Post-infection colonization and recurrent infections by ST11-KL64 carbapenem-resistant Klebsiella pneumoniae: a study of within-host evolution

Bacteria pose a serious threat to hosts through adaptive mutations that confer stress resistance and promote persistent colonization. Here, we describe an adaptive evolution event involving eight highly similar ST11-KL64 carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, isolated from a non-infected inpatient who acquired two distinct CRKP strains, CRKP-F1 and CRKP-S2 during the first hospitalization, recovered, and was discharged after receiving antimicrobial therapy but subsequently experienced two additional recurrent febrile episodes and re-admission. The strain CRKP-S2 showed significantly enhanced resistance to oxidative stress, survival within macrophages, and internalization ability, and carried an additional ~72 kb fragment containing oxidative stress response factors (including NAD(P)-dependent oxidoreductases), and a ~ 19kb plasmid fragment harboring catA2, sul2, umuC/D genes, compared to the initial strain CRKP-F1. All four strains, CRKP-B3, CRKP-U4, CRKP-F5 and CRKP-S6, from the second hospitalization exhibited higher genetic similarity to CRKP-S2 than each other, and each of these strains has its own unique mutations compared to CRKP-S2. The third-hospitalization strain CRKP-U7 displayed the highest average nucleotide identity (ANI) with CRKP-S2, and possessed unique mutations in cecR, rlmA1, and selB, distinct from second-hospitalization strains. However, the last strain, CRKP-B8, carries a new gene mutation based on CRKP-U7 and exhibits greater host adaptability than all other isolates. While these findings are suggestive, whether the ~72-kb and ~19-kb fragments and mutations in CRKP-S2 drove enhanced colonization, and whether subsequent mutations contributed to subclones linked to recurrent febrile, or merely coincided, remains unclear. The possibility of mixed colonization by co-circulating subclones cannot be excluded, and functional validation is needed.