Differences and fingerprints of ESBL-producing E. coli from chicken faeces

E. coli is an important source of β-lactam resistance. Extended Spectrum β-Lactamase (ESBL) producing E. coli and their phylogenetic transmission are an important problem for health. On the other hand, MALDI-TOF MS allows sensitive and specific applications in food safety and many clinical studies, and it is also a method approved by the Food and Drug Administration (FDA) for microbial identification. We thought that the protein phenotypic character of the bacteria might provide data on resistance. This study aims to investigate β-lactamases in E. coli and to examine the differences in protein properties of ESBL-producing bacteria. In the present study that is the first report for Duzce (Türkiye), 28.6% of 122 isolates were identified as Chicken Faeces E. coli (CFEC)-ESBL. bla_CTX-M, bla_CTX-M-1, bla_CTX-M-15, bla_SHV, bla_TEM, bla_OXA-10, bla_CIT and bla_MOX genes were determined with PCR and bla_CTX-M gene was detected with the highest rate (88.5%). At least one of the resistance genes was detected in the phenotype screening tests, except one of the isolates (CFEC-ESBL-90). On the other hand, CFEC-ESBL-38 contained bla_CTX-M-15 and the fact that this isolate was the only atypical ESBL strain with indole (-) and lac (-) characteristics among all isolates explains the highest variance (41%). It was also different from other Principle Component Analysis (PCA) components. Moreover, this isolate had a high degree of similarity (87%; CCI) with the other isolate (CFEC-ESBL-90), which had low similarity to CFEC-ESBLs. The study determined the differences and similarities between E. coli isolates with all PCA analyses. Our findings indicate that the ESBL group generally differed from susceptible strains, and the isolates had some heterogeneities and homogeneities. As a result, phyloproteomic analyses with MALDI-TOF MS are considered beneficial in characterising phenotypic bacterial behaviour. Despite that, there were some limitations in the study that need to be solved with further research.