New diagnostic methods for and the first report of its identification in clinical isolates in North America.

BACKGROUND

Genomic sequences of and differ by 10%. Discovered as an environmental "cryptic clade" of Escherichia, also occurs in human infections. Microbiological and MALDI-TOF-MS methods frequently misidentify as . Our goal was to develop methods that reliably distinguish from to improve therapeutic decisions and treatments.

METHODS

A Taqman PCR method was developed to distinguish from based on genomic sequences of uidA, uidB, and a positive control targeting adk in and . MALDI-TOF-MS spectra were obtained for environmental and clinical isolates using a bioMérieux VITEK MALDI-TOF-MS system.

RESULTS

UidA- and uidB species-specific PCR amplified DNA from with 100% specificity, and not from or other Escherichia species. The Biomérieux VITEK MALDI-TOF-MS consistently misidentified as , with median IVD confidence scores for both and of 99.9%; however, RUO scores for (median 0%) were significantly lower ( < 0.0001) than for (median = 87.4%). The spectral peak between m/z 7,250 to 7,280 consistently occurred between 7,260 and 7,268 in and only between 7,268 and 7,280 in , with no overlap ( < 0.001). Application of these spectral criteria to 176 clinical isolates revealed the first identification of a isolate from a human infection in North America. The isolate had originally been diagnosed as based on a 99.1% IVD confidence score. This first North American clinical isolate was confirmed as by Taqman-PCR and whole genome sequencing. This isolate had numerous antibiotic resistance gene markers and unlike most clinical , this isolate lacked motility at 37°C.

CONCLUSION

Clinical tests based on these methods of differentiating and may assist in determining the prevalence of this emerging pathogen and making therapeutic decisions.