In the present study, we analyzed 81 bacterial isolates of the genus Escherichia isolated from bat guano sampled in Škocjan caves at the Institute of Karst Research ZRC SAZU in 2020 and 2021. We determined the ERIC profile of the isolates, classified them into phylogenetic groups according to the original and revised methods, analyzed the presence of virulence factor genes, and tested their sensitivity to selected antimicrobial agents. We found that among the 81 isolates, 26 were nonclonal, belonging to Escherichia coli, most of which were classified into phylogenetic group B23 by the original method and into group B2 by the revised method after Clermont. Among genes for virulence factors associated with adhesions, we confirmed crl and fimH in all E. coli isolates, half of the isolates were positive for the autotransporter gene vat, and among toxins and invasins, we most frequently confirmed the astA, hlyF, and usp genes. The most frequent gene for factors related to immune defense was traT, and among genes related to iron uptake, fyuA and irp2 were confirmed in half of the isolates. Phenotypically, resistance to at least one antimicrobial agent was confirmed in 21 nonclonal E. coli isolates. We confirmed that the isolates also contained plasmids, but their isolation was difficult. For 17 strains with the same ERIC profile, we could not distinguish whether they belonged to E. coli or E. marmotae based on the 16S rRNA gene sequence. However, analysis by MALDI-TOF MS confirmed that the isolates forming white colonies on the MacConkey medium belong to the recently described species E. marmotae. This is the first report of isolation of E. marmotae from bat guano.
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