The article omits the most-important part of the story: the bacterial strains in question are “superbugs” because they contain a transmissable (between bacteria) gene that inactivates a class of potent antibiotics that most hospitals hold in reserve for very serious infections: the carbapenems (e.g., imipenem, meropenem, doripenem, ertapenem).
Thus, “CRE” stands for “carbapenem-resistant Enterobacteriaceae” - usually E. coli or Klebsiella pneumoniae.