Detection of a mixed infection in a culture-negative brain abscess by broad-spectrum bacterial 16S rRNA gene PCR

Polymicrobial brain abscesses: A complex condition with diagnostic and therapeutic challenges

Brain abscesses (BA) are focal parenchymal infections that remain life-threatening conditions. Polymicrobial BAs (PBAs) are complex coinfections of bacteria or bacterial and nonbacterial pathogens such as fungi or parasites, with diagnostic and therapeutic challenges. In this article, we comprehensively review the prevalence, pathogenesis, clinical manifestations, and microbiological, histopathological, and radiological features of PBAs, as well as treatment and prognosis. While PBAs and monomicrobial BAs have some similarities such as nonspecific clinical presentations, PBAs are more complex in their pathogenesis, pathological, and imaging presentations. The diagnostic challenges of PBAs include nonspecific imaging features at early stages and difficulties in identification of some pathogens by routine techniques without the use of molecular analysis. Imaging of late-stage PBAs demonstrates increased heterogeneity within lesions, which corresponds to variable histopathological features depending on the dominant pathogen-induced changes in different areas. This heterogeneity is particularly marked in cases of coinfections with nonbacterial pathogens such as Toxoplasma gondii. Therapeutic challenges in the management of PBAs include initial medical therapy for possibly underrecognized coinfections prior to identification of multiple pathogens and subsequent broad-spectrum antimicrobial therapy to eradicate identified pathogens. PBAs deserve more awareness to facilitate prompt and appropriate treatment.

A pulmonary abscess caused by Porphyromonas endodontalis infection:A case report and literature review

Porphyromonas endodontalis is an oral anaerobic bacterium associated with periodontitis but seldomly been detected in other diseases. Only one case of respiratory disease caused by Porphyromonas endodontalis, pyopneumothorax, has been reported so far. A 53-year-old man with refractory periodontitis was admitted due to an indeterminate lung space-occupying lesion. Following mNGS analysis of the liquefaction necrotic area and solid component of the lesion through biopsy, Porphyromonas endodontalis and Parvimonas micra were detected. Therefore, the patient was diagnosed with an aspiration lung abscess and discharged after receiving effective antibacterial treatment. The Chest computed tomography (CT) scan revealed a remarkable improvement during outpatient follow-up. In this study, we applied mNGS to diagnose a case of lung abscess attributed to an uncommon bacterium successfully, suggesting that when patients complicated with periodontal diseases and clinical respiratory symptoms, the possibility of inhalation disease caused by oral pathogens should be considered.

Oral flora meningoencephalitis diagnosis by next-generation DNA sequencing

Introduction

Standard culture methods may fail to detect the causative agents of bacterial infection for various reasons including specimen collection after antibiotic administration, or when standard techniques or environmental conditions are not appropriate for growth of the microorganisms. Conventional 16S rRNA gene sequencing is sometimes a useful alternative technique for identification of bacteria, but is confounded by polymicrobial infection. We present a case of a patient who developed a serious neurological infection for which causative oral flora organisms were observed by microscopy, failed to culture but were identified by next-generation DNA sequencing.

Case presentation

A male in his forties developed sinus pain and congestion, followed by facial and eye pain, and several weeks later acute-onset confusion and neck stiffness. Cerebrospinal fluid examination revealed pleocytosis and several bacterial morphologies, which were subsequently identified by next-generation sequencing as oral flora constituents Porphyromonas endodontalis , Fusobacterium nucleatum , Streptococcus constellatus , Prevotella species and Parvimonas micra .

Conclusion

Oral flora can cause meningoencephalitis and brain abscess formation if translocation occurs by injury or surgical procedures. Next-generation sequencing is often not available at healthcare facilities, or when available may not have been validated for a wide spectrum of specimen sources, but is available at reference laboratories and should be considered when routine methods fail to provide a diagnosis for serious infections.

Molecular diagnosis of polymicrobial brain abscesses with 16S-rDNA-based next-generation sequencing

OBJECTIVES

Brain abscesses lead to high mortality despite antibiotic and surgical treatment. Identification of causative bacteria is important to guide antibiotic therapy, but culture-based methods and molecular diagnostics by Sanger sequencing of 16S PCR products are hampered by antibiotic treatment and the often polymicrobial nature of brain abscesses. We have applied 16S-rRNA-based next-generation sequencing (NGS) for metagenomic analysis of intracranial abscess (brain and epidural) and meningitis samples.

METHODS

Seventy-nine samples from 54 patients with intracranial abscesses or meningitis were included. DNA was subjected to 16S PCR. Amplicons were analysed with the Illumina MiSeq system, sequence reads were blasted versus the NCBI 16S bacterial database and analysed using MEGAN software. Results were compared to those of gram-staining, culture and Sanger sequencing.

RESULTS

The NGS workflow was successful for 51 intracranial abscesses (46 brain and five epidural) and nine meningitis samples. Inclusion of (mono)bacterial meningitis samples allowed us to establish a cut-off criterion for the exclusion of contaminating sequences. In total 86 bacterial taxa were identified in brain abscesses by NGS, with Streptococcus intermedius and Fusobacterium nucleatum as most prevalent species; Propionibacterium and Staphylococcus spp. were associated with epidural abscesses. NGS identified two or more bacterial taxa in 31/51 intracranial abscesses, revealing the polymicrobial nature of these infections and allowing the discrimination of up to 16 bacterial taxa per sample.

