Pigrum Research Articles

Septic shock and death due to Dolosigranulum pigrum bacteremia: a case report.

We report the case of a 77-year-old Japanese woman with neuromyelitis optica spectrum disorder, treated with 15 mg of prednisolone daily, who presented with acute septic shock and altered consciousness due to Dolosigranulum pigrum bacteremia. Intravenous extracellular fluids and broad-spectrum antibiotics were administered as an initial treatment. However, the patient died shortly after admission. We performed 16S rRNA sequencing and analyzed the murJ gene. A phylogenetic tree constructed using the neighbor-joining method showed that the strain belonged to clade C3, according to the classification proposed by Flores Ramos et al. Although D. pigrum, a commensal bacterium of the upper respiratory tract, is rarely associated with infections, it occasionally causes serious infections. Accumulation of clinical and bacteriological data is crucial for understanding the pathogenicity and infections associated with this organism.

The Staphylococcus aureus-antagonizing human nasal commensal Staphylococcus lugdunensis depends on siderophore piracy

BackgroundBacterial pathogens such as Staphylococcus aureus colonize body surfaces of part of the human population, which represents a critical risk factor for skin disorders and invasive infections. However, such pathogens do not belong to the human core microbiomes. Beneficial commensal bacteria can often prevent the invasion and persistence of such pathogens by using molecular strategies that are only superficially understood. We recently reported that the commensal bacterium Staphylococcus lugdunensis produces the novel antibiotic lugdunin, which eradicates S. aureus from the nasal microbiomes of hospitalized patients. However, it has remained unclear if S. lugdunensis may affect S. aureus carriage in the general population and which external factors might promote S. lugdunensis carriage to enhance its S. aureus-eliminating capacity.ResultsWe could cultivate S. lugdunensis from the noses of 6.3% of healthy human volunteers. In addition, S. lugdunensis DNA could be identified in metagenomes of many culture-negative nasal samples indicating that cultivation success depends on a specific bacterial threshold density. Healthy S. lugdunensis carriers had a 5.2-fold lower propensity to be colonized by S. aureus indicating that lugdunin can eliminate S. aureus also in healthy humans. S. lugdunensis-positive microbiomes were dominated by either Staphylococcus epidermidis, Corynebacterium species, or Dolosigranulum pigrum. These and further bacterial commensals, whose abundance was positively associated with S. lugdunensis, promoted S. lugdunensis growth in co-culture. Such mutualistic interactions depended on the production of iron-scavenging siderophores by supportive commensals and on the capacity of S. lugdunensis to import siderophores.EJt4aqYa_PFzdC4ihACHg3Video ConclusionsThese findings underscore the importance of microbiome homeostasis for eliminating pathogen colonization. Elucidating mechanisms that drive microbiome interactions will become crucial for microbiome-precision editing approaches.

Lower respiratory tract microbiota in patients with clinically suspected nontuberculous mycobacterial pulmonary disease according to the presence of gastroesophageal reflux.

Although gastroesophageal reflux has been recognized as one of the risk factors of nontuberculous mycobacterial pulmonary disease (NTM-PD) progression, the effect of reflux on the lower respiratory tract microbiota has not been studied in detail. We investigated the composition of the lower respiratory tract microbiota in patients with clinically suspected NTM-PD, comparing them based on the presence of reflux. Forty-seven patients suspected of having NTM-PD were enrolled and assigned according to presence of reflux (n = 22) and non- reflux (n = 25). We performed a pepsin ELISA assay to identify the presence of reflux and 16S ribosomal RNA gene amplicon sequencing to evaluate the microbiota in bronchoalveolar lavage fluid. There were no significant differences in the diversity or composition of the lower respiratory microbiota between the NTM-PD and non-NTM-PD groups. Bacterial richness was observed in the non-reflux group than in the reflux group [P = 0.03] and a cluster in the reflux group was observed. The reflux group showed a predominance for Pseudomonas aeruginosa or Staphylococcus aureus among the NTM-PD group and for P. aeruginosa, Haemophilus influenzae, Klebsiella pneumoniae, or Eikenella species among the non-NTM-PD group. The non-reflux groups presented diverse patterns. A linear discriminant analysis and volcano plot demonstrated that P. aeruginosa, H. haemolyticus, Selenomonas artemidis, and Dolosigranulum pigrum were specifically associated with the NTM-PD reflux group, while P. aeruginosa was specifically associated with the non-NTM-PD reflux group. These observations confirm that the lower respiratory microbiota is consistently altered by reflux but not in NTM-PD.

