The findings suggest additional serotypes may need to be added to the current pneumococcal vaccine to provide fuller protection from ear infections.
In an attempt to reduce the number of cases of acute otitis media in children, the US began vaccinating infants with the seven-valent pneumococcal vaccine in 2000.
England and Wales followed suit, adding the pneumococcal vaccine to the childhood immunisation programme in September 2007.
The latest study focused on two populations of healthy children, aged six to 36 months, who had received the pneumococcal vaccine between 2003 and 2006.
All had received the pneumococcal vaccine between September 2003 and June 2006.
The first group of children had experienced their first or second episode of acute otitis media. The second group included children with difficult to treat otitis media.
Of the 1,816 children with acute otitis media, middle ear fluid samples were taken from 212 children. Of these 59 had S. pneumoniae infection.
The researchers found that a strain of S pneumoniae belonging to the serotype 19A was a new genotype and was resistant to all antibiotics approved in the US for use in children with ear infection.
This strain was identified in nine children, four of whom had been unsuccessfully treated with two or more antibiotics.
Lead researcher Dr Michael Pichichero, from the University of Rochester in New York, said the observations were worrying, especially as there were no new antibiotics available for acute otitis media in children.
'The study suggests an expanded pneumococcal conjugate vaccine is needed,' he said.