A Panel of Diverse Klebsiella pneumoniae Clinical Isolates for Research and Development

Abstract

Klebsiella pneumoniae are a leading cause of healthcare associated infections worldwide. In particular, strains expressing extended-spectrum β-lactamases (ESBLs) and carbapenemases pose serious treatment challenges, leading the World Health Organization (WHO) to designate ESBL and carbapenem-resistant Enterobacteriaceae (CRE) as "critical" threats to human health. Research efforts to combat these pathogens can be supported by accessibility to diverse and clinically relevant isolates for testing novel therapeutics. Here, we describe a panel of 100 diverse K. pneumoniae isolates publicly available to assist the research community in this endeavor. Whole-genome sequencing (WGS) was performed on 3,878 K. pneumoniae clinical isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. The isolates were cultured from 63 facilities in 19 countries between 2001 and 2020. Core-genome multilocus sequence typing and high-resolution single nucleotide polymorphism based phylogenetic analyses captured the genetic diversity of the collection and were used to select the final panel of 100 isolates. In addition to known multi-drug resistant (MDR) pandemic lineages, the final panel includes hypervirulent lineages and isolates with specific and diverse resistance genes and virulence biomarkers. A broad range of antibiotic susceptibilities ranging from pan-sensitive to extensively drug resistant isolates are described. The panel collection, all associated metadata and genome sequences, are available at no additional cost and will be an important for the research community and for the design and development of novel antimicrobial agents and diagnostics against this important pathogen.

Differentiation of hypervirulent and classicalKlebsiella pneumoniaewith acquired drug resistance

“…Notably, these strains were identified by clinical syndrome irrespective of their antimicrobial susceptibility profile (4). Interestingly, only 0.9% of a 3,123 MDR K. pneumoniae global strain set (27) carried all 5 biomarkers, which we find here to be most predictive of hypervirulence.…”

“…Of these 49 strains, 17 (35%) possessed all 5 biomarkers, 7 (14%) possessed 4 biomarkers, 19 (39%) possessed 2 biomarkers, and 6 (12%) possessed 1 biomarker (Supplementary Table S1). To place this in perspective, the natural prevalence of biomarkers in an unbiased collection of 3,123 MDR isolates (27) from global origins were assessed. The most represented biomarkers were peg-344 (8% of isolates), iucA (5%) rmpA2 and rmpA (each at 4%) and iroB (1%).…”

“…The metabolite transporter peg-344 was included in the agglomerative scoring due to its high association with fully virulent K. pneumoniae isolates (4). To calculate the prevalence of iroB, iucA, peg-344 , rmpA and rmpA2 in MDR K. pneumoniae, an unbiased collection of 3,123 clinical isolates (27) from global origins was queried using BLASTN and Kleborate (Supplementary Table S2). Strains also underwent antimicrobial susceptibility testing using reference broth microdilution with panels that were prepared in-house according to the Clinical and Laboratory Standards Institute (CLSI) guidelines (28) and stored at –70°C until use.…”

A heptavalent O-antigen bioconjugate vaccine exhibits differential functional antibody responses against diverseKlebsiella pneumoniaeisolates

“…K. pneumoniae strains and mutants were used for all ELISAs and serum bactericidal assays. Fourteen of the 18 strains used for this study are part of the the BEI Resources Repository Klebsiella pneumoniae diversity panel (27) which was obtained from BEI Resources, NIAID, NIH: Klebsiella pneumoniae MRSN Diversity Panel, NR-55604, provided by the Multidrug-Resistant Organism Repository and Surveillance Network (MRSN) at the Walter Reed Army Institute of Research (WRAIR), Silver Springs, Maryland, USA. BEI strains were categorized according to the BEI website for their O-antigen and capsule.…”