Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon

Sima Tokajian, Jonathan A Eisen, Guillaume Jospin, Anna Farra, David A. Coil

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


OBJECTIVE: The emergence of extended-spectrum β-lactamase (ESBL)-producing bacteria is now a critical concern. The ESBL-producing Klebsiella pneumoniae constitutes one of the most common multidrug-resistant (MDR) groups of gram-negative bacteria involved in nosocomial infections worldwide. In this study we report on the molecular characterization through whole genome sequencing of an ESBL-producing K. pneumoniae strain, LAU-KP1, isolated from a stool sample from a patient admitted for a gastrointestinal procedure/surgery at the Lebanese Amrican University Medical Center-Rizk Hospital (LAUMCRH) in Lebanon.

METHODS: Illumina paired-end libraries were prepared and sequenced, which resulted in 4,220,969 high-quality reads. All sequence processing and assembly were performed using the A5 assembly pipeline.

RESULTS: The initial assembly produced 86 contigs, for which no scaffolding was obtained. The final collection of contigs was submitted to GenBank. The final draft genome sequence consists of a combined 5,632,663 bases with 57% G+C content. Automated annotation was performed using the RAST annotation server. Sequencing analysis revealed that the isolate harbored different β-lactamase genes, including bla oxa-1, bla CTX-M-15, bla SHV-11, and bla TEM-1b. The isolate was also characterized by the concomitant presence of other resistance determinants most notably acc(6')-lb-cr and qnrb1. The entire plasmid content was also investigated and revealed homology with four major plasmids pKPN-IT, pBS512_2, pRSF1010_SL1344, and pKPN3.

CONCLUSIONS: The potential role of K. pneumonia as a reservoir for ESBL genes and other resistance determinants is along with the presence of key factors that favor the spread of antimicrobial resistance a clear cause of concern and the problem that Carbapenem-non-susceptible ESBL isolates are posing in hospitals should be reconsidered through systematic exploration and molecular characterization.

Original languageEnglish (US)
Pages (from-to)32
Number of pages1
JournalFrontiers in cellular and infection microbiology
StatePublished - 2015


  • CTX-M-15
  • ESBL
  • Klebsiella pneumoniae
  • SHV-11
  • whole genome sequencing

ASJC Scopus subject areas

  • Medicine(all)


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