Sputum production and salivary microbiome in COVID-19 patients reveals oral-lung axis.

SARS-CoV-2, a severe respiratory disease primarily targeting the lungs, was the leading cause of death worldwide during the pandemic. Understanding the interplay between the oral microbiome and inflammatory cytokines during acute infection is crucial for elucidating host immune responses. This study aimed to explore the relationship between the oral microbiome and cytokines in COVID-19 patients, particularly those with and without sputum production. Saliva and blood samples from 50 COVID-19 patients were subjected to 16S ribosomal RNA gene sequencing for oral microbiome analysis, and 65 saliva and serum cytokines were assessed using Luminex multiplex analysis. The Mann-Whitney test was used to compare cytokine levels between individuals with and without sputum production. Logistic regression machine learning models were employed to evaluate the predictive capability of oral microbiome, salivary, and blood biomarkers for sputum production. Significant differences were observed in the membership (Jaccard dissimilarity: p = 0.016) and abundance (PhILR dissimilarity: p = 0.048; metagenomeSeq) of salivary microbial communities between patients with and without sputum production. Seven bacterial genera, including Prevotella, Streptococcus, Actinomyces, Atopobium, Filifactor, Leptotrichia, and Selenomonas, were more prevalent in patients with sputum production (p<0.05, Fisher's exact test). Nine genera, including Prevotella, Megasphaera, Stomatobaculum, Selenomonas, Leptotrichia, Veillonella, Actinomyces, Atopobium, and Corynebacteria, were significantly more abundant in the sputum-producing group, while Lachnoanaerobaculum was more prevalent in the non-sputum-producing group (p<0.05, ANCOM-BC). Positive correlations were found between salivary IFN-gamma and Eotaxin2/CCL24 with sputum production, while negative correlations were noted with serum MCP3/CCL7, MIG/CXCL9, IL1 beta, and SCF (p<0.05, Mann-Whitney test). The machine learning model using only oral bacteria input outperformed the model that included all data: blood and saliva biomarkers, as well as clinical and demographic variables, in predicting sputum production in COVID-19 subjects. The performance metrics were as follows, comparing the model with only bacteria input versus the model with all input variables: precision (95% vs. 75%), recall (100% vs. 50%), F1-score (98% vs. 60%), and accuracy (82% vs. 66%).

Difference in formation of a dental multi-species biofilm according to substratum direction.

OBJECTIVES: The aim of this study was to investigate the difference in dental biofilm formation according to substratum direction, using an artificial biofilm model. METHODS: A three-species biofilm, consisting of Streptococcus mutans, Streptococcus oralis, and Actinomyces naeslundii, was formed on saliva-coated hydroxyapatite (sHA) discs oriented in three directions: downward (the discs placed in the direction of gravity), vertical (the discs placed parallel to the direction of gravity), and upward (the discs placed in opposite direction of gravity). The biofilms at 22 h and 46 h of age were analyzed using microbiological and biochemical methods, fluorescence-based assays, and scanning electron microscopy to investigate difference in bacterial adhesion, early and mature biofilm formation. RESULTS: The biofilms formed in the upward direction displayed the most complex structure, with the highest number and biovolume of bacteria, as well as the lowest pH conditions at both time points. The vertical and downward directions, however, had only scattered and small bacterial colonies. In the 22-h-old biofilms, the proportion of S. oralis was similar to, or slightly higher than, that of S. mutans in all directions of substratum surfaces. However, in the 46-h-old biofilms, S. mutans became the dominant bacteria in all directions, especially in the vertical and upward directions. CONCLUSIONS: The direction of the substratum surface could impact the proportion of bacteria and cariogenic properties of the multi-species biofilm. Biofilms in an upward direction may exhibit a higher cariogenic potential, followed by those in the vertical and downward directions, which could be related to gravity.

Intestinal Bacteria Fluctuating in Early-Stage Colorectal Cancer Carcinogenesis are Associated with Diet in Healthy Adults.

