Pangenome analysis and virulence profiling of Streptococcus intermedius

Novel Use of Metagenomic Next-Generation Sequencing in Diagnosing Streptococcus intermedius Meningitis and Ventriculitis: A Case Report and Literature Review

Background

Streptococcus intermedius is a commensal microflora commonly found in various mucosal sites in the respiratory, gastrointestinal, and genitourinary tracts. It causes invasive suppurative infections including liver and brain abscesses along with thoracic empyema. However, it rarely causes meningitis without abscess formation.

Case Presentation

A 56-year-old immunocompetent man who presented with fever and headache. Bacterial meningitis was confirmed using cerebrospinal fluid analysis. Magnetic resonance imaging of the brain revealed leptomeningitis and ventriculitis. However, conventional methods, such as microbiological culture failed to identify the causative pathogens. Metagenomic next-generation sequencing of cerebrospinal fluid revealed the presence of S. intermedius. It allowed us the optimal treatment for him. The patient underwent antibiotic treatment with 6-week duration of ceftriaxone administration accompanied by surgical intervention, resulting in a favorable prognosis.

Conclusion

Herein, we report a rare case of meningitis and ventriculitis caused by S. intermedius using metagenomic next-generation sequencing. The patient recovered well after antibiotic treatment and surgery. We present this rare case and summarize previous studies to remind clinicians that timely identification of the pathogen and optimal treatment are crucial for management of S. intermedius-induced infections.

Increasing Incidence of Streptococcus anginosus Group Intracranial Infections Associated With Sinusitis, Otitis Media, and Mastoiditis in Children

BACKGROUND

The Streptococcus anginosus group (SAG) pathogens have the potential to cause head and neck space infections, including intracranial abscesses. Several centers noted an increase in intracranial abscesses in children during the SARS-CoV-2 pandemic, prompting a Centers for Disease Control and Prevention health alert in May 2022. We examined the epidemiology of pediatric intracranial abscesses at a tertiary care center with a focus on SAG pre- and post-pandemic.

METHODS

Cases of intracranial abscesses of any microbiologic etiology admitted from January 2011 to December 2022 were identified using International Classification of Diseases 10 codes. Subjects were cross-referenced with culture results from the microbiology laboratory at Texas Children's Hospital. Cases included were those associated with either otitis media, mastoiditis or sinusitis and medical records were reviewed.

RESULTS

A total of 157 cases were identified and 59.9% (n = 94) were caused by SAG. The incidence of all sinogenic/otogenic intracranial infections ( P = 0.002), and SAG-specific infections ( P = 0.004), increased from 2011 to 2022. SAG infection was more often associated with multiple surgeries, and these subjects were more likely to require craniotomy or craniectomy. Among sinogenic abscesses, S. intermedius was the most common pathogen, while among otogenic cases, S. pyogenes predominated. From March 2020 to Dec 2022, 9/49 cases tested positive for SARS-CoV-2 (18.4%); characteristics of infection were not significantly different among cases with and without SARS-CoV-2.

CONCLUSIONS

Over the last decade, intracranial complications of sinusitis/otitis have been increasing, specifically those caused by SAG; this trend, however, predated the SARS-CoV-2 pandemic. SAG was associated with a greater need for surgical intervention, specifically neurosurgery. Further work is necessary to determine the cause for these rising infections.

Pulmonary granulomas and Mendelson syndrome in an immunocompromised patient

Granuloma formation is generally correlated with infection. Pulmonary granulomas caused by foreign bodies aspiration are uncommon. The clinical and radiologic features of such cases often lack specificity, which makes it difficult to distinguish from malignancy. Aspiration is usually not considered in the differential diagnosis of patients presenting with mass-like abnormalities on chest imaging. Occult aspiration history, diverse clinical manifestations, atypical imaging findings, and limited availability of pathogen detection techniques make the precise diagnosis a substantial challenge. Herein, we describe an older patient presenting with chest pain and worrisome lung masses/nodules that proved to be pulmonary granulomas caused by foreign matters aspiration. In addition, the patient developed Mendelson syndrome due to acute macroaspiration. Lung tissue metagenomics next-generation sequencing (mNGS) revealed Streptococcus intermedius, a normal flora of the oropharynx. The aim of this case was to underscore the importance of considering aspiration as a potential differential diagnosis of patients presenting with pulmonary granulomas, especially in patients with recurrent pneumonia or predisposing factors. In addition, mNGS act as a potential, rapid, and effective technique for diagnosing aspiration-related syndrome, showing satisfactory performance in identifying pathogens.

A Report of Two Cases of Meningoencephalitis Caused by Streptococcus intermedius

Objective

In this paper, we analyzed the clinical data of patients with meningoencephalitis caused by Streptococcus intermedius to understand better the clinical characteristics of the disease and recommend auxiliary diagnostic mode as well as treatment experience.

Methods

We reviewed the clinical data of two patients admitted to our department in 2019 with meningoencephalitis caused by S. intermedius.

