First Genome-Phenome Characterization of Two Nonencapsulated Streptococcus pneumoniae Isolates from Children with LRTI in China

Chen Cai,1,2 Hanfang Jiang,1 Wujiao Li,1 Bingjun Ye,1 Song Liang,1 Xiaoying Fu,1 Yunsheng Chen1 1Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518038, People’s Republic of China; 2Medical College, Jiaying University, Meizhou, Guangdong, 514031, People’s Republic of ChinaCorrespondence: Hanfang Jiang, Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518038, People’s Republic of China, Email [email protected]: Streptococcus pneumoniae (S.pn) is the predominant bacterial pathogen affecting children under 5 years old. Its polysaccharide capsule is the primary virulence factor, enabling the bacteria to evade the immune system and defining the serotypes that current vaccines target. Recently, nonencapsulated Streptococcus pneumoniae (NESp) have emerged as significant causes of conjunctivitis, otitis media, and invasive diseases worldwide. This report provides the first integrated genomic and phenotypic analysis of two NESp strains identified in China. The NESp colonies are characterized by their rough texture and small size, and they exhibit a slower growth rate compared to other serotypes. Whole-genome sequencing has identified these NESps strains as belonging to the ST10236 type. Notably, these strains demonstrate multidrug resistance. In comparison to encapsulated strains, NESps possess fewer coding genes related to cell wall biogenesis and basal metabolism. However, they still retain crucial virulence genes including the pspK gene. Our findings highlight the clinical significance of NESps and emphasize the need for ongoing surveillance of these “capsule-free” clones in the post-PCV era.Keywords: nonencapsulated Streptococcus pneumoniae, lower respiratory tract infection, multidrug resistance, virulence factors