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Updated: Jan 4, 2026
Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Molecular validation of clinical Pantoea isolates identified by MALDI-TOF
Craig D Soutar1, John Stavrinides1
1Department of Biology, University of Regina, Regina, Saskatchewan, Canada.
Abstract:
The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections by members of this species group are accurate. MALDI-TOF-based identification methods are commonly used in clinical laboratories as a rapid means of identification, but its reliability for identification of Pantoea species is unclear. In this study, we carried out cpn60-based molecular typing of 54 clinical isolates that had been identified as Pantoea using MALDI-TOF and other clinical typing methods. We found that 24% had been misidentified, and were actually strains of Citrobacter, Enterobacter, Kosakonia, Klebsiella, Pseudocitrobacter, members of the newly described Erwinia gerundensis, and even several unclassified members of the Enterobacteriaceae. The 40 clinical strains that were confirmed to be Pantoea were identified as Pantoea agglomerans, Pantoea allii, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica as well as the proposed species group, Pantoea latae. Some species groups considered largely environmental or plant-associated, such as P. allii and P. eucalypti were also among clinical specimens. Our results indicate that MALDI-TOF-based identification methods may misidentify strains of the Enterobacteriaceae as Pantoea.
Insights
Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) misidentified 24% of clinical Pantoea isolates. Molecular typing revealed misidentified bacteria included other Enterobacteriaceae, highlighting limitations in rapid diagnostic methods.
Area of Science:
- Clinical microbiology
- Bacterial identification
- Molecular typing
Background:
- The Enterobacterial genus Pantoea includes free-living and host-associated species.
- Accurate identification of Pantoea in clinical settings is debated.
- Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) is a common but potentially unreliable method for Pantoea identification.
Purpose of the Study:
- To assess the reliability of MALDI-TOF for identifying Pantoea species in clinical isolates.
- To molecularly characterize clinical isolates initially identified as Pantoea.
Main Methods:
- Collected 54 clinical isolates identified as Pantoea via MALDI-TOF and other clinical methods.
- Performed cpn60-based molecular typing for accurate identification.
- Compared molecular results with initial MALDI-TOF identifications.
Main Results:
- 24% of isolates initially identified as Pantoea were misidentified.
- Misidentified strains belonged to genera such as Citrobacter, Enterobacter, Kosakonia, Klebsiella, and Erwinia.
- Confirmed Pantoea strains included P. agglomerans, P. allii, P. dispersa, P. eucalypti, P. septica, and P. latae.
- Plant-associated species like P. allii and P. eucalypti were found in clinical specimens.
Conclusions:
- MALDI-TOF misidentifies a significant proportion of Enterobacteriaceae as Pantoea.
- cpn60-based molecular typing is crucial for accurate identification of Pantoea and related bacteria.
- Clinical isolates may include environmental/plant-associated Pantoea species, necessitating careful identification.