Dolosigranulum savutiense sp. nov., isolated from human upper respiratory samples collected in Botswana.

Four strains (MSK211, MSK294T, MSK312, MSK433) of a novel Dolosigranulum species were cultured from nasopharyngeal swabs collected from mother-infant dyads in southern Botswana. These strains grew optimally on tryptic soy agar with 5% sheep blood solid medium and in fastidious bacteria broth. Colonies on tryptic soy agar with 5% sheep blood agar appeared grey or white with a flat, smooth surface and variable alpha haemolysis. Cells were Gram-positive, non-spore-forming, non-motile cocci that lacked catalase or oxidase activity. Major fatty acids were C16 : 0 (palmitic acid), C18 : 1 ω9c (oleic acid), and C18 : 0 (stearic acid). Analyses of 16S rRNA gene sequences identified these strains as belonging to the genus Dolosigranulum (family Carnobacteriaceae), which currently contains only a single validly published species (Dolosigranulum pigrum). Whole-genome sequencing revealed that the genomes of these strains are 1.98-2.07 Mbp in size and have a G+C content of 39.6-39.9 mol%. Comparisons of these genomes to publicly available genomes of D. pigrum yielded average nucleotide identities and in silico DNA-DNA hybridization values of 92.3-92.9% and 49.1-51.4%, respectively. These results indicate that these strains represent a novel species of Dolosigranulum, for which we propose the name Dolosigranulum savutiense sp. nov., with the type strain MSK294T (=DSM 117171T=JCM 36673T).

Nasopharyngeal microbiota in children is associated with severe asthma exacerbations

BackgroundThe respiratory microbiome has been associated with the etiology and disease course of asthma. ObjectiveThis study assessed the nasopharyngeal microbiota in children with a severe asthma exacerbation and their associations with medication, air quality and viral infection. MethodsA cross-sectional study was performed among children aged 2-18 years admitted to the medium (MCU; n=84) or intensive care (ICU; n=78) with an asthma exacerbation. For case-control analyses, we matched all cases aged 2-6 years (n=87) to controls in a 1:2 ratio. Controls were participants of either a prospective case-control study or a longitudinal birth cohort (n=182). The nasopharyngeal microbiome was characterized by 16S-rRNA-gene sequencing. ResultsCases showed higher Shannon diversity (ICU and MCU combined; p=0.002) and a distinct microbial community composition when compared to controls (PERMANOVA R2=1.9%, p<0.001). We observed significantly higher abundance of Staphylococcus and ‘oral’ taxa, including Neisseria, Veillonella and Streptococcus spp. and lower abundance of Dolosigranulum pigrum, Corynebacterium and Moraxella spp. (MaAsLin2, q<0.25) in cases versus controls. Furthermore, Neisseria abundance was associated with more severe disease (ICU vs MCU MaAslin2 p=0.03, q=0.30). Neisseria spp. abundance was also related with fine particulate matter exposure, whereas Haemophilus and Streptoccocus abundance was related with recent inhalation corticosteroid use. We observed no correlations with viral infection. ConclusionOur results demonstrate that children admitted with asthma exacerbations harbor a microbiome characterized by overgrowth of Staphylococcus and ‘oral’ microbes, and an underrepresentation of beneficial niche-appropriate commensals. Several of these associations may be explained by (environmental or medical) exposures, although cause-consequence relationships remain unclear and requires further investigations.

Dolosigranulum Pigrum Bacteremia in an Injecting Drug User Associated with Methicillin Resistant Staphylococcus Aureus Endocarditis and Fungal Endophthalmitis

Dolosigranulum pigrum is a commensal bacterium of the upper respiratory tract. We present a case of D. Pigrum bacteremia, identified incidentally in a patient with a history of injecting drug use (IDU), chronic hepatitis C (HCV) and partially treated methicillin resistant staphylococcus aureus (MRSA) endocarditis, who presented with acute monocular vision loss. Workup was consistent with unilateral fungal endophthalmitis. The patient was initially treated with intravenous Voriconazole, Ceftriaxone and linezolid for 4 weeks with resolution of his symptoms. This case highlights the emerging role of D. Pigrum as a pathogen in the immune compromised and specifically in the IDU population. This case further illustrates that although identification of fungal growth in vitreous fluid may include culture and PCR analysis, fungal endophthalmitis remains a clinical diagnosis and that fungal cultures have lower sensitivity.

