Identification and characterization of a novel α-haemolytic streptococci, Streptococcus parapneumoniae sp. nov., which caused bacteremia with pyelonephritis

• Published in: International journal of medical microbiology Vol. 315; p. 151625
• Main Authors: Katayama, Yuri, Morita, Masatomo, Chang, Bin, Katagiri, Daisuke, Ishikane, Masahiro, Yamada, Gen, Mezaki, Kazuhisa, Kurokawa, Masami, Takano, Hideki, Akeda, Yukihiro
• Format: Journal Article
• Language: English
• Published: Germany Elsevier GmbH 01.06.2024; Elsevier
• Subjects: Anti-Bacterial Agents - pharmacology; Average nucleotide identity; Bacteremia; Bacteremia - microbiology; Bacterial Typing Techniques; DNA, Bacterial - genetics; DNA-DNA hybridization; Genome, Bacterial; Humans; Male; Microbial Sensitivity Tests; Middle Aged; Nucleic Acid Hybridization; Phylogeny; Pyelonephritis; Pyelonephritis - microbiology; Streptococcal Infections - microbiology; Streptococcus - classification; Streptococcus - genetics; Streptococcus - isolation & purification; Streptococcus parapneumoniae; Whole Genome Sequencing; α-Haemolytic streptococci; α-Haemolytic streptococci; Average nucleotide identity; Streptococcus parapneumoniae; DNA-DNA hybridization; Pyelonephritis; Bacteremia
• ISSN: 1438-4221; 1618-0607; 1618-0607
• DOI: 10.1016/j.ijmm.2024.151625

We report a case of bacteremia with pyelonephritis in an adult male with an underlying disease caused by α-hemolytic streptococci. α-Hemolytic streptococci were isolated from blood, but it was challenging to identify its species. This study aimed to characterize the causative bacterium SP4011 and to elucidate its species. The whole-genome sequence and biochemical characteristics of SP4011 were determined. Based on the genome sequence, phylogenetic analysis was performed with standard strains of each species of α-hemolytic streptococci. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were calculated. SP4011 showed optochin susceptibility and bile solubility, but did not react with pneumococcal omni antiserum. Phylogenetic analysis of the whole-genome sequence showed that SP4011 clustered with S. pneumoniae and S. pseodopneumoniae and was most closely related to S. pseodopneumoniae. Genomic analysis revealed that ANI and dDDH values between SP4011 and S. pseodopneumoniae were 94.0 % and 56.0 %, respectively, and between SP4011 and S. pneumoniae were 93.3 % and 52.2 %, respectively. Biochemical characteristics also showed differences between SP4011 and S. pseodopneumoniae and between SP4011 and S. pneumoniae. These results indicate that SP4011 is a novel species. Our findings indicate that SP4011 is a novel species of the genus Streptococcus. SP4011 has biochemical characteristics similar to S. pneumoniae, making it challenging to differentiate and requiring careful clinical diagnosis. This isolate was proposed to be a novel species, Streptococcus parapneumoniae sp. nov. The strain type is SP4011T (= JCM 36068T = KCTC 21228T).