Genomic Definition of Hypervirulent and Multidrug-ResistantKlebsiella pneumoniaeClonal Groups

Abstract

We created a Web-accessible genome database to enable rapid extraction of genotype, virulence, and resistance information from sequences.

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

“…The presence of yersiniabactin in CC258, and also in the ESBL clones ST14 and ST15, is worrying, because our data show that it not only is strongly associated with infection in humans but also appears to be a frequent first step in the acquisition of additional siderophores that augment the ability of KpI clones to cause invasive non-hospital-related infections. There also is a high risk that current hypervirulent clones may acquire AMR, and MDR ST23 already has been reported in Korea, Vietnam, China, Madagascar, and Brazil (12,(61)(62)(63). Now that the associations have been recognized, new efforts can be more focused on the task of reconstructing the mobile elements that carry the critical virulence genes, ideally using long-read sequencing approaches that have proven successful for unraveling MDR plasmids (64).…”

“…Crucially, our study shows that we can augment these surveillance efforts by using key virulence genes as strong predictors of invasive disease in humans, and by determining clonal background, so that we can identify and track XDR hypervirulent clones as they emerge. To facilitate future genome-based surveillance, the genomes presented here have been deposited in the K. pneumoniae BIGSdb database (bigsdb.web.pasteur.fr) (12), which includes a core genome MLST scheme as well as key K. pneumoniae accessory genes encoding critical determinants of AMR, virulence, and capsule type. The data presented here provide a new genomic framework with which a new and deeper understanding of the K. pneumoniae population can be developed (SI Appendix, Fig.…”

“…Moreover it can thrive in a range of plant hosts and environmental niches, including water, soil, and plant matter (4,5,11). Although it is clear that K. pneumoniae is genetically and phenotypically diverse (12,13), previous efforts to identify specific features that can distinguish human clinical isolates from plant, animal, or environmental isolates have yielded no markers of humanspecific lineages (14). Three distinct phylogroups of K. pneumoniaeKpI, KpII, and KpIII-have been defined based on sequencing of a small number of genes (15,16), and it has been proposed that these phylogroups be redesignated as distinct species, namely, K. pneumoniae (KpI), K. quasipneumoniae (KpII) (17), and K. variicola (KpIII) (18); however, all three cause infections in humans (15,19).…”

Allocation of Klebsiella pneumoniae Bloodstream Isolates into Four Distinct Groups byompK36Typing in a Taiwanese University Hospital

“…ST14 was an SLV of ST15, but they were assigned to different ompK36 groups. ST14 and ST15 were subgroup founders in the eBURST analysis using the whole MLST database and have been allocated to CG14 and CG15 (34). Moreover, 3 ST clusters (ST23-ST1905-ST1893, ST268-ST36-ST1914-ST1590, and ST292-ST1925-ST1180) included members with different ompK36 types.…”

Evaluation of Antibiotic Resistance Patterns of Clinical Klebsiella pneumoniae Isolates from Educational Hospitals in Zahedan, Iran

“…The standard strain of K. pneumoniae ATCC 700603 was used as positive control. Next, one or two K. pneumonia-positive colonies were transferred to vials containing tryptic soy broth containing 10-15% glycerol, and the vials were kept at -20 °C until analysis (11). Antibiotic resistance pattern of isolates was determined using the Kirby-Bauer disk diffusion method based on the guidelines from the Clinical and Laboratory Standards Institute (CSLI) (12).…”