Characterization of Klebsiella sp. Strain 10982, a Colonizer of Humans That Contains Novel Antibiotic Resistance Alleles and Exhibits Genetic Similarities to Plant and Clinical Klebsiella Isolates

Abstract

A unique Klebsiella species strain, 10982, was cultured from a perianal swab specimen obtained from a patient in the University of Maryland Medical Center intensive care unit. Klebsiella sp. 10982 possesses a large IncA/C multidrug resistance plasmid encoding a novel FOX AmpC ␤-lactamase designated FOX-10. A novel variant of the LEN ␤-lactamase was also identified. Genome sequencing and bioinformatic analysis demonstrated that this isolate contains genes associated with nitrogen fixation, allantoin metabolism, and citrate fermentation. These three gene regions are typically present in either Klebsiella pneumoniae clinical isolates or Klebsiella nitrogen-fixing endophytes but usually not in the same organism. Phylogenomic analysis of Klebsiella sp. 10982 and sequenced Klebsiella genomes demonstrated that Klebsiella sp. 10982 is present on a branch that is located intermediate between the genomes of nitrogen-fixing endophytes and K. pneumoniae clinical isolates. Metabolic features identified in the genome of Klebsiella sp. 10982 distinguish this isolate from other Klebsiella clinical isolates. These features include the nitrogen fixation (nif) gene cluster, which is typically present in endophytic Klebsiella isolates and is absent from Klebsiella clinical isolates. Additionally, the Klebsiella sp. 10982 genome contains genes associated with allantoin metabolism, which have been detected primarily in K. pneumoniae isolates from liver abscesses. Comparative genomic analysis of Klebsiella sp. 10982 demonstrated that this organism has acquired genes conferring new metabolic strategies and novel antibiotic resistance alleles, both of which may enhance its ability to colonize the human body.

Klebsiella variicola and Klebsiella quasipneumoniae with capacity to adapt to clinical and plant settings

“…In this work, we identified another K. pneumoniae genome (from KPNIN29) that contains the nif operon in addition to that described by Holt and colleagues. 13 Hazen and colleagues 27 identified the absence of nifJ-nifQ gene cluster in K. pneumoniae NTUH-K2044, MGH-78578, 1162281, JH1, MS 92-3, 1191100241, ATCC13884 and KCTC-2242 genomes. Here we identified a conserved genetic context and gene synteny of nifJ-nifQ operon both in K. variicola and K. quasipneumoniae genomes (data not shown).…”

Genome misclassification of Klebsiella variicola and Klebsiella quasipneumoniae isolated from plants, animals and humans

“…genomes that corresponded to K. variicola and K. quasipneumoniae Both K. variicola as K. pneumoniae and K. quasipneumoniae isolates exhibit very similar biochemical features, 1 and to date there are no reported biochemical tests for their appropriate differentiation. 3,4,10,11 The phylogenetic analysis of the rpoB gene is more adequate than the 16S rRNA for Klebsiella spp. differentiation.…”

“…genomes was first identified by whole-genome and rpoB phylogenies. 3,4 Subsequently by K. quasipneumoniae and other K. variicola genomes the misclassification was evidenced by Average Nucleotide Identity (ANI). 5 The aim of this work was detect misclassified K. variicola and K. quasipneumoniae genomes.…”

“…1.1.55 clinical isolate was previously identified as a possible K. variicola. 4 In addition, K. pneumoniae UCICRE14 corresponded to K. quasipneumoniae subsp. …”

Comparative Genomics of an IncA/C Multidrug Resistance Plasmid from Escherichia coli and Klebsiella Isolates from Intensive Care Unit Patients and the Utility of Whole-Genome Sequencing in Health Care Settings

“…The FOX-1 AmpC ␤-lactamase was first detected in a Klebsiella pneumoniae strain isolated from a hospital in Buenos Aires, Argentina, in 1989 (7). Since the initial description of FOX-1, there have been 10 bla FOX alleles characterized to date that have been designated allele numbers by the Lahey Clinic (http://www.lahey.org/Studies/) (7)(8)(9)(10)(11)(12)(13)(14). A recent study demonstrated that the bla FOX-1 gene was associated with an approximately 45-kb plasmid that could be conjugally transferred to an Escherichia coli laboratory isolate (7).…”