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

Abstract

Abstract 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.

Keywords

• Antibiotic resistance
• Fourier-transform infrared spectroscopy
• Surveillance