Results

Two female patients were examined, one of whom had a history of radiotherapy for nasopharyngeal carcinoma while the other had no underlying disease. These two patients were admitted with symptoms of meningoencephalitis. Cerebrospinal fluid examinations revealed elevated levels of leukocytes and protein. After treatment with meropenem, the condition improved for a brief time, but then worsened with a decline in mental status and limb movement. Blood and cerebrospinal fluid cultures demonstrated the absence of pathogenic bacteria, while genome sequencing of cerebrospinal fluids revealed the presence of S. intermedius. Cranial magnetic resonance imaging revealed multiple cerebral abscesses (CAs). After coadministration of linezolid as an anti-infective, clinical symptoms gradually improved, and the CAs shrank on follow-up imaging. The condition exhibited a pattern of improvement-deterioration-improvement.

Conclusion

Meningoencephalitis caused by S. intermedius is complex and prone to fluctuation and formation of multiple CAs. The definitive clinical diagnosis of this disease can be aided by genome sequencing technology, and early clarification of the etiology combined with the use of potent antibiotics is effective.

Pangenome analyses of Clostridium butyricum provide insights into its genetic characteristics and industrial application

Clostridium butyricum is a Gram-positive anaerobic bacterium known for its ability to produce butyate. In this study, we conducted whole-genome sequencing and assembly of 14C. butyricum industrial strains collected from various parts of China. We performed a pan-genome comparative analysis of the 14 assembled strains and 139 strains downloaded from NCBI. We found that the genes related to critical industrial production pathways were primarily present in the core and soft-core gene categories. The phylogenetic analysis revealed that strains from the same clade of the phylogenetic tree possessed similar antibiotic resistance and virulence factors, with most of these genes present in the shell and cloud gene categories. Finally, we predicted the genes producing bacteriocins and botulinum toxins as well as CRISPR systems responsible for host defense. In conclusion, our research provides a desirable pan-genome database for the industrial production, food application, and genetic research of C. butyricum.

Challenging Diagnosis of Streptococcus intermedius-Associated Empyema in an Immunocompetent Adult: A Case Report and Literature Review

The significance of Streptococcus intermedius in infectious diseases, especially pleural infections, is gaining recognition. While traditional risk factors like dental procedures and immunosuppression remain pivotal in differential diagnosis, there is an emerging recognition of unconventional clinical presentations and risk factors linked to infections by S. intermedius. This shift compels medical professionals to broaden their diagnostic and therapeutic strategies, underscoring the intricate and evolving nature of managing infections associated with this opportunistic bacterium. We describe the case of a 48-year-old immunocompetent woman with untreated hypertension who experienced a 15-day episode of right-sided chest pain, which worsened with a sudden onset of dyspnea, yet her daily activities remained unaffected. Physical examination suggested a pleuropulmonary syndrome due to significant pleural effusion, with a computed tomography (CT) scan of the lungs revealing about 50% effusion on the right side. Laboratory tests indicated elevated inflammatory markers. Ultrasound-guided thoracentesis extracted purulent fluid compatible with empyema, necessitating the placement of a pleural drain and multiple pleural cavity lavages using alteplase, which led to the removal of substantial infected fluid. Culture of the pleural fluid identified S. intermedius, which was pansusceptible. Treatment with intravenous ceftriaxone was administered, resulting in a favorable clinical outcome. This case highlights the critical nature of recognizing atypical clinical presentations and managing complex bacterial infections in the pleural space.

Genomic Features and Comparative Genomic Analysis of Streptococcus sp. v1. nov., Isolated from an Endophthalmitis Patient

Endophthalmitis is an acute inflammatory intraocular condition that can cause permanent vision loss. The treatment strategy and visual outcome partly depend on the identification of the agents of pathogens. In this study, metagenomic sequencing was conducted to investigate the microbial and antibiotic resistance genes (ARGs) composition in the vitreous (intraocular body fluid) of an endophthalmitis patient, who progressed rapidly and accompanied by severe pain. Metagenomic sequencing data revealed that the vitreous sample was predominated by Streptococcus, with a low-diversity microbiome in the vitreous. This strain harbor's the ARGs mainly against beta-lactam, macrolide-lincosamide-streptogramin, and multidrug. Additionally, metagenome-assembled genome sequence of Streptococcus sp. v1. nov. was identified. The Tetra Correlation Search (TCS) analysis uncovered that the closest relative of the Streptococcus sp. v1. nov. was Streptococcus mitis SK321. Pan/core genome analysis for Streptococcus sp. v1. nov. and TCS top 25 hits strains revealed that most unique genes of Streptococcus sp. v1. nov. were linked to ATP-binding cassette transport system, which could indicate unique virulence and pathogenic potentials of Streptococcus sp. v1. nov. In addition, a total of 7 virulence factors were identified, and the overwhelming of them were classified into "offensive virulence factors". The high pathogenicity of Streptococcus sp. v1. nov. could be a reason for the patient's rapid disease progression. Our study was first isolated an ocular pathogen with highly virulent based on metagenomic sequencing and bioinformatics analysis, which has important reference value for revealing the composition and genome characteristics of pathogens in endophthalmitis patient in the future.