This hospital-based, cross-sectional study aimed to explore the association between diet and fluctuating intestinal bacteria in early-stage colorectal cancer (CRC) (Atopobium parvulum, Actinomyces odontolyticus, Solobacterium moorei, and Bifidobacterium longum). Healthy participants (n = 212) who underwent total colonoscopy at National Cancer Center Hospital (Tokyo, Japan) were divided into two groups according to the relative abundance of bacteria in their feces: those in the top 25% of relative bacterial abundance as cases and the bottom 25% as controls. The participants were divided into three groups (low, medium, and high) according to their intake of food groups associated with CRC. Multivariable logistic regression analysis was conducted to estimate the association between dietary intake and higher relative abundance of bacteria. Dairy products were inversely associated with a higher relative abundance of A. parvulum, A. odontolyticus, and S. moorei, with odds ratios (high vs. low) and 95% confidence interval as follows: 0.16 (0.06-0.44), 0.25 (0.08-0.82), and 0.29 (0.11-0.78), respectively. Additionally, dietary fiber was inversely associated with a higher relative abundance of S.moorei (0.29 [0.11-0.78]). No association was observed between diet and B.longum. In conclusion, healthy adults with a higher intake of dairy products and fiber had lower odds of having a higher relative abundance of CRC-associated microbiota.

Molecular basis for dual functions in pilus assembly modulated by the lid of a pilus-specific sortase.

The biphasic assembly of Gram-positive pili begins with the covalent polymerization of distinct pilins catalyzed by a pilus-specific sortase, followed by the cell wall anchoring of the resulting polymers mediated by the housekeeping sortase. In Actinomyces oris, the pilus-specific sortase SrtC2 not only polymerizes FimA pilins to assemble type 2 fimbriae with CafA at the tip, but it can also act as the anchoring sortase, linking both FimA polymers and SrtC1-catalyzed FimP polymers (type 1 fimbriae) to peptidoglycan when the housekeeping sortase SrtA is inactive. To date, the structure-function determinants governing the unique substrate specificity and dual enzymatic activity of SrtC2 have not been illuminated. Here, we present the crystal structure of SrtC2 solved to 2.10-Å resolution. SrtC2 harbors a canonical sortase fold and a lid typical for class C sortases and additional features specific to SrtC2. Structural, biochemical, and mutational analyses of SrtC2 reveal that the extended lid of SrtC2 modulates its dual activity. Specifically, we demonstrate that the polymerizing activity of SrtC2 is still maintained by alanine-substitution, partial deletion, and replacement of the SrtC2 lid with the SrtC1 lid. Strikingly, pilus incorporation of CafA is significantly reduced by these mutations, leading to compromised polymicrobial interactions mediated by CafA. In a srtA mutant, the partial deletion of the SrtC2 lid reduces surface anchoring of FimP polymers, and the lid-swapping mutation enhances this process, while both mutations diminish surface anchoring of FimA pili. Evidently, the extended lid of SrtC2 enables the enzyme the cell wall-anchoring activity in a substrate-selective fashion.

Skin and Soft Tissue Actinomycosis in Children and Adolescents.

BACKGROUND: Pediatric actinomycosis studies are limited to case reports or small case series. In this retrospective cohort study, we aimed to describe characteristics of skin and soft tissue actinomycosis in adolescents and children. METHODS: We conducted the study from January 2019 to December 2022, including patients ≤21 years of age with at least 1-year follow-up data. All clinical cultures obtained under sterile conditions with Actinomyces growth were included. RESULTS: One hundred four patients met inclusion criteria; median age 19 (interquartile range: 17-20) years, 68.3% female, 46.2% Black and 47.1% Hispanic. The median antibiotic treatment duration was 10 (7-10) days, and majority of patients received treatment with non-first-line Actinomyces antibiotics. Infectious disease consultation was requested for only 7 patients during their initial skin and soft tissue actinomycosis treatment. One-third of the patients with skin and soft tissue actinomycosis had documented recurrence within a median of 10 (interquartile range: 6-16) months of the initial episode. Monobacterial culture growth (85.7% vs. 63.8%, P = 0.02), patients with body mass index >25 (75% vs. 52.6%, P = 0.04) and patients with prior abscess in the same area (18.8% vs. 51.4%, P = 0.001) were significantly higher in patients with recurrent actinomycosis compared to the nonrecurrent group. In a univariate logistic regression model, they were found to be significantly associated with recurrence; monobacterial growth [odds ratio (OR): 3.4; 95% confidence interval (CI): 1.2-9.9], body mass index >25 (OR: 2.7; 95% CI, 1.1-7.0) and prior abscess (OR: 4.6; 95% CI: 1.9-11.2). CONCLUSIONS: Our study results highlight the importance of considering Actinomyces species in skin and soft tissue infections, especially in recurrent ones, and risk factors for recurrence. Suboptimal antibiotic utilization, very low numbers of consultations with infectious diseases and high recurrence rate suggest that providers should be informed and updated regarding this rare but hard-to-treat infection.

