Clinical and molecular epidemiology of Streptococcus pneumoniae infections during and in early recovery phase of COVID-19 pandemic in Hong Kong

Abstract

<p>The COVID-19 pandemic has given us an unprecedented opportunity to study the clinical and molecular epidemiology of <em>Streptococcus pneumoniae</em> infections during this period, when its incidence was at its record low and started to rise again when social distancing restriction policies were lifted. A total of 64 non-duplicated <em>S. pneumoniae</em> isolates (May/2020–December/2023) from patients at the Queen Mary Hospital, Hong Kong were included. The commonest clinical manifestation was community-acquired (n = 39) and hospital-acquired (n = 9) pneumonia. The most prevalent serotypes were 3, 19A and 19F (all <em>n</em> = 11). Multilocus sequence typing revealed 34 sequence-types, including four novel ones. Resistome profiling showed that the 64 <em>S. pneumoniae</em> isolates exhibited greater abundance of resistance genes compared to 10,234 <em>S. pneumoniae</em> isolates from other countries. Antimicrobial susceptibility testing showed that the isolates were highly resistant to erythromycin and clindamycin (73.4 % and 62.5 %), concurring with resistome profiling results which showed that 73.4 % and 65.6 % had resistance genes against these two antibiotics. Despite the transient interruption of transmission during the COVID-19 pandemic, <em>S. pneumoniae</em> serotype 3 has remained as one of the most important causes of pneumococcal infections in Hong Kong. <em>S. pneumoniae</em> strains from our patients were more resistant to antibiotics compared to those from Western countries.<br></p>