Use of a national repository of Fourier-transform infrared spectroscopy spectra enables fast detection of silent outbreaks and prevention of spread of new antibiotic-resistant sequence types

Background: The reference microbiology laboratory of Israel’s National Institute for Antibiotic Resistance and Infection Control has established a national repository of isolates analyzed by Fourier-transform infrared (FTIR) spectroscopy and their spectra. Healthcare institutions send antibiotic-resistant isolates as part of outbreak investigation, periodic nation-wide collection of specific species, or point prevalence studies. Here, we describe the use of a national FTIR repository to detect the emergence and spread of new sequence types and resistance mechanisms. Methods: Using FTIR, we produced dendrograms of outbreaks and periodic country-level dendrograms of isolates from selected species. When FTIR identified new clusters that were distinct from previously characterized clusters, they were investigated further by whole genome sequencing. Results: FTIR analysis uncovered two clones new to Israel: NDM-5-producing E. coli ST650 harboring a novel plasmid, and NDM-producing K. pneumoniae ST307. Conclusions: Establishing regional or national FTIR repositories could serve as a simple and effective tool for early detection of new antibiotic-resistant clones.