Pullenvalenes A-D: Nitric Oxide-Mediated Transcriptional Activation (NOMETA) Enables Discovery of Triterpene Aminoglycosides from Australian Termite Nest-Derived Fungi.

We report on the use of nitric oxide-mediated transcriptional activation (NOMETA) as an innovative means to detect and access new classes of microbial natural products encoded within silent biosynthetic gene clusters. A small library of termite nest- and mangrove-derived fungi and actinomyces was subjected to cultivation profiling using a miniaturized 24-well format approach (MATRIX) in the presence and absence of nitric oxide, with the resulting metabolomes subjected to comparative chemical analysis using UPLC-DAD and GNPS molecular networking. This strategy prompted study of Talaromyces sp. CMB-TN6F and Coccidiodes sp. CMB-TN39F, leading to discovery of the triterpene glycoside pullenvalenes A-D (1-4), featuring an unprecedented triterpene carbon skeleton and rare 6-O-methyl-N-acetyl-d-glucosaminyl glycoside residues. Structure elucidation of 1-4 was achieved by a combination of detailed spectroscopic analysis, chemical degradation, derivatization and synthesis, and biosynthetic considerations.

Tongue-Coating Microbial and Metabolic Characteristics in Halitosis.

Halitosis is a common oral condition, which leads to social embarrassment and affects quality of life. Cumulative evidence has suggested the association of tongue-coating microbiome with the development of intraoral halitosis. The dynamic variations of tongue-coating microbiota and metabolites in halitosis have not been fully elucidated. Therefore, the present study aimed to determine the tongue-coating microbial and metabolic characteristics in halitosis subjects without other oral diseases using metagenomics and metabolomics analysis. The participants underwent oral examination, halitosis assessment, and tongue-coating sample collection for the microbiome and metabolome analysis. It was found that the microbiota richness and diversity were significantly elevated in the halitosis group. Furthermore, species from Actinomyces, Prevotella, Veillonella, and Solobacterium were significantly more abundant in the halitosis group. However, the Rothia and Streptococcus species exhibited opposite tendencies. Eleven Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched in the halitosis tongue coatings, including cysteine and methionine metabolism. Functional genes related to sulfur, indole, skatole, and cadaverine metabolic processes (such as serA, metH, metK and dsrAB) were identified to be more abundant in the halitosis samples. The metabolome analysis revealed that indole-3-acetic, ornithine, and L-tryptophan were significantly elevated in the halitosis samples. Furthermore, it was observed that the values of volatile sulfur compounds and indole-3-acetic abundances were positively correlated. The multiomics analysis identified the metagenomic and metabolomic characteristics to differentiate halitosis from healthy individuals using the least absolute shrinkage and selection operator logistic regression and random forest classifier. A total of 19 species and 39 metabolites were identified as features in halitosis patients, which included indole-3-acetic acid, Bacillus altitudinis, Candidatus Saccharibacteria, and Actinomyces species. In conclusion, an evident shift in microbiome and metabolome characteristics was observed in the halitosis tongue coating, which may have a potential etiological significance and provide novel insights into the mechanism for halitosis.

Appendecular actinomycosis: A case series of 14 patients.

