Table 2.
List of nonmolecular and molecular methods for accurate differentiation of Escherichia coli and Shigella spp
| Method for differentiation | Target | Level of differentiation between E. coli and Shigella spp. | References |
|---|---|---|---|
| MALDI-TOF MS | Biomarker-based classifiers using their protein signature | Conventional MALDI-TOF MS fails to distinguish E. coli from Shigella spp. However, advanced software analytic tools like ClinPro could distinguish inactive and other non-lactose-fermenting E. coli from Shigella spp. | Francisco et al.[16]; Khot and Fischer [4] |
| Duplex real-time PCR | uidA, lacY | Method is based on target-specific real-time PCR. EIEC and Shigella spp. can be differentiated because lacY is specific for E. coli | Pavlovic et al.[10] |
| 16S rRNA sequencing | 16S rRNA | Unacceptable for discrimination of E. coli and Shigella spp. because sequence similarities were >99% for EIEC, EHEC and Shigella spp. | Edwards et al.[12]; Chen et al.[13] |
| MLST (conventional) | Housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, recA) | Allele-based sequence type identification within E. coli and Shigella spp. without differentiating between them | Li et al.[15] |
| Specific locus variants | Housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, recA) | Uses sequence data of housekeeping genes rather than MLST allelic profiles. Can differentiate within sequence types using single-locus variant and double-locus variant approach | Gibreel et al.[17]; Otero et al.[18]; Shahsavan et al.[19] |
| k-mer | k-mer regions | Serotype-level identification and differentiation of E. coli and Shigella spp. is performed using co-occurring k-mers | Hasman et al.[23]; Larsen et al.[24]; Chattaway et al.[22] |
| SNP | SNP markers | Specific SNP markers were used for classification using SNPs with their evolutionary phylogenetic relationships | Ashton et al.[26]; Pettengill et al.[25] |
EHEC, enterohaemorrhagic Escherichia coli; EIEC, enteroinvasive Escherichia coli; MALDI-TOF MS, matrix-assisted desorption ionization–time of flight mass spectrometry; MLST, multilocus sequence typing; SNP, single nucleotide polymorphism.