CONCLUSION

These results extend earlier studies showing that NGS methods expand the spectrum of bacteria detected in brain abscesses and demonstrate that the MiSeq platform is suitable for metagenomic diagnostics of this severe infection.

Rapid brain death caused by a cerebellar abscess with Fusobacterium nucleatum in a young man with drug abuse: a case report

Background

Fusobacterium nucleatum is a strict anaerobic microorganism that causes disease entities such as periodontal and soft tissue abscesses, pulmonary and intraabdominal infections and very rarely intracerebral infections.

Case presentation

Here, we report the rare case of a previously healthy 25-year-old German man with a cerebellar abscess caused by Fusobacterium nucleatum that resulted in rapid brain death. Toxicological screening showed positivity for amphetamines and cannabis. The diagnosis was obtained by polymerase chain reaction amplification of bacterial deoxyribonucleic acid in cerebrospinal fluid.

Conclusions

In drug users clinicians should think about rare causes of brain abscesses/meningitis. Early diagnosis is necessary and justifies the use of molecular techniques.

Brain abscess

A brain abscess is defined as a localized collection of pus within the parenchyma of the brain or meninges. Brain abscesses are a complication of ear, sinus, and/or dental infections. Although they may occur in many brain locations, the most common sites are frontal and temporal lobes. Modern neuroimaging and laboratory analysis have led to prompt diagnosis and have decreased the mortality rates from brain abscess. Critical care nurses have a vital role in performing accurate neurologic assessments, timely administration of antibiotics, and management of fever.

Polymicrobial challenges to Koch's postulates: ecological lessons from the bacterial vaginosis and cystic fibrosis microbiomes

Koch's postulates have shaped our understanding of infectious diseases; however, one of the tangential consequences of them has been the emergence of a predominantly monomicrobial perspective concerning disease aetiology. This orthodoxy has been undermined by the growing recognition that some important infectious diseases have a polymicrobial aetiology. A significant new development in our understanding of polymicrobial infections is the recognition that they represent functional ecosystems and that to understand such systems and the outcome and impact of therapeutic interventions requires an understanding of how these communities arise and develop. Therefore, it is timely to explore what we can learn from other fields. In particular, ecological theory may inform our understanding of how polymicrobial communities assemble their structure and their dynamics over time. Such work may also offer insights into how such communities move from stable to unstable states, as well as the role of invasive pathogens in the progression of the disease. Ecological theory offers a theoretical framework around which testable hypotheses can be developed to clarify the polymicrobial nature and dynamics of such infections in the face of environmental change and therapeutic interventions.

Metagenomic analysis of brain abscesses identifies specific bacterial associations

BACKGROUND

The bacterial flora involved in brain abscess is often complex. In a previous study, using a metagenomic approach based on 16S ribosomal DNA (rDNA) amplification, we demonstrated that the diversity of the microbial flora involved in these infections was underestimated.

METHODS

We performed a 16S rDNA-based metagenomic analysis of cerebral abscesses from patients diagnosed from 2006 through 2010. All bacteria present in brain abscess specimens were identified, in view of the clinical and epidemiological characteristics of the patients.

RESULTS

Fifty-one patients were included in our study. By detecting polymicrobial infections in 19 patients, our strategy was significantly more discriminatory and enabled the identification of a greater number of bacterial taxa than did culture and conventional 16S rDNA polymerase chain reaction (PCR) and sequencing, respectively (P < 10(-2)). Data mining discriminated 2 distinct bacterial populations in brain abscess from dental and sinusal origin. In addition, of the 80 detected bacterial species, we identified 44 bacteria that had never been found in brain abscess specimens, including 22 uncultured bacteria. These uncultured agents mostly originated from the buccal or sinusal floras (P < 10(-2)) and were found in polymicrobial specimens (P < 10(-2)).

CONCLUSIONS

Cloning and sequencing of PCR-amplified 16S rDNA is a highly valuable method to identify bacterial agents of brain abscesses.

Microbiological spectrum of brain abscess at a tertiary care hospital in South India: 24-year data and review

Intracranial abscesses are life-threatening infections that pose a diagnostic challenge not only to the neurosurgeon but also to the microbiologists. Detailed studies documenting the spectrum of infecting agents involved in brain abscesses are limited from India. Materials and Methods. This is a retrospective analysis of 352 samples from 1987 to 2010 analyzed at a tertiary care hospital in South India from 1987 to 2010, to document the changing trends with time. Results. The age of the patients ranged from 2 to 80 years, a larger number of males being affected. Otogenic infections were the most common cause while cryptogenic abscesses were 20%. Gram stain and culture positivity were 78% each. Gram-positive and negative facultative aerobes and obligate anaerobes were also on the rise. Unusual organisms, like Burkholderia pseudomallei, Salmonella typhi, Nocardia species, Cladosporium bantiana, Fonsecaea pedrosoi, Entamoeba histolytica, and Acanthamoeba were also isolated and/or detected from the brain abscesses aspirate or resected tissue. Summary. New and emerging pathogens associated with brain abscess, especially in immunosuppressed individuals, have renewed the necessity of an early detection, and it will be of great value in appropriate management of patients with brain abscess.

Fusobacterium nucleatum prosthetic hip infection in an adult with sickle cell-beta thalassemia

Fusobacterium nucleatum is an anaerobic Gram-negative bacillus commensal to the human oropharynx and gastrointestinal tract which causes an array of human infection, yet it has never been associated with infection of prosthetic joints. We report the first case of prosthetic hip infection caused by F. nucleatum in a man with sickle cell-beta thalassemia.