| Summary: | Pneumococcal proteins unrelated to serotypes are considered to be candidates of antigens in next-generation vaccines. In the present study, the prevalence of vaccine candidate protein genes, along with serotypes and antimicrobial resistance determinants, was investigated in a total of 57 isolates obtained from a tertiary care hospital in Japan. All of the pediatric isolates and 76.6% of the adult isolates did not belong to PCV13 (a 13-valent pneumococcal conjugate vaccine) serotypes, and 70.2% of all isolates showed multidrug resistance. All of the isolates had <i>ply</i>, <i>pavA</i>, <i>nanA</i>, and <i>nanB</i>, and high prevalence was noted for the <i>pspA</i> and <i>pspC</i> genes (96.5% and 78.9%, respectively). Detection rates for the pneumococcal histidine triad protein (Pht) genes <i>phtA</i>, <i>phtB</i>, <i>phtD</i>, and <i>phtE</i> were 49.1%, 26.3%, 61.4%, and 100%, respectively. Two fusion-type genes, <i>phtA/B</i> and <i>phtA/D</i>, were identified, with a prevalence of 36.9% and 14.0%, respectively. These fusion types showed 78.1−90.0% nucleotide sequence identity with <i>phtA</i>, <i>phtB</i>, and <i>phtD</i>. The most prevalent <i>pht</i> profile was <i>phtA</i> + <i>phtD</i> + <i>phtE</i> (26.3%), followed by <i>phtA/B</i> + <i>phtE</i> (19.3%) and <i>phtA/B</i> + <i>phtD</i> + <i>phtE</i> (17.5%), while <i>pht</i> profiles including <i>phtD</i> and/or <i>phtA</i>/<i>phtD</i> were found in 71.9% of isolates. The present study revealed the presence of two fusion types of Pht and their unexpectedly high prevalence. These fusion types, as well as PhtA and PhtB, contained sequences similar to the B cell epitopes that have been previously reported for PhtD.
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