Multiple lung abscesses caused by Actinomyces graevenitzii mimicking acute pulmonary coccidioidomycosis

Anaerobic pathogens associated with OSA may contribute to pathophysiology via amino-acid depletion

BACKGROUND

The human microbiome is linked to multiple metabolic disorders such as obesity and diabetes. Obstructive sleep apnoea (OSA) is a common sleep disorder with several metabolic risk factors. We investigated the associations between the gut microbiome composition and function, and measures of OSA severity in participants from a prospective community-based cohort study: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

METHODS

Bacterial-Wide Association Analysis (BWAS) of gut microbiome measured via metagenomics with OSA measures was performed adjusting for clinical, lifestyle and co-morbidities. This was followed by functional analysis of the OSA-enriched bacteria. We utilized additional metabolomic and transcriptomic associations to suggest possible mechanisms explaining the microbiome effects on OSA.

FINDINGS

Several uncommon anaerobic human pathogens were associated with OSA severity. These belong to the Lachnospira, Actinomyces, Kingella and Eubacterium genera. Functional analysis revealed enrichment in 49 processes including many anaerobic-related ones. Severe OSA was associated with the depletion of the amino acids glycine and glutamine in the blood, yet neither diet nor gene expression revealed any changes in the production or consumption of these amino acids.

INTERPRETATION

We show anaerobic bacterial communities to be a novel component of OSA pathophysiology. These are established in the oxygen-poor environments characteristic of OSA. We hypothesize that these bacteria deplete certain amino acids required for normal human homeostasis and muscle tone, contributing to OSA phenotypes. Future work should test this hypothesis as well as consider diagnostics via anaerobic bacteria detection and possible interventions via antibiotics and amino-acid supplementation.

FUNDING

Described in methods.

Coexistence of COVID-19, Pseudomonas, and thoracic actinomycosis in a cystic bronchiectasis case

Actinomycosis often leads to cervicofacial infections, but thoracic involvement may also occur. However, the development of empyema is rare. While being followed up with the diagnosis of asthma and bronchiectasis, our case was hospitalized for infected bronchiectasis. As empyema developed in the follow-up, the pleural effusion was drained by tube thoracostomy. Actinomycosis was diagnosed through pleural effusion cytology. Growth of Pseudomonas aeruginosa was observed in sputum culture, and SARS-CoV2 RT-PCR was also positive in nasopharyngeal sampling. Polymicrobial agents can often be detected in actinomycosis. Actinomycosis cases have also been reported in the post-COVID period. Our case is presented since it would be the first in the literature regarding the coexistence of COVID-19, Pseudomonas, and thoracic Actinomycosis (empyema).

The diagnosis and management of pulmonary actinomycosis

Pulmonary actinomycosis is a rare infection caused by the bacterial species actinomyces. This paper aims to provide a comprehensive review of pulmonary actinomycosis to improve awareness and knowledge. The literature was analysed using databases including Pubmed, Medline and Embase from 1974 to 2021. After inclusion and exclusion, a total of 142 papers were reviewed. Pulmonary actinomycosis is a rare disease occurring in approximately 1 per 3,000,000 people annually. Historically, pulmonary actinomycosis was a common infection with high mortality; however, the infection has become rarer since the widespread use of penicillins. Actinomycosis is known as "the great masquerade"; however, it can be differentiated from other diseases with acid-fast negative ray-like bacilli and sulphur granules being pathognomonic. Complications of the infection include empyema, endocarditis, pericarditis, pericardial effusion, and sepsis. The mainstay of treatment is prolonged antibiotic therapy, with adjuvant surgery in severe cases. Future research should focus on multiple areas, including the potential risk secondary to immunosuppression from newer immunotherapies, the utility of newer diagnostic techniques and ongoing surveillance post-therapy.

Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential

Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify^® Platform (Illumina^® Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.

