Molecular epidemiology of extended-spectrum β-lactamase-, AmpC β-lactamase- and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae isolated from Canadian hospitals over a 5 year period: CANWARD 2007-11.

To assess the proportion of Escherichia coli and Klebsiella pneumoniae from Canadian hospitals that produce extended-spectrum β-lactamases (ESBLs), AmpC β-lactamases and carbapenemases, as well as to describe the patterns of antibiotic resistance and molecular characteristics of these organisms. Some 5451 E. coli and 1659 K. pneumoniae were collected from 2007 to 2011 inclusive as part of the ongoing CANWARD national surveillance study. Antimicrobial susceptibility testing was performed to detect putative ESBL, AmpC and carbapenemase producers, which were then further characterized by PCR and sequencing to detect resistance genes. In addition, isolates were characterized by PFGE and an allele-specific PCR to detect isolates of sequence type (ST) 131. The proportion of ESBL-producing E. coli (2007, 3.4%; 2011, 7.1%), AmpC-producing E. coli (2007, 0.7%; 2011, 2.9%) and ESBL-producing K. pneumoniae (2007, 1.5%; 2011, 4.0%) among the isolates collected increased during the study period. The majority of ESBL-producing E. coli (>95%), AmpC-producing E. coli (>97%) and ESBL-producing K. pneumoniae (>89%) remained susceptible to colistin, amikacin, ertapenem and meropenem. Isolates were generally unrelated by PFGE (<80% similarity); however, ST131 was identified among 55.8% and 28.7% (P < 0.001) of ESBL- and AmpC-producing E. coli, respectively. CTX-M-15 was the dominant genotype in both ESBL-producing E. coli (66.2%) and ESBL-producing K. pneumoniae (50.0%), while the dominant genotype in AmpC-producing E. coli was CMY-2 (55.7%). Carbapenemase production was identified in 0.04% (n = 2) of E. coli and 0.06% (n = 1) of K. pneumoniae, all of which produced KPC-3. The proportion of ESBL- and AmpC-producing E. coli and K. pneumoniae increased significantly during the study period, while the number of carbapenemase producers remained low (<1%). Compared with AmpC-producing E. coli, ESBL-producing E. coli were significantly associated with multidrug resistance and the ST131 clone.