OBJECTIVE: This study aims to assess the clinical, radiological, and histological characteristics of Actinomyces infection identified in appendectomy specimens. MATERIAL AND METHODS: Between January 2013 and November 2023, 5834 patients underwent appendectomy in our clinic, and their pathology reports were retrospectively reviewed. RESULTS: Actinomyces appendicites were reported in 14 specimens (0.23%). It was determined that appendectomy was performed in only 10 patients (71.4%), ileocecal resection was performed in two patients (14.2%) and right hemicolectomy in two patients (14.2%). The operations on five patients were performed by laparoscopy, and the operations on the other nine patients were performed by open surgery. Laparoscopy was started in three patients and converted to open surgery due to suspicion of an ileocecal mass and cecal perforation. It was found that the white blood cell count of three patients was within the normal range of reference (8-9.77mg/dL); leukocytosis was detected in other patients (10.2-18.7mg/dL). C-reactive protein was normal in one patient and high in the rest of the patients. While the first-hour erythrocyte sedimentation rate was normal in five patients, it was found to be high in the other patients. Findings on radiological imaging were reported as acute appendicitis, appendicular plastron, and ileocecal mass. As a result of the pathology findings, the patients were given oral penicillin or semi-synthetic penicillin derivatives during one month. CONCLUSION: Ileocecal and appendecular actinomycosis are rare, and preoperative diagnosis is difficult. A definitive diagnosis is usually made after a histopathological examination. After surgery, long-term antimicrobial treatment of the patient is possible with penicillin.

A rare case report of liver masses caused by Actinomyces species.

Actinomycosis is a rare infection caused by Actinomyces spp. Of all actinomycosis infections, only 5% of Hepatic Actinomycosis (HA) infection has been reported. This disease is often misdiagnosed as a malignancy. This case report presents a 45-year-old woman with diabetes, initially suspected of intrahepatic cholangiocarcinoma, but after careful tissue staining, we found the results supported HA infection.

Effect of Precursors and Their Regulators on the Biosynthesis of Antibiotics in Actinomycetes.

During the life activities of microorganisms, a variety of secondary metabolites are produced, including antimicrobials and antitumor drugs, which are widely used in clinical practice. In addition to exploring new antibiotics, this makes it one of the research priorities of Actinomycetes to effectively increase the yield of antibiotics in production strains by various means. Most antibiotic-producing strains have a variety of functional regulatory factors that regulate their growth, development, and secondary metabolite biosynthesis processes. Through the study of precursor substances in antibiotic biosynthesis, researchers have revealed the precursor biosynthesis process and the mechanism by which precursor synthesis regulators affect the biosynthesis of secondary metabolites, which can be used to obtain engineered strains with high antibiotic production. This paper summarizes the supply of antibiotic biosynthesis precursors and the progress of research on the role of regulators in the process of precursors in biosynthesis. This lays the foundation for the establishment of effective breeding methods to improve antibiotic yields through the manipulation of precursor synthesis genes and related regulators.

[Skin abscess caused by Actinomyces radingae]. / Hautabszess verursacht durch Actinomyces radingae.

We report a 77-year-old man with a skin abscess caused by Actinomyces radingae. Targeted antibiotic therapy with amoxicillin/clavulanic acid for 6 weeks resulted in clearing of the infection. A. radingae is a rare pathogenic agent of skin and soft tissue infections. As with other Actinomyces infections, the early identification of the pathogen and specific antibiotic therapy is crucial for successful resolution of the infection because of the chronic course and the long treatment time needed. Usually, A. radingae is sensitive to ß­lactam antibiotics.

Actinomyces-induced Osteomyelitis of the Mandible - A Rare Disease?

BACKGROUND: Actinomyces species are commensal oral cavity flora that can cause jaw osteomyelitis. Osteomyelitis of the jaw by Actinomyces is rare, and its presentation can be confused with many different pathologies. CASE PRESENTATION: This is the case of a 61-year-old female with breast cancer and on chemotherapy as well as non-invasive carcinoma of the tongue who initially presented to the dentist with white spots in the right mandible near the incisors associated with right mandible pain and swelling. Actinomyces-induced osteomyelitis of the mandible was diagnosed. The patient was treated with penicillin V for 6 weeks along with a course of hyperbaric oxygen therapy, which resulted in the complete resolution of the infection. CONCLUSION: In summary, jaw osteomyelitis caused by Actinomyces should always be part of the differential diagnosis; as these organisms are commensal flora. The symptoms manifested are non-specific, and such a diagnosis could be easily missed, resulting in delay of care and disease progression.

