Genomic surveillance for multidrug-resistant or hypervirulent Klebsiella pneumoniae among United States bloodstream isolates

Abstract

Background Klebsiella pneumoniae strains have been divided into two major categories: classical K. pneumoniae, which are frequently multidrug-resistant and cause hospital-acquired infections in patients with impaired defenses, and hypervirulent K. pneumoniae, which cause severe community-acquired and disseminated infections in normal hosts. Both types of infections may lead to bacteremia and are associated with significant morbidity and mortality. The relative burden of these two types of K. pneumoniae among bloodstream isolates within the United States is not well understood. Methods We evaluated consecutive K. pneumoniae isolates cultured from the blood of hospitalized patients at Northwestern Memorial Hospital (NMH) in Chicago, Illinois between April 2015 and April 2017. Bloodstream isolates underwent whole genome sequencing, and sequence types (STs), capsule loci (KLs), virulence genes, and antimicrobial resistance genes were identified in the genomes using the bioinformatic tools Kleborate and Kaptive. Patient demographic, comorbidity, and infection information, as well as the phenotypic antimicrobial resistance of the isolates were extracted from the electronic health record. Candidate hypervirulent isolates were tested in a murine model of pneumonia, and their plasmids were characterized using long-read sequencing. We also extracted STs, KLs, and virulence and antimicrobial resistance genes from the genomes of bloodstream isolates submitted from 33 United States institutions between 2007 and 2021 to the National Center for Biotechnology Information (NCBI) database. Results Consecutive K. pneumoniae bloodstream isolates (n = 104, one per patient) from NMH consisted of 75 distinct STs and 51 unique capsule loci. The majority of these isolates (n = 58, 55.8%) were susceptible to all tested antibiotics except ampicillin, but 17 (16.3%) were multidrug-resistant. A total of 32 (30.8%) of these isolates were STs of known high-risk clones, including ST258 and ST45. In particular, 18 (17.3%) were resistant to ceftriaxone (of which 17 harbored extended-spectrum beta-lactamase genes) and 9 (8.7%) were resistant to meropenem (all of which harbored a carbapenemase genes). Four (3.8%) of the 104 isolates were hypervirulent K. pneumoniae, as evidenced by hypermucoviscous phenotypes, high levels of virulence in a murine model of pneumonia, and the presence of large plasmids similar to characterized hypervirulence plasmids. These isolates were cultured from patients who had not recently traveled to Asia. Two of these hypervirulent isolates belonged to the well characterized ST23 lineage and one to the re-emerging ST66 lineage. Of particular concern, two of these isolates contained plasmids with tra conjugation loci suggesting the potential for transmission. We also analyzed 963 publicly available genomes of K. pneumoniae bloodstream isolates from locations within the United States. Of these, 465 (48.3%) and 760 (78.9%) contained extended-spectrum beta-lactamase genes or carbapenemase genes, respectively, suggesting a bias towards submission of antibiotic-resistant isolates. The known multidrug-resistant high-risk clones ST258 and ST307 were the predominant sequence types. A total of 32 (3.3%) of these isolates contained aerobactin biosynthesis genes and 26 (2.7%) contained at least two genetic features of hvKP strains, suggesting elevated levels of virulence. We identified 6 (0.6%) isolates that were STs associated with hvKP: ST23 (n = 4), ST380 (n = 1), and ST65 (n = 1). Conclusions Examination of consecutive isolates from a single center demonstrated that multidrug-resistant high-risk clones are indeed common, but a small number of hypervirulent K. pneumoniae isolates were also observed in patients with no recent travel history to Asia, suggesting that these isolates are undergoing community spread in the United States. A larger collection of publicly available bloodstream isolate genomes also suggested that hypervirulent K. pneumoniae strains are present but rare in the USA; however, this collection appears to be heavily biased towards highly antibiotic-resistant isolates (and correspondingly away from hypervirulent isolates).

Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains

“…Another large-scale study in China reported that 36% of screened carbapenem-resistant (CRKp) strains carried the hypervirulence-associated siderophore aerobactin locus [ 17 ]. Other regional studies focused on Singapore [ 18 ], India [ 19 ] and the USA [ 20 ], while the global landscape has also been investigated [ 21 ]. Our work extends the previous reports by exploring in detail the plasmid replicons associated with the CRhvKp genotype, globally.…”

Differentiation of hypervirulent and classicalKlebsiella pneumoniaewith acquired drug resistance

“…In our study, all 24 strains that possessed only iucA and/or rmpA/A2 were designated as cKp (Supplementary Table S1). Although, less pragmatic, ascites growth curves further enhance accuracy and murine infection models remain the most accurate means to identify hvKp strains (4, 50). Of note, although commonly used, the Galleria mellonella infection model is unable to differentiate hvKp from cKp (51).…”

Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395

“…Fig. 4 Structure of carbapenemase gene-carrying plasmids. BRIG images show similarities between plasmid sequences of selected ST395 isolates (central rings) and other published plasmid sequences identified by BLAST (concentric rings colored according to legends).…”

“…Klebsiella pneumoniae is an opportunistic pathogen and one of the most common causes of hospital-and community-acquired infections [1]. It has been traditionally differentiated into classic (frequently but not exclusively multidrug-resistant [MDR]) and hypervirulent K. pneumoniae (hvKp) with the latter appearing clinically as mostly antibiotic-susceptible and invasive pathogen able to induce multiple site infection [2][3][4]. However, a recent study revealed that definition boundaries are blurred and that a strict assignation to particular contexts (hospitalor community-associated) not always applies [5].…”