Using Nucleic Acid Microarrays To Perform Molecular Epidemiology and Detect Novel β-Lactamases: a Snapshot of Extended-Spectrum β-Lactamases throughout the World

The worldwide dissemination of extended-spectrum-β-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae is a major concern in both hospital and community settings. Rapid identification of these resistant pathogens and the genetic determinants they possess is needed to assist in clinical practice and epidemiological studies. A collection of Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, and Proteus mirabilis isolates, including phenotypically ESBL-positive (n = 1,093) and ESBL-negative isolates (n = 59), obtained in 2008–2009 from a longitudinal surveillance study (SMART) was examined using an in vitro nucleic acid-based microarray. This approach was used to detect and identify blaESBL (blaSHV, blaTEM, and blaCTX-M genes of groups 1, 2, 9, and 8/25) and blaKPC genes and was combined with selective PCR amplification and DNA sequencing for complete characterization of the blaESBL and blaKPC genes. Of the 1,093 phenotypically ESBL-positive isolates, 1,041 were identified as possessing at least one blaESBL gene (95.2% concordance), and 59 phenotypically ESBL-negative isolates, used as negative controls, were negative. Several ESBL variants of blaTEM (n = 5), blaSHV (n = 11), blaCTX-M (n = 19), and blaKPC (n = 3) were detected. A new blaSHV variant, blaSHV-129, and a new blaKPC variant, blaKPC-11, were also identified. The most common bla genes found in this study were blaCTX-M-15, blaCTX-M-14, and blaSHV-12. Using nucleic acid microarrays, we obtained a “molecular snapshot” of blaESBL genes in a current global population; we report that CTX-M-15 is still the dominant ESBL and provide the first report of the new β-lactamase variants blaSHV-129 and blaKPC-11.