Pneumonia and Respiratory Infections

Identifying candidate genetic determinants associated with invasion in pneumococcal lineages

The paper identifies invasion-associated genetic variants in pneumococcal lineages by separating serotype and lineage effects, highlighting candidate determinants for experimental investigation.

ALLCAPS: a scalable and accurate deep-learning method for in silico pneumococcal serotyping

ALLCAPS is a deep-learning tool for in silico pneumococcal serotyping that outperforms existing methods and identifies novel serotypes.

Upper respiratory tract bacterial microbiome features associated with Streptococcus pneumoniae colonisation, environmental and demographic factors among older children in a rural setting in The Gambia

The study examines URT microbiome features linked to S. pneumoniae colonisation in older children in The Gambia, identifying microbial associations and environmental factors influencing colonisation.

The global evolutionary dynamics of natural capsule switching in a human-restricted bacterial pathogen

This study examines capsule switching in Streptococcus pneumoniae using whole-genome sequences, finding that switching is limited to specific capsule-type pairs and influenced by genetic and ecological factors.

Genome-wide CRISPRi maps pneumococcal attachment and intracellular survival during single infection and Influenza co-infection

This study uses CRISPRi to identify pneumococcal genes critical for attachment and survival during single infection and influenza co-infection, revealing key metabolic and structural dependencies.

Real-time near-infrared imaging distinguishes nasopharyngeal colonization from aspiration of Streptococcus pneumoniae and identifies aspiration as a trigger of severe disease

This study uses real-time near-infrared imaging to distinguish nasopharyngeal colonization from aspiration of Streptococcus pneumoniae and shows aspiration triggers severe disease.

A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions

The paper develops a mathematical model to predict vaccine replacement dynamics in Streptococcus pneumoniae and identifies optimal genomic surveillance strategies.

Influenza A Virus Coinfection Alters Streptococcus pneumoniae Gene Expression during Upper Respiratory Tract Colonization

This study identifies transcriptional changes in Streptococcus pneumoniae during upper respiratory tract colonization and IAV coinfection, revealing distinct metabolic and virulence adaptations.

Biofilm formation during pneumococcal carriage imprints naturally acquired humoral immunity

The paper shows that biofilm formation during pneumococcal colonization shapes humoral immunity and protection, with the first colonizing strain imprinting immune responses toward biofilm antigens.

Lactate Oxidase (LctO) Acts as a Metabolic Checkpoint Restraining Streptococcus pneumoniae Invasion of Respiratory Epithelial Barriers

Niche-specific contribution of the branched-chain amino acid biosynthesis protein IlvD in Streptococcus pneumoniae infection

This study identifies mutations in ilvD, encoding a BCAA biosynthesis protein, as beneficial for pneumococcal survival in blood but detrimental for nasopharyngeal colonization.

Genome-wide association study of susceptibility to pneumococcal carriage amongst children

This study identifies genetic loci associated with pneumococcal carriage in children through a genome-wide association analysis.

Quantifying the mechanisms of vaccine-induced serotype replacement in Streptococcus pneumoniae using genome-informed modelling

The paper quantifies how serotype replacement in Streptococcus pneumoniae is driven by shifts in serotypes within persistent lineages rather than lineage replacement, using genome-informed modeling and longitudinal data.

Lipid-mediated regulation of pneumolysin balances vascular injury and bacterial containment during pneumococcal infection

This study shows that 25-hydroxycholesterol protects against pneumolysin-induced vascular injury, while its suppression allows bacterial containment through coagulation, with PAF acting as a compensatory antagonist.

Sorafenib, a clinically approved kinase inhibitor attenuates Streptococcus pneumoniae pathogenesis in vivo by targeting serine/threonine kinase StkP

This study shows that sorafenib, a cancer drug, targets StkP in Streptococcus pneumoniae, reducing bacterial pathogenesis and mortality in mice.

