Abstract
Shigella spp. and E. coli are closely related and cannot be distinguished using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) with commercially available databases. Here, three alternative approaches using MALDI-TOF MS to identify and distinguish Shigella spp., E. coli, and its pathotype EIEC were explored and evaluated using spectra of 456 Shigella spp., 42 E. coli, and 61 EIEC isolates. Identification with a custom-made database resulted in >94% Shigella identified at the genus level and >91% S. sonnei and S. flexneri at the species level, but the distinction of S. dysenteriae, S. boydii, and E. coli was poor. With biomarker assignment, 98% S. sonnei isolates were correctly identified, although specificity was low. Discriminating markers for S. dysenteriae, S. boydii, and E. coli were not assigned at all. Classification models using machine learning correctly identified Shigella in 96% of isolates, but most E. coli isolates were also assigned to Shigella. None of the proposed alternative approaches were suitable for clinical diagnostics for identifying Shigella spp., E. coli, and EIEC, reflecting their relatedness and taxonomical classification. We suggest the use of MALDI-TOF MS for the identification of the Shigella spp./E. coli complex, but other tests should be used for distinction.
Highlights
Introduction iationsThe E. coli pathotype entero-invasive E. coli (EIEC) is thought to cause the same disease as Shigella spp. [1]
A few biomarkers for Shigella spp. and E. coli described by Khot and Fisher [19] were present within a range of 500 ppm in isolates used in this study, i.e., 4163 Da, 7157 Da, Da, and 9227 Da, and corrected for a charge of 2 electrons, 5096 Da and 5752 Da
Current commercially available MALDI-TOF MS databases cannot distinguish between Shigella spp. and E. coli
Summary
A total of 559 isolates consisting of 36 S. dysenteriae, 156 S. flexneri, 32 S. boydii, 232 S. sonnei, 61 EIEC, and 42 other E. coli of human and animal origin comprising phylogroups. 82.49T ; STEC ci 1 ; EPEC ci 1 mussel, 3 pigeon, turkey, 1 oyster ci = clinical isolate. 2 isolated from animals, all other numbers are reference isolates. Except the references, were identified using a previously described culturebased identification algorithm [25]. They were divided into a set of training isolates (n = 288) and test isolates (n = 271), both having similar species and serotype distributions. The test set was used to test all of these algorithms in duplicate, with both direct smear and ethanol-formic acid extraction application methods
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