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•Population structure of clinical Streptococcus pneumoniaeisolates associated with invasive pneumococcal disease (IPD) ranging from 2009 to 2017 in a China metropolitan city were characterized.•We identified an independent clade CC320_SZpop (ST271) dominantly circulating in China especially in Shenzhen and possible under expansion.•Clinical feature and antibiotics susceptibility analysis revealed that CC320_SZpop might manifest much higher pathogenicity and tolerance to β-lactam, which deserve more study and surveillance.