Genome Mining and Comparative Analysis of Streptococcus intermedius Causing Brain Abscess in a Child

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.

The Antibacterial Type VII Secretion System of Bacillus subtilis: Structure and Interactions of the Pseudokinase YukC/EssB

Type VIIb secretion systems (T7SSb) were recently proposed to mediate different aspects of Firmicutes physiology, including bacterial pathogenicity and competition. However, their architecture and mechanism of action remain largely obscure. Here, we present a detailed analysis of the T7SSb-mediated bacterial competition in Bacillus subtilis, using the effector YxiD as a model for the LXG secreted toxins. By systematically investigating protein-protein interactions, we reveal that the membrane subunit YukC contacts all T7SSb components, including the WXG100 substrate YukE and the LXG effector YxiD. YukC’s crystal structure shows unique features, suggesting an intrinsic flexibility that is required for T7SSb antibacterial activity. Overall, our results shed light on the role and molecular organization of the T7SSb and demonstrate the potential of B. subtilis as a model system for extensive structure-function studies of these secretion machineries.

An Eight Year Clinico-Microbiological Retrospective Study on Brain Abscesses in India

Background:

Intracranial abscesses have been a diagnostic and therapeutic challenge since time immemorial for both the microbiologists and the neurosurgeons. There is paucity of detailed studies documenting the infecting organism causing brain abscesses in South India.

Aims:

The study aimed at identifying and assessing the prevalence of aerobic, anaerobic bacteria and fungi associated with brain abscesses at a tertiary care hospital in South India.

Methods and Material:

Eight years data was collected from the records of culture reports from 2007 to 2010 and 2013 to 2018. The corresponding clinical case records were retrieved for the assessment of risk factors. Risk factors of brain abscess development were assessed based on clinical cases records.

Results:

Data from 140 brain abscess cases obtained over a period of 8 years were analyzed. Out of the 140 samples, 66 (47.14%) were culture positive in which 33 (50%) had single aerobic/facultative anaerobic bacteria, 20 (30.3%) had mixture of more than one aerobic/facultative anaerobic bacteria, 12 (18.18%) had single obligate anaerobic bacteria and 1(1.5%) sample had Mycobacterium tuberculosis isolated. Among the total 92 isolates, Pseudomonas aeruginosa (21/92, 23%) and Staphylococcus aureus (20/92, 22%) predominated. Bacteroides fragilis group was the most common obligate anaerobe isolated. There were no fungal isolates. As there were various isolates isolated, hence there is heterogeneity of isolates detected Neuroanatomically, parietal lobe (45/140, 32%) was the most common location. Otogenic infection was the major risk factor for parietal and temporal lobe abscess (P value < .05).

Conclusions:

It has become essential for the microbiologists to be aware of unusual isolates from brain abscess and its complex nature. Obscurity and difficulty in their microbiological diagnosis calls for more such detailed studies.

Pangenome analysis and virulence profiling of Streptococcus intermedius

Background

Streptococcus intermedius, a member of the S. anginosus group, is a commensal bacterium present in the normal microbiota of human mucosal surfaces of the oral, gastrointestinal, and urogenital tracts. However, it has been associated with various infections such as liver and brain abscesses, bacteremia, osteo-articular infections, and endocarditis. Since 2005, high throughput genome sequencing methods enabled understanding the genetic landscape and diversity of bacteria as well as their pathogenic role. Here, in order to determine whether specific virulence genes could be related to specific clinical manifestations, we compared the genomes from 27 S. intermedius strains isolated from patients with various types of infections, including 13 that were sequenced in our institute and 14 available in GenBank.

Results

We estimated the theoretical pangenome size to be of 4,020 genes, including 1,355 core genes, 1,054 strain-specific genes and 1,611 accessory genes shared by 2 or more strains. The pangenome analysis demonstrated that the genomic diversity of S. intermedius represents an “open” pangenome model. We identified a core virulome of 70 genes and 78 unique virulence markers. The phylogenetic clusters based upon core-genome sequences and SNPs were independent from disease types and sample sources. However, using Principal Component analysis based on presence/ absence of virulence genes, we identified the sda histidine kinase, adhesion protein LAP and capsular polysaccharide biosynthesis protein cps4E as being associated to brain abscess or broncho-pulmonary infection. In contrast, liver and abdominal abscess were associated to presence of the fibronectin binding protein fbp54 and capsular polysaccharide biosynthesis protein cap8D and cpsB.

Conclusions

Based on the virulence gene content of 27 S. intermedius strains causing various diseases, we identified putative disease-specific genetic profiles discriminating those causing brain abscess or broncho-pulmonary infection from those causing liver and abdominal abscess. These results provide an insight into S. intermedius pathogenesis and highlights putative targets in a diagnostic perspective.

Molecular trafficking between bacteria determines the shape of gut microbial community

Complex inter-bacterial interactions largely influence the structure and function of the gut microbial community. Though several host-associated phenomena have often been shown to be involved in the stability, structure, and function of the gut microbial community, the implication of contact-dependent and contact-independent inter-bacterial interactions has been overlooked. Such interactions are tightly governed at multiple layers through several extracellular organelles, including contact-dependent inhibition (CDI), nanotubes, type VI secretion system (T6SS), and membrane vesicles (MVs). Recent advancements in molecular techniques have revealed that such extracellular organelles function beyond exhibiting competitive behavior and are also involved in manifesting cooperative behaviors. Cooperation between bacteria occurs through the sharing of several beneficial molecules including nucleic acids, proteins, metabolites, and nutrients among the members of the community, while competition occurs by means of multiple toxins. Intrinsic coordination between contact-dependent and contact-independent mechanisms collectively provides a fitness advantage and increased colonization resistance to the gut microbiota, where molecular trafficking plays a key role. This review is intended to provide a comprehensive view of the salient features of the different bacterial interactions and to highlight how microbiota deploy multifaceted organelles, for exerting both cooperative and competitive behaviors. We discuss the current knowledge of bacterial molecular trafficking and its impact on shaping the gut microbial community.

Interest of bacterial pangenome analyses in clinical microbiology

Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.

From Normal Flora to Brain Abscesses: A Review of Streptococcus intermedius

Streptococcus intermedius is a β-hemolytic Gram-positive member of the Streptococcus anginosus group (SAG). Despite being a part of the normal microbiota, it is one of the most common pathogens associated with brain and liver abscesses and thoracic empyema, increasing as a result the morbidity and mortality rates in affected patients. Though there are numerous published case reports on S. intermedius infections, it is still understudied compared to other SAG members. Our knowledge of the genomic factors contributing to its dissemination to the brain and abscess development is also limited to few characterized genes. In this review, we summarize our current knowledge on S. intermedius identification methods, virulence factors, and insight provided by the whole-genome and correlate patients’ metadata, symptoms, and disease outcome with S. intermedius infections in 101 recent case reports obtained from PubMed. This combined information highlights the gaps in our understanding of S. intermedius pathogenesis, suggesting future research directions to unveil the factors contributing to abscess development.