Outbreak Investigation of Phytobacter diazotrophicus Using Fourier Transform Infrared Spectroscopy compared to cgMLST

Phytobacter diazotrophicus is an emerging opportunistic pathogen associated with hospital outbreaks and a reservoir of antimicrobial resistance genes; however, its clonal epidemiology remains poorly understood. Accurate identification and rapid clonal typing are crucial for infection control. Core genome MLST (cgMLST) is the genomic gold standard; however, it is both costly and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy using the IR Biotyper® emerges as a rapid and accessible typing alternative. This study evaluated the performance of the IR Biotyper® in discriminating P. diazotrophicus outbreak isolates, compared to cgMLST. Eight epidemiologically relevant isolates, including two from a total parenteral nutrition (TPN) outbreak and four from a hemodialysis clinic, along with two outliers, were analyzed. Its identification was confirmed by API20E, MALDI-TOF MS, nifL gene qPCR, and WGS. Both cgMLST, based on 7,755 conserved genes, and the FT-IR. Spectroscopy by IR Biotyper® were used for clonal typing, with the spectral cutoff empirically determined based on known clonal isolates. Both methodologies demonstrated remarkable agreement in detecting clonal clusters. The two TPN outbreak isolates showed 23 allele differences (ADs) by cgMLST and consistently clustered according to the IR Biotyper. Similarly, the four isolates from the outbreak at hemodialysis clinic formed homogeneous clusters by both methods (5-27 ADs by cgMLST). The outlier isolates were consistently discriminated. FT-IR spectroscopy (IR Biotyper®) proved promising and complementary to cgMLST for typing P. diazotrophicus in outbreak scenarios, offering a rapid and cost-effective alternative for detecting clonal events. Its applicability in routine epidemiological surveillance is significant.