Screening biosurfactant-producing actinomycetes: Identification of Streptomyces sp. RP1 as a potent species for bioremediation.

This study aimed to isolate biosurfactant-producing and hydrocarbon-degrading actinomycetes from different soils using glycerol-asparagine and starch-casein media with an antifungal agent. The glycerol-asparagine agar exhibited the highest number of actinomycetes, with a white, low-opacity medium supporting pigment production and high growth. Biosurfactant analyses, such as drop collapse, oil displacement, emulsification, tributyrin agar test, and surface tension measurement, were conducted. Out of 25 positive isolates, seven could utilize both olive oil and black oil for biosurfactant production, and only isolate RP1 could produce biosurfactant when grown in constrained conditions with black oil as the sole carbon source and inducer, demonstrating in situ bioremediation potential. Isolate RP1 from oil-spilled garden soil is Gram-staining-positive with a distinct earthy odor, melanin formation, and white filamentous colonies. It has a molecular size of ~621 bp and 100% sequence similarity to many Streptomyces spp. Morphological, biochemical, and 16 S rRNA analysis confirmed it as Streptomyces sp. RP1, showing positive results in all screenings, including high emulsification activity against kerosene (27.2%) and engine oil (95.8%), oil displacement efficiency against crude oil (7.45 cm), and a significant reduction in surface tension (56.7 dynes/cm). Streptomyces sp. RP1 can utilize citrate as a carbon source, tolerate sodium chloride, resist lysozyme, degrade petroleum hydrocarbons, and produce biosurfactant at 37°C in a 15 mL medium culture, indicating great potential for bioremediation and various downstream industrial applications with optimization.

Empyema caused by Actinomyces odontolyticus: A case report.

RATIONALE: Actinomyces odontolyticus causes a rare, chronic granulomatous infection that is frequently associated with immunocompromised states. A odontolyticus can cause infection in multiple organs, but empyema is rare. PATIENT CONCERNS: We report a case of empyema caused by A odontolyticus. The patient was a 64-year-old man. He was admitted to the hospital with a 5-day history of fever and dyspnea. He had caries and sequelae of cerebral apoplexy. DIAGNOSES: Metagenome next generation sequencing of pleural effusion was positive for A odontolyticus. Pathogen was identified by biphasic culture of pleural effusion fluid. INTERVENTIONS: According to the drug sensitivity test, linezolid 0.6 g twice daily and clindamycin 0.6 g 3 times a day were administered intravenously. Thoracic drainage was initially performed, but the drainage was not sufficient. Medical thoracoscopy was performed to fully drain the pleural effusion. OUTCOMES: After anti-infection and medical thoracoscopic therapy, the symptoms of this patient improved. LESSONS: Microbial metagenome sequencing can find pathogens that are difficult to culture by traditional methods. Adequate drainage was the key to the treatment of empyema. Medical thoracoscopy was recommended to remove the pleural effusion and spoilage when thoracic drainage is difficult. The common clinical features of A odontolyticus include a mass or swelling, abdominal disease, dental disease, and subcutaneous abscesses. Microbial metagenome sequencing can find pathogens that are difficult to culture by traditional methods. Adequate drainage was the key to the treatment of empyema. Medical thoracoscopy was recommended to remove the pleural effusion and spoilage when thoracic drainage is difficult.

Intramedullary spinal cord abscess involving Actinomyces and Streptococcus: a case report and literature review.

