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

摘要

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 bla_ESBL (bla_SHV, bla_TEM, and bla_CTX-M genes of groups 1, 2, 9, and 8/25) and bla_KPC genes and was combined with selective PCR amplification and DNA sequencing for complete characterization of the bla_ESBL and bla_KPC genes. Of the 1,093 phenotypically ESBL-positive isolates, 1,041 were identified as possessing at least one bla_ESBL gene (95.2% concordance), and 59 phenotypically ESBL-negative isolates, used as negative controls, were negative. Several ESBL variants of bla_TEM (n = 5), bla_SHV (n = 11), bla_CTX-M (n = 19), and bla_KPC (n = 3) were detected. A new bla_SHV variant, bla_SHV-129, and a new bla_KPC variant, bla_KPC-11, were also identified. The most common bla genes found in this study were bla_CTX-M-15, bla_CTX-M-14, and bla_SHV-12. Using nucleic acid microarrays, we obtained a “molecular snapshot” of bla_ESBL 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 bla_SHV-129 and bla_KPC-11.