Successful Use of Phage and Antibiotics Therapy for the Eradication of Two Bacterial Pathogens from the Respiratory Tract of an Infant.

Phage therapy can be a useful approach in a number of clinical cases associated with multidrug-resistant (MDR) bacterial infections. In this study, we describe a successful consecutive phage and antibiotic application to cure a 3-month-old girl suffering from severe bronchitis after tracheostomy. Bronchitis was associated with two bacterial agents, MDR Pseudomonas aeruginosa and a rare opportunistic pathogen Dolosigranulum pigrum. The phage cocktail "Pyobacteriophage" containing at least two different phages against isolated MDR P. aeruginosa strain was used via inhalation and nasal drops. Topical application of the phage cocktail removed most of P. aeruginosa cells and contributed to a change in the antimicrobial resistance profile of surviving P. aeruginosa cells. As a result, it became possible to choose and administer an appropriate antibiotic that was effective against both infectious agents. Complete recovery of the infant was recorded.

Screening Dolosigranulum pigrum Strains for Secreted Factors that InhibitStaphylococcus aureus

Abstract Background Staphylococcus aureus is a leading cause of community-associated and hospital-acquired infections, and methicillin-resistant S. aureus (MRSA) is a significant global health concern. Approximately 30% of the human population is asymptomatically colonized by S. aureus in the upper respiratory tract, with this colonization typically preceding respiratory infections caused by S. aureus. Dolosigranulum pigrum is a putatively beneficial bacterium that is a frequent colonizer of the human upper respiratory tract. The presence and abundance of D. pigrum in the upper respiratory tract has been negatively associated with S. aureus colonization among infants and young children. Additionally, in cocultivation experiments, D. pigrum has been shown to inhibit S. aureus growth, although the mechanisms for this antistaphylococcal activity have not been identified. Methods We hypothesized that D. pigrum strains secrete a protein factor that inhibits growth of S. aureus. To evaluate this hypothesis, we screened D. pigrum strains for antistaphylococcal activity using a plate-based cocultivation assay. Briefly, 5 µL aliquots of D. pigrum strains in liquid brain heart infusion (BHI) medium (OD600=0.3) were spotted onto a BHI agar plate and incubated at 37°C and 5% CO2 for 48 hours. Next, 5 µL aliquots of S. aureus strain Newman in liquid BHI medium (OD600=0.1) were spotted onto this plate at varying distances from the D. pigrum inocula and incubated at 37°C and 5% CO2 for an additional 24 hours. Secretion of an anti-staphylococcal factor was assessed based on the presence of a visible zone of inhibition between the D. pigrum and S. aureus inocula. We excised agar fragments adjacent to 4 inhibitory and 4 non-inhibitory D. pigrum strains and submitted these samples for liquid chromatography with tandem mass spectrometry (LC-MS/MS)-based proteomics. The proteomic data were searched against the TrEMBL D. pigrum database and a common contaminant/spiked protein database, and signal intensity values for identified peptides were quantified. Results Four of 43 (9%) D. pigrum strains screened in cocultivation assays consistently produced a zone of inhibition against S. aureus. We identified 531 unique proteins from proteomic analysis of agar fragments, including 28 D. pigrum proteins that were significantly more abundant in zones adjacent to inhibitory vs. non-inhibitory strains. The most differentially abundant protein was an S8 family serine protease (112 times more abundant in fragments adjacent to inhibitory strains). Using previously generated whole-genome sequencing data from these 43 D. pigrum strains, we found that the gene encoding this serine protease was present in 41 of 43 (95%) D. pigrum strains, including all 4 strains that were inhibitory in the cocultivation assay. The predicted active domain for the final protein was highly conserved across strains. Other secreted D. pigrum proteins that were more abundant in gel fragments adjacent to inhibitory strains included a peptidoglycan hydrolase and 7 uncharacterized D. pigrum proteins. Conclusion D. pigrum inhibits S. aureus growth in vitro through secretion of inhibitory factors in a strain-dependent manner. We identified an S8 family serine protease as a possible candidate mechanism for the anti-staphylococcal activity of D. pigrum. Future experiments will screen cell-free supernatants from inhibitory D. pigrum strains for S. aureus inhibition and evaluate the effect of protease inhibitor treatment on the antistaphylococcal activity of these supernatants.