Pulmonary Actinomyces graevenitzii Infection: Case Report and Review of the Literature

Background

Pulmonary actinomycosis (PA), a chronic indolent infection, is a diagnostic challenge. Actinomyces graevenitzii is a relatively rare Actinomyces species isolated from various clinical samples.

Case Presentation

A 47-year-old patient presented with a 3-month history of mucopurulent expectoration and dyspnea and a 3-day history of fever up to 39.0°C. He had dental caries and a history of alcoholism. Computed tomography (CT) images of the chest revealed a consolidation shadow in the right upper and middle lobes, with necrosis containing foci of air. Actinomyces graevenitzii was isolated from bronchoalveolar lavage fluid (BALF) culture and was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. He received treatment with intravenous piperacillin-sulbactam for 10 days and oral amoxicillin-clavulanate for 7 months. His clinical condition had considerably improved. The consolidation shadow was gradually absorbed.

Conclusion

Early diagnosis and treatment of pulmonary actinomycosis are crucial. Bronchoscopy plays a key role in the diagnostic process, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) is an accurate tool for Actinomyces identification.

Antimicrobial Susceptibility of Clinical Oral Isolates of Actinomyces spp

Actinomyces species play an important role in the pathogenesis of oral diseases and infections. Susceptibility testing is not always routinely performed, and one may oversee a shift in resistance patterns. The aim of the study was to analyze the antimicrobial susceptibility of 100 well-identified clinical oral isolates of Actinomyces spp. against eight selected antimicrobial agents using the agar dilution (AD) and E-Test (ET) methods. We observed no to low resistance against penicillin, ampicillin-sulbactam, meropenem, clindamycin, linezolid and tigecycline (0-2% ET, 0% AD) but high levels of resistance to moxifloxacin (93% ET, 87% AD) and daptomycin (83% ET, 95% AD). The essential agreement of the two methods was very good for benzylpenicillin (EA 95%) and meropenem (EA 92%). The ET method was reliable for correctly categorizing susceptibility, in comparison with the reference method agar dilution, except for daptomycin (categorical agreement 87%). Penicillin is still the first-choice antibiotic for therapy of diseases caused by Actinomyces spp.

Enlightening clinical and therapeutic heterogeneity in thoracic actinomycosis: A review in bronchiectasis and non-bronchiectasis patients

Actinomycosis is a rare chronic infection triggered by species of Actinomyces. Although thoracic involvement represents about 15% of human actinomycosis, its true incidence may be underestimated, not only because of its challenging diagnosis, but also because it can be treated unintentionally with antibiotics for other diseases. In this sense, this work aims at providing an up-to-date literature review on thoracic actinomycoses, with particular emphasis on presentation, diagnostic and therapeutic approaches, also paving upcoming clinical interventions from findings obtained of a presentation of a case series. Data discussed here clearly denote the rarity, non-specificity and heterogeneity of clinical presentations of the disease, reinforcing the need for individualized therapeutic approaches.

More than Valley Fever: Pulmonary Actinomycosis and Coccidioidomycosis Co-infection in a Patient

Pulmonary coccidioidomycosis and pulmonary actinomycosis are unheard of as co-pathogens. Infection with these organisms on their own can mimic lung cancer, thus presenting a diagnostic challenge. We present the case of a 75-year-old woman presenting with haemoptysis with a chest CT chest finding of a lung mass suggestive of lung cancer. A diagnosis of concomitant infection by Coccidioides posadasii/immitis and Actinomyces odontolyticus was made based on culture and histopathology results. The patient was successfully treated with a combination of antifungal and antibacterial therapy. This is the first reported case of co-infection by these two microorganisms.

LEARNING POINTS

Pulmonary coccidioidomycosis and pulmonary actinomycosis can mimic lung cancer.The diagnosis of infection by Coccidioides posadasii/immitis and Actinomyces odontolyticus is best obtained by histopathology and tissue culture.Treatment comprises a combination of oral azoles and a beta-lactam antibiotic for a total of 12 months.

