TY - GEN A1 - Khan, Muhammad Moman A1 - Sidorczuk, Katarzyna A1 - Becker, Juliane A1 - Aleksandrowicz, Adrianna A1 - Baraniewicz, Karolina A1 - Ludwig, Christina A1 - Ali, Aamir A1 - Kingsley, Robert A. A1 - Schierack, Peter A1 - Kolenda, Rafał T1 - Characterization of clumpy adhesion of Escherichia coli to human cells and associated factors influencing antibiotic sensitivity T2 - Microbiology Spectrum N2 - Escherichia coli intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of E. coli strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found to be distinct from planktonic bacteria in the supernatant. A total of 622 genes in the transcriptome were differentially expressed in bacteria present in clumps relative to the planktonic bacteria. Seven genes targeted for disruption had variable distribution in different pathotypes and nonpathogenic E. coli, with the pilV and spnT genes being the least frequent or absent from most groups. Deletion (Δ) of five differentially expressed genes, flgH, ffp, pilV, spnT, and yggT, affected motility, adhesion, or antibiotic stress. ΔflgH exhibited 80% decrease and ΔyggT depicted 184% increase in adhesion, and upon complementation, adhesion was significantly reduced to 13%. ΔflgH lost motility and was regenerated when complemented, whereas Δffp had significantly increased motility, and reintroduction of the same gene reduced it to the wild-type level. The clumps produced by Δffp and ΔspnT were more resistant and protected the bacteria, with ΔspnT showing the best clump formation in terms of ampicillin stress protection. ΔyggT had the lowest tolerance to gentamicin, where the antibiotic stress completely eliminated the bacteria. Overall, we were able to investigate the influence of clump formation on cell surface adhesion and antimicrobial tolerance, with the contribution of several factors crucial to clump formation on susceptibility to the selected antibiotics. KW - Infectious Diseases KW - Cell Biology KW - Microbiology (medical) KW - Genetics KW - General Immunology and Microbiology KW - Ecology KW - Physiology Y1 - 2024 U6 - https://doi.org/10.1128/spectrum.02606-23 SN - 2165-0497 ER - TY - GEN A1 - Sidorczuk, Katarzyna A1 - Burdukiewicz, Michał A1 - Cerk, Klara A1 - Fritscher, Joachim A1 - Kingsley, Robert A. A1 - Schierack, Peter A1 - Hildebrand, Falk A1 - Kolenda, Rafał T1 - AdhesiomeR: a tool for Escherichia coli adhesin classification and analysis T2 - BMC Genomics N2 - AbstractAdhesins are crucial factors in the virulence of bacterial pathogens such as Escherichia coli. However, to date no resources have been dedicated to the detailed analysis of E. coli adhesins. Here, we provide adhesiomeR software that enables characterization of the complete adhesin repertoire, termed the adhesiome. AdhesiomeR incorporates the most comprehensive database of E. coli adhesins and facilitates an extensive analysis of adhesiome. We demonstrate that adhesiomeR achieves 98% accuracy when compared with experimental analyses. Based on analysis of 15,000 E. coli genomes, we define novel adhesiome profiles and clusters, providing a nomenclature for a unified comparison of E. coli adhesiomes. Y1 - 2024 U6 - https://doi.org/10.1186/s12864-024-10525-6 SN - 1471-2164 VL - 25 IS - 1 SP - 1 EP - 10 PB - Springer Science and Business Media LLC ER -