Deciphering salivary microbiome signature in Crohn’s disease patients with different factors contributing to dysbiosis

Crohn's disease (CD) is a chronic inflammatory bowel disease. An imbalanced microbiome (dysbiosis) can predispose to many diseases including CD. The role of oral dysbiosis in CD is poorly understood. We aimed to explore microbiome signature and dysbiosis of the salivary microbiome in CD patients, and correlate microbiota changes to the level of inflammation. Saliva samples were collected from healthy controls (HC) and CD patients (n = 40 per group). Salivary microbiome was analyzed by sequencing the entire 16S rRNA gene. Inflammatory biomarkers (C-reactive protein and calprotectin) were measured and correlated with microbiome diversity. Five dominant species were significantly enriched in CD, namely Veillonella dispar, Megasphaera stantonii, Prevotella jejuni, Dolosigranulum pigrum and Lactobacillus backii. Oral health had a significant impact on the microbiome since various significant features were cariogenic as Streptococcus mutans or periopathogenic such as Fusobacterium periodonticum. Furthermore, disease activity, duration and frequency of relapses impacted the oral microbiota. Treatment with monoclonal antibodies led to the emergence of a unique species called Simonsiella muelleri. Combining immunomodulatory agents with monoclonal antibodies significantly increased multiple pathogenic species such as Salmonella enterica, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. Loss of diversity in CD was shown by multiple diversity indices. There was a significant negative correlation between gut inflammatory biomarkers (particularly calprotectin) and α-diversity, suggesting more inflammation associated with diversity loss in CD. Salivary dysbiosis was evident in CD patients, with unique microbiota signatures and perturbed species that can serve as disease biomarkers or potential targets for microbiota modulation. The interplay of various factors collectively contributed to dysbiosis, although each factor probably had a unique effect on the microbiome. The emergence of pathogenic bacteria in the oral cavity of CD patients is alarming since they can disturb gut homeostasis and induce inflammation by swallowing, or hematogenous spread of microbiota, their metabolites, or generated inflammatory mediators.

A Fatal Infection Caused by Dolosigranulum Pigrum in a Patient with Lung Cancer: A Case Report

Dolosogranulum Pigrum is a rare gram-positive catalase-negative coccus and a commensal organism residing in the upper respiratory tract that can cause fatal opportunistic infections in immunocompromised patients. In this report, we describe a case of a 62-year-old male patient affected by metastatic lung cancer treated with chemotherapy, radiotherapy and immunotherapy, who had dyspnea and positive blood cultures for the bacterium Dolosigranulum Pigrum, associated with bilateral interstitial pneumonia, initially confused with pneumonia related to SARS-CoV-2 infection. Although Dolosigranulum Pigrum appears to be very susceptible to current antibiotics, as ampicillin, ceftriaxone, levofloxacin, and vancomycin, it can cause serious infections in humans, particularly in patients with baseline pulmonary diseases, such as lung cancer, cystic fibrosis, and severe chronic obstructive pulmonary disease, until the patient’s death.

Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome

Dolosigranulum pigrum—a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 104D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.

Microbiological Profile of Infectious Keratitis During Covid-19 Pandemic.

