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

ABSTRACTA uniqueKlebsiellaspecies strain, 10982, was cultured from a perianal swab specimen obtained from a patient in the University of Maryland Medical Center intensive care unit.Klebsiellasp. 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 pneumoniaeclinical isolates orKlebsiellanitrogen-fixing endophytes but usually not in the same organism. Phylogenomic analysis ofKlebsiellasp. 10982 and sequencedKlebsiellagenomes demonstrated thatKlebsiellasp. 10982 is present on a branch that is located intermediate between the genomes of nitrogen-fixing endophytes andK. pneumoniaeclinical isolates. Metabolic features identified in the genome ofKlebsiellasp. 10982 distinguish this isolate from otherKlebsiellaclinical isolates. These features include the nitrogen fixation (nif) gene cluster, which is typically present in endophyticKlebsiellaisolates and is absent fromKlebsiellaclinical isolates. Additionally, theKlebsiellasp. 10982 genome contains genes associated with allantoin metabolism, which have been detected primarily inK. pneumoniaeisolates from liver abscesses. Comparative genomic analysis ofKlebsiellasp. 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.