Studying bacterial infections in vivo holds high importance as it offers a window into the complex environment of host-pathogen interactions, shedding light on bacterial adaptation and maintenance of infection. Even though in vitro studies have broadened our understanding on bacterial virulence and adaptation strategies, many questions about the behaviour of bacterial pathogens in vivo remain unanswered. Human prosthetic joint infection (PJI) are challenging to treat and often necessitate reconstructive surgery and extended antibiotic therapy, leading to the emergence of antibiotic-resistant bacteria in hospital. These infections serve as prime models for biofilm-related infections, featuring a variety of bacterial types, enabling investigation of various bacterial adaptation strategies. To achieve this, we are developing novel methods to recover intact total RNA and enrich bacterial total RNA to obtain robust and complete bacterial transcriptomes from PJIs. This study does not investigate any human related transcriptome or genome.