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity

The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease.

Gut microbiome alterations have been linked to inflammatory bowel disease (IBD) and obesity. Here, the authors characterize the metagenomes of four large human cohorts and perform co-abundance network analysis showing that dysbiosis in disease is marked by the altered co-abundance relationships, suggesting that pathway coabundance networks are more heterogeneous than species network.

Evaluation of Extraction Methods for Clinical Metagenomic Assay

(1) Background: Clinical metagenomics is a promising approach that helps to identify etiological agents in cases of unknown infections. For the efficient detection of an unknown pathogen, the extraction method must be carefully selected for the maximum recovery of nucleic acid from different microorganisms. The aim of this study was to evaluate different extraction methods that have the ability to isolate nucleic acids from different types of pathogens with good quality and quantity for efficient use in clinical metagenomic identification. (2) Methods: A mock sample spiked with five different pathogens was used for the comparative evaluation of different commercial extraction kits. Extracted samples were subjected to library preparation and run on MiSeq. The selected extraction method based on the outcome of the comparative evaluation was used subsequently for the nucleic acid isolation of all infectious agents in clinical respiratory samples with multiple infections. (3) Results: The protocol using the PowerViral^® Environmental RNA-DNA Isolation Kit with a 5-min bead beating step achieved the best results with a low starting volume. The analysis of the tested clinical specimens showed the ability to successfully identify different types of pathogens. (4) Conclusions: The optimized extraction protocol in this study is recommended for clinical metagenomics application in specimens with multiple infections from different taxa.

Cigarette smoking and oral microbiota in low-income and African-American populations

BACKGROUND

Cigarette smoking is a common risk factor for diseases and cancers. Oral microbiota is also associated with diseases and cancers. However, little is known about the impact of cigarette smoking on the oral microbiota, especially among ethnic minority populations.

METHODS

We investigated cigarette smoking in relationship with the oral microbiota in a large population of predominately low-income and African-American participants. Mouth rinse samples were collected from 1616 participants within the Southern Community Cohort Study, including 592 current-smokers, 477 former-smokers and 547 never-smokers. Oral microbiota was profiled by 16S ribosomal RNA gene deep sequencing.

RESULTS

Current-smokers showed a different overall microbial composition from former-smokers (p=6.62×10-7) and never-smokers (p=6.00×10-8). The two probiotic genera, Bifidobacterium and Lactobacillus, were enriched among current-smokers when compared with never-smokers, with Bonferroni-corrected p values (PBonferroni ) of 1.28×10-4 and 5.89×10-7, respectively. The phylum Actinobacteria was also enriched in current-smokers when compared with never-smokers, with a median relative abundance of 12.35% versus 9.36%, respectively, and with a PBonferroni =9.11×10-11. In contrast, the phylum Proteobacteria was depleted in current smokers (PBonferroni =5.57×10-13), with the relative abundance being almost three times that of never-smokers (7.22%) when compared with that of current-smokers (2.47%). Multiple taxa within these two phyla showed differences in abundance/prevalence between current-smokers and never-smokers at PBonferroni <0.05. The differences in the overall microbial composition and abundance/prevalence of most taxa were observed among both African-Americans and European-Americans. Meanwhile, such differences were not observed between former-smokers and never-smokers.

CONCLUSION

Smoking has strong impacts on oral microbial community, which was recovered after smoking cessation.

Host genetic variation and its microbiome interactions within the Human Microbiome Project

Background

Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and microbiome characterization have been performed.

Methods

We performed whole-genome sequencing of 298 donors from the Human Microbiome Project (HMP) healthy cohort study to accompany existing deep characterization of their microbiomes at various body sites. This analysis yielded an average sequencing depth of 32x, with which we identified 27 million (M) single nucleotide variants and 2.3 M insertions-deletions.