A pan-serotype human monoclonal antibody protects against pneumococcal infection by targeting multiple choline binding domain proteins

This paper identifies a human monoclonal antibody that protects against multiple pneumococcal serotypes by targeting conserved choline-binding domain proteins.

Age Dependent Immunopathology Drives Pneumonia-Associated Cardiac Dysfunction During Streptococcus pneumoniae Infection

This study shows aging worsens cardiac dysfunction during Streptococcus pneumoniae infection through inflammation and impaired immune responses, with potential therapeutic targets identified.

Pathogen-specific host responses define distinct pneumonia endotypes in the human lung

This study identifies distinct pneumonia endotypes based on pathogen-specific host responses in the lung, linking them to clinical outcomes and suggesting personalized treatment strategies.

Bacterial and host factors affecting acquisition of Streptococcus pneumoniae in a murine model

This study identifies host and bacterial factors influencing acquisition of Streptococcus pneumoniae in mice, showing that prior viral infection and capsule expression enhance acquisition, while prior colonization blocks it.

Sub-phenotypes of pneumonia defined by pulmonary histopathological features

The paper defines sub-phenotypes of pneumonia using histopathological features from human lung samples and validates them in mouse models.

Global population structure and phase variation of serotype 12F Streptococcus pneumoniae following the introduction of pneumococcal conjugate vaccine

This study characterizes the global population structure and genetic diversity of serotype 12F Streptococcus pneumoniae, identifying strand-slippage mutations as a mechanism for capsule variation and vaccine evasion.

A soluble host signal drives rapid, brain-predominant capsular thickening in Streptococcus pneumoniae via a putative sodium-dependent transporter (SPD_0642) and capsular prepromoter sequence

This paper identifies a host-derived signal that induces rapid, tissue-specific capsule thickening in Streptococcus pneumoniae, independent of phase variation, and shows two genetic determinants involved in this process.

Metabolic Rewiring at the Pyruvate Node Drives Severe Pneumonia and T-Cell Suppression in Serotype 3 Streptococcus pneumoniae Infection

This study identifies a metabolic pathway in Streptococcus pneumoniae that drives pneumonia and immune evasion through oxygen-sensitive growth and membrane bleb formation.

Serotypic heterogeneity in the response to pneumococcal vaccine

This study identifies serotype-specific IgG thresholds for pneumococcal vaccine response, showing significant variability across serotypes and highlighting the need for tailored assessment.

Early metabolic reprogramming licenses Streptococcus pneumoniae for Influenza-driven superinfection

This study identifies alcohol dehydrogenases as critical for Streptococcus pneumoniae fitness during influenza-driven superinfection, revealing a metabolic dependency that can be targeted therapeutically.

The capsule and genetic background, rather than specific individual loci, strongly influence in vitro pneumococcal growth kinetics

This study shows that pneumococcal growth kinetics are influenced by capsular serotype, lineage, and genetic background rather than specific loci.

SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae

This paper introduces SeroBA(v2.0), a tool for pneumococcal serotyping, and SeroBAnk, a resource for capsular diversity, which accurately identifies 102 serotypes and supports community contributions for updates.

Alterations in Nutrient Availability in the Lungs During Streptococcus pneumoniae-Induced Pneumonia

This study examines metabolic changes in the lungs during Streptococcus pneumoniae infection, revealing shifts in metabolite levels and bacterial gene expression that correlate with disease progression.

A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline

The paper introduces GPS Pipeline, a scalable and portable genomic analysis tool for Streptococcus pneumoniae, enabling public health outputs with minimal expertise.

Streptococcus pneumoniae vaccine serotype persistence following 13-valent pneumococcal conjugate vaccine introduction in Mongolia: investigating changes in epidemiology, immunology and virulence

The paper examines persistence of vaccine serotypes of Streptococcus pneumoniae in Mongolia after PCV13 introduction, finding changes in lineage composition, virulence, and drug resistance.