Biology subjects

Szelag, M.

Publications and source records attributed to Szelag, M..

3 recordsLinked to original sources

bioRxiv2026

Precision single-cell profiling of Circulating Tumour Cells: novel markers and data-driven characterization by CTCeek

Circulating tumour cells (CTCs) represent a minimally invasive method for monitoring cancer evolution in patients. CTCs are nowadays commonly isolated using antibodies against EPCAM protein. A key limitation regards the extent of EPCAM-negative CTCs, such as those that undergo EMT or whose tumour of origin is EPCAM-low or negative. We studied 3,302 RNA single-cell transcriptomes reported as CTCs in public repositories. Using copy number variation and cell type-specific markers, we discriminated bona fide CTCs from contaminating blood cells, often mislabelled as CTCs. The integration of bona fide CTCs and PBMCs, from multiple datasets, allowed us to identify novel markers, such as CLDN4, CLDN7, EFNA1 and TACSTD2 for epithelial CTCs, KCNK15 and LY6K for epithelial B CTCs, and ITGB4 for both epithelial B and mesenchymal CTCs. We revealed PODXL, AXL, CAV1, and TGM2 as markers of mesenchymal CTCs, which might be undetectable using anti-EPCAM antibodies, and TM4SF1 as universal marker, expressed in all CTC subclasses. Additionally, we found platelets to be physically associated with the epithelial A, but not with the epithelial B or the mesenchymal subtypes. Finally, we developed and implemented CTCeek, the first web-based and public reference tool that automatically annotates bona fide CTCs from scRNA-sequencing profiles.

cancer biology↗

bioRxiv2024

A newly-identified IncY plasmid from multi-drug resistant Escherichia coli isolated from dairy cattle feces in Poland

Comprehensive whole-genome sequencing was performed on two multi-drug resistant Escherichia coli strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes (ARGs) located within many mobile genetic elements (e.g., insertional sequences or transposons), and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene tet(A), aph family aminoglycoside resistance genes aph(3")-lb and aph(6)-ld, {beta}-lactam resistance genes blaTEM-1, blaCTX-M-15, sulfonamide resistance gene sul2, fluoroquinolone resistance gene qnrS1, and the trimethoprim resistance gene dfrA14. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the Enterobacteriaceae. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. This findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant E. coli from livestock and food sources to be transmitted to humans and vice versa. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach.

microbiology↗

bioRxiv2024

The IncC and IncX1 resistance plasmids present in multi-drug resistant Escherichia coli strains isolated from poultry manure in Poland

The study describes the whole-genome sequencing of two antibiotic-resistant representative Escherichia coli strains, isolated from poultry manure in 2020. The samples were obtained from a commercial chicken meat production facility in Poland. The antibiotic resistance profile was characterized by co-resistance to {beta}-lactam antibiotics, aminoglycosides, and fluoroquinolones. The three identified resistance plasmids (R-plasmids), pECmdr13.2, pECmdr13.3 and pECmdr14.1, harbored various genes conferring resistance to tetracyclines (tetR[A]) for, aminoglycoside (aph, aac and aad families), {beta}-lactam (blaCMY-2, blaTEM-176), sulfonamide (sul1, sul2), fluoroquinolone (qnrS1), and phenicol (floR). These plasmids, which have not been previously reported in Poland, were found to carry IS26 insertion elements, the intI1-integrase gene, as well as conjugal transfer genes, facilitating horizontal gene transfer. Plasmids pECmdr13.2 and pECmdr14.1 also possessed a mercury resistance gene operon related to transposon Tn1696; this promotes plasmid persistence even without antibiotic selection pressure due to co-selection mechanisms such as co-resistance. The chicken manure-derived plasmids belonged to the IncX1 (narrow host range) and IncC (broad host range) incompatibility groups. Similar plasmids have been identified in various environments, clinical isolates, and farm animals, including cattle, swine, and poultry. This study holds significant importance for the One Health approach, as it highlights the potential for antimicrobial-resistant bacteria from livestock and food sources, particularly E. coli, to transfer through the food chain to humans and vice versa. This underscores the need for vigilant monitoring of R-plasmids prevalence in the human, animal and natural environments, and to implement strategies to mitigate the spread of antibiotic resistance.

microbiology↗