The Covid-19 pandemic introduced significant changes in our daily life, including the widespread use of face masks. The purpose of this study was to assess if significant changes occurred in the microbiological profile of infectious keratitis. A retrospective study was performed, based on a survey review of the electronic medical records of all patients with presumed infectious keratitis, between March 2020 and October 2021. The microbiological isolates in this sample (pandemic group) were compared with those obtained in our center between 2009 and 2018 (pre-pandemic group). A total of 194 samples were included in the pandemic group. We obtained a culture-positivity rate of 43.3%, which was significantly higher when compared with the pre-pandemic data (35.15%, p = 0.033). Several further significant differences were found between the pandemic and the pre-pandemic groups: the proportion of bacteria, including gram-positive and gram-negative groups, was higher in our sample (pre-pandemic vs pandemic: 76.78% vs 83.33%, p = 0.010; 53.35% vs 60.71%, p = 0.016; 23.43% vs 34.52%, p = 0.005, respectively); two populations of Gram-positive bacteria found in this study were not isolated in the pre-pandemic sample - Dolosigranulum pigrum and Propionibacterium spp.; and two bacterial isolates were significantly increased in our sample - Corynebacterium spp. (18.41% vs 29.76%, p = 0.003) and Pseudomonas aeruginosa (9.00% vs 16.66%, p = 0.012). In conclusion, significant changes were found in the microbiological profile of infectious keratitis in our center during the Covid-19 pandemic. While these changes could be related to face mask use, more observational and experimental studies are needed to explore this possible association.

Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers

Nasal decolonization procedures against the opportunistic pathogen Staphylococcus aureus rely on topical antimicrobial drug usage, whose impact on the nasal microbiota is poorly understood. We examined this impact in healthy S. aureus carriers and noncarriers. This is a prospective interventional cohort study of 8 S. aureus carriers and 8 noncarriers treated with nasal mupirocin and chlorhexidine baths. Sequential nasal swabs were taken over 6 months. S. aureus was detected by quantitative culture and genotyped using spa typing. RNA-based 16S species-level metabarcoding was used to assess the living microbial diversity. The species Dolosigranulum pigrum, Moraxella nonliquefaciens and Corynebacterium propinquum correlated negatively with S. aureus carriage. Mupirocin treatment effectively eliminated S. aureus, D. pigrum and M. nonliquefaciens, but not corynebacteria. S. aureus recolonization in carriers occurred more rapidly than recolonization by the dominant species in noncarriers (median 3 vs. 6 months, respectively). Most recolonizing S. aureus isolates had the same spa type as the initial isolate. The impact of mupirocin-chlorhexidine treatment on the nasal microbiota was still detectable after 6 months. S. aureus recolonization predated microbiota recovery, emphasizing the strong adaptation of this pathogen to the nasal niche and the transient efficacy of the decolonization procedure.

Towards the human nasal microbiome: Simulating D. pigrum and S. aureus.

The human nose harbors various microbes that decisively influence the wellbeing and health of their host. Among the most threatening pathogens in this habitat is Staphylococcus aureus. Multiple epidemiological studies identify Dolosigranulum pigrum as a likely beneficial bacterium based on its positive association with health, including negative associations with S. aureus. Carefully curated GEMs are available for both bacterial species that reliably simulate their growth behavior in isolation. To unravel the mutual effects among bacteria, building community models for simulating co-culture growth is necessary. However, modeling microbial communities remains challenging. This article illustrates how applying the NCMW fosters our understanding of two microbes' joint growth conditions in the nasal habitat and their intricate interplay from a metabolic modeling perspective. The resulting community model combines the latest available curated GEMs of D. pigrum and S. aureus. This uses case illustrates how to incorporate genuine GEM of participating microorganisms and creates a basic community model mimicking the human nasal environment. Our analysis supports the role of negative microbe-microbe interactions involving D. pigrum examined experimentally in the lab. By this, we identify and characterize metabolic exchange factors involved in a specific interaction between D. pigrum and S. aureus as an in silico candidate factor for a deep insight into the associated species. This method may serve as a blueprint for developing more complex microbial interaction models. Its direct application suggests new ways to prevent disease-causing infections by inhibiting the growth of pathogens such as S. aureus through microbe-microbe interactions.

Microbial Metagenomics of the Extubated Lacrimal Stents Following Dacryocystorhinostomy: The Lacriome Paper 4.