Hepatic Abscess in Inflammatory Bowel Disease: A Systematic Scoping Review of an Overlooked Entity

Background

Liver abscess is one of the hepatobiliary manifestations of inflammatory bowel disease (IBD) that has been scarcely described in the literature.

Objectives

To conduct a scoping review to provide a detailed description of the occurrence of hepatic abscess in patients with IBD and summarize the observed clinical features.

Methodology

Searches were carried out using relevant keywords in Medline (via PubMed) and Web of Science from inception until June 13, 2022. Only articles that reported the occurrence of hepatic abscess in patients with IBD were included.

Results

Forty-eight publications (40 case reports and 8 case series) were included, representing 73 patients with IBD who were radiologically or intraoperatively diagnosed with hepatic abscess. Patients with Crohn's disease were more predisposed to developing hepatic abscess than patients with ulcerative colitis (79.5% vs. 20.5%, respectively). Furthermore, pyogenic liver abscess was found to be more prevalent (57.9%) compared with aseptic (38.7%) and amebic (3.2%) abscesses. No clear relation was found between death or prolonged hospital stay in terms of the clinical presentation or management plan, as mortality was reported in different age groups with different managements.

Conclusion

To date, there is no consensus regarding the appropriate management of hepatic abscess as an extraintestinal manifestation of IBD. However, the condition shares several features with liver abscess diagnosed among the general population.

Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research

The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.

Clinical features of Streptococcus intermedius infection in children: a case series study

Introduction

Streptococcus intermedius is an opportunistic pathogen associated with prolonged hospital stays and high mortality rates in adults. However, little is currently known about the clinical features of Streptococcus intermedius infection in children.

Methods

This retrospective case series study included 40 children diagnosed with Streptococcus intermedius, confirmed through bacterial cultures or high-throughput sequencing. Antibiotic resistance was assessed through susceptibility testing. The site and clinical manifestations were evaluated for all patients.

Results

The common infection sites were the abdominal cavity, skin and soft tissue, intracranial, and invasive pulmonary, with the abdominal cavity being the most frequently affected. The drug susceptibility test showed 100% sensitivity to ceftriaxone, levofloxacin, chloramphenicol, vancomycin, and linezolid, 92.6% sensitivity to penicillin, 73.3% resistance to erythromycin, and 76.7% resistance to clindamycin. Besides antibiotic therapy, surgical intervention or pus drainage was often necessary. Lung imaging of four patients revealed pulmonary abscesses, nodules, or encapsulated pleura. Two cases yielded positive culture results, while three were identified as positive through high-throughput nucleotide sequencing of pleural effusion.

Discussion

In children with Streptococcus intermedius infection, emphasis should be placed on the risk of pus or abscess formation. In cases of pulmonary abscess and pleural effusion, especially in male children, Streptococcus intermedius should be suspected even if the culture is negative. Improvements in high-throughput nucleotide sequencing are required to reduce misdiagnosis rates.

Streptococcus intermedius Acute Meningitis in an Immunocompetent Child

Streptococcus intermedius is a commensal bacterium increasingly associated with brain abscesses. It can infect the brain through a direct extension of an inflammatory process or a hematogenous route. Meningitis due to this pathogen is sporadic and has not been described in children before. We report a case of an immunocompetent 6-year-old boy who developed bacterial meningitis due to S. intermedius .

Multifocal brain abscesses caused by invasive Streptococcus intermedia: A case report

Multifocal brain abscesses caused by invasive Streptococcus intermedia are relatively rare. Here, we present a 67-year-old male was admitted to the hospital for unconsciousness and fever. The computed tomography (CT) examination showed multiple intracranial space-occupying and “cavity-like” changes in the right lower lung. The examination of cerebrospinal fluid (CSF) was consistent with typical bacterial meningitis, CSF analyses revealed leukocytosis (10,300 × 10⁶/L), elevated protein levels (140.39 mg/dL), decreased glucose levels (0.27 mmol/L), and normal chloride concentration level (120.2 mmol/L), however, pathogens were not detected in the cultures. Then, the CSF and sputum samples were analyzed using meta-genomic next-generation sequencing (mNGS), and S. intermedia was detected in both samples. We adjusted the use of antibiotics according to the results of mNGS in time. After anti-infective treatment, the patient achieved good treatment results in a very short time. This case highlights the mNGS can identify pathogens of brain abscess, and provide strong evidence for clinical diagnosis and treatment strategy.

Streptococcus intermedius Bacteremia and Pyogenic Liver Abscess in a Patient With No Risk Factors

This case report depicts a 39-year-old male with no significant past medical history who was admitted for fever of unknown origin and sepsis. He was then found to have Streptococcus intermedius bacteremia and pyogenic liver abscess. The treatment course was complicated by pleural empyema leading to readmission. The case presented here adds to the medical literature, where a clear underrepresentation has been noted, and outlines a unique case of S. intermedius liver abscess complicated by pleural empyema in a patient without significant medical history, risk factors, or typical physical exam findings.