{"entity": "publication", "iuid": "ab2f96ed4c884800b4747bf303018f86", "timestamp": "2026-10-20T23:58:19.002Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab2f96ed4c884800b4747bf303018f86.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab2f96ed4c884800b4747bf303018f86"}}, "title": "A streamlined, nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing.", "authors": [{"family": "Liu", "given": "Honglian", "initials": "H"}, {"family": "Huch", "given": "Susanne", "initials": "S"}, {"family": "Hull", "given": "Ryan", "initials": "R"}, {"family": "Garcia", "given": "Fabricio Romero", "initials": "FR"}, {"family": "Nersisyan", "given": "Lilit", "initials": "L"}, {"family": "Yin", "given": "Xiushan", "initials": "X"}, {"family": "Chen", "given": "Wei-Hua", "initials": "WH"}, {"family": "Du", "given": "Juan", "initials": "J"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}], "type": "journal article", "published": "2026-03-23", "journal": {"title": "Cell Reports Methods", "issn": "2667-2375", "volume": "6", "issue": "3", "pages": "101327", "issn-l": null}, "abstract": "Antimicrobial resistance (AMR) poses a significant threat to public health. Rapid and accurate antimicrobial sensitivity testing is essential to guide effective treatment. Here, we present \"simplified 5PSeq\" (s5PSeq), a streamlined protocol for profiling 5' monophosphorylated (5'P) mRNA degradation intermediates that reflect ribosome dynamics in vivo. By capturing antibiotic-induced, context-specific ribosome stalling events, s5PSeq provides a molecular proxy for bacterial growth inhibition-offering a molecular phenotypic readout without the need for culturing. s5PSeq reduces library preparation time to under 4 h and incorporates a novel rRNA blocking strategy. We demonstrated its clinical utility by identifying erythromycin-resistant and sensitive Clostridioides difficile clinical isolates. Combining s5PSeq with real-time nanopore sequencing enables fast AMR diagnosis with as few as 3,000 reads. In addition to simplifying the study of 5'P co-translational mRNA decay, our work suggests that utilizing information-rich phenotypic molecular readouts can significantly improve AMR diagnostics.", "doi": "10.1016/j.crmeth.2026.101327", "pmid": "41825450", "labels": {"NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13030957"}, {"db": "pii", "key": "S2667-2375(26)00027-5"}], "notes": [], "created": "2026-10-14T13:03:01.667Z", "modified": "2026-10-14T13:03:01.672Z"}