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A uniqueKlebsiella 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 β-lactamase designated FOX-10. A novel variant of the LEN β-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 eitherKlebsiella pneumoniae clinical isolates orKlebsiella nitrogen-fixing endophytes but usually not in the same organism. Phylogenomic analysis ofKlebsiella sp. 10982 and sequencedKlebsiella genomes demonstrated thatKlebsiella sp. 10982 is present on a branch that is located intermediate between the genomes of nitrogen-fixing endophytes andK. pneumoniae clinical isolates. Metabolic features identified in the genome ofKlebsiella sp. 10982 distinguish this isolate from otherKlebsiella clinical isolates. These features include the nitrogen fixation (nif ) gene cluster, which is typically present in endophyticKlebsiella isolates and is absent fromKlebsiella clinical isolates. Additionally, theKlebsiella sp. 10982 genome contains genes associated with allantoin metabolism, which have been detected primarily inK. pneumoniae isolates from liver abscesses. Comparative genomic analysis ofKlebsiella 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.

antimicrobial agents and chemotherapy

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