Journal: Microbiology Spectrum

Article Title: High-resolution genomics uncovers region-specific evolution and virulence of ocular Streptococcus pneumoniae

doi: 10.1128/spectrum.03291-25

Figure Lengend Snippet: Serotype distribution of ocular S. pneumoniae in Zhejiang, China. The serotypes of S. pneumoniae strains collected in the current study are presented in the bar figure. The green bars represent the pneumococcal conjugate vaccine types (PCV12T and PCV20T), and the gray bars represent the non-vaccine serotypes (NVT). A small figure was inserted in the upper-right corner to show the proportion of PCVs covered serotypes and NVT in all isolates.

Article Snippet: An S. pneumoniae reference strain (ATCC 49619) was used as quality control for each antimicrobial susceptibility test.

Techniques:

Journal: Microbiology Spectrum

Article Title: High-resolution genomics uncovers region-specific evolution and virulence of ocular Streptococcus pneumoniae

doi: 10.1128/spectrum.03291-25

Figure Lengend Snippet: The phylogenetic analysis and distribution of major antimicrobial resistance determinants among global ocular S. pneumoniae strains and the antimicrobial resistance profile of pneumococcus in the current study. ( A ) The phylogenetic tree of global pneumococcal isolates from ocular infections ( n = 58) was constructed via PopPUNK (v2.4.0) and aligned with the metadata, including country, serotype, ST type, GPSC type, and PBP1a-2b-2x mutation type, and antimicrobial resistance determinants ( ermB, mefA, and tetM ). This panel was visualized using iTOL (v6). ( B ) The antimicrobial susceptibility test results of PEN, CRO, ERY, and LVX against isolated ocular pneumococcus (one figure for each drug), and the last figure (bottom right corner of panel B) represents the resistance proportion in all tested pneumococcal strains against each drug. Red bars represent the resistance strains, and gray bars show the susceptible strains. The red dashed line in each figure indicates the breakpoint of each drug against S. pneumoniae according to the CLSI standard 2023.

Article Snippet: An S. pneumoniae reference strain (ATCC 49619) was used as quality control for each antimicrobial susceptibility test.

Techniques: Construct, Mutagenesis, Isolation

Journal: Microbiology Spectrum

Article Title: High-resolution genomics uncovers region-specific evolution and virulence of ocular Streptococcus pneumoniae

doi: 10.1128/spectrum.03291-25

Figure Lengend Snippet: Clone distribution aligned with diagnoses and virulence factors detected in global ocular S. pneumoniae . The phylogenetic tree of global pneumococcal isolates from ocular infections ( n = 58) was constructed via PopPUNK (v2.4.0) and aligned with the metadata, including diagnoses, country, serotype, ST type, GPSC type, and virulence factors. Four major clones were identified and shaded with different colors on the branch, including CC344 (light yellow), CC448 (light red), CC271 (light blue), and CC90 (light green).

Article Snippet: An S. pneumoniae reference strain (ATCC 49619) was used as quality control for each antimicrobial susceptibility test.

Techniques: Construct, Clone Assay

Journal: Microbiology Spectrum

Article Title: High-resolution genomics uncovers region-specific evolution and virulence of ocular Streptococcus pneumoniae

doi: 10.1128/spectrum.03291-25

Figure Lengend Snippet: Recombination analysis of global ocular S. pneumoniae. ( A ) The phylogenetic tree of global pneumococcal isolates from ocular infections ( n = 58) was constructed using the SNP of the core genome of each strain, and TIGR4 was used as the reference strain (aligned at the top of panel A). The ocular pneumococcal strains from China were marked in red in the isolated ID. The serotype, country, and diagnosis data were aligned at the tree tip. Recombination data were presented in red (recombination within each clone complex on an internal branch) and blue (recombination that occurred on a terminal branch that is unique to each isolate) blocks. Due to the high diversity of serotypes, countries, and diagnostic data presented in this figure, we chose to use a gradient color scale, ranging from bright yellow to dark blue, to illustrate the differences in the data. For example, in the serotype data, NT is bright yellow, serotype 3 is green, and 10A is dark blue. Specific data corresponding to each color are presented in the legend below panel A. The total SNP number ( B ), number of SNPs inside recombination ( C ), and recombination blocks ( D ) of each isolate were calculated in different regions (China, North America, Europe, and other Asian countries) worldwide. ( E ) The strains with r/m > 1 (the ratio of SNP introduced by recombination and by mutation) were also counted in the above four regions worldwide. “***” represents a P < 0.001, “****” represents a P < 0.0001, and “ns” indicates no significant difference between compared groups.

Article Snippet: An S. pneumoniae reference strain (ATCC 49619) was used as quality control for each antimicrobial susceptibility test.

Techniques: Construct, Isolation, Biomarker Discovery, Diagnostic Assay, Mutagenesis

Journal: Microbiology Spectrum

Article Title: High-resolution genomics uncovers region-specific evolution and virulence of ocular Streptococcus pneumoniae

doi: 10.1128/spectrum.03291-25

Figure Lengend Snippet: Single-nucleotide polymorphism analysis of global ocular S. pneumoniae . ( A–D ) The top 20 SNPs accumulated genes in ocular S. pneumoniae isolated from North America ( A ), Europe ( B ), other Asian countries ( C ), and China ( D ). The light red shading indicates the top five mutated genes. The dark red shading indicates the top mutated gene. The blue star marks gene ranked in the top five in China and not in other regions. ( E ) The SNP distribution across all genes of ocular S. pneumoniae from North America, Europe, other Asian countries, and China.

Article Snippet: An S. pneumoniae reference strain (ATCC 49619) was used as quality control for each antimicrobial susceptibility test.

Techniques: Isolation