To study the metagenome of the microbes present on the extubated lacrimal stents following a dacryocystorhinostomy. A prospective study was performed on 10 consecutive extubated lacrimal stents obtained for the metagenomic analysis from the patients following an endoscopic dacryocystorhinostomy. The stents were extubated at 4 weeks postoperatively under endoscopic guidance and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMeta pipeline or MG-RAST pipeline. The taxonomic hit distribution across the stent samples showed that bacteria were the most common isolates (mean, 69.70%), followed by viruses (mean, 0.02%) and archaea (0.003%). The 3 major phyla identified were Firmicutes, Actinobacteria, and Proteobacteria. The prevalent organisms include Pseudomonas aeruginosa, Staphylococcus aureus, Corynebacterium accolens, Dolosigranulum pigrum, Citrobacter koserii, Staphylococcus epidermidis, E. coli, and Hemophilus influenza . The functional subsystem profiling demonstrated microbial genes associated with metabolism, cellular, and information processing. The functional subsystem categories were metabolism involving carbohydrates, amino acids, DNA and RNA, cell wall or cell capsule biogenesis, membrane transport, virulence, and defense mechanisms. The present study is the first whole metagenome sequencing of the microbes isolated from the extubated lacrimal stents. The stents harbor diverse microbial communities with distinct ecosystem dynamics. Further studies on microbes-host interactions in the early postoperative period would provide valuable insights.

Whole-Genome Shotgun Sequencing for Nasopharyngeal Microbiome in Pre-school Children With Recurrent Wheezing.

Microbiome mediates early life immune deviation in asthma development. Recurrent wheeze (RW) in pre-school years is a risk factor for asthma diagnosis in school-age children. Dysbiosis exists in asthmatic airways, while its origin in pre-school years and relationship to RW is not clearly defined. This study investigated metagenomics of nasopharyngeal microbiome in pre-school children with RW. We applied whole-genome shotgun sequencing and human rhinovirus (HRV) detection on nasopharyngeal samples collected from three groups of pre-school children: (i) RW group: 16 children at-risk for asthma who were hospitalized for RW, (ii) inpatient control (IC): 18 subjects admitted for upper respiratory infection, and (iii) community control (CC): 36 children without respiratory syndromes. Sequence reads were analyzed by MetaPhlAn2 and HUMAnN2 algorithm for taxonomic and functional identification. Linear discriminant analysis effect size (LEfSe) analysis was used to identify discriminative features. We identified that Moraxella catarrhalis and Dolosigranulum pigrum were predominant species in nasopharynx. RW had lower alpha diversity (Shannon diversity index) than CC (0.48 vs. 1.07; Padj = 0.039), characterized by predominant Proteobacteria. LEfSe analysis revealed D. pigrum was the only discriminative species across groups (LDA = 5.57, P = 0.002), with its relative abundance in RW, IC, and CC being 9.6, 14.2, and 37.3%, respectively (P < 0.05). LEfSe identified five (ribo)nucleotides biosynthesis pathways to be group discriminating. Adjusting for HRV status, pre-school children with RW have lower nasopharyngeal biodiversity, which is associated with Proteobacteria predominance and lower abundance of D. pigrum. Along with discriminative pathways found in RW and CC, these microbial biomarkers help to understand RW pathogenesis.

The role of respiratory microbiota in the protection against viral diseases: respiratory commensal bacteria as next-generation probiotics for COVID-19.

On March 11, 2020, the World Health Organization declared a pandemic of coronavirus infectious disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and imposed the biggest public health challenge for our civilization, with unforeseen impacts in the subsequent years. Similar to other respiratory infections, COVID-19 is associated with significant changes in the composition of the upper respiratory tract microbiome. Studies have pointed to a significant reduction of diversity and richness of the respiratory microbiota in COVID-19 patients. Furthermore, it has been suggested that Prevotella, Staphylococcus, and Streptococcus are associated with severe COVID-19 cases, while Dolosigranulum and Corynebacterium are significantly more abundant in asymptomatic subjects or with mild disease. These results have stimulated the search for new microorganisms from the respiratory microbiota with probiotic properties that could alleviate symptoms and even help in the fight against COVID-19. To date, the potential positive effects of probiotics in the context of SARS-CoV-2 infection and COVID-19 pandemics have been extrapolated from studies carried out with other viral pathogens, such as influenza virus and respiratory syncytial virus. However, scientific evidence has started to emerge demonstrating the capacity of immunomodulatory bacteria to beneficially influence the resistance against SARS-CoV-2 infection. Here we review the scientific knowledge regarding the role of the respiratory microbiota in viral infections in general and in the infection caused by SARS-CoV-2 in particular. In addition, the scientific work that supports the use of immunomodulatory probiotic microorganisms as beneficial tools to reduce the severity of respiratory viral infections is also reviewed. In particular, our recent studies that evaluated the role of immunomodulatory Dolosigranulum pigrum strains in the context of SARS-CoV-2 infection are highlighted.

