mRNAs present in the cell need to be translated to produce functional proteins. mRNA translation is a highly regulated process with multiple layers of control. Although translation initiation has been considered the rate-limiting step, and thus has been more intensively studied, recent evidence suggests that translation elongation is also highly regulated. Our lab has previously developed a method termed 5PSeq that takes advantage of the mRNA co-translational 5’-3’degradation to produce an in vivo ribosomal footprint. This approach, by sequencing the ends of 5’phosphorylated mRNA degradation intermediates, obtains a genome-wide drug-free measurement of ribosome dynamics. We have applied this approach to investigate both eukaryotic and prokaryotic mRNA degradation signatures. We are currently in the process to expand its applicability to investigate human samples, complex microbial mixtures and as a phenotypic reporter for antimicrobial resistance..