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The city's health authorities declared an outbreak on Tuesday and expressed concern the scarlet fever bacterium involved has mutated into a strain that appears to be resistant to traditional antibiotic treatment and which may also be more transmissible.
Scientists at the University of Hong Kong have warned that the strain of scarlet fever that has already killed two children and infected dozens of others has mutated and become more contagious.
"This (mutation) may nicely explain the 'unusual' large outbreak of the scarlet fever in Hong Kong recently," Thomas Tsang, director of the Centre for Health Protection (CHP) said on Monday.
He added that the Chinese mainland and Macao also face widespread outbreaks of the disease.
Scarlet fever infections have gone up around 5-fold in China, and 3-fold in Macau, about an hour by ferry from Hong Kong.