Leveraging the global genomic epidemiology of carbapenemase-producing Klebsiella pneumoniae to inform infection prevention in Tunisian hospitals

Introduction: Habib Bourguiba Hospital (HBH) in Sfax, Tunisia, a 500-bed regional medical center, experienced profound increases in carbapenemase-producing Klebsiella pneumoniae (CPK) infections over 2009-2022. Given limited resources, we leveraged Clinical microbiologic and genomic information with analyses using internationally available tools in FDA GenomeTrakr and NCBI Pathogen Detection, to facilitate high-resolution clustering of strains and carbapenemase-carrying plasmids that resolved transmission chains and reservoirs. Methods: Clinical Microbiology analyses, including carbapenemase PCR, evaluated 1013 unique CPK isolates. PFGE and plasmid conjugation profiles identified representative strains by year for genomic analyses. Genomic-epidemiologic analyses identified critical strains and plasmids mobilizing resistance, their global context, and endemic versus sporadic hospital entry over time. Results: Hospital-acquired CPK increased >10-fold over 2009-2022, from 0.95 to 9.59 cases per 10000 patient days. OXA-48-like enzymes occurred most frequently (730 strains, 56.7%), followed by NDMs (281, 43.1%), or both carbapenemases (207, 26.9%). Genomic analyses revealed 23 genomic sequence types (STs) with 70% occurring in ST101, ST147, and ST383. ST and carbapenemase-mobilizing plasmids changed significantly over time. In 2009, blaOXA-204-producing strains occurred in ST383, followed by blaOXA-48 in ST101 in 2011 and blaNDM-1 in ST147 in 2014. Since 2019, dual blaNDM-5, blaOXA-48 arose in ST383 isolates from recent epidemic international lineages. Diverse plasmids mobilized resistance genes with blaOXA-48-like carried by IncL/M (53/61; 86.8%), blaNDM-1 by IncFIB (pQIL)/IncFII multi-replicon plasmids (22/35; 62.8%), and blaNDM-5 by hybrid IncFIB/IncHI1B plasmids (13/13; 100%). Clustering with 80,252 K. pneumoniae genomes within NCBI Pathogen Detection rapidly identified strain global contexts, of which 82% of HBH's dominant STs clustered with Mediterranean and globally clusters while 18% were unique to the hospital. Conclusion: A 14-year genomic analysis of Tunisian CPK sepsis isolates defined a complex landscape of hospital-endemic and sporadically entering strains, informing the need for tailored screening programs to enable prevention programs, particularly at patient ICU admission. Our analyses identified increasingly resistant strains that contribute to global CPK outbreaks.