Results

Taxonomic composition and functional potential of the microbiome covaried significantly with genetic principal components in the gastrointestinal tract and oral communities, but not in the nares or vaginal microbiota. Example associations included validation of known associations between FUT2 secretor status, as well as a variant conferring hypolactasia near the LCT gene, with Bifidobacterium longum abundance in stool. The associations of microbial features with both high-level genetic attributes and single variants were specific to particular body sites, highlighting the opportunity to find unique genetic mechanisms controlling microbiome properties in the microbial communities from multiple body sites.

Conclusions

This study adds deep sequencing of host genomes to the body-wide microbiome sequences already extant from the HMP healthy cohort, creating a unique, versatile, and well-controlled reference for future studies seeking to identify host genetic modulators of the microbiome.

Electronic supplementary material

The online version of this article (10.1186/s13073-018-0515-8) contains supplementary material, which is available to authorized users.

Co-infection of Candidaparapsilosis in a Patient of Pulmonary Actinomycosis-A Rare Case Report

The diagnosis of pulmonary actinomycosis is difficult and less than 10% of cases are diagnosed at the initial presentation. Actinomycosis is always poly-microbial flora infection in human. On the other hand, Candida parapsilosis is an emerging fungal pathogen especially in immuno-compromised patients. Combined bacterial-fungal infection increases frequency and severity of the disease. This report is a case of a Candida parapsilosis co-infection in a 23-year-old male patient having pulmonary actinomycosis. This thereby could guide the clinicians towards an appropriate therapy.

Actinomyces and related organisms in human infections

Actinomyces israelii has long been recognized as a causative agent of actinomycosis. During the past 3 decades, a large number of novel Actinomyces species have been described. Their detection and identification in clinical microbiology laboratories and recognition as pathogens in clinical settings can be challenging. With the introduction of advanced molecular methods, knowledge about their clinical relevance is gradually increasing, and the spectrum of diseases associated with Actinomyces and Actinomyces-like organisms is widening accordingly; for example, Actinomyces meyeri, Actinomyces neuii, and Actinomyces turicensis as well as Actinotignum (formerly Actinobaculum) schaalii are emerging as important causes of specific infections at various body sites. In the present review, we have gathered this information to provide a comprehensive and microbiologically consistent overview of the significance of Actinomyces and some closely related taxa in human infections.

Pseudo-outbreak of Actinomyces graevenitzii associated with bronchoscopy

Outbreaks and pseudo-outbreaks of infection related to bronchoscopy typically involve Gram-negative bacteria, Mycobacterium species or Legionella species. We report an unusual bronchoscopy-related pseudo-outbreak due to Actinomyces graevenitzii. Extensive epidemiological and microbiological investigation failed to identify a common source. Strain typing revealed that the cluster was comprised of heterogeneous strains of A. graevenitzii. A change in laboratory procedures for Actinomyces cultures was coincident with the emergence of the pseudo-outbreak, and we determined that A. graevenitzii isolates more readily adopted a white, dry, molar tooth appearance on anaerobic colistin nalidixic acid (CNA) agar which likely facilitated its detection and identification in bronchoscopic specimens. This unusual pseudo-outbreak was related to frequent requests of bronchoscopists for Actinomyces cultures combined with a change in microbiology laboratory practices.

Actinomyces graevenitzii pulmonary abscess mimicking tuberculosis in a healthy young man

Pulmonary actinomycosis is a rare disease that is often misdiagnosed as tuberculosis or lung cancer. Actinomyces graevenitzii is a relatively new recognized Actinomyces species isolated from various clinical samples. The authors report a case of pulmonary actinomycosis caused by A graevenitzii. A computed tomography examination revealed an excavated consolidation in the middle right lobe of a previously healthy young man who presented with a long history of moderate cough. Cultures of the bronchoalveolar lavage fluid confirmed the diagnosis of pulmonary abscess caused by A gravenitzii. At the three-month follow-up consultation and, after six weeks of high-dose amoxicillin, the pulmonary lesion had completely disappeared.