Pneumonia and Respiratory Infections

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.

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.

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.

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.

Mechanisms of 10-Hydroxyoctadecanoic acid resistance in Streptococcus pneumoniae

This study identifies h18:0 as a toxic fatty acid produced by S. aureus that targets S. pneumoniae, and reveals genetic mechanisms allowing pneumococcus to resist its toxicity.

Storage stability of non-encapsulated pneumococci in saliva is dependent on null-capsule clade, with strains carrying aliC and aliD showing a competitive disadvantage during culture enrichment

This study evaluates the storage stability of non-encapsulated pneumococci in saliva, finding that NCC2 strains are less stable than NCC1, and that extraction-free methods may better detect NCC2 strains.

Large-scale global molecular epidemiology of antibiotic resistance determinants in Streptococcus pneumoniae

This study analyzes antibiotic resistance patterns in Streptococcus pneumoniae using global whole-genome sequencing data, identifying trends in multi-drug resistance and serotype distribution.

An abundance of aliC and aliD genes were identified in saliva using a novel multiplex qPCR to characterize group II non-encapsulated pneumococci with improved specificity

The paper develops a novel multiplex qPCR assay to detect and classify non-encapsulated pneumococci (NESp) by targeting aliC and aliD genes, showing high specificity and prevalence in saliva samples.

Splenic red pulp macrophages eliminate the liver-resistant Streptococcus pneumoniae during bloodstream infection

The paper identifies that splenic red pulp macrophages, aided by natural antibodies and complement, clear liver-resistant Streptococcus pneumoniae from the bloodstream in mice.

A 5-transcript signature for discriminating viral and bacterial etiology in pediatric pneumonia

The paper identifies a 5-transcript signature in blood samples that distinguishes bacterial from viral pneumonia with high accuracy.

Weakened airway epithelial junctions and enhanced neutrophil elastase release contribute to age-dependent bacteremia risk following pneumococcal pneumonia

This study identifies weakened airway epithelial junctions and increased neutrophil elastase release in aged mice as factors contributing to age-dependent bacteremia risk after pneumococcal pneumonia.

Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure

The paper develops a genomic resource and clustering methods for pneumococcal population analysis using a large curated dataset of genomes.

Nasopharyngeal competition dynamics are likely to be altered following vaccine introduction: bacteriocin prevalence and diversity among Icelandic and Kenyan pneumococci

The paper examines changes in bacteriocin prevalence and diversity in pneumococci from Iceland and Kenya before and after vaccine introduction, showing vaccine-induced shifts in bacterial population structure.

RNase R, a new virulence determinant of Streptococcus pneumoniae

This study shows that RNase R enhances pneumococcal virulence in Galleria mellonella by affecting bacterial replication and immune evasion.

The role of interspecies recombinations in the evolution of antibiotic resistant pneumococci

The paper reconstructs the evolutionary histories of antibiotic-resistant pneumococcal lineages PMEN3 and PMEN9, showing how interspecies recombination contributes to antibiotic resistance and serotype switching.

Determining the serotype composition of mixed samples of pneumococcus using whole genome sequencing

This paper introduces SeroCall, a software tool for accurately quantifying pneumococcal serotypes in mixed samples using whole-genome sequencing.

Discovery and Predictive Modeling of Urine Microbiome, Metabolite and Cytokine Biomarkers in Hospitalized Patients with Community Acquired Pneumonia

This study identifies urine microbiome, metabolite, and cytokine biomarkers to predict pneumonia etiology with high accuracy using LASSO modeling.

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

The paper uses genome-wide association studies to show human and pneumococcal genetic variation influences susceptibility and severity of pneumococcal meningitis.

Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data

This paper analyzes pneumococcal carriage genomic data before and after PCV13 introduction, showing reduced vaccine-type strains and limited serotype replacement.

Identifying Streptococcus pneumoniae genes associated with invasive disease using pangenome-based whole genome sequence typing

This study identifies 43 genes associated with invasive pneumococcal disease using whole genome sequence data and a random forest machine-learning algorithm across three geographically distinct datasets.

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

SeroBA predicts Streptococcus pneumoniae serotypes from whole genome sequencing data with high concordance and scalability.

A Comparison Of Machine Learning And Bayesian Modelling For Molecular Serotyping

The paper compares Bayesian modeling and machine learning for serotype classification of Streptococcus pneumoniae using genomic data, finding machine learning outperforms the Bayesian model with enhanced training data.

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

This paper identifies genomic variation associated with pneumococcal carriage duration using longitudinal data and genome-wide association studies.