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

The COVID-19 pandemic has given us an unprecedented opportunity to study the clinical and molecular epidemiology of Streptococcus pneumoniae 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 S. pneumoniae 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 n = 11). Multilocus sequence typing revealed 34 sequence-types, including four novel ones. Resistome profiling showed that the 64 S. pneumoniae isolates exhibited greater abundance of resistance genes compared to 10,234 S. pneumoniae 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, S. pneumoniae serotype 3 has remained as one of the most important causes of pneumococcal infections in Hong Kong. S. pneumoniae strains from our patients were more resistant to antibiotics compared to those from Western countries.