1837. Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem Resistant Klebsiella pneumoniae from Blood Cultures of Individual Patients

Abstract

Abstract Background The longstanding paradigm is that almost all bloodstream infections (BSIs) stem from a single, clonal organism. We hypothesized that carbapenem resistant K. pneumoniae (CRKP) from individual patients (pts) with BSIs are genetically diverse and manifest phenotypic differences that are not typically recognized by the clinical microbiology laboratory at time of diagnosis. Methods We streaked blood culture (BC) broth from 6 pts with CRKP BSI onto blood agar plates, and randomly picked 9 colonies (strains) for HiSeq (Illumina) whole genome sequence. Single BSI isolates recovered by the clinical micro lab from individual pts underwent short- and long-read MinION (ONT) sequencing. Results 2 pts were infected with clade 1 (B, G), and 4 with clade 2 (A, D, F, J) ST258 KPC-producing KP. Strains from individual pts clustered by cgSNP phylogeny (Fig. 1A-B). BC bottles from each pt harbored genetically heterogenous KP populations, with strains differing from each other by cgSNPs (Fig. 1B), presence/absence of specific antibiotic resistance genes (Fig. 1A), mutations of capsular genes (Fig 2) and at other loci involved in host interactions, and/or loss of plasmids or plasmid-borne genes (Fig. 1A). Differences in capsular gene composition were observed in KL107 capsule type strains from pts A, D and J (Fig. 2). Pangenome analyses showed accessory gene composition diversity among strains from all pts (Fig. 3). Intra-pt genetically diverse strains exhibited differences in antibiotic resistance (Fig. 4), viscosity and mucosity, capsular content, and resistance to serum and macrophage killing. Various strains from pts A and J differed in ability to cause target organ infections or mortality in a mouse model of intravenous disseminated infection (Fig. 5). Conclusion We identified genotypic and phenotypic variant strains of ST258 KP from BSIs of individual patients that were not recognized at time of diagnosis. Our data suggest a new, population-based paradigm for BSIs by CRKP. The findings potentially have profound implications for medical, microbiology laboratory and infection prevention practices, and for understanding emergence of antibiotic resistance and pathogenesis. Disclosures Cornelius J. Clancy, MD, receives research funding paid to his institution from Astellas and Merck: Grant/Research Support|serves as an advisory Board member for Astellas, Cidara, and Scynexis, served on the advisory board for Merck, Qpex Biopharma, and Shionogi: Advisor/Consultant|Venatorx and Needham & Associates: Advisor/Consultant.