INTRODUCTION: Intramedullary spinal cord abscesses (ISCA) are rare and caused by central nervous system infections. Although polymicrobial infections are rarely seen in ISCAs, isolation of the causative pathogen is important for treatment. Here, we describe a very rare case of ISCA resulting from a mixed Streptococcus and Actinomyces infection. CASE PRESENTATION: An 82-year-old man presented with acute posterior cervical pain and progressive quadriplegia. Radiological investigations revealed a mass lesion showing marginal enhancement at the level of the C3-4 vertebrae. Microsurgical drainage was performed, and Streptococcus and Actinomyces were identified as causative agents. Subsequent antibiotic treatment was noted to be beneficial to the patient. DISCUSSION: This case suggests that mixed infection can develop into ISCA depending on the causative agents such as Actinomyces. Prompt pathogen-directed antibacterial therapy is required for ISCA treatment.

A Case of Thoracic Empyema Caused by Actinomyces naeslundii.

BACKGROUND Actinomycosis is a clinically significant but uncommon infectious disease caused by anaerobic commensals of Actinomyces species, and the incidence of thoracic empyema is rare. We report an extremely rare case of empyema caused by Actinomyces naeslundii (A. naeslundii). CASE REPORT A 39-year-old man presented to our hospital with fever and dyspnea. He had massive pleural effusion and was diagnosed with a left lower-lobe abscess and left thoracic empyema. Thoracic drainage was performed and Ampicillin/Sulbactam was administered for 3 weeks. Four years later, the patient presented with back pain, and chest X-ray showed increased left pleural effusion. After close examination, malignant pleural mesothelioma was suspected, and computed tomography-guided needle biopsy was performed, which yielded a viscous purulent pleural effusion with numerous greenish-yellow sulfur granules. A. naeslundii was identified through anaerobic culture. Thoracoscopic surgery of the empyema cavity was conducted, and Ampicillin/Sulbactam followed by Amoxicillin/Clavulanate was administered for approximately 6 months. No recurrence has been observed for 1 year since the surgical procedure. CONCLUSIONS Actinomyces empyema is a rare condition, and this case is the second reported occurrence of empyema caused by A. naeslundii. The visual identification of sulfur granules contributed to the diagnosis. Long-term antibiotic therapy plays a crucial role in treatment.

Brain abscess caused by Actinomyces turicensis in a non-immunocompromised adult patient: a case report and systematic review of the literature.

BACKGROUND: Actinomyces turicensis is rarely responsible of clinically relevant infections in human. Infection is often misdiagnosed as malignancy, tuberculosis, or nocardiosis, therefore delaying the correct identification and treatment. Here we report a case of a 55-year-old immunocompetent adult with brain abscess caused by A. turicensis. A systematic review of A. turicensis infections was performed. METHODS: A systematic review of the literature was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The databases MEDLINE, Embase, Web of Science, CINAHL, Clinicaltrials.gov and Canadian Agency for Drugs and Technology in Health (CADTH) were searched for all relevant literature. RESULTS: Search identified 47 eligible records, for a total of 67 patients. A. turicensis infection was most frequently reported in the anogenital area (n = 21), causing acute bacterial skin and skin structure infections (ABSSSI) including Fournier's gangrene (n = 12), pulmonary infections (n = 8), gynecological infections (n = 6), cervicofacial district infections (n = 5), intrabdominal or breast infections (n = 8), urinary tract infections (n = 3), vertebral column infections (n = 2) central nervous system infections (n = 2), endocarditis (n = 1). Infections were mostly presenting as abscesses (n = 36), with or without concomitant bacteremia (n = 7). Fever and local signs of inflammation were present in over 60% of the cases. Treatment usually involved surgical drainage followed by antibiotic therapy (n = 51). Antimicrobial treatments most frequently included amoxicillin (+clavulanate), ampicillin/sulbactam, metronidazole or cephalosporins. Eighty-nine percent of the patients underwent a full recovery. Two fatal cases were reported. CONCLUSIONS: To the best of our knowledge, we hereby present the first case of a brain abscess caused by A. turicensis and P. mirabilis. Brain involvement by A. turicensis is rare and may result from hematogenous spread or by dissemination of a contiguous infection. The infection might be difficult to diagnose and therefore treatment may be delayed. Nevertheless, the pathogen is often readily treatable. Diagnosis of actinomycosis is challenging and requires prompt microbiological identification. Surgical excision and drainage and antibiotic treatment usually allow for full recovery.