Reduced virulence and enhanced host adaption during antibiotics therapy: A story of a within-host carbapenem-resistant Klebsiella pneumoniae sequence type 11 evolution in a fatal scrotal abscess patient

Abstract

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has disseminated globally and become a major threat to human life. The sequence type (ST) 11 CRKP is a dominant clone in Asia, especially China, but how this clone evolves in vivo, then adapts to host and facilitates dissemination remain largely unknown. We analyzed the genomic dynamics of 4 ST11-CRKP isolates sequencially isolated from the urine of a patient with initial fatal scrotal abscess and finally recovered without effective medication. Genomic differences were identified and their implications for pathogenesis and host adaptation were investigated. The related transcriptional pathways were further explored by RNA-Seq. Genomic analysis identified 4-24 mutations and 94%-100% were synonymous or intergenic. The mutation rate of ST11-CRKP was 2.1x10-6-1.7x10-5 substitutions/site/year over 47 days of antibiotics therapy. During this period, CRKP underwent several adaptive changes including tigecycline resistance and virulence attenuation. Tigecycline resistance was caused by ramR ribosomal binding site (RBS) deletion, which has been described by us previously. In this study, we demonstrated that mutations associated with acyltransferase (act) and ompK26 caused the virulence attenuation of ST11-CRKP. act deletion reduced the production of capsular polysaccharide and enhanced biofilm formation. RNA-Seq analysis revealed that act influenced the expression of ldhA, bglX, mtnK and metE which likely participate in capsular synthesis and biofilm formation. ompK26 affected the virulence by its overexpression caused by the deletion of upstream repressor binding site. Our finding suggested that the broad genomic diversity, high evolutionary capacity and rapid within-host adaptability of ST11-CRKP might contribute to the worldwide dissemination of this clone. IMPORTANCECarbapenem-resistant Klebsiella pneumoniae (CRKP) has disseminated worldwide and can cause life threatening infections, including pneumonia, bloodstream infections, urinary tract infections, intra-abdominal infection, liver abscess and meningitis. CRKP infection is the leading cause of high mortality in clinical. The sequence type (ST) 11 CRKP is a dominant clone and accounts for 60% of CRKP infections in China. Recently, the ST11-CRKP with high transmissibility are increasingly identified. Understanding how this clone evolved is crucial in controlling its further dissemination. The significance of our research is identifying the in vivo genomic dynamics of ST11-CRKP and the genetic basis for ST11-CRKP to facilitate persistence and dissemination, which will has broader biomedical impacts on understanding of ST11-CRKP dissemination. Furthermore, our study also highlights the importance of monitoring the development of variation in antibiotics susceptibility and virulence of bacteria in clinical practice, considering that pathogens can rapidly adapt to host during the treatment.