Dolosigranulum pigrum en absceso corneal

Dolosigranulum pigrum is a gram-positive, facultatively anaerobic coccus, which is part of the oral and upper respiratory tract microbiota. Although reports of infections by this microorganism are scarce, it has been associated with a wide spectrum of infectious diseases. The case of an elderly man with a lower corneal abscess, in which Dolosigranulum pigrum was isolated, is described. The microorganism was identified by mass spectrometry (MALDI-TOF MS) and by the sequencing of the 16S rRNA gene. Furthermore, the presumptive identification of the causative agent was achieved by using key phenotypic tests such as the cluster arrangement in Gram stain, the negative catalase test, the production of pyrrolidonyl arylamidase and leucine aminopeptidase activity, the growth in 6.5% NaCl and esculin hydrolysis. The data from the literature (and the present case) support the association of the microorganism with ocular infections, which often take a destructive course, mainly in elderly patients.

Application of nanopore sequencing in diagnosis of secondary infections in patients with severe COVID-19.

To explore the application value of nanopore sequencing technique in the diagnosis and treatment of secondary infections in patients with severe coronavirus disease 2019 (COVID-19). A total of 77 clinical specimens from 3 patients with severe COVID-19 were collected. After heat inactivation, all samples were subjected to total nucleic acid extraction based on magnetic bead enrichment. The extracted DNA was used for DNA library construction, then nanopore real-time sequencing detection was performed. The sequencing data were subjected to Centrifuge software database species matching and R program differential analysis to obtain potential pathogen identification. Nanopore sequencing results were compared with respiratory pathogen qPCR panel screening and conventional microbiological testing results to verify the effectiveness of nanopore sequencing detection. Nanopore sequencing results showed that positive pathogen were obtained in 44 specimens (57.1%). The potential pathogens identified by nanopore sequencing included , , and , et al. , , were also detected in clinical microbiological culture-based detection; was detected in respiratory pathogen screening qPCR panel; was only detected by the nanopore sequencing technique. Comprehensive considerations with the clinical symptoms, the patient was treated with antibiotics against , and the infection was controlled. Nanopore sequencing may assist the diagnosis and treatment of severe COVID-19 patients through rapid identification of potential pathogens.

Characterising clinical Staphylococcus aureus isolates from the sinuses of patients with chronic rhinosinusitis

The role of Staphylococcus aureus in the pathogenesis of the chronic sinonasal disease chronic rhinosinusitis (CRS), has not been definitively established. Comparative analyses of S. aureus isolates from CRS with those from control participants may offer insight into a possible pathogenic link between this organism and CRS. The intra- and inter-subject S. aureus strain-level diversity in the sinuses of patients with and without CRS were compared in this cross-sectional study. In total, 100 patients (CRS = 64, control = 36) were screened for S. aureus carriage. The overall carriage prevalence of S. aureus in this cohort was 24% (CRS n = 13, control n = 11). Cultured S. aureus isolates from 18 participants were strain-typed using spa gene sequencing. The bacterial community composition of the middle meatus was assessed using amplicon sequencing targeting the V3V4 hypervariable region of the bacterial 16S rRNA gene. S. aureus isolates cultured from patients were grown in co-culture with the commensal bacterium Dolosigranulum pigrum and characterised. All participants harboured a single S. aureus strain and no trend in disease-specific strain-level diversity was observed. Bacterial community analyses revealed a significant negative correlation in the relative abundances of S. aureus and D. pigrum sequences, suggesting an antagonistic interaction between these organisms. Co-cultivation experiments with these bacteria, however, did not confirm this interaction in vitro. We saw no significant associations of CRS disease with S. aureus strain types. The functional role that S. aureus occupies in CRS likely depends on other factors such as variations in gene expression and interactions with other members of the sinus bacterial community.